Li Ding

Summary

Affiliation: Washington University School of Medicine
Country: USA

Publications

  1. pmc Characterizing the cancer genome in lung adenocarcinoma
    Barbara A Weir
    Department of Medical Oncology and Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Nature 450:893-8. 2007
  2. pmc EAnnot: a genome annotation tool using experimental evidence
    Li Ding
    Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Genome Res 14:2503-9. 2004
  3. pmc VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing
    Daniel C Koboldt
    The Genome Institute, Washington University, St Louis, MO 63108, USA
    Genome Res 22:568-76. 2012
  4. 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
  5. 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
  6. 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
  7. 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
  8. pmc MuSiC: identifying mutational significance in cancer genomes
    Nathan D Dees
    The Genome Institute, Washington University, St Louis, Missouri 63108, USA
    Genome Res 22:1589-98. 2012
  9. 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
  10. 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

Detail Information

Publications41

  1. pmc Characterizing the cancer genome in lung adenocarcinoma
    Barbara A Weir
    Department of Medical Oncology and Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Nature 450:893-8. 2007
    ..More generally, our results indicate that many of the genes that are involved in lung adenocarcinoma remain to be discovered...
  2. pmc EAnnot: a genome annotation tool using experimental evidence
    Li Ding
    Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Genome Res 14:2503-9. 2004
    ..EAnnot can readily be applied to manual annotation of other eukaryotic genomes and can be used to rapidly obtain an automated gene set...
  3. pmc VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing
    Daniel C Koboldt
    The Genome Institute, Washington University, St Louis, MO 63108, USA
    Genome Res 22:568-76. 2012
    ..Taken together, our results demonstrate the robust performance of VarScan 2 for somatic mutation and CNA detection and shed new light on the landscape of genetic alterations in ovarian cancer...
  4. 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...
  5. 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...
  6. 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...
  7. 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...
  8. pmc MuSiC: identifying mutational significance in cancer genomes
    Nathan D Dees
    The Genome Institute, Washington University, St Louis, Missouri 63108, USA
    Genome Res 22:1589-98. 2012
    ..MuSiC correctly confirms many expected results, and identifies several potentially novel avenues for discovery...
  9. 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...
  10. 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...
  11. 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...
  12. pmc PathScan: a tool for discerning mutational significance in groups of putative cancer genes
    Michael C Wendl
    The Genome Institute, Washington University, St Louis, MO 63108, USA
    Bioinformatics 27:1595-602. 2011
    ..Pathway associations are especially consequential, but existing algorithms are demonstrably inadequate...
  13. pmc DGIdb: mining the druggable genome
    Malachi Griffith
    1 The Genome Institute, Washington University School of Medicine, St Louis, Missouri, USA 2 Department of Genetics, Washington University School of Medicine, St Louis, Missouri, USA 3
    Nat Methods 10:1209-10. 2013
    ..It provides an interface for searching lists of genes against a compendium of drug-gene interactions and potentially 'druggable' genes. DGIdb can be accessed at http://dgidb.org/. ..
  14. pmc Advances for studying clonal evolution in cancer
    Li Ding
    Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO 63110, USA The Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA Siteman Cancer Center, Washington University School of Medicine, St Louis, MO 63110, USA Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA Electronic address
    Cancer Lett 340:212-9. 2013
    ..In turn, these will provide both an improved framework for the understanding of cancer progression and a guide for treatment strategies aimed at the elimination of all, rather than just some, of the cancer cells within a patient. ..
  15. 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...
  16. 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...
  17. pmc Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts
    Shunqiang Li
    Section of Breast Oncology, Division of Oncology, Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA Siteman Cancer Center Breast Cancer Program, Washington University in St Louis, St Louis, MO 63110, USA
    Cell Rep 4:1116-30. 2013
    ..The originating tumor genome provides a benchmark for assessing genetic drift and clonal representation after transplantation. ..
  18. pmc Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma
    David H Gutmann
    Department of Neurology, Washington University School of Medicine, St Louis, MO 63110, USA
    Genome Res 23:431-9. 2013
    ..Importantly, we identified no additional recurrent pathogenic somatic mutations, supporting a model in which neuroglial progenitor cell NF1 loss is likely sufficient for PA formation in cooperation with a proper stromal environment...
  19. 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...
  20. 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...
  21. pmc Activating HER2 mutations in HER2 gene amplification negative breast cancer
    Ron Bose
    Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
    Cancer Discov 3:224-37. 2013
    ..These findings show that HER2 somatic mutation is an alternative mechanism to activate HER2 in breast cancer and they validate HER2 somatic mutations as drug targets for breast cancer treatment...
  22. pmc Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes
    Timothy A Graubert
    Department of Internal Medicine, Division of Oncology, Washington University, St Louis, Missouri, USA
    Nat Genet 44:53-7. 2012
    ..Mutant U2AF1 promotes enhanced splicing and exon skipping in reporter assays in vitro. This previously unidentified, recurrent mutation in U2AF1 implicates altered pre-mRNA splicing as a potential mechanism for MDS pathogenesis...
  23. 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...
  24. 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...
  25. 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...
  26. 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...
  27. pmc Analysis of next-generation genomic data in cancer: accomplishments and challenges
    Li Ding
    Department of Genetics, The Genome Center at Washington University School of Medicine, 4444 Forest Park Blvd, St Louis, MO 63108, USA
    Hum Mol Genet 19:R188-96. 2010
    ....
  28. pmc Challenges of sequencing human genomes
    Daniel C Koboldt
    The Genome Center at Washington University, St Louis, Missouri 63108, USA
    Brief Bioinform 11:484-98. 2010
    ..This review aims to describe the state of current NGS technologies, as well as the strategies that enable NGS users to characterize the full spectrum of DNA sequence variation in humans...
  29. 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...
  30. pmc DNMT3A mutations in acute myeloid leukemia
    Timothy J Ley
    Department of Genetics, Genome Center, Washington University, St Louis, MO 63110, USA
    N Engl J Med 363:2424-33. 2010
    ..The genetic alterations responsible for an adverse outcome in most patients with acute myeloid leukemia (AML) are unknown...
  31. 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...
  32. 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...
  33. 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...
  34. pmc Complete characterization of the microRNAome in a patient with acute myeloid leukemia
    Giridharan Ramsingh
    Deparment of Medicine, Washington University School of Medicine, St Louis, MO, USA
    Blood 116:5316-26. 2010
    ....
  35. pmc Co-survival of the fittest few: mosaic amplification of receptor tyrosine kinases in glioblastoma
    Feng Chen
    The Genome Institute, Washington University School of Medicine, St Louis, MO 63108, USA
    Genome Biol 13:141. 2012
    ..Mosaic amplification of receptor tyrosine kinases in glioblastoma suggests that tumor cells with different progression driver mutations may coevolve rather than compete during clonal evolution...
  36. ncbi request reprint Generation and annotation of the DNA sequences of human chromosomes 2 and 4
    Ladeana W Hillier
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 434:724-31. 2005
    ..Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions...
  37. ncbi request reprint Analysis of plasmid samples on a microchip
    Li Ding
    Caliper Technologies Corp, 605 Fairchild Drive, Mountain View, CA 94043 2234, USA
    Anal Biochem 316:92-102. 2003
    ..The measurement is semiquantitative with a CV lower than 20%. A number of applications of this assay on a Labchip will be shown...
  38. ncbi request reprint Functional analysis of the essential bifunctional tobacco enzyme 3-dehydroquinate dehydratase/shikimate dehydrogenase in transgenic tobacco plants
    Li Ding
    Institut für Pflanzengenetik und Kulturpflanzenforschung IPK, Corrensstrasse 3, 06466 Gatersleben, Germany
    J Exp Bot 58:2053-67. 2007
    ..These data are discussed in the context of current models of plant intermediary metabolism...
  39. ncbi request reprint Interferon-gamma receptor 1 promoter polymorphisms: population distribution and functional implications
    Sergio D Rosenzweig
    Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, NIH, DHHS, Bethesda, MD 20892 1886, USA
    Clin Immunol 112:113-9. 2004
    ..The IFNGR1 MPR is a polymorphic region with at least two SNPs influencing its activity, but these are not associated with increased mycobacterial susceptibility...
  40. ncbi request reprint Severe phenotype of chronic granulomatous disease presenting in a female with a de novo mutation in gp91-phox and a non familial, extremely skewed X chromosome inactivation
    Mindy Anderson-Cohen
    Laboratory of Host Defenses, NIAID, Department of Laboratory Medicine, Bethesda, MD, USA
    Clin Immunol 109:308-17. 2003
    ..Our conclusion: A presumed autosomal form of CGD has been excluded. Instead, a spontaneous mutation in gp91-phox coinciding with an extreme X chromosome inactivation ratio resulted in X-linked CGD in this young woman...