Systematic comparison of somatic variant calling performance among different sequencing depth and mutation frequency
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Yuchen Yuan | Shudai Lin | Zixi Chen | Xingsong Li | Xiaoshi Chen | Jiayun Chen | H. Du
[1] Erratum: Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. , 2020, CA: a cancer journal for clinicians.
[2] Birgit Funke,et al. Best practices for benchmarking germline small-variant calls in human genomes , 2019, Nature Biotechnology.
[3] A. Jemal,et al. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries , 2018, CA: a cancer journal for clinicians.
[4] A. Halpern,et al. Strelka2: fast and accurate calling of germline and somatic variants , 2018, Nature Methods.
[5] Christopher T. Saunders,et al. Strelka2: fast and accurate calling of germline and somatic variants , 2018, Nature Methods.
[6] Jia Gu,et al. fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.
[7] M. Tarnopolsky,et al. Whole‐exome sequencing is a valuable diagnostic tool for inherited peripheral neuropathies: Outcomes from a cohort of 50 families , 2018, Clinical genetics.
[8] C. Marshall,et al. Prospective cohort study for identification of underlying genetic causes in neonatal encephalopathy using whole-exome sequencing , 2017, Genetics in Medicine.
[9] S. Eschrich,et al. Evaluating somatic tumor mutation detection without matched normal samples , 2017, Human Genomics.
[10] Joel Pel,et al. Duplex Proximity Sequencing (Pro-Seq): A method to improve DNA sequencing accuracy without the cost of molecular barcoding redundancy , 2017, bioRxiv.
[11] V. Marx. How to deduplicate PCR , 2017, Nature Methods.
[12] J. Rosenfeld,et al. Interpreting Incidentally Identified Variants in Genes Associated With Catecholaminergic Polymorphic Ventricular Tachycardia in a Large Cohort of Clinical Whole-Exome Genetic Test Referrals , 2017, Circulation. Arrhythmia and electrophysiology.
[13] Jefferey Chen,et al. Exome sequencing covers >98% of mutations identified on targeted next generation sequencing panels , 2017, PloS one.
[14] Andrew C. Adey,et al. Sequencing thousands of single-cell genomes with combinatorial indexing , 2017, Nature Methods.
[15] Walter J Curran,et al. Lung cancer: current therapies and new targeted treatments , 2017, The Lancet.
[16] M. Weerts,et al. Somatic mutation detection using various targeted detection assays in paired samples of circulating tumor DNA, primary tumor and metastases from patients undergoing resection of colorectal liver metastases , 2016, Molecular oncology.
[17] Lin He,et al. In-depth comparison of somatic point mutation callers based on different tumor next-generation sequencing depth data , 2016, Scientific Reports.
[18] Mariella G. Filbin,et al. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma , 2016, Nature.
[19] M. Berger,et al. Reliable Detection of Mismatch Repair Deficiency in Colorectal Cancers Using Mutational Load in Next-Generation Sequencing Panels. , 2016, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.
[20] Xiaoyu Chen,et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications , 2016, Bioinform..
[21] Lincoln D. Stein,et al. Simple, multiplexed, PCR-based barcoding of DNA enables sensitive mutation detection in liquid biopsies using sequencing , 2016, Nucleic acids research.
[22] Mads Thomassen,et al. Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data , 2016, PloS one.
[23] Ash A. Alizadeh,et al. Integrated digital error suppression for improved detection of circulating tumor DNA , 2016, Nature Biotechnology.
[24] Wendy K Chung,et al. Pathogenic and likely pathogenic variant prevalence among the first 10,000 patients referred for next-generation cancer panel testing , 2015, Genetics in Medicine.
[25] O. Hofmann,et al. VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research , 2016, Nucleic acids research.
[26] Michael C. Heinold,et al. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing , 2015, Nature Communications.
[27] Geoffrey R. Oxnard,et al. Bias-Corrected Targeted Next-Generation Sequencing for Rapid, Multiplexed Detection of Actionable Alterations in Cell-Free DNA from Advanced Lung Cancer Patients , 2015, Clinical Cancer Research.
[28] S. Mundlos,et al. Comparison of Exome and Genome Sequencing Technologies for the Complete Capture of Protein‐Coding Regions , 2015, Human mutation.
[29] Michael Boutros,et al. Amplicon Sequencing of Colorectal Cancer: Variant Calling in Frozen and Formalin-Fixed Samples , 2015, PloS one.
[30] M. Tétreault,et al. Whole-exome sequencing as a diagnostic tool: current challenges and future opportunities , 2015, Expert review of molecular diagnostics.
[31] Theresa Zhang,et al. Personalized genomic analyses for cancer mutation discovery and interpretation , 2015, Science Translational Medicine.
[32] A. Iafrate,et al. Anchored multiplex PCR for targeted next-generation sequencing , 2014, Nature Medicine.
[33] Mikhail Shugay,et al. Towards error-free profiling of immune repertoires , 2014, Nature Methods.
[34] K. Robasky,et al. The role of replicates for error mitigation in next-generation sequencing , 2013, Nature Reviews Genetics.
[35] Marilyn M. Li,et al. Clinical application of amplicon-based next-generation sequencing in cancer. , 2013, Cancer genetics.
[36] Peilin Jia,et al. Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers , 2013, Genome Medicine.
[37] Mauricio O. Carneiro,et al. From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.
[38] Jay Shendure,et al. Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation , 2013, Genome research.
[39] Jesse J. Salk,et al. Detection of ultra-rare mutations by next-generation sequencing , 2012, Proceedings of the National Academy of Sciences.
[40] H. Swerdlow,et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers , 2012, BMC Genomics.
[41] T. Dallman,et al. Performance comparison of benchtop high-throughput sequencing platforms , 2012, Nature Biotechnology.
[42] P. A. Futreal,et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. , 2012, The New England journal of medicine.
[43] Christopher A. Miller,et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. , 2012, Genome research.
[44] S. Linnarsson,et al. Counting absolute numbers of molecules using unique molecular identifiers , 2011, Nature Methods.
[45] Heng Li,et al. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..
[46] K. Kinzler,et al. Detection and quantification of rare mutations with massively parallel sequencing , 2011, Proceedings of the National Academy of Sciences.
[47] M. DePristo,et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.
[48] K. Flaherty,et al. Inhibition of mutated, activated BRAF in metastatic melanoma. , 2010, The New England journal of medicine.
[49] A. Tutt,et al. Oral poly(ADP-ribose) polymerase inhibitor olaparib in patients with BRCA1 or BRCA2 mutations and recurrent ovarian cancer: a proof-of-concept trial , 2010, The Lancet.
[50] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[51] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[52] D. Busam,et al. An Integrated Genomic Analysis of Human Glioblastoma Multiforme , 2008, Science.
[53] Patricia L. Harris,et al. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. , 2004, The New England journal of medicine.
[54] R. Hansen,et al. Molecular barcodes detect redundancy and contamination in hairpin-bisulfite PCR. , 2004, Nucleic acids research.
[55] H. Hug,et al. Measurement of the number of molecules of a single mRNA species in a complex mRNA preparation. , 2003, Journal of theoretical biology.
[56] D. Bentley. Current Challenges and Future Opportunities , 1989, Infection Control & Hospital Epidemiology.