Patent SG-11201811556R-A (SG)
Title: Methods for fragmentome profiling of cell-free nucleic acids
Inventor: ABDUEVA DIANA
IPC: C12Q1/68
Filed: 2017-07-06
Abstract: INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization 1111111111111111111111111111 11111111111111111111111111111111 0111111101111 0111111 International Bureau (10) International Publication Number (43) International Publication Date .....0\"\" WO 2018/009723 Al 11 January 2018 (11.01.2018) W I PO I PCT (51) International Patent Classification: DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, C12Q 1/68 (2006.01) GOOF 19/22 (2011.01) HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, GO6F 19/18 (2011.01) GO6F 19/24 (2011.01) KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, (21) International Application Number: MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, PCT/US2017/040986 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, (22) International Filing Date: TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. 06 July 2017 (06.07.2017) (84) Designated States (unless otherwise indicated, for every (25) Filing Language: English kind of regional protection available): ARIPO (BW, GH, (26) Publication Language: English GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, (30) Priority Data: TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, 62/359,151 06 July 2016 (06.07.2016) US EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, 62/420,167 10 November 2016 (10.11.2016) US MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, 62/437,172 21 December 2016 (21.12.2016) US TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, 62/489,399 24 April 2017 (24.04.2017) US KM, ML, MR, NE, SN, TD, TG). (71) Applicant: GUARDANT HEALTH, INC. [US/US]; 505 Published: Penobscot Drive, Redwood City, CA 94063 (US). — with international search report (Art. 21(3)) (72) Inventor: ABDUEVA, Diana; 227 Orchard Road, Orinda, CA 94563 (US). = Agent: SKUBATCH, Maya et al.; Wilson Sonsini (74) Goodrich & Rosati, 650 Page Mill Road, Palo Alto, CA 94304-1050 (US). = = Designated States (unless otherwise indicated, for every = (81) 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, = = Title: METHODS FOR FRAGMENTOME PROFILING OF CELL-FREE NUCLEIC ACIDS (54) = = — benign systemic response = _ fENA tumor systemic response = = = th. 4 including bloom =tumor tumor microenvir onment = FIG. 1A Il M N IN (57) : The present disclosure contemplates various uses of cell-free DNA. Methods provided herein may use sequence infor- C:N mation in a macroscale and global manner, with or without somatic variant information, to assess a fragmentome profile that can be © representative of a tissue of origin, disease, progression, etc. In an aspect, disclosed herein is a method for determining a presence or ot .---- absence of a genetic aberration in deoxyribonucleic acid (DNA) fragments from cell-free DNA obtained from a subject, the method Il comprising: (a) constructing a multi-parametric distribution of the DNA fragments over a plurality of base positions in a genome; and C:::: ) (b) without taking into account a base identity of each base position in a first locus, using the multi-parametric distribution to determine ei _ the presence or absence of the genetic aberration in the first locus in the subject.