Olivier Harismendy

Summary

Affiliation: University of California
Country: USA

Publications

  1. 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
  2. pmc Genomics in 2011: challenges and opportunities
    David J Adams
    Wellcome Trust Sanger Institute
    Genome Biol 12:137. 2011
  3. 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
  4. 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
  5. pmc A covering method for detecting genetic associations between rare variants and common phenotypes
    Gaurav Bhatia
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
    PLoS Comput Biol 6:e1000954. 2010
  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 Biomarkers of endocannabinoid system activation in severe obesity
    Jack C Sipe
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
    PLoS ONE 5:e8792. 2010
  8. 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
  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 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

Collaborators

Detail Information

Publications20

  1. 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...
  2. 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?..
  3. 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...
  4. 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
    ....
  5. pmc A covering method for detecting genetic associations between rare variants and common phenotypes
    Gaurav Bhatia
    Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
    PLoS Comput Biol 6:e1000954. 2010
    ..The data suggests that the RVs help disrupt the expression of the two genes, leading to lowered metabolism of the corresponding cannabinoids. Overall, our results point to the power of including RVs in measuring genetic associations...
  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 Biomarkers of endocannabinoid system activation in severe obesity
    Jack C Sipe
    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
    PLoS ONE 5:e8792. 2010
    ....
  8. 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...
  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 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. ..
  11. 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...
  12. 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
    ....
  13. 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%...
  14. 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...
  15. 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...
  16. 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...
  17. 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...
  18. pmc Identification of liver cancer progenitors whose malignant progression depends on autocrine IL-6 signaling
    Guobin He
    Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, University of California San Diego, School of Medicine, 9500 Gilman Drive, San Diego, CA 92093, USA
    Cell 155:384-96. 2013
    ..This may be a general mechanism that drives other IL-6-producing malignancies. ..
  19. 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...