Patent SG-11201910046S-A (SG)
Title: Process for aligning targeted nucleic acid sequencing data
Inventor: BEAN GORDON JEFF
IPC: G07D11/28
Filed: 2019-01-07
Abstract: INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 11 July 2019 (11.07.2019) WIPO I PCT 11111111111110111111111111111101111101011111111011111111011111111111111111011110111111 (10) International Publication Number WO 2019/136364 Al (51) International Patent Classification: G16B 25/20 (2019.01) GI6B 30/10 (2019.01) (21) International Application Number: PCT/US2019/012511 (22) International Filing Date: 07 January 2019 (07.01.2019) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/614,088 05 January 2018 (05 01 2018) US (71) Applicant: ILLUMINA, INC. [US/US]; 5200 Illumina Way, San Diego, California 92122 (US). (72) Inventors: BEAN, Gordon Jeff; 5200 Illumina Way, San Diego, California 92122 (US). BRUAND, Jocelyn; 5200 Illumina Way, San Diego, California 92122 (US). KEL- LEY, Ryan Matthew; 5200 Illumina Way, San Diego, Cal- ifornia 92122 (US). LEE, Chih; 5200 Illumina Way, San Diego, California 92122 (US). EMIG-AGIUS, Dorothea Margherita; 5200 Illumina Way, San Diego, California 92122 (US). ALLEN, Eric; 5200 Illumina Way, San Diego, California 92122 (US). SUN, Youting; 5200 Illumina Way, San Diego, California 92122 (US). (74) Agent: SHEEHAN, Teige P.; Heslin Rothenberg Farley & Mesiti P.C., 5 Columbia Circle, Albany, New York 12203 (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. (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, 1E, 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). (54) Title: PROCESS FOR ALIGNING TARGETED NUCLEIC ACID SEQUENCING DATA Generate target sequences amplifiable from transcript sequences Receive sequence reads (57) : Provided is a computer-implemented method of aligning RNA including receiving onto a data storage unit primer sequences and transcript sequences transcribable from a reference genome based on a gene model, generating target sequences to be amplified from a combination of the primer sequences and the tran- script sequences, generating a modified reference genome based on 2620 the plurality of target sequences, aligning sequence reads generated from a test sample comprising RNA amplicon molecules to the of target sequences, and generating an alignment profile for the test sample based on the aligning Also provided is a computer system for performing the foregoing method. 4— 2640 Receive primer sequences and transcript sequences from reference genome 4— 2610 2600 Generate modified reference genome from amplifiable target sequences 4— 2530 W O 20 19/ 13636 4 Al Align sequence reads with modified reference genome Generate alignment profile FIG. 26 1 — 2650 1- 2660 [Continued on next page] WO 2019/136364 Al I IllIl 111111110111111 II III 11111 II 111 1101 II 111 OM Dill IIIII Dill 1101 HIME1111111111111 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))