Identification of single nucleotide variants using position-specific error estimation in deep sequencing data

[1]  Shivakumar Keerthikumar,et al.  Patient-derived Models of Abiraterone- and Enzalutamide-resistant Prostate Cancer Reveal Sensitivity to Ribosome-directed Therapy. , 2018, European urology.

[2]  George D. Cresswell,et al.  The Spatiotemporal Evolution of Lymph Node Spread in Early Breast Cancer , 2018, Clinical Cancer Research.

[3]  Hanna Lee,et al.  AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing , 2018, Bioinform..

[4]  Chang Xu,et al.  A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data , 2018, Computational and structural biotechnology journal.

[5]  Jing Wang,et al.  Strategies for identification of somatic variants using the Ion Torrent deep targeted sequencing platform , 2018, BMC Bioinformatics.

[6]  M. Gerlinger,et al.  Ultra-Sensitive Mutation Detection and Genome-Wide DNA Copy Number Reconstruction by Error-Corrected Circulating Tumor DNA Sequencing. , 2018, Clinical chemistry.

[7]  Ellen Heitzer,et al.  The potential of liquid biopsies for the early detection of cancer , 2017, npj Precision Oncology.

[8]  D. Amadori,et al.  Androgen receptor gene status in plasma DNA associates with worse outcome on enzalutamide or abiraterone for castration-resistant prostate cancer: a multi-institution correlative biomarker study , 2017, Annals of oncology : official journal of the European Society for Medical Oncology.

[9]  James D. Brenton,et al.  Liquid biopsies come of age: towards implementation of circulating tumour DNA , 2017, Nature Reviews Cancer.

[10]  N. McGranahan,et al.  Clonal Heterogeneity and Tumor Evolution: Past, Present, and the Future , 2017, Cell.

[11]  J. McPherson,et al.  Coming of age: ten years of next-generation sequencing technologies , 2016, Nature Reviews Genetics.

[12]  Ash A. Alizadeh,et al.  Integrated digital error suppression for improved detection of circulating tumor DNA , 2016, Nature Biotechnology.

[13]  Delila Gasi Tandefelt,et al.  Plasma AR and abiraterone-resistant prostate cancer , 2015, Science Translational Medicine.

[14]  A. Sboner,et al.  ASEQ: fast allele-specific studies from next-generation sequencing data , 2015, BMC Medical Genomics.

[15]  F. Demichelis,et al.  Tumor clone dynamics in lethal prostate cancer , 2014, Science Translational Medicine.

[16]  G. McVean,et al.  Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications , 2014, Nature Genetics.

[17]  Shuifang Zhu,et al.  Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads , 2014, BMC Bioinformatics.

[18]  Philip Hugenholtz,et al.  Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data , 2013, PLoS Comput. Biol..

[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]  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.

[22]  M. Gerstung,et al.  Reliable detection of subclonal single-nucleotide variants in tumour cell populations , 2012, Nature Communications.

[23]  Joshua S. Paul,et al.  Genotype and SNP calling from next-generation sequencing data , 2011, Nature Reviews Genetics.

[24]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[25]  A. Hills,et al.  Detection of subtelomere imbalance using MLPA: validation, development of an analysis protocol, and application in a diagnostic centre , 2007, BMC Medical Genetics.

[26]  M. Dowsett,et al.  The spatio-temporal evolution of lymph node spread in early breast cancer , 2018 .

[27]  Faraz Hach,et al.  SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA , 2017, Bioinform..

[28]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..