SG11201811159SA - Methods for multi-resolution analysis of cell-free nucleic acids - Google Patents

Abstract

Uniq ue mo lecu le cou n t () INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 05 April 2018 (05.04.2018) WIP0 I PCT olimion °nolo III oiloo VIII imio oimIE (10) International Publication Number WO 2018/064629 Al (51) International Patent Classification: C12Q 1/68 (2018.01) (21) International Application Number: PCT/US2017/054607 (22) International Filing Date: 29 September 2017 (29.09.2017) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/402,940 30 September 2016 (30.09.2016) US 62/468,201 07 March 2017 (07.03.2017) US 62/489,391 24 April 2017 (24.04.2017) US (71) Applicant: GUARDANT HEALTH, INC. [US/US]; 505 Penobscot Drive, Redwood City, CA 94063 (US). (72) Inventors: CHUDOVA, Darya; 5931 Taormino Avenue, San Jose, CA 95123 (US). ELTOUKHY, Helmy; 2 Barry Lane, Atherton, CA 94027 (US). MORTIMER, Stefanie Ann, Ward; 2000 Willow Springs Road, Morgan Hill, CA 95037 (US). ABDUEVA, Diana; 227 Orchard Road, Orin- da, CA 94563 (US). SIKORA, Marcin; 505 Penobscot Dri- ve, Redwood City, CA 94063 (US). (74) Agent: AMODEO, Gabriele, A. et al.; Wilson Sonsini Goodrich & Rosati, 650 Page Mill Road, Palo Alto, CA 94304-1050 (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. (54) Title: METHODS FOR MULTI-RESOLUTION ANALYSIS OF CELL-FREE NUCLEIC ACIDS 0.2X 0.8X 3X 5X 12X FIG. 6 (57) : The present disclosure provides a method for enriching for multiple genomic regions using a first bait set that selectively hybridizes to a first set of genomic regions of a nucleic acid sample and a second bait set that selectively hybridizes to a second set of genomic regions of the nucleic acid sample. These bait set panels can selectively enrich for one or more nucleosome-associated regions of a genome, said nucleosome-associated regions comprising genomic regions having one or more genomic base positions with differential nucleosomal occupancy, wherein the differential nucleosomal occupancy is characteristic of a cell or tissue type of origin or disease state. [Continued on next page] WO 2018/064629 Al MIDEDIMOMMIDIIMERIONIMMIEIDEICHINVOIMIE (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)) with sequence listing part of description (Rule 5.2(a))