Patent SG-11201407888R-A (SG)
Title: Method of sequence determination using sequence tags
Inventor: FAHAM MALEK
IPC: C12Q1/68
Filed: 2013-06-11
Abstract: (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 19 December 2013 (19.12.2013) WIPOIPCT (10) International Publication Number WO 2013/188471 A2 (51) International Patent Classification: C12Q 1/68 (2006.01) (21) International Application Number: (22) International Filing Date: (25) Filing Language: (26) Publication Language: PCT/US2013/045276 11 June 2013 (11.06.2013) English English (30) Priority Data: 61/658,317 61/738,277 61/776,647 13/835,093 61/829,054 11 June 2012 (11.06.2012) US 17 December 2012 (17.12.2012) US 11 March 2013 (11.03.2013) US 15 March 2013 (15.03.2013) US 30 May 2013 (30.05.2013) US (71) Applicant (72) Inventors; and (71) Applicants (for all designated States except US): SE- QUENTA, INC. [US/US]; 400 East Jamie Court, Suite 301, South San Francisco, CA 94080 (US). (for US only): FAHAM, Malek [US/US]; 400 East Jamie Court, Suite 301, South San Francisco, CA 94080 (US). MOORHEAD, Martin [CH/US]; 400 East Jamie Court, Suite 301, South San Francisco, CA 94080 (US). WILLIS, Thomas [US/US]; 400 East Jamie Court, Suite 301, South San Francisco, CA 94080 (US). ZHENG, Jianbiao [US/US]; 400 East Jamie Court, Suite 301, South San Francisco, CA 94080 (US). (74) Agents: EASTERDAY, Mathew et al.; Wilson Sonsini Goodrich & Rosati, 650 Page Mill Road, Palo Alto, CA 94304-1050 (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, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KN, KP, KR, KZ, LA, LC, LK, LR, LS, LT, 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, 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, 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, [Continued on next page] (54) Title: METHOD OF SEQUENCE DETERMINATION USING SEQUENCE TAGS 1 dA incorporated Wash (414) , dGTPAddition (416) CJ i-H l> •t 00 00 i-H en i-H o CJ o & 1 dG incorporated 0 dC incorporated Wash (422) dTTP Addition (424) Fig. 4A (57) Abstract: The invention is directed to the use of sequence tags to im­ prove sequence determination of amplicons of related sequences, particularly large and complex amplicons, such as those comprising recombined nucleic acids encoding immune receptor molecules. In one aspect, sequence reads having the same sequence tags are aligned after which final base calls are de­ termined from a (possibly weighted) average base call from sequence read base calls at each position. Similarly, in another aspect, sequence reads com­ prising series of incorporation signals are aligned by common sequence tags and base calls in homopolymer regions are made as a function incorporation signal values each at \"flow\" position. WO 2013/188471 A2 I lllll llllllll II llllll III lllll lllll III III III lllll lllll lllll llll llll lllll lllll lllllll llll llll MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Published: — without international search report and to be republished upon receipt of that report (Rule 48.2(g)) — with sequence listing part of description (Rule 5.2(a))