Research Topics
Genomes and GenesSpecies | David W CraigSummaryAffiliation: Translational Genomics Research Institute Country: USA Publications
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Detail Information
Publications
Applications of whole-genome high-density SNP genotypingDavid 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...
Identification of somatic chromosomal abnormalities in hypothalamic hamartoma tissue at the GLI3 locusDavid 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...- Assessing and managing risk when sharing aggregate genetic variant dataDavid 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... 
Identification of disease causing loci using an array-based genotyping approach on pooled DNADavid W Craig
Neurogenomics Division, Translational Genomics Research Institute TGen, Phoenix, Arizona 85004, USA
BMC Genomics 6:138. 2005....- Identification of genetic variants using bar-coded multiplexed sequencingDavid 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... - Evidence for an association between KIBRA and late-onset Alzheimer's diseaseJason 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... - 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... - Whole-genome analysis of sporadic amyotrophic lateral sclerosisTravis 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... - SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arraysJianping 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... - GAB2 alleles modify Alzheimer's risk in APOE epsilon4 carriersEric 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... - Statistical comparison framework and visualization scheme for ranking-based algorithms in high-throughput genome-wide studiesWaibhav 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... - Chromosomal abnormality at 6p25.1-25.3 identifies a susceptibility locus for hypothalamic hamartoma associated with epilepsyJohn 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... - SNiPer: improved SNP genotype calling for Affymetrix 10K GeneChip microarray dataMatthew 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... - Identification of the genetic basis for complex disorders by use of pooling-based genomewide single-nucleotide-polymorphism association studiesJohn V Pearson
Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
Am J Hum Genet 80:126-39. 2007.... - Association of CR1, CLU and PICALM with Alzheimer's disease in a cohort of clinically characterized and neuropathologically verified individualsJason 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.... - SNP-based chromosomal copy number ascertainment following multiple displacement whole-genome amplificationJason 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... - A high-density whole-genome association study reveals that APOE is the major susceptibility gene for sporadic late-onset Alzheimer's diseaseKeith D Coon
Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Ariz 85004, USA
J Clin Psychiatry 68:613-8. 2007.... - Calmodulin-binding transcription activator 1 (CAMTA1) alleles predispose human episodic memory performanceMatthew 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... - Common sequence variants on 20q11.22 confer melanoma susceptibilityKevin 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... - Genetic control of human brain transcript expression in Alzheimer diseaseJennifer 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... 
Microarray-based genome-wide association studies using pooled DNASzabolcs Szelinger
Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
Methods Mol Biol 700:49-60. 2011....- 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 studyRobert 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... - Induction of pluripotent stem cells from autopsy donor-derived somatic cellsBrooke 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... - The Autism Genome Project: goals and strategiesDiane 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... - Bar-coded, multiplexed sequencing of targeted DNA regions using the Illumina Genome AnalyzerSzabolcs Szelinger
Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
Methods Mol Biol 700:89-104. 2011.... - Genome-wide characterization of pancreatic adenocarcinoma patients using next generation sequencingWinnie S Liang
Translational Genomics Research Institute TGen, Phoenix, Arizona, United States of America
PLoS ONE 7:e43192. 2012.... - Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumorsChristiane 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... - Common Kibra alleles are associated with human memory performanceAndreas 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... - Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarraysNils 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... - Polyhydramnios, megalencephaly and symptomatic epilepsy caused by a homozygous 7-kilobase deletion in LYK5Erik G Puffenberger
Clinic for Special Children, 535 Bunker Hill Road, Strasburg, PA 17579, USA
Brain 130:1929-41. 2007.... - A survey of genetic human cortical gene expressionAmanda 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.... - Mapping of sudden infant death with dysgenesis of the testes syndrome (SIDDT) by a SNP genome scan and identification of TSPYL loss of functionErik 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... - The nuts and bolts of gene array technology and its application to drug abuse researchDavid Shurtleff
Drug Alcohol Depend 91:102-6. 2007 - Identification of a novel risk locus for progressive supranuclear palsy by a pooled genomewide scan of 500,288 single-nucleotide polymorphismsStacey 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... - 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-q35Demetra 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..This single family may be promising for narrowing the search for NTD susceptibility genes... - Genome-wide SNP arrays as a diagnostic tool: clinical description, genetic mapping, and molecular characterization of Salla disease in an Old Order Mennonite populationKevin 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...