Establishing reference samples for detection of somatic mutations and germline variants with NGS technologies
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Hugo Y. K. Lam | Daoud M. Meerzaman | S. Sherry | G. Schroth | W. Xiao | M. Mohiyuddin | Leming Shi | R. Jensen | H. Hong | B. Ning | Z. Tezak | C. Xiao | Charles Lu | M. Cam | A. Scherer | M. Pirooznia | Yuanting Zheng | M. Sultan | J. Shetty | Erich B Jaeger | O. Abaan | Ying Yu | Bao Tran | J. Lack | R. Maestro | S. Stanbouly | Charles Wang | L. Ren | S. Kõks | B. Zhu | D. Meerzaman | Eric Donaldson | Lei Song | Yunfei Guo | R. Kusko | Lijing Yao | C. Nguyen | U. Liljedahl | J. Drabek | R. Kalamegham | J. Nordlund | Li Tai Fang | Virginie Petitjean | D. Gasparotto | Eric F. Donaldson | Yongmei Zhao | E. Reimann | Keyur Talsania | K. Idler | Zhaowei Yang | Wanqiu Chen | Zhipan Li | Zhong Chen | Jing Li | L. Kerrigan | K. Langenbach | M. D. Mars | H. Jacob | Tsai-Wei Shen | T. Hung | E. Peters | Sayed Mohammad Ebrahim Sahraeian | Malcolm Moos | Penelope Duerken-Hughes | Erich Jaeger | Bin Zhu | J. Drábek | Tsai-wei Shen | L. Song | Wenming Xiao | Seta Stanbouly | Chunlin Xiao | Jyoti Shetty | Luyao Ren
[1] Chunlin Xiao,et al. An open resource for accurately benchmarking small variant and reference calls , 2019, Nature Biotechnology.
[2] Tingting Jiang,et al. Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity , 2018, bioRxiv.
[3] Thomas Colthurst,et al. A universal SNP and small-indel variant caller using deep neural networks , 2018, Nature Biotechnology.
[4] Christopher T. Saunders,et al. Strelka2: fast and accurate calling of germline and somatic variants , 2018, Nature Methods.
[5] Isabelle Salmon,et al. Methods of measurement for tumor mutational burden in tumor tissue. , 2018, Translational lung cancer research.
[6] Renke Pan,et al. TNscope: Accurate Detection of Somatic Mutations with Haplotype-based Variant Candidate Detection and Machine Learning Filtering , 2018, bioRxiv.
[7] Mauricio O. Carneiro,et al. Scaling accurate genetic variant discovery to tens of thousands of samples , 2017, bioRxiv.
[8] P. Stephens,et al. Tumor Mutational Burden as an Independent Predictor of Response to Immunotherapy in Diverse Cancers , 2017, Molecular Cancer Therapeutics.
[9] Jack Kuipers,et al. Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers , 2017, BMC Bioinformatics.
[10] P. A. Futreal,et al. MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data , 2016, Genome Biology.
[11] G. McVean,et al. A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree , 2016, bioRxiv.
[12] Steven J. M. Jones,et al. A somatic reference standard for cancer genome sequencing , 2016, Scientific Reports.
[13] 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.
[14] R. Wilson,et al. INTEGRATE: gene fusion discovery using whole genome and transcriptome data , 2016, Genome research.
[15] O. Hofmann,et al. VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research , 2016, Nucleic acids research.
[16] Hugo Y. K. Lam,et al. An ensemble approach to accurately detect somatic mutations using SomaticSeq , 2015, Genome Biology.
[17] P. Taschner,et al. Recommendations for Analyzing and Reporting TP53 Gene Variants in the High‐Throughput Sequencing Era , 2014, Human mutation.
[18] Heng Li,et al. Toward better understanding of artifacts in variant calling from high-coverage samples , 2014, Bioinform..
[19] Heng Li. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.
[20] A. Sivachenko,et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.
[21] A. Vincent-Salomon,et al. Ploidy and large-scale genomic instability consistently identify basal-like breast carcinomas with BRCA1/2 inactivation. , 2012, Cancer research.
[22] A. Chinnaiyan,et al. Gene fusions associated with recurrent amplicons represent a class of passenger aberrations in breast cancer. , 2012, Neoplasia.
[23] Gabor T. Marth,et al. Haplotype-based variant detection from short-read sequencing , 2012, 1207.3907.
[24] N. Gooderham,et al. Abstract 5454: Genotoxic consequences of exposure to mixtures of food-derived chemical carcinogens , 2012 .
[25] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[26] Ken Chen,et al. SomaticSniper: identification of somatic point mutations in whole genome sequencing data , 2012, Bioinform..
[27] A. Chinnaiyan,et al. Functionally Recurrent Rearrangements of the MAST Kinase and Notch Gene Families in Breast Cancer , 2011, Nature Medicine.
[28] Toshihiro Tanaka. The International HapMap Project , 2003, Nature.
[29] †The International HapMap Consortium. The International HapMap Project , 2003, Nature.
[30] M. Westerfield,et al. Characterization of paired tumor and non‐tumor cell lines established from patients with breast cancer , 1998, International journal of cancer.