Patent SG-11201903272X-A (SG)
Title: Method and systems for the representation and processing of bioinformatics data using reference sequences
Inventor: ALBERTI CLAUDIO
IPC: G16B45/00
Filed: 2017-07-11
Abstract: INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property 1111111111111 0 11011111111111 OH 10 1 0 1111111 1111 010 111110111111110 1110111111 Organization International Bureau (10) International Publication Number (43) International Publication Date .....0\"\" WO 2018/071080 A2 19 April 2018 (19.04.2018) WIP0 1 PCT (51) International Patent Classification: (74) Agent: BILICKI, Byron et al.; The Bilicki Law Firm, P.C., GOOF 19/20 (2011.01) 1285 North Main Street, Jamestown, NY 14701 (US). (21) International Application Number: (81) Designated States (unless otherwise indicated, for every PCT/US2017/041591 kind of national protection available): AE, AG, AL, AM, (22) International Filing Date: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, 11 July 2017 (11.07.2017) 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, (25) Filing Language: English HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, (26) Publication Language: English 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, (30) Priority Data: OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, PCT/EP2016/074311 SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 11 October 2016 (11.10.2016) EP TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. PCT/EP2016/074297 (84) Designated States (unless otherwise indicated, for every 11 October 2016 (11.10.2016) EP kind of regional protection available): ARIPO (BW, GH, PCT/EP2016/074307 GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, 11 October 2016 (11.10.2016) EP UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, PCT/EP2016/074301 — 11 October 2016 (11.10.2016) EP TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, PCT/US2017/017841 EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, 14 February 2017 (14.02.2017) US MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, PCT/US2017/017842 TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). 14 February 2017 (14.02.2017) US = Applicant: GENOMSYS SA [CH/CH]; chemin de la Raye Declarations under Rule 4.17: (71) = 13, 1024 Ecublens VD (CH). — as to the identity of the inventor (Rule 4.17(i)) (72) Inventor; and Published: (71) Applicant: BALUCH, Mohamed, Khoso [US/US]; 4439 — without international search report and to be republished Woodsedge Ct, Chantilly, VA 20151 (US). upon receipt of that report (Rule 48.2(g)) = Inventors: ALBERTI, Claudio; Chemin des Esserts 1, = (72) — 1213 Petit-Lancy (CH). ZOIA, Giorgio; Chemin des Croix- = Rouges 10, 1007 Lausanne (CH). RENZI, Daniele; Route Aloys-Fauquez 105, 1018 Lausanne (CH). = = = Title: METHOD AND SYSTEMS FOR THE REPRESENTATION AND PROCESSING OF BIOINFORMATICS DATA (54) = USING REFERENCE SEQUENCES = = The left-most read has N alignments The right-most read has M alignments = • ' / •-.. _ N, / / Reference <= Ili a, b, aN, bm GC 0 11 Figure 15. IN © . - 6,-- t) (57) : Method and apparatus for the representation and processing of genome sequence data, produced by genome sequencing 1-1 machines, when aligned on one or more reference sequences. Sequence reads are coded by aligning them with respect to pre-existing or constructed reference sequences. After the alignment, the coding process is composed of a classification of the reads into data classes, ei followed by the coding of each data class in terms of a multiplicity of descriptors layers. Specific source models and entropy coders 0 are used for the coding of the sub-sets of descriptors used to represent each data class.