{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina Genome Analyzer IIx;"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001001108"],"sample_count":["218"],"description":["EGA dataset EGAD00001001108"],"repository":["EGA"],"title":["MMP-seq tumor samples (FASTQ)"],"pubmed_abstract":["<h4>Purpose</h4>Tailoring cancer treatment to tumor molecular characteristics promises to make personalized medicine a reality. However, reliable genetic profiling of archived clinical specimens has been hindered by limited sensitivity and high false-positive rates. Here, we describe a novel methodology, MMP-seq, which enables sensitive and specific high-throughput, high-content genetic profiling in archived clinical samples.<h4>Experimental design</h4>We first validated the technical performance of MMP-seq in 66 cancer cell lines and a Latin square cross-dilution of known somatic mutations. We next characterized the performance of MMP-seq in 17 formalin-fixed paraffin-embedded (FFPE) clinical samples using matched fresh-frozen tissue from the same tumors as benchmarks. To demonstrate the potential clinical utility of our methodology, we profiled FFPE tumor samples from 73 patients with endometrial cancer.<h4>Results</h4>We demonstrated that MMP-seq enabled rapid and simultaneous profiling of a panel of 88 cancer genes in 48 samples, and detected variants at frequencies as low as 0.4%. We identified DNA degradation and deamination as the main error sources and developed practical and robust strategies for mitigating these issues, and dramatically reduced the false-positive rate. Applying MMP-seq to a cohort of endometrial tumor samples identified extensive, potentially actionable alterations in the PI3K (phosphoinositide 3-kinase) and RAS pathways, including novel PIK3R1 hotspot mutations that may disrupt negative regulation of PIK3CA.<h4>Conclusions</h4>MMP-seq provides a robust solution for comprehensive, reliable, and high-throughput genetic profiling of clinical tumor samples, paving the way for the incorporation of genomic-based testing into clinical investigation and practice."],"pubmed_title":["High-throughput detection of clinically relevant mutations in archived tumor samples by multiplexed PCR and next-generation sequencing."],"pubmed_authors":["Bourgon Richard R, Lu Shan S, Yan Yibing Y, Lackner Mark R MR, Wang Weiru W, Weigman Victor V, Wang David D, Guan Yinghui Y, Ryner Lisa L, Koeppen Hartmut H, Patel Rajesh R, Hampton Garret M GM, Amler Lukas C LC, Wang Yulei Y"],"name_synonyms":["F20P5_11, benign mucous membrane pemphigoid, Malignant Neoplasm, Malignancy, ocular pemphigoid, matrix metalloproteinase 7 activity, Metalloproteinases, metalloproteinase pump-1, PUMP, uterine metalloendopeptidase activity, Neoplasms, Benign Neoplasm, Matrix, Benign Neoplasms, Cancers, putative metalloproteinase activity, Tumor, Metalloproteinase, Malignant, cicatricial pemphigoid with ocular involvement, PUMP-1 activity, Neoplasias, ocular pemphigus, matrix metalloproteinase pump 1, benign mucosal pemphigoid, MMP 7, MMPs, Benign, putative (or punctuated) metalloproteinase-1 activity, PUMP-1 proteinase activity, Matrix Metalloproteinase, Neoplasm, MMP, Malignancies, benign mucous membrane pemphigoid with ocular involvement, F20P5.11, matrix metalloproteinase, other neoplasm, Neoplasia, matrin activity, Cancer, Tumors, Malignant Neoplasms."],"description_synonyms":["F20P5_11, benign mucous membrane pemphigoid, Malignant Neoplasm, Malignancy, ocular pemphigoid, matrix metalloproteinase 7 activity, Metalloproteinases, metalloproteinase pump-1, PUMP, uterine metalloendopeptidase activity, Neoplasms, Benign Neoplasm, Matrix, Benign Neoplasms, Cancers, putative metalloproteinase activity, Tumor, Metalloproteinase, Malignant, cicatricial pemphigoid with ocular involvement, PUMP-1 activity, Neoplasias, ocular pemphigus, matrix metalloproteinase pump 1, benign mucosal pemphigoid, MMP 7, MMPs, Benign, putative (or punctuated) metalloproteinase-1 activity, PUMP-1 proteinase activity, Matrix Metalloproteinase, Neoplasm, MMP, Malignancies, benign mucous membrane pemphigoid with ocular involvement, F20P5.11, matrix metalloproteinase, other neoplasm, Neoplasia, matrin activity, Cancer, Tumors, Malignant Neoplasms."],"pubmed_title_synonyms":["polymerase chain reaction., Anchored, Anchored Polymerase Chain Reaction, Malignant Neoplasm, Reactions, Nested, Malignancy, Nested Polymerase Chain Reaction, Neoplasms, Benign Neoplasm, Inverse Polymerase Chain Reaction, Benign Neoplasms, Polymerase Chain Reactions, Cancers, Tumor, Inverse, Malignant, Malignant Neoplasms, Mutations, Neoplasias, Inverse PCR, Benign, Reaction, Neoplasm, Nested PCR, Malignancies, Anchored PCR, Polymerase Chain, other neoplasm, Neoplasia, PCR, Cancer, Tumors"],"pubmed_abstract_synonyms":["Experimental Designs, Formol, RAS, Ras, l(1)G0098, Materials, dP60, Adjustments, endometrium neoplasm (disease), Vps34, Design, Error Sources, BcDNA:LD15217, Tumor, Ras-1, VPS34, 11621, Medical Specialties, Mutations, PI-3 kinase, p110-alpha, ras, benign mucosal pemphigoid, c-ras2, Method, Methanal, Parafilm, AGM7, Line, Kinase, treatment, Dp60, benign mucous membrane pemphigoid, PI3K_59F, Matched Group, Tissue, Oxomethane, Matched, composition, PI3-kinase activity, procedures, cicatricial pemphigoid with ocular involvement, D17Mit170, PI3Kgamma, allergic reaction, ENDMC, MCAP, Inositol Phospholipids, medicine, Reporting, PI3K 68D, Medicine, Cancer of Endometrium, ATP Phosphotransferases, ATP - 1-phosphatidyl-1D-myo-inositol 3-phosphotransferase activity, Data Reporting, CG1799, Tumors, dVps34, Ras2, RAS2, Research Technic, Ras1, RAS1, Research Methodology, rea, familial, DNA catabolism, p50alpha, Tl3, Tl2, CG2699, DmelCG5373, Research Proposal, Medical Speciality, matrix metalloproteinase pump 1, Experimental, Benign, C530050K14, tumor of Endometrium, type-1 PI3K, primary malignant neoplasm of endometrium, dRas85D, Technics, simple tissue, Problem Formulation, ras1, PI3KA, ras2, DNA degradation, BcDNA:RE36103, Carcinomas, CG11621, matrix metalloproteinase 7 activity, content, Hras-1, Benign Neoplasms, Dm Ras1, DmelCG4141, F8A5_4, Malignant Neoplasms, Formulations, APDS, Phosphoinositides, RasI, Material, PI3KBETA, PUMP-1 proteinase activity, other neoplasm, Data Adjustments, Harvey-ras, Hras1, Inositide, Neoplasms, dRas, Matched Groups, Phosphatidylinositol, CG1167, H-ras, DRAS1, DRas2, putative metalloproteinase activity, IMPDH, LD06825, endometrial neoplasm, Dras2, Dras1, Adjustment, PIK3, Medical Specialities, dVps34/PI3K59F, Pi3Kp60, D-Ras, sensitive, Sources, deamination, PI3K-dp110, Kras-2, Phosphatidyl, dPI3K, anon-92Ed, IMPdH, Medical, Ha-ras, Technique, class I, Dras, ras 1, Endometrial cancer, raspberry/impd, study., Pi3Kp110, Ras[V12], Metalloproteinase, EK3-4, Solution, Research Strategy, P110BETA, DRas, Neoplasias, DRas85D/Ras, neoplasm of endometrium, Dmras64B, Endometrial, drugs, PI3K21B, Formalin, putative (or punctuated) metalloproteinase-1 activity, benign mucous membrane pemphigoid with ocular involvement, Insurance, MCM, constitutitional genetic, Cancer, Cpk, p85-ALPHA, Malignant Neoplasm, cou, AA414921, class II, type III phosphoinositide 3-kinase activity, Phosphoglycerides, compositionality, D-ras-1, Cell, PI(3)K, cpk, E(faf), Research Strategies, PI3K-92E/Dp110, malignant endometrial neoplasm, PIK3C1, DmelCG1167, Lr, MT, CWS5, Inositol Phosphoglycerides, Neoplasm, endometrial Ca, S35097, Endometrial Neoplasm, RAS85D, primary cancer, Dmras85D, underdeveloped, Phospholipids, l(1)9Eb, ocular pemphigoid, Metalloproteinases, Specificity, Research Designs, Deaminations, Cancers, Research Technics, DmelCG11621, malignant tumor, Data Adjustment, caPI3K, CLOVE, Error, Oxomethylene, DmVps34, IMD14, PI3K_68D, PI3K-92D, structure, Bra, Dmp110, endometrium tumor, matrix metalloproteinase, Strategy, hereditary, Neoplasia, Endometrial Cancer, Ras1/RAs85D, Research Technique, Problem Formulations, CG5373, ATVPS34, Feature, PI3K, c-rasHa, Dp110, E(sev)3C, Technic, PtdIns, composed of, endometrial tumour, CG11485, Speciality, Techniques, PHOSPHATIDYLINOSITOL 3-KINASE, DmelCG2699, F8A5.4, Specialities, IMD36, p110alpha, phosphatidylinositol 3-kinase activity, D-Ras1, Experimental Design, Group, me75, Insurance Medicine, RTK, Endometrium Carcinomas, Pi3K92D, CG4141, metalloproteinase pump-1, PUMP, Endometrium Cancers, endometrium tumour, l(1)G0436, catalyst activity, Formaldehyd, Designs, hypoplasia, Pi3k, ras85B, Groups, ras85D, experimental design, Endometrium Cancer, PI[[3]]K, T1, Phosphatidyl Inositol, genetic, p55alpha, D-ras-2, tumor of the endometrium, malignant neoplasm, Endometrium Carcinoma, disease management, Therapies, Research Techniques, Malignancies, Pi3K, PI3k, Medicines, MCMTC, GRB1, matrin activity, ATP, Endometrial Carcinoma, Therapy, Carcinoma, Specialties, PI3K68D, l(3)s1747, P110DELTA, Ki-ras, PtdIns-3-kinase activity, Research Proposals, results, vacuolar protein sorting 34, PUMP-1 activity, dPIK, 1-phosphatidylinositol 3-kinase activity, MMP 7, Specialty, MMP, Genetic Materials, p21[Ras1], Phosphoglyceride, dRas1, dRAS1, F20P5.11, Problem, fixed, Dras85D, Genetic Material, ras-2, Lines, Transphosphorylases, F20P5_11, l(1)G0351, LD02673, p85alpha, DmelCG1799, c-Ha-ras, D-ras1, l(1)G0238, D-ras2, C-ras1, PI3K 68_D, Dras64B, endometrial tumor, Features, Endometrial Cancers, Treatments, C-ras2, Endometrium, l(3)06677, l(1)G0002, Insurance Medicines, ocular pemphigus, l(1)G0482, p110D, Specificity and Sensitivity, Patient, c-H-ras, l(1)G0127, Inositide Phospholipids, Cistron, inherited genetic, p120-PI3K, droPIK57, RasV12, PI3K92E, Kras2, Benign Neoplasm, Matrix, Gene, Pi3K_59F, Scoring Method, DmelCG9375, type I phosphatidylinositol kinase activity, Malignant, phosphatidylinositol 3-kinase, l(1)G0388, reduced, Scoring Methods, p60, DNA breakdown, PHOSPATIDYLINOSITOL 3-KINASE, Low, neoplasm of the endometrium, tiny, endometrial cancer, Inositide Phospholipid, l(1)G0380, sensitivity, Phosphotransferase, Dp110/PI3K, PI3K-68D/E, p21B, Methodology, Cancer of the Endometrium, dras1, Dm-ras-64B, Genetic, Phospholipid, Scoring, Malignancy, Research, Proposals, PI3'K, Transphosphorylase, l(1)G0391, Ras 85D, PI3K-68D, Clients, p85, Matrix Metalloproteinase, Error Source, Sensitivity, Characteristics, Strategies, ras-l, Carcinoma of Endometrium, small, l(1)G0056, dP110, Inositol Phosphoglyceride, 6330412C24Rik, Medical Specialty, CG9375, p120, Cell Lines, p110, K-ras, Formulation, Vps34p, Cistrons, Client, Phosphotransferases, Inositol, malignant neoplasm of endometrium, fs(3)05703, ATP:1-phosphatidyl-1D-myo-inositol 3-phosphotransferase activity, Characteristic, vps34, EP(X)1093, dp110, FORMALIN, techniques, PI3CG, AI929937, Proposal, Methods, PI-3-K, Phosphoinositide, tumour of endometrium, PI3K-59F, PI3K-Dp110, Endometrial Carcinomas, Kinases, uterine metalloendopeptidase activity, Source, class III, p110gamma, Su(tor)3-2, Methylene oxide, MMPs, Inositol Phospholipid, Therapeutic, Data, tumour of the endometrium, tumor of endometrium, Treatment, methodology"],"additional_accession":[]},"is_claimable":false,"name":"MMP-seq tumor samples (FASTQ) - samples","description":"MMP-seq tumor samples (FASTQ)","dates":{"updated":"2017-07-26 15:39:25"},"accession":"EGAD00001001108","cross_references":{"TAXONOMY":["9606"],"pubmed":["24573554"],"EGA":["EGAC00001000055","EGAS00001000674"]}}