Ken Chen

Summary

Affiliation: Washington University School of Medicine
Country: USA

Publications

  1. pmc PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data
    Ken Chen
    Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Genome Res 17:659-66. 2007
  2. pmc BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
    Ken Chen
    The Genome Center, Washington University School of Medicine, St Louis, Missouri, USA
    Nat Methods 6:677-81. 2009
  3. pmc SomaticSniper: identification of somatic point mutations in whole genome sequencing data
    David E Larson
    The Genome Institute, Washington University, St Louis, MO 63108, USA
    Bioinformatics 28:311-7. 2012
  4. pmc CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data
    Qunyuan Zhang
    Division of Statistical Genomics, Washington University School of Medicine, St Louis, MO, USA
    Bioinformatics 26:464-9. 2010
  5. pmc The origin and evolution of mutations in acute myeloid leukemia
    John S Welch
    Department of Medicine, Washington University, St Louis, MO 63110, USA
    Cell 150:264-78. 2012
  6. pmc Clonal architecture of secondary acute myeloid leukemia
    Matthew J Walter
    Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO 63110, USA
    N Engl J Med 366:1090-8. 2012
  7. pmc Genome remodelling in a basal-like breast cancer metastasis and xenograft
    Li Ding
    The Genome Center at Washington University, St Louis, Missouri 63108, USA
    Nature 464:999-1005. 2010
  8. pmc VarScan: variant detection in massively parallel sequencing of individual and pooled samples
    Daniel C Koboldt
    The Genome Center at Washington University School of Medicine, St Louis, MO 63108, USA
    Bioinformatics 25:2283-5. 2009
  9. pmc DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome
    Timothy J Ley
    Department of Medicine, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 456:66-72. 2008
  10. pmc Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells
    Margaret A Young
    Department of Internal Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St Louis, MO 63110, USA
    Cell Stem Cell 10:570-82. 2012

Detail Information

Publications22

  1. pmc PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data
    Ken Chen
    Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Genome Res 17:659-66. 2007
    ..Moreover, SNP identification improves when reprocessing the results of other programs. These results suggest that PolyScan may play a useful role in the post human genome project research era...
  2. pmc BreakDancer: an algorithm for high-resolution mapping of genomic structural variation
    Ken Chen
    The Genome Center, Washington University School of Medicine, St Louis, Missouri, USA
    Nat Methods 6:677-81. 2009
    ..BreakDancer sensitively and accurately detected indels ranging from 10 base pairs to 1 megabase pair that are difficult to detect via a single conventional approach...
  3. pmc SomaticSniper: identification of somatic point mutations in whole genome sequencing data
    David E Larson
    The Genome Institute, Washington University, St Louis, MO 63108, USA
    Bioinformatics 28:311-7. 2012
    ..Despite this fact, there remains a dearth of available software tools designed to compare sequences in pairs of samples and identify sites that are likely to be unique to one sample...
  4. pmc CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data
    Qunyuan Zhang
    Division of Statistical Genomics, Washington University School of Medicine, St Louis, MO, USA
    Bioinformatics 26:464-9. 2010
    ..We propose a population-based approach for RCNA detection with no need of single-sample analysis, which is statistically powerful, computationally efficient and particularly suitable for high-resolution and large-population studies...
  5. pmc The origin and evolution of mutations in acute myeloid leukemia
    John S Welch
    Department of Medicine, Washington University, St Louis, MO 63110, USA
    Cell 150:264-78. 2012
    ..Cells from the founding clone can acquire additional cooperating mutations, yielding subclones that can contribute to disease progression and/or relapse...
  6. pmc Clonal architecture of secondary acute myeloid leukemia
    Matthew J Walter
    Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO 63110, USA
    N Engl J Med 366:1090-8. 2012
    ..The genetic changes that underlie progression from the myelodysplastic syndromes to secondary AML are not well understood...
  7. pmc Genome remodelling in a basal-like breast cancer metastasis and xenograft
    Li Ding
    The Genome Center at Washington University, St Louis, Missouri 63108, USA
    Nature 464:999-1005. 2010
    ..The differential mutation frequencies and structural variation patterns in metastasis and xenograft compared with the primary tumour indicate that secondary tumours may arise from a minority of cells within the primary tumour...
  8. pmc VarScan: variant detection in massively parallel sequencing of individual and pooled samples
    Daniel C Koboldt
    The Genome Center at Washington University School of Medicine, St Louis, MO 63108, USA
    Bioinformatics 25:2283-5. 2009
    ..We demonstrate VarScan's ability to detect SNPs and indels with high sensitivity and specificity, in both Roche/454 sequencing of individuals and deep Illumina/Solexa sequencing of pooled samples...
  9. pmc DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome
    Timothy J Ley
    Department of Medicine, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 456:66-72. 2008
    ..Our study establishes whole-genome sequencing as an unbiased method for discovering cancer-initiating mutations in previously unidentified genes that may respond to targeted therapies...
  10. pmc Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells
    Margaret A Young
    Department of Internal Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St Louis, MO 63110, USA
    Cell Stem Cell 10:570-82. 2012
    ..These findings have implications for the development and therapeutic use of cells that are reprogrammed by any method...
  11. pmc Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing
    Li Ding
    The Genome Institute, Washington University, St Louis, Missouri 63108, USA
    Nature 481:506-10. 2012
    ..These data demonstrate that AML relapse is associated with the addition of new mutations and clonal evolution, which is shaped, in part, by the chemotherapy that the patients receive to establish and maintain remissions...
  12. pmc Massively parallel sequencing approaches for characterization of structural variation
    Daniel C Koboldt
    The Genome Institute at Washington University School of Medicine, St Louis, MO, USA
    Methods Mol Biol 838:369-84. 2012
    ..We describe visualization and de novo assembly strategies for characterizing SV breakpoints and removing false positives...
  13. pmc Recurring mutations found by sequencing an acute myeloid leukemia genome
    Elaine R Mardis
    Department of Genetics, Washington University, St Louis, MO 63110, USA
    N Engl J Med 361:1058-66. 2009
    ..The full complement of DNA mutations that are responsible for the pathogenesis of acute myeloid leukemia (AML) is not yet known...
  14. pmc Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression
    Lukas D Wartman
    Department of Internal Medicine, Division of Oncology, Stem Cell Biology Section, Washington University School of Medicine, Siteman Cancer Center, St Louis, Missouri, USA
    J Clin Invest 121:1445-55. 2011
    ..In conclusion, whole genome sequencing of mouse cancer genomes can provide an unbiased and comprehensive approach for discovering functionally relevant mutations that are also present in human leukemias...
  15. pmc Whole-genome analysis informs breast cancer response to aromatase inhibition
    Matthew J Ellis
    Department of Internal Medicine, Division of Oncology, Washington University, St Louis, Missouri 63110, USA
    Nature 486:353-60. 2012
    ..Prospective clinical trials based on these findings will require comprehensive genome sequencing...
  16. pmc Use of whole-genome sequencing to diagnose a cryptic fusion oncogene
    John S Welch
    Department of Medicine, Washington University, St Louis, Missouri, USA
    JAMA 305:1577-84. 2011
    ..Whole-genome sequencing is becoming increasingly available for research purposes, but it has not yet been routinely used for clinical diagnosis...
  17. pmc Genomic landscape of non-small cell lung cancer in smokers and never-smokers
    Ramaswamy Govindan
    Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO 63110, USA
    Cell 150:1121-34. 2012
    ..Cell-cycle and JAK-STAT pathways are significantly altered in lung cancer, along with perturbations in 54 genes that are potentially targetable with currently available drugs...
  18. pmc BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data
    Ken Chen
    Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, USA
    Bioinformatics 28:1923-4. 2012
    ..Here, we present a software package, BreakFusion that combines the strength of reference alignment followed by read-pair analysis and de novo assembly to achieve a good balance in sensitivity, specificity and computational efficiency...
  19. pmc Somatic mutations affect key pathways in lung adenocarcinoma
    Li Ding
    The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 455:1069-75. 2008
    ..Our findings shed further light on several important signalling pathways involved in lung adenocarcinoma, and suggest new molecular targets for treatment...
  20. pmc Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML
    Daniel C Link
    Department of Medicine, Siteman Cancer Center, Washington University, St Louis, Missouri, USA
    JAMA 305:1568-76. 2011
    ..However, in many cases of suspected cancer susceptibility, the family history is unclear and genetic testing of common cancer susceptibility genes is unrevealing...
  21. pmc On the detection of functionally coherent groups of protein domains with an extension to protein annotation
    William A McLaughlin
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, 9500 Gilman Drive La Jolla, CA 92093 0359, USA
    BMC Bioinformatics 8:390. 2007
    ..Further effort is needed to identify groups of domains that span across two or more proteins and are linked by a cooperative function. Such functional domain combinations can be useful for protein annotation...
  22. ncbi Conditional deletion of the colony stimulating factor-1 receptor (c-fms proto-oncogene) in mice
    Jia Li
    Department of Development and Molecular Biology, Center for the Study of Reproductive Biology and Women s Health, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Genesis 44:328-35. 2006
    ..This conditional allele will prove extremely valuable to study the spatial and temporal roles of CSF-1R...