{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Complete Genomics - CG Build 1.4.2.8"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00010000220"],"sample_count":["2"],"description":["EGA dataset EGAD00010000220"],"repository":["EGA"],"title":["Title not provided"],"pubmed_abstract":["DNA replication errors that persist as mismatch mutations make up the molecular fingerprint of mismatch repair (MMR)-deficient tumors and convey them with resistance to standard therapy. Using whole-genome and whole-exome sequencing, we here confirm an MMR-deficient mutation signature that is distinct from other tumor genomes, but surprisingly similar to germ-line DNA, indicating that a substantial fraction of human genetic variation arises through mutations escaping MMR. Moreover, we identify a large set of recurrent indels that may serve to detect microsatellite instability (MSI). Indeed, using endometrial tumors with immunohistochemically proven MMR deficiency, we optimize a novel marker set capable of detecting MSI and show it to have greater specificity and selectivity than standard MSI tests. Additionally, we show that recurrent indels are enriched for the 'DNA double-strand break repair by homologous recombination' pathway. Consequently, DSB repair is reduced in MMR-deficient tumors, triggering a dose-dependent sensitivity of MMR-deficient tumor cultures to DSB inducers."],"pubmed_title":["Mismatch repair deficiency endows tumors with a unique mutation signature and sensitivity to DNA double-strand breaks."],"pubmed_authors":["Zhao Hui H, Thienpont Bernard B, Yesilyurt Betül Tuba BT, Moisse Matthieu M, Reumers Joke J, Coenegrachts Lieve L, Sagaert Xavier X, Schrauwen Stefanie S, Smeets Dominiek D, Matthijs Gert G, Aerts Stein S, Cools Jan J, Metcalf Alex A, Spurdle Amanda A, Amant Frederic F, Lambrechts Diether D"],"name_synonyms":["average, Genogroups, Genotypes., Genogroup"],"pubmed_title_synonyms":["mismatch repair cancer syndrome 1, mismatch repair cancer syndrome 3, mismatch repair cancer syndrome 2, mismatch repair cancer syndrome 4, MMRCS1, Malignant Neoplasm, DNS, Mismatch Repair Deficiency, (Deoxyribonucleotide)n, Neoplasms, DNAn+1, Benign Neoplasm, mismatch repair cancer syndrome, CNS tumours with familial polyposis of the colon, MMRCS2, Double-Stranded, MMRCS3, Tumor, MMRCS4, Malignant, CNS tumors with familial polyposis of the colon, glioma-polyposis syndrome, Mutations, (Deoxyribonucleotide)n+m, CNS tumors with Familial polyposis of the colon, Benign, Deoxyribonucleic Acid, sensitive, MMR deficiency, Neoplasm, Mismatch Repair Cancer Syndrome, brain tumor-polyposis syndrome, ds-DNA, desoxyribose nucleic acid, sensitivity, MMR Deficiency, MMRCS, thymus nucleic acid, Malignancy, malignant tumors of the central nervous system associated with familial polyposis of the colon, Deoxyribonucleic acids., Specificity, Brain Tumor-Polyposis Syndrome 1, Benign Neoplasms, Double Stranded, Deoxyribonucleic acid, Cancers, malignant tumours of the central nervous system associated with familial polyposis of the colon, Malignant Neoplasms, Neoplasias, allergic reaction, childhood cancer syndrome, Specificity and Sensitivity, ds DNA, Desoxyribonukleinsaeure, Turcot syndrome, Sensitivity, Malignancies, Double-Stranded DNA, (Deoxyribonucleotide)m, DNA, deoxyribonucleic acids, DNAn, Neoplasia, mismatch repair deficiency, Cancer, Tumors"],"description_synonyms":["average, Genogroups, Genotypes., Genogroup"],"pubmed_abstract_synonyms":["mismatch repair cancer syndrome 1, mismatch repair cancer syndrome 3, chromosomal crossover, mismatch repair cancer syndrome 2, IPP2A2, mismatch repair cancer syndrome 4, MMRCS1, acetylglucosaminyltransferase-like protein, Mbp1, cd206, MMRCS2, Tumor, MMRCS3, MMRCS4, Repair, CNS tumors with familial polyposis of the colon, Mutations, 5730420M11Rik, Recombinations, Mismatch Repair Cancer Syndrome, Whole Transcriptome, Transcriptome Sequencing, 4, Autonomous Replication, myd, treatment, SET, thymus nucleic acid, Man (Taxonomy), like-acetylglucosaminyltransferase, Genomes, TAF-I, Homologous, Complete Exome Sequencing, Whole Transcriptome Sequencing, hypoplasia, Mbp-1, Brain Tumor-Polyposis Syndrome 1, Replication Error, Autonomous, DmelCG4299, allergic reaction, IGAAD, set, Replication Error Phenotype, DmelCG10574, disease management, Therapies, Malignancies, Double-Stranded DNA, deoxyribonucleic acids, Error Phenotypes, DNAn, CD206, Mismatch, Tumors, Therapy, distinct from, phapii, gyltl1b-b, Modern, Exome, StF-IT-1, Diversities, mismatch repair cancer syndrome, Double-Stranded, 2-pyrazolidinediyl)bis-, glioma-polyposis syndrome, (Deoxyribonucleotide)n+m, Replication Error Phenotypes, Benign, MDDGA6, mKIAA0609, MMR, macrophage mannose receptor 1-like protein 1, brain tumor-polyposis syndrome, desoxyribose nucleic acid, KIAA0609, CLEC13DL, acetylglucosaminyltransferase-like 1A, MMR Deficiency, fg, long patch mismatch repair system, Recombination, MMRCS, Complete Transcriptome, gyltl1b, HLA-DR-associated protein II, mismatch repair, DI-2, I-2Dm, Mismatch Repair, mdc1d, mmr, Benign Neoplasms, whole genome, CG4299, Genetic Diversity, LARGE_HUMAN, Treatments, human, Malignant Neoplasms, I-2PP1, Phenotypes, MDC1D, Replications, TAF-IBETA, enr, 4'-(4-butyl-3, Specificity and Sensitivity, ds DNA, Whole Exome Sequencing, Turcot syndrome, Autonomous Replications, TAF-Ibeta, DNA, other neoplasm, Transcriptome Sequencings, i2pp2a, 5-dioxo-1, human being, DNS, (Deoxyribonucleotide)n, Mismatch Repair Deficiency, Complete Exome, Neoplasms, Benign Neoplasm, C-type lectin domain family 13 member D-like, Malignant, LARGE1, Deoxyribonucleic acids, froggy, PHAPII, Gyltl1a, Human, CNS tumors with Familial polyposis of the colon, Deoxyribonucleic Acid, Homo sapiens, reduced, sensitive, Core Genome, MMR deficiency, tiny, DNA Replications, Man, sensitivity, WES, Complete, Exome Sequencings, Diversity, MutS/MutL/MutH pathway, Genetic, clec13d, Malignancy, MDDGB6, malignant tumors of the central nervous system associated with familial polyposis of the colon, Accessory Genome, ipp2a2, DNA Mismatch, Double Stranded, 2pp2a, Deoxyribonucleic acid, LARGE, malignant tumours of the central nervous system associated with familial polyposis of the colon, Sequencing, CG10574, MRC1L1, Neoplasias, BPFD#36, Whole Exome, 2PP2A, taf-ibeta, Whole, dSET, dSet, Sensitivity, (Deoxyribonucleotide)m, Variation, mismatch repair deficiency, Cancer, Genetic Variations, small, Malignant Neoplasm, Complete Exome Sequencings, Variations, Homologous Recombinations, DNAn+1, igaad, DSB, CNS tumours with familial polyposis of the colon, Pangenome, group, Microsatellite, Exome Sequencing, I-2PP2A, 2-pyrazolidinediyl)bis-., Dm I-2, Genetic Diversities, I2PP2A, Neoplasm, Phenotype, ds-DNA, Replication, Complete Transcriptome Sequencing, ensemble, underdeveloped, Benzenesulfonamide, reciprocal DNA recombination, Specificity, MutL-like pathway, Error Phenotype, Cancers, dSET/TAF-Ibeta, 2610030F17Rik, CLEC13D, Pan-genome, childhood cancer syndrome, like-glycosyltransferase, Therapeutic, Modern Man, Desoxyribonukleinsaeure, Treatment, AA407739, Instability, Neoplasia, glycosyltransferase-like protein LARGE1"],"additional_accession":[]},"is_claimable":false,"name":"Ovarian & matched normal (Genotypes) - samples","description":"Ovarian & matched normal (Genotypes)","dates":{"updated":"2017-07-26 15:39:24"},"accession":"EGAD00010000220","cross_references":{"TAXONOMY":["9606"],"pubmed":["25085081"],"EGA":["EGAC00001000042","EGAS00001000158"]}}