Patent SG-11201900253T-A (SG)
Title: Method and system for microbial pharmacogenomics
Inventor: APTE ZACHARY
IPC: A61K35/74
Filed: 2017-07-13
Abstract: INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) -., (19) World Intellectual Property MD HIM 01110101011111 3E1 0 10111110111 OM 11111H10111111011110111111 Organization . International Bureau (10) International Publication Number (43) International Publication Date ......'\"' WO 2018/013865 Al 18 January 2018 (18.01.2018) W I P0 I PC T (51) International Patent Classification: (74) Agent: SCHOX, Jeffrey; 500 3rd Street, Suite 215, San A61B 5/00 (2006.01) A61K 35/74 (2015.01) Francisco, CA 94107 (US). (21) International Application Number: (81) Designated States (unless otherwise indicated, for every PCT/US2017/042015 kind of national protection available): AE, AG, AL, AM, (22) International Filing Date: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, 13 July 2017 (13.07.2017) 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, (25) Filing Language: English HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, (26) Publication Language: English 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, (30) Priority Data: OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, 62/361,943 13 July 2016 (13.07.2016) US SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 15/606,743 26 May 2017 (26.05.2017) US TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (71) Applicant: UBIOME, INC. [US/US]; 360 Langton Street, (84) Designated States (unless otherwise indicated, for every #301, San Francisco, CA 94103 (US). kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, (72) Inventors: APTE, Zachary; 360 Langton Street, #301, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, San Francisco, CA 94103 (US). RICHMAN, Jessica; 360 TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, Langton Street, #301, San Francisco, CA 94103 (US). EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, — ALMONACID, Daniel; 360 Langton Street, #301, San MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, Francisco, CA 94103 (US). PEDROSO, Inti; 360 Lang- TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, = ton Street, #301, San Francisco, California 94103 (US). KM, ML, MR, NE, SN, TD, TG). _ UGALDE, Juan; 360 Langton Street, #301, San Francis- = co, California 94103 (US). ORTIZ, Rodrigo; 360 Langton Published: — Street, #301, San Francisco, California 94103 (US). — with international search report (Art. 21(3)) = = = (54) Title: METHOD AND SYSTEM FOR MICROBIAL PHARMACOGENOMICS = 00 (57) : Embodiments of a method and system for microbial pharma- — 1 — \...\"-\ cogenomics can include: a sample handling system operable to collect contain- ers including biological samples from a set of users, the handling system includ- = = — ta set determining at least one of a microbiome pharmacogenomics da microbiome composition dataset, and a microbiome functional diversity dataset based on processing biological samples associated with a set of users S110 —de- ing a sequencing system operable to determine microorganism sequences from the biological samples; a microbiome characterization system operable to: terrine microbiome pharmacogenomics data based on the microorganism se- = — quences, collect supplementary data associated with the antibiotics- associated = processing a supplementary dataset informative of the antibiotics- associated condition for the set of users S120 condition for the set of users, and transform the supplementary data and features = i extracted from the microbiome pharmacogenomics data into a characterization = = _ — performing a characterization process associated with the antibiotics-associated condition based on the supplementary dataset and features extracted from the at least one of the microbiome 4.. pharmacogenomics dataset, the i m crobiome composition dataset. and the microbiome functional diversity . dataset Si 30 determining a treatment configured to modulate microorganism abundance, distributions, functional diversity and/ or pharmacogenomics diversity in subjects characterized according to the characterization model associated with the antibiotics-associated condition; and a treatment sys- tem operable to promote a treatment to the user for the antibiotics-associated condition based on characterizing user biological material with the characteriza- . F tion model in relation to the antibiotics-associated condition. It ir) GC M It © r.„.... GC li © N processing a biological sample from . , a subject S150 i identifying a characterization of the user in relation to the antibiotics-associated condition based upon processing at least one of a user microbiome pharmacogenomics dataset, a user morobioroe composition dataset, and a user microbiome functional diversity dataset derived from the biological sample from the user, with the characterization process 6160 — monitoring effectiveness of a treatment for points, based upon processing biological samples, a microbiome pharmacogenomics profile, microbiome composition, mIcroblome functional diversity FIGURE 1A 4 the P rocess S140 P promoting a the subject based upon 1 subject at different time to assess at least one of 5180 the characterization 5170 i treatment to X and r O