Title:
COMPUTATIONAL METHODS FOR TRANSLATING A SEQUENCE OF MULTI-BASE COLOR CALLS TO A SEQUENCE OF BASES
Document Type and Number:
WIPO Patent Application WO/2011/143525
Kind Code:
A3
Abstract:
Disclosed are systems and methods for resequencing using color calls. A DNA sample is encoded and sequenced according to a multi-base code producing a string of read color calls for a fragment of the sample. A reference sequence is obtained. The string of read color calls is mapped to the reference sequence. A base sequence is extracted from the reference sequence. The base sequence is encoded as a string of reference color codes according to the multi-base code. The string of read color calls is aligned with the string of reference color codes and mismatches in the alignment are detected. One or more mismatches of the string of read color calls are annotated as inconsistent. The one or more inconsistent mismatches of the string of read color calls are corrected. The string of corrected read color calls is decoded to bases producing a read sequence.
Inventors:
BREU HEINZ (US)
GUO DANWEI (US)
GUO DANWEI (US)
Application Number:
PCT/US2011/036393
Publication Date:
April 19, 2012
Filing Date:
May 13, 2011
Export Citation:
Assignee:
LIFE TECHNOLOGIES CORP (US)
BREU HEINZ (US)
GUO DANWEI (US)
BREU HEINZ (US)
GUO DANWEI (US)
International Classes:
C12Q1/68; G16B30/10
Domestic Patent References:
| WO2006084132A2 | 2006-08-10 |
Other References:
RUMBLE, S. M. ET AL.: "SHRiMP Accurate mapping of short color-space reads.", PLOS COMPUTATIONAL BIOLOGY, vol. 5, no. ISSUE, 22 May 2009 (2009-05-22), pages E1000385
ONDOV, B. D. ET AL.: "Efficient mapping of applied biosystems SOLiD sequence data to a reference genome for functional genomic applications.", BIOINFORMATICS, vol. 24, no. 23, 7 October 2008 (2008-10-07), pages 2776 - 2777
LI, H. ET AL.: "Mapping short DNA sequencing reads and calling variants using mapping quality scores.", GENOME RESEARCH, vol. 18, 19 August 2008 (2008-08-19), pages 1851 - 1858, XP001503357, doi:10.1101/GR.078212.108
SALMELA, L. ET AL.: "Correction of sequencing errors in a mixed set of reads.", BIOINFORMATICS, vol. 26, no. 10, 8 April 2010 (2010-04-08), pages 1284 - 1290
BREU, H. ET AL.: "A theoretical understainding of 2 base color codes and its application to annotation, error detection, and error corredtion.", July 2010 (2010-07-01), Retrieved from the Internet
ONDOV, B. D. ET AL.: "Efficient mapping of applied biosystems SOLiD sequence data to a reference genome for functional genomic applications.", BIOINFORMATICS, vol. 24, no. 23, 7 October 2008 (2008-10-07), pages 2776 - 2777
LI, H. ET AL.: "Mapping short DNA sequencing reads and calling variants using mapping quality scores.", GENOME RESEARCH, vol. 18, 19 August 2008 (2008-08-19), pages 1851 - 1858, XP001503357, doi:10.1101/GR.078212.108
SALMELA, L. ET AL.: "Correction of sequencing errors in a mixed set of reads.", BIOINFORMATICS, vol. 26, no. 10, 8 April 2010 (2010-04-08), pages 1284 - 1290
BREU, H. ET AL.: "A theoretical understainding of 2 base color codes and its application to annotation, error detection, and error corredtion.", July 2010 (2010-07-01), Retrieved from the Internet
Attorney, Agent or Firm:
SCHELL, David et al. (Attention: IP Department5791 Van Allen Wa, Carlsbad CA, US)
Download PDF: