WO2007070482A2 - Procede de detection d'anormalites chromosomiques a l'aide de microreseaux pour le diagnostic genetique preimplantatoire - Google Patents

Procede de detection d'anormalites chromosomiques a l'aide de microreseaux pour le diagnostic genetique preimplantatoire Download PDF

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WO2007070482A2
WO2007070482A2 PCT/US2006/047254 US2006047254W WO2007070482A2 WO 2007070482 A2 WO2007070482 A2 WO 2007070482A2 US 2006047254 W US2006047254 W US 2006047254W WO 2007070482 A2 WO2007070482 A2 WO 2007070482A2
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microarray
chromosomal
probes
dna
sample
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WO2007070482A3 (fr
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Xueliang Xia
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Xueliang Xia
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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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase

Definitions

  • the present invention relates generally to methods of detecting and analyzing chromosomal abnormalities in a single cell or a few cells using microarray technology for preimplantation genetic diagnosis (PGD) and cancer diagnostics, and kits are provided.
  • PPD genetic diagnosis
  • IVF in vitro fertilization
  • Chromosomal abnormalities include chromosomal aneuploidy, amplification, translocation, insertion/deletion, inversion, short tandem repeat polymorphisms, microsatellite polymorphisms, single nucleotide polymorphisms (SNPs), and other structural abnormalities. Chromosomal abnormalities can cause many phenotypic diseases and some are even lethal. If chromosomal abnormalities occur in embryos, many types of prenatal conditions and congenital diseases are likely to develop. Screening these abnormalities for preimplantation genetic diagnosis (PGD) is very important to ensure a structurally normal embryo selection and viable implantation.
  • PDD genetic diagnosis
  • FISH fluorescence in situ hybridization
  • metalphase CGH metaphase-based comparative genomic hybridization
  • Chromosomal translocations are the commonest form of structural abnormality in chromosomes and occur about once in every 500 live births. For any chromosomal rearrangement, genetically unbalanced gametes are likely to be produced during oocyte meiosis. For reciprocal translocations, the prevalence of these unbalanced gametes is estimated to be between 50% and 70%. The genetically unbalanced gametes produced by some translocations are incompatible with a viable pregnancy.
  • PGD technology has played an important role in improving clinical outcome.
  • PDG largely depends on chromosomal smears and other cytogenetic techniques. Development of new technology to improve embryo selection and transfer is highly desirable.
  • chromosomal aberrations similar to those described above, some of which are related to prognosis.
  • Two important translocations are t(4;l 1) for MLL and AF4 genes and t(l:19) for E2A and PBX genes.
  • MLL mixed-lineage leukemia
  • the multi-lineage gene is a chromosomal translocation located on segment 1 Iq23.
  • the AF-4 gene (located at 4q21) has been implicated in myeloid/lymphoid leukemia translation.
  • Pbxl which is a proto-oncogene which is translocated in pre-B acute lymphoblastoid leukemias.
  • the chromosomal translocation involves chromosomes 1 and 19 and results in a fusion protein in which the N-terminal portion of E2A is fused to Pbxl, converting a nontranscriptional activator into a transcriptional activator (E2A-Pbxl).
  • FISH in situ chromosomes
  • Microarrays also referred to as arrays or biochips, have been widely used for gene expression and other genomic research.
  • the features of high density, flexible design, uniform hybridization efficiency, and massively parallel detection are but a few of their superior characteristics.
  • Microarray-based comparative genomic hybridization has the potential to be more flexible, cost-effective, and efficient than traditional CGH methods that depend on metaphase chromosomes, as in most PDG protocols. From published genomic information, probes can be flexibly designed at any position along chromosomes for specific disorders and applications. Oligonucleotide DNA or RNA probes are readily manufactured at high quality.
  • the inventions described herein provide objective methods for determining chromosomal abnormalities, which up to now have mainly been subjective observations by trained cytogenetic technicians reporting on chromosomal spreads or limited FISH display of one or more chromosomes.
  • These embodiments feature methods and a kit to analyze chromosomal abnormalities for preimplantation genetic diagnosis (PGD) using microarrays.
  • PGD genetic diagnosis
  • the method is able to analyze all kinds of chromosomal abnormalities including aneuploidy, gene amplification, translocation, insertion, deletion, reversion, short tandem repeats, and single nucleotide polymorphisms.
  • a comprehensive microarray for detecting major and minor chromosomal abnormalities for preimplantation genetic diagnosis (PGD) research and clinical application comprising pre-in vitro fertilization (FVF).
  • the microarray has a) a surface for adhering oligonucleotide probes; b) the oligonucleotide probes on the surface said probes designed to hybridize to selected known abnormal amplified and labeled XIA - OOlPCT
  • oligonucleotides probes being capable of detecting at least three of aneuploidy, translocation, gene/locus amplification, insertions, deletions, reversions, short tandem repeat (STR) polymorphisms, mycrosatellite polymorphisms, single nucleotide polymorphisms (SNPs), single genetic mutations of selected inherited diseases, or a combination thereof.
  • STR short tandem repeat
  • a method of analyzing with a microarray chromosomal abnormalities for preimplantation genetic diagnosis (PGD) research and clinical applications comprising in vitro fertilization (IVF).
  • This method has the steps of a) providing a suitable PDG microarray coated with oligonucleotide probes designed to hybridize with chromosomal abnormalities; b) providing a small sample comprising a single cell, a few cells, body fluids or a small piece of tissue; c) lysing at least one cell in the small sample to free the genomic DNA; d) amplifying the DNA to produce a nucleotide sample; e) labeling the amplified DNA to produce a labeled nucleotide sample; f) incubating the labeled nucleotide sample with the PDG microarray to permit the labeled nucleotides to hybridize to the PDG microarray; g) exposing the hybridized PDG microarray to a scanner to
  • steps d and e are performed as one step, in that labeling occurs as the sequences are amplified.
  • the chromosomal abnormalities include aneuploidy; translocation; gene/locus amplification; insertion/deletion; reversion; short tandem repeat (STR) polymorphisms, microsatellite polymorphisms; single nucleotide polymorphisms (SNPs) or a combination thereof.
  • STR short tandem repeat
  • SNPs single nucleotide polymorphisms
  • kits for analyzing chromosomal abnormalities in single cells has at least the following: a) reagents for preimplantation genetic diagnosis, said reagents comprising nucleotide sequences capable of hybridizing with known chromosomal abnormalities; and b) at least one slide with a microarray designed to hybridize with a plurality of chromosomal abnormalities, said microarray comprising a plurality of spots, each containing the same oligonucleotides; and the oligonucleotides in a spot having been designed to hybridize with a single chromosomal XlA - OOlPCT
  • abnormality corresponding normal sequence, or flanking sequences neighboring the chromosomal abnormality.
  • a process of analyzing chromosomal abnormalities in cancer using microarray technology has at least the following steps: a) providing a suitable microarray comprising oligonucleotide probes designed for the detection of selected known cancer cell chromosomal abnormalities; b) providing a small sample comprising a single cell, a few cells, body fluid or a small piece of tissue; c) lysing at least one cell in the small sample to release genomic DNA; d) amplifying the genomic DNA to produce a nucleotide sample; e) labeling the nucleotide sample; f) incubating the labeled nucleotide sample with the microarray to permit the labeled nucleotides to hybridize with the oligonucleotide probes; and g) exposing the hybridized microarray to a scanner equipped with software to transform the scanned data into an indication of the presence or absence of a variety of chromosome abnormal
  • a method of analyzing chromosomal aberrations associated with excess or missing chromosomes has at least the following steps: a) providing a microarray comprising oligonucleotide probes for individual chromosomes; b) providing a normal control and a small sample comprising a single cell, a few cells, body fluid or a small piece of tissue in separate containers; c) lysing the control and small samples to free genomic DNA; d) priming the genomic DNA with oligos comprising RNA promoter sequences; e) amplifying the genomic DNA in the control and small samples to produce amplified nucleotides; f) labeling the amplified nucleotides in the control sample with one color of dye and in the small sample with another color of dye; g) mixing the labeled control and small samples so that the labeled nucleotides are in approximately equal quantities; h) adding mixed or non-mixed labeled sample to
  • T7 or T3 promoters from T7 or T3 promoters.
  • the promoter is specific for the polymerase, and an RNA polymerase is selected from T7 RNA polymerase and T3 RNA polymerase.
  • the type of detectable label is a fluorescent dye or a radioactive moiety.
  • a method of designing and manufacturing a microarray suitable for diagnosis of chromosomal abnormalities includes at least the following steps: a) designing sequences for oligonucleotides suitable for arraying with steps comprising i. selecting known chromosomal sequences associated with chromosomal abnormalities, such as gene mutations associated with inherited diseases, chromosomal breaks, chromosomal translocations, chromosomal or gene amplification, insertions, reversions, short tandem repeats (STR) polymorphisms, microsatellite polymorphisms, single nucleotide polymorphisms (SNPs) and combinations thereof; ii.
  • STR short tandem repeats
  • a method of linear amplification of genomic DNA having the steps of a) obtaining genomic DNA; b) priming genomic DNA with degenerate oligonucleotide primers (DOP) with a T7 RNA promoter sequence at the 5' end of the primers; c) reacting the DOP-primed DNA with DNA polymerase for at least one cycle to amplify by PCR; d) amplifying the PCR product with T7 RNA polymerase; and e) labeling the amplified product with a detectable moiety.
  • DOP degenerate oligonucleotide primers
  • T7 RNA promoter can be replaced with T3 promoter
  • T7 RNA polymerase can be replaced with T3 RNA XIA - OOlPCT
  • steps d and e are combined for labeling during the amplification of the PCR product.
  • oligonucleotide microarrays used for this invention have advantages as to flexibility of design and coverage from fine points of polymorphism to the whole genome, which gives more advantages than other currently used detection methods used for this application such as FISH (fluorescence in situ hybridization) and metaphase comparative genome hybridization.
  • aliquots of amplified genome can be further amplified using specific primers for specific genetic diagnosis by uniplexing or multiplexing PCR (polymerase chain reaction).
  • PCR polymerase chain reaction
  • This method applies not only to PGD, but also other applications using single cells, such as stem cells, differentiated cells, and transformed cells for culture, tissue, and body fluid.
  • Figures Ia- Id are schematic diagrams for aneuploidy detection.
  • Fig Ia shows a chromosome which can be detected by a probe.
  • Fig Ib shows equal numbers of test and reference pairs of chromosomes, or a normal number of copies for the test sample.
  • Fig Ic shows hyperhaploid test cells, compared to the normal number of reference chromosomes, for a ratio of 3:2.
  • Fig Id illustrates hypoploidy (condition of having only one or a few chromosomes fewer than normal), in which fewer or no test DNA signals should be seen for XIA -OOlPCT
  • the detected chromosome or arm If diploid cell lines are used, the ratio between test and reference for a trisomy is expected to be 3:2, or 1.5, and for monosomy 1:2, or 0.67, theoretically.
  • Figure 2 is a graph of the representation of all the chromosomes of cell lines having trisomy 13 (47, XX, +13), 18 (47, XX, +18), and 21 (47, XX, +21). The average ratio greater than 1.33 was obtained for trisomy, which was significant (p ⁇ 0.05) compared to ratio range of 0.86 - 1.16 for normal chromosome pairs.
  • Figures 3a-3d are schematic figures showing the rationale for translocation detection.
  • Fig 3a shows the regimen for probe design of the normal chromosome. Probes flanking and spanning the breakpoints of translocation are labeled 1, 2, 3.
  • Fig 3b illustrates the types of translocations. The normal chromosome is labeled A. Two types of translocations occur: unbalanced translocation or deletion is shown for chromosome B, and balanced translocation or reciprocal translocation is shown between chromosomes C (open) and D (diagonal lines).
  • Fig 3c shows an inventive biochip layout. The numbered probes (see Fig 3a) are spotted on biochips.
  • Fig 3d shows hybridization results.
  • probe 1 there are hybridization signals on all 1, 2, and 3 probes for the normal chromosome; for a deletion, only probe 1 has a signal because no target for probe 3 was amplified and shorter targets for probe 2 washed off after hybridization; probe 1 and 3 but not probe 2 show signals for both chromosomes C and D. Probe 1 and 3 hybridized with the full target sequences. Half portion of targets that are homologous to probe 2 hybridizes to the probe (chiramic targets due to translocations) and targets are washed away.
  • Figures 4a-4c show microarray design and results for translocations of chromosomes 1 1 and 16.
  • Fig 4a illustrates the probe layout on a chip of probes designed as shown in Fig 3a.
  • Fig 4b shows signals only for normal chromosomal probes for the reference samples.
  • Fig 4c shows no signals on breakpoint probes, but do show a signal on the fused probe for test samples.
  • Figures 5a-5c illustrate multiplex PCR for. translocation.
  • Fig 5a shows spots in triplicate on an array for probes for four genes from different chromosomes as well as XIA-OOlPCT
  • Fig 5b shows t(4;l 1) translocation
  • Fig 5c shows the other t(l;19) translocation.
  • Microarrays disclosed herein employ smaller oligonucleotides have designed to assess not only the whole chromosomal structure but also the finer chromosomal changes including aneuploidies, translocations, insertion/deletion, reversion, local amplification, even single nucleotide polymorphisms..
  • This invention provides a method to detect chromosomal abnormalities in a single cell, a few cells or small tissues on oHgonucleotide-based microarrays.
  • One specific technical platform used herein was the microarray (or biochip or chip), because microarrays afford a powerful system for massive and parallel detection of hundreds to thousands to even millions of chromosomal segments at one time on one sample, providing maximal genomic information for cells. Whole genome information and chromosomal abnormalities can be detected and studied.
  • the other technical aspect of this invention is genomic amplification and labeling. Limited initial genetic material from only a few cells poses a major analytical challenge.
  • the invention provides a method to amplify the whole genome from a single cell or a few cells, then to label them for the hybridization.
  • Standard techniques for cloning, DNA isolation, amplification and purification, for enzymatic reactions involving DNA Iigase, DNA polymerase, restriction endonucleases and the like, and various separation techniques are those known and commonly employed by those skilled in the art.
  • a number of standard techniques are described in Sambrook et al., 1989 MOLECULAR CLONING, Second Edition, Cold Spring Harbor Laboratory, Ptainview, New York; Maniatis et al, 1982 MOLECULAR CLONING, Cold Spring Harbor Laboratory, Plainview, New York; Wu (Ed.) 1993 Meth. Enzymol. 218, Part I; Wu (Ed.) 1979 Meth Enzymol. 68; Wu et al., (Eds.) 1983 Meth.
  • PCR polymerase chain reaction
  • LCR Iigase chain reaction
  • LCR Iigase chain reaction
  • LCR Iigase chain reaction
  • transcription amplification Kwoh Proc. Natl. Acad. Sci. USA 1989; 86:1173
  • self-sustained sequence replication Guatelli Proc. Natl. Acad. Sci. USA 1990; 87:1874
  • Q Beta replicase amplification Smith J. CHn. Microbiol. 1997; 35:1477-1491
  • other RNA polymerase mediated techniques such as nucleic acid XIA- OOlPCT
  • NASBA sequence based amplification
  • Adenine (A or a) - 6-Aminopurine A Nitrogenous Base, One Member of the Base Pair AT (Adenine-thymine); One of the Two Major Purines (the Other Being Guanine) Found in Both RNA and DNA
  • Alzheimer's Disease - AD Adult-onset Dementia Characterized by Disorientation and Impaired Memory, Judgment, and Intellect Due to Pathological Changes in the Brain
  • BAC Bacterial Artificial Chromosome
  • Beta-globulin Gene The Gene Associated with Sickle Cell Trait and Anemia, Also Known as the HBB Gene
  • Biochip A Two-dimensional Configuration to Screen For or Identify Specific Genes or Genomic Regions of Interest by Chemical Reactions (Array; Microarray)
  • Chromosome The Self-replicating Genetic Structure of Cells That Contains Cellular DNA and Bears the Portions of the Genetic Code
  • Cystic Fibrosis A Common Hereditary Disease Caused by a Mutation in a Gene (i.e., the Cystic Fibrosis Transmembrane Conductance Regulator) That Affects the Entire Body, Causing Chronic Pulmonary Disease, Progressive Disability, and Premature Death
  • DeGeorge (DiGeorge) Syndrome A Rare Congenital Disease, Caused by a Large Deletion from Chromosome 22 Affecting Multiple Genes, Characterized by Variable Signs and Symptoms That Commonly Include Recurrent Infection, Heart Defects, and Abnormal Facial Features.
  • DNA ⁇ Deoxyribonucleic Acid - DNA.
  • DNA Is a Double-stranded Molecule Held Together by Weak Bonds Between Base Pairs of Nucleotides.
  • ⁇ Down (Down's) Syndrome - Trisomy 21 A Genetic Disorder Caused by the Presence of All or Part of an Extra 21 st Chromosome.
  • the Condition is Characterized by a Combination of Major and Minor Differences in Body Structure and Appearance, Including the Face, and Is Associated with Impairment of Cognitive Function, Frank Mental Retardation, and Altered Physical Growth
  • Gamete A Mature Male or Female Reproductive Cell (i.e., sperm or ovum) with a Haploid Set of Chromosomes (23 Pairs for Humans)
  • Genome The Diploid Human Genome Consists of 23 Pairs of Chromosomes (A Total of 46 Chromosomes): 22 Pairs of Autosomes, and One Pair of Sex Chromosomes (X and Y Chromosomes). The Entire Chromosomal Genetic Material of an Organism.
  • Haploid A Single Set of Chromosomes (i.e., One-half of the Full Set of Chromosomes) Present in an Ovum or Sperm
  • Huntington's (Huntington) Disease - HD A Rare Inherited Neurological Disorder, Previously Known as Huntington's Chorea and Chorea Major, is caused by a trinucleotide Repeat Expansion in the Huntington (Htt) Gene and is Characterized by Abnormal Body Movements Called Chorea, Lack of Coordination, and Abnormalities of Cognitive Function and Behavior.
  • Hybridization The Process of Combining Two Complementary Strands of DNA (or One Each of DNA and RNA) to Form a Double-stranded Molecule.
  • Lymphocytes Immunologically Important White Blood Cells Formed in Lymphatic Tissue Throughout the Body, (e.g., lymph nodes, the spleen, and the thymus)
  • XIA -OOlPCT XIA -OOlPCT
  • Microarray A Small, Miniaturized, Two- or three-dimensional Configuration to Screen For or Identify Specific Genes or Genomic Regions of Interest by Chemical Reactions (Array; Biochip; Chip; beads, etc.)
  • Nucleoside - A Compound Composed of a Sugar, Usually Ribose or Deoxyribose, with a Purine or Pyrimidine Base by Way of an 2V ⁇ glycosyl link
  • Nitrogenous Base i.e., Adenine, Cytosine, Guanine, or Thymine in DNA, and Adenine, Cytosine, Guanine, or Uracil in RNA
  • Phosphate Moiety i.e., Deoxyribose in DNA and Ribose in RNA
  • Oligonucleotides A Molecule Composed of about 100 or Fewer Nucleotides, Used as a DNA Synthesis Primer; "Oligo" for short
  • Phagemids Vectors Based on Hybrids Between Phages and Plasmids That Are Used in DNA Cloning and Sequencing
  • Phenotype The Physical Characteristics of an Organism or the Presence of a Disease That May or May Not Be Genetic
  • RNA Ribonucleic Acid - RNA. A Macromolecule Found in All Cells, Both in the Nucleus and the Cytoplasm That Is Composed of Ribonucleosides and Is Similar in Structure to DNA. RNA Plays an Important Role in Protein Synthesis and Other Chemical Activities Within the Cell. RNA is Divided into Several Classes with Different Functions, Including Messenger RNA and Transfer RNA
  • Sickle-cell Anemia - Sickle-cell Anemia or Disease Is an Inherited Disorder of the Hemoglobin in Red Blood Cells That Is Characterized by Abnormally Shaped Red Blood Cells and by Anemia and Painful Sickle-cell Crises, Especially Prevalent in African Americans XIA - OOlPCT
  • SNP Single Nucleotide Polymorphism - SNP.
  • SNPs make up 90% of all human genetic variations and can affect how humans develop diseases, respond to pathogens, chemicals, drugs, etc.
  • Nucleic acid samples disclosed herein also comprise a detectable composition referred to herein as a label.
  • the label can be biological molecule, such as a nucleic acid.
  • This nucleic acid samples can have detectable labeled bases incorporated into the nucleic acid by, for example, nick translation, random primer extension, amplification with degenerate primers, and the like.
  • the label can be detectable by any means, including but not limited to, visual, spectroscopic, photochemical, biochemical, immunochemical, physical or chemical means.
  • Non-limiting examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; a non-Hmiting example of a luminescent material includes luminol; non-limiting examples of bioluminescent materials include luciferase, luciferin, and aequorin.
  • oligonucleotide probes were designed to hybridize with those loci.
  • the designed probe sequences were subjected to a BLAST (Basic XIA - OOlPCT
  • Probes were designed to detect the intact breaking points of genes 11 and 16 (1 Iq23 and 16pl3, respectively), flanking regions around the breaking points, and the fused point of new MLL-CBP gene. According to the terminology in Fig 3, probes across the breaking points were designated 11- 2 and 16-2 for chromosomes 11 and 16, respectively. Upstream and downstream probes were designed for the flanking regions 11-1 and 11-3, and 16-1 and 16-3, respectively. The fused probe was designed across the fusion point of the new gene and was named fused-2.
  • Probe 11-1 ctttatattcccatagctctttgtttataccactcttagg (SEQ ID NO: 1),
  • fiised-2 ttctatttccactggtattaggggaccatcttgaagagta (SEQ ED NO: 7)
  • the probe design can be readily adapted to detect more abnormalities including aneuploidies, translocations, single nucleotide polymorphisms (SNPs), single nucleotide mutations (such as the substitution of A>T at codon 7 in the beta-globin gene for sickle-cell anemia) and short repeat polymorphisms (e.g., Huntington's disease).
  • SNPs single nucleotide polymorphisms
  • short repeat polymorphisms e.g., Huntington's disease.
  • oligo probes can be designed based on the any specific chromosomal or genetic information, instead of mere selection of whole-genome cloned probes orlibraries (such as BACs or YACs), thus maximally reducing cost and being more practical.
  • the other advantage from the use of oligo probes is to be able to provide the detailed information of fine structural abnormalities of chromosomes. For specific, small chromosomal abnormalities, multiple oligo probes can be designed for those fine locations to provide the most detailed structural information available.
  • the oligo probes can be DNA or RNA oligonucleotides, PNA, LNA or modified DNA or RNA or other types of analogs to meet the required specificity and product stability.
  • DNA oligo probes were used in this study. Biochips were manufactured in a class 100 clean room. DNA oligo probes were synthesized with a 5' amine group for chip attachment and were purified by HPLC. Their concentration was normalized at 20 mM per chemical probe. The probes were dissolved in 50 mM phosphate buffer pH 8.3. The probes were spotted on the microarray surface in triplicate. After post-printing processes, the biochips were stored at 4° C in a desiccator's container and can be used for hybridization.
  • Lymphocytes were also obtained from peripheral blood of a normal female (46, XX).
  • Single cells were isolated as described (Hussey et al, MoI Hum Reprod 1999;5: 1089-94). Lysis of single cells was carried out by the addition of 5 ⁇ l of lysis buffer (200 mM KOH, 50 mM DTT) and incubation at 65 0 C for 10 min followed by neutralization using 5 ⁇ l of neutralization solution (300 mM KCl, 900 mM Tris-HCl, pH 8.3, 200 mM HCl) (Cui et al. Proc Natl Acad Sci USA 1989; 86:9389-93).
  • lysis buffer 200 mM KOH, 50 mM DTT
  • neutralization solution 300 mM KCl, 900 mM Tris-HCl, pH 8.3, 200 mM HCl
  • DOPs degenerated oligonucleotide primers
  • T7 RNA promoter sequences at the 5' end T7-sequence-CTGACTCGACNNNNNNATGTGG
  • SEQ ID NO: 8 T7-sequence-CTGACTCGACNNNNNNATGTGG
  • the degenerated oligonucleotide primed-PCR (DOP-PCR) reaction was conducted in a volume of 50 ⁇ l with a final concentration of 50 mM KCl, 100 mM Tris-HCI, pH 8.3, 0.1 mg/ml gelatin, 2.5 mM MgCl 2 , 200 ⁇ M of each dNTP, 2 ⁇ M T7-DOP, and 5 IU of Taq polymerase (Perkin Elmer, Wellesley, MA).
  • PCR products were purified with a PCR purification kit (Qiagen, Valencia, CA), following the manufacturer's directions. The purified products were either stored at or below — 20 0 C, or were directly used in the next step.
  • IVT was carried out in a volume of 40 ⁇ l with a final concentration of Ix IVT buffer (Ambion, Austin, TX), 5 mM each NTP, 1.25 mM UTP-Cy5 or -Cy3 (Amersham), 4 ⁇ l enzyme mix (Ambion), and 16.9 ⁇ l amplified genome products (see above for preferred method). The mix was incubated at 37°C for 14 hours.
  • PBX-reverse acagcatgttgtccagccgc (SEQ ID NO: 12)
  • Probe sequences on the arrays were:
  • MLL aaagcagcctccaccaccagaatcaggtccagagcagagc (SEQ ID NO: 13)
  • E2A gacgaggccatccacgtgctccgcagccacgccgtgggca (SEQ ID NO: 15)
  • PBX cgaggagcccaggaggaggaacccacagacccccagctga (SEQ ID NO: 16)
  • the IVT products were purified (Qiagen Rneasy Mini kit) and then quantified using Beckman DU800 LJV spectrophotometry (Beckman Coulter, Fullerton, CA). XIA - OOlPCT
  • the hybridization chamber volume was 140 ⁇ l (Genomic Solutions, Inc., Ann Arbor, MI). Ten micrograms of each labeled target was added into the hybridization chambers at the final buffer concentration 6xSSPE and 50% formamide. Hybridization was performed at 37 0 C for 15-20 hours with constant agitation.
  • the chips were washed twice in washing buffers containing 2x SSC/2% SDS at 37 0 C for 15 min, then twice in 0.2x SSC/0.2% SDS at 37 0 C for 15 min, then once in O.lx SSC at room temperature for 15 min, followed by three brief rinses in deionized H 2 O. After drying, the chips were scanned by the Axon scanner 4000B (Axon Instrument/Molecular Devices, Sunnyvale, CA) at different laser channels for Cy5 and Cy3 dyes.
  • Axon scanner 4000B Axon Instrument/Molecular Devices, Sunnyvale, CA
  • This experiment tested the model for detecting aneuploidies using the inventive array-based CGH.
  • Microarrays were designed as described in Fig 1. Three trisomy cell lines (see above), for trisomy 13 (47, XX, +13), 18 (47, XX, +18) and 21 (47, XX, +21), were selected along with normal lymphocyte (46, XX) reference cells.
  • Genomic DNA was isolated and amplified with T7-DOP PCR as described above.
  • the PCR products were then further amplified and labeled with Cy5 and Cy3 fluorescent dyes for the test and reference samples, respectively, by the in vitro transcription method described above.
  • the test and reference samples with the differently labeled RNA were then mixed and added to the biochip chambers for hybridization. After post-hybridization washes, XIA - OOlPCT
  • the SN-I cell line was selected to demonstrate translocation detection. Chips were designed to delineate the different possible types of translocations and are summarized in Fig 3. The experimental method was described as above. The chip images for the translocation t(l I;16)(q23;pl3) detection are displayed in Fig 4.
  • the genomic information on the sequences around the translocation was obtained from NCBI 5 and probes were designed for the intact break point, flanking sequences and for the fused sequence, utilizing the in-house developed software.
  • the probes were synthesized using an ABI 394 DNA synthesizer with the DNA oligonucleotides of 40 nt length.
  • the probes were dissolved in lO ⁇ l of 5OmM sodium phosphate buffer at pH 8.3 for a final concentration of 20 mM.
  • the microarrays were spotted using an OmniGrid Arrayer (Genomic Solutions) with the layout pattern shown in Fig 4.a, with triplicate spots for each probe.
  • the printed arrays were incubated overnight in a 70% humidity chamber. After blocking and repeated washes, the arrays were dried and used for hybridization assays.
  • An Axon scanner 4000B was used for scanning the slide at different laser channels for Cy5 and Cy3. Data analysis was performed by the GenePix Pro 5.0 software. Ratios of Cy5 and Cy3 were determined.
  • ratio data for all chromosomes were collected from three different cell lines, and the data are presented in Fig 2. Ratios greater than 1.33 (on average) were obtained for the extra chromosome known to be in trisomy, which is significant (p ⁇ 0.05) compared to the ratio range of 0.86 - 1.16 for normal chromosome pairs.
  • Fig 3 The array design and experimental methods for translocation were described in Fig 3 and above.
  • the cell line SN-I was selected. This cell line has a reciprocal translocation t(l I;16)(q23;pl3), where Ilq23 was fused to 16pl3 to form a new gene.
  • probes were designed for the breakpoint and flanking regions. Probes crossing the breakpoints were designed 11-2 and 16-2 for chromosomes 11 and 16, respectively. Upstream and downstream probes were designed in the flanking regions 11-1 and 11-3, and 16-1 and 16-3, respectively.
  • a fused probe (fused-2) was also designed across the fusion point of the two chromosomes. Chip layout for these triple-printed probes is displayed in Fig 4a. Hybridization signals were scanned and reproduced in Figs 4b and 4c).
  • SN-I cells (Fig 4c) showed signals at probes -1, -3 and fused-2, but no signals at probe —2, suggesting that breaking chromosomes occurred at the position corresponding to probe —2 and that a new fused sequence had formed.
  • the normal reference cells (Fig 4b) presented the expected hybridization signals on all normal chromosomal probes, but not on the fused-2 probes.
  • Probes for four genes (see above) on different chromosomes were designed and printed on the arrays in the formation shown in Fig 5.a. Positive and negative controls were also included. Probes were printed in triplicate.
  • Single lymphocytes were selected from leukemia patients. Cells were lysed, and first round genomic amplification was performed. Five microliters of amplified genetic material was transferred to a new PCR tube containing multiplex primers designed for specific translocation tests. Because four genes, MLL and AF4, and PBX and E2A from four different chromosomes were believed to be involved in translocation, four primers were designed, one based on each gene (see above). When the four primers were pooled together, they generated products for the fused genes if translocation(s) were present. Multiplex PCR was performed and the PCR products were hybridized to the microarray probes. Positive hybridization signals were observed, but negative samples did not show signals (Fig 5). Fig XIA - OOlPCT

Abstract

La présente invention décrit un procédé d'analyse d'anormalités chromosomiques dans une cellule unique ou quelques cellules pour la recherche et le diagnostic génétique préimplantatoire. Le procédé est aussi utilisable pour d'autres applications utilisant une cellule unique telle une cellule-souche, le diagnostic et la recherche de cellules transformées et le diagnostic du cancer. L'invention fait usage de l'amplification génomique, du marquage génomique et/ou de techniques de marquage de gènes spécifiques. Le matériel génétique amplifié est détecté sur des plates-formes de microréseaux à différents formats. L'invention concerne des dosages multiplexes et la détection de multiples types d'anormalités chromosomiques.
PCT/US2006/047254 2005-12-14 2006-12-12 Procede de detection d'anormalites chromosomiques a l'aide de microreseaux pour le diagnostic genetique preimplantatoire WO2007070482A2 (fr)

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