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Method for Determining the Origin of a Sample

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Method for Determining the Origin of a Sample University of Central Florida STARS UCF Patents Technology Transfer 1-20-2015 Method for Determining the Origin of a Sample John Ballantyne University of Central Florida Erin Hanson University of Central Florida Helge Lubenow QIAGEN GmbH Find similar works at: https://stars.library.ucf.edu/patents University of Central Florida Libraries http://library.ucf.edu This Patent is brought to you for free and open access by the Technology Transfer at STARS. It has been accepted for inclusion in UCF Patents by an authorized administrator of STARS. For more information, please contact [email protected]. Recommended Citation Ballantyne, John; Hanson, Erin; and Lubenow, Helge, "Method for Determining the Origin of a Sample" (2015). UCF Patents. 335. https://stars.library.ucf.edu/patents/335 Illlll llllllll Ill lllll lllll lllll lllll lllll 111111111111111111111111111111111 US008936909B2 c12) United States Patent (IO) Patent No.: US 8,936,909 B2 Lubenow et al. (45) Date of Patent: Jan.20,2015 (54) METHOD FOR DETERMINING THE ORIGIN (58) Field of Classification Search OF A SAMPLE None See application file for complete search history. (75) Inventors: Helge Lubenow, Langenfeld (DE); Jack Ballantyne, Chuluota, FL (US); Erin K. (56) References Cited Hanson, Oviedo, FL (US) U.S. PATENT DOCUMENTS (73) Assignees: Qiagen GmbH, Hilden (DE); 7,270,983 Bl 9/2007 Ballantyne University of Central Florida Research 8,039,234 Bl* 10/2011 Fang et al. 435/91.1 Foundation Inc., Orlando, FL (US) 2005/0123952 Al 6/2005 Griffrey ( *) Notice: Subject to any disclaimer, the term ofthis FOREIGN PATENT DOCUMENTS patent is extended or adjusted under 35 U.S.C. 154(b) by 448 days. WO WO 2007/073737 A 7/2007 WO WO 2007073737 Al * 7/2007 WO WO 2008/020008 2/2008 (21) Appl. No.: 13/054,721 WO WO 2008/029295 3/2008 OTHER PUBLICATIONS (22) PCT Filed: Jul. 20, 2009 Hanson et al., "Identification of forensically relevant body fluids (86) PCT No.: PCT/EP2009/005254 using a panel of differentially expressed microRNAs," Anal. § 371 (c)(l), Biochem. 2009, 387:303-314.* (2), ( 4) Date: Jan.4,2012 Zubakov et al., "MicroRNA markers for forensic body fluid identi­ fication obtained from microarray screening and quantitative RT­ (87) PCT Pub. No.: W02010/006814 PCR confirmation," Int. J. Legal Med. 2010, 124:217-226.* (Continued) PCT Pub. Date: Jan. 21, 2010 Primary Examiner - Samuel Woolwine (65) Prior Publication Data Assistant Examiner - Kaijiang Zhang US 2012/0094850Al Apr. 19, 2012 (74) Attorney, Agent, or Firm - Fanelli Haag & Kilger PLLC Related U.S. Application Data (57) ABSTRACT A method for determining the nature of a sample is provided, (60) Provisional application No. 61/082,056, filed on Jul. wherein the presence or absence of at least one marker small 18, 2008. non-coding RNA in the sample is detected. Suitable marker (51) Int. Cl. small non-coding RNAs for different samples such as blood, C12Q 1168 (2006.01) saliva, semen and vaginal secretions are provided. Also pro­ vided are suitable kits and methods for identifying marker (52) U.S. Cl. small-non coding RNAs. CPC .................................... C12Q 116881 (2013.01) USPC ........................................... 435/6.1; 435/6.12 7 Claims, 15 Drawing Sheets Table 1: Small non-coding RNAa sullllble u blood mark&!'$ miRNA Huma~ miRNAe tet7a hsa-laHa-UGAGGUAGUAGGUUGUAUAGUU - SEQ ID NO , let7b tisa·let-7t>-UGAGGUAGUAGGUUGUGUGGUU - SEQ 10 NO 2 iet7c Ma-lat-7c-UGAGGUAGUAGGUUGUAUGGUU - SEQ ID NO 3 let7d Ma-tet-711-AGAGGUAGUAGGUUGCAUAGUU. SEQ ID NO 4 hsa-let-7&-UGAGGUAGGAGGUUGUAUAGUU ·SEO 10 NO S 1817f~" hsa-~t-7!-UGAGGUAGUAGAUUGUAUAGUU ·SEQ ID NO 6 hsa-ieH~UGAGGUAGUAGUUUGUACAGUU ·SEQ ID NO 7 ~~~ hS8·1et-7~UGAGGUAGUAGUUUGUGCUGUU ·SEQ ID NO· 8 hsa-mlR-7-UGGAAGACUAGUGAUUUUGUUGU. SEQ ID NO: 9 m•R7 mlR1Ga hsa-mlR-158-UAGCAGCACAUAAUGGUUUGUG - SEQ ID NO 10 mlR15b hsa·mlR-15b·UAGCAGCACAUCAUGGUUUACA ·SEQ 10 NO. 11 miR1S nsa-m•R-16-UAGCAGCACGUAAAUAUUGGCG. SEQ 10 NO 12 mlR17 Ma-mlR-17-CAAAGUGCUUACAGUGCAGGUAG - SEQ ID NO 13 mlR18alb hsa·'™R-11!a·UAAGGUGCAUCUAGUGCAGAUAG - SEQ ID NO 14 h""·m1R-181l.UAAGGUGCAUCUAGUGCAGUUAG ·SEQ ID NO· 15 mlR18a" hsa-m1R-11!a"-ACUGCCCUAAGUGCUCCUUCUGG ·SEQ ID NO 16 mlR19a h ...m1R-19a.UGUGCAAAUCUAUGCAAAACUGA- SEQ ID NO 17 mrR20a hsa-mlR-20..-UAAAGUGCUUAUAGUGCAGGUAG ·SEQ ID NO. 18 mlR25 h.. ·ITllR-25-CAUUGCACUUGUCUCGGUCUGA - sea ID NO 19 mlR26b h:;a-m!A-25b--UUCAAGUAAUUCAGGAUAGGU ·SEQ ID NO· 20 m<R30b hsa-miR-JOb-UGUAMCAUCCUACACUCAGCU - SEO ID NO 21 m1R30ale· hsa-mlR-30a-UGUAAACAUCCUCGACUGGAAG - SEO ID NO· 22 '" hsa-mll'l-3Cle- UGUAAACAUCCUUGACUGGAAG- pr~IB!Ted ·SEO ID NO· 23 miR93 hsa-mll'l-93-CAMGUGCUGUUCGUGCAGGUAG ·SEQ ID NO· 24 mrR96 hsa-m•R-95-UUUOOCACUAGCACAUUUUUGCU ·SEQ ID NO. 25 m1R103 hsa-moR-103-AGCAGCAUUGUACAGGGCUAUGA- sea ID NO 26 //hsa-miR-107-AGCAGCAUUGUACAGGGCUAUCA. sea ID NO 29 h$1i-mlR-106o-AAAAGUGCUUACAGUGCAGGUAG - sea ID NO 27 // hsa-m•Fl-1 7-CAAAGUGCUUACAGUGCAGGUAG • SEQ 10 NO 13 mlR106b hsa-m1R-106~UAAAGUGCUGACAGUGCAGAU - SEQ ID NO 28 m1R107 hsa-mlR-107-AGCAGCAUUGUACAGGGCUAUCA- SEQ 10 NO 29 mlR126 h:!<l·mlR· 126-UCGUACCGUGAGUAAUAAUGCG • SEO ID NO 30 m1R125" hsa-mlR-12e·-CAUUAUUACUUUUGGUACOCG-SEOIDNO 31 miR12B has-miR-128-UCACAGUGAACCGGUCUCUUU ·SEQ ID NO. 32 mlfl130a hsa-mlR-130a-CAGUGCAAUGUUAAAAOGGCAU - SEQ 10 NO: 33 miR149b hs'1-m1R-14aa-UCAGUGCACUACAGAACUUUGU ·SEO ID NO 34 hs•-mlR-14&-UCAGUGCAUCACAGAACUUUGU ·SEQ ID NO: 35 hsi0-m1R·14Sa'·AAAGUUCUGAGACACUCCGACU ·SEQ ID NO 36 hsa·miR-148b'-AAGUUCUGUUAUACACUCAGGC ·SEQ ID NO 37 miR150 hsa-mlR-150-UCUCCCAACCCUUGUACCAGUG. sea 10 NO 36 mlR151 hsa-m1R-151-5p·UCGAGGAGCUCACAGUCUAGU - SEQ ID NO 39 hsa-mJR-151-Jp-CUAGACUGAAGCUCCUUGAGG- preferred - SEQ 10 NO: 40 m<R181a hsa-m<R-1S1a·AACAUUCAACGCUGUCGGUGAGU ·SEQ ID NO 41 m<R181c hsa-mlR-161c-AACAUUCAACCUGUCGGUGAGU -SEQ ID NO 42 US 8,936,909 B2 Page 2 (56) References Cited Suh, Mi-ra et al., "Human embryonic stem cells express a unique set of microRNAs," Developmental Biology, Academic Press, New OTHER PUBLICATIONS York, NY, US vol. 270 No. 2, May 6, 2004, pp. 488-498. Lagos-Quintana, Mariana et al., "New microRNAs from mouse and Wang et al., "A model for data analysis of microRNA expression in human, RNA," Cold Spring Harbor Laboratory Press Woodbury, NY, US vol. 9 No. 2, Feb. 1, 2003, pp. 175-179. forensic body fluid identification," Forensic Sci. Int. Genet. 2012, Jobling et al., "Encoded Evidence: DNA in Forensic Analysis," 6:419-423.* Nature Reviews in Genetics, vol. 5, p. 739; 2004. Chajut, A. et al., "MicroRNA profiles in body fluids as a novel class Mattick et al., "Non-coding RNA," Human Molecular Genetics 2006, ofbiomarkers," Proceedings of the Annual Meeting of the American vol. 15, Review Issue 1Rl7-R29. Association for Cancer Research, New York, NY, US vol. 49, Apr. 16, Cummins et al., "Implications of micro-RNA profiling for cancer 2008, p. 1231. diagnosis," Oncogene (2006) 25, pp. 6220-6227. Labourier, E. and Goldrick, M., "MiRNA Expression in White Blood Berezikov et al., "Approaches to microRNA discovery," Nature Cells," Applied Biosystems Technotes [Online] vol. 11 No. 3, May Genetics Supplement, vol. 38, Jun. 2006, pp. S2-S7. 2004, pp. 2-3. Kloosterman eta!., "The Diverse Functions of Micro RNAs in Animal Beuvink, Iwan et al., "A novel microarray approach reveals new Development and Disease," Developmental Cell 11, Oct. 2006 pp. tissue-specific signatures of known and predicted mammalian 441-450. microRNAs," Nucleic Acids Research vol. 35 No. 7, Apr. 2007, p. 3. Chomczynski et al., "The single-step method of RNA isolation by Lagos-Quintana, M et al., "Identification of novel genes coding for acid guanidinium thiocyanate-phenol-chloroform extraction: small expressed RNAs," Science, American Association for the twenty-something years on," Analytical Biochemistry Apr. 1987; Advancement of Science, US, Washington, DC vol. 294 No. 5543, 162: pp. 156-159. Oct. 26, 2001, pp. 853-858. Nussbaumer et al., "Messenger RNA profiling: A novel method for Sewer, Alain et al., "Identification of clustered microRNAs using an body fluid identification by Real-Time PCR," Forensic Science Inter­ ab initio prediction method," BMC Bioinformatics 2005, vol. 6, p. national, 157 (2006) pp. 181-186. 267. Juusola et al., "Multiplex mRNA profiling for the identification of Weber, Michel J, "New human and mouse microRNA genes found by body fluids," Forensic Science International, 152 (2005) pp. 1-12. homology search," FEBS Journal vol. 272 No. 1, Jan. 2005, pp. 59-73. * cited by examiner U.S. Patent Jan.20,2015 Sheet 1of15 US 8,936,909 B2 Table 1: Small non-coding RN As suitable as blood markers mi RNA Human miRNAs let7a hsa-let-7a-UGAGGUAGUAGGUUGUAUAGUU - SEQ ID NO: 1 let7b hsa-let-7b-UGAGGUAGUAGGUUGUGUGGUU - SEQ ID NO 2 let7c hsa-let-7c-UGAGGUAGUAGGUUGUAUGGUU - SEQ ID NO: 3 let7d hsa-let-7d-AGAGGUAGUAGGUUGCAUAGUU - SEQ ID NO: 4 let7e hsa-let-7e-UGAGGUAGGAGGUUGUAUAGUU - SEQ ID NO: 5 let7f hsa-let-7f-UGAGGUAGUAGAUUGUAUAGUU - SEQ ID NO: 6 let7g hsa-let-7g-UGAGGUAGUAGUUUGUACAGUU - SEQ ID NO: 7 let7i hsa-let-7i-UGAGGUAGUAGUUUGUGCUGUU - SEQ ID NO: 8 miR7 hsa-miR-7-UGGAAGACUAGUGAUUUUGUUGU - SEQ ID NO: 9 miR15a hsa-miR-15a-UAGCAGCACAUAAUGGUUUGUG - SEQ ID NO: 10 miR15b hsa-miR-15b-UAGCAGCACAUCAUGGUUUACA- SEQ ID NO: 11 miR16 hsa-miR-16-UAGCAGCACGUAAAUAUUGGCG - SEQ ID NO: 12 miR17 hsa-miR-17-CAAAGUGCUUACAGUGCAGGUAG - SEQ ID NO: 13 miR18a/b hsa-miR-18a-UAAGGUGCAUCUAGUGCAGAUAG - SEQ ID NO: 14 hsa-miR-18b-UAAGGUGCAUCUAGUGCAGUUAG ·SEQ ID NO: 15 miR1Ba· hsa-miR-18a*-ACUGCCCUMGUGCUCCUUCUGG - SEQ ID NO: 16 miR19a hsa-miR-19a-UGUGCMAUCUAUGCAAAACUGA- SEQ ID NO: 17 miR20a hsa-m1R-20a-UAAAGUGCUUAUAGUGCAGGUAG ·SEQ ID NO:
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