US20120190582A1 - Method for designing probe in dna microarray, and dna microarray provided with probe designed thereby - Google Patents

Method for designing probe in dna microarray, and dna microarray provided with probe designed thereby Download PDF

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Publication number
US20120190582A1
US20120190582A1 US13/499,618 US201013499618A US2012190582A1 US 20120190582 A1 US20120190582 A1 US 20120190582A1 US 201013499618 A US201013499618 A US 201013499618A US 2012190582 A1 US2012190582 A1 US 2012190582A1
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Prior art keywords
genomic dna
restriction enzyme
probe
designing
adaptor
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Hiroyuki Enoki
Satoru Nishimura
Aya Murakami
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Toyota Motor Corp
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Toyota Motor Corp
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Assigned to TOYOTA JIDOSHA KABUSHIKI KAISHA reassignment TOYOTA JIDOSHA KABUSHIKI KAISHA ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: ENOKI, HIROYUKI, MURAKAMI, AYA, NISHIMURA, SATORU
Publication of US20120190582A1 publication Critical patent/US20120190582A1/en
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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
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • C12Q1/683—Hybridisation assays for detection of mutation or polymorphism involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
    • 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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] 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
    • 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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • 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
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • C12Q1/6855—Ligating adaptors

Definitions

  • a method for detecting such a mutation in genomic DNA a method of directly determining a sequence of a mutation site, a method of using a restriction enzyme fragment length polymorphism (RFLP), a method of using an amplification fragment length polymorphism (AFLP) and the like are known.
  • RFLP restriction enzyme fragment length polymorphism
  • AFLP a method of using an amplification fragment length polymorphism
  • DArT Diversity Array Technology
  • FIG. 5 is a characteristic view showing alignment of A — 1 and A — 2 and the site of the designed probe.
  • the amplified genomic DNA fragment is sequenced (Step 1 e ), one or more regions having a shorter nucleotide length than the genomic DNA fragments and covering at least a part of the genomic DNA fragments are specified; and a probe for the one or more regions specified are designed for detecting the amplified genomic DNA fragment of an organism to be tested (Step 1 f ).
  • a method for sequencing a genomic DNA fragment is not particularly limited. A method known in the art employing the Sanger method etc. and a DNA sequencer can be used.
  • more than one region is preferably set so as to cover the entire region of the sequenced genomic DNA fragment.
  • more than one probe responds to a genomic DNA fragment obtained by a restriction enzyme treatment from genomic DNA derived from a predetermined organism to detect the genomic DNA fragment by these more than one probe.
  • more than one region covering at least a part of the genomic DNA fragments obtained by digesting genomic DNA with restriction enzyme A and restriction enzyme B can be specified by more than one DNA fragment without sequencing.
  • region to be specified those having, for example, a 20 to 100 nucleotide length, preferably a 30 to 90 nucleotide length, and more preferably, a 50 to 75 nucleotide length are mentioned, as mentioned above.
  • the stringent conditions can be controlled by a reaction temperature and a salt concentration. More specifically, further higher stringent conditions can be obtained by increasing the temperature and further higher stringent conditions can be obtained by reducing a salt concentration. For example, when a probe having a 50 to 75 nucleotide length is used, further higher stringent conditions are prepared if conditions of 40 to 44° C., 0.21SDS, 6 ⁇ SSC are employed.
  • a mutation rate was calculated based on homology of the genome sequence of the loci regions of NiF8 and Ni9 alleles within respective probes.
  • Probes were prepared by separately inserting, deleting and substituting with 1, 2, 3, 4, 5, 10, 15, 20 and 25 nucleotides into, from and for the basic probes of the step (2).
  • 59,462 probes were designed from 5,848 genomic sequence data. Of them, the number of probes in the case where a signal intensity ratio was beyond 2, was 5,596. Sequence data having at least one of such a probe was 1,497. Of these sequence data, the number of data providing a signal intensity ratio of 2 or more in all probes were 189, which was 12.6% of the total ( FIG. 8 ). It was considered that mutation within the sequence data is caused by a large insertion/deletion of several kbp within a restriction enzyme recognition sequence. On the other hand, the sequence data in which a mutation was detected in a part of probes was 87.4% of all data.

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  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Biophysics (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Physics & Mathematics (AREA)
  • Genetics & Genomics (AREA)
  • Immunology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
US13/499,618 2009-12-14 2010-12-13 Method for designing probe in dna microarray, and dna microarray provided with probe designed thereby Abandoned US20120190582A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
JP2009-283430 2009-12-14
JP2009283430A JP5799484B2 (ja) 2009-12-14 2009-12-14 Ｄｎａマイクロアレイにおけるプローブ設計方法、当該方法により設計されたプローブを有するｄｎａマイクロアレイ
PCT/JP2010/072322 WO2011074510A1 (ja) 2009-12-14 2010-12-13 Dnaマイクロアレイにおけるプローブ設計方法、当該方法により設計されたプローブを有するdnaマイクロアレイ

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PCT/JP2010/072322 A-371-Of-International WO2011074510A1 (ja) 2009-12-14 2010-12-13 Dnaマイクロアレイにおけるプローブ設計方法、当該方法により設計されたプローブを有するdnaマイクロアレイ

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EP (1) EP2514820B1 (ja)
JP (1) JP5799484B2 (ja)
CN (1) CN102753686B (ja)
AU (1) AU2010331393B2 (ja)
BR (1) BR112012014466B1 (ja)
WO (1) WO2011074510A1 (ja)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2018053573A1 (en) * 2016-09-22 2018-03-29 Garvan Institute Of Medical Research Device for presenting sequencing data

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JP5653957B2 (ja) * 2011-04-28 2015-01-14 トヨタ自動車株式会社 サトウキビ属植物の黒穂病抵抗性関連マーカーとその利用
JP6253132B2 (ja) 2013-09-09 2017-12-27 国立研究開発法人農業・食品産業技術総合研究機構 イチゴ属植物の炭疽病抵抗性関連マーカーとその利用
WO2017120750A1 (zh) * 2016-01-12 2017-07-20 中国科学院生物物理研究所 一种针对东亚人群全基因组范围内的非编码区的SNPs的DNA芯片
JP6515884B2 (ja) 2016-06-29 2019-05-22 トヨタ自動車株式会社 Ｄｎａプローブの作製方法及びｄｎａプローブを用いたゲノムｄｎａ解析方法

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WO2000034518A1 (en) * 1998-12-04 2000-06-15 Keygene N.V. Array and method for analysing nucleic acid sequences
US20080187912A1 (en) * 1999-06-17 2008-08-07 Fred Hutchinson Cancer Research Center Oligonucleotide arrays for high resolution HLA typing
US6958225B2 (en) * 1999-10-27 2005-10-25 Affymetrix, Inc. Complexity management of genomic DNA
US20030044791A1 (en) * 2001-06-13 2003-03-06 Flemington Erik Kolstad Adaptor kits and methods of use
US20030162181A1 (en) * 2002-02-28 2003-08-28 Eastman Kodak Company DNA sequencing and gene identification
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US20070016382A1 (en) * 2004-01-16 2007-01-18 Affymetrix, Inc. Methods for Selecting a Collection of Single Nucleotide Polymorphisms
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* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2018053573A1 (en) * 2016-09-22 2018-03-29 Garvan Institute Of Medical Research Device for presenting sequencing data

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EP2514820A4 (en) 2013-08-07
CN102753686A (zh) 2012-10-24
BR112012014466A2 (pt) 2015-11-24
US10214769B2 (en) 2019-02-26
EP2514820A1 (en) 2012-10-24
JP2011120558A (ja) 2011-06-23
AU2010331393B2 (en) 2014-06-19
EP2514820B1 (en) 2020-05-06
BR112012014466B1 (pt) 2020-12-29
US20170166951A1 (en) 2017-06-15
CN102753686B (zh) 2015-09-09
WO2011074510A1 (ja) 2011-06-23
JP5799484B2 (ja) 2015-10-28
AU2010331393A1 (en) 2012-07-12

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