ANNOVAR: functional annotation of genetic variants from high-throughput sequencing dataKai Wang
Center for Applied Genomics, Children s Hospital of Philadelphia, PA 19104, USA
Nucleic Acids Res 38:e164. 2010
..7 million variants, making it practical to handle hundreds of human genomes in a day. ANNOVAR is freely available at http://www.openbioinformatics.org/annovar/...
- Comparative genetic analysis of inflammatory bowel disease and type 1 diabetes implicates multiple loci with opposite effects
Kai Wang
Center for Applied Genomics, The Children s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Hum Mol Genet 19:2059-67. 2010
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A genome-wide association study identifies a locus for nonsyndromic cleft lip with or without cleft palate on 8q24Struan F A Grant
Center for Applied Genomics, Abramson Research Center, The Children s Hospital of Philadelphia, Philadelphia, PA 19104 4318, USA
J Pediatr 155:909-13. 2009
..To identify, in a non-hypothesis manner, novel genetic factors associated with nonsyndromic cleft lip with or without cleft palate (NSCL/P)...
- A genome-wide association study on obesity and obesity-related traits
Kai Wang
Center for Applied Genomics, Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
PLoS ONE 6:e18939. 2011
..67 × 10(-9)), previously associated with body weight and fat distribution. Our study demonstrated how a relatively small sample ascertained through extreme phenotypes can detect genuine associations in a GWAS...
- Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms
Sharon J Diskin
Center for Childhood Cancer Research, Children s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Nucleic Acids Res 36:e126. 2008
..With the wide application of whole-genome SNP genotyping techniques, our wave adjustment method will be important for taking full advantage of genotyped samples for CNV analysis...
- Gene-based interaction analysis by incorporating external linkage disequilibrium information
Jing He
Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
Eur J Hum Genet 19:164-72. 2011
..As our method operates at the gene level, it can be applied to a genome-wide association setting and used as a screening tool to detect gene-gene interactions...
- Integrative genomics identifies LMO1 as a neuroblastoma oncogene
Kai Wang
The Center for Applied Genomics, Children s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
Nature 469:216-20. 2011
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- Modeling genetic inheritance of copy number variations
Kai Wang
Department of Genetics, Division of Human Genetics, Center for Applied Genomics, The Children s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
Nucleic Acids Res 36:e138. 2008
..In conclusion, our method produces accurate CNV calls, gives probabilistic estimates of CNV transmission and builds a solid foundation for the development of linkage and association tests utilizing CNVs...
- Phenotype restricted genome-wide association study using a gene-centric approach identifies three low-risk neuroblastoma susceptibility Loci
Le B Nguyen
Division of Oncology and Center for Childhood Cancer Research, Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
PLoS Genet 7:e1002026. 2011
..2 (P = 4.20 × 10⁻⁷) as being associated with the less aggressive form of the disease. These data demonstrate the importance of robust phenotypic data in GWAS analyses and identify additional susceptibility variants for neuroblastoma...
- Large copy-number variations are enriched in cases with moderate to extreme obesity
Kai Wang
Center for Applied Genomics, Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
Diabetes 59:2690-4. 2010
..We investigated whether large and rare copy-number variations (CNVs) differentiate moderate to extreme obesity from never-overweight control subjects...
- Analysing biological pathways in genome-wide association studies
Kai Wang
Center for Applied Genomics, The Childrens Hospital of Philadelphia, Pennsylvania 19104, USA
Nat Rev Genet 11:843-54. 2010
..Here we review the development of pathway-based approaches for GWA studies, discuss their practical use and caveats, and suggest that pathway-based approaches may also be useful for future GWA studies with sequencing data...
- Variants of DENND1B associated with asthma in children
Patrick M A Sleiman
Center for Applied Genomics, Philadelphia, PA 19104 4318, USA
N Engl J Med 362:36-44. 2010
..Asthma is a complex disease that has genetic and environmental causes. The genetic factors associated with susceptibility to asthma remain largely unknown...
- Common variants at five new loci associated with early-onset inflammatory bowel disease
Marcin Imielinski
Center for Applied Genomics, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
Nat Genet 41:1335-40. 2009
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- ATOM: a powerful gene-based association test by combining optimally weighted markers
Mingyao Li
Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, The Children s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Bioinformatics 25:497-503. 2009
..One particularly challenging yet important question is how to best use all genetic information to test whether a gene or a region is associated with the trait of interest...
- Pathway-based approaches for analysis of genomewide association studies
Kai Wang
Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
Am J Hum Genet 81:1278-83. 2007
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- Diverse genome-wide association studies associate the IL12/IL23 pathway with Crohn Disease
Kai Wang
Center for Applied Genomics, Children s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Am J Hum Genet 84:399-405. 2009
..Our study suggests that examination beyond individual SNP hits, by focusing on genetic networks and pathways, is important to unleashing the true power of GWA studies...
- Pathway-Wide Association Study Implicates Multiple Sterol Transport and Metabolism Genes in HDL Cholesterol Regulation
Kai Wang
Center for Applied Genomics, Children s Hospital of Philadelphia Philadelphia, PA, USA
Front Genet 2:41. 2011
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- Interpretation of association signals and identification of causal variants from genome-wide association studies
Kai Wang
Center for Applied Genomics, Children s Hospital of Philadelphia, Philadelphia, PA 19104, USA
Am J Hum Genet 86:730-42. 2010
..Our results suggest that thinking beyond common variants is essential in interpreting GWAS signals and identifying causal variants...
- Autism genome-wide copy number variation reveals ubiquitin and neuronal genes
Joseph T Glessner
Center for Applied Genomics, Children s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
Nature 459:569-73. 2009
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Convergent mechanisms of somatic mutations in polycythemia veraKai Wang
Center for Applied Genomics, Children s Hospital of Philadelphia, Pennsylvania 19104, USA
Discov Med 12:25-32. 2011
..We argue that PV represents a unique disease model to study the interplay between germline risk variants and convergent mechanisms of somatic mutations...
