{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"technology_type":["Illumina HiScanSQ, Illumina_Human660W-Quad_v1_A-Not supplied"],"study_type":["Other"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001000558"],"host":["EGA"],"description":["EGA study EGAS00001000558"],"dataset_title":["DNA sequencing of samples from tumoural tissue of colon biopsies","Title not provided","DNA sequencing of samples from normal tissue of colon biopsies"],"category":["restricted"],"repository":["EGA"],"pubmed_abstract":["<h4>Background</h4>Deviations in the amount of genomic content that arise during tumorigenesis, called copy number alterations, are structural rearrangements that can critically affect gene expression patterns. Additionally, copy number alteration profiles allow insight into cancer discrimination, progression and complexity. On data obtained from high-throughput sequencing, improving quality through GC bias correction and keeping false positives to a minimum help build reliable copy number alteration profiles.<h4>Results</h4>We introduce seqCNA, a parallelized R package for an integral copy number analysis of high-throughput sequencing cancer data. The package includes novel methodology on (i) filtering, reducing false positives, and (ii) GC content correction, improving copy number profile quality, especially under great read coverage and high correlation between GC content and copy number. Adequate analysis steps are automatically chosen based on availability of paired-end mapping, matched normal samples and genome annotation.<h4>Conclusions</h4>seqCNA, available through Bioconductor, provides accurate copy number predictions in tumoural data, thanks to the extensive filtering and better GC bias correction, while providing an integrated and parallelized workflow."],"pubmed_title":["seqCNA: an R package for DNA copy number analysis in cancer using high-throughput sequencing."],"pubmed_authors":["Mosen-Ansorena David D, Telleria Naiara N, Veganzones Silvia S, De la Orden Virginia V, Maestro Maria Luisa ML, Aransay Ana M AM"],"name_synonyms":["Adenocarcinoma, colon tumor, Colon Neoplasm, cg11478, human being, DNS, malignant neoplasm of colon, (Deoxyribonucleotide)n, Colon Adenocarcinomas, malignant, DNAn+1, Neoplasms, Modern, Colon Cancer, Double-Stranded, Colon Adenocarcinoma, CG30327, Adenocarcinomas, autosomal dominant, Deoxyribonucleic acids, Dmel_CG30327., Human, (Deoxyribonucleotide)n+m, colon neoplasm, CG11478, malignant colonic neoplasm, Colonic Cancers, Deoxyribonucleic Acid, Homo sapiens, CG6393, Neoplasm, Colon Neoplasms, malignant tumor of colon, malignant colonic tumor, malignant tumour of colon, CRC, ds-DNA, desoxyribose nucleic acid, Man, malignant tumor of the colon, malignant colon tumour, average, Dmel_CG6393, DmelCG42257, Colon Cancers, thymus nucleic acid, Colonic, Man (Taxonomy), susceptibility to, Colonic Neoplasm, Colon cancer, Double Stranded, Deoxyribonucleic acid, Colonic Cancer, Cancers, Cancer of the Colon, Colon, human, large intestine cancer, malignant colon tumor, malignant colonic tumour, colon cancer, Cancer of Colon, 65K, malignant tumour of the colon, Modern Man, ds DNA, malignant neoplasm of the colon, CG42257, Desoxyribonukleinsaeure, Double-Stranded DNA, snp, (Deoxyribonucleotide)m, DNA, deoxyribonucleic acids, cancer of colon, DNAn, malignant colon neoplasm, somatic mutation, Cancer"],"description_synonyms":["Adenocarcinoma, colon tumor, Colon Neoplasm, human being, DNS, malignant neoplasm of colon, Procedures, (Deoxyribonucleotide)n, Colon Adenocarcinomas, Neoplasms, number, Colon Cancer, CG30327, autosomal dominant, presence, Deoxyribonucleic acids, Human, colon neoplasm, CG11478, malignant colonic neoplasm, Techniques, Deoxyribonucleic Acid, Homo sapiens, Method, Studies, Colon Neoplasms, malignant tumor of colon, malignant tumour of colon, Man, Technique, malignant tumor of the colon, malignant colon tumour, average, study, DmelCG42257, thymus nucleic acid, Colonic, Man (Taxonomy), Double Stranded, Deoxyribonucleic acid, Colonic Cancer, procedures, Cancer of the Colon, large intestine cancer, Study, malignant colon tumor, malignant colonic tumour, Methodological Studies, 65K, malignant neoplasm of the colon, CG42257, Dmel_CG30327, Double-Stranded DNA, snp, (Deoxyribonucleotide)m, deoxyribonucleic acids, cancer of colon, DNAn, somatic mutation, Cancer, cg11478, malignant, DNAn+1, Modern, Double-Stranded, Colon Adenocarcinoma, Procedure, Adenocarcinomas, results, (Deoxyribonucleotide)n+m, count in organism, Colonic Cancers, microarray., CG6393, Neoplasm, malignant colonic tumor, CRC, techniques, ds-DNA, desoxyribose nucleic acid, Dmel_CG6393, Colon Cancers, susceptibility to, Colonic Neoplasm, Colon cancer, Cancers, Methodological, Colon, Methodological Study, human, colon cancer, Cancer of Colon, malignant tumour of the colon, Modern Man, ds DNA, cardinality, Desoxyribonukleinsaeure, DNA, malignant colon neoplasm, methodology"],"pubmed_title_synonyms":["thymus nucleic acid, primary cancer, DNS, Malignant Neoplasm, (Deoxyribonucleotide)n, determination, Malignancy, DNAn+1, Neoplasms, number, Benign Neoplasm, Double Stranded, Benign Neoplasms, Deoxyribonucleic acid, Cancers, Double-Stranded, Tumor, Malignant, presence, malignant tumor, Deoxyribonucleic acids, (Deoxyribonucleotide)n+m, Neoplasias, count in organism, MT, Benign, Deoxyribonucleic Acid, malignant neoplasm, ds DNA, cardinality, chemical analysis, Desoxyribonukleinsaeure, Neoplasm, Double-Stranded DNA, Malignancies, (Deoxyribonucleotide)m, assay, DNA, deoxyribonucleic acids, DNAn, ds-DNA, desoxyribose nucleic acid, Neoplasia, Cancer, Tumors, Malignant Neoplasms."],"pubmed_abstract_synonyms":["Extensive, Scientific Bias, determination, Data Mapping, Tumor, Integral, composed of, Pack, Integrated, Pack Dosing Unit, copy_number, sequencing assay, Epidemiologic Biase, Correlated, Work Flows., MIN, Ecological, correlation, Work Flow, Obtained, INSL3R, Progression, Correlation, Ecological Biases, Copy Number Reported, F, Selection, Gene Expressions, and Cellular and Tissue-Based Products Packing, Genomes, availability, Moods, IMPROVED, copy number variant, min, composition, Oncogeneses, procedures, Elected, Selected, Based, Minangkabau Language, paired, Novel, GREAT, Pick, STEPS to Enhance Physical Activity (STEPS), malignant neoplasm, Statistical Biases, COPYNUM, Great, CS, Ecological Bias, Copy Number Alteration, Malignancies, Systematic, Choose, Better, Select, Epidemiologic Biases, Tumors, sequencing_assay, Scientific, Epidemiologic, Package Dosing Unit, CORRECTION, PACKAGE, Ecological Fallacies, copy number, results, Human Cells, Outcome Measurement Errors, Drug Package, Mathematical Integral, Workflows, Experimental, Benign, STEPS to Enhance Physical Activity, Tumor Progression, Disease Progression, Obtain, Copy Number Polymorphism, NOS, Truncation Bias, END, LGR8, Lgr8, Bias, Nucleic Acid Sequencing, Cancer Disease Progression, Copy Number Variation, Correction, content, Benign Neoplasms, whole genome, Outcome Measurement, Picked, Program Package, {PACKAGE}, Improved, Genomic, Malignant Neoplasms, Experimental Bias, Outcome Measurement Error, HCT/P Packing, Oncogenesis, packaging, Matched Normal, Election, Base, Sequence Analysis, Minangkabau, CHOSEN, Tumorigeneses, Step Unit of Distance, {STEP}, False, Ecological Fallacy, Neoplasms, Correction Report, Truncation, Benign Neoplasm, Correlative, Gene, Systematic Bias, Available, Malignant, STEPS Intervention, Aid, mapping, SEQUENCING, Structural, Biopolymer Sequencing, It improved, Minimal, Mood, CNA, Assisted, Package, Fallacies, Minimum, Help, CNP, Gpr106, CNV, Malignancy, disease progression, Tissues, Profile, Aggregation, Matched_Normal, Better than Others, BETTER/IMPROVED/RECOVERING, RXFPR2, Expressions, Structure, Sequencing, Neoplasias, Annotation, genome, Expression, Chosen Chinese, GPR106, HHT1, Cancer, Biase, New, Fallacy, Choice, Molecular Biology, Copy Number Variant, adequate, Malignant Neoplasm, Edg, Mapping, Affects, Truncation Biases, Build, compositionality, Tumorigenesis, Assistance, Availability, read, MT, chemical analysis, Neoplasm, Errors, background, techniques, Packaging, Chose, STEPS, Basic, Copy Number, primary cancer, progression, Pre-Release Version, copy_number_variant, Chosen, Carcinogeneses, MINIMUM, Basis, Biases, Matched Tissues, Accuracy, Cancers, LGR8.1, malignant tumor, {Step}, introduction, NUCLEIC ACID SEQUENCING, Accurate, Minimum Value Derivation Technique, LAB_SEQ_METHOD, Cancer Progression, Error, Aggregation Bias, structure, Statistical Bias, {Package}, assay, Statistical, ORW1, Genome, Neoplasia, Assist, methodology"],"additional_accession":[]},"is_claimable":false,"name":"DNA from colon cancer samples and matched normal samples was hybridized on Human 660W-Quad SNP arrays and sequenced in Illumina HiScanSQ.","description":"DNA from colon cancer samples and matched normal samples was hybridized on Human 660W-Quad SNP arrays and sequenced in Illumina HiScanSQ. The objective of the study was to introduce methodology for the detection of genomic copy number alterations (CNAs) using high-throughput sequencing data. The samples in this study allow the comparison of the results from the seqCNA R package with those from other methods that detect copy number alterations (CNAs) in tumoural samples, either using SNP-array data or high-throughput sequencing data.","dates":{"updated":"2017-07-26 15:39:25"},"accession":"EGAS00001000558","cross_references":{"TAXONOMY":["9606"],"pubmed":["24597965"],"EGA":["EGAD00010000492","EGAD00001000643","EGAD00001000642","EGAD00010000494","EGAC00001000124"]}}