Kelly A Frazer

Summary

Affiliation: The Scripps Research Institute
Country: USA

Publications

  1. doi request reprint Human genetic variation and its contribution to complex traits
    Kelly A Frazer
    Scripps Genomic Medicine, Scripps Translational Science Institute and The Scripps Research Institute, La Jolla, California 92037, USA
    Nat Rev Genet 10:241-51. 2009
  2. pmc Accurate detection and genotyping of SNPs utilizing population sequencing data
    Vikas Bansal
    Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
    Genome Res 20:537-45. 2010
  3. pmc Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level
    Olivier Harismendy
    Moores UCSD Cancer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Genome Biol 11:R118. 2010
  4. pmc 9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response
    Olivier Harismendy
    Department of Pediatrics and Rady s Children s Hospital, University of California at San Diego, School of Medicine, La Jolla, California 92093, USA
    Nature 470:264-8. 2011
  5. pmc Common vs. rare allele hypotheses for complex diseases
    Nicholas J Schork
    Scripps Genomic Medicine, and Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, United States
    Curr Opin Genet Dev 19:212-9. 2009
  6. pmc Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing
    Shawn E Yost
    Bioinformatics Graduate Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA
    Bioinformatics 29:1908-9. 2013
  7. pmc Evaluation of next generation sequencing platforms for population targeted sequencing studies
    Olivier Harismendy
    Scripps Genomic Medicine, Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
    Genome Biol 10:R32. 2009
  8. pmc Enrichment of sequencing targets from the human genome by solution hybridization
    Ryan Tewhey
    Scripps Genomic Medicine, Scripps Translational Science Institute, The Scripps Research Institute, 3344 N Torrey Pines Court, La Jolla, CA 92037, USA
    Genome Biol 10:R116. 2009
  9. pmc Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas
    Christopher Deboever
    Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
    PLoS ONE 8:e73956. 2013
  10. pmc Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens
    Shawn E Yost
    Moores UCSD Cancer Center, Bioinformatics and Systems Biology Graduate Program, Department of Pediatrics and Rady Children s Hospital, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Nucleic Acids Res 40:e107. 2012

Detail Information

Publications16

  1. doi request reprint Human genetic variation and its contribution to complex traits
    Kelly A Frazer
    Scripps Genomic Medicine, Scripps Translational Science Institute and The Scripps Research Institute, La Jolla, California 92037, USA
    Nat Rev Genet 10:241-51. 2009
    ..Technological advances, such as the ability to detect rare and structural variants, and a clear understanding of the challenges in linking different types of variation with phenotype, will be essential for future progress...
  2. pmc Accurate detection and genotyping of SNPs utilizing population sequencing data
    Vikas Bansal
    Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
    Genome Res 20:537-45. 2010
    ..Collectively, these results suggest that analysis of population sequencing data is a powerful approach for the accurate detection of SNPs and the assignment of genotypes to individual samples...
  3. pmc Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level
    Olivier Harismendy
    Moores UCSD Cancer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Genome Biol 11:R118. 2010
    ....
  4. pmc 9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response
    Olivier Harismendy
    Department of Pediatrics and Rady s Children s Hospital, University of California at San Diego, School of Medicine, La Jolla, California 92093, USA
    Nature 470:264-8. 2011
    ....
  5. pmc Common vs. rare allele hypotheses for complex diseases
    Nicholas J Schork
    Scripps Genomic Medicine, and Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, United States
    Curr Opin Genet Dev 19:212-9. 2009
    ..Both hypotheses have their place in current research efforts...
  6. pmc Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing
    Shawn E Yost
    Bioinformatics Graduate Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA
    Bioinformatics 29:1908-9. 2013
    ..Using datasets reproducing tumor genetic heterogeneity, we demonstrate that Mutascope has a higher sensitivity and generates fewer false-positive calls than tools designed for shotgun sequencing or diploid genomes...
  7. pmc Evaluation of next generation sequencing platforms for population targeted sequencing studies
    Olivier Harismendy
    Scripps Genomic Medicine, Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
    Genome Biol 10:R32. 2009
    ..To evaluate these platforms for this application, we analyzed human sequence generated by the Roche 454, Illumina GA, and the ABI SOLiD technologies for the same 260 kb in four individuals...
  8. pmc Enrichment of sequencing targets from the human genome by solution hybridization
    Ryan Tewhey
    Scripps Genomic Medicine, Scripps Translational Science Institute, The Scripps Research Institute, 3344 N Torrey Pines Court, La Jolla, CA 92037, USA
    Genome Biol 10:R116. 2009
    ..9 Mb of sequence target. We demonstrate that the tiling probe frequency is important for generating sequence data with high uniform coverage of targets. We obtained 93% sensitivity to detect SNPs, with a calling accuracy greater than 99%...
  9. pmc Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas
    Christopher Deboever
    Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
    PLoS ONE 8:e73956. 2013
    ..This study demonstrates the ability of next generation transcriptome sequencing to accurately identify viruses, including DNA viruses, in solid human cancer tissue samples. ..
  10. pmc Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens
    Shawn E Yost
    Moores UCSD Cancer Center, Bioinformatics and Systems Biology Graduate Program, Department of Pediatrics and Rady Children s Hospital, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Nucleic Acids Res 40:e107. 2012
    ..Our study demonstrates the feasibility of performing genome-wide deep sequencing analysis of FFPE archived tumors of limited sample size such as residual cancer after treatment or metastatic biopsies...
  11. pmc Genetic determinants of phenotypic diversity in humans
    Nazli G Rahim
    Scripps Genomic Medicine, The Scripps Research Institute, North Torrey Pines Road MEM 275, La Jolla, CA 92037, USA
    Genome Biol 9:215. 2008
    ..These same technologies have also resulted in the identification of common genetic variants associated with more than 30 human diseases and traits...
  12. pmc Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs
    Marcus Kinsella
    Bioinformatics and Systems Biology Program, Moores UCSD Cancer Center, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
    Bioinformatics 27:1068-75. 2011
    ..Previous methods to find gene fusions either ignored these reads or required additional longer single reads. This can obscure up to 30% of fusions and unnecessarily discards much of the data...
  13. pmc Microdroplet-based PCR enrichment for large-scale targeted sequencing
    Ryan Tewhey
    Scripps Genomic Medicine, Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, California, USA
    Nat Biotechnol 27:1025-31. 2009
    ..Our results demonstrate that microdroplet technology is well suited for processing DNA for massively parallel enrichment of specific subsets of the human genome for targeted sequencing...
  14. pmc A second generation human haplotype map of over 3.1 million SNPs
    Kelly A Frazer
    The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA
    Nature 449:851-61. 2007
    ..Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations...
  15. ncbi request reprint The genomics gold rush
    Eric J Topol
    Scripps Genomic Medicine, Scripps Health, and The Scripps Research Institute, La Jolla, California 92037, USA
    JAMA 298:218-21. 2007
  16. pmc Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing
    Olivier Harismendy
    Moores UCSD Cancer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Genome Biol 12:R124. 2011
    ..With an improved performance when run on the Illumina Miseq, the UDT-Seq assay is well suited for clinical applications to guide therapy and study clonal selection in heterogeneous samples...