SG11201907417WA - Method and systems for the efficient compression of genomic sequence reads - Google Patents

Abstract

rodIng rarrcters 1312 1304 305 1 bete once based alagoress4 f. \"2 , 11 (descr;pcors1 generator. C '77 3 , igr , ,mnts 1311 (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 23 August 2018 (23.08.2018) WIP0 I PCT O V SID o OH Em VIII VII IE (10) International Publication Number WO 2018/151788 Al (51) International Patent Classification: C4OB 50/02 (2006.01) GOOF 19/22 (2011.01) GOOF 19/26 (2011.01) (21) International Application Number: PCT/US2017/066863 (22) International Filing Date: 15 December 2017 (15.12.2017) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: PCT/US2017/017842 14 February 2017 (14.02.2017) US PCT/US2017/041579 11 July 2017 (11.07.2017) US (71) Applicant: GENOMSYS SA [CH/CH]; Chemin de la Raye 13, 1024 Ecublens VD (CH). (72) Inventor; and (71) Applicant: BLAUCH, Mohamed, Khoso [US/US]; 4439 Woodsedge Ct, Chantilly, VA 20151 (US). (72) Inventor: ALBERTI, Claudio; Chemin des Esserts 1, 1213 Petit-Laney (Geneva) (CH). (74) Agent: BILICKI, Byron et al.; 1285 North Main St, Jamestown, NY 14750 (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. (54) Title: METHOD AND SYSTEMS FOR THE EFFICIENT COMPRESSION OF GENOMIC SEQUENCE READS 1309 a ding parameter.e.ncotie, Boad.tion Rinnnzation Binanzation —` ti `AI >inorintion ender Binallzatiop Entropy coder Binatt,ation —' Entropy Binaribdio ntrnp coder Entropy coder 1307 I nd Figure 13. (57) : Method and apparatus for the compression of genome sequence data produced by genome sequencing machines. Se- quence reads are coded by aligning them with respect to pre-existing or constructed reference sequences, the coding process is composed of a classification of the reads into data classes followed by the coding of each class in terms of a multiplicity of genomic descriptors. Genomic descriptors of the same type are organized in blocks which are compressed by applying successive transformation stages, bi- narization and entropy coding. Specific source models and entropy coders are used for each data class and for each associated descriptor. [Continued on next page] WO 2018/151788 Al MIDEDIMOMMIDIREEM3111111111111111111111101111111111111111111 (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, 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)) before the expiration of the time limit for amending the claims and to be republished in the event of receipt of amendments (Rule 48.2(h))