Kelly A Frazer

Summary

Affiliation: The Scripps Research Institute
Country: USA

Publications

  1. 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
  2. pmc In vitro human keratinocyte migration rates are associated with SNPs in the KRT1 interval
    Heng Tao
    Perlegen Sciences, Mountain View, California, United States of America
    PLoS ONE 2:e697. 2007
  3. 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
  4. ncbi request reprint A sequence-based variation map of 8.27 million SNPs in inbred mouse strains
    Kelly A Frazer
    Perlegen Sciences, 2021 Stierlin Court, Mountain View, California 94043, USA
    Nature 448:1050-3. 2007
  5. ncbi request reprint Whole-genome patterns of common DNA variation in three human populations
    David A Hinds
    Perlegen Sciences Inc, 2021 Stierlin Court, Mountain View, CA 94043, USA
    Science 307:1072-9. 2005
  6. 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
  7. 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
  8. pmc Application of pooled genotyping to scan candidate regions for association with HDL cholesterol levels
    David A Hinds
    Perlegen Sciences, 2021 Stierlin Court, Mountain View, CA 94043, USA
    Hum Genomics 1:421-34. 2004
  9. 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
  10. 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

Detail Information

Publications31

  1. 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...
  2. pmc In vitro human keratinocyte migration rates are associated with SNPs in the KRT1 interval
    Heng Tao
    Perlegen Sciences, Mountain View, California, United States of America
    PLoS ONE 2:e697. 2007
    ..Furthermore we show that in vitro cell assays can successfully be used to deconstruct complex traits into simple biological model systems for genetic association studies...
  3. 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...
  4. ncbi request reprint A sequence-based variation map of 8.27 million SNPs in inbred mouse strains
    Kelly A Frazer
    Perlegen Sciences, 2021 Stierlin Court, Mountain View, California 94043, USA
    Nature 448:1050-3. 2007
    ..The considerable regional redundancy of the SNP data will facilitate imputation of the majority of these genotypes in less-densely typed classical inbred strains to provide a complete view of variation in additional strains...
  5. ncbi request reprint Whole-genome patterns of common DNA variation in three human populations
    David A Hinds
    Perlegen Sciences Inc, 2021 Stierlin Court, Mountain View, CA 94043, USA
    Science 307:1072-9. 2005
    ..Our data provide a tool for exploring many questions that remain regarding the causal role of common human DNA variation in complex human traits and for investigating the nature of genetic variation within and between human populations...
  6. 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...
  7. 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
    ....
  8. pmc Application of pooled genotyping to scan candidate regions for association with HDL cholesterol levels
    David A Hinds
    Perlegen Sciences, 2021 Stierlin Court, Mountain View, CA 94043, USA
    Hum Genomics 1:421-34. 2004
    ..Our study is among the first to demonstrate the application of pooled genotyping followed by confirmation with individual genotyping to identify genetic determinants of a complex trait...
  9. 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
    ....
  10. 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...
  11. 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...
  12. pmc Allele-specific KRT1 expression is a complex trait
    Heng Tao
    Perlegen Sciences, Mountain View, California, USA
    PLoS Genet 2:e93. 2006
    ....
  13. pmc Analysis of allelic differential expression in human white blood cells
    P V Krishna Pant
    Perlegen Sciences, Mountain View, California 94043, USA
    Genome Res 16:331-9. 2006
    ....
  14. 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...
  15. pmc Segmental phylogenetic relationships of inbred mouse strains revealed by fine-scale analysis of sequence variation across 4.6 mb of mouse genome
    Kelly A Frazer
    Perlegen Sciences, Mountain View, California 94043, USA
    Genome Res 14:1493-500. 2004
    ....
  16. 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...
  17. ncbi request reprint Common deletions and SNPs are in linkage disequilibrium in the human genome
    David A Hinds
    Perlegen Sciences, Inc, 2021 Stierlin Court, Mountain View, California 94043, USA
    Nat Genet 38:82-5. 2006
    ....
  18. pmc Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional
    Kelly A Frazer
    Perlegen Sciences, Mountain View, California 95051, USA
    Genome Res 14:367-72. 2004
    ..These findings suggest that functional conserved noncoding human sequences can be missing in other mammals, even closely related primate species...
  19. 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
  20. pmc High-resolution mutational profiling suggests the genetic validity of glioblastoma patient-derived pre-clinical models
    Shawn E Yost
    Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
    PLoS ONE 8:e56185. 2013
    ....
  21. 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%...
  22. pmc Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders
    Dan Zhou
    Division of Respiratory Medicine, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
    Am J Hum Genet 93:452-62. 2013
    ..Our study provides an unbiased framework to identify and validate the genetic basis of adaptation to high altitudes and identifies potentially targetable mechanisms for CMS treatment. ..
  23. pmc Transcriptome sequencing of tumor subpopulations reveals a spectrum of therapeutic options for squamous cell lung cancer
    Christian L Barrett
    Moores UCSD Cancer Center, University of California San Diego, La Jolla, California, United States of America
    PLoS ONE 8:e58714. 2013
    ..Here, we analyze the transcriptome of CSC and non-CSC subpopulations by RNA-seq to identify new potential therapeutic strategies for SCC...
  24. 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...
  25. 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...
  26. 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. ..
  27. pmc VISTA: computational tools for comparative genomics
    Kelly A Frazer
    Perlegen Sciences, Inc, 2021 Stierlin Court, Mountain View, CA 94043, USA
    Nucleic Acids Res 32:W273-9. 2004
    ..We illustrate capabilities of the VISTA site by the analysis of a 180 kb interval on human chromosome 5 that encodes for the kinesin family member 3A (KIF3A) protein...
  28. 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...
  29. pmc Experimental selection of hypoxia-tolerant Drosophila melanogaster
    Dan Zhou
    Department of Pediatrics, University of California at San Diego, La Jolla, CA 92093, USA
    Proc Natl Acad Sci U S A 108:2349-54. 2011
    ..Unique analytical tools and genetic and bioinformatic strategies allowed us to discover that Notch activation plays a major role in this hypoxia tolerance in Drosophila melanogaster...
  30. pmc Genomic DNA insertions and deletions occur frequently between humans and nonhuman primates
    Kelly A Frazer
    Perlegen Sciences, Mountain View, California 94043, USA
    Genome Res 13:341-6. 2003
    ..These DNA rearrangements are commonly found in genic intervals, and thus provide natural starting points for focused investigations of qualitative and quantitative gene expression differences between humans and other primates...
  31. 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...