Patent SG-11201807117W-A (SG)
Title: Generation of phased read-sets for genome assembly and haplotype phasing
Inventor: GREEN RICHARD E
IPC: C40B40/08
Filed: 2017-02-23
Abstract: INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization 11111111011110111010101111101011111011101011101111101011111101111101111011111 International Bureau ... ...... (10) International Publication Number (43) International Publication Date ..... ...r .....1 WO 2017/147279 Al 31 August 2017 (31.08.2017) WI PO I PCT (51) International Patent Classification: (72) Inventors: GREEN, Richard E., Jr.; 223 Wavecrest Av- C12Q 1/68 (2006.01) C40B 40/08 (2006.01) enue, Santa Cruz, California 95060 (US). ROKHSAR, C40B 30/04 (2006.01) Daniel S.; 15 Norwood Avenue, Kensington, California (21) International Application Number: 94707 (US). HARTLEY, Paul; 4265 Mountcastle Way, PCT/US2017/019099 San Jose, California 95136 (US). BLANCHETTE, Marco; 707 Pelton Avenue, Apt. 307, Santa Cruz, Califor- (22) International Filing Date: nia 95060 (US). 23 February 2017 (23.02.2017) (74) Agent: ANDERSON, Garrett H.; Wilson Sonsini (25) Filing Language: English Goodrich & Rosati, 650 Page Mill Road, Palo Alto, Cali- fornia 94304 (US). (26) Publication Language: English (81) Designated States (unless otherwise indicated, for every (30) Priority Data: kind of national protection available): AE, AG, AL, AM, 62/298,906 23 February 2016 (23.02.2016) US AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, 62/298,966 23 February 2016 (23.02.2016) US BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, 62/305,957 9 March 2016 (09.03.2016) US DO, DZ, EC, EE, EG, ES, FL GB, GD, GE, GH, GM, GT, (71) Applicant: DOVETAIL GENOMICS LLC [US/US]; HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KH, KN, 2161 Delaware Avenue, Suite A2, Santa Cruz, California KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, 95060 (US). 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, [Continued on next page] (54) Title: GENERATION OF PHASED READ-SETS FOR GENOME ASSEMBLY AND HAPLOTYPE PHASING (57) Sample 1 Sample 2 and systems that facilitate accurate phasing of sequence data such : Disclosed herein are methods, compositions as genomic sequence data through the segmentation and rearrangement of nucleic acid molecules in such a way as to BF AF BF AF preserve individual molecules phase or physical linkage in- formation. This is variously accomplished by binding mo- lecules independent of their phosphodiester backbones, cleaving the molecules, ligating, and sequencing the mo- lecules through long-read sequencing technology to recover segment sequence information spanning at least more than one segment. ,-1 C:r IN ei IN ii- 1-1 FIG. 7 IN 1-1 0 ei C WO 2017/147279 Al 1#1110111011101011MMEMOMMHOHNEHOMOVOIS TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, Declarations under Rule 4.17: VN, ZA, ZM, ZW. — as to applicant's entitlement to apply for and be granted (84) Designated States (unless otherwise indicated, for every a patent (Rule 43 7(ii)) kind of regional protection available): ARIPO (BW, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, GH, SZ, as to the applicant's entitlement to claim the the earlier application (Rule 4.17(iii)) priority of TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, Published: DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, LT, SE, GA, with international search report (Art. 21(3)) GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG).