Patent SG-11201907415S-A (SG)
Title: Method and systems for the reconstruction of genomic reference sequences from compressed genomic sequence reads
Inventor: ALBERTI CLAUDIO
Filed: 2017-12-14
Abstract: Genomicsequences mapped on the reference genome Contig constructed from the mapped sequences Differences with respect to the reference gen ome . 47 505 504 T AC CfiTCG GT AC G G Entropy coding of genomic descriptors for reads Entropy coding of positions and type of differences ••••i 503 (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 IiiimmommionotiolomolEmoloitioiliflovoimIE (10) International Publication Number WO 2018/151786 Al N 501 M n 502 (51) International Patent Classification: C4OB 50/02 (2006.01) G06F 19/22 (2011.01) G06F 19/26 (2011.01) (21) International Application Number: PCT/US2017/066458 (22) International Filing Date: 14 December 2017 (14.12.2017) (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 (CH). (72) Inventor; and (71) Applicant: BALUCH, mohamed khoso [US/US]; 4439 Woodsedge Ct., Chantilly, Virginia 20151 (US). (72) Inventor: ALBERTI, Claudio; chemin des Esserts 1, 1213 petit-lancy (CH). (74) Agent: BILICKI, Byron et al.; The Bilicki Law Firm, P.C., 1285 North Main Street, JAMESTOWN, New York 14701 (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, (54) Title: METHOD AND SYSTEMS FOR THE RECONSTRUCTION OF GENOMIC REFERENCE SEQUENCES FROM COM- = PRESSED GENOMIC SEQUENCE READS Genomic sequences generated by sequencing devices Reference genome T AGT AC AGTCGC GT AC GAGGTC Figure 5. (57) : The method and apparatus described in this disclosure include representing a reference genome in terms of syntax elements describing the differences between said reference genome and previously aligned genomic sequences. Each of the aligned genomic sequence is described by means of a subset of syntax elements. Syntax elements describing all the genomic sequences are partitioned in blocks according to their statistical properties. Each block of syntax elements is entropy coded. The entropy coded blocks are then concatenated to form a compressed bitstream. The differences between the reference genome and the aligned sequences are expressed in terms of syntax elements, which are embedded in the bitstream of coded blocks of syntax elements describing aligned reads. The disclosed method enables the reconstruction of the reference genome used for alignment when decoding the compressed genomic sequences while preserving different options of random access on the compressed data and enabling efficient compression. [Continued on next page] WO 2018/151786 Al MIDEDIMOMMIONER1311011010MMOVOIMIE 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, 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))