Patent SG-11201806757X-A (SG)
Title: Systems, methods, and media for de novo assembly of whole genome sequence data
Inventor: JAFFE DAVID
IPC: G01N33/68
Filed: 2016-08-19
Abstract: INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2017/138984 Al 17 August 2017 (17.08.2017) WIPO I PCT 1111111111111101110111111111110101111101111111101111101111111101111111111111110111111 (51) International Patent Classification: C12Q 1/68 (2006.01) C4OB 50/16 (2006.01) C12P 19/34 (2006.01) G01N 33/68 (2006.01) C04B 40/06 (2006.01) (21) International Application Number: PCT/US2016/047899 (22) International Filing Date: 19 August 2016 (19.08.2016) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/294,184 11 February 2016 (11.02.2016) 62/332,914 6 May 2016 (06.05.2016) (71) Applicant: 10X GENOMICS, INC. [US/US]; 7068 Koll Center Parkway, Suite 401, Pleasanton, CA 94566 (US). (72) Inventors: JAFFE, David; 3517 Touriga Drive, Pleas- anton, CA 94566 (US). MARKS, Patrick; 760 Treat Street #1, San Francisco, CA 94110 (US). SCHNALL- LEVIN, Michael; 3945 20th Street #4, San Francisco, CA 94114 (US). WEISENFELD, Neil; 103 Lowell Road, Apt. 301, North Reading, MA 01864 (US). (74) Agents: LAM, Amy 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, IR, IS, JP, KE, KG, KN, KP, KR, 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. 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, 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)) US US (84) (54) Title: SYSTEMS, METHODS, AND MEDIA FOR DE NOVO ASSEMBLY OF WHOLE GENOME SEQUENCE DATA ill •1 , :e2, J79.023- , E! EJA, , ,,,Avv...k4AAAAAJoill.\"4.4.4CC\"CTCA;TC7TCAVACCAGT - TCAAA.4\" , :l: 4-,. .TATIITTA,A TAMA 1.A.A:,AAAAAPJAAAAAAAAAAAAI ( TrAvr. - 11.514 . I AAAATAr. 1G1' T :II.. 7 .450 waIng 055e$l IGACTCCUCAAAA' , AAA , AAA , A.VJAAATAAA ,, AAA WTAAAVAVAAAT.l.,,C.,C4. 4 .4.1' 4 '\"AT TCCATCA AAPA.Al.\"4....:4.TA',.47.4.41, , AAA , AAATAAArAAA , AAATAAAC,:s6AAAMTAT 1440 Tae: , :ilg bassi , :c. , ,,y,cYGTAArCATAACTTACTGC.CLITTGAATTCCI\"-iaA \"LAACIWTCCV. '7(.1.CCT , 79C., ..44GTAA1CA AAC ! A'. I l,CA likA Hill!! . CACl:AGCTCOGATTA::•45 '4 , \"A.TrcA.cct.ac,.kiitc.wicTuti ilmiGTAGA4n.\").GGC:T17170:7710 -7 '\" i C. I CAAAl. r4; • I I.AAA(. , :,(. I Cll;iA: !ALA.* ill ll . .. . AUCTC4 T• 4-1( 4CAGAC.I7CIACTATCTGTAA ITTCACA AGGC.CTICATTCIT ICACCTATAAA ill! I i I li!li I: I t 1111 ' •i, •1 11 .11 (57) : Described are computer-implemented methods, systems, and media for de novo phased diploid assembly of nucleic acid sequence data generated from a nucleic acid sample of an individual utilizing nucleic acid tags to preserve long-range sequence context for the individual such that a subset of short-read sequence data derived from a common starting sequence shares a common tag. The phased diploid assembly is achieved without alignment to a reference sequence derived from organisms other than the in- dividual. The methods, systems, and media described are computer-resource efficient, allowing scale-up. W O 20 17 / 13898 4 Al I AA I MAA,AAAA1A AAA , ' (AGC.xl,A1 • 4/..Th.TAATICAl,01:1AALVATAI' l.AAti ITTAAATUTA...\"CAAAP.014:11.CCATTAA HA( AMIGAA.SIMCO:. inn 1•Alld! iiir A AS.AS •410A.4.1:AAAl f:ALAA I MU. A HAW C.: l'I'll(CT(..CTICAT:371GTAATA , TTCTTRIGINAUCCAAlie'CCAVTVICA.CACriVO.'.00.7. , :77tiC X1 5 : A1461 , \" 1GTICTGLI , AAC.7 - :,: \"A. lTITTAAAA,... AA LIG,A : E : I cAG6T4:T ,- C1G77CTGTATAP,C , ..Z.7 , -, - . - arTinkAaMMTV.:007 , A.A;, 211 matchirr, '7,05 FIG. 1