{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HiSeq 2000;ILLUMINA"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001002885"],"sample_count":["26"],"description":["EGA dataset EGAD00001002885"],"repository":["EGA"],"title":["CPC-GENE Prostate Cancer Heterogeneity Study"],"pubmed_abstract":["Short tandem repeat (STR) analysis, such as the AmpFlSTR® Identifiler® Plus kit, is a standard, PCR-based human genotyping method used in the field of forensics. Misidentification of cell line and tissue DNA can be costly if not detected early; therefore it is necessary to have quality control measures such as STR profiling in place. A major issue in large-scale research studies involving archival formalin-fixed paraffin embedded (FFPE) tissues is that varying levels of DNA degradation can result in failure to correctly identify samples using STR genotyping. PCR amplification of STRs of several hundred base pairs is not always possible when DNA is degraded. The Sample ID Plus® panel from Sequenom allows for human DNA identification and authentication using SNP genotyping. In comparison to lengthy STR amplicons, this multiplexing PCR assay requires amplification of only 76-139 base pairs, and utilizes 47 SNPs to discriminate between individual samples. In this study, we evaluated both STR and SNP genotyping methods of sample identification, with a focus on paired FFPE tumor/normal DNA samples intended for next-generation sequencing (NGS). The ability to successfully validate the identity of FFPE samples can enable cost savings by reducing rework."],"pubmed_title":["Use of Sequenom sample ID Plus® SNP genotyping in identification of FFPE tumor samples."],"pubmed_authors":["Miller Jessica K JK, Buchner Nicholas N, Timms Lee L, Tam Shirley S, Luo Xuemei X, Brown Andrew M K AM, Pasternack Danielle D, Bristow Robert G RG, Fraser Michael M, Boutros Paul C PC, McPherson John D JD"],"pubmed_title_synonyms":["Dmel_CG6393, DmelCG42257, cg11478, Malignant Neoplasm, Malignancy, Neoplasms, Benign Neoplasm, Benign Neoplasms, Cancers, CG30327, Tumor, Malignant, sample population, Neoplasias, CG11478, Benign, 65K, sample, CG6393, CG42257, Dmel_CG30327, Neoplasm, snp, Malignancies, other neoplasm, Neoplasia, Cancer, Tumors, Malignant Neoplasms."],"name_synonyms":["TSSC5, Svc, nmf250, study, ITM, Bru, BWR1A, Col4a-1, ORCTL2, Raw, GP91-3, AW260131, het, SAFB1, Slc22a1l, p45-BWR1A, 3110021E02Rik, Impt1, IMPT1, E130307D12, D18386, sequence, SAF-B1, primary structure of sequence macromolecule., Del(8)44H, HET, HAP, SLC22A1L, 5330423C17Rik, AU018122, Orctl2, BWSCR1A"],"pubmed_abstract_synonyms":["Atr25D, AI747449, scale tissue, Formol, Activity, determination, Laboratory, acetylglucosaminyltransferase-like protein, Str, Mbp1, Xkl-1, CG30327, Tumor, H105E3, CG11478, KL receptor activity, Techniques, serRS, Gsfsco1, Saving, Method, Methanal, Parafilm, str, SCO5, Line, SCO1, Polymerase Chain, Research Activity, Gsfsow3, Fs(3)Hor, myd, Gsfsco5, Laboratory Research, SOW3, Priorities, average, Savings, DmelCG42257, thymus nucleic acid, DmelCG2684, Man (Taxonomy), like-acetylglucosaminyltransferase, DmelCG14026, developmental field, plant peltate hair, Tissue, Formaldehyd, Oxomethane, Inverse Polymerase Chain Reaction, Mbp-1, W, procedures, NTef2, Sars1, Methodological Studies, scientific observation, Reaction, sample, Bs, Double-Stranded DNA, Malignancies, deoxyribonucleic acids, Research Priority, DNAn, Sl, Tumors, Base Pairings, Anchored Polymerase Chain Reaction, Cost Saving., functional failure, gyltl1b-b, Modern, DNA catabolism, Tr-kit, Research Priorities, future organ, Double-Stranded, Procedure, Fs(3)Sz11, (Deoxyribonucleotide)n+m, shortened, PBT, Strs, Benign, MDDGA6, mKIAA0609, CG6393, kl1-A, simple tissue, failure, KIT, desoxyribose nucleic acid, KIAA0609, fixed, acetylglucosaminyltransferase-like 1A, DNA degradation, TKV, Tkv, PCR, Lines, Research and Development, tyrosine-protein kinase Kit, fg, pbt, Dmel_CG6393, gyltl1b, Nested Polymerase Chain Reaction, mdc1d, Control, Benign Neoplasms, Quality, kit, Methodological, Controls, Methodological Study, LARGE_HUMAN, human, polymerase chain reaction, early, Malignant Neoplasms, Activities, Atkv, MDC1D, enr, Horka, ds DNA, CG2684, Fs(3)Horka, DNA, short, other neoplasm, krk1, tkv1, human being, DNS, Procedures, (Deoxyribonucleotide)n, Neoplasms, peltate hair, Benign Neoplasm, SCF receptor activity, Polymerase Chain Reactions, disfunctional, Inverse, Malignant, LARGE1, Deoxyribonucleic acids, froggy, Gyltl1a, Human, method, organ field, Inverse PCR, scfr, Homo sapiens, Deoxyribonucleic Acid, DNA breakdown, method used in an experiment, Studies, field, DmF2, SCFR, Man, Technique, lod, study, Fdc, FOCUS, Malignancy, Research, MDDGB6, stubby, tkva, Double Stranded, Deoxyribonucleic acid, LARGE, Dtfr, Study, Neoplasias, BPFD#36, Quality Controls, Formalin, kv, Base Pair, 65K, CG42257, Dmel_CG30327, dtfr, snp, TKV1, Anchored PCR, (Deoxyribonucleotide)m, Development and Research, Cancer, measuring, proto-oncogene c-Kit, cg11478, STK-A, Malignant Neoplasm, DNAn+1, Brk25D, Cell Lines, defective, Cell, Priority, KIT ligand receptor activity, chemical analysis, Research Activities, l(2)25Da, Neoplasm, Bpa, Brk25D2, FORMALIN, Brk25D1, techniques, ds-DNA, scales, CG14026, XKrk1, Anchored, Base Pairs, c-KIT, Reactions, Nested, scale, Cost, Cancers, CD117, Lds, Methylene oxide, sample population, plan specification, c-kit, like-glycosyltransferase, C-Kit, Oxomethylene, Ssm, XAP104, Modern Man, xkl-1, Desoxyribonukleinsaeure, Nested PCR, assay, l(2)04415, Neoplasia, glycosyltransferase-like protein LARGE1, methodology"],"description_synonyms":["Raw., Svc, Bru, Del(8)44H, Col4a-1"],"additional_accession":[]},"is_claimable":false,"name":"CPCG Het Study, Raw Fastq Sequence - samples","description":"Raw sequence data, fastq format","dates":{"updated":"2017-07-26 15:39:29"},"accession":"EGAD00001002885","cross_references":{"TAXONOMY":["9606"],"pubmed":["24551080"],"EGA":["EGAC00001000010","EGAS00001000549"]}}