{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"contact_person":["Dr Andreas Schreiber"],"full_dataset_link":["https://ega-archive.org/dacs/EGAC00001000220"],"host":["EGA"],"description":["EGA DAC EGAC00001000220"],"repository":["EGA"],"email":["andreas.schreiber@adelaide.edu.au"],"pubmed_abstract":["<h4>Motivation</h4>With the advent of relatively affordable high-throughput technologies, DNA sequencing of cancers is now common practice in cancer research projects and will be increasingly used in clinical practice to inform diagnosis and treatment. Somatic (cancer-only) single nucleotide variants (SNVs) are the simplest class of mutation, yet their identification in DNA sequencing data is confounded by germline polymorphisms, tumour heterogeneity and sequencing and analysis errors. Four recently published algorithms for the detection of somatic SNV sites in matched cancer-normal sequencing datasets are VarScan, SomaticSniper, JointSNVMix and Strelka. In this analysis, we apply these four SNV calling algorithms to cancer-normal Illumina exome sequencing of a chronic myeloid leukaemia (CML) patient. The candidate SNV sites returned by each algorithm are filtered to remove likely false positives, then characterized and compared to investigate the strengths and weaknesses of each SNV calling algorithm.<h4>Results</h4>Comparing the candidate SNV sets returned by VarScan, SomaticSniper, JointSNVMix2 and Strelka revealed substantial differences with respect to the number and character of sites returned; the somatic probability scores assigned to the same sites; their susceptibility to various sources of noise; and their sensitivities to low-allelic-fraction candidates.<h4>Availability</h4>Data accession number SRA081939, code at http://code.google.com/p/snv-caller-review/<h4>Contact</h4>david.adelson@adelaide.edu.au<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online."],"pubmed_title":["A comparative analysis of algorithms for somatic SNV detection in cancer."],"pubmed_authors":["Roberts Nicola D ND, Kortschak R Daniel RD, Parker Wendy T WT, Schreiber Andreas W AW, Branford Susan S, Scott Hamish S HS, Glonek Garique G, Adelson David L DL"],"pubmed_title_synonyms":["Neoplasias, primary cancer, MT, Benign, Malignant Neoplasm, determination, malignant neoplasm, Malignancy, Algorithm, chemical analysis, Neoplasms, Neoplasm, Benign Neoplasm, Malignancies, Benign Neoplasms, assay, Cancers, Tumor, Malignant, malignant tumor, Neoplasia, Cancer, Tumors, Malignant Neoplasms."],"name_synonyms":["cytopathology, biopsy, histopathology, Pathologies."],"pubmed_abstract_synonyms":["Myelocytic, Chronic Myelocytic Leukemia, Antemortem Diagnosis, Chronic Granulocytic Leukemia, Activity, determination, Chronic Myeloid Leukemia, Laboratory, Myeloid, Sequence Determination, Myelocytic Leukemia, Philadelphia-Positive Myeloid Leukemias, Tumor, Diagnosis, Mutations, Personal, chronic myelogenous, symptoms, Whole Transcriptome, Transcriptome Sequencing, Ph1 Positive, Analysis, Research Activity, Laboratory Research, BCR1, Chronic Myelocytic Leukemias, Priorities, treatment, average, me75, F, Analyses, Determination, availability, Complete Exome Sequencing, Whole Transcriptome Sequencing, Chronic Myelogenous Leukemias, Myelogenous Leukemia, Sequence Determinations, adult chronic leukaemia, D17Mit170, T1, Granulocytic, DNA Sequence Analysis, malignant neoplasm, disease management, Therapies, adult chronic leukemia, Ph1-Positive Myeloid Leukemia, Malignancies, Research Priority, Nucleotide, Diagnose, Tumors, Therapy, Myelogenous, screening, Noise, Granulocytic Leukemias, Exome, Ph1-Positive Myelogenous Leukemia, Pollution, Research Priorities, Philadelphia-Positive, Tl3, Tl2, results, Determinations, Diagnoses, Incentive, Ph1-Positive, D22S662, Ph1-Positive Myeloid Leukemias, Benign, Postmortem, Screenings, Examinations and Diagnoses, Algorithm, Philadelphia-Positive Myeloid, DNA Sequence Determinations, DNA Sequence, Postmortem Diagnosis, nucleotides, DNA sequencing, Research and Development, Diagnoses and Examination, Chronic granulocytic leukemia, Postmortem Diagnoses, Complete Transcriptome, Chronic Granulocytic, Chronic Myelogenous, Disincentive, Chronic Myeloid Leukemias, Review, Ph1-Positive Myelogenous, Dignity, signs, common, Benign Neoplasms, Ph1-Positive Myeloid, Treatments, Malignant Neoplasms, Activities, chronic granulocytic leukemia, Patient, CML - chronic Myelogenous Leukemia, Whole Exome Sequencing, Noise Pollution, DNA, Review of Reported Cases, Multicase., other neoplasm, Transcriptome Sequencings, Myelogenous Leukemias, CLL, Incentives, Respect, Philadelphia Positive, Complete Exome, False, Neoplasms, Benign Neoplasm, number, chronic granulocytic leukaemia, Malignant, presence, CML, Mass, Screening, atypical, Philadelphia-Positive Myeloid Leukemia, Low, Antemortem, Chronic Granulocytic Leukemias, WES, Motivations, chronic myeloid, Complete, Leukemia, Exome Sequencings, Malignancy, Research, Academic, D22S11, Granulocytic Leukemia, PHL, Diagnoses and Examinations, Sequencing, Probabilities, Neoplasias, Whole Exome, Ph1-Positive Myelogenous Leukemias, Clients, Whole, Personal Respect, heterogeneity, Myeloid Leukemia, Myelocytic Leukemias, Chronic, Development and Research, Disincentives, Sequence Analyses, Cancer, leukemia, ALL, Antemortem Diagnoses, findings, Characters, Malignant Neoplasm, Complete Exome Sequencings, cou, Chronic Myelocytic, Client, Examination and Diagnoses, chronic, Leukemias, Exome Sequencing, count in organism, Priority, Lr, MT, Review Literature, Chronic myelogenous leukemia, chronic myelogenous leukemia, Mass Screenings, DNA Sequencing, chemical analysis, Myeloid Leukemias, Research Activities, Neoplasm, Xcml, susceptibility, primary cancer, Complete Transcriptome Sequencing, Chronic Myelogenous Leukemia, cml-A, patient, Cancers, malignant tumor, DNA Sequence Determination, Noises, DNA Sequence Analyses, Therapeutic, chronic myelogenous leukaemia, cardinality, chronic myeloid leukaemia, Bra, Treatment, assay, Neoplasia, Chronic Myeloid"],"additional_accession":[]},"is_claimable":false,"name":"SA Pathology Data Access Committee","description":"Data Access Committee EGAC00001000220","dates":{"output":"2025-1-9"},"accession":"EGAC00001000220","cross_references":{"TAXONOMY":["9606"],"pubmed":["23842810"],"EGA":["EGAS00001004145","EGAS00001003547","EGAS00001000927","EGAS00001004176","EGAS00001004793","EGAS00001003861","EGAS00001004273","EGAS00001003071","EGAD00001005364","EGAD00001000967","EGAD00001005937","EGAD00001006578","EGAD00001004861","EGAD00001005775","EGAD00001006010","EGAD00001004179"]}}