US20120077200A1 - Primers for diagnosing avellino corneal dystrophy - Google Patents

Primers for diagnosing avellino corneal dystrophy Download PDF

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US20120077200A1
US20120077200A1 US13/264,784 US200913264784A US2012077200A1 US 20120077200 A1 US20120077200 A1 US 20120077200A1 US 200913264784 A US200913264784 A US 200913264784A US 2012077200 A1 US2012077200 A1 US 2012077200A1
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nos
corneal dystrophy
avellino corneal
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Gene Lee
Jung Kuk Yun
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AVELLINO CO Ltd
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    • 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
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C—CHEMISTRY; METALLURGY
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    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
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    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]
    • 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
    • C12Q2561/00—Nucleic acid detection characterised by assay method
    • C12Q2561/113—Real time assay
    • 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
    • C12Q2600/112—Disease subtyping, staging or classification
    • 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

  • the present invention relates to a real-time PCR primer pair and probe for diagnosing Avellino corneal dystrophy, and more particularly to such a real-time PCR primer pair and probe for diagnosing Avellino corneal dystrophy, which can accurately diagnose the presence or absence of a mutation in exon 4 of BIGH3 gene, which is responsible for Avellino corneal dystrophy.
  • Corneal dystrophy is an autosomal dominant hereditary disease, which begins with a blurry symptom in the center of cornea and gradually spreads and thus ends up vision loss as a patient gets older. It includes Avellino corneal dystrophy, Granular corneal dystrophy, lattice type I corneal dystrophy, Reis-bucklers corneal dystrophy, etc., and is caused by mutation of a gene coding ⁇ IG-H3 protein.
  • Avellino corneal dystrophy is a newly named disease in 1988, divided from generally called Granular corneal dystrophy because it was found to have discrete symptoms and genetic foundation. Also, it has been known to be the most common corneal dystrophy worldwide, 1/340 to 1/1000 of prevalence rate in Korea (the case of heterozygote) based on genetic analysis indicates that it is a common dystrophy (Holland, E. J. et al., Ophthalmology, 99:1564, 1992; Kennedy, S. M. et al., Br. J.
  • the present inventors has found that if a patient suffering from heterozygous Avellino corneal dystrophy has LASIK surgery, 2 years later, opacity of cornea starts to develop aggressively and eventually results in vision loss (Jun, R. M. et al., Opthalmology, 111:463, 2004).
  • eye surgery has been performed with an expectation that LASIK or Excimer Laser surgery would get rid of vision blurriness of a patient suffering from corneal dystrophy.
  • approximately 3 hundred thousand cases of LASIK surgery have been performed, which leads to the assumption that 300 people lost their vision, based on 1/1000 of minimum estimation of heterozygous patients suffering from Avellino corneal dystrophy.
  • Patients who have undergone LASIK surgery are mainly in their 20's and 30's carrying out productive activities; therefore, their vision loss causes serious troubles in both society and economics.
  • Avellino corneal dystrophy is required to prevent the progression of Avellino corneal dystrophy by LASIK surgery
  • diagnosis of Avellino corneal dystrophy is just conducted by microscopic observation of corneal opacity and thus often doctors miss latent symptoms of patients to perform LASIK surgery, which results in vision loss. Therefore, rapid and precise diagnosis of corneal dystrophy is urgent in need.
  • the diagnosis of Avellino corneal dystrophy using said DNA chip disadvantageously require several steps, including a step of amplifying DNA in a sample, a step of hybridizing the amplified DNA with the DNA chip, a step of washing the hybridized DNA chip, and a step of detecting a positive response.
  • the present inventors have made extensive efforts to develop a method capable of more efficiently diagnosing Avellino corneal dystrophy, and as a result, have found that, if the diagnosis of Avellino corneal dystrophy is performed using a pair of primers having nucleotide sequences of SEQ ID NO: 1 and SEQ ID NO: 2 and probes having nucleotide sequences of SEQ ID NO: 13 and SEQ ID NO: 14 by a real-time PCR method, Avellino corneal dystrophy can be diagnosed in a more rapid and accurate manner than a conventional method, thereby completing the present invention.
  • a main object of the present invention is to provide a primer pair and probe for more efficiently and accurately diagnosing Avellino corneal dystrophy using a real-time PCR method.
  • the present invention provides a real-time PCR primer pair for diagnosing Avellino corneal dystrophy, which is represented by nucleotide sequences selected from the group consisting of SEQ ID NOs: 1 and 2, SEQ ID NOs: 3 and 4, SEQ ID NOs: 5 and 6, SEQ ID NOs: 7 and 8, SEQ ID NOs: 9 and 10, SEQ ID NOs: 11 and 12, SEQ ID NOs: 13 and 14, SEQ ID NOs: 15 and 16, SEQ ID NOs: 17 and 18, SEQ ID NOs: 19 and 20, SEQ ID NOs: 21 and 22, and SEQ ID NOs: 23 and 24.
  • the present invention also provides a real-time PCR probe for diagnosing Avellino corneal dystrophy, which is represented by a nucleotide sequence selected from the group consisting of SEQ ID NO: 25 to SEQ ID NO: 42.
  • FIG. 1 shows the results obtained from the design of real-time PCR primers and probes.
  • “A” shows the results of real-time PCR carried out using optimal primers and probes
  • “B” and “C” show the results of real-time PCR carried out using primers different from those in “A”.
  • FIG. 2 shows the results of real-time PCR carried out using real-time PCR primers according to the present invention in order to detect a gene mutation causing Avellino corneal dystrophy.
  • the present invention is directed to a real-time PCR primer pair for diagnosing Avellino corneal dystrophy, which is represented by nucleotide sequences selected from the group consisting of SEQ ID NOs: 1 and 2, SEQ ID NOs: 3 and 4, SEQ ID NOs: 5 and 6, SEQ ID NOs: 7 and 8, SEQ ID NOs: 9 and 10, SEQ ID NOs: 11 and 12, SEQ ID NOs: 13 and 14, SEQ ID NOs: 15 and 16, SEQ ID NOs: 17 and 18, SEQ ID NOs: 19 and 20, SEQ ID NOs: 21 and 22, and SEQ ID NOs: 23 and 24.
  • Avellino corneal dystrophy is a disease caused by genetic abnormality in which the sequence CGC in exon 4 of BIGH3 gene is mutated to CAC so that arginine at residue of BIGH3 protein is mutated to histidine (R124H).
  • Avellino corneal dystrophy can be diagnosed in a more rapid and accurate manner than a conventional method that uses a DNA chip.
  • FIG. 1A shows the results of using well-designed primers and probes
  • FIGS. 1B and 1C shows the results of using primers different from those used in FIG. 1A while using the same probes as those used in FIG. 1A .
  • the design of the primers and the probes has a significant effect on reading.
  • pairs of primers of SEQ ID NOs: 1 and 2, SEQ ID NOs: 3 and 4, SEQ ID NOs: 5 and 6, SEQ ID NOs: 7 and 8, SEQ ID NOs: 9 and 10, SEQ ID NOs: 11 and 12, SEQ ID NOs: 13 and 14, SEQ ID NOs: 15 and 16, SEQ ID NOs: 17 and 18, SEQ ID NOs: 19 and 20, SEQ ID NOs: 21 and 22 and SEQ ID NOs: 23 and 24 were designed, and real-time PCR was performed using each of the designed primer pairs. As a result, it was found that the use of the pair of primers of SEQ ID NOs: 1 and 2 showed the optimal results.
  • the present invention is directed to a real-time PCR probe for diagnosing Avellino corneal dystrophy, which is represented by a nucleotide sequence selected from the group consisting of SEQ ID NO: 25 to SEQ ID NO: 42.
  • probes of SEQ ID NOs: 25 to 42 were designed, and real-time PCR was performed each of the designed primers. As a result, it was found that the use of the probes of SEQ ID NOs: 13 and 14 showed the optimal results.
  • ACD Fw primer (SEQ ID NO: 1) 5′-TCC ACC ACC ACT CAG CTG TA ACD Re primer: (SEQ ID NO: 2) 5′-CCA TCT CAG GCC TCA GCT T (60 bp) AV Fw primer: (SEQ ID NO: 3) 5′-TGC AGC CCT ACC ACT CTC AA AV Re primer: (SEQ ID NO: 4) 5′-AGG CCT CGT TGC TAG G (150 bp) Real Fw primer: (SEQ ID NO: 5) 5′-TAG TCT CTT ATT CTA ATA GA Real Re primer: (SEQ ID NO: 6) 5′-GCT GCA GAC TCT GTG TTT AA (860 bp) ACD Fw2 primer: (SEQ ID NO: 7) 5′-CCA TCC CTC CTT CTG TCT TCT G ACD Re2 primer: (SEQ ID NO: 8) 5′-CGG GCC CCT CCA TCT C (140
  • probes of SEQ ID NOs: 25 to 42 were constructed.
  • the probe binding to a normal gene fragment having no mutation was labeled with VIC, and the probe binding to a gene fragment having a mutation was labeled with FAM, and a minor groove binder (MGB) was attached to the probe so as to facilitate binding to a complementary gene fragment.
  • VIC VIC
  • FAM FAM
  • MGB minor groove binder
  • Normal probe 1 (SEQ ID NO: 25) VIC-CAC GGA CC G CAC GGA-NFQ (15 bp) Mutant probe 1: (SEQ ID NO: 26) FAM-CAC GGA CC A CAC GGA-NFQ Normal probe 2: (SEQ ID NO: 27) VIC-ACA CGG ACC G CA CG-NFQ Mutant probe 2: (SEQ ID NO: 28) FAM-ACA CGG ACC A CA CG-NFQ (14 bp) Normal probe 3: (SEQ ID NO: 29) VIC-TAC ACG GAC C G C A-NFQ Mutant probe 3: (SEQ ID NO: 30) FAM-TAC ACG GAC C A C A-NFQ (13 bp) Normal probe 4: (SEQ ID NO: 31) VIC-CTG TAC ACG GAC C G C ACG-NFQ Mutant probe 4: (SEQ ID NO: 32) FAM-CTG TAC ACG GAC C A C ACG-NFQ (18 bp
  • Samples were taken from the blood, hair root and oral epithelial cells of test subjects, and DNA was isolated from the samples.
  • the isolation and purification of DNA were performed using a partial modification of the phenol/chloroform extraction method (Miller, SA et al., Nucl. Acids Res. 16:1215, 1988), and the isolated DNA was dissolved in a suitable amount of TE buffer (10 mM Tris-Cl, 1 mM EDTA, pH7.4) and confirmed by electrophoresis on 1% agarose gel and used as template DNA in PCR.
  • TE buffer 10 mM Tris-Cl, 1 mM EDTA, pH7.4
  • the PCR reactions were performed using the primers (SEQ ID NOs: 1 to 12) for amplifying the fragment containing the mutation region, and the probes (SEQ ID NOs: 13 to 24), constructed in Example 1.
  • the real-time PCR reaction was performed in the following conditions: 36 cycles each consisting of 10 min at 95° C., 15 sec at 92° C. and 1 min at 60° C., followed by a reaction for 5 min at 60° C.
  • the use of the primer pair and probe according to the present invention can diagnose Avellino corneal dystrophy in a more rapid and accurate manner than a conventional method that uses a DNA chip or PCR.

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KR1020090033528A KR101251538B1 (ko) 2009-04-17 2009-04-17 아벨리노 각막이상증 진단용 프라이머
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US15/947,473 Active 2030-02-26 US11268146B2 (en) 2009-04-17 2018-04-06 Primers for diagnosing Avellino corneal dystrophy
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US17/584,701 Pending US20220205044A1 (en) 2009-04-17 2022-01-26 Primers for Diagnosing Avellino Corneal Dystrophy

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Cited By (4)

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EP3068908A4 (en) * 2013-11-15 2017-08-23 Avellino Lab USA, Inc. Methods for multiplex detection of alleles associated with ophthalmic conditions
CN108085375A (zh) * 2016-11-07 2018-05-29 北京宏微特斯生物科技有限公司 检测角膜营养不良基因多态性位点的基因型的方法及其试剂盒
EP3486328A1 (en) 2013-03-15 2019-05-22 Avellino Lab USA, Inc. Methods for improved isolation of genomic dna templates for allele detection
US11987809B2 (en) 2015-11-13 2024-05-21 Avellino Lab Usa, Inc. Methods for the treatment of corneal dystrophies

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KR101251538B1 (ko) * 2009-04-17 2013-04-08 (주)아벨리노 아벨리노 각막이상증 진단용 프라이머
KR101125212B1 (ko) * 2010-10-01 2012-03-21 (주)아벨리노 아벨리노 각막이상증 진단용 시스템
KR101480522B1 (ko) * 2013-02-15 2015-01-08 솔젠트 (주) 아벨리노 각막 이상증 판별용 진단 키트
KR101577109B1 (ko) * 2013-04-23 2015-12-11 주식회사 녹십자엠에스 아벨리노 각막이상증 진단용 조성물 및 이의 진단방법
CN106480200A (zh) * 2016-10-25 2017-03-08 北京亿昊基因技术有限公司 一种快速高效的与角膜营养不良相关基因突变位点的检测方法
KR101957919B1 (ko) * 2017-01-02 2019-03-13 부산대학교 산학협력단 각막이상증 진단용 바이오센서 및 이의 용도
KR20200129539A (ko) 2019-05-09 2020-11-18 주식회사 왓슨알앤디 Pcr 및 제한효소를 이용한 각막이상증 분자 진단 방법.
KR102249878B1 (ko) * 2019-09-24 2021-05-11 주식회사 에이엠에스바이오 과립형 각막이상증 진단용 조성물

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