A patient-driven clinicogenomic partnership for metastatic prostate cancer

[1]  P. Kantoff,et al.  Tackling Diversity in Prostate Cancer Clinical Trials: A Report From the Diversity Working Group of the IRONMAN Registry , 2021, JCO global oncology.

[2]  S. Ramsey,et al.  Persistent Disparity: Socioeconomic Deprivation and Cancer Outcomes in Patients Treated in Clinical Trials , 2021, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[3]  H. Krumholz,et al.  Prevalence of Missing Data in the National Cancer Database and Association With Overall Survival , 2020, JAMA network open.

[4]  E. V. Van Allen,et al.  Detection of Pathogenic Variants With Germline Genetic Testing Using Deep Learning vs Standard Methods in Patients With Prostate Cancer and Melanoma. , 2020, JAMA.

[5]  F. Saad,et al.  Olaparib for Metastatic Castration-Resistant Prostate Cancer. , 2020, The New England journal of medicine.

[6]  Brendan Reardon,et al.  CoMut: visualizing integrated molecular information with comutation plots , 2020, bioRxiv.

[7]  F. Feng,et al.  Non-BRCA DNA Damage Repair Gene Alterations and Response to the PARP Inhibitor Rucaparib in Metastatic Castration-Resistant Prostate Cancer: Analysis From the Phase II TRITON2 Study , 2020, Clinical Cancer Research.

[8]  Z. Szallasi,et al.  Detection of Molecular Signatures of Homologous Recombination Deficiency in Prostate Cancer with or without BRCA1/2 Mutations , 2020, Clinical Cancer Research.

[9]  Yevgeniy Feyman,et al.  Disparities in Clinical Trial Access Across US Urban Areas , 2020, JAMA network open.

[10]  A. Jemal,et al.  Cancer statistics, 2020 , 2020, CA: a cancer journal for clinicians.

[11]  A. Wyatt,et al.  Identification of Hypermutation and Defective Mismatch Repair in ctDNA from Metastatic Prostate Cancer , 2019, Clinical Cancer Research.

[12]  S. AlDubayan.  Considerations of multigene test findings among men with prostate cancer - knowns and unknowns. , 2019, The Canadian journal of urology.

[13]  E. Lander,et al.  The Angiosarcoma Project: enabling genomic and clinical discoveries in a rare cancer through patient-partnered research , 2019, Nature Medicine.

[14]  R. Basha,et al.  Diversity in the Era of Precision Medicine - From Bench to Bedside Implementation. , 2019, Ethnicity & disease.

[15]  E. Hawk,et al.  Mind the Gap: Precision Oncology and Its Potential to Widen Disparities. , 2019, Journal of oncology practice.

[16]  Yi Mi Wu,et al.  Genomic correlates of clinical outcome in advanced prostate cancer , 2019, Proceedings of the National Academy of Sciences.

[17]  G. Pond,et al.  Circulating tumor DNA alterations in patients with metastatic castration‐resistant prostate cancer , 2019, Cancer.

[18]  Prashanth Rawla,et al.  Epidemiology of Prostate Cancer , 2019, World journal of oncology.

[19]  G. Getz,et al.  Comprehensive analysis of tumour initiation, spatial and temporal progression under multiple lines of treatment , 2018, bioRxiv.

[20]  Takafumi N. Yamaguchi,et al.  Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories. , 2018, Cancer cell.

[21]  J. C. Love,et al.  Tumor fraction in cell-free DNA as a biomarker in prostate cancer. , 2018, JCI insight.

[22]  C. Cole,et al.  The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers , 2018, Nature Reviews Cancer.

[23]  G. Scagliotti,et al.  Enzalutamide-resistant castration-resistant prostate cancer: challenges and solutions , 2018, OncoTargets and therapy.

[24]  Thomas Colthurst,et al.  A universal SNP and small-indel variant caller using deep neural networks , 2018, Nature Biotechnology.

[25]  T. Rebbeck.  Prostate Cancer Disparities by Race and Ethnicity: From Nucleotide to Neighborhood. , 2018, Cold Spring Harbor perspectives in medicine.

[26]  Nicolai J. Birkbak,et al.  Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancer , 2018, npj Breast Cancer.

[27]  William R. Buckingham,et al.  Making Neighborhood-Disadvantage Metrics Accessible - The Neighborhood Atlas. , 2018, The New England journal of medicine.

[28]  N. Lennon,et al.  DeTiN : Overcoming Tumor in Normal Contamination , 2018, Nature Methods.

[29]  Natalie S. Fox,et al.  The Evolutionary Landscape of Localized Prostate Cancers Drives Clinical Aggression , 2018, Cell.

[30]  A. Lapuk,et al.  Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice , 2018, PloS one.

[31]  Steven J. M. Jones,et al.  Pathogenic Germline Variants in 10,389 Adult Cancers. , 2018, Cell.

[32]  Yi Mi Wu,et al.  The long tail of oncogenic drivers in prostate cancer , 2018, Nature Genetics.

[33]  Chunlei Liu,et al.  ClinVar: improving access to variant interpretations and supporting evidence , 2017, Nucleic Acids Res..

[34]  M. Nykter,et al.  Circulating Tumor DNA Genomics Correlate with Resistance to Abiraterone and Enzalutamide in Prostate Cancer. , 2018, Cancer discovery.

[35]  Nikhil Wagle,et al.  Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors , 2017, Nature Communications.

[36]  E. Lander,et al.  A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer , 2017, Nature Genetics.

[37]  Mark S. Litwin,et al.  The Diagnosis and Treatment of Prostate Cancer: A Review , 2017, JAMA.

[38]  N. Krieger,et al.  Structural racism and health inequities in the USA: evidence and interventions , 2017, The Lancet.

[39]  A. Jemal,et al.  Socioeconomic and Racial/Ethnic Disparities in Cancer Mortality, Incidence, and Survival in the United States, 1950–2014: Over Six Decades of Changing Patterns and Widening Inequalities , 2017, Journal of environmental and public health.

[40]  Alain Bergeron,et al.  Genomic hallmarks of localized, non-indolent prostate cancer , 2017, Nature.

[41]  Thao M. Doan,et al.  Integrating Social Determinants of Health With Treatment and Prevention: A New Tool to Assess Local Area Deprivation , 2016, Preventing chronic disease.

[42]  Levi Waldron,et al.  Racial/Ethnic Disparities in Genomic Sequencing. , 2016, JAMA oncology.

[43]  Ahmet Zehir,et al.  Inherited DNA-Repair Gene Mutations in Men with Metastatic Prostate Cancer. , 2016, The New England journal of medicine.

[44]  N. Lennon,et al.  The Metastatic Breast Cancer Project: A national direct-to-patient initiative to accelerate genomics research. , 2016 .

[45]  V. Seshan,et al.  FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing , 2016, Nucleic acids research.

[46]  A. McGuire,et al.  Barriers to clinical adoption of next generation sequencing: Perspectives of a policy Delphi panel , 2016, Applied & translational genomics.

[47]  Rachel G Liao,et al.  Facilitating a culture of responsible and effective sharing of cancer genome data , 2016, Nature Medicine.

[48]  F. Cunningham,et al.  The Ensembl Variant Effect Predictor , 2016, Genome Biology.

[49]  B. Taylor,et al.  deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution , 2016, Genome Biology.

[50]  G. Parmigiani,et al.  Familial Risk and Heritability of Cancer Among Twins in Nordic Countries. , 2016, JAMA.

[51]  Steven J. M. Jones,et al.  The Molecular Taxonomy of Primary Prostate Cancer , 2015, Cell.

[52]  Wei Yuan,et al.  DNA-Repair Defects and Olaparib in Metastatic Prostate Cancer. , 2015, The New England journal of medicine.

[53]  C. Swanton,et al.  APOBEC Enzymes: Mutagenic Fuel for Cancer Evolution and Heterogeneity. , 2015, Cancer discovery.

[54]  A. McKenna,et al.  Paired Exome Analysis of Barrett’s Esophagus and Adenocarcinoma , 2015, Nature Genetics.

[55]  Trevor J Pugh,et al.  Oncotator: Cancer Variant Annotation Tool , 2015, Human mutation.

[56]  M. Nykter,et al.  The Evolutionary History of Lethal Metastatic Prostate Cancer , 2015, Nature.

[57]  S. Fröhling,et al.  Stakeholders’ perspectives on biobank-based genomic research: systematic review of the literature , 2015, European Journal of Human Genetics.

[58]  S. Chakradhar.  Tumor sequencing takes off, but insurance reimbursement lags , 2014, Nature Medicine.

[59]  Nazneen Rahman,et al.  Realizing the promise of cancer predisposition genes , 2014, Nature.

[60]  S. Gabriel,et al.  Discovery and saturation analysis of cancer genes across 21 tumor types , 2014, Nature.

[61]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[62]  David T. W. Jones,et al.  Signatures of mutational processes in human cancer , 2013, Nature.

[63]  A. Sivachenko,et al.  Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples , 2013, Nature Biotechnology.

[64]  Yann Joly,et al.  Data Sharing in the Post-Genomic World: The Experience of the International Cancer Genome Consortium (ICGC) Data Access Compliance Office (DACO) , 2012, PLoS Comput. Biol..

[65]  A. Børresen-Dale,et al.  Mutational Processes Molding the Genomes of 21 Breast Cancers , 2012, Cell.

[66]  Wendy S. W. Wong,et al.  Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs , 2012, Bioinform..

[67]  A. McKenna,et al.  Absolute quantification of somatic DNA alterations in human cancer , 2012, Nature Biotechnology.

[68]  Benjamin J. Raphael,et al.  The Mutational Landscape of Lethal Castrate Resistant Prostate Cancer , 2016 .

[69]  P. A. Kelly,et al.  To share or not to share: A randomized trial of consent for data sharing in genome research , 2011, Genetics in Medicine.

[70]  C. Cole,et al.  COSMIC: the catalogue of somatic mutations in cancer , 2011, Genome Biology.

[71]  Kristian Cibulskis,et al.  ContEst: estimating cross-contamination of human samples in next-generation sequencing data , 2011, Bioinform..

[72]  G. Getz,et al.  GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers , 2011, Genome Biology.

[73]  Shicai Wang,et al.  COSMIC: the Catalogue Of Somatic Mutations In Cancer , 2018, Nucleic Acids Res..

[74]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[75]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[76]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[77]  E. Demidenko,et al.  Determinants of NCI Cancer Center Attendance in Medicare Patients with Lung, Breast, Colorectal, or Prostate Cancer , 2009, Journal of General Internal Medicine.

[78]  Ahmedin Jemal,et al.  Cancer Disparities by Race/Ethnicity and Socioeconomic Status , 2004, CA: a cancer journal for clinicians.