Patent SG-11201810924W-A (SG)
Title: System and method for secondary analysis of nucleotide sequencing data
Inventor: GARCIA FRANCISCO
IPC: G16B30/10
Filed: 2017-10-06
Abstract: ReceiveImaging Data of a Sequencing Cycle V Determine Bases and Quay Scores for Bases Determined 615 W O 20 18/0680 14 A9 (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) CORRECTED VERSION (19) World Intellectual Property Organization International Bureau (43) International Publication Date 111111111111011010101111101111010 0111011011 101 IIMOEHRM110111 (10) International Publication Number WO 2018/068014 A9 12 April 2018 (12.04.2018) Wi P 0 I PCT START ) - 1 05 (51) International Patent Classification: GO6F 19/18 (2011.01) G06F 19/22 (2011.01) (21) International Application Number: PCT/US2017/055653 (22) International Filing Date: 06 October 2017 (06.10.2017) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/405,824 07 October 2016 (07.10.2016) US (71) Applicant: ILLUMINA, INC. [US/US]; 5200 Illumina Way, San Diego, CA 92122 (US). (72) Inventors: GARCIA, Francisco, Jose; C/o Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122 (US). RACZY, Come; C/o Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122 (US). DAY, Aaron; C/o Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122 (US). CARNEY, Michael, J.; C/o Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122 (US). (74) Agent: FULLER, Michael, L.; Knobbe Martens Olson & Bear LLP, 2040 Main Street, Fourteenth Floor, Irvine, CA 92614 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, (54) Title: SYSTEM AND METHOD FOR SECONDARY ANALYSIS OF NUCLEOTIDE SEQUENCING DATA (57) : Disclosed herein are systems and methods for performing sec- ondary analyses of nucleotide sequencing data in a time-efficient manner. Some embodiments include performing a secondary analysis iteratively while sequence reads are generated by a sequencing system. Secondary analyses can encompass both alignment of sequence reads to a reference sequence (e.g., the human ref- erence genome sequence) and utilization of this alignment to detect differences between a sample and the reference. Secondary analysis can enable detection of genetic differences, variant detection and genotyping, identification of sin- gle nucleotide polymorphisms (SNPs), small insertions and deletion (indels) and structural changes in the DNA, such as copy number variants (CNVs) and chro- Ye 620 mosomal rearrangements. Perform AI gnment 625 Perform Valiant Calling 630 Yes 635 No ( End )1 40 FIG. 6 [Continued on next page] WO 2018/068014 A9 11111111111111011101111111111101111101001110111111011111010111111111011111101111 TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Published: with international search report (Art. 21(3)) with information concerning authorization of rectification of an obvious mistake under Rule 91.3 (b) (Rule 48.2(0) (48) Date of publication of this corrected version: 30 August 2018 (30.08.2018) (15) Information about Correction: see Notice of 30 August 2018 (30.08.2018)