# US 9,040,243 B2 · Method for detecting and/or quantifying human DNA > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 9,040,243 B2 - Document ID: US9040243B2 - Status: Granted - Kind: B2 - Application number: 13/825,226 - Filed: 2011-09-22 - Published: 2013-08-29 - Granted: 2015-05-26 - Earliest claimed: 2010-09-23 - Assignees: Qiagen GmbH - Applicants: Andy Wende; Francesca Dipasquale; Sabine Werner; Sascha Strauss - Inventors: Andy Wende; Francesca Dipasquale; Sabine Werner; Sascha Strauss - Web page: https://patentgrep.com/patent/US9040243B2 ## CPC - C12Q 1/6853: using modified primers or templates - C12Q 1/6846: {Common amplification features} - C12Q 1/6851: Quantitative amplification - C12Q 1/686: Polymerase chain reaction [PCR] - C12Q 1/6865: Promoter-based amplification, e.g. nucleic acid sequence amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS] - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES ## Abstract The present invention relates to a method, kit and use of various nucleic acid sequences for deleting and/or quantifying one or more nucleic acids of a genome in a sample. Wherein the nucleic acid is amplified and the locus that is amplified is a multi copy locus within the genome, the multicopy locus has copies on at least two different chromosomes and the amplification product is detected and/or quantified. ## Claims ### Claim 1 A method of quantifying one or more nucleic acids of a genome in a sample comprising: a. amplifying a nucleic acid comprising a non-repetitive, multicopy locus, the locus having copies on at least 2 chromosomes and a sequence that shares at least 80% sequence identity over a stretch of 80 base pairs to a nucleic acid sequence of SEQ ID NO.1 or SEQ ID NO.52 to produce an amplification product; b. detecting the amplification product; and c. quantifying the amplification product. ### Claim 2 A method of detecting one or more nucleic acids of a genome in a sample comprising: a. amplifying a nucleic acid comprising a non-repetitive, multicopy locus, the locus having copies on at least 2 chromosomes and a sequence that shares at least 80% sequence identity over a stretch of 80 base pairs to a nucleic acid sequence of SEQ ID NO.1 or SEQ ID NO.52 to produce an amplification product; and b. detecting the amplification product. ### Claim 3 A method of analyzing the state of possible degradation of human DNA comprising: a. amplifying a nucleic acid comprising a non-repetitive, multicopy locus, the locus having copies on at least 2 chromosomes and a sequence that shares at least 80% sequence identity over a stretch of 80 base pairs to a nucleic acid sequence of SEQ ID NO.1 or SEQ ID NO.52 to produce an amplification product; b. detecting the amplification product; c. quantifying the amplification product; and d. determining the state of possible degradation of human DNA in the quantified amplification product. ### Claim 4 A method of analyzing Copy Number Variation (CNV) comprising: a. amplifying a nucleic acid comprising a non-repetitive, multicopy locus, the locus having copies on at least 2 chromosomes and a sequence that shares at least 80% sequence identity over a stretch of 80 base pairs to a nucleic acid sequence of SEQ ID NO.1 or SEQ ID NO.52 to produce an amplification product; b. detecting the amplification product; c. quantifying the amplification product; and d. determining the CNV of the quantified amplification product. ### Claim 5 (depends on 1) The method according to claim 1, wherein at least 4 different copies of the multicopy locus are amplified. ### Claim 6 (depends on 2) The method according to claim 2, wherein at least 4 different copies of the multicopy locus are amplified. ### Claim 7 (depends on 3) The method according to claim 3, wherein at least 4 different copies of the multicopy locus are amplified. ### Claim 8 (depends on 4) The method according to claim 4, wherein at least 4 different copies of the multicopy locus are amplified. ### Claim 9 (depends on 1) The method according to claim 1, wherein the amplifying is a non-isothermal amplifying. ### Claim 10 (depends on 2) The method according to claim 2, wherein the amplifying is a non-isothermal amplifying. ### Claim 11 (depends on 3) The method according to claim 3, wherein the amplifying is a non-isothermal amplifying. ### Claim 12 (depends on 4) The method according to claim 4, wherein the amplifying is a non-isothermal amplifying. ### Claim 13 (depends on 1) The method according to claim 1, wherein the amplifying is an isothermal amplifying. ### Claim 14 (depends on 2) The method according to claim 2, wherein the amplifying is an isothermal amplifying. ### Claim 15 (depends on 3) The method according to claim 3, wherein the amplifying is an isothermal amplifying. ### Claim 16 (depends on 4) The method according to claim 4, wherein the amplifying is an isothermal amplifying. ### Claim 17 (depends on 1) The method according to claim 1, wherein the amplifying is selected from the group consisting of quantitative real-time PCR (rtPCR), ligase chain reaction (LCR), strand displacement amplification (SDA), multiple displacement amplification (MDA), roHingcircle amplification (RCA), loop mediated isothermal amplification (LAMP), transcription mediated amplification (TMA), helicase-dependent amplification (HDA), smart-amplification process (SMAP), single primer isothermal amplification (SPIA), nicking enzyme amplification reaction (NEAR), exponential amplification reaction (EXPAR), recombinase polymerase amplification (RPA), and nucleic acid sequence based amplification (NASBA). ### Claim 18 (depends on 2) The method according to claim 2, wherein the amplifying is selected from the group consisting of quantitative real-time PCR (rtPCR), ligase chain reaction (LCR), strand displacement amplification (SDA), multiple displacement amplification (MDA), roHingcircle amplification (RCA), loop mediated isothermal amplification (LAMP), transcription mediated amplification (TMA), helicase-dependent amplification (HDA), smart-amplification process (SMAP), single primer isothermal amplification (SPIA), nicking enzyme amplification reaction (NEAR), exponential amplification reaction (EXPAR), recombinase polymerase amplification (RPA), and nucleic acid sequence based amplification (NASBA). ### Claim 19 (depends on 3) The method according to claim 3, wherein the amplifying is selected from the group consisting of quantitative real-time PCR (rtPCR), ligase chain reaction (LCR), strand displacement amplification (SDA), multiple displacement amplification (MDA), roHingcircle amplification (RCA), loop mediated isothermal amplification (LAMP), transcription mediated amplification (TMA), helicase-dependent amplification (HDA), smart-amplification process (SMAP), single primer isothermal amplification (SPIA), nicking enzyme amplification reaction (NEAR), exponential amplification reaction (EXPAR), recombinase polymerase amplification (RPA), and nucleic acid sequence based amplification (NASBA). ### Claim 20 (depends on 4) The method according to claim 4, wherein the amplifying is selected from the group consisting of quantitative real-time PCR (rtPCR), ligase chain reaction (LCR), strand displacement amplification (SDA), multiple displacement amplification (MDA), roHingcircle amplification (RCA), loop mediated isothermal amplification (LAMP), transcription mediated amplification (TMA), helicase-dependent amplification (HDA), smart-amplification process (SMAP), single primer isothermal amplification (SPIA), nicking enzyme amplification reaction (NEAR), exponential amplification reaction (EXPAR), recombinase polymerase amplification (RPA), and nucleic acid sequence based amplification (NASBA). ### Claim 21 (depends on 17) The method according to claim 17, wherein the amplifying is a helicase-dependent amplification. ### Claim 22 (depends on 18) The method according to claim 18, wherein the amplifying is a helicase-dependent amplification. ### Claim 23 (depends on 19) The method according to claim 19, wherein the amplifying is a helicase-dependent amplification. ### Claim 24 (depends on 20) The method according to claim 20, wherein the amplifying is a helicase-dependent amplification. ### Claim 25 (depends on 17) The method according to claim 17, wherein the amplifying is real-time PCR (rtPCR). ### Claim 26 (depends on 18) The method according to claim 18, wherein the amplifying is real-time PCR (rtPCR). ### Claim 27 (depends on 19) The method according to claim 19, wherein the amplifying is real-time PCR (rtPCR). ### Claim 28 (depends on 20) The method according to claim 20, wherein the amplifying is real-time PCR (rtPCR). ### Claim 29 (depends on 1) The method according to claim 1, wherein the amplification product is between 60 base pairs and 200 base pairs long. ### Claim 30 (depends on 2) The method according to claim 2, wherein the amplification product is between 60 base pairs and 200 base pairs long. ### Claim 31 (depends on 3) The method according to claim 3, wherein the amplification product is between 60 base pairs and 200 base pairs long. ### Claim 32 (depends on 4) The method according to claim 4, wherein the amplification product is between 60 base pairs and 200 base pairs long. ### Claim 33 (depends on 1) The method according to claim 1, wherein the amplifying comprises amplifying with primers that have a nucleotide sequence that differs from SEQ ID NO. 2, 3, 5, 6, 8, 9, 10, 11, and/or 12 by no more than 5 nucleotides over a stretch of 18 nucleotides. ### Claim 34 (depends on 2) The method according to claim 2, wherein the amplifying comprises amplifying with primers that have a nucleotide sequence that differs from SEQ ID NO. 2, 3, 5, 6, 8, 9, 10, 11, and/or 12 by no more than 5 nucleotides over a stretch of 18 nucleotides. ### Claim 35 (depends on 3) The method according to claim 3, wherein the amplifying comprises amplifying with primers that have a nucleotide sequence that differs from SEQ ID NO. 2, 3, 5, 6, 8, 9, 10, 11, and/or 12 by no more than 5 nucleotides over a stretch of 18 nucleotides. ### Claim 36 (depends on 4) The method according to claim 4, wherein the amplifying comprises amplifying with primers that have a nucleotide sequence that differs from SEQ ID NO. 2, 3, 5, 6, 8, 9, 10, 11, and/or 12 by no more than 5 nucleotides over a stretch of 18 nucleotides. ### Claim 37 (depends on 1) The method according to claim 1, wherein the amplification product shares at least 95% sequence identity over a stretch of 80 base pairs to a nucleic acid sequence of SEQ ID NO.1 or SEQ ID NO.52. ### Claim 38 (depends on 2) The method according to claim 2, wherein the amplification product shares at least 95% sequence identity over a stretch of 80 base pairs to a nucleic acid sequence of SEQ ID NO.1 or SEQ ID NO.52. ### Claim 39 (depends on 3) The method according to claim 3, wherein the amplification product shares at least 95% sequence identity over a stretch of 80 base pairs to a nucleic acid sequence of SEQ ID NO. 1 or SEQ ID NO.52. ### Claim 40 (depends on 4) The method according to claim 4, wherein the amplification product shares at least 95% sequence identity over a stretch of 80 base pairs to a nucleic acid sequence of SEQ ID NO.1 or SEQ ID NO.52.