US20020106657A1 - Genetic test to determine non-responsiveness to statin drug treatment - Google Patents

Genetic test to determine non-responsiveness to statin drug treatment Download PDF

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US20020106657A1
US20020106657A1 US09/898,779 US89877901A US2002106657A1 US 20020106657 A1 US20020106657 A1 US 20020106657A1 US 89877901 A US89877901 A US 89877901A US 2002106657 A1 US2002106657 A1 US 2002106657A1
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oligonucleotide primer
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Kent Taylor
Maren Scheuner
Jerome Rotter
Huiying Yang
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • This invention relates to the medical arts. In particular, it relates to the field of genetic testing methods and diagnostic kits.
  • Statin drugs the most potent lipid-lowering agents currently available—are 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitors. They include lovastatin, pravastatin, simvastatin, atorvastatin, fluvastatin, and cerivastatin. All these statin drugs share a common mechanism of action and have similar toxicity profiles. (E. von Kreutz and G. Schluter, Preclinical safety evaluation of cerivastatin, a novel HMG-CoA reductase inhibitor, Am. J. Cardiol. 82(4B):11J-17J [1998];A. G. Ollson [1998]).
  • statin drugs are effective in reducing the primary and secondary risk of coronary artery disease and coronary events, such as heart attack, in middle-aged and older men and women (under 76 years), in both diabetic and non-diabetic patients, and are often prescribed for patients with hyperlipidemia.
  • A. G. Ollson Addressing the challenge, Eur. Heart J. Suppl. M:M29-35 [1998]; M. Kornitzer, Primary and secondary prevention of coronary artery disease: a follow-up on clinical controlled trials, Curr. Opin. Lipidol. 9(6):557-64 [1998]; M. Farnier and J. Davignon, Current and future treatment of hyperlipidemia: the role of statins, Am. J.
  • statins used in secondary prevention of coronary artery or heart disease significantly reduce the risk of stroke, total mortality and morbidity and attacks of myocardial ischemia; the use of statins is also associated with improvements in endothelial and fibrinolytic functions and decreased platelet thrombus formation.
  • CABG coronary artery bypass graft
  • the patient's own saphenous vein, or brachial or mammary artery is used to bypass the affected coronary artery.
  • the majority of CABG patients experience good long-term results, but 30-40% require a second CABG within 10-12 years after surgery, and continuing atherosclerosis in the graft is an important factor in late graft failure.
  • L. Campeau et al The effect of aggressive lowering of low-density lipoprotein cholesterol levels and low-dose anticoagulation on obstructive changes in saphenous-vein coronary-artery bypass grafts, N. Eng. J. Med. 336(3):153-62 [1997]).
  • Atherosclerosis in bypass grafts is associated with elevated serum levels of very low density lipoproteins (VLDL), low density lipoprotein cholesterol (LDL-C), and triglycerides, and low levels of high density lipoprotein cholesterol (HDL-C).
  • VLDL very low density lipoproteins
  • LDL-C low density lipoprotein cholesterol
  • HDL-C high density lipoprotein cholesterol
  • Lipid lowering therapy has been demonstrated to delay the progression of atherosclerosis in coronary arteries.
  • G. Brown et al. Regression of coronary artery disease as a result of intensive lipid lowering therapy in men with high levels of apolipoprotein B, N. Engl. J. Med. 323:1289-98 [1990]
  • J. P. Kane et al Regression of coronary atherosclerosis during treatment of familial hypercholesterolemia with combined drug regimens, JAMA 264:3007-12 ([1990]; Jukema et al., 1995).
  • Low-dose anticoagulation therapy prevented emboli after major surgery (A. G. G. Turpie et al, Randomised comparison of two intensities of oral anticoagulant therapy after tissue heart valve replacement, Lancet 1:1242-45 [1988]; L. Poller et al., Fixed minidose warfarin: a new approach to prophylaxis against venous thrombosis after major surgery, Br. Med. J. 295:1309-12 [1987]), and this implied that low-dose anticoagulation treatment would also be able to delay graft obstruction.
  • Statin drug treatment beneficially affects the long-term outcome for most CABG patients.
  • CABG patients received statin drug treatment to lower serum LDL-C; in comparing patients who had received aggressive lovastatin treatment (LDL-C lowered to 93-97 mg/dl) to those who had only received moderate lovastatin treatment (LDL-C lowered to 132-136 mg/dl), the percentages of patients with atherosclerotic worsening of grafts within 4 years were 39% and 51%, respectively,. (L. Campeau et al. [1997]). The number of patients in the aggressive lovastatin-treatment group who required a second CABG procedure was 29% lower than the number in the moderate-treatment group.
  • Lipoprotein lipase (LPL; E.C. 3.1.1.34), also known as triacylglycerol acylhydrolase, is a heparin-releasable glycoprotein enzyme bound to glycosaminoglycan components of macrophages and to the luminal surface of capillary epithelial cells in a variety of human tissues, including heart, skeletal muscle, adipose, lung, and brain.
  • LPL Lipoprotein lipase
  • E.C. 3.1.1.34 also known as triacylglycerol acylhydrolase
  • Lipoprotein lipase is active as a dimer of identical subunits, each approximately 62,500 D in unglycosylated form.
  • M. R. Taskinen et al. Enzymes involved in triglyceride hydrolysis. In: James Shepard (Ed.), Bailliere's Clinical Endocrinology and Metabolism, Vol. 1, No.3, Bailliere Tindall, London, pp.639-66 [1987]).
  • Lipoprotein lipase is the rate-limiting enzyme for the hydrolysis and removal of triglyceride-rich lipoproteins, such as chylomicrons, VLDL, and LDL-C from the blood stream.
  • triglyceride-rich lipoproteins such as chylomicrons, VLDL, and LDL-C from the blood stream.
  • LPL polymorphisms are known to affect LPL activity.
  • the D9N mutation in exon 2 has been associated with increased triglyceride levels and with the occurrence of coronary atherosclerosis, attenuating the ability of pravastatin to lower LDL-C. (J. Jukema et al. [1996]).
  • the N291 S mutation in exon 6 has been associated with reduced HDL-C levels.
  • a lipoprotein lipase mutation [asn 291ser] is associated with reduced HDL cholesterol levels in premature atherosclerosis, Nat. Gen. 10:28-34 [1995]; H. H.
  • Some genetic variation can be associated with the accumulation of toxic products, for example treatment of TPMT-deficient (thiopurine methyltransferase) patients with 6-mercaptopurine or azathioprine can lead to a potentially fatal hematopoietic toxicity due to higher than normal levels of thioguanine nucleotides.
  • TPMT-deficient (thiopurine methyltransferase) patients with 6-mercaptopurine or azathioprine can lead to a potentially fatal hematopoietic toxicity due to higher than normal levels of thioguanine nucleotides.
  • the present invention relates to a method of detecting a genetic predisposition in a human subject for non-responsiveness to statin drug treatment for coronary artery disease.
  • This genetic testing method involves analyzing amplification products of the nucleic acids in a human tissue sample that includes a non-coding or untranslated region within the 3′ end of the human LPL gene.
  • Homozygosity for a variant allele in a non-coding or untranslated region within the 3′ end of the human LPL gene indicates a genetic predisposition for non-responsiveness to treatment with statin-class drugs, such as lovastatin, pravastatin, simvastatin, atorvastatin, fluvastatin, and cerivastatin, which are typically prescribed to treat atherosclerotic stenosis in subjects with coronary artery disease, or to prevent graft worsening (stenosis) in CABG patients.
  • statin-class drugs such as lovastatin, pravastatin, simvastatin, atorvastatin, fluvastatin, and cerivastatin
  • the present invention also relates to oligonucleotide primer sequences, primer sets, and genetic testing kits for practicing the method.
  • FIG. 1 shows graft worsening in subjects related to different LPL variant alleles in the LPL gene.
  • FIG. 1( a ) shows the location of some variant alleles in the LPL gene. Vertical bars represent exons.
  • FIG. 1( b ) shows the percentage of subjects with graft worsening. Each pair of vertical bars represents two genotype groups for each marker as defined in the box at the base of the bar. The number of subjects in each genotype group (N) is given below each bar.
  • FIG. 1( c ) represents the odds ratios and 95% confidence limits for graft worsening for each polymorphism.
  • FIG. 2 shows graft worsening in subjects by HindIII genotype and drug treatment groups. The total number of subjects in each group is given on each vertical bar.
  • the present invention is directed to a method of detecting a genetic predisposition in a human subject for non-responsiveness to statin drug treatment for coronary artery disease or high blood pressure.
  • This genetic testing method involves analyzing amplification products of the nucleic acids in a human tissue sample for homozygosity with respect to a variant allele in a non-coding or untranslated region of the 3′ end of the human LPL gene.
  • the present invention does not rely on and is not committed to any particular mechanism by which a variant allele or LPL polymorphism in a non-coding or untranslated region of the 3′ end of the human LPL gene produces a phenotype of non-responsiveness to statin drug treatment.
  • the LPL gene is located on the short arm of human chromosome 8, at 8p22.
  • Human genes involved lipolysis of plasma lipoproteins Mapping of loci for lipoprotein lipase to 8p22 and hepatic lipase to 15q21, Genomics 1:138-44 [1987]).
  • the gene is near microsatellite marker D8S1715 and flanked by microsatellites D8S261 and D8S280. Closer flanking sequences of human LPL are defined by GenBank accession numbers M94221 and M94222 (S.
  • Wood et al. Support for founder effect for two lipoprotein lipase [LPL] gene mutations in French Canadians by analysis of GT microsatellites flanking the LPL gene, unpublished [1992]).
  • the gene spans about 30 kb and contains 10 exons encoding a 475 amino acid protein including a 27 amino acid secretory signal peptide.
  • S. Deeb and R. Peng Structure of the human lipoprotein lipase gene, Biochemistry 28(10) :4131-35 [1989]
  • T. G. Kirchgessner et al. Organization of the human lipoprotein lipase gene and evolution of the lipase gene family, Proc. Natl. Acad. Sci. USA 86:9647-51 [1989]).
  • the 3′ end of the human lipoprotein lipase gene includes nucleotide positions 4801 through 9734 of the Nickerson reference sequence extending from intron 6 into intron 9. (GenBank accession No. AF050163). (D. A. Nickerson et al., DNA sequence diversity in a 9.7- kb region of the human lipoprotein lipase gene, Nat. Genet. 19:233-40 [1998]).
  • the complete Nickerson reference sequence is the following: 1 TGTAACACAA AATTAAAATA AGTAGAATTA GTTTTCAGTA TTTCCTATAT TTGGAAAACA (SEQ.ID.No.:80) 61 ATATTTATAT TCATTTTGTT TCTTTTAGTT TTATTTTTGG CAGAACTGTA AGCACCTTCA 121 TTTTCTTTTT CTTCCAAAGG AGGAGTTTAA CTACCCTCTG GACAATGTCC ATCTCTTGGG 181 ATACAGCCTT GGAGCCCATG CTGCTGGCAT TGCAGGAAGT CTGACCAATA AGAAAGTCAA 241 CAGAATTACT GGTAAGAAAG CAATTTCGTT GGTCTTATCA TAAGAGGTGA AAAGACTGTC 301 ATTCTGAGAG AGAATCAGAA CAAATTTTGT TAAATACCCA CATGTGTGGT GTTCTTCCCG 361 GAGACATGAC CAGCACTTGA TTATCTCATT GTAGGGCTCT TTATTAGGGA TAAGAA
  • the 3′ end of the human lipoprotein lipase gene includes exon 10 and the 3′ untranslated region (3′UTR), at least partially defined by nucleotide positions 1 through 3240 of the reference sequence of Oka et al., (GenBank accession No. X52978 and X53518; K. Oka et al., Structure and polymorphic map of human lipoprotein lipase gene, Biochim. Biophys. Acta 1049(1):21-26 [1990], Erratum: [Biochirn Biophys Acta 1991 Nov. 11;1090(3):357]).
  • the first and second polyadenylation signals are at nt.
  • the 3′ end of the human lipoprotein lipase gene includes the intervening nucleotide sequence between the end of the Nickerson reference sequence in intron 9 and the beginning of the reference sequence of Oka et al.
  • a non-coding or untranslated region of the 3′ end of the human LPL gene includes any non-transcribed or untranslated nucleotide sequence within the 3′ end, including all intronic sequences. Included are the part of intron 6 extending from Nickerson reference sequence position nt. 4801 through nt. 6086; intron 7 from nt. 6208 through nt. 7729, intron 8 from nt. 7913 through nt. 8941; and intron 9 from nt. 9047 through nt. 9734. Also included is exon 10 and the 3′UTR.
  • a variant allele in a non-coding or untranslated region of the 3′ end of the human LPL gene is a mutation or polymorphism with respect to the Nickerson or Oka et al. reference sequences, of any class, such as, but not limited to, a single nucleotide polymorphism (SNP). Included among the sources of variant alleles in a non-coding or untranslated region of the 3′ end of the human LPL gene are deletion mutations, insertion mutations, inversions, translocations, transitions, tranversions, or repeats.
  • SNP single nucleotide polymorphism
  • Examples of homozygous genotypes that indicate a genetic predisposition to non-responsiveness to statin drug treatment, in accordance with the present method include, but are not limited to, the HindIII 2/2 and (TTTA) n 4/4 genotypes.
  • the HindIII 2 variant allele is created by a T to G transition in the single HindIII recognition site mapped in intron 8, i.e., AAGC T T to AAGC G T, at position 8393 of the Nickerson reference sequence.
  • AAGC T T AAGC T T
  • AAGC G T AAGC G T
  • RFLP for the human lipoprotein lipase [LPL] gene HindIII, Nuc. Acids Res. 15:6763 [1987]; D. A. Nickerson et al. [1998]).
  • nucleic acids comprising the normal locus of the HindIII recognition site in intron 8 of the human LPL gene are any nucleic acid sequences that overlap the entire six-basepair region at positions 8389-8394 of the Nickerson reference sequence, whether or not the nucleic acid sequence of a particular human subject at that locus is AAGCTT.
  • TTTA tetranucleotide
  • Allele 4 yields a 131 bp nucleotide fragment when PCR amplification is done using a primer set comprising reverse primer GZ-15 (5′-CCT GGG TAA CTG AGC GAG ACT GTG TC-3′; SEQ. ID. NO.: 33) and forward primer GZ-14 (5′-ATC TGA CCA AGG ATA GTG GGA TAT A-3′; SEQ. ID. NO.: 34).
  • a statin drug is any 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitor, including, but not limited to, lovastatin, pravastatin, simvastatin, atorvastatin, fluvastatin, and cerivastatin.
  • HMG-CoA 3-hydroxy-3-methylglutaryl coenzyme A
  • a human subject particularly a CABG patient, who has a genetic predisposition for non-responsiveness to statin drug treatment possesses an hereditary inclination, susceptibility, or tendency to develop atherosclerotic stenosis of coronary blood vessels, including of a native coronary artery, or of any coronary artery bypass graft using a saphenous vein or any other vein or artery, in a manner that does not respond to statin drug treatment. It does not mean that at any time such a person will actually develop stenosis of a coronary blood vessel, or graft worsening (graft lumen narrowing).
  • a CABG patient is a human subject who is a candidate for coronary artery bypass graft surgery or one who has undergone a coronary artery bypass graft procedure.
  • tissue samples can be sampled and collected for the purpose of practicing the methods of the present invention.
  • a most preferred and convenient tissue for collecting is blood.
  • Collecting a tissue sample includes in vitro harvest of cultured human cells derived from a subject's tissue or any means of in vivo sampling directly from a subject, for example, by blood draw, spinal tap, tissue smear or tissue biopsy.
  • tissue samples are stored before analysis by well known storage means that will preserve a sample's nucleic acids in an analyzable condition, such as quick freezing, or a controlled freezing regime, in the presence of a cryoprotectant, for example, dimethyl sulfoxide (DMSO), glycerol, or propanediol-sucrose.
  • DMSO dimethyl sulfoxide
  • glycerol glycerol
  • propanediol-sucrose propanediol-sucrose.
  • Amplifying nucleic acids from a tissue sample of a subject to obtain amplification products includes any conventional means of amassing sufficient nucleic acid material for analysis. Most preferably, amplification is by conventional polymerase chain reaction (PCR) methods. Alternatively, amplification of nucleic acids is by in vitro cell culture and harvest of the subject's cultured cells, or by multiple sampling from the subject's tissues in vivo and pooling of multiple tissue samples from a subject.
  • PCR polymerase chain reaction
  • Nucleic acids thus amplified are amplification products if they include a non-coding or untranslated nucleotide sequence from the 3′ end of the LPL gene, for example, the normal locus of the HindIII recognition site in intron 8, or the tetranucleotide (TTTA) n repeat region of intron 6, of the human LPL gene.
  • TTTA tetranucleotide
  • nucleotide sequencing is used to analyze the amplification products of the nucleic acids in a tissue sample to detect homozygosity for a mutation in the 3′ end of humanLPL.
  • the skilled artisan can detect the mutation by any nucleotide sequencing means, for example conventional dideoxy sequencing or preferably by using a commercially available automated sequencer, then comparing the subject's nucleotide sequences to other known human LPL sequences available in genomic sequence databases, such as GenBank.
  • sequencing of 3′ end LPL sequences is accomplished by using fluorescence-based single strand conformation polymorphism analysis (SSCP), a routine and reliable means of identifying point mutations, small insertions or deletions.
  • SSCP fluorescence-based single strand conformation polymorphism analysis
  • J. S. Ellison Fluorescence-based mutation detection. Single-strand conformation polymorphism analysis [F - SSCP], Mol. Biotechnol. 5(1):17-31 [1996]; H. Iwahana et al., Multiple fluorescence - based PCR - SSCP analysis using internal fluorescent labeling of PCR products, Biotechniques 21(3):510-14,516-19 [1996]; R.
  • F - SSCP fluorescence - based polymerase chain reaction - single - strand conformation polymorphism [ PCR-SSCP], PCR Methods Appl. 2(1):10-13 [1992]).
  • An automated system may be used, such as an Applied Biosystems DNA sequencer, equipped with GENESCAN 672®, Genotyper®, or another appropriate analytical software package.
  • high throughput analysis may be achieved by PCR multiplexing techniques well known in the art. (E.g., Z. Lin et al., Multiplex genotype determination at a large number of gene loci, Proc. Natl. Acad. Sci. USA 93(6):2582-87 [1996]).
  • nucleotide sequencing is unnecessary for analyzing the amplification products.
  • heteroduplex analysis on high resolution gel matrices are employed to detect even single nucleotide polymorphisms.
  • the PCR/OLA procedure can be used for analyzing amplification products to detect SNPs in the 3′ end of the human LPL gene.
  • Conformation-sensitive gel electrophoresis of amplification products may also be employed as a means of analysis by the skilled artisan in practicing the methods of the present invention.
  • A. Markoff et al. Comparison of conformation-sensitive gel electrophoresis and single strand conformation polymorphism analysis for detection of mutations in the BRCA 1 gene using optimized conformation analysis protocols, Eur. J. Genet. 6(2):145-50 [1998]).
  • Electrophoresis for analyzing amplification products is done rapidly and with high sensitivity by using any of various methods of conventional slab or capillary electrophoresis, with which the practitioner can optionally choose to employ any facilitating means of nucleic acid fragment detection, including, but not limited to, radionuclides, UV-absorbance or laser-induced fluorescence.
  • any facilitating means of nucleic acid fragment detection including, but not limited to, radionuclides, UV-absorbance or laser-induced fluorescence.
  • any of diverse fluorescent dyes can optionally be used to label primers of the present invention or amplification products for ease of analysis, including but not limited to, SYBR Green I, Y1O-PRO-1, thiazole orange, Hex (i.e., 6-carboxy- 2′,4′,7′,4,7- -hexachlorofluoroscein), pico green, edans, fluorescein, FAM (i.e., 6-carboxyfluorescein), or TET (i.e., 4,7,2′,7′-tetrachloro-6-(carboxyfluoroscein).
  • SYBR Green I i.e., 6-carboxy- 2′,4′,7′,4,7- -hexachlorofluoroscein
  • Hex i.e., 6-carboxy- 2′,4′,7′,4,7- -hexachlorofluoroscein
  • pico green i.e., 6-car
  • Analyzing the amplification products can also be done by means of restricting the amplification products with one or more restriction enzymes.
  • the restriction enzyme employed is preferably HindIII. Restriction of nucleic acids is followed by separation of the resulting fragments and analysis of fragment length or differential fragment migration in denaturing high-performance liquid chromatography (DHPLC) or gel electrophoresis, as above, including restriction-capillary electrophoresis.
  • DPLC denaturing high-performance liquid chromatography
  • gel electrophoresis as above, including restriction-capillary electrophoresis.
  • this can be achieved by techniques known in the art, such as PCR-restriction fragment-SSCP, which can detect single base substitutions, deletions or insertions.
  • the present invention also relates to an oligonucleotide primer for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human.
  • Useful oligonucleotide primers for amplifying the nucleic acids include any 15 to 28-mer nucleotide sequence that hybridizes with a nucleic acid fragment of the Nickerson or Oka reference sequences, under conventional conditions of stringency used for hybridization in PCR, and together in a set with another primer sequence amplifies a non-coding or untranslated region within the 3′ end of the human LPL gene.
  • a preferred primer is a 20 to 24-mer.
  • oligonucleotide primers having nucleotide sequences that are fragments of the nucleotide sequences in GenBank accession numbers M76722 (below) and M76723 (opposite strand).
  • the nucleotide sequence of M76722 is the following: 1 GAATTCAAGG TCTGCATTTT CTAGGTATGA ACACTGTGCA TGATGAAGTC TTTCCAAGCC (SEQ.ID.NO.:81).
  • oligonucleotide primer sequences that are useful for amplifying nucleic acids that comprise the normal locus of the HindIII recognition site in LPL intron 8, include but are not limited to the following sequences (designation after the SEQ. ID. NO.
  • Any 15-to 28-mer primer sequence overlapping any of SEQ. ID. NOS: 1-32 or 35-79 can also be used to amplify nucleic acids comprising the normal locus of the HindIII recognition site in LPL intron 8.
  • the primer sequence can overlap the entire sequence of any of SEQ. ID. NOS.: 1-32 and 35-79 or can overlap at one or more contiguous nucleotide positions of any of SEQ. ID. NOS.: 1-32 and 35-79 and additional nucleotides adjacent to the position(s) based upon the Nickerson reference sequence.
  • primer sequences are useful for amplifying nucleic acid sequences including the (TTTA) n tetranucleotide repeat region in intron 6. These include SEQ. ID. NOS.: 33 and 34, described above and the following primer sequences (designation includes the nucleotide position within the Nickerson reference sequence in Genbank accession AF050163, e.g., 4644 or 4934, at which the 5′-terminus of the primer sequence begins if it is an upper [“U”; i.e., forward] primer; or the position complementary to a position in AF050163 at which its 3′-terminus ends if it is a lower [“L”; i.e., reverse] primer; and primer length, e.g., 24 bases): 5′-CTG GAC AAG AGT CTA AAG CAG CAT-3′ (SEQ.
  • Any 15-to 28-mer primer sequence overlapping any of SEQ. ID. NOS:33 and 34 or 82-92 can also be used to amplify nucleic acids comprising the (TTTA) n tetranucleotide repeat region in LPL intron 6.
  • the primer sequence can overlap the entire sequence of any of SEQ. ID. NOS.: 33-34 and 82-92 or can overlap at one or more contiguous nucleotide positions of any of SEQ. ID. NOS.: 33-34 and 82-92 and additional nucleotides adjacent to the position(s) based upon the Nickerson reference sequence.
  • primer sequences are useful for amplifying nucleic acid sequences in exon 10 and the 3′-UTR. These include the following primer sequences (SEQ. ID. NOS.: 95-106) (designation includes the nucleotide position within the Oka reference sequence in GenBank accession X52978 X53518, e.g., 2564, at which the 5′-terminus of the primer sequence begins if it is an upper [“U”; i.e., forward] primer; or the position complementary to a position in X52978 X53518 at which its 3′-terminus ends if it is a lower [“L”; i.e., reverse] primer; and primer length, e.g., 22 bases): 5′-ATG AAA AGA GCA TAT GGT GGT T-3′ (SEQ.
  • Any 15-to 28-mer primer sequence overlapping any of SEQ. ID. NOS: 95-106 with respect to its position on the Oka reference sequence can also be used to amplify nucleic acids comprising LPL exon 10 and the 3′UTR.
  • the primer sequence can overlap the entire sequence of any of SEQ. ID. NOS.: 95-106 or can overlap at one or more contiguous nucleotide positions of any of SEQ. ID. NOS.: 95-106 and additional nucleotides adjacent to the position(s) based upon the Oka reference sequence.
  • the present invention also relates to a primer set for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human.
  • the primer set functions to initiate nucleic acid synthesis in PCR from both the 5′ and 3′ ends of a nucleic acid template comprising a non-coding or untranslated region of the 3′ end of the human LPL gene.
  • the primer set comprises any two suitable oligonucleotide primers of the present invention, as described herein, as long as the primer set includes both a forward (upper or “U”) and a reverse (lower or “L”) primer.
  • a preferred primer set for amplifying nucleic acids comprising the normal locus of the HindIII recognition site in intron 8 of LPL includes any pair lower and upper primers from among SEQ. ID. NOS.: 1-32 or 35-79 (described above), or primer sequences overlapping any of them with respect to the Nickerson reference sequence.
  • a most preferred set of primers is reverse (lower) primer SEQ. ID. NO.: 1 and forward (upper) primer SEQ. ID. NO. : 2.
  • Additional primer sets that are useful for amplifying the region of the (TTTA) n tetranucleotide repeat include any pair of lower and upper primers from among SEQ. ID. NOS.: 33-34 and 82-92 (described above), or primer sequences overlapping any of them with respect to the Nickerson reference sequence.
  • a most preferred embodiment of a primer set for detecting the presence of the (TTTA) n 4 allele includes primers comprising SEQ. ID. NOS.: 33 and 34.
  • Additional primer sets that are useful for amplifying exon 10 and the 3′UTR include any pair of lower and upper primers from among SEQ. ID. NOS.: 95-106 (described above), or primer sequences overlapping any of them with respect to the Oka reference sequence.
  • the present invention also relates to a genetic testing kit for detecting in a human subject a genetic predisposition for non-responsiveness to statin drug treatment.
  • the genetic testing kit is a ready assemblage of materials for facilitating the amplifying of nucleic acids from a human subject comprising a nucleotide sequence from a non-coding or untranslated region of the 3′ end of the human LPL gene and/or analyzing amplification products thereof
  • a genetic testing kit of the present invention contains at least one oligonucleotide primer of the present invention and preferably comprises a primer set of the present invention, as described above, together with instructions for the practice of the present method.
  • the materials or components assembled in the genetic testing kit are provided to the practitioner stored in any convenient and suitable way that preserves their operability and utility.
  • the components can be in dissolved, dehydrated, or lyophilized form; they can be provided at room, refrigerated or frozen temperatures.
  • Another preferred embodiment of the genetic testing kit incorporates an array of oligonucleotide primers specific for single nucleotide polymorphisms in the human nucleotide sequence of the 3′ end of LPL, particularly of non-coding or untranslated regions, preassembled in a “DNA chip” (or “gene chip”) configuration for facilitating the amplifying of nucleic acids and the analyzing of amplification products.
  • a “DNA chip” or “gene chip”
  • homozygosity for a mutation in a non-coding or untranslated region of the 3′ end of the human LPL gene is a risk factor for atherosclerotic stenosis in coronary artery disease independent and additive to the use of statin drugs to reduce LDL.
  • the effect of the LPL HindIII 2/2 genotype on atherosclerotic graft worsening is of the same magnitude as the use of moderate rather than aggressive drug therapy to lower LDL.
  • Such a genotype apparently does not act via an effect on lipid levels, nor the amount of drug needed to achieve lower levels. However, it is associated with a modest effect on blood pressure.
  • the practitioner can identify patients homozygous for a variant allele in a non-coding or untranslated region of the 3′ end of LPL, for example those with the HindIII 2/2 or (TTTA) 4 4/4 genotype. These patients are predisposed to develop atherosclerotic progression despite their compliance with aggressive lipid lowering therapy with lovastatin or other statin class drugs.
  • a high level of LDL-C is an important risk factor of heart disease and atherosclerosis, but it is not the sole risk factor.
  • the present invention provides the practitioner a valuable tool for better characterizing individual patients and identifying those patients likely to need individualized alternative interventions other than LDL-C lowering therapy with statin class drugs.
  • direct blood pressure lowering therapy may be indicated for patients identified as homozygous for a variant genotype in accordance with the present invention, because they tend to have blood pressures at the high end of the normal range.
  • Such treatment can include, for example, angiotensinogen converting enzyme (ACE) inhibitors or Ca 2+ channel blockers.
  • ACE angiotensinogen converting enzyme
  • beta blockers, diuretics, or a combination of modalities can be a more appropriate blood pressure lowering therapy for a given patient.
  • Blood pressure lowering in conjunction with aspirin treatment can prevent heart disease in some patients.
  • HOT hypertension Optimal Treatment
  • Thrombosis prevention trial randomised trial of low - intensity oral anticoagulation with warfarin and low - dose aspirin in the primary prevention of ischemic heart disease in men at increased risk, Lancet 351(9098):233-41 [1998]).
  • LDL-C levels are amenable to treatment in an individual patient.
  • small LDL particle sizes may be amenable to treatment with fibric acid-derivative drugs, e.g., lopid, or high dose niacin.
  • fibric acid-derivative drugs e.g., lopid
  • High Lp(a) levels may be treatable with niacin, or estrogen replacement therapy in women or testosterone replacement in men.
  • statin drugs In view of the substantial cost of statin drugs, a secondary benefit to be derived from identifying patients having a genetic predisposition to non-responsiveness to statin drug treatment, for coronary artery disease or high blood pressure, is the cost savings to patients and health care systems that can be gained by relying on more individually suited alternative treatments instead of statin treatment regimens, for those individuals for whom statins are likely to be ineffective.
  • a secondary benefit to be derived from identifying patients having a genetic predisposition to non-responsiveness to statin drug treatment, for coronary artery disease or high blood pressure is the cost savings to patients and health care systems that can be gained by relying on more individually suited alternative treatments instead of statin treatment regimens, for those individuals for whom statins are likely to be ineffective.
  • Participants were randomly assigned, following a two by two design, to receive 1) lovastatin therapy to lower the LDL-cholesterol level to within the range of 93-97 mg/dl (aggressive treatment group) or 132-136 mg/dl (moderate treatment group), and 2) placebo or low-dose warfarin (Post-CABG, 1997).
  • Coronary angiograms of 1351 subjects at enrollment and an average of 4.3 years later were compared using a quantitative assessment of the severity of graft stenosis. Graft worsening was defined as a decrease in lumen diameter of 0.6mm or more.
  • the percentage of subjects with worsening of one or more grafts was 39% in the aggressive treatment group compared to 51% in the moderate treatment group (p ⁇ 0.00 1) and the mean percentage of grafts per patient showing worsening was 27% in the aggressive treatment group compared to 39% in the moderate treatment group (p ⁇ 0.001).
  • Subjects were randomly assigned in a two by two factorial design for treatment to lower LDL-cholesterol levels aggressively (target LDL 93-97 mg/dl) or moderately (target LDL 132-136 mg/dl) with lovastatin and cholestyramine if needed, and for treatment with either placebo or warfarin sufficient to maintain an international normalized ratio of less than 2.
  • graft worsening was determined by comparing the initial angiogram at enrollment with a follow-up angiogram repeated an average of 4.3 years later. “Worsening” was defined as a reduction in diameter ⁇ 0.6mm in diameter. “Subjects with worsening” were defined as those subjects with one or more grafts showing worsening.
  • Marker genotypes were determined using a PCR with primers listed below as recommended by the manufacturer of Ampli-Taq Gold (Perkin Elmer, Foster City, Calif.) in a Perkin Elmer 9600 thermocycler. (All PCR runs began with 95° for 10 min. to activate the polymerase). After digestion with the appropriate restriction enzyme, PCR products for each subject were pooled from all five genotyping reactions and run together on 6% Long Ranger gels in a semi-automated DNA sequencer (ABI 373 DNA sequencer, Applied Biosystems, Foster City, Calif.) with gel processing using Genescan and Genotyper software.
  • HindIII (intron 8)
  • Adjusted variables for this trait included age, gender, body mass index, smoking status, number of years since CABG, systolic and diastolic blood pressure, current medicine use, and family history as listed in Table 1. All statistical analyses were carried out with SAS software (version 6.12, SAS Institute, Cary, N.C.).
  • (TTTA) n intron 6; allele 1 is 119 bp, 2 is 123 bp, 3 is 127 bp, 4 is 131 bp, 5 is 135 bp, D.
  • a designation of “X ” is an abbreviation for “other” genotypes.
  • the percent of subjects with graft worsening is the percent of subjects with one or more grafts showing a reduction in diameter ⁇ 0.6 mm.
  • the (TTTA) n 4 allele was found to be in strong linkage disequilibrium with the HindIII 2 allele (p ⁇ 0.001, data not shown). Consequently, the combined genotype of (TTTA) n 4/4 and HindIII 2/2 was also associated with graft worsening at a significance level similar to the (TTTA) n 4/4 or HindIII 2/2 genotypes alone.

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Abstract

In a method for detecting a genetic predisposition in a human for non-responsiveness to statin drug treatment for coronary artery disease, nucleic acids comprising nucleotide sequences of the human lipoprotein lipase (LPL) gene are amplified and analyzed. Homozygosity for a variant allele in a non-coding or untranslated region of the 3′ end of LPL, for example, LPL HindIII 2/2 or (TTTA)n 4/4 genotypes, is linked to non-responsiveness to treatment with statin drugs, including lovastatin, pravastatin, simvastatin, atorvastatin, fluvastatin, or cerivastatin. Oligonucleotide primer sequences, primer sets, and genetic testing kits allow the practitioner to practice the method and thus better individualize the treatment and improve the care of patients with coronary artery disease.

Description

    BACKGROUND OF THE INVENTION
  • Throughout this application various publications are referenced within parentheses. The disclosures of these publications in their entireties are hereby incorporated by reference in this application in order to more fully describe the state of the art to which this invention pertains. [0001]
  • 1. The Field of the Invention [0002]
  • This invention relates to the medical arts. In particular, it relates to the field of genetic testing methods and diagnostic kits. [0003]
  • 2. Discussion of the Related Art [0004]
  • Statin drugs—the most potent lipid-lowering agents currently available—are 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitors. They include lovastatin, pravastatin, simvastatin, atorvastatin, fluvastatin, and cerivastatin. All these statin drugs share a common mechanism of action and have similar toxicity profiles. (E. von Kreutz and G. Schluter, [0005] Preclinical safety evaluation of cerivastatin, a novel HMG-CoA reductase inhibitor, Am. J. Cardiol. 82(4B):11J-17J [1998];A. G. Ollson [1998]).
  • The statin drugs are effective in reducing the primary and secondary risk of coronary artery disease and coronary events, such as heart attack, in middle-aged and older men and women (under 76 years), in both diabetic and non-diabetic patients, and are often prescribed for patients with hyperlipidemia. (A. G. Ollson, [0006] Addressing the challenge, Eur. Heart J. Suppl. M:M29-35 [1998]; M. Kornitzer, Primary and secondary prevention of coronary artery disease: a follow-up on clinical controlled trials, Curr. Opin. Lipidol. 9(6):557-64 [1998]; M. Farnier and J. Davignon, Current and future treatment of hyperlipidemia: the role of statins, Am. J. Cardiol. 82(4B):3J-10J [1998]). Statins used in secondary prevention of coronary artery or heart disease significantly reduce the risk of stroke, total mortality and morbidity and attacks of myocardial ischemia; the use of statins is also associated with improvements in endothelial and fibrinolytic functions and decreased platelet thrombus formation. (M. Kornitzer [1998]; M. Farnier and J. Davignon, Current and future treatment of hyperlipidemia: the role of statins, Am. J. Cardiol. 82(4B):3J-10J [1998]).
  • The use of statin drugs has recently decreased the need for surgical coronary revascularization, known as coronary artery bypass graft (CABG). (B. M. Rifkind, [0007] Clinical trials of reducing low-density lipoprotein concentrations, Endocrinol. Metab. Clin. North Am. 27(3):585-95, viii-ix [1998]). But CABG is still a common surgical intervention for patients who develop atherosclerotic occlusion in coronary arteries. Approximately 12,000-14,000 CABG procedures are performed annually. (G. F. Neitzel et al., Atherosclerosis in Aortocoronary Bypass Grafts, Atherosclerosis 6(6):594-600 [1986]). The patient's own saphenous vein, or brachial or mammary artery, is used to bypass the affected coronary artery. The majority of CABG patients experience good long-term results, but 30-40% require a second CABG within 10-12 years after surgery, and continuing atherosclerosis in the graft is an important factor in late graft failure. (L. Campeau et al, The effect of aggressive lowering of low-density lipoprotein cholesterol levels and low-dose anticoagulation on obstructive changes in saphenous-vein coronary-artery bypass grafts, N. Eng. J. Med. 336(3):153-62 [1997]).
  • Atherosclerosis in bypass grafts is associated with elevated serum levels of very low density lipoproteins (VLDL), low density lipoprotein cholesterol (LDL-C), and triglycerides, and low levels of high density lipoprotein cholesterol (HDL-C). (J. T. Lie et al., [0008] Aortocoronary bypass saphenous vein atherosclerosis: Anatomic study of99 vein grafts from normal and hyperlipoproteinemic patients up to 75 months postoperatively, Am. J. Cardiol. 40:906 [1977]; L. Campeau et al, The relation of risk factors to the development of atherosclerosis in saphenous vein bypass grafts and the progression of disease in the native circulation, N. Eng. J. Med. 311(21):1329-32 [1984]). It is standard for CABG patients to be prescribed statin drugs to lower their serum LDL-C.
  • Lipid lowering therapy has been demonstrated to delay the progression of atherosclerosis in coronary arteries. (E.g., G. Brown et al., [0009] Regression of coronary artery disease as a result of intensive lipid lowering therapy in men with high levels of apolipoprotein B, N. Engl. J. Med. 323:1289-98 [1990]; J. P. Kane et al, Regression of coronary atherosclerosis during treatment of familial hypercholesterolemia with combined drug regimens, JAMA 264:3007-12 ([1990]; Jukema et al., 1995). Prior to the Post-CABG Trial, few data were available to determine the efficacy of LDL-lowering therapy to delay the obstruction of saphenous-vein grafts. (D. H. Blankenhom et al., Beneficial effects of combined colestipol-niacin therapy on coronary atherosclerosis and coronary venous bypass grafts, JAMA 257:3233-40 [1987]). Furthermore, thrombosis had also been observed to contribute to graft obstruction (G. F. Neitzel et al., Atherosclerosis in aortocoronary bypass grafts: morphologic study and risk factor analysis 6 to 12 years after surgery, Arteriosclerosis 6:594-600 [1986]). Low-dose anticoagulation therapy prevented emboli after major surgery (A. G. G. Turpie et al, Randomised comparison of two intensities of oral anticoagulant therapy after tissue heart valve replacement, Lancet 1:1242-45 [1988]; L. Poller et al., Fixed minidose warfarin: a new approach to prophylaxis against venous thrombosis after major surgery, Br. Med. J. 295:1309-12 [1987]), and this implied that low-dose anticoagulation treatment would also be able to delay graft obstruction.
  • Statin drug treatment beneficially affects the long-term outcome for most CABG patients. In a large clinical study, the Post-CABG Trial, CABG patients received statin drug treatment to lower serum LDL-C; in comparing patients who had received aggressive lovastatin treatment (LDL-C lowered to 93-97 mg/dl) to those who had only received moderate lovastatin treatment (LDL-C lowered to 132-136 mg/dl), the percentages of patients with atherosclerotic worsening of grafts within 4 years were 39% and 51%, respectively,. (L. Campeau et al. [1997]). The number of patients in the aggressive lovastatin-treatment group who required a second CABG procedure was 29% lower than the number in the moderate-treatment group. [0010]
  • In addition to serum lipid concentrations, there are other risk factors, that may have a genetic basis, and that may independently affect atherosclerotic coronary artery disease and occlusion of bypass grafts or that interact with statin treatment to lower serum lipids, which can affect atherosclerotic stenosis. Several laboratories have observed a link between variant alleles of the lipoprotein lipase gene (LPL) and the occurrence and/or progression of atherosclerosis. The involvement of LPL in coronary artery disease was suspected, since rare homozygotes for defects in this gene have type I hyperlipoproteinemia (OMIM 238600) and premature coronary artery disease. (P. Benlian et al., [0011] Premature atherosclerosis in patients with familial chylomicronemia caused by mutations in the lipoprotein lipase gene, N. Engl. J. Med. 335:848-54 [1996]).
  • Lipoprotein lipase (LPL; E.C. 3.1.1.34), also known as triacylglycerol acylhydrolase, is a heparin-releasable glycoprotein enzyme bound to glycosaminoglycan components of macrophages and to the luminal surface of capillary epithelial cells in a variety of human tissues, including heart, skeletal muscle, adipose, lung, and brain. (K. L. Wion et al., [0012] Human lipoprotein lipase complementary DNA sequence, Science 235:1638 [1987]; C. Heizmann et al., DNA polymorphism haplotypes of the human lipoprotein lipase gene: possible association with high density lipoprotein levels, Hum. Genet. 86:578-84 [1991]). Lipoprotein lipase is active as a dimer of identical subunits, each approximately 62,500 D in unglycosylated form. (M. R. Taskinen et al., Enzymes involved in triglyceride hydrolysis. In: James Shepard (Ed.), Bailliere's Clinical Endocrinology and Metabolism, Vol. 1, No.3, Bailliere Tindall, London, pp.639-66 [1987]).
  • Lipoprotein lipase is the rate-limiting enzyme for the hydrolysis and removal of triglyceride-rich lipoproteins, such as chylomicrons, VLDL, and LDL-C from the blood stream. (Jukema et al., [0013] The Asp 9 Asn Mutation in the Lipoprotein Lipase Gene Is Associated With Increased Progression of coronary Atherosclerosis, Circulation 94(8): 1913-18 [1996]). The enzymatic action of LPL results in the generation of mono—and diglycerides and free fatty acids that can be used as fuel for energy or reesterified for storage in peripheral adipose tissue.
  • The gene sequence of human LPL is known, including the 3′ region through [0014] exon 10 and the 3′ untranslated region (3′-UTR). (K. L. Wion et al., Human lipoprotein lipase complementary DNA sequence, Science 235:1638-41 [1987]; T. G. Kirchgessner et al., The sequence of cDNA encoding lipoprotein lipase, J. Biol. Chem. 262(18):8463-66 [1987]; K. Oka et al., Structure and polymorphic map of human lipoprotein lipase gene, Biochim. Biophys. Acta 1049:21-26 [1990]; D. A. Nickerson et al., DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene, Nat. Genet. 19:233-40 [1998]). Nickerson et al. sequenced the region of the LPL gene spanning exons 4-9 (containing the major catalytic portion of the enzyme) of 71 individuals taken from 3 different populations and observed 88 different DNA variants or polymorphisms, with 78 of these present at an allele frequency greater than 1% (D. A. Nickerson et al., [1998]).
  • Two LPL polymorphisms are known to affect LPL activity. The D9N mutation in [0015] exon 2 has been associated with increased triglyceride levels and with the occurrence of coronary atherosclerosis, attenuating the ability of pravastatin to lower LDL-C. (J. Jukema et al. [1996]). The N291 S mutation in exon 6 has been associated with reduced HDL-C levels. (P. Reymer et al., A lipoprotein lipase mutation [asn291ser] is associated with reduced HDL cholesterol levels in premature atherosclerosis, Nat. Gen. 10:28-34 [1995]; H. H. Wittrup et al., A common substitution [asn291ser] in lipoprotein lipase is associated with increased risk of ischemic heart disease, J. Clin. Inves. 99:1606-13 [1997]). The N291S mutation is also linked with increased coronary stenosis (narrowing of arterial lumen) seen on angiography in women with verified ischemic heart disease compared to controls. (H. H. Wittrup et al [1997]).
  • Two other LPL polymorphisms have demonstrated association with the development of atherosclerosis, although their functional significance is unknown. The first is the PvuII polymorphism in [0016] intron 6, which is linked with the number of coronary blood vessels with greater than 50% obstruction. (X. Wang et al., Common DNA polymorphisms at the lipoprotein lipase gene: association with severity of coronary artery disease and diabetes, Circulation 93:1339-45 [1996]). The second is the HindIII polymorphism in intron 8, associated with the angiographic severity of coronary artery disease. (R. Mattu et al., DNA variants at the LPL gene locus associate with angiographically defined severity of atherosclerosis and serum lipoprotein levels in a Welsh population, Arterno. Thromb. 14:1090-97 [1994]; R. Peacock et al., Associations between lipoprotein lipase, lipoproteins and lipase activities in young myocardial infarction survivors and age-matched healthy individuals from Sweden, Atherosclerosis 97:171-85 [1992]).
  • Progress in pharmacogenetics has shown that human genetic variation underlies different individual responses to drug treatment within a population. (Reviewed in G. Alvan, [0017] Genetic polymorphisms in drug metabolism, J. Int. Med. 231:571-73 [1992]; P. W. Kleyn and E. S. Vesell, Genetic variation as a guide to drug development, Science 281:1820-22 [1998]). For example, alleles of the NAT1 and NAT2 genes (N-Acetyltransferases) create a “slow acetylator” phenotype in 40-60% of Caucasians, resulting in a slow clearance and associated toxicity of many drugs including isoniazid and procainamide (K. P. Vatsis et al., Diverse point mutations in the human gene for polymorphic N-acetyltransferase, Proc. Natl. Acad. Sci. USA 88(14):6333-37 [1991]). A defect in CYP2D6 (a member of the cytochrome P450 family) leads to the “poor metabolizer” phenotype in 5-10% of Caucasians, affecting the metabolism of many drugs including some beta-blockers and antiarrhythmics. (Reviewed in A. K. Daly et al., Metabolic polymorphisms, Pharmac. Ther.57:129-60 [1993]). Some genetic variation can be associated with the accumulation of toxic products, for example treatment of TPMT-deficient (thiopurine methyltransferase) patients with 6-mercaptopurine or azathioprine can lead to a potentially fatal hematopoietic toxicity due to higher than normal levels of thioguanine nucleotides. (R. Weinshilboum, Methyltransferase pharmacogenetics, Pharmac. Ther. 43:77-90 [1989]; E. S. Vesell, Therapeutic lessonsfrompharmacogenetics, Ann. Intem. Med. 126:653-55 [1997]).
  • The presence of multiple genetic and environmental factors capable of creating such large variations in how drugs operate in the patient argues that individualization of the choice of drug and dosage is required for optimal treatment of disease, including atherosclerotic coronary artery disease. Jukema et al. (1996) reported that the HMG-CoA reductase inhibitor pravastatin did not lower the LDL-cholesterol level in subjects with the LPL N9 polymorphism to the same extent as in those with the LPL D9 polymorphism. In addition, J. A. Kuivenhoven et al. (1998) observed that pravastatin slowed the progression of atherosclerosis in subjects with the CETP B1B1genotype, but not in those with the CETP B2B2 genotype. (J. A. Kuivenhoven et al., [0018] The role of a common variant of the cholesteryl ester transfer protein gene in the progression of coronary atherosclerosis, N. Engl. J. Med. 338:86-93 [1998]). These reports suggest that there are interactions between statin drugs and some genetic determinants of atherosclerosis.
  • There has been a definite need for a reliable predictive test for determining which patients suffering from coronary artery disease, or which CABG patients, will likely not respond positively to statin drug treatment with respect to stenosis of a coronary artery or bypass graft. Such a genetic testing method can provide useful information so that patients can be given more individually suited alternative treatments to prevent further injury. [0019]
  • This and other benefits of the present invention are described herein. [0020]
    • SUMMARY OF THE INVENTION
  • The present invention relates to a method of detecting a genetic predisposition in a human subject for non-responsiveness to statin drug treatment for coronary artery disease. This genetic testing method involves analyzing amplification products of the nucleic acids in a human tissue sample that includes a non-coding or untranslated region within the 3′ end of the human LPL gene. Homozygosity for a variant allele in a non-coding or untranslated region within the 3′ end of the human LPL gene indicates a genetic predisposition for non-responsiveness to treatment with statin-class drugs, such as lovastatin, pravastatin, simvastatin, atorvastatin, fluvastatin, and cerivastatin, which are typically prescribed to treat atherosclerotic stenosis in subjects with coronary artery disease, or to prevent graft worsening (stenosis) in CABG patients. [0021]
  • The present invention also relates to oligonucleotide primer sequences, primer sets, and genetic testing kits for practicing the method.[0022]
    • BRIEF DESCRIPTION OF THE DRAWINGS
  • FIG. 1 shows graft worsening in subjects related to different LPL variant alleles in the LPL gene. [0023]
  • FIG. 1([0024] a) shows the location of some variant alleles in the LPL gene. Vertical bars represent exons. FIG. 1(b) shows the percentage of subjects with graft worsening. Each pair of vertical bars represents two genotype groups for each marker as defined in the box at the base of the bar. The number of subjects in each genotype group (N) is given below each bar. FIG. 1(c) represents the odds ratios and 95% confidence limits for graft worsening for each polymorphism.
  • FIG. 2 shows graft worsening in subjects by HindIII genotype and drug treatment groups. The total number of subjects in each group is given on each vertical bar.[0025]
    • DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
  • The present invention is directed to a method of detecting a genetic predisposition in a human subject for non-responsiveness to statin drug treatment for coronary artery disease or high blood pressure. This genetic testing method involves analyzing amplification products of the nucleic acids in a human tissue sample for homozygosity with respect to a variant allele in a non-coding or untranslated region of the 3′ end of the human LPL gene. The present invention does not rely on and is not committed to any particular mechanism by which a variant allele or LPL polymorphism in a non-coding or untranslated region of the 3′ end of the human LPL gene produces a phenotype of non-responsiveness to statin drug treatment. [0026]
  • The LPL gene is located on the short arm of [0027] human chromosome 8, at 8p22. (R. S. Sparkes et al., Human genes involved lipolysis of plasma lipoproteins: Mapping of loci for lipoprotein lipase to 8p22 and hepatic lipase to 15q21, Genomics 1:138-44 [1987]). The gene is near microsatellite marker D8S1715 and flanked by microsatellites D8S261 and D8S280. Closer flanking sequences of human LPL are defined by GenBank accession numbers M94221 and M94222 (S. Wood et al., Support for founder effect for two lipoprotein lipase [LPL] gene mutations in French Canadians by analysis of GT microsatellites flanking the LPL gene, unpublished [1992]). The gene spans about 30 kb and contains 10 exons encoding a 475 amino acid protein including a 27 amino acid secretory signal peptide. (S. Deeb and R. Peng, Structure of the human lipoprotein lipase gene, Biochemistry 28(10) :4131-35 [1989]; T. G. Kirchgessner et al., Organization of the human lipoprotein lipase gene and evolution of the lipase gene family, Proc. Natl. Acad. Sci. USA 86:9647-51 [1989]).
  • The 3′ end of the human lipoprotein lipase gene, for purposes of the present invention, includes nucleotide positions 4801 through 9734 of the Nickerson reference sequence extending from [0028] intron 6 into intron 9. (GenBank accession No. AF050163). (D. A. Nickerson et al., DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene, Nat. Genet. 19:233-40 [1998]). The complete Nickerson reference sequence is the following:
       1 TGTAACACAA AATTAAAATA AGTAGAATTA GTTTTCAGTA TTTCCTATAT TTGGAAAACA (SEQ.ID.No.:80)
      61 ATATTTATAT TCATTTTGTT TCTTTTAGTT TTATTTTTGG CAGAACTGTA AGCACCTTCA
     121 TTTTCTTTTT CTTCCAAAGG AGGAGTTTAA CTACCCTCTG GACAATGTCC ATCTCTTGGG
     181 ATACAGCCTT GGAGCCCATG CTGCTGGCAT TGCAGGAAGT CTGACCAATA AGAAAGTCAA
     241 CAGAATTACT GGTAAGAAAG CAATTTCGTT GGTCTTATCA TAAGAGGTGA AAAGACTGTC
     301 ATTCTGAGAG AGAATCAGAA CAAATTTTGT TAAATACCCA CATGTGTGGT GTTCTTCCCG
     361 GAGACATGAC CAGCACTTGA TTATCTCATT GTAGGGCTCT TTATTAGGGA TAAGAAAAAA
     421 CACAGACGCT CTCACTGGCT TACTATCCAC TGGCAATAGC ACAGAAATAA AGCATAATTA
     481 CACACAATGC CTGCAGATTT CTCTGGGAAG CCTGTTTCCT CCCACTCTCA GCTCTGTGTT
     541 TTAGTAGTGT AAATGCACAT CAGTACTAGG AGAAAAGAAG AAGGACCAAT TCCAGAGGCC
     601 ACTTCGAAAG AAGACCGTCA TCTAGGCAAA GGTGTGGCAT ACACACAGAG AGAAAGAACC
     661 CACCACTGTT TATACATCTT CTCGACATAT TCAGAAATAA TCTACAAAAG GAAATCCAGC
     721 CATCCTGAGT GGAAATTGCT GCATAAGGCT AGTTTAAGAG ACTCAAATTC ATTTTAGAAG
     781 GAGCCAAGCC TCCTTTTATG TCTCTCTAAG TAAAGATACC ATGACTGTAG AATAGGAGCT
     841 AATAAGAATC TAAATAGCTG CCAGTGCATT CAAATGATGA GCAGTGACAT GCGAATGTCA
     901 TACGAATGGA AATTTACAAA TCTGTGTTCC TGCTTTTTTC CCTTTTAAGG CCTCGATCCA
     961 GCTGGACCTA ACTTTGAGTA TGCAGAAGCC CCGAGTCGTC TTTCTCCTGA TGATGCAGAT
    1021 TTTGTAGACG TCTTACACAC ATTCACCAGA GGGTCCCCTG GTCGAAGCAT TGGAATCCAG
    1081 AAACCAGTTG GGCATGTTGA CATTTACCCG AATGGAGGTA CTTTTCAGCC AGGATGTAAC
    1141 ATTGGAGAAG CTATCCGCGT GATTGCAGAG AGAGGACTTG GAGGTAAATA TTATTTAGAA
    1201 GCGAATTAAA TGTGACTCTT ATCCTTAACC CTTATTGACC CAATGTCCTA CTCAGTAGCT
    1261 TCAAAGTATG TAGTTTTCAT ATACACATTT GGCCAAATTA TGTTTCTGAA GAATTCTGCA
    1321 ATGTTCAGCA TGACCACCTT AGAGCCAGGC AGACAGCCAT TTTATCTTTT ATTTACTATA
    1381 CTGTAGGCTA CACTGAGCAG TGCACTTACA GTAGCAAGAG AAAAAGGTGG GATTTTAGAC
    1441 AGGAAGACTC CACTGACCTC AATAATGGCA TCATAAAATG CTATCTGGCC ACATGTTGTC
    1501 ATACCTTGAA TGTAGCTGCA AAGCCAATGG AAAGATTTTA GATGTTACTG GAACAGAAGA
    1561 TGTTAATTAG CATAAATCTT CCAAAATGTT CAGAACATAA TGTTAGCTTA ATGTTTTACT
    1621 TTAATAATGT TAGCTTGTGT TAAATTTATG ATTTTTGTTT GTTTGTTTTT TGAGATAGAG
    1681 TCTTATTCTA TTGCCCAAGC TGGGGTGCAG TCACACAATC ACAGGGACTT GCAATGTTGC
    1741 CCAGGCTGGT CTCAAACTCC TGGCCTCAAG TGATCCTCCT GCCTCAGCCT CCCAAAGTTC
    1801 TGGGATTGCA GCTGTGAGCC ACCACGCCCA GTTTACGATT TATTTTTAAG AGCCCCTTGC
    1861 ATACTTTATA GACATTGGGA CCTACCTAGG ATATTCTCGT TATTTTTGTG CACGTAATAG
    1921 AACTTAGAGC ATATTGTTAC TATTTTCGAT TGTCCTAAAA ACTTACAAGG AATTCATTCT
    1981 TATGGCATTG CTGATTATTT CTATGTTCAT TTGATATAAA AGAGTGTTAG TAGGGGCAGA
    2041 ACCCTCAATT GTACATAATA TCAATGATAA AATACAATTC ATTTAACAAT TACCCTCTTA
    2101 AGATGTGGTT TCTAGAAATA CAAATTGTCC CTAACTTACA GTTTTCCAAC TTTACAATTG
    2161 GGCTGTAACA CCATTTTAAG TTGAGAAGCA CGTGATGGTT TGACTTAAAA CTTTTTGACA
    2221 TTATGATGGG TTTTGGGGGT ATTAAGTGCA TTTTGACTTA CAGTATTTTT GACTTATGAA
    2281 GAATTTATTG TAAGGCAAGG GGCAGGTATA TGTTTCTAGA AGCACCTAGA AGTGTTAGAC
    2341 ACTTTCAATG TAAGAGAAGG ATGAGATAAA CAAGGAAATC ACACCTCCAC CTTGGAGGCT
    2401 TATTACAGCT TCATAAACAT ACTCATAAAT ATAAGAAGCA CAAAAGTCAA AAATTCCCTG
    2461 TGAACTTGCA ACTTTCACTC TCTTGAAGGT GGGTGGGCCG CTACCACCAA GAATATCTCC
    2521 TGAAATAGGG CCTACAATCA TAAATGCACA GGACTATATC CTTGGGTGAT TCTACTCTAA
    2581 CACCACATCT CACCTATTTT AGACATGCCA AATGAAACAC TCTTTGTGAA TTTCTGCCGA
    2641 GATACAATCT TGGTGTCTCT TTTTTACCCA GATGTGGACC AGCTAGTGAA GTGCTCCCAC
    2701 GAGCGCTCCA TTCATCTCTT CATCGACTCT CTGTTGAATG AAGAAAATCC AAGTAAGGCC
    2761 TACAGGTGCA GTTCCAAGGA AGCCTTTGAG AAAGGGCTCT GCTTGAGTTG TAGAAAGAAC
    2821 CGCTGCAACA ATCTGGGCTA TGAGATCAAT AAAGTCAGAG CCAAAAGAAG CAGCAAAATG
    2881 TACCTGAAGA CTCGTTCTCA GATGCCCTAC AAAGGTAGGC TGGAGACTGT TGTAAATAAG
    2941 GAAACCAAGG AGTCCTATTT CATCATGCTC ACTGCATCAC ATGTACTGAT TCTGTCCATT
    3001 GGAACAGAGA TGATGACTGG TGTTACTAAA CCCTGAGCCC TGGTGTTTCT GTTGATAGGG
    3061 GGTTGCATTG ATCCATTTGT CTGAGGCTTC TAATTCCCAT TGTCAGCAAG GTCCCAGTGC
    3121 TCAGTGTGGG ATTTGCAGCC TTGCTCGCTG CCCTCCCCTG TAAATGTGGC CATTAGCATG
    3181 GGCTAGGCTA TCAGCACAGA GCTCAGAGCT CATTTGGAAC CATCCACCTC GGGTCAACAA
    3241 ACTATAACCC TTGTGCCAAA TCCAGCCTAC TTCCTGCTTT TGTAAATAGT TTTTTTAAAA
    3301 CTTTTAAGTT CAGGGGTACG TATGTAGGTT TGCTAAAAAG GTAAACTTGT GACATGGGAG
    3361 TTTGTTGTCC AGAATATTCC ATCACCCAGG TATTAAGCTT AGTACCCATT AGTTACTTTT
    3421 CCTGAAGCTC TCCCTCCTCC CACCCTCTGG GAGGCCCCAG TGTCTGTTGT TCCCCTCTAT
    3481 GTGCTCATGC AAAGTTTTAT TAGGACACAG CCACACACAT TCATTACCAT ATTGTCAAAG
    3541 GCTGGTTTCA TGCCACCATA ACAGAGTTGA TAGCCCACAG AGCCTAAAAT ATTTACTCCC
    3601 TGGCCCTTTA CAGAATGTTC ACAACTTACA TAAAGGCAAG GACCATCTGT CTTATTTATT
    3661 TATTTATTTA ATTTGAGATG AAGTCTAGCT TTCTCCTAGG CTGGAGGAGA GGGGCATGAT
    3721 CTTGGCTCAC CACAACCTCT GCCTCCCGGG TTCAAATGAT TCCCCTGCCT CAGCCTCCGG
    3781 AGTAGCTGGG ATAACAGGCA TGCACCATCA TGCCCAGCTA ATTTTTGTAT TTTTAGTAGA
    3841 GAGGGGGTTT CACCGTGTTG ACCAGGCTGG TCTCGAACTG CTGACCTCAG GTGATCTGCC
    3901 CTCCTTGGCC TCATCTGTCT TTTTAAATGC AACTATTCCT GGAAGGCAAG AATATCTCAC
    3961 ACCTTCTAAG ATACTGCCAT TTTGCCAGGA GTTTGTTTCA CACTTGAATT TCAAGCTTGG
    4021 CCTCTTGTTT AGAGGCAGAC CTAAAGGAAT GGTCGGAAAA TGAGAGAGGA GGTCTTCGGA
    4081 TAAATCCGGT GAGAGGGACC AACTTCAGGA AGGGTGGCTT TTGTGGAATC CAGATGGAAA
    4141 CCTGAGGGAA GGGATGATAT TAAAGAACAG TGGCCCCAGG TAAAACATAT GGCACCCATG
    4201 TGTAAGGTGA TTCTTAGAAT CTGTAGAGGT GTCTTTCGTG GTATAGAGGT TGAGGCACCT
    4261 GTGCTTCAAG GAAACCTTAA CTCTTCAAAA TCAGGCAATG CGTATGAGGT AAAGAGAGGA
    4321 CTGTGGGACC ATAATCTTGA AGACACAGAC AGGCTTCACT CATCCCTGCC TCCTGCACCA
    4381 GTGGGTTCAA GGCTCTGTCA GTGTCCCCTA GGGGCACCTC ACCACTCCCA GCTTCTTCAG
    4441 CTCTGGCCTG TCCTGCTGCC TGCAAGGGTT TTGCTTAATT CTCAATTCAA TGTCTCTTCA
    4501 TCTTTTAGTA GCTGTGGGGT TTTGTTGTTG TTCTTCTGTT TTTGCTTAGT ATCTGACTAC
    4561 TTTTTAATTA TAAAAAGAGA TGTATCTAAA CAAAATAGAG ATTGTTATCA GAAGTTCACA
    4621 ACATTTATTA AAAATTTTTT CACCTGGACA AGAGTCTAAA GCAGCATAAA AATATGGTCT
    4681 GCTATATTCT AAACCATCAG TCTTAAGAGA TCTGTGTCTC AGCTTAAGAG AAAATACATT
    4741 TAATAGACAG TAACACAAAT AAGAAAAAAA TCTGACCAAG GATAGTGGGA TATAGAAGAA
    4801 AAAACATTCC AAGAATTATT TTATTTATTT ATTTATTTAT TTATTTATTT ATTTATTTAT
    4861 TTTTGAGACA CGGTCTCGCT CAGTTACCCA GGCTGGAGTG CAGCGGCGCA ATCTTAACTC
    4921 ACTGCAACCT CTGCTTTCCG GTTCAAGCGA TTCTCCTGCC TCAGCCTCCT GAGTAACTGG
    4981 GATTACAGGC ACCCGCCACC ACGCCCAACT AATTTCTGTA TTTTTCTTAG TAGAAACAGG
    5041 GTTTCACCAT GTTGGCCAAG CTAGTCTCAA ACTCCTGACC TCAGGTGATT CACCCACCAA
    5101 GGCCTCCCAA AGTGCTGGGA TTACAGGCAT GAGCCACCAT GCCTGGCCTC CAAAAACTCT
    5161 TTTTTCCTCC ATCATCATGG TTCTATTTTA GTCCTGCTGC CTTTCCTTTT AACCTCTCCC
    5221 CAGGCCCATT TGCTCAGGGT TTTTGGTAGA GACCAGAGGA GGGGCAGGGA GGAGATATAG
    5281 AAGTTCAACT ACCTGCTTCC AGAGGCTGTC CCTAGTATAG AATACTTTAG GGGCTGGCTT
    5341 TACAAGGCAG TCCTTGTGGC CTCACTGATG GCTCAATGAA ATAAGTTCTT TTTTAAAAAA
    5401 AATTTTATTT ATTTCCATAG GTTATTGGGG GAACAGGTGG TGTTTGGTTA CATGAGTAAG
    5461 TTCTTTAGTA GTGATTTGTG AGATTTTGGT GTGCCCATTA CGGAATGGAA AAATCAACGA
    5521 AATAAGTTCT ATGATGCACC TACTAGACAC CTAATCTGCA CTAGATGGTG GGGGAATTAA
    5581 GAGCATGGGC ATGATCCTGT GACCGGAAGC CCGCTTACAG TCAGGGTGGA GGACAGACCT
    5641 ACTCATGAAA CAAACACAGT GACATATAGT GACACAGAAG CAAATGTCAA ATATGCTTGC
    5701 TCCAGATGCT AAGGCACAAG ATGGCCAAGG ATGGCGGAGT TCATGGAGAA AGCATCATGA
    5761 GTGTTTTGGC CTTCTGATTT GATCTCCCTA GCACCCCTCA AAGATGGCTA CTTCCTAATG
    5821 CTGCTTGGCA ATTCAGACAC ATTTGGGTTT TTCCTATGCA TATAACCACA CTTTTCTGAA
    5881 AGGGAGTAGA ATTCAAGGTC TGCATTTTCT AGGTATGAAC ACTGTGCATG ATGAAGTCTT
    5941 TCCAAGCCAC ACCAGTGGTT CCATGTGTGT GCACTTCCGG TTTGAGTGCT AGTGAGATAC
    6001 TTCTGTGGTT CTGAATTGCC TGACTATTTG GGGTTGTGAT ATTTTCATAA AGATTGATCA
    6061 ACATGTTCGA ATTTCCTCCC CAACAGTCTT CCATTACCAA GTAAAGATTC ATTTTTCTGG
    6121 GACTGAGAGT GAAACCCATA CCAATCAGGC CTTTGAGATT TCTCTGTATG GCACCGTGGC
    6181 CGAGAGTGAG AACATCCCAT TCACTCTGTG AGTAGCACAG GGGGGCGGTC ATCATGGCAC
    6241 CAGTCCCTCC CCTGCCATAA CCCTTGGTCT GAGCAGCAGA AGCAGAGAGC GATGCCTAGA
    6301 AAACAAGTCT TTAGTTAAAA AAATCAGAAT TTCAAAATTG AGGTCTTTCC TCTATTTGAT
    6361 ATTGAGAAAA AAATGCTTCA AATTGGCCAT TTTATTTTCA CTTACTAGTT ATATTTTTTT
    6421 ATTTATCATC TTATATCTGT TTATTTCTTT TATAAAGCTG CTGTTAAACA ATATAATTAA
    6481 ACTATCTCAA AAGGTTTGAC ATTAAAGAAA ATGAGCAATG GTAACAGGAA ACCACTCTAT
    6541 AGATGTACAT ATAATATGTA CAGAAAATAT AAGTAGTAAG AAGTCCATGA CAAAGTGTTA
    6601 GCTCTTTTTT TTTTTTTTTT TTTTTTTTTT TTTGAGATGG AGTCTCTCTC CTATTGCCCA
    6661 GGCTGGAGTG CAGTGATTCG ATCTCAGCTC ACTGCAACCT CTACCTCCCG AGTTCAAACA
    6721 ATTCTTCTGT CTCAGCCTCC CGAGTAGCTG GGGCTGCAGG TGCCCACCAC CATGCCCAGC
    6781 TAATTTTTGT ATTTTTAGTA GCGACAGGGT CTCACCATGT TGGCCAAGCT GGTCTTGAAT
    6841 TCCTGATCTC AGGTGATCCA CCCGCCTCGG CCTCCCAAAG TGCTGGGATT ACAGGTGTGA
    6901 GCCACCATGC CCAGCCTACC CTTTACTACT AATCAAAGAA ATAAAAGTAA GGCAACTTGA
    6961 TACTTTTACA ATTACTAGAT GAACAAATCT TTAAAAATAG CCAGTGCAGA CAAGGTGGTG
    7021 AAGCAGAACA TGCGAACCTA CCATGCATCA TTCACGGCTA GAACCCTCCA GGTGCGGAAG
    7081 GTAGTATTTT AATAACTTTC CATAGCTACA AAATATTATT ACATAGAAGG GAGTGATTTT
    7141 TTTCTAATAT TTATCCTAAA GAAATAGTCA ACAAACATTT TTAAAAAACA TCAATTACAG
    7201 TCGTACCTAT ACTAGCATAA ATTAGAAACC CAGTATCCAA CATTGAGGCA GTGGGTAAAT
    7261 GAATCGTGGT TTATCAAGTC ATTAAAATCA ATCTAGCCTT TAAAAACTAT AATTGTAGGA
    7321 AACCCAGGAA AACATAGTAA AAAATGGAAT ATAAAATCTA AAGAGAATAA AGAATAGAGA
    7381 ATCGTATGTG TGCTATGATT GTAGCTAAAT AATGTTCAAG TATCAACACA AATTGAAAAG
    7441 GAATACATGA AAATGAAAAT TATATTTCTG AATGATTGAC TTCAGGATTT TCTTTTAGAA
    7501 TTGTATTAAA TAGTTCATGT CATTAGGATA AATGCTGGAA TGTGGATATA ATTTAAAATA
    7561 TACTAAATGC CATCGACCTT CATTTTGAGT TCTTTGTTGG ACATTTTTGT GCATTTTTAA
    7621 AATATCCCCT AAATAATAAA GCTATTTATA TTTGGAGAGG AGAAAAAAAA GTGGGGGGCA
    7681 GGGAGAGCTG ATCTCTATAA CTAACCAAAT TTATTGCTTT TTTGTTTAGG CCTGAAGTTT
    7741 CCACAAATAA GACATACTCC TTCCTAATTT ACACAGAGGT AGATATTGGA GAACTACTCA
    7801 TGTTGAAGCT CAAATGGAAG AGTGATTCAT ACTTTAGCTG GTCAGACTGG TGGAGCAGTC
    7861 CCGGCTTCGC CATTCAGAAG ATCAGAGTAA AAGCAGGAGA GACTCAGAAA AAGTAATTAA
    7921 ATGTATTTTT CTTCCTTCAC TTTAGACCCC CACCTGATGT CAGGACCTAG GGGCTGTATT
    7981 TCAGGGGCCT TCACAATTCA GGGAGAGCTT TAGGAAACCT TGTATTTATT ACTGTATGAT
    8041 GTAGATTTTC TTTAGGAGTC TTCTTTTATT TTCTTATTTT TGGGGGGCGG GGGGGGAAGT
    8101 GACAGTATTT TTGTATTTCA TGTAAGGAAA ACATAAGCCC TGAATCGCTC ACAGTTATTC
    8161 AGTGAGAGCT GGGATTAGAA GTCAGGAATC TCAGCTTCTC ATTTGGCACT GTTTCTTGTA
    8221 AGTACAAAAT AGTTAGGGAA CAAACCTCCG AGATGCTACC TGGATAATCA AAGATTCAAA
    8281 CCAACCTCTT CAAGAAGGGT GAGATTCCAA GATAATCTCA ACCTGTCTCC GCAGCCCCAC
    8341 CCATGTGTAC CCATAAAATG AATTACACAG AGATCGCTAT AGGATTTAAA GCTTTTATAC
    8401 TAAATGTGCT GGGATTTTGC AAACTATAGT GTGCTGTTAT TGTTAATTTA AAAAAACTCT
    8461 AAGTTAGGAT TGACAAATTA TTTCTCTTTA GTCATTTGCT TGTATCACCA AAGAAGCAAA
    8521 CAAACAAACA AAAAAAAAAA GAAAAAGATC TTGGGGATGG AAATGTTATA AAGAATCTTT
    8581 TTTACACTAG CAATGTCTAG CTGAAGGCAG ATGCCCTAAT TCCTTAATGC AGATGCTAAG
    8641 AGATGGCAGA GTTGATCTTT TATCATCTCT TGGTGAAAGC CCAGTAACAT AAGACTGCTC
    8701 TAGGCTGTCT GCATGCCTGT CTATCTAAAT TAACTAGCTT GGTTGCTGAA CACCGGGTTA
    8761 GGCTCTCAAA TTACCCTCTG ATTCTGATGT GGCCTGAGTG TGACAGTTAA TTATTGGGAA
    8821 TATCAAAACA ATTACCCAGC ATGATCATGT ATTATTTAAA CAGTCCTGAC AGAACTGTAC
    8881 CTTTGTGAAC AGTGCTTTTG ATTGTTCTAC ATGGCATATT CACATCCATT TTCTTCCACA
    8941 GGGTGATCTT CTGTTCTAGG GAGAAAGTGT CTCATTTGCA GAAAGGAAAG GCACCTGCGG
    9001 TATTTGTGAA ATGCCATGAC AAGTCTCTGA ATAAGAAGTC AGGCTGGTGA GCATTCTGGG
    9061 CTAAAGCTGA CTGGGCATCC TGAGCTTGCA CCCTAAGGGA GGCAGCTTCA TGCATTCCTC
    9121 TTCACCCCAT CACCAGCAGC TTGCCCTGAC TCATGTGATC AAAGCATTCA ATCAGTCTTT
    9181 CTTAGTCCTT CTGCATATGT ATCAAATGGG TCTGTTGCTT TATGCAATAC TTCCTCTTTT
    9241 TTTCTTTCTC CTCTTGTTTC TCCCAGCCCG GACCTTCAAC CCAGGCACAC ATTTTAGGTT
    9301 TTATTTTACT CCTTGAACTA CCCCTGAATC TTCACTTCTC CTTTTTTCTC TACTGCGTCT
    9361 CTGCTGACTT TGCAGATGCC ATCTGCAGAG CATGTAACAC AAGTTTAGTA GTTGCCGTTC
    9421 TGGCTGTGGG TGCAGCTCTT CCCAGGATGT ATTCAGGGAA GTAAAAAGAT CTCACTGCAT
    9481 CACCTGCAGC CACATAGTTC TTGATTCTCC AAGTGCCAGC ATACTCCGGG ACACACAGCC
    9541 AACAGGGCTG CCCCAAGCAC CCATCTCAAA ACCCTCAAAG CTGCCAAGCA AACAGAATGA
    9601 GAGTTATAGG AAACTGTTCT CTCTTCTATC TCCAAACAAC TCTGTGCCTC TTTCCTACCT
    9661 GACCTTTAGG GCTAATCCAT GTGGCAGCTG TTAGCTGCAT CTTTCCAGAG CGTCAGTACT
    9721 GAGAGGACAC TAAG
  • Also for purposes of the present invention, the 3′ end of the human lipoprotein lipase gene includes [0029] exon 10 and the 3′ untranslated region (3′UTR), at least partially defined by nucleotide positions 1 through 3240 of the reference sequence of Oka et al., (GenBank accession No. X52978 and X53518; K. Oka et al., Structure and polymorphic map of human lipoprotein lipase gene, Biochim. Biophys. Acta 1049(1):21-26 [1990], Erratum: [Biochirn Biophys Acta 1991 Nov. 11;1090(3):357]). In the reference sequence of Oka et al., the first and second polyadenylation signals are at nt. 15-20 and 411-416, respectively (in bold), and two analogous AGTAAA sequences are at nt. 468-473 and 529-534 (in bold). The poly(A) addition site is at nt. 439. The following is the reference sequence of Oka et al.:
    1 GAATTCTCTC TAAAAATAAA ATGATGTATG ATTTGTTGTT GGCATCCCCT TTATTAATTC (SEQ.ID.NO.:94).
    61 ATTAAATTTC TGGATTTGGG TTGTGACCCA GGGTGCATTA ACTTAAAAGA TTCACTAAAG
    121 CAGCACATAG CACTGGGAAC TCTGGCTCCG AAAAACTTTG TTATATATAT CAAGGATGTT
    181 CTGGCTTTAC ATTTTATTTA TTAGCTGTAA ATACATGTGT GGATGTGTAA ATGGAGCTTG
    241 TACATATTGG AAAGGTCATT GTGGCTATCT GCATTTATAA ATGTGTGGTG CTAACTGTAT
    301 GTGTCTTTAT CAGTGATGGT CTCACAGAGC CAACTCACTC TTATGAAATG GGCTTTAACA
    361 AAACAAGAAA GAAACGTACT TAACTGTGTG AAGAAATGGA ATCAGCTTTT AATAAAATTG
    421 ACAACATTTT ATTACCACAC TAAGTCATTA TTTTGTATCA TTTTTAAAGT AAATTTATTC
    481 TTAGGTCAGA TTCACTCAGC ATATTTTGAC TAAGTAACCA CTGTACTTAG TAAACCGAAG
    541 AGCTTCTGAG AATTATAGTG TACCGTATAG ATATTTTTAA CATTTATATT TGTATAAAGC
    601 TAAAGAAAGC CTTACATATC CTTTAAACTG ACTATAGAAG AAAATGATAC AGAATTTTGC
    661 CTGCATAAAG TACACAGGAC TATTCTTGCC TACAATATGC TTTTTCACAA GCAAAATGTT
    721 AGACTAATAT AAGGCATCTT TGGCCATTTT ATAGTGTACA TCATCTCTAT TTCTGAGGCC
    781 TCATTGTTAG CTGTAACGCA AGTAGCATTT GTGCAATAAA ATGAACTATT TGGGATGGGA
    841 GGGTACATTT TTTAGAACTT TGCTTTGGGT TGCCTTGATA ATTAATAGCA TATAGTCCAT
    901 TTATGCAGCT AAGTAGGGAT TGCTTCTTAG TACAGTCAGG AAGAATTTAG CCCAGAAAAC
    961 AATTATTTCA ATGGCCACTG ACCCAAACTT CCAGGCTGAA GAGCAATGGC GTGATCATGG
    1021 CTCACTGCAC CTCCACCTCC CAGGCTCAAG TGATTCTCCT GCCTCAGCCT CCCAAGTAGA
    1081 TGGTACTACA AGCACACGCC ACTGCACCCA GCTAATTTTT GTATTTTTTG TAGAGATGGG
    1141 GGTTTCACCA TGTTGCCCAG GCTGGTCTTA AATTCCTGGC CTCAAGTGTC TGCCCCCCTT
    1201 GGCCTCCCAA AGTGCTGGAA TTACAGGCAT GAGCCACCAT GTCCAGCCTT GACCCAAACT
    1261 TTTATTGTCA GTTAGCTATT GGGGGCTTCT GGAGTTTGGG TCTCCCCTGA CAGGAGGGGG
    1321 CTCCCCAGTT CACACTTGGC CACTGCCCAT CAATTCCTGT TGATATGATC AACAAGATAG
    1381 ACAATTGCAA ATGTTGCTGA GGATGTGGAG AAGTGTGAAC CTGTGTAAGT GGCTGATGGG
    1441 AATGTAAAAT GGCACAGCCA CTATGGAGAA CAATTTGGTA GTATTTCCAA AGTTAAGCAT
    1501 AGAGTTTAAC CCATATGACC CAGCAATTCC ACTCCTAGAT ATATACCCAA GAGAAATGAA
    1561 AACACAGATC CACAAAGATT TGCACACACA GGTTCATAGC AGCATTAATC AGATTAGTCC
    1621 CAAAGTGGAC AACCCAAATG TCCATGAACT TGTGAAAGAG ATAAGGAAAA TGTGACAAAT
    1681 TCACATAATA AAATATTATT CAGAAGTAAA AAGAACAAGC AGCAGATATA TGATACAACA
    1741 CGATGCGCCT TGAAAACGTT TAGCCATATG AAAGAAACCA GATGCAAAAT GGAACCATGG
    1801 CTTAGGGGAG GAGAACGGCA CAATGGTGTA AAAGTTGCAG AGAGGAACAA AAAGGCTACC
    1861 TGCCTCGCTC CCAGGCCAAG TAACACAGGA GGAAAGAAAA TATCCACATA TGCGAGGGCT
    1921 AAAGGAAAGA GGTGTTCTCA AGCTGAAGCA GGAGGTGGGA CTCAACTCTG GAGGTGGGCC
    1981 TCACACACTG TACCAAATTG AGGACTAGCT AAAACAGGGA TGGGGGTGAA AGCACCTTTT
    2041 CGTAAGACAT GCCCACCATT GTCCCGTTCT CCTCCCTTAA GCCCTTGTCT TGCTCATGTC
    2101 AGCAAGCTTA TTGCCATCTA TTCTTCCTAG TTACAGACAT CTGTGGAGCT CTGAGTTTTT
    2161 TGCCTAATCA TTATTTTAGA ACCTGGTTCA CTCTCTCTCC CTTCTACACT AGTTCTGTCA
    2221 TTATTATTAC TGATTTCAGT ACCTCTGAGG TGATAGATTT TATTTTCCAA TGGCAGCCAC
    2281 AACACTACCT CCCATTCTAT ATGTTCCCCT GCAATGTTGC CTTGACATCC CTATTAAGAG
    2341 TTGGAATCTA GTCACCCCGC TTTTCTAGTC TCCCCACTCC TTTGAACTTG TGTGGGCCCT
    2401 AAGATTGCTT CTACTAGTAG AATAGAACTA AAATGACCCT GGACCAGTGT GGGGTGCAGC
    2461 CCTTAACTGG CCTGGCAGCT TCTGCTTTTG GTTCCTTGGG GCACTCACTC TTGGGAAACT
    2521 TCCCTTTGGA ACTCAGCATT CATGATGCGG AAGTTGAAGC CACATGAAAA GAGCATATGG
    2581 TGGTTCTCTC AGCTCCCAGC CAACAACCAG TCTCGACTGT CAGCCATGTG AGTGAGGCAT
    2641 CTTGGACCTC CGGCCAGTTG AGTGTTCAGA AGACTGCAGC TCGAGCTGGC ATCTGGATGC
    2701 AACCACATGA GAGACGCTCT GCCCAGCCAA GCCCAGCCAA CTCACAGTAC TATGAGAGAT
    2761 ACTAATAACT TGTTGTTGTT GTTGTTGTTG TTGTTTTTAT TATTAAACTT TAAGTTTTAG
    2821 CATACACGTG CACAACGTGC AGGTTAGTTA CATATGTATA CCTGGGCCAT GTTGGTGTGC
    2881 TGCACCCAGT AACTCGTCAT TTAACATTAG GTATATCTCC AAATGCTATC CCTCCCCCCT
    2941 CCCTAAGTTT TTAGGAGTTT GCTTTGCAAC GATAGATAGT TGAAACATCT GGATGATGCA
    3001 TCCAGTATTC TGGCTTCTCA CTGCCTTTAC CTCCTCTCTC CCATGGCCTT GTCTTCTAAA
    3061 TCTACCTTTA CATAGAAACA TTCAGTCACG TGCTATACTA TATCATGCCA TTACTAATAA
    3121 CTCATAAACT CAATTTCAAC TTCTCCCTTC TTTGACTACC ACATGCTATC TTTTTACTTT
    3181 AATCAGTCTA GTGCTCTCAG TTCAACAGCT CCTCAACTGC CCCAGGACCT CCAATACATT//
  • Also for purposes of the present invention, the 3′ end of the human lipoprotein lipase gene includes the intervening nucleotide sequence between the end of the Nickerson reference sequence in [0030] intron 9 and the beginning of the reference sequence of Oka et al.
  • A non-coding or untranslated region of the 3′ end of the human LPL gene includes any non-transcribed or untranslated nucleotide sequence within the 3′ end, including all intronic sequences. Included are the part of [0031] intron 6 extending from Nickerson reference sequence position nt. 4801 through nt. 6086; intron 7 from nt. 6208 through nt. 7729, intron 8 from nt. 7913 through nt. 8941; and intron 9 from nt. 9047 through nt. 9734. Also included is exon 10 and the 3′UTR.
  • A variant allele in a non-coding or untranslated region of the 3′ end of the human LPL gene is a mutation or polymorphism with respect to the Nickerson or Oka et al. reference sequences, of any class, such as, but not limited to, a single nucleotide polymorphism (SNP). Included among the sources of variant alleles in a non-coding or untranslated region of the 3′ end of the human LPL gene are deletion mutations, insertion mutations, inversions, translocations, transitions, tranversions, or repeats. [0032]
  • Examples of homozygous genotypes that indicate a genetic predisposition to non-responsiveness to statin drug treatment, in accordance with the present method, include, but are not limited to, the [0033] HindIII 2/2 and (TTTA)n 4/4 genotypes.
  • The [0034] HindIII 2 variant allele, is created by a T to G transition in the single HindIII recognition site mapped in intron 8, i.e., AAGCTT to AAGCGT, at position 8393 of the Nickerson reference sequence. (K. Oka et al. [1990]; C. Heinzmann et al., RFLP for the human lipoprotein lipase [LPL] gene: HindIII, Nuc. Acids Res. 15:6763 [1987]; D. A. Nickerson et al. [1998]). For purposes of the present invention, nucleic acids comprising the normal locus of the HindIII recognition site in intron 8 of the human LPL gene are any nucleic acid sequences that overlap the entire six-basepair region at positions 8389-8394 of the Nickerson reference sequence, whether or not the nucleic acid sequence of a particular human subject at that locus is AAGCTT.
  • The tetranucleotide (TTTA)[0035] n repeat sequence in intron 6 of the LPL gene begins at position 4819 of the Nickerson reference sequence and extending to position 4864. There are five known (TTTA)n alleles or polymorphisms. Allele 4 yields a 131 bp nucleotide fragment when PCR amplification is done using a primer set comprising reverse primer GZ-15 (5′-CCT GGG TAA CTG AGC GAG ACT GTG TC-3′; SEQ. ID. NO.: 33) and forward primer GZ-14 (5′-ATC TGA CCA AGG ATA GTG GGA TAT A-3′; SEQ. ID. NO.: 34).
  • In the (TTTA)[0036] n 4 variant allele, two additional TTTA repeats (shown below in underlined boldface type) are added to give the (TTTA)4 4 allele length of 131 bp. Nucleotide position numbers with respect to the Nickerson reference sequence will be off from that point on:
    4501 TCTTTTAGTA GCTGTGGGGT TTTGTTGTTG TTCTTCTGTT TTTGCTTAGT ATCTGACTAC (SEQ.ID.NO.:93).
    4561 TTTTTAATTA TAAAAAGAGA TGTATCTAAA CAAAATAGAG ATTGTTATCA GAAGTTCACA
    4621 ACATTTATTA AAAATTTTTT CACCTGGACA AGAGTCTAAA GCAGCATAAA AATATGGTCT
    4681 GCTATATTCT AAACCATCAG TCTTAAGAGA TCTGTGTCTC AGCTTAAGAG AAAATACATT
    4741 TAATAGACAG TAACACAAAT AAGAAAAAAA TCTGACCAAG GATAGTGGGA TATAGAAGAA
    4801 AAAACATTCC AAGAATTATT TTA TTTATTTA TTTATTT ATTTATTTAT TTATTTATTT ATTTATTTAT
    4861 TTTTGAGACA CGGTCTCGCT CAGTTACCCA GGCTGGAGTG CAGCGGCGCA ATCTTAACTC
    4921 ACTGCAACCT CTGCTTTCCG GTTCAAGCGA TTCTCCTGCC TCAGCCTCCT GAGTAACTGG
    4981 GATTACAGGC ACCCGCCACC ACGCCCAACT AATTTCTGTA TTTTTCTTAG TAGAAACAGG
    5041 GTTTCACCAT GTTGGCCAAG CTAGTCTCAA ACTCCTGACC TCAGGTGATT CACCCACCAA
    5101 GGCCTCCCAA AGTGCTGGGA TTACAGGCAT GAGCCACCAT GCCTGGCCTC CAAAAACTCT//
  • A statin drug is any 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitor, including, but not limited to, lovastatin, pravastatin, simvastatin, atorvastatin, fluvastatin, and cerivastatin. [0037]
  • A human subject, particularly a CABG patient, who has a genetic predisposition for non-responsiveness to statin drug treatment possesses an hereditary inclination, susceptibility, or tendency to develop atherosclerotic stenosis of coronary blood vessels, including of a native coronary artery, or of any coronary artery bypass graft using a saphenous vein or any other vein or artery, in a manner that does not respond to statin drug treatment. It does not mean that at any time such a person will actually develop stenosis of a coronary blood vessel, or graft worsening (graft lumen narrowing). It merely means that he or she has a greater likelihood of developing stenosis, when statin treatment is given; this is in comparison to the general population of individuals who are not homozygous for a mutation in the 3′ end of the LPL gene, for example for the [0038] HindIII 2 allele or (TTTA)n 4 allele, including those who have atherosclerotic coronary artery disease, who are coronary artery bypass graft patients.
  • A CABG patient is a human subject who is a candidate for coronary artery bypass graft surgery or one who has undergone a coronary artery bypass graft procedure. [0039]
  • Any human tissue containing nucleic acids can be sampled and collected for the purpose of practicing the methods of the present invention. A most preferred and convenient tissue for collecting is blood. Collecting a tissue sample includes in vitro harvest of cultured human cells derived from a subject's tissue or any means of in vivo sampling directly from a subject, for example, by blood draw, spinal tap, tissue smear or tissue biopsy. Optionally, tissue samples are stored before analysis by well known storage means that will preserve a sample's nucleic acids in an analyzable condition, such as quick freezing, or a controlled freezing regime, in the presence of a cryoprotectant, for example, dimethyl sulfoxide (DMSO), glycerol, or propanediol-sucrose. Tissue samples can also be pooled before or after storage for purposes of amplifying them for analysis. [0040]
  • Amplifying nucleic acids from a tissue sample of a subject to obtain amplification products includes any conventional means of amassing sufficient nucleic acid material for analysis. Most preferably, amplification is by conventional polymerase chain reaction (PCR) methods. Alternatively, amplification of nucleic acids is by in vitro cell culture and harvest of the subject's cultured cells, or by multiple sampling from the subject's tissues in vivo and pooling of multiple tissue samples from a subject. Nucleic acids thus amplified are amplification products if they include a non-coding or untranslated nucleotide sequence from the 3′ end of the LPL gene, for example, the normal locus of the HindIII recognition site in [0041] intron 8, or the tetranucleotide (TTTA)n repeat region of intron 6, of the human LPL gene.
  • In a preferred embodiment of the present method, nucleotide sequencing is used to analyze the amplification products of the nucleic acids in a tissue sample to detect homozygosity for a mutation in the 3′ end of humanLPL. The skilled artisan can detect the mutation by any nucleotide sequencing means, for example conventional dideoxy sequencing or preferably by using a commercially available automated sequencer, then comparing the subject's nucleotide sequences to other known human LPL sequences available in genomic sequence databases, such as GenBank. [0042]
  • In a most preferred embodiment that employs nucleotide sequencing, sequencing of 3′ end LPL sequences is accomplished by using fluorescence-based single strand conformation polymorphism analysis (SSCP), a routine and reliable means of identifying point mutations, small insertions or deletions. (J. S. Ellison, [0043] Fluorescence-based mutation detection. Single-strand conformation polymorphism analysis [F-SSCP], Mol. Biotechnol. 5(1):17-31 [1996]; H. Iwahana et al., Multiple fluorescence-based PCR-SSCP analysis using internal fluorescent labeling of PCR products, Biotechniques 21(3):510-14,516-19 [1996]; R. Makino et al., F-SSCP: fluorescence-based polymerase chain reaction-single-strand conformation polymorphism [PCR-SSCP], PCR Methods Appl. 2(1):10-13 [1992]). An automated system may be used, such as an Applied Biosystems DNA sequencer, equipped with GENESCAN 672®, Genotyper®, or another appropriate analytical software package.
  • Optionally, high throughput analysis may be achieved by PCR multiplexing techniques well known in the art. (E.g., Z. Lin et al., [0044] Multiplex genotype determination at a large number of gene loci, Proc. Natl. Acad. Sci. USA 93(6):2582-87 [1996]).
  • In a most preferred embodiment, nucleotide sequencing is unnecessary for analyzing the amplification products. For example, heteroduplex analysis on high resolution gel matrices are employed to detect even single nucleotide polymorphisms. (M. T. Hauser et al., [0045] Generation of co-dominant PCR-based markers by duplex analysis on high resolution gels, Plant. J. 16(1):117-25 [1998]). The PCR/OLA procedure can be used for analyzing amplification products to detect SNPs in the 3′ end of the human LPL gene. (B. R. Glick and J. J. Pastemak, Molecular Biotechnology: Principles and Applications of Recombinant DNA, ASM Press, Washington, D.C., pp. 197-200 [1994]). Conformation-sensitive gel electrophoresis of amplification products may also be employed as a means of analysis by the skilled artisan in practicing the methods of the present invention. (A. Markoff et al., Comparison of conformation-sensitive gel electrophoresis and single strand conformation polymorphism analysis for detection of mutations in the BRCA1 gene using optimized conformation analysis protocols, Eur. J. Genet. 6(2):145-50 [1998]).
  • Electrophoresis for analyzing amplification products is done rapidly and with high sensitivity by using any of various methods of conventional slab or capillary electrophoresis, with which the practitioner can optionally choose to employ any facilitating means of nucleic acid fragment detection, including, but not limited to, radionuclides, UV-absorbance or laser-induced fluorescence. (K. Keparnik et al., [0046] Fast detection of a (CA) 18 microsatellite repeat in the IgE receptor gene by capillary electrophoresis with laser-inducedfluorescence detection, Electrophoresis 19(2);249-55 [1998]; H. Inoue et al, Enhanced separation of DNA sequencing products by capillary electrophoresis using a stepwise gradient of electric field strength, J. Chromatogr. A. 802(1):179-84 [1998]; N. J. Dovichi, DNA sequencing by capillary electrophoresis, Electrophoresis 18(12-13):2393-99 [1997]; H. Arakawa et al., Analysis of single-strand conformation polymorphisms by capillary electrophoresis with laser inducedfluorescence detection, J. Pharm. Biomed. Anal. 15(9-10):1537-44 [1997]; Y. Baba, Analysis of disease-causing genes and DNA-based drugs by capillary electrophoresis. Towards DNA diagnosis and gene therapy for human diseases, J. Chromatgr B. Biomed. Appl. 687(2):271-302 [1996]; K. C. Chan et al., High-speed electrophoretic separation of DNA fragments using a short capillary, J. Chromatogr B. Biomed. Sci. Appl. 695(1): 13-15 [1997]). Any of diverse fluorescent dyes can optionally be used to label primers of the present invention or amplification products for ease of analysis, including but not limited to, SYBR Green I, Y1O-PRO-1, thiazole orange, Hex (i.e., 6-carboxy-2′,4′,7′,4,7--hexachlorofluoroscein), pico green, edans, fluorescein, FAM (i.e., 6-carboxyfluorescein), or TET (i.e., 4,7,2′,7′-tetrachloro-6-(carboxyfluoroscein). (E.g., J. Skeidsvoll and P. M. Ueland, Analysis of double-stranded DNA by capillary electrophoresis with laser-inducedfluorescence detection using the monomeric dye SYBR green I, Anal. Biochem. 231(20):359-65 [1995]; H. Iwahana et al., Multiple fluorescence-based PCR-SSCP analysis using internalfluorescent labeling of PCR products, Biotechniques 21(30:510-14, 516-19 [1996]).
  • Analyzing the amplification products can also be done by means of restricting the amplification products with one or more restriction enzymes. When the amplification products comprise the normal locus of the HindIII recognition site in [0047] intron 8 of the human LPL gene, the restriction enzyme employed is preferably HindIII. Restriction of nucleic acids is followed by separation of the resulting fragments and analysis of fragment length or differential fragment migration in denaturing high-performance liquid chromatography (DHPLC) or gel electrophoresis, as above, including restriction-capillary electrophoresis. For example, this can be achieved by techniques known in the art, such as PCR-restriction fragment-SSCP, which can detect single base substitutions, deletions or insertions. (M. Tawata et al., A mass screening device of genome by polymerase chain reaction-restriction fragment-single strand conformation polymorphism analysis, Genet. Anal. 12(3-4): 125-27 [1996]; H. H. Lee et al., Mutational analysis by a combined application of the multiple restriction fragment-single strand conformation polymorphism and the direct linear amplification DNA sequencing protocols, Anal. Biochem. 205(2);289-93 [1992]).
  • The present invention also relates to an oligonucleotide primer for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human. Useful oligonucleotide primers for amplifying the nucleic acids include any 15 to 28-mer nucleotide sequence that hybridizes with a nucleic acid fragment of the Nickerson or Oka reference sequences, under conventional conditions of stringency used for hybridization in PCR, and together in a set with another primer sequence amplifies a non-coding or untranslated region within the 3′ end of the human LPL gene. A preferred primer is a 20 to 24-mer. [0048]
  • Useful for amplifying non-coding or untranslated nucleic acid sequences from intron 6 ( beginning at position 5988 of the Nickerson reference sequence) through [0049] intron 9, is a set of oligonucleotide primers having nucleotide sequences that are fragments of the nucleotide sequences in GenBank accession numbers M76722 (below) and M76723 (opposite strand). The nucleotide sequence of M76722 is the following:
       1 GAATTCAAGG TCTGCATTTT CTAGGTATGA ACACTGTGCA TGATGAAGTC TTTCCAAGCC (SEQ.ID.NO.:81).
      61 ACACCAGTGG TTCCATGTGT GTGCACTTCC GGTTTGAGTG CTAGTGAGAT ACTTCTGTGG
     121 TTCTGAATTG CCTGACTATT TGGGGTTGTG ATATTTTCAT AAAGATTGAT CAACATGTTC
     181 GAATTTCCTC CCCAACAGTC TTCCATTACC AAGTAAAGAT TCATTTTTCT GGGACTGAGA
     241 GTGAAACCCA TACCAATCAG GCCTTTGAGA TTTCTCTGTA TGGCACCGTG GCCGAGAGTG
     301 AGAACATCCC ATTCACTCTG TGAGTAGCAC AGGGGGGCGG TCATCATGGC ACCAGTCCCT
     361 CTCCTGCCAT AACCCTTGGT CTGAGCAGCA GAAGCAGAGA GCGATGCCTA GAAAACAAGT
     421 CTTTAGTTAA AAAAATCAGA ATTTCAAAAT TGAGGTCTTT CCTCTATTTG ATATTGAGAA
     481 AAAAATGCTT CAAATTGGCC ATTTTATTTT CACTTACTAG TTATATTTTT TTATTTATCA
     541 TCTTATATCT GTTTATTTCT TTTATAAAGC TGCTGTTAAA CAATATAATT AAACTATCTC
     601 AAAAGGTTTG ACATTAAAGA AAATGAGCAA TGGTAACAGG AAACCACTCT ATAGATGTAC
     661 ATATAATATG TACAGAAAAT ATAAGTAGTA AGAAGTCCAT GACAAAGTGT TAGCTCTTTT
     721 TTTTTTTTTT TTTTTTTTTT TTTTTGAGAT GGAGTCTCTC TCTATTGCCC AGGCTGGAGT
     781 GCAGTGATTC GATCTCAGCT CACTGCAACC TCTACCTCCC GAGTTCAAAC AATTCTTCTG
     841 TCTCAGCCTC CCGAGTAGCT GGGGCTGCAG GTGCCCACCA CCATGCCCAG CTAATTTTTG
     901 TATTTTTAGT AGCGACAGGG TCTCACCATG TTGGCCAAGC TGGTCTTGAA TTCCTGATCT
     961 CAGGTGATCC ACCCGCCTCG GCCTCCCAAA GTGCTGGGAT TACAGGTGTG AGCCACCATG
    1021 CCCAGCCTAC CCTTTACTAC TAATCAAAGA AATAAAAGTA AGGCAACTTG ATACTTTTAC
    1081 AATTACTAGA TGAACAAATC TTTAAAAATA GCCAGTGCAG ACAAGGTGGT GAAGCAGAAC
    1141 ATGCGAACCT ACCATGCATC ATTCACGGCT AGAACCCTCC AGGTGCGGAA GGTAGTATTT
    1201 TAATAACTTT CCATAGCTAC AAAATATTAT TACATAGAAG GGAGTGATTT TTTTCTAATA
    1261 TTTATCCTAA AGAAATAGTC AACAAACATT TTTAAAAACA TCAATTACAG TCGTACCTAT
    1321 ACTAGCATAA ATTAGAAACC CAGTATCCAA CATTGAGGCA GTGGGTAAAT GAATCGTGGT
    1381 TTATCAAGTC ATTAAAATCA ATCTAGCCTT TAAAAACTAT AATTGTAGGA AACCCAGGAA
    1441 AACATAGTAA AAAATGGAAT ATAAAATCTG AAGAGAATAA AGAATAGAGA ATCGTATGTG
    1501 TGCTATGATT GTAGCTAAAT AATGTTCAAG TATCAACACA AATTGAAAAG GAATACATGA
    1561 AAATGAAAAT TATATTTCTG AATGATTGAC TTCAGGATTT TCTTTTAGAA TTGTATTAAA
    1621 TAGTTCATGT CATTAGGATA AATGCTGGAA TGTGGATATA ATTTAAAATA TACTAAATGC
    1681 CATCGACCTT CATTTTGAGT TCTTTGTTGG ACATTTTTGT GCATTTTTAA AATATCCCCT
    1741 AAATAATAAA GCTATTTATA TTTGGAGAGG AGAAAAAAAA GTGGGGGGCA GGGAGAGCTG
    1801 ATCTCTATAA CTAACCAAAT TTATTGCTTT TTTGTTTAGG CCTGAAGTTT CCACAAATAA
    1861 GACCTACTCC TTCCTAATTT ACACAGAGGT AGATATTGGA GAACTACTCA TGTTGAAGCT
    1921 CAAATGGAAG AGTGATTCAT ACTTTAGCTG GTCAGACTGG TGGAGCAGTC CCGGCTTCGC
    1981 CATTCAGAAG ATCAGAGTAA AAGCAGGAGA GACTCAGAAA AAGTAATTAA ATGTATTTTT
    2041 CTTCCTTCAC TTTAGACCCC CACCTGATGT CAGGACCTAG GGGCTGTATT TCAGGGGCCT
    2101 TCACAATTCA GGGAGAGCTT TAGGAAACCT TGTATTTATT ACTGTATGAT GTAGATTTTC
    2161 TTTAGGAGTC TTCTTTTATT TTCTTATTTT TGGGGGGCGG GGGGGGAAGT GACAGTATTT
    2221 TTGTATTTCA TGTAAGGAAA ACATAAGCCC TGAATCGCTC ACAGTTATTC AGTGAGAGCT
    2281 GGGATTAGAA GTCAGGAATC TCAGCTTCTC ATTTGGCACT GTTTCTTGTA AGTACAAAAT
    2341 AGTTAGGGAA CAAACCTCCG AGATGCTACC TGGATAATCA AAGATTCAAA CCAACCTCTT
    2401 CCAGAAGGGT GAGATTCCAA GATAATCTCA ACCTGTCTCC GCAGCCCCAC CCATGTGTAC
    2461 CCATAAAATG AATTACACAG AGATCGCTAT AGGATTTAAA GCTTTTATAC TAAATGTGCT
    2521 GGGATTTTGC AAACTATAGT GTGCTGTTAT TGTTAATTTA AAAAAACTCT AAGTTAGGAT
    2581 TGACAAATTA TTTCTCTTTA GTCATTTGCT TGTATCACCA AAGAAGCAAA CAAACAAACA
    2641 AAAAAAAAAA GAAAAAGATC TTGGGGATGG AAATGTTATA AAGAATCTTT TTTACACTAG
    2701 CAATGTCTAG CTGAAGGCAG ATGCCCTAAT TCCTTAATGC AGATGCTAAG AGATGGCAGA
    2761 GTTGATCTTT TATCATCTCT TGGTGAAAGC CCAGTAACAT AAGACTGCTC TAGGCTGTCT
    2821 GCATGCCTGT CTATCTAAAT TAACTAGCTT GGTTGCTGAA CACCAGGTTA GGCTCTCAAA
    2881 TTACCCTCTG ATTCTGATGT GGCCTGAGTG TGACAGTTAA TTATTGGGAA TATCAAAACA
    2941 ATTACCCAGC ATGATCATGT ATTATTTAAA CAGTCCTGAC AGAACTGTAC CTTTGTGAAC
    3001 AGTGCTTTTG ATTGTTCTAC ATGGCATATT CACATCCATT TTCTTCCACA GGGTGATCTT
    3061 CTGTTCTAGG GAGAAAGTGT CTCATTTGCA GAAAGGAAAG GCACCTGCGG TATTTGTGAA
    3121 ATGCCATGAC AAGTCTCTGA ATAAGAAGTC AGGCTGGTGA GCATTCTGGG CTAAAGCTGA
    3181 CTGGGCATCC TGAGCTTGCA CCCTAAGGGA GGCAGCTTCA TGCATTCCTC TTCACCCCAT
    3241 CACCAGCAGC TTGCCCTGAC TCATGTGATC AAAGCATTCA ATCAGTCTTT CTTAGTCCTT
    3301 CTGCATATGT ATCAAATGGG TCTGTTGCTT TATGCAATAC TTCCTCTTTT TTTCTTTCTC
    3361 CTCTTGTTTC TCCCAGCCCG GACCTTCAAC CCAGGCACAC ATTTTAGGTT TTATTTTACT
    3421 CCTTGAACTA CCCCTGAATC TTCACTTCTC CTTTTTTCTC TACTGCGTCT CTGCTGACTT
    3481 TGCAGATGCC ATCTGCAGAG CATGTAACAC AAGTTTAGTA GTTGCCGTTC TGGCTGTGGG
    3541 TGCAGCTCTT CCCAGGATGT ATTCAGGGAA GTAAAAAGAT CTCACTGCAT CACCTGCAGC
    3601 CACATAGTTC TTGATTCTCC AAGTGCCAGC ATACTCCGGG ACACACAGCC AACAGGGCTG
    3661 CCCCAAGCAC CCATTCTCAA AACCCTCAAA GCTGCCAAGC AAACAGAATG AGAGTTATAG
    3721 GAAACTGTTC TCTCTTCTAT CTCCAAACAA CTCTGTGCCT CTTTCCTACC TGACCTTTAG
    3781 GGCTAATCCA TGTGGCAGCT GTTAGCTGCA TCTTTCCAGA GCGTCAGTAC TGAGAGGACA
    3841 CTAAGCATGT GACCTTCACT ACTCCTGTTC TGAATTC
  • For example, oligonucleotide primer sequences that are useful for amplifying nucleic acids that comprise the normal locus of the HindIII recognition site in [0050] LPL intron 8, include but are not limited to the following sequences (designation after the SEQ. ID. NO. includes the nucleotide position within M76722, e.g., 2701 or 2397, at which the 5′-terminus of the primer sequence begins if it is an upper [“U”; i.e., forward] primer; at which position complementary to a position within M76722 its 3′-terminus ends if it is a lower [“L”; i.e., reverse] primer; and the primer length, e.g., 24 bases):
    5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′ (SEQ. ID. NO.:1; LPL HindIII:2701L24);
    5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′ (SEQ. ID. NO.:2; LPL HindIII:2397U24);
    5′-GGA AAA CAT AAG CCC TGA ATC-3′ (SEQ. ID. NO.:3; LPL HindIII:2236U21);
    5′-GAA AAC ATA AGC CCT GAA TCG-3′ (SEQ. ID. NO.:4; LPL HindIII:2237U21);
    5′-AAC ATA AGC CCT GAA TCG CTC-3′ (SEQ. ID. NO.:5, LPL HindIII:2240U21);
    5′-CCT GAA TCG CTC ACA GTT ATT-3′ (SEQ. ID. NO.:6; LPL HindIII:2249U21);
    5′-CTG AAT CGC TCA CAG TTA TTC-3′ (SEQ. ID. NO.:7; LPL HindIII:2250U21);
    5′-AAT CGC TCA CAG TTA TTC AGT-3′ (SEQ. ID. NO.:8; LPL HindIII:2253U21);
    5′-TTG GCA CTG TTT CTT GTA AGT-3′ (SEQ. ID. NO.:9, LPL HindIII:2313U21);
    5′-CAC TAT AGT TTG CAA AAT CCC-3′ (SEQ. ID. NO.:1O; LPL HindIII:2521L21);
    5′-CAAACCTCC GAG ATG CTA CCT GGA-3′ (SEQ. ID. NO.:11; LPL HindIII:2351U24);
    5′-AGATGCTACCTG GAT AAT CAA AGA-3′ (SEQ. ID. NO.:12; LPL HindIII:2361U24);
    5′-GATGCTACC TGG ATA ATC AAA GAT-3′ (SEQ. ID. NO.:13; LPL HindIII:2362U24);
    5′-CTTCCAGAA GGG TGA GAT TCC AAG-3′ (SEQ. ID. NO.:14; LPL HindIII:2398U24);
    5′-CCAGAAGGGTGA GAT TCC AAG ATA-3′ (SEQ. ID. NO.:15; LPL HindIII:2401U24);
    5′-CAGAAGGGTGAG ATT CCA AGA TAA-3′ (SEQ. ID. NO.:16, LPL HindIII:2402U24);
    5′-CCCACCCAT GTG TAC CCA TAA AAT-3′ (SEQ. ID. NO.:17; LPL HindIII:2446U24);
    5′-CCACCCATG TGT ACC CAT AAA ATG-3′ (SEQ. ID. NO.:18; LPL HindIII:2447U24);
    5′-CCCATGTGT ACC CAT AAA ATG AAT-3′ (SEQ. ID. NO.:19; LPL HindIII:2450U24);
    5′-GTACCCATA AAA TGA ATT ACA CAG-3′ (SEQ. ID. NO.:20; LPL HindIII:2457U24);
    5′-CCCATAAAATGA ATT ACA CAG AGA-3′ (SEQ. ID. NO.:21; LPL HindIII:2460U24);
    5′-ATGAATTAC ACA GAG ATC GCT ATA-3′ (SEQ. ID. NO.:22; LPL HindIII:2468U24);
    5′-ACACAGAGA TCG CTA TAG GAT TTA-3′ (SEQ. ID. NO.:23; LPL HindIII:2475U24),
    5′-TTATAA CAT TTC CAT CCC CAA GAT-3′ (SEQ. ID. NO.:24; LPL HindIII:2658L24);
    5′-CATCTG CCT TCA GCT AGA CAT TGC-3′ (SEQ. ID. NO.:25; LPL HindIII:2700L24);
    5′-CTGCAT TAA GGA ATT AGG GCA TCT-3′ (SEQ. ID. NO.:26; LPL HindIII:2719L24);
    5′-AGATCA ACT CTG CCA TCT CTT AGC-3′ (SEQ. ID. NO.:27; LPL HindIII:2745L24);
    5′-TCT TAT GTT ACT GGG CTT TCA CCA-3′ (SEQ. ID. NO.:28; LPL HindIII:2781L24);
    5′-AGCCTA GAG CAG TCT TAT GTT ACT-3′ (SEQ. ID. NO.:29; LPL HindIII:2793L24);
    5′-CAGCCT AGA GCA GTC TTA TGT TAC-3′ (SEQ. ID. NO.:30; LPL HindIII:2794L24);
    5′-ACAGCC TAG AGC AGT CTT ATG TTA-3′ (SEQ. ID. NO.:31; LPL HindIII:2795L24);
    5′-AGACAGCCT AGA GCA GTC TTA TGT-3′ (SEQ. ID. NO.:32; LPL HindIII:2797L24);
    5′-CTTTATAACATTTCCATCCCCAAG AT-3′ (SEQ. ID. NO.:35; LPL HindIII:2658L26),
    5′-TGTACCCATAAAATGAATTACACAGA-3′ (SEQ. ID. NO.:36; LPL HindIII:2456U26);
    5′-ACCCATAAAATGAATTACACAGAGAT-3′ (SEQ. ID. NO.:37; LPL HindIII:2459U26);
    5′-AAAATGAATTACACAGAGATCGCTAT-3′ (SEQ. ID. NO.:38; LPL HindIII:2465U26);
    5′-TTACACAGAGATCGCTATAGGATTTA-3′ (SEQ. ID. NO.:39; LPL HindIII:2473U26);
    5′-CAGCCTAGAGCAGTCTTA TGT TAC T-3′ (SEQ. ID. NO.:40; LPL HindIII:2793L25);
    5′-ACAGCCTAGAGCAGTCTTATG TTA C-3′ (SEQ. ID. NO.:41; LPL HindIII:2794L25);
    5′-GACAGCCTAGAGCAGTCTTAT GTT A-3′ (SEQ. ID. NO.:42; LPL HindIII:2795L25);
    5′-ATAAAATGAATTACACAGAGATCGCTAT-3′ (SEQ. ID. NO.:43 ;LPL HindIII:2463U28);
    5′-AAGATTCTTTATAACATTTCCATC CC-3′ (SEQ. ID. NO.:44; LPL HindIII:2664L26),
    5′-AATTACACAGAGATCGCTATAGGATTTA-3′ (SEQ. ID. NO.:45;LPL HindIII:2471U28);
    5′-ACAGCCTAGAGCAGTCTTATGTTACT-3′ (SEQ. ID. NO.:46; LPL HindIII:2793L26);
    5′-CCC ACC CAT GTG TAC CCA T-3′ (SEQ. ID. NO.:47; LPL HindIII:2446U19);
    5′-CCA CCC ATG TGT ACC CAT-3′ (SEQ. ID. NO.:48; LPL HindIII:2447U18);
    5′-CAC CCA TGT GTA CCC ATA AAA-3′ (SEQ. ID. NO.:49; LPL HindIII:2448U21);
    5′-ACC CAT GTG TAC CCA TAA AA-3′ (SEQ. ID. NO.:50; LPL HindIII:2449U20);
    5′-GGC TTT CAC CAA GAG ATG ATA A-3′ (SEQ. ID. NO.:51; LPL HindIII:2770L22);
    5′-GGG CTT TCA CCA AGA GAT GAT A-3′ (SEQ. ID. NO.:52; LPL HindIII:2771L22);
    5′-TGA ATT ACA CAG AGA TCG CTA T-3′ (SEQ. ID. NO.:53; LPL HindIII:2469U22);
    5′-ACA GAG ATC GCT ATA GGA TTT A-3′ (SEQ. ID. NO.:54; LPL HindIII:2477U22);
    5′-GTT ACT GGG CTT TCA CC-3′ (SEQ. ID. NO.:55; LPL HindIII:2782L17);
    5′-CTT ATG TTA CTG GGC TTT CA-3′ (SEQ. ID. NO.:56; LPL HindIII:2784L20);
    5′-TCT TAT GTT ACT GGG CTT TC-3′ (SEQ. ID. NO.:57; LPL HindIII:2785L20);
    5′-CCA CCC ATG TGT ACC CAT A-3′ (SEQ. ID. NO.:58; LPL HindIII:2447U19);
    5′-CAC CCA TGT GTA CCC ATA-3′ (SEQ. ID. NO.:59; LPL HindIII:2448U18);
    5′-ACC CAT GTG TAC CCA TAA-3′ (SEQ. ID. NO.:60; LPL HindIII:2449U18);
    5′-CCC ATG TGT ACC CAT AAA-3′ (SEQ. ID. NO.:61; LPL HindIII:2450U18);
    5′-CAA CTC TGC CAT CTC TTA GC-3′ (SEQ. ID. NO.:62; LPL HindIII:2745L20);
    5′-TCA ACT CTG CCA TCT CTT AG-3′ (SEQ. ID. NO.:63; LPL HindIII:2746L20);
    5′-ATC AAC TCT GCC ATC TCT TA-3′ (SEQ. ID. NO.:64; LPL HindIII:2747L20),
    5′-GAA AAC ATA AGC CCT GAA-3′ (SEQ. ID. NO.:65; LPL HindIII:2237U18),
    5′-AAA ACA TAA GCC CTG AAT C-3′ (SEQ. ID. NO.:66; LPL HindIII:2238U19);
    5′-ACA TAA GCC CTG AAT CG-3′ (SEQ. ID. NO.:67; LPL HindIII:2241U17);
    5′-CTG AAT CGC TCA CAG TT-3′ (SEQ. ID. NO.:68; LPL HindIII:2250U17);
    5′-TGA ATC GCT CAC AGT TAT T-3′ (SEQ. ID. NO.:69; LPL HindIII:2251U19);
    5′-ATC GCT CAC AGT TAT TCA G-3′ (SEQ. ID. NO.:70; LPL HindIII:2254U19);
    5′-TCG CTC ACA GTT ATT CAG T-3′ (SEQ. ID. NO.:71; LPL HindIII:2255U19);
    5′-CGC TCA CAG TTA TTC AGT G-3′ (SEQ. ID. NO.:72, LPL HindIII:2256U19);
    5′-AAT CCC AGC ACA TTT AGT AT-3′ (SEQ. ID. NO.:73; LPL HindIII:2507L20);
    5′-ACT ATA GTT TGC AAA ATC CC-3′ (SEQ. ID. NO.:74; LPL HindIII:2521L20);
    5′-TGA GAG CTG GGA TTA GAA-3′ (SEQ. ID. NO.:75; LPL HindIII:2273U18);
    5′-GAG AGC TGG GAT TAG AAG T-3′ (SEQ. ID. NO.:76; LPL HindIII:2274U19);
    5′-AGA GCT GGG ATT AGA AGT C-3′ (SEQ. ID. NO.:77; LPL HindIII:2275U19);
    5′-AAT CCC AGC ACA TTT AGT AT-3′ (SEQ. ID. NO.:78, LPL HindIII:2507L20); and
    5′-CCC ACC CAT GTG TAC CCA TA-3′ (SEQ. ID. NO.:79; LPL HindIII:2446U20).
  • Any 15-to 28-mer primer sequence overlapping any of SEQ. ID. NOS: 1-32 or 35-79 can also be used to amplify nucleic acids comprising the normal locus of the HindIII recognition site in [0051] LPL intron 8. The primer sequence can overlap the entire sequence of any of SEQ. ID. NOS.: 1-32 and 35-79 or can overlap at one or more contiguous nucleotide positions of any of SEQ. ID. NOS.: 1-32 and 35-79 and additional nucleotides adjacent to the position(s) based upon the Nickerson reference sequence.
  • Other primer sequences are useful for amplifying nucleic acid sequences including the (TTTA)[0052] n tetranucleotide repeat region in intron 6. These include SEQ. ID. NOS.: 33 and 34, described above and the following primer sequences (designation includes the nucleotide position within the Nickerson reference sequence in Genbank accession AF050163, e.g., 4644 or 4934, at which the 5′-terminus of the primer sequence begins if it is an upper [“U”; i.e., forward] primer; or the position complementary to a position in AF050163 at which its 3′-terminus ends if it is a lower [“L”; i.e., reverse] primer; and primer length, e.g., 24 bases):
    5′-CTG GAC AAG AGT CTA AAG CAG CAT-3′ (SEQ. ID. NO.:82; LPL:4644U24);
    5′-GAA TCG CTT GAA CCG GAA AG-3′ (SEQ. ID. NO.:83; LPL:4934L20:),
    5′-ACC ATC AGT CTT AAG AGA TCT GTG-3′ (SEQ. ID. NO.:84; LPL:4934L24);
    5′-CAC AGA TCT CTT AAG ACT GAT GGT-3′ (SEQ. ID. NO.:85; LPL:4693L24);
    5′-TTT TTC ACC TGG ACA AGA GT-3′ (SEQ. ID. NO.:86; LPL:4636U20);
    5′-GGG TAA CTG AGC GAG ACC GT-3′ (SEQ. ID. NO.:87; LPL:4870L20);
    5′-TTC ACC TGG ACA AGA GTC TA-3′ (SEQ. ID. NO.:88; LPL:4639U20);
    5′-GCT TGA ACC GGA AAG-3′ (SEQ. ID. NO.:89;LPL:4934L15);
    5′-TCA CCT GGA CAA GAG TCT AA-3′ (SEQ. ID. NO.:90; LPL:4640U20);
    5′-CTC CAG CCT GGG TAA CT-3′ (SEQ. ID. NO :91, LPL:4882L17); and
    5′-ACA AGA GTC TAA AGC AGC AT-3′ (SEQ. ID NO.:92; LPL:4648U20).
  • Any 15-to 28-mer primer sequence overlapping any of SEQ. ID. NOS:33 and 34 or 82-92 can also be used to amplify nucleic acids comprising the (TTTA)[0053] n tetranucleotide repeat region in LPL intron 6. The primer sequence can overlap the entire sequence of any of SEQ. ID. NOS.: 33-34 and 82-92 or can overlap at one or more contiguous nucleotide positions of any of SEQ. ID. NOS.: 33-34 and 82-92 and additional nucleotides adjacent to the position(s) based upon the Nickerson reference sequence.
  • Other primer sequences are useful for amplifying nucleic acid sequences in [0054] exon 10 and the 3′-UTR. These include the following primer sequences (SEQ. ID. NOS.: 95-106) (designation includes the nucleotide position within the Oka reference sequence in GenBank accession X52978 X53518, e.g., 2564, at which the 5′-terminus of the primer sequence begins if it is an upper [“U”; i.e., forward] primer; or the position complementary to a position in X52978 X53518 at which its 3′-terminus ends if it is a lower [“L”; i.e., reverse] primer; and primer length, e.g., 22 bases):
    5′-ATG AAA AGA GCA TAT GGT GGT T-3′ (SEQ. ID. NO.:95; LPL 3′ end Oka 2564U22);
    5′-TGG CCC AGG TAT ACA TAT GTA ACT A-3′ (SEQ. ID. NO.:96; LPL 3′ end Oka 2845L25);
    5′-GGC CCA GGT ATA CAT ATG TAA CTA A 3′ (SEQ. ID. NO.:97; LPL-3′ end Oka 2844L25);
    5′-TGA AAA GAG CAT ATG GTG GTT C 3′ (SEQ. ID. NO.:98; LPL-3′ end Oka 2565U22);
    5′-GAA AAG AGC ATA TGG TGG TTC-3′ (SEQ. ID. NO.:99; LPL 3′ end Oka 2566U21);
    5′-GCC CAG GTA TAC ATA TGT AAC TAA C-3′ (SEQ. ID. NO.:100; LPL 3′ end Oka 2843L25);
    5′-AAA AGA GCA TAT GGT GGT TC-3′ (SEQ. ID. NO.:101; LPL 3′ end Oka 2567U20);
    5′-GGT TCT CTC AGC TCC CAG CCA ACA A-3′ (SEQ. ID. NO.:102; LPL 3′ end Oka 2582U25);
    5′-AGC ACA CCA ACA TGG CCC AGG TA-3′ (SEQ. ID. NO.:103; LPL 3′ end Oka 2869L23);
    5′-CTC AGC TCC CAG CCA ACA ACC AGT C-3′ (SEQ. ID. NO.:104; LPL 3′ end Oka 2588U25);
    5′-CAG CAC ACC AAC ATG GCC CAG GTA-3′ (SEQ. ID. NO.:105; LPL 3′ end Oka 2859L24); and
    5′-AGC TCC CAG CCA ACA ACC AGT CTC G-3′ (SEQ. ID. NO.:106; LPL 3′ end Oka 2591U25).
  • Any 15-to 28-mer primer sequence overlapping any of SEQ. ID. NOS: 95-106 with respect to its position on the Oka reference sequence can also be used to amplify nucleic acids comprising [0055] LPL exon 10 and the 3′UTR. The primer sequence can overlap the entire sequence of any of SEQ. ID. NOS.: 95-106 or can overlap at one or more contiguous nucleotide positions of any of SEQ. ID. NOS.: 95-106 and additional nucleotides adjacent to the position(s) based upon the Oka reference sequence.
  • The present invention also relates to a primer set for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human. The primer set functions to initiate nucleic acid synthesis in PCR from both the 5′ and 3′ ends of a nucleic acid template comprising a non-coding or untranslated region of the 3′ end of the human LPL gene. The primer set comprises any two suitable oligonucleotide primers of the present invention, as described herein, as long as the primer set includes both a forward (upper or “U”) and a reverse (lower or “L”) primer. [0056]
  • For example, a preferred primer set for amplifying nucleic acids comprising the normal locus of the HindIII recognition site in [0057] intron 8 of LPL includes any pair lower and upper primers from among SEQ. ID. NOS.: 1-32 or 35-79 (described above), or primer sequences overlapping any of them with respect to the Nickerson reference sequence. A most preferred set of primers is reverse (lower) primer SEQ. ID. NO.: 1 and forward (upper) primer SEQ. ID. NO. : 2.
  • Additional primer sets that are useful for amplifying the region of the (TTTA)[0058] n tetranucleotide repeat include any pair of lower and upper primers from among SEQ. ID. NOS.: 33-34 and 82-92 (described above), or primer sequences overlapping any of them with respect to the Nickerson reference sequence. A most preferred embodiment of a primer set for detecting the presence of the (TTTA)n 4 allele includes primers comprising SEQ. ID. NOS.: 33 and 34.
  • Additional primer sets that are useful for amplifying [0059] exon 10 and the 3′UTR include any pair of lower and upper primers from among SEQ. ID. NOS.: 95-106 (described above), or primer sequences overlapping any of them with respect to the Oka reference sequence.
  • The present invention also relates to a genetic testing kit for detecting in a human subject a genetic predisposition for non-responsiveness to statin drug treatment. The genetic testing kit is a ready assemblage of materials for facilitating the amplifying of nucleic acids from a human subject comprising a nucleotide sequence from a non-coding or untranslated region of the 3′ end of the human LPL gene and/or analyzing amplification products thereof A genetic testing kit of the present invention contains at least one oligonucleotide primer of the present invention and preferably comprises a primer set of the present invention, as described above, together with instructions for the practice of the present method. The materials or components assembled in the genetic testing kit are provided to the practitioner stored in any convenient and suitable way that preserves their operability and utility. For example the components can be in dissolved, dehydrated, or lyophilized form; they can be provided at room, refrigerated or frozen temperatures. [0060]
  • Another preferred embodiment of the genetic testing kit incorporates an array of oligonucleotide primers specific for single nucleotide polymorphisms in the human nucleotide sequence of the 3′ end of LPL, particularly of non-coding or untranslated regions, preassembled in a “DNA chip” (or “gene chip”) configuration for facilitating the amplifying of nucleic acids and the analyzing of amplification products. (E.g., J. G. Hacia et al, [0061] Enhanced high density oligonucleotide array-based sequence analysis using modified nucleoside triphosphates, Nucleic Acids Res. 26(2):4975-82 [1998]; R. W. Wallace, DNA on a chip: serving up the genome for diagnostics and research, Mol. Med. Today 3(9):384-89 [1997]; T. Pastinen et al., Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays, Genome Res. 7(6):606-14 [1997]; M. T. Cronin et al, Cystic fibrosis mutation detection by hybridization to light-generated DNA probe arrays, Hum. Mutat. 7(3):244-55 [1996]; A.C. Pease et al., Light-generated oligonucleotide arrays for rapid DNA sequence analysis, Proc. Natl. Acad. Sci. USA 91(11):5022-26 [1994]; E.M . Southern et al, Arrays of complementary oligonucleotides for analyzing the hybridisation behaviour of nucleic acids, Nucleic Acids Res. 22(8):1368-73 [1994]).
  • The skilled practitioner will appreciate that homozygosity for a mutation in a non-coding or untranslated region of the 3′ end of the human LPL gene, such as the [0062] HindIII 2/2 or (TTTA)n 4/4 genotypes, is a risk factor for atherosclerotic stenosis in coronary artery disease independent and additive to the use of statin drugs to reduce LDL. For example, the effect of the LPL HindIII 2/2 genotype on atherosclerotic graft worsening is of the same magnitude as the use of moderate rather than aggressive drug therapy to lower LDL. Such a genotype apparently does not act via an effect on lipid levels, nor the amount of drug needed to achieve lower levels. However, it is associated with a modest effect on blood pressure.
  • Using the methods, primers, primer sets, and genetic testing kits of the present invention for detecting a genetic predisposition in a human for non-responsiveness to statin drug treatment for coronary artery disease, the practitioner can identify patients homozygous for a variant allele in a non-coding or untranslated region of the 3′ end of LPL, for example those with the [0063] HindIII 2/2 or (TTTA)4 4/4 genotype. These patients are predisposed to develop atherosclerotic progression despite their compliance with aggressive lipid lowering therapy with lovastatin or other statin class drugs.
  • A high level of LDL-C is an important risk factor of heart disease and atherosclerosis, but it is not the sole risk factor. The present invention provides the practitioner a valuable tool for better characterizing individual patients and identifying those patients likely to need individualized alternative interventions other than LDL-C lowering therapy with statin class drugs. For example, direct blood pressure lowering therapy may be indicated for patients identified as homozygous for a variant genotype in accordance with the present invention, because they tend to have blood pressures at the high end of the normal range. Such treatment can include, for example, angiotensinogen converting enzyme (ACE) inhibitors or Ca[0064] 2+channel blockers. Alternatively, beta blockers, diuretics, or a combination of modalities can be a more appropriate blood pressure lowering therapy for a given patient. Blood pressure lowering in conjunction with aspirin treatment can prevent heart disease in some patients. (See L. Hansson et al., Effects of intensive blood-pressure lowering and low-dose aspirin in patients with hypertension: principle results of the hypertension Optimal Treatment [HOT] randomised trial, Lancet 351(9118):1755-62 [1998]; Thrombosis prevention trial: randomised trial of low-intensity oral anticoagulation with warfarin and low-dose aspirin in the primary prevention of ischemic heart disease in men at increased risk, Lancet 351(9098):233-41 [1998]).
  • For patients identified as homozygous for a variant allele in accordance with the present invention, the practitioner can look at a variety of other known or suspected atherogenic risk factors, beyond LDL-C levels, that may be amenable to treatment in an individual patient. For example, small LDL particle sizes may be amenable to treatment with fibric acid-derivative drugs, e.g., lopid, or high dose niacin. (See J. R. Guyton et al., [0065] Effectiveness of once-nightly dosing of extended-release niacin alone and in combination for hypercholesterolemia, Am. J. Cardiol. 82(6):737-43 [1998]). High Lp(a) levels may be treatable with niacin, or estrogen replacement therapy in women or testosterone replacement in men.
  • For some patients identified as homozygous for a variant allele in accordance with the present invention, such as the [0066] HindIII 2/2 or (TTTA)n 4/4 genotype, the practitioner can appropriately focus on altering atherogenic life style factors such as diet, smoking, and exercise. (E.g., see J.C. LaRosa, The role of diet and exercise in the statin era, Prog. Cardiovasc. Dis. 41(2): 137-50 [1998]).
  • In view of the substantial cost of statin drugs, a secondary benefit to be derived from identifying patients having a genetic predisposition to non-responsiveness to statin drug treatment, for coronary artery disease or high blood pressure, is the cost savings to patients and health care systems that can be gained by relying on more individually suited alternative treatments instead of statin treatment regimens, for those individuals for whom statins are likely to be ineffective. (See D. M. Huse et al., [0067] Cost-effectiveness of statins, Am. J. Cardiol. 82(11): 1357-63 [1998]; P. N. Durrington, Can we afford to treat hyperlipida as we should? Strategies for rational treatment, Atherosclerosis 139(Suppl. 1):S1-5 [1998]; J. A. Farmer, Economic implications of lipid-lowering trials: current considerations in selecting a statin, Am J. Cardiol. 82(6A):26M-31M [1998]).
  • By using the methods, primers, primer sets, and genetic testing kits of the present invention, the practitioner can better individualize the treatment and improve the care of patients with coronary artery disease. [0068]
  • The detailed examples which follow describe the genetic association between variant alleles in non-coding or untranslated regions of the 3′ end of the human LPL gene and atherosclerotic stenosis in coronary artery disease that is non-responsive to statin drug treatment. These examples are intended merely to illustrate and in no way limit the present invention. [0069]
    • EXAMPLES
  • Genetic Link Between Mutant LPL Genotypes and Phenotypic Atherosclerotic Stenosis in Coronary Artery Disease that is Non-Responsive to Statin Drug Treatment. [0070]
  • The following examples describe further data and analyses that support a genetic association between the [0071] LPL HindIII 2/2 or (TTTA)n 4/4 genotypes and a phenotype of atherosclerotic stenosis in coronary artery disease that is non-responsive to statin drug treatment.
    • Example 1 Study Design
  • A genetic association study was conducted by a within-case comparison ancillary to the Post Coronary Artery Bypass Graft Trial. (The Post Coronary Artery Bypass Graft Trial Investigators. [0072] The effect of aggressive lowering of low-density lipoprotein cholesterol levels and low-dose anticoagulation on obstructive changes in saphenous-vein coronary-artery bypass grafts, N. Engl. J. Med. 336:153-62 [1997]). A two stage design was followed. First, EBV-transformed lymphoblastoid cell lines were established for subjects from the Los Angeles (L.A.) cohort providing a permanent source of DNA for testing hypotheses related to atherosclerosis-related candidate genes. Then, significant results were tested in a second stage by genotyping all available subjects in the post-CABG trial using DNA isolated from whole blood shipped to Cedars-Sinai Medical Center from the other participating centers.
  • Participants were randomly assigned, following a two by two design, to receive 1) lovastatin therapy to lower the LDL-cholesterol level to within the range of 93-97 mg/dl (aggressive treatment group) or 132-136 mg/dl (moderate treatment group), and 2) placebo or low-dose warfarin (Post-CABG, 1997). Coronary angiograms of 1351 subjects at enrollment and an average of 4.3 years later were compared using a quantitative assessment of the severity of graft stenosis. Graft worsening was defined as a decrease in lumen diameter of 0.6mm or more. The percentage of subjects with worsening of one or more grafts was 39% in the aggressive treatment group compared to 51% in the moderate treatment group (p<0.00 1) and the mean percentage of grafts per patient showing worsening was 27% in the aggressive treatment group compared to 39% in the moderate treatment group (p<0.001). [0073]
  • These results demonstrated the efficacy of lowering LDL-cholesterol levels with statin drug treatment in reducing the risk of graft worsening in most CABG patients. No effect of the warfarin treatment on graft worsening was observed. [0074]
    • Example 2 Subjects
  • A total of 1351 subjects from seven clinical centers throughout North America were included in the clinical trial and all were eligible as participants. Genetic material was received from 891 subjects who were included in this ancillary study. Inclusion criteria for the clinical trial were: bypass surgery 1 -11 years prior to the study; an LDL-cholesterol level of 130-175 mg/dl; and at least one patent vein graft as determined by angiography. Subjects were excluded if there was: (a) the likelihood of revascularization or death within the study period of 5 years; (b) unstable angina or myocardial infarction within six months before the start of the trial; (c) severe angina; (d) heart failure; or (e) contraindications to the study medications. Id. Subjects were randomly assigned in a two by two factorial design for treatment to lower LDL-cholesterol levels aggressively (target LDL 93-97 mg/dl) or moderately (target LDL 132-136 mg/dl) with lovastatin and cholestyramine if needed, and for treatment with either placebo or warfarin sufficient to maintain an international normalized ratio of less than 2. Id. Graft worsening was determined by comparing the initial angiogram at enrollment with a follow-up angiogram repeated an average of 4.3 years later. “Worsening” was defined as a reduction in diameter ≧0.6mm in diameter. “Subjects with worsening” were defined as those subjects with one or more grafts showing worsening. [0075]
    • Example 3 Data Collection
  • Questionnaire data regarding demographics, family and medical history, and angiographic and clinical data were collected as part of the post-CABG trial. Additional family history data were collected from 891 subjects in the genetic ancillary study. [0076]
    • Example 4 DNA
  • During years 2-3 of the clinical trial, cell lines from 224 subjects in the L.A. cohort were established by transformation of peripheral blood lymphocytes with Epstein-Barr virus (EBV). (M. A. Anderson and J. F. Gusella, [0077] Use of cyclosporin-A in establishing Epstein-Barr virus transformed human lymphoblastoid cell lines. In Vitro 21:856-58 [1984]; S. Pressman and J. I. Rotter, Epstein-Barr virus transformation of cryopreserved lymphocytes, prolonged experience with technique, letter to the editor,Am. J. Hum. Genet. 49:467 [1991]). During years 4-5, whole blood was collected from an additional 667 subjects from the other centers. Thus, DNA was available from a total of 891 subjects. DNA was isolated following standard protocols. (B. G. Herrman and A. Frischauf, Isolation of Genomic DNA, Methods in Enzymology 152:180-83 [1987]).
    • Example 5 Genotyping
  • Conventional agarose gel techniques were used to genotype the LA cohort for the biallelic LPL HindIII polymorphism following Heizmann et al. (C. Heizmann et al., [0078] RFLP for the human lipoprotein lipase (LPL) gene: HindIII, Nucleic Acids Res. 15:6763 [1987]). DNA samples from the remaining subjects were genotyped for this polymorphism as well as four additional LPL polymorphisms using fluorescent semi-automated technology. In FIG. 1(a), the location of polymorphisms in the LPL gene was assembled from information in GenBank, accession numbers G187209, G34390, M76722, and M76723, and other published sources. (F. Mailly et al., A common variant in the gene for lipoprotein lipase (asp9-asn): functional implications and prevalence in normal and hyperlipidemic subjects, Arterioscler. Thromb. Vasc. Biol. 15:468-78 [1995]; P. W. A. Reymer et al., A lipoprotein lipase mutation (asn291ser) is associated with reduced HDL cholesterol levels in premature atherosclerosis, Nat Genet 1995; 10:28-34 [1995]; C. Herimann et al., DNA polymorphism haplotypes of the human lipoprotein lipase gene: possible association with high density lipoprotein levels, Hum. Genet. 86:578-84 [1991]; G. Zuliani and H. H. Hobbs, Tetranucleotide repeat polymorphism in the LPL gene, Nucleic Acids Res. 18:4958 [1990]).
  • Marker genotypes were determined using a PCR with primers listed below as recommended by the manufacturer of Ampli-Taq Gold (Perkin Elmer, Foster City, Calif.) in a Perkin Elmer 9600 thermocycler. (All PCR runs began with 95° for 10 min. to activate the polymerase). After digestion with the appropriate restriction enzyme, PCR products for each subject were pooled from all five genotyping reactions and run together on 6% Long Ranger gels in a semi-automated DNA sequencer (ABI 373 DNA sequencer, Applied Biosystems, Foster City, Calif.) with gel processing using Genescan and Genotyper software. [0079]
  • D9N (exon 2) [0080]
  • The assay of Mailley et al. (1995) was redesigned using the sequence in GenBank accession G187209 so that the forward primer (5′-Hex-ACT CCG GGA ATG AGG T; SEQ. ID. NO.: 107) carried the detection dye and the reverse primer (CCA GAA AGA AGA GAT TTT GTC; SEQ. ID. NO.: 108) introduced a SalI restriction site if the PCR fragment carried the mutated D9N allele, and resulted in a 98 bp fragment for the D allele (1 allele) and a 77 bp fragment for the N allele (2 allele) after SalI digestion. PCR conditions were 35 cycles of 94° C. 30 sec, 46° C. 30 sec, 72° C. 30 sec. [0081]
  • N291S (exon 6) [0082]
  • The procedure of Reymer et al. (1995) was followed with Hex added to the forward primer. PCR conditions were 35 cycles of 94° C. 30 sec, 60° C. 30 sec, 72° C. 30 sec. The reverse primer introduces a partial RsaI site so that the N allele gave a 242 bp fragment (1 allele) and the S allele gave a 218 bp fragment (2 allele) after the RsaI digestion. [0083]
  • PvuII (intron 6). [0084]
  • The assay of Li et aL (S. Li et al., [0085] PvuII RFLP at the human lipoprotein [LPL] gene locus, Nucleic Acids Res. 16:2358 [1988]) was redesigned using the sequence in GenBank accession number g34390 so that the resulting fragments would run less than 350 bp in size on the ABI 373. The forward primer was 5′-Tet-CTG CTT TAG ACT CTT GTC CAG GTG (SEQ. ID. NO.: 109) and the reverse primer was 5′-GGG TTC AAG GCT CTG TCA GTG TCC (SEQ. ID. NO.: 110). PCR conditions were 35 cycles of 94° C. 30 sec, 55° C. 30 sec, 72° C. 30 sec. A 155 bp fragment was detected if the PvuII site was present (1 allele) and a 282 bp fragment was detected if the PvuII site was absent (2 allele).
  • (TTTA)[0086] n(intron 6)
  • The procedure of Zuliani and Hobbs (1990) was followed using FAM-labeled GZ-15 primer (5′-CCT GGG TAA CTG AGC GAG ACT GTG TC-3′; SEQ. ID. NO. : 33) and GZ-14 primer (5′-ATC TGA CCA AGG ATA GTG GGA TAT A-3′; SEQ. ID. NO. : 34). PCR conditions were 35 cycles of 94° C. 30 sec, 68° C. 3 min. [0087] Allele 1 ran at a size of 119 bp, 2 at 123 bp, 3 at 127 bp, 3at 127 bp, 4 at 131 bp, and 5 at 135 bp.
  • HindIII (intron 8) [0088]
  • The assay of Heinzmann et al. (1987) was used for [0089] stage 1 and then was redesigned for stage 2 using the sequence in GenBank accession numbers M76722 and M76723. Reverse primer was 5′-Fam-GCA TCT GCC TTC AGC TAG ACA TTG (SEQ. ID. NO.: 1) and forward primer was 5′-TCT TCC AGA AGG GTG AGA TTC CAA (SEQ. ID. No.: 2). PCR conditions were the same as described above for PvuII. Using this primer set of SEQ. ID. NOS.: 1 and 2, a 228 bp fragment was detected if the HindIII restriction site was present (1 allele) and a 330 bp fragment if absent (2 allele).
    • Example 6 Statistical Methods
  • Differences in baseline characteristics between treatment groups and between genotype groups were tested by one-way analysis of variance or Chi-square tests. Log-transformed HDL and TG values were used to perform all statistical analyses in order to adjust for their skewed distributions, but are presented in the tables as untransformed means ±SE. The association between graft worsening and LPL genotype was tested by Chi-square test. Mantel-Haenszel statistics were used for testing the interactions between genotypes and treatment groups. The proportion of grafts showing worsening per subject was used as the quantitative measurement of graft worsening, and multiple regression was performed to for this proportion as a function of genotype and treatment group to identify predictors. Adjusted variables for this trait included age, gender, body mass index, smoking status, number of years since CABG, systolic and diastolic blood pressure, current medicine use, and family history as listed in Table 1. All statistical analyses were carried out with SAS software (version 6.12, SAS Institute, Cary, N.C.). [0090]
    • Example 7 Baseline Characteristics
  • Table 1(a) compares the baseline characteristics of the subjects in the aggressive and moderate drug treatment groups. Minor differences were observed in the percent of subjects with a history of stroke, percent using diabetic therapies, systolic and diastolic blood pressures, and baseline LDL levels. The highly significant difference in the steady state levels of total cholesterol and LDL-cholesterol between these two groups reflects the effect of the drug treatment. As shown in Table 1(b), significant differences were observed between the 891 subjects in the genetic study and the 460 subjects who were not included: frequency of prior myocardial infarction, 46% vs. 55%, p=0.001; smoking 9% vs. 14%, p=0.005; mean years from CABG to enrollment, 4.7 vs. 5.2 years, p<0.001; and aspirin use, 79% vs. 69%, p=0.001. [0091]
    TABLE 1
    Characteristics of Subjects by Treatment Group (1a) or by Inclusion or Exclusion in Genetic Study (1b).
    1b: By Inclusion or Exclusion
    1a: By Treatment Group in Genetic Study
    Aggessive Moderate Included Excluded
    Characteristic (N = 430) (N = 406) p (N = 891) (N = 460) p
    Age (yr, mean(SE) 62.2 ± 0.4  61.5 ± 0.4  62 61
    Caucasian (%) 94 96 94 96
    Male (%) 91 92 92 93
    Body mass index (kg/m2, mean(SE) 27.2 ± 0.2  27.3 ± 0.2 
    Current smoking (%) 15  9 9 14 0.005
    History of myocardial infarction (%) 45 48 46 55 0.001
    Time between CABG and enrollment 4.7 ± 0.1 4.8 ± 0.1 4.7 5.2 <0.001  
    (yr, mean(SE)
    Ejection fraction (%): 56 57 57 57
    Family history of (%):
    Coronary artery disease 76 70 70 71
    Diabetes 36 33 *
    Hypertension 58 56
    Peripheral vascular disease 19 21
    Stroke 41 48 0.05 
    Current medications (%):
    Aspirin 82 77 79 69 0.001
    Beta-blocker 25 24 24 26
    Calcium-channel blocker 27 21 24 23
    Insulin or oral antidiabetic agent 10  6 0.03  10 8
    Thiazide diuretic 12  9 11 11
    Systolic blood pressure 134.4 ± 0.8  133.0 ± 0.9  0.03  134.0 134.8
    (mmHg, mean(SE)
    Diastolic blood pressure 79.3 ± 0.4  79.7 ± 0.4  0.02  79.6 80.1
    (mmHg, mean(SE)
    Baseline lipid levels (mg/dl):†
    Total cholesterol 227.3 ± 1.2  227.4 ± 1.3  226.9 226.4
    LDL cholesterol 156.1 ± 1.0  155.3 ± 1.0  0.04  155.3 155.8
    HDL cholesterol 39.3 ± 0.5  39.5 ± 0.5  39.4 39.0
    Triglycerides 160.3 ± 73.2  162.2 ± 3.7  161.1 157.6
    Steady state lipid levels (mg/dl):
    Total cholesterol 172.6 ± 1.6  209.5 ± 1.6  0.001 191.1 194.3
    LDL cholesterol 97.1 ± 1.3  133.0 ± 1.3  0.001 120.4 114.6 0.002
    HDL cholesterol 44.9 ± 0.6  43.7 ± 0.6  44.3 42.0 0.001
    Triglycerides 157.4 ± 4.5  164.5 ± 4.4  163.1 160.6
    • Example 8 LPL HindIII and Graft Worsening in L. A. Cohort
  • Genotyping of the L. A. cohort for the LPL HindIII polymorphism demonstrated that the proportion of subjects with graft worsening increased with the number of [0092] HindIII 2 alleles: 42% in those with no HindIII 2 allele, 54% in those with one, and 72% in those with two (X 22 ×3 test of association, p=0.05). Further, the percent of grafts showing worsening was calculated per subject and the mean of this percentage also increased with the number of LPL HindIII 2 alleles, with 22% in the subjects with HindlII 1/1, 31% in subjects with 1/2, and 53% in subjects with 2/2 (analysis of variance, p=0.001).
    • Example 9 LPL HindIII and Graft Worsening in All Subjects
  • With this result, the remaining 667 subjects were genotyped. A comparison of the percent of subjects with graft worsening for the two LPL HindIII genotypes for all 891 subjects is shown in Table 2. A significant difference in the percent of subjects showing graft worsening was observed between those with the [0093] LPL HindIII 2/2 genotype compared to those with the LPL HindIII 1/1 and 1/2 genotypes combined; 58% of those with the LPL HindIII 2/2 genotype exhibited worsening compared with 42% of those with either 1/1 or 1/2 (odds ratio=1.9, 95% confidence interval 1.2-3.2, p=0.011). The mean proportion of grafts showing worsening per subject was also significantly increased for those with the LPL HindIll 2/2 genotype (40% for HindIII 2/2 compared with 27% for LPL HindIII 1/1 and 1/2; p=0.0066). There were no significant differences in graft worsening between subjects with the LPL HindIII 1/1 and 1/2 genotypes.
    TABLE 2
    Graft Worsening and LPL HindIII Genotype.
    LPL HindIII Genotype
    2/2 1/1 & 1/2
    Phenotype (N = 65) (N = 723) p value
    Subjects with Worsening (%) 58 41 0.011 
    Mean Grafts with Worsening/ 40 27 0.0066
    Subject (%)
  • Example 10 [0094]
    • LPL Genotypes and Graft Worsening
  • Four additional LPL polymorphisms were tested for association with graft worsening in the entire genetic study cohort (FIG. 1). Complete worsening data were available for 792 subjects; complete genotyping data for each marker represented in FIG. 1: D9N ([0095] exon 2; Mailley et al. [1995], N291S (exon 6; Reymer et al. [1995]), PvuII (intron 6; “1”=site is present, “2”=site is absent; S. Li et al. [1988]), (TTTA)n (intron 6; allele 1 is 119 bp, 2 is 123 bp, 3 is 127 bp, 4 is 131 bp, 5 is 135 bp, D. A. Wu et al, Quantitative trait locus mapping of human blood pressure to a genetic region at or near the lipoprotein gene locus on chromosome 8p22, J. Clin. Invest. 97:2111-18 [1996]), HindIII (intron 8; “1”=site is present, “2”=site is absent; C. Heizmann et al. [1987]). A designation of “X ” is an abbreviation for “other” genotypes. The percent of subjects with graft worsening is the percent of subjects with one or more grafts showing a reduction in diameter ≧0.6 mm.
  • Only the (TTTA)[0096] n and HindIII polymorphisms were significantly associated with graft worsening by the Chi square test of association. There was no association between graft worsening and the functional D9N and N291S polymorphisms and also no association with the PvuII polymorphism.
  • In contrast, the 4/4 genotype of the (TTTA)[0097] n polymorphism was associated with graft worsening: 63% of (TTTA)n 4/4 subjects had worsening of one or more grafts compared to 43% of subjects with other (TTTA)n genotypes (OR=2.2, 95%CI 1.1-4.6; p=0.027). The (TTTA)n 4 allele was found to be in strong linkage disequilibrium with the HindIII 2 allele (p<0.001, data not shown). Consequently, the combined genotype of (TTTA)n 4/4 and HindIII 2/2 was also associated with graft worsening at a significance level similar to the (TTTA)n 4/4 or HindIII 2/2 genotypes alone.
  • Graft worsening was significantly associated with the [0098] LPL HindIII 2/2 genotype and tetranucleotide (TTTA)n 4/4 polymorphisms, both individually and together. The LPL HindIII 2/2 polymorphism did not appear to be acting through any lipid variables, but was associated with significant differences in systolic and diastolic blood pressure.
  • In contrast, no associations between clinical endpoints and the LPL D9N, N29 IS, or PvuII polymorphisms were observed, indicating that the as yet unknown functional mutation associated with graft worsening is in linkage disequilibrium with the (TTTA)[0099] n and HindIII polymorphisms, and thus resides in the 3′-end of the LPL gene.
  • Multiple regression analysis demonstrated that there were no differences in the baseline or steady-state serum lipid values, or the response to lipid-lowering therapy between those subjects with the [0100] LPL HindIII 2/2 genotype and those with the other HindIII genotypes (i.e., 1/1 or 1/2). While the present invention is not committed to any particular mechanism, this observation indicates that the LPL polymorphism does not act through an effect on LDL-cholesterol. This result is congruent with that of Peacock et al. (1992) who observed an association between the LPL HindIII 2 allele and the angiographic severity of atherosclerosis without observing concomitant differences in the mean fasting serum lipid levels in a comparison of young myocardial infarction survivors and age-matched controls.
  • Some significant differences in important risk factors for atherosclerosis were observed among the group of subjects in the genetic study described herein, including: the frequency of prior myocardial infarction, smoking, aspirin use, and mean years from CABG to enrollment. But if a survival bias occurred, it would lead to an underestimate of the effect of the [0101] LPL HindIII 2/2 genotype on the risk of graft worsening. Further, in the 891 subjects for which DNA was available, there were no important differences between the aggressive and moderate treatment groups as to the effect of HindIII 2/2 upon responsiveness to statin treatment, as described below.
    • Example 11 Characteristics of the HindIII 2/2 Genotype Group
  • To investigate potential mechanisms for the association between the [0102] LPL HindIII 2/2 genotype and graft worsening, baseline characteristics and response of the subjects to the lipid-lowering action of lovastatin were compared between subjects (Table 3). There were no differences observed between the baseline values for total cholesterol, HDL-cholesterol, and triglycerides. However, a small difference in LDL-cholesterol was observed, 159.6±2.1 mg/dl for subjects with HindIII 2/2 compared with 155.0±0.7 for 1/1 and 1/2, p=0.04. There were no differences in any of the lipid values attained as a result of drug treatment during the trial, nor was the amount of drug necessary to achieve target lipid values significantly different between the two genotype groups. In contrast to the essentially similar lipid profile of the LPL HindIII genotype groups, the HindIII 2/2 subjects did vary consistently on one set of physiologic parameters. They had a higher average blood pressure, systolic pressure 138.6±2.1 mmHg vs. 133.7±0.6 for subjects with other genotypes, p=0.03; and diastolic pressure 82.1±1.0 mmHg vs. 79.4±0.3 for subjects with other genotypes, p=0.02.
  • Multiple regression analysis showed that graft worsening or stenosis was associated with an interaction between the LPL genotype and blood pressure. The [0103] LPL HindIII 2/2 effect on blood pressure observed here probably has little effect in normal subjects. However, in the presence of ongoing vascular pathology or clinical atherosclerosis, a modest change due to a genetic factor might exert a greater effect. For example, while a blood pressure increase within the normal range has little effect in the general population, slight increases in blood pressure are a significant risk factor for nephropathy in type I diabetes, such that blood-pressure lowering intervention is recommended for some normotensive type I diabetic subjects. (J. Barzilay et al., Predisposition to hypertension: risk factor for nephropathy and hypertension in IDDM, Kidney Int. 42:723-30 [1992]; E. J. Lewis et al., The effect of angiotensin-converting enzyme inhibition on diabetic nephropathy, N. Engl. J. Med. 329:1456-62 [1993]). Thus, for those patients with an unfavorable LPL genotype (e.g., HindIII 2/2) other therapies may be indicated in addition to or instead of lipid-lowering statin treatment for prevention of atherosclerotic stenosis.
    TABLE 3
    Characteristics of Subjects with HindIII 2/2 Genotype
    LPL HindIII Genotype
    2/2 1/1 & 1/2
    Characteristic (N = 74) (N = 817)
    Age (yr, mean(SE) 62.2 ± 0.8  61.7 ± 0.3 
    Caucasian (%) 97 94
    Male (%) 92 92
    Current smoking (%) 15  9
    Body mass index (kg/m2, mean(SE) 26.7 ± 0.4  27.3 ± 0.2 
    History of myocardial infarction (%) 47 46
    Time between CABG and enrollment 5.0 ± 0.3 4.7 ± 0.1
    (yr, mean(SE)
    Ejection fraction (%): 57 57
    Family history of (%):
    Coronary artery disease 76 70
    Diabetes 36 33
    Hypertension 58 56
    Peripheral vascular disease 19 21
    Stroke 41 45
    Current medications (%):
    Aspirin 82 79
    Beta-blocker 23 24
    Calcium-channel blocker 26 24
    Insulin or oral antidiabetic agent  7  8
    Thiazide diuretic  7 11
    Systolic blood pressure 138.6 ± 2.1  133.7 ± 0.6 
    (mmHg, mean(SE)*
    Diastolic blood pressure 82.1 ± 1.0  79.4 ± 0.3 
    (mmHg, mean(SE)*
    Baseline lipid levels (mg/dl):
    Total cholesterol 230.7 ± 2.7  226.7 ± 0.9 
    LDL cholesterol* 159.6 ± 2.1  155.0 ± 0.7 
    HDL cholesterol 41.0 ± 1.1  39.3 ± 0.3 
    Triglycerides 150.8 ± 7.3  161.7 ± 2.4 
    Steady state lipid levels (mg/dl):†
    Total cholesterol 191.1 ± 4.8  191.0 ± 1.3 
    LDL cholesterol 115.1 ± 4.3  114.7 ± 1.1 
    HDL cholesterol 46.7 ± 1.6  44.1 ± 0.4 
    Triglycerides 151.0 ± 9.6  163.6 ± 3.4 
    Lipid change (%):
    Total cholesterol 16.9 ± 2.0  15.2 ± 0.6 
    LDL cholesterol 53.5 ± 6.9  45.1 ± 1.5 
    HDL cholesterol 14.1 ± 3.1  14.2 ± 1.0 
    Triglycerides 6.0 ± 5.8 8.2 ± 2.0
    Mean lovastatin dose required to
    reach target lipid levels (mg/day):
    Aggressive treatment group 37 36
    Moderate treatment group 6.0 6.5
    • Example 12 HindIII 2/2 Genotype and Statin Drug Treatment
  • The percent of subjects with graft worsening when stratified by lovastatin treatment group and LPL HindIII genotype is shown in FIG. 2. Complete LPL HindIII genotype data and worsening data were available for 786 subjects. [0104]
  • The highest percentage of subjects with worsening were those with the [0105] HindIII 2/2 genotype assigned to the moderate lipid-lowering treatment group (65%). The lowest percentage of subjects with worsening were those with the HindIII 1/1 or 1/2 genotype assigned to the aggressive lipid-lowering treatment group (35%). Within the LPL HindIII 1/1 and 1/2 genotype group, the moderate drug treatment group had a significantly higher percent of subjects with graft worsening than the aggressive treatment group, 49% compared with 35%, odds ratio=1.8, 95% confidence interval 1.3 to 2.4, p<0.00 1. Within the aggressive treatment group, the LPL HindIII 2/2 genotype group had a significantly higher percent of subjects with graft worsening, 54% vs. 35%; OR=2.14, 95% CI 1.11-4.11, p=0.023. The effect of genotype on graft worsening, adjusted for treatment, was significant at p=0.006, OR=2.06, 95% CI 1.23-3.43, and the effect of treatment on graft worsening, adjusted for genotype was significant at p=0.001, OR=1.78, 95% CI 1.32-2.4. The combined effect of both the unfavorable LPL HindIII genotype with moderate drug treatment yielded an odds ratio of 3.5 for graft worsening, 95% CI 1.4-8.7, p=0.002.
  • Using the proportion of grafts with worsening per subject as the dependent variable, the interactions between factors were tested using multiple regression analysis. After adjustments were made for age, sex, body mass index (BMI), smoking, current medication usage, medical history, and family history, the drug treatment group (p=0.0001) and the interaction between the [0106] LPL HindIII 2/2 genotype and diastolic blood pressure (p=0.0046) remained significant. No interaction between the dose of lovastatin required to bring each subject to their target LDL-cholesterol level and the HindIII 2/2 genotype was observed.
  • When subjects were stratified by their LPL HindIII genotype and drug treatment group, each factor had a similar effect on graft worsening, with odds ratios of 2.1 and 1.8 respectively. The combined effect of both the unfavorable LPL HindlII genotype and moderate lipid-lowering yielded an odds ratio for graft worsening of 3.5 (95% CI 1.4-8.7, p=0.002). This analysis demonstrates that the [0107] LPL HindIII 2/2 genotype is an independent and additive risk factor for worsening of grafts with an odds ratio of the same magnitude as that for lipid-lowering in the post-CABG trial.
  • The foregoing examples being illustrative but not an exhaustive description of the embodiments of the present invention, the following claims are presented. [0108]
  • 1 110 1 24 DNA Homo sapiens 1 gcatctgcct tcagctagac attg 24 2 24 DNA Homo sapiens 2 tcttccagaa gggtgagatt ccaa 24 3 21 DNA Homo sapiens 3 ggaaaacata agccctgaat c 21 4 21 DNA Homo sapiens 4 gaaaacataa gccctgaatc g 21 5 21 DNA Homo sapiens 5 aacataagcc ctgaatcgct c 21 6 21 DNA Homo sapiens 6 cctgaatcgc tcacagttat t 21 7 21 DNA Homo sapiens 7 ctgaatcgct cacagttatt c 21 8 21 DNA Homo sapiens 8 aatcgctcac agttattcag t 21 9 21 DNA Homo sapiens 9 ttggcactgt ttcttgtaag t 21 10 21 DNA Homo sapiens 10 cactatagtt tgcaaaatcc c 21 11 24 DNA Homo sapiens 11 caaacctccg agatgctacc tgga 24 12 24 DNA Homo sapiens 12 agatgctacc tggataatca aaga 24 13 24 DNA Homo sapiens 13 gatgctacct ggataatcaa agat 24 14 24 DNA Homo sapiens 14 cttccagaag ggtgagattc caag 24 15 24 DNA Homo sapiens 15 ccagaagggt gagattccaa gata 24 16 24 DNA Homo sapiens 16 cagaagggtg agattccaag ataa 24 17 24 DNA Homo sapiens 17 cccacccatg tgtacccata aaat 24 18 24 DNA Homo sapiens 18 ccacccatgt gtacccataa aatg 24 19 24 DNA Homo sapiens 19 cccatgtgta cccataaaat gaat 24 20 24 DNA Homo sapiens 20 gtacccataa aatgaattac acag 24 21 24 DNA Homo sapiens 21 cccataaaat gaattacaca gaga 24 22 24 DNA Homo sapiens 22 atgaattaca cagagatcgc tata 24 23 24 DNA Homo sapiens 23 acacagagat cgctatagga ttta 24 24 24 DNA Homo sapiens 24 ttataacatt tccatcccca agat 24 25 24 DNA Homo sapiens 25 catctgcctt cagctagaca ttgc 24 26 24 DNA Homo sapiens 26 ctgcattaag gaattagggc atct 24 27 24 DNA Homo sapiens 27 agatcaactc tgccatctct tagc 24 28 24 DNA Homo sapiens 28 tcttatgtta ctgggctttc acca 24 29 24 DNA Homo sapiens 29 agcctagagc agtcttatgt tact 24 30 24 DNA Homo sapiens 30 cagcctagag cagtcttatg ttac 24 31 24 DNA Homo sapiens 31 acagcctaga gcagtcttat gtta 24 32 24 DNA Homo sapiens 32 agacagccta gagcagtctt atgt 24 33 26 DNA Homo sapiens 33 cctgggtaac tgagcgagac tgtgtc 26 34 25 DNA Homo sapiens 34 atctgaccaa ggatagtggg atata 25 35 26 DNA Homo sapiens 35 ctttataaca tttccatccc caagat 26 36 26 DNA Homo sapiens 36 tgtacccata aaatgaatta cacaga 26 37 26 DNA Homo sapiens 37 acccataaaa tgaattacac agagat 26 38 26 DNA Homo sapiens 38 aaaatgaatt acacagagat cgctat 26 39 26 DNA Homo sapiens 39 ttacacagag atcgctatag gattta 26 40 25 DNA Homo sapiens 40 cagcctagag cagtcttatg ttact 25 41 25 DNA Homo sapiens 41 acagcctaga gcagtcttat gttac 25 42 25 DNA Homo sapiens 42 gacagcctag agcagtctta tgtta 25 43 28 DNA Homo sapiens 43 ataaaatgaa ttacacagag atcgctat 28 44 26 DNA Homo sapiens 44 aagattcttt ataacatttc catccc 26 45 28 DNA Homo sapiens 45 aattacacag agatcgctat aggattta 28 46 26 DNA Homo sapiens 46 acagcctaga gcagtcttat gttact 26 47 19 DNA Homo sapiens 47 cccacccatg tgtacccat 19 48 18 DNA Homo sapiens 48 ccacccatgt gtacccat 18 49 21 DNA Homo sapiens 49 cacccatgtg tacccataaa a 21 50 20 DNA Homo sapiens 50 acccatgtgt acccataaaa 20 51 22 DNA Homo sapiens 51 ggctttcacc aagagatgat aa 22 52 22 DNA Homo sapiens 52 gggctttcac caagagatga ta 22 53 22 DNA Homo sapiens 53 tgaattacac agagatcgct at 22 54 22 DNA Homo sapiens 54 acagagatcg ctataggatt ta 22 55 17 DNA Homo sapiens 55 gttactgggc tttcacc 17 56 20 DNA Homo sapiens 56 cttatgttac tgggctttca 20 57 20 DNA Homo sapiens 57 tcttatgtta ctgggctttc 20 58 19 DNA Homo sapiens 58 ccacccatgt gtacccata 19 59 18 DNA Homo sapiens 59 cacccatgtg tacccata 18 60 18 DNA Homo sapiens 60 acccatgtgt acccataa 18 61 18 DNA Homo sapiens 61 cccatgtgta cccataaa 18 62 20 DNA Homo sapiens 62 caactctgcc atctcttagc 20 63 20 DNA Homo sapiens 63 tcaactctgc catctcttag 20 64 20 DNA Homo sapiens 64 atcaactctg ccatctctta 20 65 18 DNA Homo sapiens 65 gaaaacataa gccctgaa 18 66 19 DNA Homo sapiens 66 aaaacataag ccctgaatc 19 67 17 DNA Homo sapiens 67 acataagccc tgaatcg 17 68 17 DNA Homo sapiens 68 ctgaatcgct cacagtt 17 69 19 DNA Homo sapiens 69 tgaatcgctc acagttatt 19 70 19 DNA Homo sapiens 70 atcgctcaca gttattcag 19 71 19 DNA Homo sapiens 71 tcgctcacag ttattcagt 19 72 19 DNA Homo sapiens 72 cgctcacagt tattcagtg 19 73 20 DNA Homo sapiens 73 aatcccagca catttagtat 20 74 20 DNA Homo sapiens 74 actatagttt gcaaaatccc 20 75 18 DNA Homo sapiens 75 tgagagctgg gattagaa 18 76 19 DNA Homo sapiens 76 gagagctggg attagaagt 19 77 19 DNA Homo sapiens 77 agagctggga ttagaagtc 19 78 20 DNA Homo sapiens 78 aatcccagca catttagtat 20 79 20 DNA Homo sapiens 79 cccacccatg tgtacccata 20 80 9734 DNA Homo sapiens 80 tgtaacacaa aattaaaata agtagaatta gttttcagta tttcctatat ttggaaaaca 60 atatttatat tcattttgtt tcttttagtt ttatttttgg cagaactgta agcaccttca 120 ttttcttttt cttccaaagg aggagtttaa ctaccctctg gacaatgtcc atctcttggg 180 atacagcctt ggagcccatg ctgctggcat tgcaggaagt ctgaccaata agaaagtcaa 240 cagaattact ggtaagaaag caatttcgtt ggtcttatca taagaggtga aaagactgtc 300 attctgagag agaatcagaa caaattttgt taaataccca catgtgtggt gttcttcccg 360 gagacatgac cagcacttga ttatctcatt gtagggctct ttattaggga taagaaaaaa 420 cacagacgct ctcactggct tactatccac tggcaatagc acagaaataa agcataatta 480 cacacaatgc ctgcagattt ctctgggaag cctgtttcct cccactctca gctctgtgtt 540 ttagtagtgt aaatgcacat cagtactagg agaaaagaag aaggaccaat tccagaggcc 600 acttcgaaag aagaccgtca tctaggcaaa ggtgtggcat acacacagag agaaagaacc 660 caccactgtt tatacatctt ctcgacatat tcagaaataa tctacaaaag gaaatccagc 720 catcctgagt ggaaattgct gcataaggct agtttaagag actcaaattc attttagaag 780 gagccaagcc tccttttatg tctctctaag taaagatacc atgactgtag aataggagct 840 aataagaatc taaatagctg ccagtgcatt caaatgatga gcagtgacat gcgaatgtca 900 tacgaatgga aatttacaaa tctgtgttcc tgcttttttc ccttttaagg cctcgatcca 960 gctggaccta actttgagta tgcagaagcc ccgagtcgtc tttctcctga tgatgcagat 1020 tttgtagacg tcttacacac attcaccaga gggtcccctg gtcgaagcat tggaatccag 1080 aaaccagttg ggcatgttga catttacccg aatggaggta cttttcagcc aggatgtaac 1140 attggagaag ctatccgcgt gattgcagag agaggacttg gaggtaaata ttatttagaa 1200 gcgaattaaa tgtgactctt atccttaacc cttattgacc caatgtccta ctcagtagct 1260 tcaaagtatg tagttttcat atacacattt ggccaaatta tgtttctgaa gaattctgca 1320 atgttcagca tgaccacctt agagccaggc agacagccat tttatctttt atttactata 1380 ctgtaggcta cactgagcag tgcacttaca gtagcaagag aaaaaggtgg gattttagac 1440 aggaagactc cactgacctc aataatggca tcataaaatg ctatctggcc acatgttgtc 1500 ataccttgaa tgtagctgca aagccaatgg aaagatttta gatgttactg gaacagaaga 1560 tgttaattag cataaatctt ccaaaatgtt cagaacataa tgttagctta atgttttact 1620 ttaataatgt tagcttgtgt taaatttatg atttttgttt gtttgttttt tgagatagag 1680 tcttattcta ttgcccaagc tggggtgcag tcacacaatc acagggactt gcaatgttgc 1740 ccaggctggt ctcaaactcc tggcctcaag tgatcctcct gcctcagcct cccaaagttc 1800 tgggattgca gctgtgagcc accacgccca gtttacgatt tatttttaag agccccttgc 1860 atactttata gacattggga cctacctagg atattctcgt tatttttgtg cacgtaatag 1920 aacttagagc atattgttac tattttcgat tgtcctaaaa acttacaagg aattcattct 1980 tatggcattg ctgattattt ctatgttcat ttgatataaa agagtgttag taggggcaga 2040 accctcaatt gtacataata tcaatgataa aatacaattc atttaacaat taccctctta 2100 agatgtggtt tctagaaata caaattgtcc ctaacttaca gttttccaac tttacaattg 2160 ggctgtaaca ccattttaag ttgagaagca cgtgatggtt tgacttaaaa ctttttgaca 2220 ttatgatggg ttttgggggt attaagtgca ttttgactta cagtattttt gacttatgaa 2280 gaatttattg taaggcaagg ggcaggtata tgtttctaga agcacctaga agtgttagac 2340 actttcaatg taagagaagg atgagataaa caaggaaatc acacctccac cttggaggct 2400 tattacagct tcataaacat actcataaat ataagaagca caaaagtcaa aaattccctg 2460 tgaacttgca actttcactc tcttgaaggt gggtgggccg ctaccaccaa gaatatctcc 2520 tgaaataggg cctacaatca taaatgcaca ggactatatc cttgggtgat tctactctaa 2580 caccacatct cacctatttt agacatgcca aatgaaacac tctttgtgaa tttctgccga 2640 gatacaatct tggtgtctct tttttaccca gatgtggacc agctagtgaa gtgctcccac 2700 gagcgctcca ttcatctctt catcgactct ctgttgaatg aagaaaatcc aagtaaggcc 2760 tacaggtgca gttccaagga agcctttgag aaagggctct gcttgagttg tagaaagaac 2820 cgctgcaaca atctgggcta tgagatcaat aaagtcagag ccaaaagaag cagcaaaatg 2880 tacctgaaga ctcgttctca gatgccctac aaaggtaggc tggagactgt tgtaaataag 2940 gaaaccaagg agtcctattt catcatgctc actgcatcac atgtactgat tctgtccatt 3000 ggaacagaga tgatgactgg tgttactaaa ccctgagccc tggtgtttct gttgataggg 3060 ggttgcattg atccatttgt ctgaggcttc taattcccat tgtcagcaag gtcccagtgc 3120 tcagtgtggg atttgcagcc ttgctcgctg ccctcccctg taaatgtggc cattagcatg 3180 ggctaggcta tcagcacaga gctcagagct catttggaac catccacctc gggtcaacaa 3240 actataaccc ttgtgccaaa tccagcctac ttcctgcttt tgtaaatagt ttttttaaaa 3300 cttttaagtt caggggtacg tatgtaggtt tgctaaaaag gtaaacttgt gacatgggag 3360 tttgttgtcc agaatattcc atcacccagg tattaagctt agtacccatt agttactttt 3420 cctgaagctc tccctcctcc caccctctgg gaggccccag tgtctgttgt tcccctctat 3480 gtgctcatgc aaagttttat taggacacag ccacacacat tcattaccat attgtcaaag 3540 gctggtttca tgccaccata acagagttga tagcccacag agcctaaaat atttactccc 3600 tggcccttta cagaatgttc acaacttaca taaaggcaag gaccatctgt cttatttatt 3660 tatttattta atttgagatg aagtctagct ttctcctagg ctggaggaga ggggcatgat 3720 cttggctcac cacaacctct gcctcccggg ttcaaatgat tcccctgcct cagcctccgg 3780 agtagctggg ataacaggca tgcaccatca tgcccagcta atttttgtat ttttagtaga 3840 gagggggttt caccgtgttg accaggctgg tctcgaactg ctgacctcag gtgatctgcc 3900 ctccttggcc tcatctgtct ttttaaatgc aactattcct ggaaggcaag aatatctcac 3960 accttctaag atactgccat tttgccagga gtttgtttca cacttgaatt tcaagcttgg 4020 cctcttgttt agaggcagac ctaaaggaat ggtcggaaaa tgagagagga ggtcttcgga 4080 taaatccggt gagagggacc aacttcagga agggtggctt ttgtggaatc cagatggaaa 4140 cctgagggaa gggatgatat taaagaacag tggccccagg taaaacatat ggcacccatg 4200 tgtaaggtga ttcttagaat ctgtagaggt gtctttcgtg gtatagaggt tgaggcacct 4260 gtgcttcaag gaaaccttaa ctcttcaaaa tcaggcaatg cgtatgaggt aaagagagga 4320 ctgtgggacc ataatcttga agacacagac aggcttcact catccctgcc tcctgcacca 4380 gtgggttcaa ggctctgtca gtgtccccta ggggcacctc accactccca gcttcttcag 4440 ctctggcctg tcctgctgcc tgcaagggtt ttgcttaatt ctcaattcaa tgtctcttca 4500 tcttttagta gctgtggggt tttgttgttg ttcttctgtt tttgcttagt atctgactac 4560 tttttaatta taaaaagaga tgtatctaaa caaaatagag attgttatca gaagttcaca 4620 acatttatta aaaatttttt cacctggaca agagtctaaa gcagcataaa aatatggtct 4680 gctatattct aaaccatcag tcttaagaga tctgtgtctc agcttaagag aaaatacatt 4740 taatagacag taacacaaat aagaaaaaaa tctgaccaag gatagtggga tatagaagaa 4800 aaaacattcc aagaattatt ttatttattt atttatttat ttatttattt atttatttat 4860 ttttgagaca cggtctcgct cagttaccca ggctggagtg cagcggcgca atcttaactc 4920 actgcaacct ctgctttccg gttcaagcga ttctcctgcc tcagcctcct gagtaactgg 4980 gattacaggc acccgccacc acgcccaact aatttctgta tttttcttag tagaaacagg 5040 gtttcaccat gttggccaag ctagtctcaa actcctgacc tcaggtgatt cacccaccaa 5100 ggcctcccaa agtgctggga ttacaggcat gagccaccat gcctggcctc caaaaactct 5160 tttttcctcc atcatcatgg ttctatttta gtcctgctgc ctttcctttt aacctctccc 5220 caggcccatt tgctcagggt ttttggtaga gaccagagga ggggcaggga ggagatatag 5280 aagttcaact acctgcttcc agaggctgtc cctagtatag aatactttag gggctggctt 5340 tacaaggcag tccttgtggc ctcactgatg gctcaatgaa ataagttctt ttttaaaaaa 5400 aattttattt atttccatag gttattgggg gaacaggtgg tgtttggtta catgagtaag 5460 ttctttagta gtgatttgtg agattttggt gtgcccatta cggaatggaa aaatcaacga 5520 aataagttct atgatgcacc tactagacac ctaatctgca ctagatggtg ggggaattaa 5580 gagcatgggc atgatcctgt gaccggaagc ccgcttacag tcagggtgga ggacagacct 5640 actcatgaaa caaacacagt gacatatagt gacacagaag caaatgtcaa atatgcttgc 5700 tccagatgct aaggcacaag atggccaagg atggcggagt tcatggagaa agcatcatga 5760 gtgttttggc cttctgattt gatctcccta gcacccctca aagatggcta cttcctaatg 5820 ctgcttggca attcagacac atttgggttt ttcctatgca tataaccaca cttttctgaa 5880 agggagtaga attcaaggtc tgcattttct aggtatgaac actgtgcatg atgaagtctt 5940 tccaagccac accagtggtt ccatgtgtgt gcacttccgg tttgagtgct agtgagatac 6000 ttctgtggtt ctgaattgcc tgactatttg gggttgtgat attttcataa agattgatca 6060 acatgttcga atttcctccc caacagtctt ccattaccaa gtaaagattc atttttctgg 6120 gactgagagt gaaacccata ccaatcaggc ctttgagatt tctctgtatg gcaccgtggc 6180 cgagagtgag aacatcccat tcactctgtg agtagcacag gggggcggtc atcatggcac 6240 cagtccctcc cctgccataa cccttggtct gagcagcaga agcagagagc gatgcctaga 6300 aaacaagtct ttagttaaaa aaatcagaat ttcaaaattg aggtctttcc tctatttgat 6360 attgagaaaa aaatgcttca aattggccat tttattttca cttactagtt atattttttt 6420 atttatcatc ttatatctgt ttatttcttt tataaagctg ctgttaaaca atataattaa 6480 actatctcaa aaggtttgac attaaagaaa atgagcaatg gtaacaggaa accactctat 6540 agatgtacat ataatatgta cagaaaatat aagtagtaag aagtccatga caaagtgtta 6600 gctctttttt tttttttttt tttttttttt tttgagatgg agtctctctc ctattgccca 6660 ggctggagtg cagtgattcg atctcagctc actgcaacct ctacctcccg agttcaaaca 6720 attcttctgt ctcagcctcc cgagtagctg gggctgcagg tgcccaccac catgcccagc 6780 taatttttgt atttttagta gcgacagggt ctcaccatgt tggccaagct ggtcttgaat 6840 tcctgatctc aggtgatcca cccgcctcgg cctcccaaag tgctgggatt acaggtgtga 6900 gccaccatgc ccagcctacc ctttactact aatcaaagaa ataaaagtaa ggcaacttga 6960 tacttttaca attactagat gaacaaatct ttaaaaatag ccagtgcaga caaggtggtg 7020 aagcagaaca tgcgaaccta ccatgcatca ttcacggcta gaaccctcca ggtgcggaag 7080 gtagtatttt aataactttc catagctaca aaatattatt acatagaagg gagtgatttt 7140 tttctaatat ttatcctaaa gaaatagtca acaaacattt ttaaaaaaca tcaattacag 7200 tcgtacctat actagcataa attagaaacc cagtatccaa cattgaggca gtgggtaaat 7260 gaatcgtggt ttatcaagtc attaaaatca atctagcctt taaaaactat aattgtagga 7320 aacccaggaa aacatagtaa aaaatggaat ataaaatcta aagagaataa agaatagaga 7380 atcgtatgtg tgctatgatt gtagctaaat aatgttcaag tatcaacaca aattgaaaag 7440 gaatacatga aaatgaaaat tatatttctg aatgattgac ttcaggattt tcttttagaa 7500 ttgtattaaa tagttcatgt cattaggata aatgctggaa tgtggatata atttaaaata 7560 tactaaatgc catcgacctt cattttgagt tctttgttgg acatttttgt gcatttttaa 7620 aatatcccct aaataataaa gctatttata tttggagagg agaaaaaaaa gtggggggca 7680 gggagagctg atctctataa ctaaccaaat ttattgcttt tttgtttagg cctgaagttt 7740 ccacaaataa gacatactcc ttcctaattt acacagaggt agatattgga gaactactca 7800 tgttgaagct caaatggaag agtgattcat actttagctg gtcagactgg tggagcagtc 7860 ccggcttcgc cattcagaag atcagagtaa aagcaggaga gactcagaaa aagtaattaa 7920 atgtattttt cttccttcac tttagacccc cacctgatgt caggacctag gggctgtatt 7980 tcaggggcct tcacaattca gggagagctt taggaaacct tgtatttatt actgtatgat 8040 gtagattttc tttaggagtc ttcttttatt ttcttatttt tggggggcgg ggggggaagt 8100 gacagtattt ttgtatttca tgtaaggaaa acataagccc tgaatcgctc acagttattc 8160 agtgagagct gggattagaa gtcaggaatc tcagcttctc atttggcact gtttcttgta 8220 agtacaaaat agttagggaa caaacctccg agatgctacc tggataatca aagattcaaa 8280 ccaacctctt caagaagggt gagattccaa gataatctca acctgtctcc gcagccccac 8340 ccatgtgtac ccataaaatg aattacacag agatcgctat aggatttaaa gcttttatac 8400 taaatgtgct gggattttgc aaactatagt gtgctgttat tgttaattta aaaaaactct 8460 aagttaggat tgacaaatta tttctcttta gtcatttgct tgtatcacca aagaagcaaa 8520 caaacaaaca aaaaaaaaaa gaaaaagatc ttggggatgg aaatgttata aagaatcttt 8580 tttacactag caatgtctag ctgaaggcag atgccctaat tccttaatgc agatgctaag 8640 agatggcaga gttgatcttt tatcatctct tggtgaaagc ccagtaacat aagactgctc 8700 taggctgtct gcatgcctgt ctatctaaat taactagctt ggttgctgaa caccgggtta 8760 ggctctcaaa ttaccctctg attctgatgt ggcctgagtg tgacagttaa ttattgggaa 8820 tatcaaaaca attacccagc atgatcatgt attatttaaa cagtcctgac agaactgtac 8880 ctttgtgaac agtgcttttg attgttctac atggcatatt cacatccatt ttcttccaca 8940 gggtgatctt ctgttctagg gagaaagtgt ctcatttgca gaaaggaaag gcacctgcgg 9000 tatttgtgaa atgccatgac aagtctctga ataagaagtc aggctggtga gcattctggg 9060 ctaaagctga ctgggcatcc tgagcttgca ccctaaggga ggcagcttca tgcattcctc 9120 ttcaccccat caccagcagc ttgccctgac tcatgtgatc aaagcattca atcagtcttt 9180 cttagtcctt ctgcatatgt atcaaatggg tctgttgctt tatgcaatac ttcctctttt 9240 tttctttctc ctcttgtttc tcccagcccg gaccttcaac ccaggcacac attttaggtt 9300 ttattttact ccttgaacta cccctgaatc ttcacttctc cttttttctc tactgcgtct 9360 ctgctgactt tgcagatgcc atctgcagag catgtaacac aagtttagta gttgccgttc 9420 tggctgtggg tgcagctctt cccaggatgt attcagggaa gtaaaaagat ctcactgcat 9480 cacctgcagc cacatagttc ttgattctcc aagtgccagc atactccggg acacacagcc 9540 aacagggctg ccccaagcac ccatctcaaa accctcaaag ctgccaagca aacagaatga 9600 gagttatagg aaactgttct ctcttctatc tccaaacaac tctgtgcctc tttcctacct 9660 gacctttagg gctaatccat gtggcagctg ttagctgcat ctttccagag cgtcagtact 9720 gagaggacac taag 9734 81 3867 DNA Homo sapiens 81 gaattcaagg tctgcatttt ctaggtatga acactgtgca tgatgaagtc tttccaagcc 60 acaccagtgg ttccatgtgt gtgcacttcc ggtttgagtg ctagtgagat acttctgtgg 120 ttctgaattg cctgactatt tggggttgtg atattttcat aaagattgat caacatgttc 180 gaatttcctc cccaacagtc ttccattacc aagtaaagat tcatttttct gggactgaga 240 gtgaaaccca taccaatcag gcctttgaga tttctctgta tggcaccgtg gccgagagtg 300 agaacatccc attcactctg tgagtagcac aggggggcgg tcatcatggc accagtccct 360 ctcctgccat aacccttggt ctgagcagca gaagcagaga gcgatgccta gaaaacaagt 420 ctttagttaa aaaaatcaga atttcaaaat tgaggtcttt cctctatttg atattgagaa 480 aaaaatgctt caaattggcc attttatttt cacttactag ttatattttt ttatttatca 540 tcttatatct gtttatttct tttataaagc tgctgttaaa caatataatt aaaaggtttg 600 acattaaaga aaatgagcaa tggtaacagg aaaccactct atagatgtac atataatatg 660 tacagaaaat ataagtagta agaagtccat gacaaagtgt tagctctttt tttttttttt 720 tttttttttt tttttgagat ggagtctctc tctattgccc aggctggagt gcagtgattc 780 gatctcagct cactgcaacc tctacctccc gagttcaaac aattcttctg tctcagcctc 840 ccgagtagct ggggctgcag gtgcccacca ccatgcccag ctaatttttg tatttttagt 900 agcgacaggg tctcaccatg ttggccaagc tggtcttgaa ttcctgatct caggtgatcc 960 acccgcctcg gcctcccaaa gtgctgggat tacaggtgtg agccaccatg cccagcctac 1020 cctttactac taatcaaaga aataaaagta aggcaacttg atacttttac aattactaga 1080 tgaacaaatc tttaaaaata gccagtgcag acaaggtggt gaagcagaac atgcgaacct 1140 accatgcatc attcacggct agaaccctcc aggtgcggaa ggtagtattt taataacttt 1200 ccatagctac aaaatattat tacatagaag ggagtgattt ttttctaata tttatcctaa 1260 agaaatagtc aacaaacatt tttaaaaaca tcaattacag tcgtacctat actagcataa 1320 attagaaacc cagtatccaa cattgaggca gtgggtaaat gaatcgtggt ttatcaagtc 1380 attaaaatca atctagcctt taaaaactat aattgtagga aacccaggaa aacatagtaa 1440 aaaatggaat ataaaatctg aagagaataa agaatagaga atcgtatgtg tgctatgatt 1500 gtagctaaat aatgttcaag tatcaacaca aattgaaaag gaatacatga aaatgaaaat 1560 tatatttctg aatgattgac ttcaggattt tcttttagaa ttgtattaaa tagttcatgt 1620 cattaggata aatgctggaa tgtggatata atttaaaata tactaaatgc catcgacctt 1680 cattttgagt tctttgttgg acatttttgt gcatttttaa aatatcccct aaataataaa 1740 gctatttata tttggagagg agaaaaaaaa gtggggggca gggagagctg atctctataa 1800 ctaaccaaat ttattgcttt tttgtttagg cctgaagttt ccacaaataa gacctactcc 1860 ttcctaattt acacagaggt agatattgga gaactactca tgttgaagct caaatggaag 1920 agtgattcat actttagctg gtcagactgg tggagcagtc ccggcttcgc cattcagaag 1980 atcagagtaa aagcaggaga gactcagaaa aagtaattaa atgtattttt cttccttcac 2040 tttagacccc cacctgatgt caggacctag gggctgtatt tcaggggcct tcacaattca 2100 gggagagctt taggaaacct tgtatttatt actgtatgat gtagattttc tttaggagtc 2160 ttcttttatt ttcttatttt tggggggcgg ggggggaagt gacagtattt ttgtatttca 2220 tgtaaggaaa acataagccc tgaatcgctc acagttattc agtgagagct gggattagaa 2280 gtcaggaatc tcagcttctc atttggcact gtttcttgta agtacaaaat agttagggaa 2340 caaacctccg agatgctacc tggataatca aagattcaaa ccaacctctt ccagaagggt 2400 gagattccaa gataatctca acctgtctcc gcagccccac ccatgtgtac ccataaaatg 2460 aattacacag agatcgctat aggatttaaa gcttttatac taaatgtgct gggattttgc 2520 aaactatagt gtgctgttat tgttaattta aaaaaactct aagttaggat tgacaaatta 2580 tttctcttta gtcatttgct tgtatcacca aagaagcaaa caaacaaaca aaaaaaaaaa 2640 gaaaaagatc ttggggatgg aaatgttata aagaatcttt tttacactag caatgtctag 2700 ctgaaggcag atgccctaat tccttaatgc agatgctaag agatggcaga gttgatcttt 2760 tatcatctct tggtgaaagc ccagtaacat aagactgctc taggctgtct gcatgcctgt 2820 ctatctaaat taactagctt ggttgctgaa caccaggtta ggctctcaaa ttaccctctg 2880 attctgatgt ggcctgagtg tgacagttaa ttattgggaa tatcaaaaca attacccagc 2940 atgatcatgt attatttaaa cagtcctgac agaactgtac ctttgtgaac agtgcttttg 3000 attgttctac atggcatatt cacatccatt ttcttccaca gggtgatctt ctgttctagg 3060 gagaaagtgt ctcatttgca gaaaggaaag gcacctgcgg tatttgtgaa atgccatgac 3120 aagtctctga ataagaagtc aggctggtga gcattctggg ctaaagctga ctgggcatcc 3180 tgagcttgca ccctaaggga ggcagcttca tgcattcctc ttcaccccat caccagcagc 3240 ttgccctgac tcatgtgatc aaagcattca atcagtcttt cttagtcctt ctgcatatgt 3300 atcaaatggg tctgttgctt tatgcaatac ttcctctttt tttctttctc ctcttgtttc 3360 tcccagcccg gaccttcaac ccaggcacac attttaggtt ttattttact ccttgaacta 3420 cccctgaatc ttcacttctc cttttttctc tactgcgtct ctgctgactt tgcagatgcc 3480 atctgcagag catgtaacac aagtttagta gttgccgttc tggctgtggg tgcagctctt 3540 cccaggatgt attcagggaa gtaaaaagat ctcactgcat cacctgcagc cacatagttc 3600 ttgattctcc aagtgccagc atactccggg acacacagcc aacagggctg ccccaagcac 3660 ccattctcaa aaccctcaaa gctgccaagc aaacagaatg agagttatag gaaactgttc 3720 tctcttctat ctccaaacaa ctctgtgcct ctttcctacc tgacctttag ggctaatcca 3780 tgtggcagct gttagctgca tctttccaga gcgtcagtac tgagaggaca ctaagcatgt 3840 gaccttcact actcctgttc tgaattc 3867 82 24 DNA Homo sapiens 82 ctggacaaga gtctaaagca gcat 24 83 20 DNA Homo sapiens 83 gaatcgcttg aaccggaaag 20 84 24 DNA Homo sapiens 84 accatcagtc ttaagagatc tgtg 24 85 24 DNA Homo sapiens 85 cacagatctc ttaagactga tggt 24 86 20 DNA Homo sapiens 86 tttttcacct ggacaagagt 20 87 20 DNA Homo sapiens 87 ggtaactga gcgagaccgt 20 88 20 DNA Homo sapiens 88 ttcacctgga caagagtcta 20 89 15 DNA Homo sapiens 89 gcttgaaccg gaaag 15 90 20 DNA Homo sapiens 90 tcacctggac aagagtctaa 20 91 17 DNA Homo sapiens 91 ctccagcctg ggtaact 17 92 20 DNA Homo sapiens 92 acaagagtct aaagcagcat 20 93 668 DNA Homo sapiens 93 tcttttagta gctgtggggt tttgttgttg ttcttctgtt tttgcttagt atctgactac 60 tttttaatta taaaaagaga tgtatctaaa caaaatagag attgttatca gaagttcaca 120 acatttatta aaaatttttt cacctggaca agagtctaaa gcagcataaa aatatggtct 180 gctatattct aaaccatcag tcttaagaga tctgtgtctc agcttaagag aaaatacatt 240 taatagacag taacacaaat aagaaaaaaa tctgaccaag gatagtggga tatagaagaa 300 aaaacattcc aagaattatt ttatttattt atttatttat ttatttattt atttatttat 360 ttatttattt ttgagacacg gtctcgctca gttacccagg ctggagtgca gcggcgcaat 420 cttaactcac tgcaacctct gctttccggt tcaagcgatt ctcctgcctc agcctcctga 480 gtaactggga ttacaggcac ccgccaccac gcccaactaa tttctgtatt tttcttagta 540 gaaacagggt ttcaccatgt tggccaagct agtctcaaac tcctgacctc aggtgattca 600 cccaccaagg cctcccaaag tgctgggatt acaggcatga gccaccatgc ctggcctcca 660 aaaactct 668 94 3240 DNA Homo sapiens 94 gaattctctc taaaaataaa atgatgtatg atttgttgtt ggcatcccct ttattaattc 60 attaaatttc tggatttggg ttgtgaccca gggtgcatta acttaaaaga ttcactaaag 120 cagcacatag cactgggaac tctggctccg aaaaactttg ttatatatat caaggatgtt 180 ctggctttac attttattta ttagctgtaa atacatgtgt ggatgtgtaa atggagcttg 240 tacatattgg aaaggtcatt gtggctatct gcatttataa atgtgtggtg ctaactgtat 300 gtgtctttat cagtgatggt ctcacagagc caactcactc ttatgaaatg ggctttaaca 360 aaacaagaaa gaaacgtact taactgtgtg aagaaatgga atcagctttt aataaaattg 420 acaacatttt attaccacac taagtcatta ttttgtatca tttttaaagt aaatttattc 480 ttaggtcaga ttcactcagc atattttgac taagtaacca ctgtacttag taaaccgaag 540 agcttctgag aattatagtg taccgtatag atatttttaa catttatatt tgtataaagc 600 taaagaaagc cttacatatc ctttaaactg actatagaag aaaatgatac agaattttgc 660 ctgcataaag tacacaggac tattcttgcc tacaatatgc tttttcacaa gcaaaatgtt 720 agactaatat aaggcatctt tggccatttt atagtgtaca tcatctctat ttctgaggcc 780 tcattgttag ctgtaacgca agtagcattt gtgcaataaa atgaactatt tgggatggga 840 gggtacattt tttagaactt tgctttgggt tgccttgata attaatagca tatagtccat 900 ttatgcagct aagtagggat tgcttcttag tacagtcagg aagaatttag cccagaaaac 960 aattatttca atggccactg acccaaactt ccaggctgaa gagcaatggc gtgatcatgg 1020 ctcactgcac ctccacctcc caggctcaag tgattctcct gcctcagcct cccaagtaga 1080 tggtactaca agcacacgcc actgcaccca gctaattttt gtattttttg tagagatggg 1140 ggtttcacca tgttgcccag gctggtctta aattcctggc ctcaagtgtc tgcccccctt 1200 ggcctcccaa agtgctggaa ttacaggcat gagccaccat gtccagcctt gacccaaact 1260 tttattgtca gttagctatt gggggcttct ggagtttggg tctcccctga caggaggggg 1320 ctccccagtt cacacttggc cactgcccat caattcctgt tgatatgatc aacaagatag 1380 acaattgcaa atgttgctga ggatgtggag aagtgtgaac ctgtgtaagt ggctgatggg 1440 aatgtaaaat ggcacagcca ctatggagaa caatttggta gtatttccaa agttaagcat 1500 agagtttaac ccatatgacc cagcaattcc actcctagat atatacccaa gagaaatgaa 1560 aacacagatc cacaaagatt tgcacacaca ggttcatagc agcattaatc agattagtcc 1620 caaagtggac aacccaaatg tccatgaact tgtgaaagag ataagcaaaa tgtgacaaat 1680 tcacataata aaatattatt cagaagtaaa aagaacaagc agcagatata tgatacaaca 1740 cgatgcgcct tgaaaacgtt tagccatatg aaagaaacca gatgcaaaat ggaaccatgg 1800 cttaggggag gagaacggca caatggtgta aaagttgcag agaggaacaa aaaggctacc 1860 tgcctcgctc ccaggccaag taacacagga ggaaagaaaa tatccacata tgcgagggct 1920 aaaggaaaga ggtgttctca agctgaagca ggaggtggga ctcaactctg gaggtgggcc 1980 tcacacactg taccaaattg aggactagct aaaacaggga tgggggtgaa agcacctttt 2040 cgtaagacat gcccaccatt gtcccgttct cctcccttaa gcccttgtct tgctcatgtc 2100 agcaagctta ttgccatcta ttcttcctag ttacagacat ctgtggagct ctgagttttt 2160 tgcctaatca ttattttaga acctggttca ctctctctcc cttctacact agttctgtca 2220 ttattattac tgatttcagt acctctgagg tgatagattt tattttccaa tggcagccac 2280 aacactacct cccattctat atgttcccct gcaatgttgc cttgacatcc ctattaagag 2340 ttggaatcta gtcaccccgc ttttctagtc tccccactcc tttgaacttg tgtgggccct 2400 aagattgctt ctactagtag aatagaacta aaatgaccct ggaccagtgt ggggtgcagc 2460 ccttaactgg cctggcagct tctgcttttg gttccttggg gcactcactc ttgggaaact 2520 tccctttgga actcagcatt catgatgcgg aagttgaagc cacatgaaaa gagcatatgg 2580 tggttctctc agctcccagc caacaaccag tctcgactgt cagccatgtg agtgaggcat 2640 cttggacctc cggccagttg agtgttcaga agactgcagc tcgagctggc atctggatgc 2700 aaccacatga gagacgctct gcccagccaa gcccagccaa ctcacagtac tatgagagat 2760 actaataact tgttgttgtt gttgttgttg ttgtttttat tattaaactt taagttttag 2820 catacacgtg cacaacgtgc aggttagtta catatgtata cctgggccat gttggtgtgc 2880 tgcacccagt aactcgtcat ttaacattag gtatatctcc aaatgctatc cctcccccct 2940 ccctaagttt ttaggagttt gctttgcaac gatagatagt tgaaacatct ggatgatgca 3000 tccagtattc tggcttctca ctgcctttac ctcctctctc ccatggcctt gtcttctaaa 3060 tctaccttta catagaaaca ttcagtcacg tgctatacta tatcatgcca ttactaataa 3120 ctcataaact caatttcaac ttctcccttc tttgactacc acatgctatc tttttacttt 3180 aatcagtcta gtgctctcag ttcaacagct cctcaactgc cccaggacct ccaatacatt 3240 95 22 DNA Homo sapiens 95 atgaaaagag catatggtgg tt 22 96 25 DNA Homo sapiens 96 tggcccaggt atacatatgt aacta 25 97 25 DNA Homo sapiens 97 ggcccaggta tacatatgta actaa 25 98 22 DNA Homo sapiens 98 tgaaaagagc atatggtggt tc 22 99 21 DNA Homo sapiens 99 gaaaagagca tatggtggtt c 21 100 25 DNA Homo sapiens 100 gcccaggtat acatatgtaa ctaac 25 101 20 DNA Homo sapiens 101 aaaagagcat atggtggttc 20 102 25 DNA Homo sapiens 102 ggttctctca gctcccagcc aacaa 25 103 23 DNA Homo sapiens 103 agcacaccaa catggcccag gta 23 104 25 DNA Homo sapiens 104 ctcagctccc agccaacaac cagtc 25 105 24 DNA Homo sapiens 105 cagcacacca acatggccca ggta 24 106 25 DNA Homo sapiens 106 agctcccagc caacaaccag tctcg 25 107 16 DNA Homo sapiens 107 actccgggaa tgaggt 16 108 21 DNA Homo sapiens 108 ccagaaagaa gagattttgt c 21 109 24 DNA Homo sapiens 109 ctgctttaga ctcttgtcca ggtg 24 110 24 DNA Homo sapiens 110 gggttcaagg ctctgtcagt gtcc 24

Claims (102)

We claim:
1. A method of detecting a genetic predisposition in a human subject for non-responsiveness to statin drug treatment, comprising:
a) collecting a tissue sample from a human subject;
b) amplifying nucleic acids that include a non-coding or untranslated region within the 3′ end of the human lipoprotein lipase gene from said tissue sample to obtain amplification products; and
c) analyzing the amplification products for homozygosity for a variant allele in a non-coding or untranslated region at the 3′ end of the human lipoprotein lipase gene, homozygosity for the variant allele indicating a genetic predisposition for non-responsiveness to treatment with a statin drug.
2. The method of claim 1, wherein the tissue sample is a blood sample.
3. The method of claim 1, further comprising restricting the amplification products with a restriction enzyme before analyzing the amplification products.
4. The method of claim 3, wherein the restriction enzyme is HindIII.
5. The method of claim 1, wherein an oligonucleotide primer is used in amplifying said nucleic acids.
6. The method of claim 1, wherein the variant allele is in the HindIII recognition site in intron 8 or the (TTTA)n tetranucleotide repeat region of intron 6.
7. The method of claim 1, wherein an oligonucleotide comprising the sequence 5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′(SEQ. ID. NO. 1) is used in amplifying said nucleic acids.
8. The method of claim 1, wherein an oligonucleotide primer comprising the sequence 5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′(SEQ. ID. NO. 2) is used in amplifying said nucleic acids.
9. The method of claim 1, wherein an oligonucleotide primer having the sequence 5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′(SEQ. ID. NO. 1) or 5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′(SEQ. ED. NO. 2) is used in amplifying said nucleic acids.
10. The method of claim 1, wherein a reverse primer oligonucleotide primer having the sequence 5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′(SEQ. ID. NO. 1) and a forward oligonucleotide primer having the sequence 5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′ (SEQ. ID. NO. 2) are used in amplifying said nucleic acids.
11. The method of claim 1, wherein an oligonucleotide primer is used in amplifying said nucleic acids, said primer comprising a nucleotide sequence of (SEQ. ID. NO.: 1), (SEQ. ID. NO.: 2), (SEQ. ID. NO.: 3), (SEQ. ID. NO.: 4), (SEQ. ID. NO.: 5), (SEQ. ID. NO.-:6), (SEQ. ID. NO.: 7), (SEQ. ID. NO.: 8), (SEQ. ID. NO.: 9), (SEQ. ID. NO.: I10), (SEQ. ID. NO.:I 1), (SEQ. ID. NO.: 12), (SEQ. ID. NO.: 13), (SEQ. ID. NO.: 14), (SEQ. ID. NO.: 15), (SEQ. ID. NO.: 16), (SEQ. ID. NO.: 17), (SEQ. ID. NO.: 18), (SEQ.NO.: 19), (SEQ. ID. NO.: 20), (SEQ. ID. NO.: 21), (SEQ. ID. NO.: 22), (SEQ. ID. NO.:23), (SEQ. ID. NO. 24 ), (SEQ. ID. NO.: 25), (SEQ. ID. NO.: 26), (SEQ. ID. NO.: 27), (SEQ. ID. NO.: 28), (SEQ. ID. NO.: 29), (SEQ. ID NO.: 30), (SEQ. ID. NO.: 31), (SEQ. ID. NO.: 32), (SEQ. ID. NO.: 35), (SEQ. ID. NO.:36), (SEQ. ID. NO.:37 ), (SEQ. ID. NO.: 38), (SEQ. ID. NO.: 39), (SEQ. ID. NO.: 40), (SEQ. ID. NO.: 41), (SEQ. ID. NO.: 42), (SEQ. ID NO.: 43), (SEQ. ID. NO.: 44), (SEQ. ID. NO.: 45),(SEQ. ID. NO.: 46), (SEQ. ID. NO.: 47), (SEQ. ID. NO.: 48) (SEQ. ID. NO.: 49), (SEQ. ID. NO.: 50), (SEQ. ID. NO.: 51), (SEQ. ID. NO.: 52), (SEQ. ID. NO.: 53), (SEQ. ID. NO.-54), (SEQ. ID. NO.-:55), (SEQ. ID. NO.: 56), (SEQ. ID. NO.: 57), (SEQ. ID. NO.: 58), (SEQ. ID. NO.:59), (SEQ. ID. NO.: 60), (SEQ. ID. NO.: 61), (SEQ. ID. NO.: 62), (SEQ. ID. NO.: 63), (SEQ. ID. NO.: 64), (SEQ. ID. NO.: 65), (SEQ. ID. NO.: 66), (SEQ ID. NO.: 67), (SEQ. ID. NO. :.68), (SEQ. ID. NO.:69), (SEQ. ID. NO.: 70) (SEQ ID. NO. : 71), (SEQ. ID. NO.: 72), (SEQ. ID. NO.: 73), (SEQ. ID. NO.: 74), (SEQ. ID. NO.: 75), (SEQ. ID. NO.: 76), (SEQ ID. NO.: 77), (SEQ. ID NO.: 78), or (SEQ. ID. NO. :79), or comprising a sequence overlapping the sequence of any of these with respect to its position on the Nickerson reference sequence.
12. The method of claim 1, wherein an oligonucleotide comprising the sequence 5′-CCT GGG TAA CTG AGC GAG ACT GTG TC-3′ (SEQ. ID. NO. :33) is used in amplifying said nucleic acids.
13. The method of claim 1, wherein an oligonucleotide primer comprising the sequence 5′-ATC TGA CCA AGG ATA GTG GGA TAT A-3′ (SEQ. ID. NO. :34) is used in amplifying said nucleic acids.
14. The method of claim 1, wherein an oligonucleotide primer having the sequence 5′-CCT GGG TAA CTG AGC GAG ACT GTG TC-3′ (SEQ. ID. NO.: 33) is used in amplifying said nucleic acids.
15. The method of claim 1, wherein an oligonucleotide primer having the sequence 5′-ATC TGA CCA AGG ATA GTG GGA TAT A-3′ (SEQ. ID. NO. :34) is used in amplifying said nucleic acids.
16. The method of claim 1, wherein amplifying said nucleic acids is done using an oligonucleotide primer comprising a nucleotide sequence of (SEQ. ID. NO.: 33), (SEQ. ID. NO.: 34), (SEQ. ID. NO.: 82), (SEQ. ID. NO.83), (SEQ. ID. NO.: 84), (SEQ. ID. NO.: 85), (SEQ. ID. NO.: 86), (SEQ. ID. NO. 87), (SEQ. ID. NO.: 88), (SEQ. ID NO.: 89), (SEQ. ID. NO.: 90), (SEQ. ID. NO.: 91), or (SEQ. ID. NO.: 92), or a sequence overlapping the sequence of any of these with respect to its position on the Nickerson reference sequence.
17. The method of claim 1, wherein amplifying said nucleic acids is done using an oligonucleotide primer comprising a nucleotide sequence of (SEQ. ID. NO.: 95), (SEQ. ID. NO.: 96), (SEQ. ID. NO.: 97), (SEQ. ID. NO.: 98), (SEQ. ID. NO.: 99), (SEQ. ID. NO.: 100), (SEQ. ID. NO.: 101), (SEQ. ID. NO.: 102), (SEQ. ID. NO.: 103), (SEQ. ID. NO.: 104), (SEQ. ID. NO.: 105), or (SEQ. ID. NO.: 106), or a sequence overlapping the sequence of any of these with respect to its position on the Oka reference sequence.
18. The method of claim 5, wherein said oligonucleotide primer is labeled with a fluorescent dye.
19. The method of claim 18, wherein said dye is SYBR Green I, YO-PRO- 1, thiazole orange, Hex, pico green, edans, fluorescein, FAM, or TET.
20. The method of claim 1, wherein said statin drug is lovastatin, pravastatin, simvastatin, atorvastatin, fluvastatin, or cerivastatin.
21. A method of detecting a genetic predisposition in a human subject for non-responsiveness to statin drug treatment, comprising:
a) collecting a tissue sample from a human subject;
b) amplifying nucleic acids that include the normal locus of the HindIII recognition site in intron 8 of the human lipoprotein lipase gene (LPL) from said tissue sample to obtain amplification products; and
c) analyzing the amplification products for the absence of a HindIII recognition site in intron 8 of the human lipoprotein lipase gene, homozygosity for an absence of said HindlIl recognition site indicating a genetic predisposition for non-responsiveness to treatment with a statin drug.
22. The method of claim 21, wherein the tissue sample is a blood sample.
23. The method of claim 21, further comprising restricting the amplification products with a restriction enzyme before analyzing the amplification products.
24. The method of claim 21, wherein the restriction enzyme is HindIII.
25. The method of claim 21, wherein an oligonucleotide primer is used in amplifying said nucleic acids.
26. The method of claim 21, wherein an oligonucleotide primer comprising the sequence 5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′ (SEQ. ID. NO. 1) is used in amplifying said nucleic acids.
27. The method of claim 21, wherein an oligonucleotide primer comprising the sequence 5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′ (SEQ. ID. NO. 2) is used in amplifying said nucleic acids.
28. The method of claim 21, wherein an oligonucleotide primer having the sequence 5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′ (SEQ ID. NO. 1) or 5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′ (SEQ. ID. NO. 2) is used in amplifying said nucleic acids.
29. The method of claim 21, wherein a reverse oligonucleotide primer having the sequence 5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′ (SEQ. ID. NO. 1) and a forward oligonucleotide primer having the sequence 5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′ (SEQ. ID. NO. 2) are used in amplifying said nucleic acids.
30. The method of claim 21, wherein an oligonucleotide primer is used in amplifying said nucleic acids, said primer comprising a sequence selected from the group essentially consisting of (SEQ. ID. NO.: 1), (SEQ. ID. NO.: 2), (SEQ. ID. NO.: 3), (SEQ. ID. NO.: 4), (SEQ. ID NO.: 5), (SEQ. ID. NO.: 6), (SEQ. ID. NO.: 7), (SEQ. ID. NO.:8), (SEQ. ID. NO.-: 9), (SEQ. ID. NO.: 10), (SEQ. ID. NO.: 10), (SEQ. ID. NO.: 11), (SEQ. ID. NO.: 12), (SEQ. ID. NO.: 13), (SEQ. ID. NO.: 14), (SEQ. ID. NO.: 15), (SEQ. ID. NO. : 16), (SEQ. ID. NO.: 17), (SEQ. ID. NO.: 18), (SEQ. ID. NO.: 19), (SEQ. ID. NO.: 20), (SEQ. ID. NO.: 21), (SEQ. ID. NO.: 22), (SEQ. ID. NO.: 23), (SEQ. ID. NO.: 24), (SEQ. 10. NO.:25), (SEQ. ID. NO.:26), (SEQ. ID. NO.: 27), (SEQ. ID. NO.: 28), (SEQ. ID. NO.: 29), (SEQ. ID. NO.: 30), (SEQ. ID. NO.:31), (SEQ. ID. NO.:32), (SEQ. ID. NO.: 35), (SEQ. ID. NO.: 36), (SEQ. ID. NO.: 37), (SEQ. ID. NO.: 38), (SEQ. ID NO.: 39), (SEQ. ID. NO.: 40), (SEQ. ID. NO.: 41), (SEQ. ID. NO.: 42), (SEQ. ID. NO.: 43), (SEQ. ID. NO.: 44), (SEQ. ID. NO.: 45),(SEQ. ID. NO.: 46), (SEQ. ID. NO. :47), (SEQ. ID. NO. :48), (SEQ. ID. NO.: 49), (SEQ. ID. NO.:50), (SEQ. ID. NO.: 51), (SEQ. ID NO.: 52), (SEQ. ID. NO.: 53), (SEQ. ID. NO.: 54), (SEQ. ID. NO.: 55), (SEQ. ID. NO. : 56), (SEQ. ID. NO.: 57), (SEQ. ID. NO.: 58), (SEQ. ID. NO.: 59), (SEQ. ID. NO.: 60), (SEQ ID. NO.: 61), (SEQ. ID. NO.: 62), (SEQ. ID. NO.: 63), (SEQ. ID. NO.-:64), (SEQ. ID. NO.: 65), (SEQ. ID. NO.: 66), (SEQ. ID. NO. :67), (SEQ. ID. NO.: 68), (SEQ. ID. NO.: 69), (SEQ. ID. NO.: 70), (SEQ ID. NO.: 71), (SEQ. ID. NO.:72), (SEQ. ID. NO.: 73), (SEQ. ID. NO.: 74), (SEQ. ID. NO.: 75), (SEQ. ID NO.:76), (SEQ. ID. NO.:77), (SEQ. ID. NO.: 78), or (SEQ. ID. NO.: 79), or comprising a sequence overlapping the sequence of any of these with respect to its position on the Nickerson reference sequence.
31. The method of claim 25, wherein said oligonucleotide primer is labeled with a fluorescent dye.
32. The method of claim 31, wherein said dye is SYBR Green I, YO-PRO-1, thiazole orange, Hex, pico green, edans, fluorescein, FAM, or TET.
33. The method of claim 21, wherein said statin drug is lovastatin, pravastatin, simvastatin, atorvastatin, fluvastatin, or cerivastatin.
34. A method of detecting a genetic predisposition for non-responsiveness to lovastatin treatment in a human subject with coronary artery disease, comprising:
a) collecting a tissue sample from a human subject;
b) amplifying nucleic acids comprising the HindIII restriction site in intron 8 of the human lipoprotein lipase gene (LPL) from said tissue sample to obtain amplification products; and
c) analyzing the amplification products for the absence of a HindIII recognition site in intron 8 of the human lipoprotein lipase gene, homozygosity for an absence of said HindIII recognition site indicating a genetic predisposition in said human subject for non-responsiveness to lovastatin treatment for coronary artery disease.
35. The method of claim 34, wherein the tissue sample is a blood sample.
36. The method of claim 34, further comprising restricting the amplification products with a restriction enzyme before analyzing the amplification products.
37. The method of claim 34, wherein the restriction enzyme is HindllI.
38. The method of claim 34, wherein an oligonucleotide primer is used in amplifying said nucleic acids.
39. The method of claim 34, comprising the sequence 5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′(SEQ. ID. NO.1) is used in amplifying said nucleic acids.
40. The method of claim 34, wherein an oligonucleotide primer comprising the sequence 5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′(SEQ. ID. NO.2) is used in amplifying said nucleic acids.
41. The method of claim 34, wherein an oligonucleotide primer having the sequence 5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′ (SEQ. ID. NO. 1) or 5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′ (SEQ. ID. NO. 2) is used in amplifying said nucleic acids.
42. The method of claim 34, wherein a reverse oligonucleotide primer having the sequence 5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′ (SEQ. ID. NO. 1) and a forward oligonucleotide primer having the sequence 5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′ (SEQ. ID. NO. 2) are used in amplifying said nucleic acids.
43. The method of claim 34, wherein an oligonucleotide primer is used in amplifying said nucleic acids, said primer comprising a nucleotide sequence of (SEQ. ID. NO: :1), (SEQ. ID. NO. :2), (SEQ. ID. NO.: 3), (SEQ. ID. NO.: 4), (SEQ. ID. NO.: 5), (SEQ ID. NO.: 6), (SEQ. ID. NO.: 7), (SEQ. ID. NO.: 8), (SEQ. ID. NO.: 9), (SEQ. ID. NO.:I0), (SEQ. ID. NO.: 11), (SEQ. ID. NO.: 12), (SEQ. ID. NO.: 13), (SEQ. ID. NO.: 14), (SEQ. ID. NO.: 15), (SEQ. ID. NO.: 16), (SEQ. ID. NO.: 17), (SEQ. ID. NO.: 18), (SEQ. ID. NO.: 19), (SEQ. ID. NO.: 20), (SEQ. ID. NO.: 21), (SEQ. ID. NO.: 22), (SEQ. ID. NO.: 23), (SEQ. ID. NO.:24), (SEQ. ID. NO.: 25), (SEQ. ID. NO.: 26), (SEQ. ID. NO.: 27), (SEQ. ID. NO :28), (SEQ. ID. NO.: 29), (SEQ. ID. NO. : 30), (SEQ. ID. NO.: 31), (SEQ. ED. NO.: 32), (SEQ. ID. NO.: 35), (SEQ. ID. NO.: 36), (SEQ. ID. NO.:37), (SEQ. ID. NO.: 38), (SEQ. ID. NO.: 39), (SEQ. ID. NO.: 40), (SEQ. ID. NO.: 41), (SEQ. ID. NO.: 42), (SEQ. ID. NO. : 43), (SEQ. ID. NO. : 44), (SEQ. ID. NO.: 45),(SEQ. ID. NO.: 46), (SEQ. ID. NO. : 47), (SEQ. ID. NO.: 48) (SEQ. ID. NO.: 49), (SEQ. ID. NO.: 50), (SEQ. ID. NO.:.51), (SEQ. ID. NO.: 52), (SEQ. ID. NO.: 53), (SEQ. ID. NO.: 54), (SEQ. ID. NO.: 55), (SEQ. ID. NO.: 56), (SEQ. ID. NO.: 57), (SEQ. ID. NO.:58), (SEQ. ID. NO.:59), (SEQ. ID. NO.: 60), (SEQ. ID. NO.: 61), (SEQ. ID. NO.: 62), (SEQ. ID. NO.: 63), (SEQ. ID. NO.: 64), (SEQ. ID. NO. : 65), (SEQ. ID. NO.: 66), (SEQ. ID. NO.: 67), (SEQ. ID. NO.: 68), (SEQ. ID. NO.: 69), (SEQ ID. NO.: 70), (SEQ. ID. NO.: 7), (SEQ. ID. NO.: 72), (SEQ. ID. NO.: 73), (SEQ. ID. NO.: 74), (SEQ. ID. NO.: 75), (SEQ. ID. NO.: 76), (SEQ. ID. NO.: 77), (SEQ. ID. NO.: 78), or (SEQ. ID. NO.: 79), or comprising a sequence overlapping the sequence of any of these with respect to its position on the Nickerson reference sequence.
44. The method of claim 34, wherein said oligonucleotide primer is labeled with a fluorescent dye.
45. The method of claim 44, wherein said dye is SYBR Green I, YO-PRO-1, thiazole orange, Hex, pico green, edans, fluorescein, FAM, or TET.
46. The method of claim 34, wherein said statin drug is lovastatin, pravastatin, simvastatin, atorvastatin, fluvastatin, or cerivastatin .
47. The method of claim 34, wherein said human subject is a coronary artery bypass graft patient.
48. A method of detecting genetic predisposition in a CABG patient for non-responsiveness to statin drug treatment, comprising:
a) collecting a tissue sample from a CABG patient;
b) amplifying nucleic acids comprising the locus of the HindIII recognition site in intron 8 of the human lipoprotein lipase (LPL) gene from said blood sample to obtain amplification products; and
c) analyzing the amplification products for the absence of the HindIIl recognition site in intron 8 of the human lipoprotein lipase gene, homozygosity for an absence of said HindIll recognition site indicating a genetic predisposition in said CABG patient for non-responsiveness to statin drug treatment for coronary artery disease.
49. The method of claim 48, wherein said tissue sample is a blood sample.
50. The method of claim 48, further comprising restricting the amplification products with a restriction enzyme before analyzing the amplification products.
51. The method of claim 50, wherein the restriction enzyme is HindIll.
52. The method of claim 48, wherein an oligonucleotide primer is used in amplifying said nucleic acids.
53. The method of claim 48, comprising the sequence 5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′(SEQ. ID. NO.1) is used in amplifying said nucleic acids.
54. The method of claim 48, wherein an oligonucleotide primer comprising the sequence 5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′(SEQ. ID. NO.2) is used in amplifying said nucleic acids.
55. The method of claim 48, wherein an oligonucleotide primer having the sequence 5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′(SEQ. ID. NO. 1) or 5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′(SEQ ID. NO.2) is used in amplifying said nucleic acids.
56. The method of claim 48, wherein a reverse oligonucleotide primer having the sequence 5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′(SEQ. ID. NO.1) and a forward oligonucleotide primer having the sequence 5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′(SEQ. ID. NO.2) are used in amplifying said nucleic acids.
57. The method of claim 48, wherein an oligonucleotide primer is used in amplifying said nucleic acids, said primer comprising a sequence of (SEQ. ID. NO.: 1), (SEQ. ID. NO.: 2), (SEQ ID. NO.: 3), (SEQ ID. NO.: 4), (SEQ. ID. NO.: 5), (SEQ. ID. NO.: 6), (SEQ. ID. NO.: 7), (SEQ. ID. NO.: 8), (SEQ. ID. NO.: 9), (SEQ. ID. NO.: 10), (SEQ. ID. NO.: 11), (SEQ. ID. NO.: 12), (SEQ. ID NO.: 13), (SEQ. ID. NO.: 14), (SEQ. ID. NO.: 15), (SEQ. ID. NO.: 16), (SEQ. ID. NO. 17), (SEQ. ID. NO.:18), (SEQ. ID. NO.: 19), (SEQ. ID. NO. 20), (SEQ. ID. NO.: 21), (SEQ. ID. NO.: 22), (SEQ. ID. NO.: 23), (SEQ. ID. NO.: 24), (SEQ. ID. NO.: 25), (SEQ. ID. NO.: 26), (SEQ. ID. NO.: 27), (SEQ. ID. NO.: 28), (SEQ. ID. NO. 29), (SEQ. ID. NO. 30), (SEQ. ID. NO.: 31), (SEQ. ID. NO.: 32), (SEQ. ID. NO.35), (SEQ. ID. NO.: 36), (SEQ. ID. NO.: 37), (SEQ. ID. NO.: 38), (SEQ. ID. NO.: 39), (SEQ. ID. NO.: 40), (SEQ. ID. NO.: 41), (SEQ. ID. NO.:42), (SEQ. ID. NO.:43), (SEQ. ID. NO.: 44), (SEQ. ID. NO.: 45),(SEQ. ID. NO.: 46), (SEQ. ID. NO.: 47), (SEQ. ID. NO.: 48), (SEQ. ID. NO.: 49), (SEQ. ID. NO.: 50), (SEQ. ID. NO.: 51), (SEQ. ID. NO.: 52), (SEQ. ID. NO.:53), (SEQ. ID. NO.:54), (SEQ. ID. NO.: 55), (SEQ. ID. NO.: 56), (SEQ. ID. NO.: 57), (SEQ. ID. NO.: 58), (SEQ ID. NO.: 59), (SEQ. ID. NO.: 60), (SEQ. ID. NO.: 61), (SEQ. ID. NO.: 62), (SEQ. ID. NO.: 63), (SEQ. ID. NO.:64), (SEQ. ID. NO.:65), (SEQ. ID. NO.: 66), (SEQ. ID. NO.: 67), (SEQ. ID. NO.: 68), (SEQ. ID. NO.: 69), (SEQ. ID. NO.: 70), (SEQ. ID. NO.: 71), (SEQ. ID. NO.: 72), (SEQ. ID. NO.: 73), (SEQ. ID. NO.:74), (SEQ. ID. NO.: 75), (SEQ. ID. NO.:76), (SEQ. ID. NO. :77), (SEQ. ID. NO.: 78), or (SEQ. ID. NO. :79), or comprising a sequence overlapping the sequence of any of these with respect to its position on the Nickerson reference sequence.
58. The method of claim 52, wherein said oligonucleotide primer is labeled with a fluorescent dye.
59. The method of claim 58, wherein said dye is SYBR Green I, YO-PRO-1, thiazole orange, Hex, pico green, edans, fluorescein, FAM, or TET.
60. The method of claim 48, wherein said statin drug is lovastatin, pravastatin, simvastatin, atorvastatin, fluvastatin, or cerivastatin.
61. A method of detecting genetic predisposition in a CABG patient for non-responsiveness to statin drug treatment, comprising:
a) collecting a tissue sample from a CABG patient;
b) amplifying nucleic acids comprising the normal locus of the Hindll recognition site in intron 8 of the human lipoprotein lipase (LPL) gene from said blood sample to obtain amplification products, by using a reverse oligonucleotide primer having the sequence 5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′ (SEQ. ID. NO. 1) and a forward oligonucleotide primer having the sequence 5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′ (SEQ. ID, NO. 2); and
c) analyzing the amplification products for the absence of the HindIII recognition site in intron 8 of the human lipoprotein lipase gene, homozygosity for an absence of said HindIII recognition site indicating a genetic predisposition in said CABG patient for non-responsiveness to statin drug treatment for coronary artery disease.
62. The method of claim 61, wherein said tissue sample is a blood sample.
63. The method of claim 61, wherein said oligonucleotide primer is labeled with a fluorescent dye.
64. The method of claim 63, wherein said dye is SYBR Green I, YO-PRO- 1, thiazole orange, Hex, pico green, edans, fluorescein, FAM, or TET.
65. The method of claim 61, wherein said statin drug is lovastatin, pravastatin, simvastatin, atorvastatin, fluvastatin, or cerivastatin.
66. A method of detecting in a human subject a genetic predisposition for non-responsiveness to statin drug treatment for coronary artery disease, comprising:
a) collecting a tissue sample from a human subject;
b) amplifying nucleic acids comprising the normal locus of the HindIII recognition site in intron 8 of the human lipoprotein lipase (LPL) gene from said blood sample to obtain amplification products, by using a reverse oligonucleotide primer having the sequence 5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′ (SEQ. ID. NO.1) and a forward oligonucleotide primer having the sequence 5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′ (SEQ. ID. NO.2);
c) restricting said amplification products with HindIII; and
d) analyzing the restriction fragments for the absence of the HindIII recognition site in intron 8 of the human lipoprotein lipase gene, wherein homozygosity for an absence of said HindIll recognition site indicates a genetic predisposition for non-responsiveness to statin drug treatment for coronary artery disease.
67. The method of claim 66, wherein the tissue sample is a blood sample.
68. The method of claim 66, wherein said oligonucleotide primer is labeled with a fluorescent dye.
69. The method of claim 66, wherein said dye is SYBR Green I, YO-PRO-1, thiazole orange, Hex, pico green, edans, fluorescein, FAM, or TET.
70. The method of claim 66, wherein said statin drug is lovastatin, pravastatin, simvastatin, atorvastatin, fluvastatin, or cerivastatin.
71. A method of detecting a genetic predisposition in a human subject for non-responsiveness to statin drug treatment, comprising:
a) collecting a tissue sample from a human subject;
b) amplifying nucleic acids comprising the normal locus of the (TTTA)n tetranucleotide repeat sequence in intron 6 of the human lipoprotein lipase gene (LPL) from said tissue sample to obtain amplification products; and
c) analyzing the amplification products for (TTTA)n tetranucleotide repeat alleles present in said nucleic acids, homozygosity for a (TTTA)n 4 allele indicating a genetic predisposition for non-responsiveness to treatment with a statin drug for coronary artery disease.
72. The method of claim 71, wherein the tissue sample is a blood sample.
73. The method of claim 71, wherein an oligonucleotide primer is used in amplifying said nucleic acids.
74. The method of claim 71, comprising the sequence 5′-CCT GGG TAA CTG AGC GAG ACT GTG TC-3′(SEQ ID. NO.: 33) is used in amplifying said nucleic acids.
75. The method of claim 71, wherein an oligonucleotide primer comprising the sequence 5′-ATC TGA CCA AGG ATA GTG GGA TAT A-3′(SEQ ID. NO.: 34) is used in amplifying said nucleic acids.
76. The method of claim 71, wherein an oligonucleotide primer having the sequence 5′-CCT GGG TAA CTG AGC GAG ACT GTG TC-3′ (SEQ. ID. NO. :33) or 5′-ATC TGA CCA AGG ATA GTG GGA TAT A-3′ (SEQ. ID. NO.: 34) is used in amplifying said nucleic acids.
77. The method of claim 71, wherein a reverse oligonucleotide primer having the sequence 5′-CCT GGG TAA CTG AGC GAG ACT GTG TC-3′ (SEQ. ID. NO.: 33) and a forward oligonucleotide primer having the sequence 5′-ATC TGA CCA AGG ATA GTG GGA TAT A-3′ (SEQ. ID. NO.: 34) are used in amplifying said nucleic acids.
78. The method of claim 71, wherein amplifying said nucleic acids is done using an oligonucleotide primer comprising a nucleotide sequence of (SEQ. ID. NO.: 33), (SEQ. ID. NO.: 34), (SEQ. ID. NO.: 82), (SEQ. ID. NO :83), (SEQ. ID. NO.: 84), (SEQ. ID. NO.: 85), (SEQ. ID. NO.: 86), (SEQ. ID. NO.: 87), (SEQ. ID. NO.: 88), (SEQ. ID. NO.: 89), (SEQ. ID. NO.: 90), (SEQ. ID. NO.: 91), or (SEQ. ID. NO. :92), or comprising a sequence overlapping the sequence of any of these with respect to its position on the Nickerson reference sequence.
79. The method of claim 73, wherein said oligonucleotide primer is labeled with a fluorescent dye.
80. The method of claim 79, wherein said dye is SYBR Green I, YO-PRO-1, thiazole orange, Hex, pico green, edans, fluorescein, FAM, or TET.
81. The method of claim 71, wherein said statin drug is lovastatin, pravastatin, simvastatin, atorvastatin, fluvastatin, or cerivastatin.
82. (Once Amended) An oligonucleotide primer for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human, said primer consisting essentially of the nucleotide sequence 5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′ (SEQ. ID. NO.: 1).
83. (Once Amended) An oligonucleotide primer for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human, said primer consisting essentially of the nucleotide sequence 5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′ (SEQ. ID. NO.: 2).
84. (Once Amended) An oligonucleotide primer for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human, said primer consisting of sequence 5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′ (SEQ. ID. NO. 1).
85. (Once Amended) An oligonucleotide primer for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human, said primer consisting of sequence 5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′(SEQ. ID. NO. :2).
86. (Once Amended) An oligonucleotide primer for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human, said primer consisting essentially of a nucleotide sequence of (SEQ. ID. NO.: 1), (SEQ. ID. NO. :2), (SEQ. ID. NO.: 3), (SEQ. ID. NO. :4), (SEQ. ID. NO. :5), (SEQ. ID. NO. :6), (SEQ. ID. NO. :7), (SEQ. ID. NO. :8), (SEQ. ID. NO.: 9), (SEQ. ID. NO.: 10), (SEQ. ID. NO.: 11), (SEQ. ID. NO.: 12), (SEQ. ID. NO.: 13), (SEQ. ID. NO.: 14), (SEQ. ID. NO.: 15), (SEQ. ID. NO.: 16), (SEQ. ID. NO.: 17), (SEQ. ID. NO.: 18), (SEQ. ID. NO.: 19), (SEQ. ID. NO.: 20), (SEQ. ID. NO.: 21), (SEQ. ID. NO. :22), (SEQ. ID. NO. :23), (SEQ. ID. NO.: 24), (SEQ. ID. NO.: 25), (SEQ. ID. NO.: 26), (SEQ. ID. NO. :27), (SEQ. ID. NO. :28), (SBQ. ID. NO.: 29), (SEQ. ID. NO.: 30), (SEQ. ID. NO.: 31), (SEQ. ID. NO.: 32), (SEQ. ID. NO.: 35), (SEQ. ID. NO.: 36), (SEQ. ID. NO.: 37), (SEQ. ID. NO.: 38), (SEQ. ID. NO.: 39), (SEQ. ID. NO.: 40), (SEQ. ID. NO.: 41), (SEQ. ID. NO.: 42), (SEQ. ID. NO.: 43), (SEQ. ID. NO.: 44), (SEQ. ID. NO.: 45), (SEQ. ID. NO.: 46), (SEQ. ID. NO.: 47), (SEQ. ID. NO.: 48), (SEQ. ID. NO.: 49), (SEQ. ID. NO.: 50), (SEQ. ID. NO.: 51), (SEQ. ID. NO.: 52), (SEQ. ID. NO.: 53), (SEQ. ID. NO.: 54), (SEQ. ID. NO.: 55), (SEQ. ID. NO.: 56), (SEQ. ID. NO.: 57), (SEQ. ID. NO.: 58), (SEQ. ID. NO.: 59), (SEQ. ID. NO.: 60), (SEQ. ID. NO.: 61), (SEQ. ID. NO.: 62), (SEQ. ID. NO.: 63), (SEQ. ID. NO.: 64), (SEQ. ID. NO.: 65), (SEQ. ID. NO.: 66), (SEQ. ID. NO.: 67), (SEQ. ID. NO.: 68), (SEQ. ID. NO.: 69), (SEQ. ID. NO.: 70), (SEQ. ID. NO.: 71), (SEQ. ID. NO.: 72), (SEQ. ID. NO.: 73), (SEQ. ID. NO.: 74), (SEQ. ID. NO.: 75), (SEQ. ID. NO.: 76), (SEQ. ID. NO.: 77), (SEQ. ID. NO.: 78), or (SEQ. ID. NO.: 79).
87. An oligonucleotide primer for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human, comprising the sequence 5′-CCT GGG TAA CTG AGC GAG ACT GTG TC-3′ (SEQ. ID. NO. :33) or 5′-ATC TGA CCA AGG ATA GTG GGA TAT A-3′ (SEQ. ID. NO.: 34).
88. An oligonucleotide primer for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human, having the sequence 5′-CCT GGG TAA CTG AGC GAG ACT GTG TC-3′ (SEQ. ID. NO. :33) or 5′-ATC TGA CCA AGG ATA GTG GGA TAT A-3′ (SEQ. ID. NO.: 34).
89. (Once Amended) An oligonucleotide primer for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human, said primer consisting essentially of a nucleotide sequence of (SEQ. ID. NO.: 82), (SEQ. ID. NO.: 83), (SEQ. ID. NO.: 84), (SEQ. ID. NO.: 85), (SEQ. ID. NO.: 86), (SEQ. ID. NO.: 87), (SEQ. ID. NO.: 88), (SEQ. ID. NO.: 89), (SEQ. ID. NO.: 90), (SEQ. ID. NO.: 91), or (SEQ. ID. NO.: 92).
90. An oligonucleotide primer for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human, said primer comprising a nucleotide sequence of (SEQ. ID. NO.: 95), (SEQ. ID. NO.: 96), (SEQ. ID. NO.: 97), (SEQ. ID. NO.: 98), (SEQ. ID. NO.: 99), (SEQ. ID. NO.: 100), (SEQ. ID. NO. :101), (SEQ. ID. NO.: 102), (SEQ. ID. NO.: 103), (SEQ. ID. NO.: 104), (SEQ. ID. NO.: 105), or (SEQ. ID. NO.: 106), or comprising a sequence overlapping the sequence of any of these with respect to its position on the Oka reference sequence.
91. (Once Amended) An oligonucleotide primer for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human, said primer consisting essentially of a nucleotide sequence of (SEQ. ID. NO.: 95), (SEQ. ID. NO.: 96), (SEQ. ID. NO.: 97), (SEQ. ID. NO.: 98), (SEQ. ID. NO.: 99), (SEQ. ID. NO.: 100), (SEQ. ID. NO.: 101), (SEQ. ID. NO.: 102), (SEQ. ID. NO.: 103), (SEQ. ID. NO.: 104), (SEQ. ID. NO.: 105), or (SEQ. ID. NO.: 106).
92. (Once Amended) An oligonucleotide primer set for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human, said primer set having a reverse primer consisting essentially of the nucleotide sequence 5′-GCA TCT GCC TTC AGC TAG ACA TTG-3′ (SEQ. ID. NO.: 1); and a forward primer consisting essentially of the nucleotide sequence 5′-TCT TCC AGA AGG GTG AGA TTC CAA-3′ (SEQ. ID. NO.: 2).
93. (Once Amended) An oligonucleotide primer set for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human, having a forward primer consisting essentially of a nucleotide sequence of (SEQ. ID. NO.: 2), (SEQ. ID. NO.: 3), (SEQ. ID. NO.: 4), (SEQ. ID. NO.: 5), (SEQ. ID. NO.: 6), (SEQ. ID. NO.: 7), (SEQ. ID. NO.: 8), (SEQ. ID. NO.: 9), (SEQ. ID. NO.: 11), (SEQ. ID. NO.: 12), (SEQ. ID. NO.: 13), (SEQ. ID. NO.: 14), (SEQ. ID. NO.: 15), (SEQ. ID. NO.: 16), (SEQ. ID. NO.: 17), (SEQ. ID. NO.: 18), (SEQ. ID. NO.: 19), (SEQ. ID. NO.: 20), (SEQ. ID. NO.: 21), (SEQ. ID. NO.: 22), (SEQ. ID. NO.: 23), (SEQ. ID. NO.: 36), (SEQ. ID. NO.: 37), (SEQ. ID. NO.: 38), (SEQ. ID. NO.: 39), (SEQ. ID. NO.: 43), (SEQ. ID. NO.: 45), (SEQ. ID. NO.: 47), (SEQ. ID. NO.: 48), (SEQ. ID. NO.: 49), (SEQ. ID. NO.: 50), (SEQ. ID. NO.: 53), (SEQ. ID. NO.: 54), (SEQ. ID. NO.: 58), (SEQ. ID. NO.: 59), (SEQ. ID. NO.: 60), (SEQ. ID. NO.: 61), (SEQ. ID. NO.: 65), (SEQ. ID. NO.: 66), (SEQ. ID. NO. :67), (SEQ. ID. NO. :68), (SEQ. ID. NO.: 69), (SEQ. ID. NO.: 70), (SEQ. ID. NO.: 71), (SEQ. ID. NO.: 72), (SEQ. ID. NO.: 75), (SEQ. ID. NO.: 76), (SEQ. ID. NO.: 77), or (SEQ. ID. NO.: 79);
and having a reverse primer consisting essentially of a nucleotide sequence of (SEQ. ID. NO.: 1),(SEQ. ID. NO.: 10), (SEQ. ID. NO.: 24), (SEQ. ID. NO.: 25), (SEQ. ID. NO.: 26), (SEQ. ID. NO.: 27), (SEQ. ID. NO.: 28), (SEQ. ID. NO.: 29), (SEQ. ID. NO.: 30), (SEQ. ID. NO.: 31), (SEQ. ID. NO.: 32), (SEQ. ID. NO.: 35), (SEQ. ID. NO.: 40), (SEQ. ID. NO.: 41), (SEQ. ID. NO.: 42), (SEQ. ID. NO.: 44), (SEQ. ID. NO.: 46), (SEQ. ID. NO.: 51), (SEQ. ID. NO.: 52), (SEQ. ID. NO.: 55), (SEQ. ID. NO.: 56), (SEQ. ID. NO.: 57), (SEQ. ID. NO.: 62), (SEQ. ID. NO.: 63), (SEQ. ID. NO.: 64), (SEQ. ID. NO.: 73), (SEQ. ID. NO.: 74), or (SEQ. ID. NO.: 78).
94. An oligonucleotide primer set for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human, having a forward primer comprising a nucleotide sequence of (SEQ. ID. NO. :34),(SEQ. ID. NO. :82), (SEQ. ID. NO. :86), (SEQ. ID. NO. :88), (SEQ. ID. NO. :90), or (SEQ. ID. NO. :92), or comprising a sequence overlapping the sequence of any of these with respect to its position on the Nickerson reference sequence;
and having a reverse primer comprising a nucleotide sequence of (SEQ. ID. NO.: 33), (SEQ. ID. NO.: 83), (SEQ. ID. NO.: 84), (SEQ. ID. NO.: 85), (SEQ. ID. NO.: 87), (SEQ. ID. NO.: 89), or (SEQ.
ID. NO.: 91), or comprising a sequence overlapping the sequence of any of these with respect to its position on the Nickerson reference sequence.
95. (Once Amended) An oligonucleotide primer set for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human, having a forward primer consisting essentially of a nucleotide sequence of (SEQ. ID. NO.: 82), (SEQ. ID. NO.: 86), (SEQ. ID. NO.: 88), (SEQ. ID. NO.: 90), or (SEQ. ID. NO.: 92);
and having a reverse primer consisting essentially of a nucleotide sequence of (SEQ. ID. NO.: 83), (SEQ. ID. NO.: 84), (SEQ. ID. NO.: 85), (SEQ. ID. NO.: 87), (SEQ. ID. NO.: 89), or (SEQ. ID. NO.: 91).
96. (Once Amended) An oligonucleotide primer set for detecting a genetic predisposition for non-responsiveness to statin drug treatment in a human, having a forward primer consisting essentially of a nucleotide sequence of (SEQ. ID. NO.: 95),(SEQ. ID. NO.: 98), (SEQ. ID. NO.: 99), (SEQ. ID. NO.: 101), (SEQ. ID. NO.: 102), (SEQ. ID. NO.: 104), or (SEQ. ID. NO.: 106);
and having a reverse primer consisting essentially of a nucleotide sequence of (SEQ. ID. NO.: 96), (SEQ. ID. NO.: 97), (SEQ. ID. NO.: 100), (SEQ. ID. NO.: 103), or (SEQ. ID. NO.: 105).
97. (Once Amended) A genetic testing kit comprising a primer comprising a nucleotide sequence of (SEQ. ID. NO.: 1), (SEQ. ID. NO.: 2), (SEQ. ID. NO. :3), (SEQ. ID. NO. :4), (SEQ. ID. NO.: 5), (SEQ. ID. NO.: 6), (SEQ. ID. NO.: 7), (SEQ. ID. NO.: 8), (SEQ. ID. NO.: 9), (SEQ. ID. NO.: 10), (SEQ. ID. NO.: 11), (SEQ. ID. NO.: 12), (SEQ. ID. NO.: 13), (SEQ. ID. NO.: 14), (SEQ. ID. NO.: 15), (SEQ. ID. NO.: 16), (SEQ. ID. NO.: 17), (SEQ. ID. NO.: 18), (SEQ. ID. NO.: 19), (SEQ. ID. NO.: 20), (SEQ. ID. NO.: 21), (SEQ. ID. NO.: 22), (SEQ. ID. NO.: 23), (SEQ. ID. NO.: 24), (SEQ. ID. NO.: 25), (SEQ. ID. NO.: 26), (SEQ. ID. NO.: 27), (SEQ. ID. NO.: 28), (SEQ. ID. NO.: 29), (SEQ. ID. NO.: 30), (SEQ. ID. NO.: 31), (SEQ. ID. NO.: 32),(SEQ. ID. NO.: 33), (SEQ. ID. NO.: 34),(SEQ. ID. NO.: 35), (SEQ. ID. NO.: 36), (SEQ. ID. NO.: 37), (SEQ. ID. NO.: 38), (SEQ. ID. NO.: 39), (SEQ. ID. NO.: 40), (SEQ. ID. NO.: 41), (SEQ. ID. NO.: 42), (SEQ. ID. NO.: 43), (SEQ. ID. NO.: 44), (SEQ. ID. NO.: 45), (SEQ. ID. NO.: 46), (SEQ. ID. NO.: 47), (SEQ. ID. NO.: 48), (SEQ. ID. NO.: 49), (SEQ. ID. NO.: 50), (SEQ. ID. NO.: 51), (SEQ. ID. NO.: 52), (SEQ. ID. NO.: 53), (SEQ. ID. NO.: 54), (SEQ. ID. NO.: 55), (SEQ. ID. NO.: 56), (SEQ. ID. NO.: 57), (SEQ. ID. NO.: 58), (SEQ. ID. NO.: 59), (SEQ. ID. NO.: 60), (SEQ. ID. NO.: 61), (SEQ. ID. NO.: 62), (SEQ. ID. NO.: 63), (SEQ. ID. NO.: 64), (SEQ. ID. NO.: 65), (SEQ. ID. NO.: 66), (SEQ. ID. NO.: 67), (SEQ. ID. NO.: 68), (SEQ. ID. NO.: 69), (SEQ. ID. NO.: 70), (SEQ. ID. NO.: 71), (SEQ. ID. NO.: 72), (SEQ. ID. NO.: 73), (SEQ. ID. NO.: 74), (SEQ. ID. NO.: 75), (SEQ. ID. NO.: 76), (SEQ. ID. NO.: 77), (SEQ. ID. NO.: 78), or (SEQ. ID. NO.: 79), or comprising a sequence overlapping the sequence of any of these with respect to its position on the Nickerson reference sequence; and
instructions for using the primer to detect a genetic predisposition in a human subject for non-responsiveness to treatment with a statin drug selected from the group consisting of lovastatin, pravastatin, and simvastatin.
98. (Once Amended) A genetic testing kit comprising:
a primer comprising a nucleotide sequence of (SEQ. ID. NO.: 82), (SEQ. ID. NO.: 83), (SEQ. ID. NO.: 84), (SEQ. ID. NO.: 85), (SEQ. ID. NO.: 86), (SEQ. ID. NO.: 87), (SEQ. ID. NO.: 88), (SEQ. SD. NO.: 89), (SEQ. ID. NO.: 90), (SEQ. ID. NO.: 91), or (SEQ. ID. NO.: 92), or comprising a sequence overlapping the sequence of any of these with respect to its position on the Nickerson reference sequence; and
instructions for using the primer to detect a genetic predisposition in a human subject for non-responsiveness to treatment with a statin drug selected from the group consisting of lovastatin, pravastatin, and simvastatin.
99. (Once Amended) A genetic testing kit comprising:
a primer comprising a nucleotide sequence of (SEQ. ID. NO. :95), (SEQ. ID. NO. :96), (SEQ. ID. NO.: 97), (SEQ. ID. NO.: 98), (SEQ. ID. NO.: 99), (SEQ. ID. NO.: 100), (SEQ. ID. NO.: 101), (SEQ. ID. NO.: 102), (SEQ. ID. NO.: 103), (SEQ. ID. NO.: 104), (SEQ. ID. NO.: 105), or (SEQ. ID. NO.: 106), or comprising a sequence overlapping the sequence of any of these with respect to its position on the Oka reference sequence; and
instructions for using the primer to detect a genetic predisposition in a human subject for non-responsiveness to treatment with a statin drug selected from the group consisting of lovastatin, pravastatin, and simvastatin.
100. (Once Amended) A genetic testing kit comprising:
a forward primer comprising a nucleotide sequence of (SEQ. ID. NO. :2), (SEQ. ID. NO.: 3), (SEQ. ID. NO.: 4), (SEQ. ID. NO.: 5), (SEQ. ID. NO.: 6), (SEQ. ID. NO.: 7), (SEQ. ID. NO.: 8), (SEQ. ID. NO.: 9), (SEQ. ID. NO.:11), (SEQ. ID. NO.: 12), (SEQ. ID. NO.: 13), (SEQ. ID. NO.: 14), (SEQ. ID. NO.: 15), (SEQ. ID. NO.: 16), (SEQ. ID. NO.: 17), (SEQ. ID. NO.: 18), (SEQ. ID. NO.: 19), (SEQ. ID. NO.: 20), (SEQ. ID. NO.: 21), (SEQ. ID. NO.: 22), (SEQ. ID. NO.: 23), (SEQ. ID. NO.: 36), (SEQ. ID. NO.: 37), (SEQ. ID. NO.: 38), (SEQ. ID. NO.: 39), (SEQ. ID. NO.: 43), (SEQ. ID. NO.: 45), (SEQ. ID. NO.: 47), (SEQ. ID. NO.: 48), (SEQ. ID. NO.: 49), (SEQ. ID. NO.: 50), (SEQ. ID. NO.: 53), (SEQ. ID. NO.: 54), (SEQ. ID. NO.: 58), (SEQ. ID. NO.: 59), (SEQ. ID. NO.: 60), (SEQ. ID. NO.: 61), (SEQ. ID. NO.: 65), (SEQ. ID. NO.: 66), (SEQ. ID. NO.: 67), (SEQ. ID. NO.: 68), (SEQ. ID. NO.: 69), (SEQ. ID. NO.: 70), (SEQ. ID. NO.: 71), (SEQ. ID. NO.: 72), (SEQ. ID. NO.: 75), (SEQ. ID. NO.: 76), (SEQ. ID. NO.: 77), or (SEQ. ID. NO.: 79), or comprising a sequence overlapping the sequence of any one of these with respect to its position on the Nickerson reference sequence;
a reverse primer comprising a nucleotide sequence of (SEQ. ID. NO.: 1),(SEQ. ID. NO.: 10), (SEQ. ID. NO.: 24), (SEQ. ID. NO.: 25), (SEQ. ID. NO.: 26), (SEQ. ID. NO.: 27), (SEQ. ID. NO.: 28), (SEQ. ID. NO.: 29), (SEQ. ID. NO.: 30), (SEQ. ID. NO.: 31), (SEQ. ID. NO.: 32), (SEQ. ID. NO.: 35), (SEQ. ID. NO.: 40), (SEQ. ID. NO.: 41), (SEQ. ID. NO.: 42), (SEQ. ID. NO.: 44), (SEQ. ID. NO.: 46), (SEQ. ID. NO.: 51), (SEQ. ID. NO.: 52), (SEQ. ID. NO.: 55), (SEQ. ID. NO.: 56), (SEQ. ID. NO.: 57), (SEQ. ID. NO.: 62), (SEQ. ID. NO.: 63), (SEQ. ID. NO.: 64), (SEQ. ID. NO.: 73), (SEQ. ID. NO. :74), or (SEQ. ID. NO. :78), or comprising a sequence overlapping the sequence of any of these with respect to its position on the Nickerson reference sequence; and
instructions for using the forward and reverse primers to detect a genetic predisposition in a human subject for non-responsiveness to treatment with a statin drug selected from the group consisting of lovastatin, pravastatin, and simvastatin.
101. A genetic testing kit comprising:
a forward primer comprising a nucleotide sequence of (SEQ. ID. NO.: 82), (SEQ. ID. NO.: 86), (SEQ. ID. NO.: 88), (SEQ. ID. NO.: 90), or (SEQ. ID. NO.: 92), or comprising a sequence overlapping the sequence of any of these with respect to its position on the Nickerson reference sequence;
a reverse primer comprising a nucleotide sequence of (SEQ. ID. NO.: 83), (SEQ. ID. NO.: 84), (SEQ. ID. NO.: 85), (SEQ. ID. NO.: 87), (SEQ. ID. NO.: 89), or (SEQ. ID. NO.: 91), or comprising a sequence overlapping the sequence of any of these with respect to its position on the Nickerson reference sequence; and
instructions for using the forward and reverse primers to detect a genetic predisposition in a human subject for non-responsiveness to treatment with a statin drug selected from the group consisting of lovastatin, pravastatin, and simvastatin.
102. A genetic testing kit comprising:
a forward primer comprising a nucleotide sequence of (SEQ. ID. NO.: 95),(SEQ. ID. NO.: 98), (SEQ. ID. NO.: 99), (SEQ. ID. NO.: 101), (SEQ. ID. NO.: 102), (SEQ. ID. NO.: 104), or (SEQ. ID. NO.: 106), or comprising a sequence overlapping the sequence of any of these with respect to its position on the Oka reference sequence;
a reverse primer comprising a nucleotide sequence of (SEQ. ID. NO.: 96), (SEQ. ID. NO. :97), (SEQ. ID. NO.: 100), (SEQ. ID. NO.: 103), or (SEQ. ID. NO.: 105), or comprising a sequence overlapping the sequence of any of these with respect to its position on the Oka reference sequence; and
instructions for using the forward and reverse primers to detect a genetic predisposition in a human subject for non-responsiveness to treatment with a statin drug selected from the group consisting of lovastatin, pravastatin, and simvastatin.
US09/898,779 1999-07-02 2001-07-03 Genetic test to determine non-responsiveness to statin drug treatment Abandoned US20020106657A1 (en)

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US20080032291A1 (en) * 2002-06-14 2008-02-07 Taylor Kent D Method of haplotype-based genetic analysis for determining risk for developing insulin resistance, coronary artery disease and other phenotypes
US20100130600A1 (en) * 2007-03-30 2010-05-27 Cedars-Sinai Medical Center Lipoprotein lipase and its effect on statin treatments

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US20020164598A1 (en) * 2001-05-03 2002-11-07 Ihc Health Services, Inc. Method for evaluating and applying an individual's genetic characteristics to determine response to cardiovascular medication therapy
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US6723527B2 (en) * 2001-10-26 2004-04-20 Board Of Regents, The University Of Texas System Methods for determining toxicity reversing agents
WO2003106652A2 (en) * 2002-06-14 2003-12-24 Cedars-Sinai Medical Center Method of haplotype-based genetic analysis for determining risk for developing insulin resistance, coronary artery disease and other phenotypes
US20040110241A1 (en) * 2002-12-06 2004-06-10 Segal Mark S. Materials and methods for monitoring vascular endothelial function
EP1592706A2 (en) * 2003-02-03 2005-11-09 Bayer HealthCare AG Genetic polymorphisms as predictive diagnostics for adverse drug reactions (adr) and drug efficacy
US8688385B2 (en) * 2003-02-20 2014-04-01 Mayo Foundation For Medical Education And Research Methods for selecting initial doses of psychotropic medications based on a CYP2D6 genotype
WO2004074456A2 (en) * 2003-02-20 2004-09-02 Mayo Foundation For Medical Education And Research Methods for selecting medications
WO2006022882A2 (en) * 2004-04-16 2006-03-02 Idexx Laboratories, Inc. Canine pancreatic lipse
WO2005110039A2 (en) * 2004-05-07 2005-11-24 Applera Corporation Genetic polymorphisms associated with vascular diseases, methods of detection and uses thereof
DK2508621T3 (en) * 2005-11-29 2015-01-12 Childrens Hosp Medical Center Optimization and individualization of drug selection and dosage
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US4988617A (en) 1988-03-25 1991-01-29 California Institute Of Technology Method of detecting a nucleotide change in nucleic acids
CA2013317A1 (en) 1989-04-17 1990-10-17 Fred T. Oakes Diagnostic kit, primer composition and their use for replication or detection of nucleic acids

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US20080032291A1 (en) * 2002-06-14 2008-02-07 Taylor Kent D Method of haplotype-based genetic analysis for determining risk for developing insulin resistance, coronary artery disease and other phenotypes
US8178294B2 (en) 2002-06-14 2012-05-15 Cedars-Sinai Medical Center Method of haplotype-based genetic analysis for determining risk for developing insulin resistance, coronary artery disease and other phenotypes
US20070054275A1 (en) * 2004-01-15 2007-03-08 Dogulu Cigdem F Method evolved for recognition of thrombophilia (mert)
US20090054256A1 (en) * 2004-01-15 2009-02-26 The Government Of The United States Of America As Represented By The Method evolved for recognition of thrombophilia (mert)
US20100130600A1 (en) * 2007-03-30 2010-05-27 Cedars-Sinai Medical Center Lipoprotein lipase and its effect on statin treatments

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