David Larson, Ph.D.,  McDonnell Genome Institute

Dr. David Larson joined the McDonnell Genome Institute in 2008 after completing his graduate work in Developmental Biology at Washington University in St. Louis. Since joining the institute, he has been working primarily on somatic single nucleotide variant discovery using next-generation sequencing data. He is currently Assistant Director of Informatics.

Dr. Larson's research focuses on the genetic basis of cancer. He is particularly interested in the role of cellular adhesion molecules in tumorigenesis. On a technical level, his research interests encompass improving sensitivity and specificity of somatic variant calling and detection of small indels in sequencing data. He also is interested in novel methods for visualizing next-generation sequencing information.

Dr. Larson graduated from Indiana University in Bloomington with a B.S. in Biology in 2003. During his time there, he researched cellular polarity in the bacterium Caulobacter crescentus. In 2007, he received his Ph.D. in Developmental Biology from Washington University in St. Louis for work on live visualization of the Drosophila retina.

Publications

title citation publication date
CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer Nat Genet. 2017 Jan 31;49(2):170-174. doi: 10.1038/ng.3774. 2017-01-31
The role of rare protein-coding variants to anti-TNF treatment response in rheumatoid arthritis. Arthritis Rheumatol. 2016 Oct 27. doi: 10.1002/art.39966. [Epub ahead of print] 2016-10-24
Truncating Prolactin Receptor Mutations Promote Tumor Growth in Murine Estrogen Receptor-Alpha Mammary Carcinomas. Cell Rep. 2016 Sep 27;17(1):249-60. doi: 10.1016/j.celrep.2016.08.076. 1970-08-22
CIViC: A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer doi: http://dx.doi.org/10.1101/072892
Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B-lymphoblastic leukemia Exp Hematol. 2016 Jul;44(7):603-13. doi: 10.1016/j.exphem.2016.04.011. Epub 2016 May 13 2016-07-01
Rare Variation in TET2 Is Associated with Clinically Relevant Prostate Carcinoma in African-Americans Cancer Epidemiol Biomarkers Prev. 2016 Aug 2. pii: cebp.0373.2016. [Epub ahead of print] 2016-08-02
Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers Nat Commun. 2016 Aug 9;7:12498. doi: 10.1038/ncomms12498 2016-08-09
A genomic case study of mixed fibrolamellar hepatocellular carcinoma. Ann Oncol. 2016 Mar 30. pii: mdw135. [Epub ahead of print] 2016-03-30
Patterns and functional implications of rare germline variants across 12 cancer types. Nat Commun. 2015 Dec 22;6:10086. doi: 10.1038/ncomms10086. 2015-12-15
Optimizing cancer genome sequencing and analysis. Cell Syst. 2015 Sep 23;1(3):210-223. 2015-09-23
A global reference for human genetic variation. Nature. 2015 Oct 1;526(7571):68-74. doi: 10.1038/nature15393. 2015-10-01
Association Between Mutation Clearance After Induction Therapy and Outcomes in Acute Myeloid Leukemia. JAMA. 2015 Aug 25;314(8):811-22. doi: 10.1001/jama.2015.9643. 2015-08-25
Genome Modeling System: A Knowledge Management Platform for Genomics. PLoS Comput Biol. 2015 Jul 9;11(7):e1004274. doi: 10.1371/journal.pcbi.1004274. eCollection 2015. 2015-07-09
TYK2 Protein-Coding Variants Protect against Rheumatoid Arthritis and Autoimmunity, with No Evidence of Major Pleiotropic Effects on Non-Autoimmune Complex Traits. PLoS One. 2015 Apr 7;10(4):e0122271. doi: 10.1371/journal.pone.0122271. eCollection 2015. 2015-04-07
Identification of Functional Variants for Cleft Lip with or without Cleft Palate in or near PAX7, FGFR2, and NOG by Targeted Sequencing of GWAS Loci. Am J Hum Genet. 2015 Mar 5;96(3):397-411. doi: 10.1016/j.ajhg.2015.01.004. Epub 2015 Feb 19. 2015-03-05
Using SomaticSniper to Detect Somatic Single Nucleotide Variants. Curr Protoc Bioinformatics. 2014 Mar 21;15(155):15.5.1-15.5.8. 2014-03-21
BreakDancer: Identification of Genomic Structural Variation from Paired-End Read Mapping Curr. Protoc. Bioinform. 45:15.6.1-15.6.11. DOI: 10.1002/0471250953.bi1506s45 2014-03-21
Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection Curr. Protoc. Bioinform. 44:15.4.1?15.4.17. DOI: 10.1002/0471250953.bi1504s44 2013-12-12
Application of Next-Generation Sequencing to Identify Genes and Mutations Causing Autosomal Dominant Retinitis Pigmentosa (adRP). Adv Exp Med Biol. 2014;801:123-9. doi: 10.1007/978-1-4614-3209-8_16. 2014-04-01
Exome-Based Mapping and Variant Prioritization for Inherited Mendelian Disorders. Am J Hum Genet. 2014 Feb 19. pii: S0002-9297(14)00054-8. doi: 10.1016/j.ajhg.2014.01.016. [Epub ahead of print] 2014-02-20
Re-sequencing Expands Our Understanding of the Phenotypic Impact of Variants at GWAS Loci. PLoS Genet. 2014 Jan 30;10(1):e1004147. doi: 10.1371/journal.pgen.1004147. eCollection 2014. 2014-01-30
Integrated analysis of germline and somatic variants in ovarian cancer. Nat Commun. 2014 Jan 22;5:3156. doi: 10.1038/ncomms4156. 2014-01-22
DGIdb: mining the druggable genome. Nat Methods. 2013 Oct 13. doi: 10.1038/nmeth.2689. [Epub ahead of print] 2013-10-13
The next-generation sequencing revolution and its impact on genomics. Cell. 2013 Sep 26;155(1):27-38. doi: 10.1016/j.cell.2013.09.006. 2013-09-26
The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Sep 26;45(10):1113-20. doi: 10.1038/ng.2764. 2013-09-26
Endocrine-Therapy-Resistant ESR1 Variants Revealed by Genomic Characterization of Breast-Cancer-Derived Xenografts. Cell Rep. 2013 Sep 18. pii: S2211-1247(13)00463-4. doi: 10.1016/j.celrep.2013.08.022. [Epub ahead of print] 2013-09-18
Identification of a rare coding variant in complement 3 associated with age-related macular degeneration. Nat Genet. 2013 Sep 15. doi: 10.1038/ng.2758. [Epub ahead of print] 2013-09-15
Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia. N Engl J Med. 2013 May 1. [Epub ahead of print] 2013-05-01
The origin and evolution of mutations in acute myeloid leukemia. Cell. 2012 Jul 20;150(2):264-78. 2012-07-20
Background Mutations in Parental Cells Account for Most of the Genetic Heterogeneity of Induced Pluripotent Stem Cells. Cell Stem Cell. 2012 Apr 26. [Epub ahead of print] 2012-04-26
Clonal Architecture of Secondary Acute Myeloid Leukemia. N Engl J Med. 2012 Mar 22;366(12):1090-8. doi: 10.1056/NEJMoa1106968. Epub 2012 Mar 14. 2012-03-14
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012 Feb 2. [Epub ahead of print] 2012-02-12
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature. 2012 Jan 11. doi: 10.1038/nature10738. [Epub ahead of print] 2012-01-11
Massively parallel sequencing approaches for characterization of structural variation. Methods Mol Biol. 2012;838:369-84. 2012-01-06
SomaticSniper: Identification of Somatic Point Mutations in Whole Genome Sequencing Data. Bioinformatics. 2011 Dec 6. [Epub ahead of print] 2011-12-06
Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes. Nat Genet. 2011 Dec 11. doi: 10.1038/ng.1031. [Epub ahead of print] 2011-12-11
Use of Whole-Genome Sequencing to Diagnose a Cryptic Fusion Oncogene JAMA. 2011 Apr 20;305(15):1577-84. 2011-04-20
Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression. J Clin Invest. 2011 Mar 23. pii: 45284. doi: 10.1172/JCI45284. [Epub ahead of print] 2011-03-23
DNMT3A Mutations in Acute Myeloid Leukemia N Engl J Med. 2010 Nov 10. 2010-11-10
Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature. 2010 Apr 15;464(7291):989-90. 2010-04-15
CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data. Bioinformatics. 2009 Dec 23. [Epub ahead of print] 2009-12-23
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009 Sep;6(9):677-81. Epub 2009 Aug 9. 2009-09-06
Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med. 2009 Sep 10;361(11):1058-66. Epub 2009 Aug 5. 2009-09-10
VarScan: Variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009 Sep 1;25(17):2283-5. Epub 2009 Jun 19. 2009-06-19
DNA sequencing of a cytogenetically normal acute myeloid leukaemia (AML) genome. Nature. 2008 Nov 6;456(7218):66-72. 2008-11-06
Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008 Oct 23;455(7216):1069-75. 2008-10-23
Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008 Oct 23;455(7216):1061-8. Epub 2008 Sep 4. 2008-10-23