EGAGenomicsIllumina HiSeq 2000;https://ega-archive.org/datasets/EGAD000010009674EGA dataset EGAD00001000967EGA<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.A comparative analysis of algorithms for somatic SNV detection in cancer.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 DLVasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASPNeoplasias, 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.leukemia, Antemortem Diagnoses, screening, Antemortem Diagnosis, findings, DNS, Data Set, (Deoxyribonucleotide)n, Effects, DNAn+1, Longterm Effect, chronic granulocytic leukaemia, Double-Stranded, Diagnosis, Client, chronic, Examination and Diagnoses, Deoxyribonucleic acids, Long Term, Diagnoses, (Deoxyribonucleotide)n+m, CML, chronic myelogenous, Postmortem, Screenings, medulla ossium, Deoxyribonucleic Acid, chronic myelogenous leukemia, Mass Screenings, Marrow, medulla ossea, Examinations and Diagnoses, Long Term Effects, Mass, symptoms, Screening, Yellow, atypical, ds-DNA, Antemortem, Postmortem Diagnosis, desoxyribose nucleic acid, Effect, Diagnoses and Examination, Yellow Marrow, Postmortem Diagnoses, thymus nucleic acid, chronic myeloid, Longterm, medullary bone, medulla of bone, signs, Double Stranded, Deoxyribonucleic acid, patient, Long-Term, Diagnoses and Examinations, Longterm Effects, Red Marrow, chronic granulocytic leukemia, Patient, chronic myelogenous leukaemia, Clients, ds DNA, CML - chronic Myelogenous Leukemia, Myeloid Leukemia, chronic myeloid leukaemia, Red, Desoxyribonukleinsaeure, Double-Stranded DNA, Long-Term Effect, (Deoxyribonucleotide)m, DNA, deoxyribonucleic acids, DNAn, Diagnoses., Bone, Long-Term Effects, DiagnoseMyelocytic, Single Nucleotide Variant, Quantity Final Containers Returned, Chronic Myelocytic Leukemia, Antemortem Diagnosis, Chronic Granulocytic Leukemia, determination, Chronic Myeloid Leukemia, Myeloid, CG 1618, Sequence Determination, clinical data, Characterization, Myelocytic Leukemia, dNSF, Philadelphia-Positive Myeloid Leukemias, Tumor, R01 Program, Diagnosis, Molecular Biologies, aa, Assigned, Mutations, Personal, chronic myelogenous, Compared, DmNSF, Bio Informatics, sequencing assay, eTMF Content Model Code, Code, Likely, symptoms, dNSF1, dNsf1, Whole Transcriptome, Transcriptome Sequencing, Ph1 Positive, Analysis, Detection, BCR1, Chronic Myelocytic Leukemias, treatment, average, Multicase, me75, F, Analyses, Identification, Biology, Determination, availability, Illumina Sequencing, Complete Exome Sequencing, Whole Transcriptome Sequencing, Matched, Chronic Myelogenous Leukemias, Of Each, Myelogenous Leukemia, Comparison, Sequence Determinations, Research Project Grants, Bio-Informatic, adult chronic leukaemia, D17Mit170, T1, Computational, Granulocytic, 5-Ethyl-2'-Deoxyuridine, Returned, DNA Sequence Analysis, Code Name, malignant neoplasm, Bio-Informatics, disease management, Therapies, adult chronic leukemia, Ph1-Positive Myeloid Leukemia, Malignancies, Assign, Computational Molecular Biologies, Diagnose, Tumors, Therapy, Myelogenous, screening, Noise, Apply, sequencing_assay, Granulocytic Leukemias, Exome, Biologies, Ph1-Positive Myelogenous Leukemia, Pollution, Sequencing Data, Research Grants, Philadelphia-Positive, somatic, DETECTION, Tl3, Tl2, HTT Protein Measurement, results, Computational Molecular, Determinations, Diagnoses, Incentive, Candidate, Contact Person, Ph1-Positive, D22S662, Ph1-Positive Myeloid Leukemias, Postmortem, Screenings, Benign, Edoxudine, HTTP, Examinations and Diagnoses, Algorithm, Philadelphia-Positive Myeloid, Computational Molecular Biology, DNA Sequence Determinations, NOS, DNA Sequence, Postmortem Diagnosis, Uridine, accessionNumberText, Clinical Data, DNA sequencing, dnsf1, Diagnoses and Examination, Chronic granulocytic leukemia, Postmortem Diagnoses, Complete Transcriptome, Chronic Granulocytic, Chronic Myelogenous, Bioinformatic, Disincentive, Chronic Myeloid Leukemias, Nucleic Acid Sequencing, Review, Biological Detection Test, Ph1-Positive Myelogenous, Dignity, signs, common, Benign Neoplasms, Ph1-Positive Myeloid, Treatments, class, Malignant Neoplasms, Identified, Characterized, Huntingtin Protein Measurement, Return, chronic granulocytic leukemia, Patient, Info, CML - chronic Myelogenous Leukemia, Whole Exome Sequencing, NSF-1, PointOfContact, Noise Pollution, DNA, Review of Reported Cases, Detected, snv variant, Transcriptome Sequencings, Sequence Analysis, Myelogenous Leukemias, CLL, Incentives, Clinical Batch, Respect, Philadelphia Positive, Material Identification, Complete Exome, Remove, False, Neoplasms, Assignment, Benign Neoplasm, number, Comt, NSF1, chronic granulocytic leukaemia, Compare, RWJ 15817, Available, Malignant, presence, Illumina, Computational., EUDR, NSF, Nsf, CML, CG1618, SEQUENCING, Biopolymer Sequencing, Sites, Mass, Screening, atypical, Philadelphia-Positive Myeloid Leukemia, Low, Antemortem, Application, Site, Somatic, Chronic Granulocytic Leukemias, snv_variant, WES, Motivations, chronic myeloid, Complete, Leukemia, Exome Sequencings, Clinical, Malignancy, Academic, D22S11, EDOXUDINE, Granulocytic Leukemia, PHL, Diagnoses and Examinations, SNV, Sequencing, Probabilities, Neoplasias, Whole Exome, Accession, Ph1-Positive Myelogenous Leukemias, Clients, Whole, Personal Respect, heterogeneity, Myeloid Leukemia, Myelocytic Leukemias, DmelCG1618, Chronic, Disincentives, Sequence Analyses, Cancer, Removal, com, ALL, leukemia, Antemortem Diagnoses, Probably, Molecular Biology, ORF 15817, findings, Characters, Malignant Neoplasm, Complete Exome Sequencings, cou, R-Series, Chronic Myelocytic, Matching, EDU, Personal Contact, Assigned Value, Client, Examination and Diagnoses, Leukemias, chronic, Bioinformatics, R01 Mechanism, Availability, Communication Contact, Exome Sequencing, count in organism, Lr, MT, Review Literature, Clinical Lot, Chronic myelogenous leukemia, chronic myelogenous leukemia, Physical Contact, Mass Screenings, DNA Sequencing, Applied, chemical analysis, Myeloid Leukemias, Research Projects, Neoplasm, Huntingtin Protein, clinical, Sequence Data, Ana, Coding System, Illumina Sequencing Technology, dNSF-1, Xcml, susceptibility, code, primary cancer, Complete Transcriptome Sequencing, RPG, Chronic Myelogenous Leukemia, Information, Single Nucleotide Variants, Match, cml-A, Likeliness, myeloid, patient, Cancers, 2'-Deoxy-5-Ethyl-, malignant tumor, DNA Sequence Determination, NUCLEIC ACID SEQUENCING, Noises, DNA Sequence Analyses, socioeconomic factors, Therapeutic, chronic myelogenous leukaemia, cardinality, chronic myeloid leukaemia, Contact, Bra, Accession Number, CODE, Treatment, assay, Neoplasia, Chronic Myeloidfalseena-DATASET-sacgf-04-08-2014-08:35:16:587-100 - samplesThis dataset contains the fastq sequencing data collected from bone marrow DNA of a chronic myeloid leukaemia patient at time of diagnosis.2017-07-26 15:39:25EGAD00001000967960623842810EGAC00001000220EGAS00001000927