# US 11,441,176 B2 · Methods and control compositions for a quantitative polymerase chain reaction > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 11,441,176 B2 - Document ID: US11441176B2 - Status: Granted - Kind: B2 - Application number: 16/714,125 - Filed: 2019-12-13 - Published: 2020-07-09 - Granted: 2022-09-13 - Earliest claimed: 2018-12-13 - Assignees: Battelle Memorial Institute - Applicants: Battelle Memorial Institute - Inventors: Rachel R. Spurbeck - Web page: https://patentgrep.com/patent/US11441176B2 ## CPC - C12Q 1/6851: Quantitative amplification - C12N 15/10: Processes for the isolation, preparation or purification of DNA or RNA (chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34) - C12Q 1/6818: involving interaction of two or more labels, e.g. resonant energy transfer - C12Q 1/6823: Release of bound markers - C12Q 1/686: Polymerase chain reaction [PCR] - C12Q 1/6806: Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence) - C12Q 1/6809: Methods for determination or identification of nucleic acids involving differential detection - C12Q 1/6813: Hybridisation assays - 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 - C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00) ## Abstract The invention relates to control compositions for a quantitative polymerase chain reaction. More particularly, the invention relates to control compositions for a quantitative polymerase chain reaction having at least one barcode sequence fragment and at least a first and a second primer binding site fragment, and to methods of their use. ## Claims ### Claim 1 A qPCR control composition, said control composition comprising i) a first nucleic acid construct comprising at least one barcode sequence fragment and at least one GC content fragment, wherein the first nucleic acid construct further comprises at least a first and a second primer binding site fragment, and ii) a second nucleic acid construct comprising the same barcode sequence fragment as in the first nucleic acid construct and at least one GC content fragment with a different percent GC content than the GC content fragment in the first nucleic acid construct, wherein the second nucleic acid construct further comprises at least a first and a second primer binding site fragment. ### Claim 2 (depends on 1) The control composition of claim 1 wherein the control composition is used to determine if cross-contamination between samples for qPCR has occurred or if sample swapping has occurred for qPCR samples. ### Claim 3 (depends on 1) The control composition of claim 1 wherein the first and the second nucleic acid constructs further comprise at least a first and a second universal sequence fragment and wherein the first universal sequence fragment is linked to the 5′ end of the barcode sequence fragment, the barcode sequence fragment is between the first universal sequence fragment and the GC content fragment, and the second universal sequence fragment is linked to the 3′ end of the GC content fragment. ### Claim 4 (depends on 3) The control composition of claim 3 wherein the first primer binding site fragment is linked at its 3′end to the 5′ end of the first universal sequence fragment and the second primer binding site fragment is linked at its 5′ end to the 3′ end of the second universal sequence fragment. ### Claim 5 (depends on 1) The control composition of claim 1 wherein the barcode sequence fragments comprise a unique sequence not present in any known genome. ### Claim 6 (depends on 2) The control composition of claim 2 wherein sample cross-contamination and/or sample swapping can be monitored over all steps of a qPCR protocol including collection of the sample, extraction of total DNA, purification of the extracted total DNA, and qPCR. ### Claim 7 (depends on 1) The control composition of claim 1 wherein one or more of the GC content fragments has a GC content of about 1 to about 40 percent. ### Claim 8 (depends on 1) The control composition of claim 1 wherein one or more of the GC content fragments has a GC content of about 40 to about 60 percent. ### Claim 9 (depends on 1) The control composition of claim 1 wherein one or more of the GC content fragments has a GC content of about 60 to about 100 percent. ### Claim 10 (depends on 1) The control composition of claim 1 further comprising a third nucleic acid construct with a GC content fragment with a different percent GC content than the GC content fragments in the first and the second nucleic acid constructs. ### Claim 11 (depends on 10) The control composition of claim 10 further comprising a fourth nucleic acid construct with a GC content fragment with a different percent GC content than the GC content fragments in the first, the second, and the third nucleic acid constructs. ### Claim 12 (depends on 10) The control composition of claim 10 wherein the percent GC contents are about 1 to about 40 percent, about 40 percent to about 60 percent, and about 60 percent to about 100 percent. ### Claim 13 (depends on 1) The control composition of claim 1 wherein the control composition is used to determine if cross-contamination between samples for qPCR has occurred. ### Claim 14 (depends on 1) The control composition of claim 1 wherein the control composition is used to determine if sample swapping has occurred for qPCR samples. ### Claim 15 (depends on 1) The control composition of claim 1 wherein the GC content fragments are used to control for polymerase GC content bias. ### Claim 16 (depends on 1) The control composition of claim 1 in combination with a probe. ### Claim 17 (depends on 1) The control composition of claim 1 wherein the first and second nucleic acid constructs are deoxyribonucleic acid constructs. ### Claim 18 (depends on 1) The control composition of claim 1 wherein the first and second nucleic acid constructs further comprise at least a first and a second universal sequence fragment. ### Claim 19 (depends on 16) The control composition of claim 16 wherein the probe is a TaqMan probe.