Patent SG-11201901730Q-A (SG)
Title: Method and system for crispr-based library preparation and sequencing
Inventor: APTE ZACHARY
IPC: G06G7/58
Filed: 2017-09-27
Abstract: ligatingthe set of end regions with a set of adapters sharing an adapter sequence amplifying the set of targets based on the ligated set of end regions and a set of primers sharing a primer sequence associated with the adapter sequence — S - S140 performing a characterization process for at least one of microbiome composition, microbiome functional diversity and/or an associated condition based on a microbiome dataset derived from the amplification of the set of targets 5150 promoting a therapy for the user based on the characterization process 5160 W O 20 18/06 4226 Al (12) 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) WIPO I PCT °Ens °nolo omoiloomiomomomovoimill (10) International Publication Number WO 2018/064226 Al generating guide RNA (gRNA) complexes for a set of targets corresponding to a set of taxa associated with the microorganism- related condition processing a biological sample with the gRNA complexes to generate microorganism nucleic acid fragments including a set of end regions associated with the set of targets (22) International Filing Date: 27 September 2017 (27.09.2017) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/400,401 27 September 2016 (27.09.2016) US (71) Applicant: UBIOME, INC. [US/US]; 360 Langton Street, #301, San Francisco, CA 94103 (US). (72) Inventors: APTE, Zachary; 360 Langton Street, #301, San Francisco, CA 94103 (US). RICHMAN, Jessica; 360 Langton Street, #301, San Francisco, CA 94103 (US). AL- MONACID, Daniel; 360 Langton Street, #301, San Fran- sisco, CA 94103 (US). ORTIZ, Rodrigo; 360 Langton Street, #301, San Francisco, CA 94103 (US). GODDARD, Audrey; 360 Langton Street, #301, San Francisco, CA 94103 (US). BIRD, Sara; 360 Langton Street, #301, San Francisco, CA 94103 (US). MORALES, Eduardo; 360 Langton Street, #301, San Francisco, CA 94103 (US). (74) Agent: SCHOX, Jeffrey; 500 3rd Street, Suite 215, San Francisco, CA 94107 (US). 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). (51) International Patent Classification: C12Q 1/68 (2018.01) GOOF 19/28 (2011.01) G01N 33/48 (2006.01) G06G 7/58 (2006.01) GOOF 19/00 (2018.01) (21) International Application Number: PCT/US2017/053822 (81) (54) Title: METHOD AND SYSTEM FOR CRISPR-BASED LIBRARY PREPARATION AND SEQUENCING (57) : Embodiments of a method and system for improved mi- loo crobiome sequencing can include: generating guide RNA complexes for a set of targets corresponding to a set of taxa associated with the microor- - ganism-related condition; processing the biological sample with the gRNA complexes to generate microorganism nucleic acid fragments comprising a set of end regions associated with the set of targets; ligating the set of end S1 regions with a set of adapters sharing an adapter sequence; and amplifying - 20 the set of targets based on the ligated set of end regions and a set of primers sharing a primer sequence associated with the adapter sequence. FIGURE 1 [Continued on next page] WO 2018/064226 Al MIDEDIMOMMIDIREIEMINIEHOIMMOIMIE 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))