David W Craig

Summary

Affiliation: Translational Genomics Research Institute
Country: USA

Publications

  1. pmc Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs
    Alexis Christoforides
    Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA
    BMC Genomics 14:302. 2013
  2. ncbi request reprint Applications of whole-genome high-density SNP genotyping
    David W Craig
    The Translational Genomics Research Institute, Neurogenomics Division, 445 North Fifth Street, Phoenix, AZ 85004, USA
    Expert Rev Mol Diagn 5:159-70. 2005
  3. pmc Assessing and managing risk when sharing aggregate genetic variant data
    David W Craig
    Translational Genomics Research Institute TGen, Phoenix, Arizona 85004, USA
    Nat Rev Genet 12:730-6. 2011
  4. pmc Identification of genetic variants using bar-coded multiplexed sequencing
    David W Craig
    The Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
    Nat Methods 5:887-93. 2008
  5. pmc Identification of disease causing loci using an array-based genotyping approach on pooled DNA
    David W Craig
    Neurogenomics Division, Translational Genomics Research Institute TGen, Phoenix, Arizona 85004, USA
    BMC Genomics 6:138. 2005
  6. pmc Identification of somatic chromosomal abnormalities in hypothalamic hamartoma tissue at the GLI3 locus
    David W Craig
    The Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA
    Am J Hum Genet 82:366-74. 2008
  7. pmc Evidence for an association between KIBRA and late-onset Alzheimer's disease
    Jason J Corneveaux
    Translational Genomics Research Institute TGen, Neurogenomics Division, Phoenix, AZ 85004, USA
    Neurobiol Aging 31:901-9. 2010
  8. ncbi request reprint Sorl1 as an Alzheimer's disease predisposition gene?
    Jennifer A Webster
    Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Ariz, USA
    Neurodegener Dis 5:60-4. 2008
  9. ncbi request reprint Whole-genome analysis of sporadic amyotrophic lateral sclerosis
    Travis Dunckley
    Translational Genomics Research Inst, Phoenix, AZ 85004, USA
    N Engl J Med 357:775-88. 2007
  10. ncbi request reprint SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays
    Jianping Hua
    Computational Biology Division Phoenix, 445 N 5th Street, Phoenix, AZ, USA
    Bioinformatics 23:57-63. 2007

Detail Information

Publications39

  1. pmc Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs
    Alexis Christoforides
    Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA
    BMC Genomics 14:302. 2013
    ....
  2. ncbi request reprint Applications of whole-genome high-density SNP genotyping
    David W Craig
    The Translational Genomics Research Institute, Neurogenomics Division, 445 North Fifth Street, Phoenix, AZ 85004, USA
    Expert Rev Mol Diagn 5:159-70. 2005
    ..In this review, the immediate applications and implications of the rapidly changing high-density, whole-genome single nucleotide polymorphism genotyping field on translational research will be described...
  3. pmc Assessing and managing risk when sharing aggregate genetic variant data
    David W Craig
    Translational Genomics Research Institute TGen, Phoenix, Arizona 85004, USA
    Nat Rev Genet 12:730-6. 2011
    ..Here we discuss mechanisms and resources for sharing data from GWASs, particularly focusing on approaches for assessing and quantifying the privacy risks to participants that result from the sharing of summary-level data...
  4. pmc Identification of genetic variants using bar-coded multiplexed sequencing
    David W Craig
    The Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
    Nat Methods 5:887-93. 2008
    ..These results suggest that >90% of genetic variants are discoverable using multiplexed sequencing provided sufficient coverage at the polymorphic base...
  5. pmc Identification of disease causing loci using an array-based genotyping approach on pooled DNA
    David W Craig
    Neurogenomics Division, Translational Genomics Research Institute TGen, Phoenix, Arizona 85004, USA
    BMC Genomics 6:138. 2005
    ....
  6. pmc Identification of somatic chromosomal abnormalities in hypothalamic hamartoma tissue at the GLI3 locus
    David W Craig
    The Translational Genomics Research Institute, Neurogenomics Division, Phoenix, AZ 85004, USA
    Am J Hum Genet 82:366-74. 2008
    ..Chromosomal abnormalities including the GLI3 locus were seen in 8 of 55 (15%) of the resected HH tissue samples. These somatic mutations appear to be highly variable...
  7. pmc Evidence for an association between KIBRA and late-onset Alzheimer's disease
    Jason J Corneveaux
    Translational Genomics Research Institute TGen, Neurogenomics Division, Phoenix, AZ 85004, USA
    Neurobiol Aging 31:901-9. 2010
    ..034; OR=1.29) and in a combined analysis of 1026 additional living and expired subjects (P=0.039; OR=1.26). Our findings suggest that KIBRA is associated with both individual variation in normal episodic memory and predisposition to AD...
  8. ncbi request reprint Sorl1 as an Alzheimer's disease predisposition gene?
    Jennifer A Webster
    Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Ariz, USA
    Neurodegener Dis 5:60-4. 2008
    ..Here we present the results of our large case-control whole-genome scan at over 500,000 polymorphisms which presents weak evidence for association and potentially narrows the association interval...
  9. ncbi request reprint Whole-genome analysis of sporadic amyotrophic lateral sclerosis
    Travis Dunckley
    Translational Genomics Research Inst, Phoenix, AZ 85004, USA
    N Engl J Med 357:775-88. 2007
    ..Approximately 90% of persons with amyotrophic lateral sclerosis (ALS) have the sporadic form, which may be caused by the interaction of multiple environmental factors and previously unknown genes...
  10. ncbi request reprint SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays
    Jianping Hua
    Computational Biology Division Phoenix, 445 N 5th Street, Phoenix, AZ, USA
    Bioinformatics 23:57-63. 2007
    ..However, we find that some errors introduced by commonly employed genotyping algorithms may lead to inflation of false associations between markers and phenotype...
  11. pmc GAB2 alleles modify Alzheimer's risk in APOE epsilon4 carriers
    Eric M Reiman
    Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
    Neuron 54:713-20. 2007
    ..Our findings suggest that GAB2 modifies LOAD risk in APOE epsilon4 carriers and influences Alzheimer's neuropathology...
  12. pmc Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays
    Nils Homer
    Translational Genomics Research Institute, Phoenix, Arizona, United States of America
    PLoS Genet 4:e1000167. 2008
    ..These findings also suggest that composite statistics across cohorts, such as allele frequency or genotype counts, do not mask identity within genome-wide association studies. The implications of these findings are discussed...
  13. pmc Statistical comparison framework and visualization scheme for ranking-based algorithms in high-throughput genome-wide studies
    Waibhav D Tembe
    Translational Genomics Research Institute TGen, Phoenix, Arizona 85004, USA
    J Comput Biol 16:565-77. 2009
    ..The results provide a theoretical basis to compare the accuracy of various methods and to identify redundant methods, thus providing guidance for selecting the most suitable analysis method in genome-wide studies...
  14. ncbi request reprint Chromosomal abnormality at 6p25.1-25.3 identifies a susceptibility locus for hypothalamic hamartoma associated with epilepsy
    John F Kerrigan
    Epilepsy Center and Division of Pediatric Neurology, Barrow Neurological Institute and Children s Health Center, St Joseph s Hospital and Medical Center, Phoenix, AZ 85013, USA
    Epilepsy Res 75:70-3. 2007
    ..8 Mb to 9.7 Mb. There are 38 RefSeq genes within the duplicated regions, and no known coding sequences within the deletion. This unique patient helps identify 6p25.1-25.3 as a possible susceptibility locus for sporadic HH...
  15. pmc SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray data
    Matthew J Huentelman
    Neurogenomics Division, The Translational Genomics Research Institute TGen, Phoenix, Arizona 85004, USA
    BMC Genomics 6:149. 2005
    ..We describe here the implementation of clustering algorithms on large training datasets resulting in improved SNP call rates on the 10K GeneChip...
  16. pmc Identification of the genetic basis for complex disorders by use of pooling-based genomewide single-nucleotide-polymorphism association studies
    John V Pearson
    Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
    Am J Hum Genet 80:126-39. 2007
    ....
  17. ncbi request reprint SNP-based chromosomal copy number ascertainment following multiple displacement whole-genome amplification
    Jason J Corneveaux
    The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
    Biotechniques 42:77-83. 2007
    ..We recommend that small amounts of patient cohort DNA stocks be set aside and not subjected to whole genome amplification in order to facilitate the unbiased determination of chromosomal copy numbers when desired...
  18. pmc Association of CR1, CLU and PICALM with Alzheimer's disease in a cohort of clinically characterized and neuropathologically verified individuals
    Jason J Corneveaux
    Neurogenomics Division, The Translational Genomics Research Institute Gen, 445 N Fifth Street, Phoenix, AZ 85004, USA
    Hum Mol Genet 19:3295-301. 2010
    ....
  19. ncbi request reprint A high-density whole-genome association study reveals that APOE is the major susceptibility gene for sporadic late-onset Alzheimer's disease
    Keith D Coon
    Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Ariz 85004, USA
    J Clin Psychiatry 68:613-8. 2007
    ....
  20. pmc Common sequence variants on 20q11.22 confer melanoma susceptibility
    Kevin M Brown
    Integrated Cancer Genomics Division, The Translational Genomics Research Institute, Phoenix, Arizona 85028, USA
    Nat Genet 40:838-40. 2008
    ..The per allele odds ratio was 1.75 (1.53, 2.01), with evidence for stronger association in early-onset cases...
  21. ncbi request reprint Calmodulin-binding transcription activator 1 (CAMTA1) alleles predispose human episodic memory performance
    Matthew J Huentelman
    Neurogenomics Division, The Translational Genomics Research Institute, 445 N Fifth Street, Phoenix, AZ 85004, USA
    Hum Mol Genet 16:1469-77. 2007
    ..Our validated genomic and functional biological findings described herein suggest a role for CAMTA1 in human episodic memory...
  22. pmc Genome-wide characterization of pancreatic adenocarcinoma patients using next generation sequencing
    Winnie S Liang
    Translational Genomics Research Institute TGen, Phoenix, Arizona, United States of America
    PLoS ONE 7:e43192. 2012
    ....
  23. pmc Genetic control of human brain transcript expression in Alzheimer disease
    Jennifer A Webster
    Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
    Am J Hum Genet 84:445-58. 2009
    ..We suggest that studying the transcriptome as a quantitative endo-phenotype has greater power for discovering risk SNPs influencing expression than the use of discrete diagnostic categories such as presence or absence of disease...
  24. doi request reprint Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities
    David W Craig
    Translational Genomics Research Institute, Phoenix, AZ 85004, USA
    Mol Cancer Ther 12:104-16. 2013
    ..These genomic data have guided patients to investigational treatment trials and provide hypotheses for future trials in this irremediable cancer...
  25. ncbi request reprint 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
    Robert L Hanson
    Translational Genomics Research Institute, 445 North Fifth St, Phoenix, AZ 85004, USA
    Diabetes 56:975-83. 2007
    ..01. The strongest evidence for association was found for rs2648875 (P = 0.0000018; 2.97 [1.90-4.65]), which maps to intron 8 of PVT1. Together, these results suggest that PVT1 may contribute to ESRD susceptibility in diabetes...
  26. doi request reprint Microarray-based genome-wide association studies using pooled DNA
    Szabolcs Szelinger
    Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
    Methods Mol Biol 700:49-60. 2011
    ....
  27. doi request reprint Bar-coded, multiplexed sequencing of targeted DNA regions using the Illumina Genome Analyzer
    Szabolcs Szelinger
    Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
    Methods Mol Biol 700:89-104. 2011
    ....
  28. pmc Induction of pluripotent stem cells from autopsy donor-derived somatic cells
    Brooke E Hjelm
    Neurogenomics Division, The Translational Genomics Research Institute TGen, Phoenix, AZ, USA
    Neurosci Lett 502:219-24. 2011
    ..These results provide evidence that autopsy donor-derived fibroblasts can be successfully reprogrammed into iPSCs, and may provide an advantageous approach for generating iPSC-based neurological disease models...
  29. ncbi request reprint The Autism Genome Project: goals and strategies
    Diane Hu-Lince
    Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
    Am J Pharmacogenomics 5:233-46. 2005
    ..From this knowledge, therapeutic targets for drug treatments, and ultimately, a newborn screening diagnostic that would allow for early intervention, can begin to be developed...
  30. pmc Plasma cytokine profiling in sibling pairs discordant for autism spectrum disorder
    Valerio Napolioni
    Neurogenomics Division, The Translational Genomics Research Institute TGen, 445 N Fifth Street, Phoenix, AZ 85004, USA
    J Neuroinflammation 10:38. 2013
    ..In the current study, we used plasma-cytokine profiling for 25 discordant sibling pairs to evaluate whether these alterations occur within families with ASD...
  31. pmc Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors
    Christiane M Robbins
    Division of Integrated Cancer Genomics, Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
    Genome Res 21:47-55. 2011
    ..Our study represents a deep genomic analysis of advanced metastatic prostate tumors and has revealed candidate somatic alterations, possibly contributing to lethal prostate cancer...
  32. ncbi request reprint Polyhydramnios, megalencephaly and symptomatic epilepsy caused by a homozygous 7-kilobase deletion in LYK5
    Erik G Puffenberger
    Clinic for Special Children, 535 Bunker Hill Road, Strasburg, PA 17579, USA
    Brain 130:1929-41. 2007
    ....
  33. ncbi request reprint A survey of genetic human cortical gene expression
    Amanda J Myers
    Laboratory of Neurogenetics, National Institute on Aging, Porter Neuroscience Building, National Institutes of Health Main Campus, Bethesda, Maryland 20892, USA
    Nat Genet 39:1494-9. 2007
    ....
  34. ncbi request reprint Common Kibra alleles are associated with human memory performance
    Andreas Papassotiropoulos
    Division of Psychiatry Research, University of Zurich, Zurich 8057, Switzerland
    Science 314:475-8. 2006
    ..Functional magnetic resonance imaging detected KIBRA allele-dependent differences in hippocampal activations during memory retrieval. Evidence from these experiments suggests a role for KIBRA in human memory...
  35. pmc Mapping of sudden infant death with dysgenesis of the testes syndrome (SIDDT) by a SNP genome scan and identification of TSPYL loss of function
    Erik G Puffenberger
    Clinic for Special Children, Strasburg, PA 17579, USA
    Proc Natl Acad Sci U S A 101:11689-94. 2004
    ..These results shed light on the pathogenesis of a disorder of sexual differentiation and brainstem-mediated sudden death, as well as give insight into a mechanism of transcriptional regulation...
  36. ncbi request reprint Genome-wide SNP arrays as a diagnostic tool: clinical description, genetic mapping, and molecular characterization of Salla disease in an Old Order Mennonite population
    Kevin A Strauss
    Clinic for Special Children, Strasburg, PA 17579, USA
    Am J Med Genet A 138:262-7. 2005
    ..In families with shared genetic heritage, genome-wide SNP arrays with relatively high marker density allow disease gene mapping studies to be incorporated into routine diagnostic evaluations...
  37. pmc Identification of a novel risk locus for progressive supranuclear palsy by a pooled genomewide scan of 500,288 single-nucleotide polymorphisms
    Stacey Melquist
    Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, FL 32224, USA
    Am J Hum Genet 80:769-78. 2007
    ..Since DNA damage and lysosomal dysfunction have been implicated in aging and neurodegenerative processes, both genes are viable candidates for conferring risk of disease...
  38. ncbi request reprint High-density single nucleotide polymorphism screen in a large multiplex neural tube defect family refines linkage to loci at 7p21.1-pter and 2q33.1-q35
    Demetra S Stamm
    Center for Human Genetics, Duke University Medical Center, Durham, North Carolina 27710, USA
    Birth Defects Res A Clin Mol Teratol 76:499-505. 2006
    ..Further investigation of the genomic screen data identified a single large multiplex family, pedigree 8776, as primarily driving the linkage results on chromosome 7...
  39. ncbi request reprint The nuts and bolts of gene array technology and its application to drug abuse research
    David Shurtleff
    Drug Alcohol Depend 91:102-6. 2007