Title:
GENE IDENTIFICATION METHOD IN FRAGMENTOME ANALYSIS AND EXPRESSION ANALYSIS METHOD
Document Type and Number:
WIPO Patent Application WO/2012/157778
Kind Code:
A1
Abstract:
A database construction method, including a stage that fragments genomic DNA contained in a sample or cDNA obtained from a transcription product and obtains a fragment DNA mixture by applying an identifiable index array, a stage that performs high-speed DNA sequencing of a portion of the fragment DNA mixture and acquires read array data for all fragment DNA contained therein, a stage that detects the presence of the index array portion for all read array data and extracts the read array data having the index array, and a stage that performs clustering and assembling of the sequences using sequence similarity and sequence length parameters, forms a plurality of clusters, and acquires the number of structural sequences of the cluster, consensus sequence and consensus sequence length, and alignment information for the clusters.
Inventors:
ABE MASUMI (JP)
YUNOKAWA HARUNOBU (JP)
SATO SHINJI (JP)
KONDO KAZUHIRO (JP)
HIEIDA TAKASHI (JP)
YUNOKAWA HARUNOBU (JP)
SATO SHINJI (JP)
KONDO KAZUHIRO (JP)
HIEIDA TAKASHI (JP)
Application Number:
PCT/JP2012/062963
Publication Date:
November 22, 2012
Filing Date:
May 21, 2012
Export Citation:
Assignee:
NAT INST RADIOLOG (JP)
MAZE INC (JP)
ABE MASUMI (JP)
YUNOKAWA HARUNOBU (JP)
SATO SHINJI (JP)
KONDO KAZUHIRO (JP)
HIEIDA TAKASHI (JP)
MAZE INC (JP)
ABE MASUMI (JP)
YUNOKAWA HARUNOBU (JP)
SATO SHINJI (JP)
KONDO KAZUHIRO (JP)
HIEIDA TAKASHI (JP)
International Classes:
C12Q1/68; G01N33/53; G01N37/00; C12N15/09
Foreign References:
| JP2005250615A | 2005-09-15 |
Other References:
HARUNOBU YUNOKAWA ET AL.: "An effective way to build a high quality HiCEP peak database (peak:gene) using GS454FLX", DAI 33 KAI THE MOLECULAR BIOLOGY SOCIETY OF JAPAN, DAI 83 KAI ANNUAL MEETING OF THE JAPANESE BIOCHEMICAL SOCIETY GODO TAIKAI YOSHI (4P-1181), 19 November 2010 (2010-11-19), Retrieved from the Internet
FUKUMURA R. ET AL.: "A sensitive transcriptome analysis method that can detect unknown transcripts", NUCLEIC ACIDS RES., vol. 31, no. 16, 2003, pages E94
ARAKI R. ET AL.: "More than 40,000 transcripts, including novel and noncoding transcripts, in mouse embryonic stem cells", STEM CELLS, vol. 24, no. 11, 2006, pages 2522 - 2528
BRAUTIGAM A. ET AL.: "Critical assessment of assembly strategies for non-model species mRNA-Seq data and application of next-generation sequencing to the comparison of C(3) and C(4) species", J. EXP. BOT., vol. 62, no. 9, March 2011 (2011-03-01), pages 3093 - 3102
FRANSSEN SU. ET AL.: "Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing", BMC GENOMICS, vol. 12, 11 May 2011 (2011-05-11), pages 227
FUKUMURA R. ET AL.: "A sensitive transcriptome analysis method that can detect unknown transcripts", NUCLEIC ACIDS RES., vol. 31, no. 16, 2003, pages E94
ARAKI R. ET AL.: "More than 40,000 transcripts, including novel and noncoding transcripts, in mouse embryonic stem cells", STEM CELLS, vol. 24, no. 11, 2006, pages 2522 - 2528
BRAUTIGAM A. ET AL.: "Critical assessment of assembly strategies for non-model species mRNA-Seq data and application of next-generation sequencing to the comparison of C(3) and C(4) species", J. EXP. BOT., vol. 62, no. 9, March 2011 (2011-03-01), pages 3093 - 3102
FRANSSEN SU. ET AL.: "Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing", BMC GENOMICS, vol. 12, 11 May 2011 (2011-05-11), pages 227
Attorney, Agent or Firm:
KURATA, Masatoshi et al. (JP)
Masatoshi Kurata (JP)
Masatoshi Kurata (JP)
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