Olivier Harismendy

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Genomics in 2011: challenges and opportunities
    David J Adams
    Wellcome Trust Sanger Institute
    Genome Biol 12:137. 2011
  2. 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
  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 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
  5. 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
  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 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
  8. 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
  9. 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
  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

Collaborators

Detail Information

Publications13

  1. pmc Genomics in 2011: challenges and opportunities
    David J Adams
    Wellcome Trust Sanger Institute
    Genome Biol 12:137. 2011
    ..What was their favorite paper of 2011? What are the challenges in their particular research area? Who has had the biggest influence on their careers? What advice would they give to young researchers embarking on a career in research?..
  2. 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...
  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 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%...
  5. 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...
  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 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. ..
  8. 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...
  9. 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
    ....
  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 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 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...
  13. doi request reprint Method for improving sequence coverage uniformity of targeted genomic intervals amplified by LR-PCR using Illumina GA sequencing-by-synthesis technology
    Olivier Harismendy
    Scripps Genomic Medicine, Scripps Translational Science Institute, Scripps Research Institute, La Jolla, CA, USA
    Biotechniques 46:229-31. 2009
    ..The capability to increase sequence coverage uniformity greatly improves the effective throughput of NGS platforms...