Patent SG-11201811504P-A (SG)
Title: Single cell whole genome libraries and combinatorial indexing methods of making thereof
Inventor: STEEMERS FRANK
IPC: C12N15/10
Filed: 2017-07-21
Abstract: Provide isolated nuclei 1 13 Deplete nucleosomes Distribute subsets of nucleosome- depleted nuclei {Index nuclei by tagmentation 14 15 17 W O 20 18/0 18008 Al (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 25 January 2018 (25.01.2018) WIP0 I PCT 0111111010 0111 °nolo ommolmoilommionio oimIE (10) International Publication Number WO 2018/018008 Al (51) International Patent Classification: Cl 2N 15/10 (2006.01) (21) International Application Number: PCT/US2017/043381 (22) International Filing Date: 21 July 2017 (21.07.2017) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/365,916 22 July 2016 (22.07.2016) US 62/451,305 27 January 2017 (27.01.2017) US (71) Applicants: OREGON HEALTH & SCIENCE UNIVERSITY [US/US]; 3181 S.W. Sam Jackson Park Road, Portland, OR 97239 (US). ILLUMINA, INC. [US/US]; 5200 Illumina Way, San Diego, CA 92122 (US). (72) Inventors; and (71) Applicants: ADEY, Andrew, C. [US/US]; 3181 S.W. Sam Jackson Park Road, Portland, OR 97239 (US). VITAK, Sarah, A. [US/US]; 3181 S.W. Sam Jackson Park Road, Portland, OR 97239 (US). (72) Inventor: STEEMERS, Frank, J.; 5200 Illumina Way, San Diego, CA 92122 (US). (74) Agent: PROVENCE, David, L.; Mueting, Raasch & Gebhardt, P.A., P.O. Box 581336, Minneapolis, MN 55458-1336 (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, (54) Title: SINGLE CELL WHOLE GENOME LIBRARIES AND COMBINATORIAL INDEXING METHODS OF MAKING = THEREOF (57) : Provided herein are methods for preparing a se- quencing library that includes nucleic acids from a plurality of single cells. In one embodiment, the sequencing library includes whole genome nucleic acids from the plurality of single cells. In one embodiment, the method includes generating nucleosome-de- pleted nuclei by chemical treatment while maintaining integrity of the nuclei. Also provided herein are compositions, such as compo- sitions that include chemically treated nucleosome-depleted isolat- ed nuclei. 16 Pool and distribute indexed nuclei Index fragments by PCR or adapter ligation 18 Immobilize library and sequence FIG. 1 [Continued on next page] WO 2018/018008 Al MIDEDIMOMMIDIREIDINIROMMIEHMEMOIMIE 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)) with sequence listing part of description (Rule 5.2(a))