Patent SG-11201909697T-A (SG)
Title: Optimal index sequences for multiplex massively parallel sequencing
Inventor: KELLEY RYAN
IPC: C12Q1/6869
Filed: 2018-05-01
Abstract: INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 08 November 2018 (08.11.2018) WIPO I PCT ~~ll~~~~~~~~ 011101010VIIIOH olo oi olo Ho °moo mom ow (10) International Publication Number WO 2018/204423 Al (51) International Patent Classification: C12Q 1/6869 (2018.01) Cl 2N 15/10 (2006.01) GOOF 19/22 (2011.01) (21) International Application Number: PCT/US2018/030539 (22) International Filing Date: 01 May 2018 (01.05.2018) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/492,851 01 May 2017 (01.05.2017) US 62/524,390 23 June 2017 (23.06.2017) US (71) Applicant: ILLUMINA, INC. [US/US]; 5200 Illumina Way, San Diego, California 92122 (US). (72) Inventors: KELLEY, Ryan; 5200 Illumina Way, San Diego, California 92122 (US). BEAN, Gordon; 5200 Illu- mina Way, San Diego, California 92122 (US). VERMAAS, Eric; 5200 Illumina Way, San Diego, California 92122 (US). (74) Agent: ZHOU, Feng et al.; WEAVER AUSTIN VIL- LENEUVE & SAMPSON LLP, P.O. Box 70250, Oakland, California 94612-0250 (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, 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). (54) Title: OPTIMAL INDEX SEQUENCES FOR MULTIPLEX MASSIVELY PARALLEL SEQUENCING (57) : The disclosed embodiments concern index oligonucleotides con- 400 figured to identify sources of samples of nucleic acids and methods, apparatus, sys- 402 , tems and computer program products for identifying and making the index oligonu- cleotides. In some implementations, the index oligonucleotides include a set of in- 404 dex sequences, a Hamming distance between any two index sequences of the set of index sequences meeting one or more criteria. System, apparatus, and computer 406 program products are also provided for determining a sequence of interest using the index oligonucleotides. Add the pair of color-balanced sequences to a candidate set and remove. the pair from the pool Sort index scecences remaining in the pool of index sequences based on minimum Hamming distance to members in the candidate not Remove any remaining index sapience whose minimum Hamming distance to the members in the candidate set is less than a first criterion value or minimum edit distance to the members in the candidate set is Ices than a third criterion Making Index Oligonueleotides Provide a pool of all possible n-rear sequences ibsee of in dorsequences from th po nd Randomlyoose a pair of color-balanced sequences from the pool f soquoncos 408 - 410 — 412 Arty Seigtenceilefthl Yes -ILle P. 01 7— No Separate the candidate set into a plurality of groups of color-balanced pairs Partition each group into two subgroups of color- balanced pairs using a bipanite graph matching algorithm. each color-balanced pair being a node in the bipartite graph Synthesize a plurality of oligonucleotides, wherein each oligonucleotide has at least one index sequence in the candidate set W O 20 18/ 20 4423 Al 416 — 418 420 - - Figure 5 414 [Continued on next page] WO 2018/204423 Al MIDEDIMOMMIONEIEHIMINHOEHMEHMOVOE# Declarations under Rule 4.17: as to applicant's entitlement to apply for and be granted a patent (Rule 4.17(11)) as to the applicant's entitlement to claim the priority of the earlier application (Rule 4.17(iii)) Published: — with international search report (Art. 21(3)) with sequence listing part of description (Rule 5.2(a))