SG11201408434QA - Targeted rna-seq methods and materials for the diagnosis of prostate cancer - Google Patents

Abstract

(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 3 January 2014 (03.01.2014) WIPOIPCT (10) International Publication Number WO 2014/003580 A1 (51) International Patent Classification: C12Q 1/68 (2006.01) C12N15/11 (2006.01) (21) International Application Number: (22) International Filing Date: (25) Filing Language: (26) Publication Language: PCT/NZ2013/000114 28 June 2013 (28.06.2013) English English (30) Priority Data: 61/665,849 61/691,743 61/709,517 28 June 2012 (28.06.2012) US 21 August 2012 (21.08.2012) US 4 October 2012 (04.10.2012) US (71) Applicant: CALDERA HEALTH LTD [NZ/NZ]; PO Box 11664, Ellerslie, Auckland, 1542 (NZ). (72) Inventors: WATSON, James Douglas; Appartment 3, 18 Eltham Road, Kohimarama, Auckland, 1071 (NZ). ELTON, Clare; 17a Jacaranda Avenue, Beach Haven, Auckland, 0626 (NZ). MUSGRAVE, David Rex; 48a Queenswood Avenue, Hamilton, 3210 (NZ). (74) Agent: CALVERT, Jane; In-Legal Limited, PO Box 8026, The Terrace, Wellington, 6143 (NZ). (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, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KN, KP, KR, KZ, LA, LC, LK, LR, LS, LT, 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, 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, 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)) (54) Title: TARGETED RNA-SEQ METHODS AND MATERIALS FOR THE DIAGNOSIS OF PROSTATE CANCER Figure 1: Four novel adaptations to the RNA-seq technology o 00 m o o o CJ o & cONA then purified (to is adapters and primers), or and cDNA is amplified with adaptor primers if necessary) cONA purified, and size selected if necessary cDNA library sequenced (57) Abstract: Methods for diagnosing the presence of a disorder, such as prostate cancer, in a subject are provided, such methods including detecting the relative frequency of expression of RNA biomarkers in biological a sample obtained from the subject using RNA-Seq technology and comparing the relative levels of expression with predetermined threshold levels. Levels of expression of at least two of the RNA biomarkers that are above the predetermined threshold levels are indicative of the presence of prostate cancer in the subject. The methods involve the use of at least one gene-specific primer in at least one point of the RNA-Seq protocol for tar­ geted sequencing of relevant transcripts.