Keck School Faculty

David Wesley Craig
David Wesley Craig
Professor of Translational Genomics;Co-Director, Institute of Translational Genomics
Department of Translational Genomics
1450 Biggy Street Health Sciences Campus Los Angeles
David Craig serves as Vice-Chair of USC's new Department of Translational Genomics ( http://dtg.usc.edu ) within the USC Keck School of Medicine. Dr. Craig's expertise is in genomics, bioinformatics, and data analysis of high-throughput genomics data. His laboratory consists of both a wet-lab and dry-lab. Within his group, lab personnel have the opportunity to either specialize or become dual trained in bioinformatics and molecular biology.

His group pioneered cost-effective GWAS methods leading to genetic associations reported in Science, Nature Genetics, and New England Journal of Medicine. His publications include some of the most significant papers addressing the challenges of data sharing and data privacy (Homer et al, PLOS Genetics 2008). Since 2006, his group has been developing tools based on NGS beginning with publishing one of the first papers for targeted variant calling in humans (Craig et al Nature Methods, 2008). In the past 8 years, his group has published and collaborated on over 60 NGS publications balanced between the wet and dry-labs. During this time, he has served in several international genomics projects including as PI on a U01 responsible for developing bioinformatic pipelines for the Phase I and Phase II portions of the 1000 Genomes Project.

With collaborators, his group was among the first to implement NGS in molecular profiling for cancer patient treatment recommendations in a feasibility study in metastatic triple negative breast cancer (Craig et al., Mol Cancer Ther. 2013). Building upon this and other efforts his group developed an end-to-end platform for personalized medicine, NGS data management, analysis, and clinical genomic interpretation following CAP/CLIA guidelines. Within this framework, they completed analytical validation for integrated RNA/DNA analysis of tumor/normal sets. Community resources from these efforts included include a collaborative release of COLO829 tumor/normal sequencing reference sets. He also was a founding scientific director for TGen's Center for Rare Childhood Disorders - a research clinic enrolling over 1000 individuals into a study developing integrative RNA/DNA approaches for identifying the germline genetic basis of disease.

Dr. Craig's laboratory has openings for post-doctoral fellows and graduate students, and can be reached at davidwcr at symbol usc.edu.

Neonatal epileptic encephalopathy caused by de novo GNAO1 mutation misdiagnosed as atypical Rett syndrome: Cautions in interpretation of genomic test results Semin Pediatr Neurol. 2018 Jul; 26:28-32. . View in PubMed

Misperceived norms and personal sugar-sweetened beverage consumption and fruit and vegetable intake among students in the United States Appetite. 2018 Jun 08. . View in PubMed

Accuracy of Estimated Blood Alcohol Concentration Norms From College Student Drinking Survey Data: Verification Using Matched Late-Night Breath Measurements J Stud Alcohol Drugs. 2018 May; 79(3):455-464. . View in PubMed

Author Correction: A population-specific reference panel empowers genetic studies of Anabaptist populations Sci Rep. 2018 Apr 25; 8(1):6771. . View in PubMed

Prospective Feasibility Trial for Genomics-Informed Treatment in Recurrent and Progressive Glioblastoma Clin Cancer Res. 2018 Jan 15; 24(2):295-305. . View in PubMed

Comparative analysis of primary versus relapse/refractory DLBCL identifies shifts in mutation spectrum Oncotarget. 2017 Nov 21; 8(59):99237-99244. . View in PubMed

Exploring genome-wide DNA methylation patterns in Aicardi syndrome Epigenomics. 2017 Nov; 9(11):1373-1386. . View in PubMed

Comprehensive molecular profiling of 718 Multiple Myelomas reveals significant differences in mutation frequencies between African and European descent cases PLoS Genet. 2017 Nov; 13(11):e1007087. . View in PubMed

A method to reduce ancestry related germline false positives in tumor only somatic variant calling BMC Med Genomics. 2017 Oct 19; 10(1):61. . View in PubMed

Enrichment of PI3K-AKT-mTOR Pathway Activation in Hepatic Metastases from Breast Cancer Clin Cancer Res. 2017 Aug 15; 23(16):4919-4928. . View in PubMed

A population-specific reference panel empowers genetic studies of Anabaptist populations Sci Rep. 2017 Jul 20; 7(1):6079. . View in PubMed

A gain-of-function mutation in the GRIK2 gene causes neurodevelopmental deficits Neurol Genet. 2017 Feb; 3(1):e129. . View in PubMed

Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease Nat Genet. 2017 09; 49(9):1373-1384. . View in PubMed

Comprehensive Genomic Analysis of Metastatic Mucinous Urethral Adenocarcinoma Guides Precision Oncology Treatment: Targetable EGFR Amplification Leading to Successful Treatment With Erlotinib Clin Genitourin Cancer. 2017 08; 15(4):e727-e734. . View in PubMed

Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma Genome Res. 2017 04; 27(4):524-532. . View in PubMed

A prospective pilot study of genome-wide exome and transcriptome profiling in patients with small cell lung cancer progressing after first-line therapy PLoS One. 2017; 12(6):e0179170. . View in PubMed

Case Report: Novel mutations in TBC1D24 are associated with autosomal dominant tonic-clonic and myoclonic epilepsy and recessive Parkinsonism, psychosis, and intellectual disability F1000Res. 2017; 6:553. . View in PubMed

Case report: whole exome sequencing of primary cardiac angiosarcoma highlights potential for targeted therapies BMC Cancer. 2017 01 05; 17(1):17. . View in PubMed

A de novo missense mutation in ZMYND11 is associated with global developmental delay, seizures, and hypotonia Cold Spring Harb Mol Case Stud. 2016 Sep; 2(5):a000851. . View in PubMed

Molecular Genetic Profiling of Adolescent Glassy Cell Carcinoma of the Cervix Reveals Targetable EGFR Amplification with Potential Therapeutic Implications J Adolesc Young Adult Oncol. 2016 Sep; 5(3):297-302. . View in PubMed

An International Standard for holotranscobalamin (holoTC): international collaborative study to assign a holoTC value to the International Standard for vitamin B12 and serum folate Clin Chem Lab Med. 2016 Sep 01; 54(9):1467-72. . View in PubMed

Genome-wide association study of 40,000 individuals identifies two novel loci associated with bipolar disorder Hum Mol Genet. 2016 Aug 01; 25(15):3383-3394. . View in PubMed

Dystonia in ATP2B3-associated X-linked spinocerebellar ataxia Mov Disord. 2016 11; 31(11):1752-1753. . View in PubMed

Clinical Implementation of Integrated Genomic Profiling in Patients with Advanced Cancers Sci Rep. 2016 12 23; 6(1):25. . View in PubMed

Age-Related Macular Degeneration-Associated Genes in Alzheimer Disease Am J Geriatr Psychiatry. 2015 Dec; 23(12):1290-1296. . View in PubMed

Plasma Complement factor H in Alzheimer's Disease J Alzheimers Dis. 2015; 45(2):369-72. . View in PubMed

Amyloid pathway-based candidate gene analysis of [(11)C]PiB-PET in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort Brain Imaging Behav. 2012 Mar; 6(1):1-15. . View in PubMed

Germline mutations in HOXB13 and prostate-cancer risk N Engl J Med. 2012 Jan 12; 366(2):141-9. . View in PubMed

Paired tumor and normal whole genome sequencing of metastatic olfactory neuroblastoma PLoS One. 2012; 7(5):e37029. . View in PubMed

Deep clonal profiling of formalin fixed paraffin embedded clinical samples PLoS One. 2012; 7(11):e50586. . View in PubMed

Genome-wide characterization of pancreatic adenocarcinoma patients using next generation sequencing PLoS One. 2012; 7(10):e43192. . View in PubMed

Cancer of the ampulla of Vater: analysis of the whole genome sequence exposes a potential therapeutic vulnerability Genome Med. 2012; 4(7):56. . View in PubMed

Induction of pluripotent stem cells from autopsy donor-derived somatic cells Neurosci Lett. 2011 Sep 20; 502(3):219-24. . View in PubMed

Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4 Nat Genet. 2011 Sep 18; 43(10):977-83. . View in PubMed

The functional spectrum of low-frequency coding variation Genome Biol. 2011 Sep 14; 12(9):R84. . View in PubMed

Demographic history and rare allele sharing among human populations Proc Natl Acad Sci U S A. 2011 Jul 19; 108(29):11983-8. . View in PubMed

Variation in genome-wide mutation rates within and between human families Nat Genet. 2011 Jun 12; 43(7):712-4. . View in PubMed

Genome-wide association of bipolar disorder suggests an enrichment of replicable associations in regions near genes PLoS Genet. 2011 Jun; 7(6):e1002134. . View in PubMed

Autism and increased paternal age related changes in global levels of gene expression regulation PLoS One. 2011 Feb 17; 6(2):e16715. . View in PubMed

Mapping copy number variation by population-scale genome sequencing Nature. 2011 Feb 03; 470(7332):59-65. . View in PubMed

Introduction to genetic epidemiology Optometry. 2011 Feb; 82(2):83-91. . View in PubMed

Accuracy of CNV Detection from GWAS Data PLoS One. 2011 Jan 13; 6(1):e14511. . View in PubMed

Genome-wide association study of CSF biomarkers Abeta1-42, t-tau, and p-tau181p in the ADNI cohort Neurology. 2011 Jan 04; 76(1):69-79. . View in PubMed

Genomic Copy Number Analysis in Alzheimer's Disease and Mild Cognitive Impairment: An ADNI Study Int J Alzheimers Dis. 2011; 2011:729478. . View in PubMed

Bar-coded, multiplexed sequencing of targeted DNA regions using the Illumina Genome Analyzer Methods Mol Biol. 2011; 700:89-104. . View in PubMed

Exonic DNA sequencing of ERBB4 in bipolar disorder PLoS One. 2011; 6(5):e20242. . View in PubMed

Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors Genome Res. 2011 Jan; 21(1):47-55. . View in PubMed

Microarray-based genome-wide association studies using pooled DNA Methods Mol Biol. 2011; 700:49-60. . View in PubMed

Assessing and managing risk when sharing aggregate genetic variant data Nat Rev Genet. 2011 09 16; 12(10):730-6. . View in PubMed

Decreased serum arylesterase activity in autism spectrum disorders Psychiatry Res. 2010 Dec 30; 180(2-3):105-13. . View in PubMed

Misperceptions of peer norms as a risk factor for sugar-sweetened beverage consumption among secondary school students J Am Diet Assoc. 2010 Dec; 110(12):1916-21. . View in PubMed

Whole genome association study of brain-wide imaging phenotypes for identifying quantitative trait loci in MCI and AD: A study of the ADNI cohort Neuroimage. 2010 Nov 15; 53(3):1051-63. . View in PubMed

Voxelwise genome-wide association study (vGWAS) Neuroimage. 2010 Nov 15; 53(3):1160-74. . View in PubMed

Diversity of human copy number variation and multicopy genes Science. 2010 Oct 29; 330(6004):641-6. . View in PubMed

A map of human genome variation from population-scale sequencing Nature. 2010 Oct 28; 467(7319):1061-73. . View in PubMed

Association of CR1, CLU and PICALM with Alzheimer's disease in a cohort of clinically characterized and neuropathologically verified individuals Hum Mol Genet. 2010 Aug 15; 19(16):3295-301. . View in PubMed

Whole-genome association mapping of gene expression in the human prefrontal cortex Mol Psychiatry. 2010 Aug; 15(8):779-84. . View in PubMed

Genome-wide analysis reveals novel genes influencing temporal lobe structure with relevance to neurodegeneration in Alzheimer's disease Neuroimage. 2010 Jun; 51(2):542-54. . View in PubMed

Evidence for an association between KIBRA and late-onset Alzheimer's disease Neurobiol Aging. 2010 Jun; 31(6):901-9. . View in PubMed

A commonly carried allele of the obesity-related FTO gene is associated with reduced brain volume in the healthy elderly Proc Natl Acad Sci U S A. 2010 May 04; 107(18):8404-9. . View in PubMed

Alzheimer's Disease Neuroimaging Initiative biomarkers as quantitative phenotypes: Genetics core aims, progress, and plans Alzheimers Dement. 2010 May; 6(3):265-73. . View in PubMed

Genetic control of individual differences in gene-specific methylation in human brain Am J Hum Genet. 2010 Mar 12; 86(3):411-9. . View in PubMed

Cerebellar telomere length and psychiatric disorders Behav Genet. 2010 Mar; 40(2):250-4. . View in PubMed

Whole genome association analysis shows that ACE is a risk factor for Alzheimer's disease and fails to replicate most candidates from Meta-analysis Int J Mol Epidemiol Genet. 2010; 1(1):19-30. . View in PubMed

Genome-wide SNP genotyping study using pooled DNA to identify candidate markers mediating susceptibility to end-stage renal disease attributed to Type 1 diabetes Diabet Med. 2009 Nov; 26(11):1090-8. . View in PubMed

Genetic variants at 6p2133 are associated with susceptibility to follicular lymphoma. Nat Genet. 2009 Aug; 41(8):873-5. . View in PubMed

Genome-wide scan of 500,000 single-nucleotide polymorphisms among responders and nonresponders to interferon beta therapy in multiple sclerosis Arch Neurol. 2009 Aug; 66(8):972-8. . View in PubMed

Singleton deletions throughout the genome increase risk of bipolar disorder Mol Psychiatry. 2009 Apr; 14(4):376-80. . View in PubMed

Genetic control of human brain transcript expression in Alzheimer disease Am J Hum Genet. 2009 Apr; 84(4):445-58. . View in PubMed

Statistical comparison framework and visualization scheme for ranking-based algorithms in high-throughput genome-wide studies J Comput Biol. 2009 Apr; 16(4):565-77. . View in PubMed

A genome-wide analysis identifies genetic variants in the RELN gene associated with otosclerosis Am J Hum Genet. 2009 Mar; 84(3):328-38. . View in PubMed

GRM7 variants confer susceptibility to age-related hearing impairment Hum Mol Genet. 2009 Feb 15; 18(4):785-96. . View in PubMed

A novel reciprocal and biphasic relationship between membrane cholesterol and beta-secretase activity in SH-SY5Y cells and in human platelets J Neurochem. 2009 Jan; 108(2):341-9. . View in PubMed

Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies J Neural Transm (Vienna). 2008 Nov; 115(11):1573-85. . View in PubMed

Identification of genetic variants using bar-coded multiplexed sequencing Nat Methods. 2008 Oct; 5(10):887-93. . View in PubMed

Multimarker analysis and imputation of multiple platform pooling-based genome-wide association studies Bioinformatics. 2008 Sep 01; 24(17):1896-902. . View in PubMed

Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays PLoS Genet. 2008 Aug 29; 4(8):e1000167. . View in PubMed

Common sequence variants on 20q1122 confer melanoma susceptibility. Nat Genet. 2008 Jul; 40(7):838-40. . View in PubMed

Genome-wide linkage analysis of ADHD using high-density SNP arrays: novel loci at 5q131 and 14q12. Mol Psychiatry. 2008 May; 13(5):522-30. . View in PubMed

Identification of somatic chromosomal abnormalities in hypothalamic hamartoma tissue at the GLI3 locus Am J Hum Genet. 2008 Feb; 82(2):366-74. . View in PubMed

Identification of a novel risk locus for multiple sclerosis at 13q313 by a pooled genome-wide scan of 500,000 single nucleotide polymorphisms. PLoS One. 2008; 3(10):e3490. . View in PubMed

Sorl1 as an Alzheimer's disease predisposition gene? Neurodegener Dis. 2008; 5(2):60-4.. View in PubMed

A survey of genetic human cortical gene expression Nat Genet. 2007 Dec; 39(12):1494-9. . View in PubMed

The nuts and bolts of gene array technology and its application to drug abuse research Drug Alcohol Depend. 2007 Nov 02; 91(1):102-6. . View in PubMed

Whole-genome analysis of sporadic amyotrophic lateral sclerosis N Engl J Med. 2007 Aug 23; 357(8):775-88. . View in PubMed

Polyhydramnios, megalencephaly and symptomatic epilepsy caused by a homozygous 7-kilobase deletion in LYK5 Brain. 2007 Jul; 130(Pt 7):1929-41. . View in PubMed

Calmodulin-binding transcription activator 1 (CAMTA1) alleles predispose human episodic memory performance Hum Mol Genet. 2007 Jun 15; 16(12):1469-77. . View in PubMed

GAB2 alleles modify Alzheimer's risk in APOE epsilon4 carriers Neuron. 2007 Jun 07; 54(5):713-20. . View in PubMed

Chromosomal abnormality at 6p251-25. 3 identifies a susceptibility locus for hypothalamic hamartoma associated with epilepsy. Epilepsy Res. 2007 Jun; 75(1):70-3. . View in PubMed

Identification of a novel risk locus for progressive supranuclear palsy by a pooled genomewide scan of 500,288 single-nucleotide polymorphisms Am J Hum Genet. 2007 Apr; 80(4):769-78. . View in PubMed

A high-density whole-genome association study reveals that APOE is the major susceptibility gene for sporadic late-onset Alzheimer's disease J Clin Psychiatry. 2007 Apr; 68(4):613-8. . View in PubMed

Identification of PVT1 as a candidate gene for end-stage renal disease in type 2 diabetes using a pooling-based genome-wide single nucleotide polymorphism association study Diabetes. 2007 Apr; 56(4):975-83. . View in PubMed

SNP-based chromosomal copy number ascertainment following multiple displacement whole-genome amplification Biotechniques. 2007 Jan; 42(1):77-83. . View in PubMed

Identification of the genetic basis for complex disorders by use of pooling-based genomewide single-nucleotide-polymorphism association studies Am J Hum Genet. 2007 Jan; 80(1):126-39. . View in PubMed

SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays Bioinformatics. 2007 Jan 01; 23(1):57-63. . View in PubMed

Common Kibra alleles are associated with human memory performance Science. 2006 Oct 20; 314(5798):475-8. . View in PubMed

High-density single nucleotide polymorphism screen in a large multiplex neural tube defect family refines linkage to loci at 7p211-pter and 2q33. 1-q35. Birth Defects Res A Clin Mol Teratol. 2006 Jun; 76(6):499-505. . View in PubMed

SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray data BMC Genomics. 2005 Oct 31; 6:149. . View in PubMed

Genome-wide SNP arrays as a diagnostic tool: clinical description, genetic mapping, and molecular characterization of Salla disease in an Old Order Mennonite population Am J Med Genet A. 2005 Oct 15; 138A(3):262-7. . View in PubMed

Identification of disease causing loci using an array-based genotyping approach on pooled DNA BMC Genomics. 2005 Sep 30; 6:138. . View in PubMed

Applications of whole-genome high-density SNP genotyping Expert Rev Mol Diagn. 2005 Mar; 5(2):159-70. . View in PubMed

The genetics of tethered cord syndrome Am J Med Genet A. 2005 Feb 01; 132A(4):450-3. . View in PubMed

The Autism Genome Project: goals and strategies Am J Pharmacogenomics. 2005; 5(4):233-46. . View in PubMed

Structural insights into how the MIDAS ion stabilizes integrin binding to an RGD peptide under force Structure. 2004 Nov; 12(11):2049-58. . View in PubMed

Mapping of sudden infant death with dysgenesis of the testes syndrome (SIDDT) by a SNP genome scan and identification of TSPYL loss of function Proc Natl Acad Sci U S A. 2004 Aug 10; 101(32):11689-94. . View in PubMed

Tuning the mechanical stability of fibronectin type III modules through sequence variations Structure. 2004 Jan; 12(1):21-30. . View in PubMed

Structure and functional significance of mechanically unfolded fibronectin type III1 intermediates Proc Natl Acad Sci U S A. 2003 Dec 09; 100(25):14784-9. . View in PubMed

Identifying unfolding intermediates of FN-III(10) by steered molecular dynamics J Mol Biol. 2002 Nov 08; 323(5):939-50. . View in PubMed

A structural model for force regulated integrin binding to fibronectin's RGD-synergy site Matrix Biol. 2002 Mar; 21(2):139-47. . View in PubMed

Structural insights into the mechanical regulation of molecular recognition sites Trends Biotechnol. 2001 Oct; 19(10):416-23. . View in PubMed

Comparison of the early stages of forced unfolding for fibronectin type III modules Proc Natl Acad Sci U S A. 2001 May 08; 98(10):5590-5. . View in PubMed

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