# US 2020/0399705 A1 · Biomarker panel and methods for detecting microsatellite instability in cancers > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2020/0399705 A1 - Document ID: US20200399705A1 - Status: Published application - Kind: A1 - Application number: 16/767,968 - Filed: 2019-01-22 - Published: 2020-12-24 - Earliest claimed: 2018-01-23 - Assignees: Biocartis NV - Applicants: Biocartis NV - Inventors: Bram De Craene; Klaas Decanniere; Jan Van De Velde - Web page: https://patentgrep.com/patent/US20200399705A1 ## CPC - C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575) - C12Q 2600/156: Polymorphic or mutational markers - 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 generally relates to the field of cancer, in particular to cancers having microsatellite instability (MSI) and/or mismatch repair (MMR-) deficiency. Examples of such cancers include many colorectal, gastric, and endometrial tumors. Accordingly, the present invention provides a novel diagnostic marker panel for analyzing MSI loci, together with methods and kits of using said panel in the detection of cancers having microsatellite instability (MSI) and/or mismatch repair (MMR-) deficiency. ## Claims ### Claim 1 A biomarker panel for analyzing MSI loci in a biological sample, the panel comprising the following homopolymeric repeat regions, or mutated forms thereof, as mapped to GRCh38/hg38 human reference genome: homopolymeric repeat comprising 11 consecutive adenines localized to human DIDO1 gene and starting at position chr20:62,905,340; homopolymeric repeat comprising 11 consecutive adenines localized to human MRE11 gene and starting at position chr11:94,479,765; homopolymeric repeat comprising 10 consecutive adenines localized to human SULF2 gene and starting at position chr20:47,657,577; and homopolymeric repeat comprising 8 consecutive adenines localized to human ACVR2A gene and starting at position chr2:147,926,117. ### Claim 2 (depends on 1) The panel according to claim 1, further comprising any one, two, or all of the following homopolymeric repeat regions, or mutated forms thereof, as mapped to GRCh38/hg38 human reference genome: homopolymeric repeat comprising 9 consecutive thymines localized to human SEC31A gene and starting at position chr4:82,864,412; homopolymeric repeat comprising 10 consecutive adenines localized to human BTBD7 gene and starting at position chr14:93,241,685; homopolymeric repeat comprising 10 consecutive adenines localized to human RYR3 gene and starting at position chr15:33,865,341. ### Claim 3 A method of analyzing MSI loci in a biological sample, comprising the step of: determining the number of nucleotides in the following homopolymeric repeats as mapped to GRCh38/hg38 human reference genome: homopolymeric repeat comprising 11 consecutive adenines localized to human DIDO1 gene and starting at position chr20:62,905,340; homopolymeric repeat comprising 11 consecutive adenines localized to human MRE11 gene and starting at position chr11:94,479,765; homopolymeric repeat comprising 10 consecutive adenines localized to human SULF2 gene and starting at position chr20:47,657,577; and homopolymeric repeat comprising 8 consecutive adenines localized to human ACVR2A gene and starting at position chr2:147,926,117. ### Claim 4 (depends on 3) The method according to claim 3, further comprising determining the number of nucleotides in any one, two, or all of the following homopolymeric repeat regions as mapped to GRCh38/hg38: homopolymeric repeat comprising 9 consecutive thymines localized to human SEC31A gene and starting at position chr4:82,864,412; homopolymeric repeat comprising 10 consecutive adenines localized to human BTBD7 gene and starting at position chr14:93,241,685; homopolymeric repeat comprising 10 consecutive adenines localized to human RYR3 gene and starting at position chr15:33,865,341. ### Claim 5 (depends on 3) The method according to claim 3, further comprising the step of amplifying nucleic acid regions comprising the homopolymeric repeats or mutated forms thereof. ### Claim 6 (depends on 5) The method according to claim 5, wherein the step of amplifying results in generating melting curve data. ### Claim 7 (depends on 6) The method according to claim 6, further comprising the steps of: (a) applying wavelet transform on the melting curve data; and (b) using the results obtained from (a) in determination of the number of nucleotides in any of the homopolymeric repeats. ### Claim 8 (depends on 5) The method according to claim 5, wherein the step of amplifying comprises use of at least one molecular beacon probe. ### Claim 9 (depends on 5) The method according to claim 5, wherein the step of amplifying comprises use of at least one primer having sequence identified by any of the following SEQ ID NO. 1-14. ### Claim 10 (depends on 5) The method according to claim 5, wherein the step of amplifying comprises at least one duplex amplification of a pair of homopolymeric repeats, or mutated forms thereof, said pair being selected from the following combinations: duplex amplification of the homopolymeric repeat comprising 11 consecutive adenines localized to human DIDO1 gene and starting at position chr20:62,905,340 together with the homopolymeric repeat comprising 11 consecutive adenines localized to human MRE11 gene and starting at position chr11:94,479,765; duplex amplification of the homopolymeric repeat comprising 8 consecutive adenines localized to human ACVR2A gene and starting at position chr2:147,926,117; together with the homopolymeric repeat comprising 9 consecutive thymines localized to human SEC31A gene and starting at position chr4:82,864,412; and duplex amplification of the homopolymeric repeat comprising 10 consecutive adenines localized to human BTBD7 gene and starting at position chr14:93,241,685; together with homopolymeric repeat comprising 10 consecutive adenines localized to human SULF2 gene and starting at position chr20:47,657,577. ### Claim 11 (depends on 3, 4) The method according to claim 3, wherein the determining the number of nucleotides in any of the homopolymeric repeats as listed in claims 3-4 is further also performed in a control biological sample comprising material derived from HTC116 cl.110268743 cell line. ### Claim 12 (depends on 4) The method according to claim 4, wherein the biological sample is a tumor or a potential tumor sample, preferably being a colorectal, gastric, or endometrial tumor. ### Claim 13 (depends on 12) The method according to claim 12, wherein the tumor sample is a stage I tumor, preferably being stage I colorectal tumor. ### Claim 14 (depends on 3) The method according to claim 3, further comprising a step of using the information obtained about the number of the homopolymeric repeats to deduce tumor mutation load or tumor indel load. ### Claim 15 (depends on 14) The method according to claim 14, wherein the deduced tumor mutation load or the tumor indel load is provided as an estimation of the total number of mutations or is provided as a score. ### Claim 16 (depends on 3) The method according to claim 3, further comprising a step of using the information obtained about the number of the homopolymeric repeats, or the tumor mutation load, or the tumor indel load, or the estimation of the total number of mutations, or the score to decide about subjecting the person from whom the biological sample was obtained to immunotherapy. ### Claim 17 (depends on 16) The method according to claim 16, wherein the immunotherapy comprises a treatment with an immune checkpoint-targeting antibody. ### Claim 18 (depends on 17) The method according to claim 17, wherein the antibody is specific to any of the following: PD-1, PD-L1, or PD-L2. ### Claim 19 (depends on 4) Kit for analyzing MSI loci in a biological sample, the kit comprising tools for detecting nucleic acid regions comprising the homopolymeric repeats as listed in claim 4. ### Claim 20 (depends on 19) The kit according to claim 19 further comprising material derived from cell line HTC116 cl.110268743. ### Claim 21 (depends on 19) The kit according to claim 19 further comprising a cartridge. ### Claim 22 Cell or any other material derived from cell line HTC116 cl.110268743.