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„ 2011/026194 Al O (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau „ (10) International Publication Number (43) International Publication Date Ι 10 March 2011 (10.03.2011) 201 1/026194 Al (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12N 15/10 (2006.01) C12Q 1/68 (2006.01) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, (21) International Application Number: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, PCT/AU2010/001 15 1 DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (22) International Filing Date: HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, 7 September 2010 (07.09.2010) KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, (25) Filing Language: English NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, (26) Publication Language: English SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: 2009904275 7 September 2009 (07.09.2009) AU (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (71) Applicant (for all designated States except US): RE¬ GM, KE, LR, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, PRODUCTIVE HEALTH SCIENCE PTY LTD [AU/ ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, AU]; PO Box 470, Mary Street, Unley, South Australia TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, 5061 (AU). EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, SE, SI, SK, (72) Inventor; and SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, (75) Inventor/Applicant (for US only): MCCARTHY, GW, ML, MR, NE, SN, TD, TG). Christina [AU/AU]; 34 Mendez Street, Paralowie, South Australia 5108 (AU). Published: (74) Agent: PHILLIPS ORMONDE FITZPATRICK; Level — with international search report (Art. 21(3)) 21, 22 & 23, 367 Collins Street, Melbourne, Victoria — with sequence listing part of description (Rule 5.2(a)) 3000 (AU). o (54) Title: NUCLEIC ACID EXTRACTION (57) Abstract: The present invention relates generally to methods for extracting a nucleic acid from a sample comprising one or more cells containing the nucleic acid. The present invention also contemplates amplification of the extracted nucleic acids, par- ticularly whole genome amplification of the extracted nucleic acids. The methods of the present invention are generally predicated ¾ on Iysing the one or more cells in a sample to release a nucleic acid and contacting the nucleic acid with a protease under condi - tions suitable for the protease to digest one or more proteins associated with the nucleic acid. NUCLEIC ACID EXTRACTION PRIORITY CLAIM This application claims priority to Australian provisional patent application 2009904275, filed 7 September 2009, the content of which is hereby incorporated by reference. FIELD The present invention relates generally to methods for extracting a nucleic acid from a sample comprising one or more cells containing the nucleic acid. The present invention also contemplates amplification of the extracted nucleic acids, particularly whole genome amplification of the extracted nucleic acids. BACKGROUND Whole Genome Amplification (WGA) may be used to amplify a genomic DNA template to generate amplicons that are representative of the genomic DNA template. In some instances, WGA is used to amplify rare and/or low concentration genomic DNA templates, thus enabling a range of genotyping techniques that could not otherwise be performed. For example, WGA may be used to amplify genomic DNA derived from single cells for comparative genomic hybridisation. Many approaches to WGA have been described and can be generally classified as PCR-based or strand displacement amplification techniques. Regardless of the methodology, for successful WGA, the amplicons generated by WGA must be representative of the original genomic DNA template. However, many WGA methodologies generate amplicons that have significant amplification bias and/or poorly represent or misrepresent the original genomic DNA. These problems limit the usefulness of WGA in methods such as comparative genomic hybridisation. Thus, it would be desirable to reduce amplification bias in WGA and/or to make WGA amplicons more representative of the original genomic DNA. Reference to any prior art in this specification is not, and should not be taken as, an acknowledgment or any form of suggestion that this prior art forms part of the common general knowledge in any country. SUMMARY In a first aspect, the present invention provides a method for extracting a nucleic acid from a sample comprising one or more cells containing the nucleic acid, the method comprising the steps of: lysing the one or more cells in the sample to release the nucleic acid from the one or more cells into a supernatant; and contacting the supernatant containing the nucleic acid with a protease under conditions suitable for the protease to digest one or more proteins associated with the nucleic acid. Digestion of one or more proteins associated with the nucleic acid is beneficial for further processing of the extracted nucleic acid. For example, digestion of one or more proteins associated with the nucleic acid may lead to higher quality amplicons being generated from amplification of the extracted nucleic acid and/or improved hybridisation of the extracted nucleic acid to a probe or primer. In some embodiments, the method of the present invention is adapted to the extraction of a nucleic acid from a single cell. In a second aspect, the present invention also provides a method for amplifying a nucleic acid, the method comprising: extracting a nucleic acid from a sample comprising one or more cells containing the nucleic acid using the method of the first aspect of the invention; and amplifying the extracted nucleic acid. In some embodiments, the amplification comprises whole genome amplification. In whole genome amplification methods, nucleic acids extracted according to the first aspect of the invention have been demonstrated to lead to the generation of amplicons having a smaller size and which are more representative of the original genomic DNA. In some embodiments, the amplicons produced according to the second aspect of the invention may be used in a comparative genomic hybridisation method. The use of amplicons produced according to the second aspect of the invention in a method for comparative genomic hybridisation can increase the sensitivity, reproducibility and/or reliability of the results generated in the comparative genomic hybridisation method. In a third aspect, the present invention also provides a kit for performing the method of the first aspect and/or second aspect of the invention, the kit comprising a protease together with instructions for performing the method of the first aspect and/or second aspect of the invention. DESCRIPTION It is to be understood that the following description is for the purpose of describing particular embodiments only and is not intended to be limiting with respect to the above description. In a first aspect, the present invention provides a method for extracting a nucleic acid from a sample comprising one or more cells containing the nucleic acid, the method comprising the steps of: lysing the one or more cells in the sample to release the nucleic acid from the one or more cells into a supernatant; and contacting the supernatant containing the nucleic acid with a protease under conditions suitable for the protease to digest one or more proteins associated with the nucleic acid. As described later, digestion of one or more proteins associated with the nucleic acid is beneficial for further processing of the extracted nucleic acid. For example, digestion of one or more proteins associated with the nucleic acid may lead to higher quality amplicons being generated from amplification of the extracted nucleic acid and/or improved hybridisation of the extracted nucleic acid to a probe or primer, relative to an extracted nucleic acid which has not been contacted with a protease under conditions suitable for the protease to digest one or more proteins associated with the nucleic acid. As set out above, the present invention contemplates a method for extracting a nucleic acid from a sample comprising one or more cells containing the nucleic acid. However, in some embodiments, the method of the present invention is adapted to the extraction of a nucleic acid from a single cell. As such, in some embodiments, the sample comprises a single cell. The cell or cells for use in the method may be any suitable eukaryotic or prokaryotic cell. Examples of suitable eukaryotic cells include animal, plant or fungal cells, while examples of suitable prokaryotic cells include bacterial or archaeal cells. In some embodiments, the one or more cells comprise an animal cell. In some embodiments, the one or more cells comprise a mammalian cell. In some embodiments the one or more cells comprise a human cell. In some embodiments, the one or more cells may be derived from a multicellular organism. In some embodiments the one or more cells may be somatic cells derived from an adult form of the organism. Methods for the isolation of various types of somatic cells from an organism are well known in the art and the present invention contemplates any such methods. In some embodiments, the one or more cells may be derived from an immature form of the organism and/or may be a germ cell. For example, in some embodiments, the cell may be a foetal cell, a cell derived from an embryo (including a blastomere) or a germ cell (including oocytes and sperm).
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