Elaine R Mardis

Summary

Affiliation: Washington University School of Medicine
Country: USA

Publications

  1. doi request reprint Next-generation DNA sequencing methods
    Elaine R Mardis
    Department of Genetics and Molecular Microbiology and Genome Sequencing Center, Washington University School of Medicine, St Louis MO 63108, USA
    Annu Rev Genomics Hum Genet 9:387-402. 2008
  2. doi request reprint A decade's perspective on DNA sequencing technology
    Elaine R Mardis
    The Genome Center at Washington University School of Medicine, Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 470:198-203. 2011
  3. 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
  4. doi request reprint Next-generation sequencing platforms
    Elaine R Mardis
    The Genome Institute at Washington University School of Medicine, St Louis, Missouri 63108, USA
    Annu Rev Anal Chem (Palo Alto Calif) 6:287-303. 2013
  5. pmc Genome sequencing and cancer
    Elaine R Mardis
    The Genome Institute at Washington University School of Medicine, St Louis, MO 63108, United States
    Curr Opin Genet Dev 22:245-50. 2012
  6. doi request reprint Applying next-generation sequencing to pancreatic cancer treatment
    Elaine R Mardis
    The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
    Nat Rev Gastroenterol Hepatol 9:477-86. 2012
  7. pmc The functional spectrum of low-frequency coding variation
    Gabor T Marth
    Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
    Genome Biol 12:R84. 2011
  8. pmc Genome-wide diversity and selective pressure in the human rhinovirus
    Amy L Kistler
    Department of Microbiology and Immunology, University of California, San Francisco, California, USA
    Virol J 4:40. 2007
  9. pmc Design and implementation of a generalized laboratory data model
    Michael C Wendl
    Genome Sequencing Center, Washington University, St, Louis, MO 63108, USA
    BMC Bioinformatics 8:362. 2007
  10. pmc Anticipating the 1,000 dollar genome
    Elaine R Mardis
    Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Boulevard, St, Louis, MO 63108, USA
    Genome Biol 7:112. 2006

Detail Information

Publications105 found, 100 shown here

  1. doi request reprint Next-generation DNA sequencing methods
    Elaine R Mardis
    Department of Genetics and Molecular Microbiology and Genome Sequencing Center, Washington University School of Medicine, St Louis MO 63108, USA
    Annu Rev Genomics Hum Genet 9:387-402. 2008
    ..Taken together, an astounding potential exists for these technologies to bring enormous change in genetic and biological research and to enhance our fundamental biological knowledge...
  2. doi request reprint A decade's perspective on DNA sequencing technology
    Elaine R Mardis
    The Genome Center at Washington University School of Medicine, Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA
    Nature 470:198-203. 2011
    ..The continuing upward trajectory of sequencing technology development is enabling clinical applications that are aimed at improving medical diagnosis and treatment...
  3. 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...
  4. doi request reprint Next-generation sequencing platforms
    Elaine R Mardis
    The Genome Institute at Washington University School of Medicine, St Louis, Missouri 63108, USA
    Annu Rev Anal Chem (Palo Alto Calif) 6:287-303. 2013
    ....
  5. pmc Genome sequencing and cancer
    Elaine R Mardis
    The Genome Institute at Washington University School of Medicine, St Louis, MO 63108, United States
    Curr Opin Genet Dev 22:245-50. 2012
    ..This review outlines the history of the past several years of development in this realm, and discusses the current and future applications that will further elucidate cancer's genomic causes...
  6. doi request reprint Applying next-generation sequencing to pancreatic cancer treatment
    Elaine R Mardis
    The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
    Nat Rev Gastroenterol Hepatol 9:477-86. 2012
    ..As a means to improve patient outcomes, the application of comprehensive next-generation sequencing and analysis to the genomes of patients with pancreatic cancer to identify therapeutic options is proposed...
  7. pmc The functional spectrum of low-frequency coding variation
    Gabor T Marth
    Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
    Genome Biol 12:R84. 2011
    ....
  8. pmc Genome-wide diversity and selective pressure in the human rhinovirus
    Amy L Kistler
    Department of Microbiology and Immunology, University of California, San Francisco, California, USA
    Virol J 4:40. 2007
    ..Previous comparative genome sequence analyses indicate that recombination drives diversification in multiple genera of the picornavirus family, yet it remains unclear if this holds for HRV...
  9. pmc Design and implementation of a generalized laboratory data model
    Michael C Wendl
    Genome Sequencing Center, Washington University, St, Louis, MO 63108, USA
    BMC Bioinformatics 8:362. 2007
    ..Designing and implementing such systems is non-trivial and it appears that in many cases a database project ultimately proves unserviceable...
  10. pmc Anticipating the 1,000 dollar genome
    Elaine R Mardis
    Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Boulevard, St, Louis, MO 63108, USA
    Genome Biol 7:112. 2006
    ..Here, I examine why the 1,000 dollar human genome is an important goal for research and clinical diagnostics, and what will be required to achieve it...
  11. pmc Cancer genome sequencing: a review
    Elaine R Mardis
    The Genome Center, Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA
    Hum Mol Genet 18:R163-8. 2009
    ..Although, we anticipate that there will be many exciting discoveries in the near future, the ultimate success of these endeavors rests on our ability to translate what is learned into better diagnosis, treatment and prevention of cancer...
  12. pmc Cancer genomics identifies determinants of tumor biology
    Elaine R Mardis
    The Genome Center, Washington University School of Medicine, St Louis, MO 63108, USA
    Genome Biol 11:211. 2010
    ..Unbiased sequencing and analysis of human tumors is revealing unsuspected somatic changes that, upon further study, are elucidating aspects of tumor biology and identifying new biomarkers...
  13. pmc New strategies and emerging technologies for massively parallel sequencing: applications in medical research
    Elaine R Mardis
    The Genome Center at Washington University School of Medicine, Department of Genetics, 4444 Forest Park Boulevard, St Louis, MO 63108, USA
    Genome Med 1:40. 2009
    ..Taken together, these approaches are dramatically accelerating the pace of human disease research and are already impacting patient care...
  14. 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...
  15. pmc contribution of genetically restricted, methicillin-susceptible strains to the ongoing epidemic of community-acquired Staphylococcus aureus infections
    Rachel C Orscheln
    Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Clin Infect Dis 49:536-42. 2009
    ..We characterize methicillin-susceptible strains that also contribute to this epidemic...
  16. 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...
  17. pmc Evolution of a distinct genomic domain in Drosophila: comparative analysis of the dot chromosome in Drosophila melanogaster and Drosophila virilis
    Wilson Leung
    Department of Biology, Washington University, St Louis, Missouri 63130, USA
    Genetics 185:1519-34. 2010
    ..Collectively, despite the heterochromatin-like properties of this domain, genes on the dot evolve to maintain function while being responsive to changes in their local environment...
  18. 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...
  19. 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...
  20. 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...
  21. 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...
  22. pmc Somatic mutations and germline sequence variants in the expressed tyrosine kinase genes of patients with de novo acute myeloid leukemia
    Michael H Tomasson
    Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
    Blood 111:4797-808. 2008
    ..Additional studies will be required to define the roles that these somatic and germline TK gene variants play in AML pathogenesis...
  23. 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...
  24. 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/. ..
  25. 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...
  26. pmc The genome of a songbird
    Wesley C Warren
    The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 464:757-62. 2010
    ..These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour...
  27. 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...
  28. 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...
  29. 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...
  30. 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...
  31. pmc Expression of a bcr-1 isoform of RARalpha-PML does not affect the penetrance of acute promyelocytic leukemia or the acquisition of an interstitial deletion on mouse chromosome 2
    Matthew J Walter
    Department of Medicine, Division of Oncology, Siteman Cancer Center, Washington University School of Medicine, St Louis, MO 63110 1093, USA
    Blood 109:1237-40. 2007
    ..38-compared with 11 of 11 for mice coexpressing PML-RARalpha and bcr-3 RARalpha-PML). The bcr-1 and bcr-3 isoforms of RARalpha-PML, therefore, have different biological activities that may be relevant for the pathogenesis of murine APL...
  32. 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...
  33. 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...
  34. 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. ..
  35. 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...
  36. ncbi request reprint Functional heterogeneity of genetically defined subclones in acute myeloid leukemia
    Jeffery M Klco
    Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
    Cancer Cell 25:379-92. 2014
    ..These data demonstrate the importance of integrating genetic and functional data in studies of primary cancer samples, both in xenograft models and in patients. ..
  37. 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...
  38. pmc Comprehensive genetic variant discovery in the surfactant protein B gene
    Aaron Hamvas
    Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St Louis Children s Hospital, St Louis, Missouri 63110, USA
    Pediatr Res 62:170-5. 2007
    ....
  39. pmc Comparative and demographic analysis of orang-utan genomes
    Devin P Locke
    The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA
    Nature 469:529-33. 2011
    ..Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts...
  40. 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...
  41. 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...
  42. ncbi request reprint Panton-Valentine Leukocidin-positive methicillin-resistant Staphylococcus aureus lung infection in patients with cystic fibrosis
    Arnon Elizur
    Department of Pediatrics, Washington University School of Medicine, Campus Box 8116, 660 S Euclid Ave, Saint Louis, MO 63110, USA
    Chest 131:1718-25. 2007
    ..Following two cases of patients with CF admitted with lung abscesses in association with PVL+ MRSA, we examined the incidence and the clinical characteristics of MRSA acquisition in our CF patient population...
  43. pmc Next-generation sequencing identifies the natural killer cell microRNA transcriptome
    Todd A Fehniger
    Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, Missouri 63110, USA
    Genome Res 20:1590-604. 2010
    ..Thus, the sequenced NK cell miRNA transcriptome provides a valuable framework for further elucidation of miRNA expression and function in NK cell biology...
  44. 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...
  45. pmc Acquired copy number alterations in adult acute myeloid leukemia genomes
    Matthew J Walter
    Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 106:12950-5. 2009
    ....
  46. pmc The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression
    Jung D Oh
    Center for Genome Sciences, Washington University School of Medicine, 4444 Forest Park, St Louis, MO 63108, USA
    Proc Natl Acad Sci U S A 103:9999-10004. 2006
    ..pylori's adaptation to ChAG...
  47. pmc Genome analysis of the platypus reveals unique signatures of evolution
    Wesley C Warren
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 453:175-83. 2008
    ..Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation...
  48. pmc A vertebrate case study of the quality of assemblies derived from next-generation sequences
    Liang Ye
    The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
    Genome Biol 12:R31. 2011
    ..Nonetheless, these assemblies are sufficient for the identification of the majority of genes and can reveal novel sequences when compared to existing assembly references...
  49. pmc A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysis
    Shana R Leopold
    Department of Pediatrics, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 106:8713-8. 2009
    ..However, constrained radiations raise the possibility of making false associations between isolates...
  50. 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...
  51. ncbi request reprint cDNA hybrid capture improves transcriptome analysis on low-input and archived samples
    Christopher R Cabanski
    The Genome Institute, Washington University School of Medicine, St Louis, Missouri Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri
    J Mol Diagn 16:440-51. 2014
    ..We conclude that cDNA hybrid capture has the potential to significantly improve transcriptome analysis from low-yield FFPE material. ..
  52. doi request reprint Whole-genome sequencing and variant discovery in C. elegans
    Ladeana W Hillier
    Washington University School of Medicine, Department of Genetics and Genome Sequencing Center, 4444 Forest Park Blvd, St Louis, Missouri 63108, USA
    Nat Methods 5:183-8. 2008
    ..This study demonstrates the utility of massively parallel short read sequencing for whole genome resequencing and for accurate discovery of genome-wide polymorphisms...
  53. pmc Distinct patterns of mutations occurring in de novo AML versus AML arising in the setting of severe congenital neutropenia
    Daniel C Link
    Division of Oncology, Department of Medicine, Washington University, St Louis, MO 63110, USA
    Blood 110:1648-55. 2007
    ..These data support the hypothesis that mutations of CSF3R may provide the "activated tyrosine kinase signal" that is thought to be important for leukemogenesis...
  54. pmc Reduced PU.1 expression causes myeloid progenitor expansion and increased leukemia penetrance in mice expressing PML-RARalpha
    Matthew J Walter
    Department of Medicine, Division of Oncology, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 102:12513-8. 2005
    ..1 through a deletional mechanism, plus down-regulation of the residual allele caused by PR expression, may synergize to expand the pool of myeloid progenitors that are susceptible to transformation, increasing the penetrance of APL...
  55. ncbi request reprint Integrated analysis of germline and somatic variants in ovarian cancer
    Krishna L Kanchi
    1 The Genome Institute, Washington University, St Louis, Missouri 63108, USA 2
    Nat Commun 5:3156. 2014
    ..Finally, integrated analyses of germline and somatic variants identify significantly altered pathways, including the Fanconi, MAPK and MLL pathways. ..
  56. 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...
  57. 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...
  58. 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...
  59. doi request reprint Large-scale sequencing and analytical processing of ESTs
    Makedonka Mitreva
    Genome Sequencing Center, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
    Methods Mol Biol 533:153-87. 2009
    ..With appropriate bioinformatics tools, each of these platforms either used independently or coupled together provide a powerful combination for comprehensive exploration of an organism's transcriptome...
  60. 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...
  61. pmc Identification of somatic JAK1 mutations in patients with acute myeloid leukemia
    Zhifu Xiang
    Department of Medicine, Washington University School of Medicine, St Louis, St Louis, MO 63110, USA
    Blood 111:4809-12. 2008
    ..This is the first report to demonstrate somatic JAK1 mutations in AML and suggests that JAK1 mutations may function as disease-modifying mutations in AML pathogenesis...
  62. 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...
  63. pmc The draft genome of the parasitic nematode Trichinella spiralis
    Makedonka Mitreva
    The Genome Center, Washington University School of Medicine, St Louis, Missouri, USA
    Nat Genet 43:228-35. 2011
    ..This genome sequence and the identified pan-phylum characteristics will contribute to genome evolution studies of Nematoda as well as strategies to combat global parasites of humans, food animals and crops...
  64. 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
    ....
  65. 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...
  66. ncbi request reprint A physical map of the chicken genome
    John W Wallis
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 432:761-4. 2004
    ..This map represents approximately 91% of the chicken genome and enables identification of chicken clones aligned to positions in other sequenced genomes...
  67. doi request reprint The next-generation sequencing revolution and its impact on genomics
    Daniel C Koboldt
    The Genome Institute, School of Medicine, Washington University, St Louis, MO 63108, USA
    Cell 155:27-38. 2013
    ..This Review explores the current state of genomics in the massively parallel sequencing era. ..
  68. ncbi request reprint Direct genomic selection
    Stavros Bashiardes
    Department of Genetics, Washington University School of Medicine, Box 8232, 4566 Scott Avenue, St Louis, Missouri 63110, USA
    Nat Methods 2:63-9. 2005
  69. ncbi request reprint Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  70. ncbi request reprint An obesity-associated gut microbiome with increased capacity for energy harvest
    Peter J Turnbaugh
    Center for Genome Sciences, Washington University, St Louis, Missouri 63108, USA
    Nature 444:1027-31. 2006
    ..These results identify the gut microbiota as an additional contributing factor to the pathophysiology of obesity...
  71. ncbi request reprint The DNA sequence of human chromosome 7
    Ladeana W Hillier
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 424:157-64. 2003
    ..Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame...
  72. 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
    ....
  73. ncbi request reprint Advances in genome biology and technology
    Elaine R Mardis
    Washington University School of Medicine, Department of Genetics, 4444 Forest Park Blvd, Box 8501, St Louis, MO 63108, USA
    Pharmacogenomics 5:355-6. 2004
  74. pmc Genome science: a video tour of the Washington University Genome Sequencing Center for high school and undergraduate students
    Susan K Flowers
    Department of Biology, Washington University, St Louis, MO 63130, USA
    Cell Biol Educ 4:291-7. 2005
    ..Initial feedback on the video from undergraduate students, high school teachers, and high school students provides suggestions for use of this video in a classroom setting to supplement present curricula...
  75. pmc Genomics of acute myeloid leukemia
    Timothy A Graubert
    Division of Oncology, Department of Internal Medicine, Washington University, St Louis, MO, USA
    Cancer J 17:487-91. 2011
    ....
  76. pmc Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting
    Hirokazu Matsushita
    Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, Missouri 63110, USA
    Nature 482:400-4. 2012
    ....
  77. pmc Demographic history and rare allele sharing among human populations
    Simon Gravel
    Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 5120, USA
    Proc Natl Acad Sci U S A 108:11983-8. 2011
    ..Our results emphasize that replication of disease association for specific rare genetic variants across diverged populations must overcome both reduced statistical power because of rarity and higher population divergence...
  78. pmc Biome representational in silico karyotyping
    Valliammai Muthappan
    Department of Ophthalmology and Visual Science, Washington University, St Louis, MO 63110, USA
    Genome Res 21:626-33. 2011
    ..These results suggest that BRISK is a powerful technique for the analysis of complex microbiomes and potentially for pathogen discovery...
  79. pmc Blinded comparison of repetitive-sequence PCR and multilocus sequence typing for genotyping methicillin-resistant Staphylococcus aureus isolates from a children's hospital in St. Louis, Missouri
    Robert S Liao
    Department of Pathology, Washington University School of Medicine, St Louis, MO 63110, USA
    J Clin Microbiol 44:2254-7. 2006
    ..The MRSA strains that were sequence type 8 (ST8), staphylococcal cassette chromosome mec (SCCmec) type IV, and Panton-Valentine leukocidin-positive clustered separately from those that were ST5 and SCCmec type II...
  80. pmc Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains
    Elizabeth E Slawson
    Biology Department, Washington University, St Louis, MO 63130, USA
    Genome Biol 7:R15. 2006
    ..In contrast, the absence of HP1 and H3K9me from the dot chromosome in D. virilis suggests that this region is euchromatic. D. virilis diverged from D. melanogaster 40 to 60 million years ago...
  81. 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...
  82. pmc Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach
    Swaine L Chen
    Center for Genome Sciences, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 103:5977-82. 2006
    ..coli isolates from patients with UTI. These studies outline a computational approach that may be broadly applicable for studying strain-specific adaptation and pathogenesis in other bacteria...
  83. pmc Histidine protects against zinc and nickel toxicity in Caenorhabditis elegans
    John T Murphy
    Department of Developmental Biology, Washington University School of Medicine, St Louis, Missouri, United States of America
    PLoS Genet 7:e1002013. 2011
    ..These studies identify a novel role for haly-1 and histidine in zinc metabolism and may be relevant for other animals...
  84. doi request reprint The impact of next-generation sequencing technology on genetics
    Elaine R Mardis
    Genome Sequencing Center, Washington University School of Medicine, St Louis, MO 63108, USA
    Trends Genet 24:133-41. 2008
    ..Here I survey next-generation sequencing technologies and consider how they can provide a more complete picture of how the genome shapes the organism...
  85. pmc A pilot study of high-throughput, sequence-based mutational profiling of primary human acute myeloid leukemia cell genomes
    Timothy J Ley
    Department of Medicine, Siteman Cancer Center, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 100:14275-80. 2003
    ..This strategy represents a viable approach for the detection of potentially relevant, nonrandom mutations in primary human cancer cell genomes...
  86. pmc Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa
    Ryan D Morin
    Genome Sciences Centre, BC Cancer Agency, Vancouver V5Z 1L3, Canada
    Genome Res 18:571-84. 2008
    ..Genomic mapping of all sequences to the O. sativa genome can be viewed at http://microrna.bcgsc.ca/cgi-bin/gbrowse/rice_build_3/...
  87. pmc The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics
    Lincoln D Stein
    Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
    PLoS Biol 1:E45. 2003
    ..elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes...
  88. pmc The repetitive landscape of the chicken genome
    Thomas Wicker
    Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    Genome Res 15:126-36. 2005
    ..This study also exemplifies the power of the CBCS method to create representative databases for the repetitive fractions of genomes for which only limited sequence data is available...
  89. ncbi request reprint Evolutionary and biomedical insights from the rhesus macaque genome
    Richard A Gibbs
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Science 316:222-34. 2007
    ..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species...
  90. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  91. pmc Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    Elliott H Margulies
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Genome Res 17:760-74. 2007
    ..Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization...
  92. pmc Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach
    Matthew N Bainbridge
    British Columbia Cancer Agency BCCA Genome Sciences Centre, Vancouver, British Columbia, Canada
    BMC Genomics 7:246. 2006
    ..Although the sequence reads are short, they can readily be used for re-sequencing. By re-sequencing the mRNA products of a cell, one may rapidly discover polymorphisms and splice variants particular to that cell...
  93. ncbi request reprint Extending assembly of short DNA sequences to handle error
    William R Jeck
    Department of Biology, University of Carolina Chapel Hill, Chapel Hill, NC 27599, USA
    Bioinformatics 23:2942-4. 2007
    ..Though it is a simple modification of a previous approach, we show significant improvements in assembly results on simulated and experimental datasets that include error...
  94. pmc Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma
    Jenifer L Marks
    Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Cancer Res 68:5524-8. 2008
    ..MEK1 mutants have not previously been reported in lung cancer and may provide a target for effective therapy in a small subset of patients with lung adenocarcinoma...
  95. pmc Conifers have a unique small RNA silencing signature
    Elena V Dolgosheina
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A 1S6
    RNA 14:1508-15. 2008
    ..No evidence for DCL3, an enzyme that matures 24-nt RNAs in angiosperms, was found. We hypothesize that the diverse class of 21-nt RNAs found in conifers may help to maintain organization of their unusually large genomes...
  96. 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...
  97. pmc Molecular refinement of gibbon genome rearrangements
    Roberta Roberto
    Department of Genetics and Microbiology, University of Bari, 70126 Bari, Italy
    Genome Res 17:249-57. 2007
    ..Our data emphasize the synergistic effect of combining computational genomics and cytogenetics and provide a framework for ultimate sequence and assembly of the gibbon genome...