A machine learning approach to optimizing cell-free DNA sequencing panels: with an application to prostate cancer

[1]  Jun Yu,et al.  Analyses of non-coding somatic drivers in 2,658 cancer whole genomes , 2020, Nature.

[2]  David R. Jones,et al.  High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants , 2019, Nature Medicine.

[3]  Adrian V. Lee,et al.  Whole genome amplification of cell-free DNA enables detection of circulating tumor DNA mutations from fingerstick capillary blood , 2018, Scientific Reports.

[4]  Keval Patel,et al.  Enhanced detection of circulating tumor DNA by fragment size analysis , 2018, Science Translational Medicine.

[5]  E. Diamandis,et al.  Utility of circulating tumor DNA in cancer diagnostics with emphasis on early detection , 2018, BMC Medicine.

[6]  J. Flowers,et al.  Origins and geographic diversification of African rice (Oryza glaberrima) , 2018, bioRxiv.

[7]  G. Marth,et al.  Automated size selection for short cell-free DNA fragments enriches for circulating tumor DNA and improves error correction during next generation sequencing , 2018, PloS one.

[8]  Chuang Tan,et al.  Universal Patterns of Selection in Cancer and Somatic Tissues , 2018, Cell.

[9]  Steven J. M. Jones,et al.  Comprehensive Characterization of Cancer Driver Genes and Mutations , 2018, Cell.

[10]  John S. Witte,et al.  Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations , 2018, Bioinform..

[11]  Jakob Skou Pedersen,et al.  Optimized targeted sequencing of cell-free plasma DNA from bladder cancer patients , 2018, Scientific Reports.

[12]  P. Gibbs,et al.  Circulating tumor DNA as a biomarker to guide therapy in post-operative locally advanced rectal cancer: the best option? , 2018, Expert review of molecular diagnostics.

[13]  A. Atala.  Re: Genomic Hallmarks of Localized, Non-Indolent Prostate Cancer. , 2017, The Journal of urology.

[14]  Sam Angiuoli,et al.  Direct detection of early-stage cancers using circulating tumor DNA , 2017, Science Translational Medicine.

[15]  R. Rosell,et al.  Development of a gene panel for next-generation sequencing of clinically relevant mutations in cell-free DNA from cancer patients , 2017, British Journal of Cancer.

[16]  S Joshua Swamidass,et al.  Unsupervised detection of cancer driver mutations with parsimony-guided learning , 2016, Nature Genetics.

[17]  Ryan D. Morin,et al.  Cell-free DNA (cfDNA): Clinical Significance and Utility in Cancer Shaped By Emerging Technologies , 2016, Molecular Cancer Research.

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

[19]  Meizhuo Zhang,et al.  Plasma EGFR T790M ctDNA status is associated with clinical outcome in advanced NSCLC patients with acquired EGFR-TKI resistance , 2016, Scientific Reports.

[20]  Marc J. Williams,et al.  Identification of neutral tumor evolution across cancer types , 2016, Nature Genetics.

[21]  Joon-Oh Park,et al.  Prospective blinded study of somatic mutation detection in cell-free DNA utilizing a targeted 54-gene next generation sequencing panel in metastatic solid tumor patients , 2015, Oncotarget.

[22]  Nicolai J. Birkbak,et al.  Clonal status of actionable driver events and the timing of mutational processes in cancer evolution , 2015, Science Translational Medicine.

[23]  J. van Helden,et al.  Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape , 2014, Nucleic acids research.

[24]  L. Diaz,et al.  Liquid biopsies: genotyping circulating tumor DNA. , 2014, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[25]  Michael P. Schroeder,et al.  IntOGen-mutations identifies cancer drivers across tumor types , 2013, Nature Methods.

[26]  Edward Y. Chen,et al.  Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool , 2013, BMC Bioinformatics.

[27]  Carlos Caldas,et al.  Analysis of circulating tumor DNA to monitor metastatic breast cancer. , 2013, The New England journal of medicine.

[28]  G. Parmigiani,et al.  Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing , 2012, Science Translational Medicine.

[29]  A. Sivachenko,et al.  Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer , 2012, Nature Genetics.

[30]  P. Greer,et al.  Pathological significance and predictive value for biochemical recurrence of c‐Fes expression in prostate cancer , 2012, The Prostate.

[31]  Kikuya Kato,et al.  Quantitative Detection of EGFR Mutations in Circulating Tumor DNA Derived from Lung Adenocarcinomas , 2011, Clinical Cancer Research.

[32]  J. Xie,et al.  LITAF and TNFSF15, two downstream targets of AMPK, exert inhibitory effects on tumor growth , 2011, Oncogene.

[33]  H. Ohtsuki,et al.  Accumulation of driver and passenger mutations during tumor progression , 2009, Proceedings of the National Academy of Sciences.

[34]  O. Rath,et al.  MAP kinase signalling pathways in cancer , 2007, Oncogene.

[35]  E. Birney,et al.  Patterns of somatic mutation in human cancer genomes , 2007, Nature.

[36]  Li Ding,et al.  Comprehensive Characterization of Cancer Driver Genes and Mutations (vol 173, 371.e1, 2018) , 2018 .

[37]  Peter Ulz,et al.  Circulating tumor DNA as a liquid biopsy for cancer. , 2015, Clinical chemistry.

[38]  David A. Cheresh,et al.  Integrins in cancer: biological implications and therapeutic opportunities , 2010, Nature Reviews Cancer.

[39]  S. Goodman,et al.  Circulating mutant DNA to assess tumor dynamics , 2008, Nature Medicine.

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