Positions
- Professor
-
Molecular & Human Genetics
Baylor College of Medicine
Houston, TX US
- Joint Professor
-
Department of Statistics
Rice University
Houston, Texas United States
- Director
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D2K Laboratory
Rice University
- Investigator
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Jan and Dan Duncan Neurological Research Institute
- Faculty Member
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Stem Cells and Regenerative Medicine (STaR) Center
Baylor College of Medicine
- Faculty Member
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Graduate Program in Quantitative & Computational Biosciences
Baylor College of Medicine
Education
- BS from Duke University
- 01/1995 - Durham, NC United States
- Mathematics
- PhD from Rice University
- 01/2001 - Houston, TX United States
- Statistics
Professional Interests
- Statistics, Genomics, Systems Biology, Bioinformatics
Professional Statement
Chad Shaw is trained as a mathematical statistician, and he has worked in statistical genomics and bioinformatics for approximately 20 years. He is currently a professor of molecular and human genetics at Baylor and a joint professor of statistics at Rice University. He is also the Director of the D2K Laboratory at Rice University.He has experience in next-generation sequencing, variant analysis, multi-omic data integration, gene expression profiling and variant functionalization. He also has expertise in copy-number analysis and has worked in the area of mechanistic studies of structural variation, with a focus on the role of repetitive elements in new mutations.
He led the development and analysis of an applied probabilistic model for the transmission of new mutations in the context of human genetic disease, which led to the elucidation of the dependency of recurrence risk on parent of origin, parental somatic mosaicism and paternal age. This fundamental contribution to human genetics was featured in many reviews and in the New York Times as a lay press article.
He has been an author on approximately 200 peer-reviewed publications, and his work has been cited approximately 17,000 times. He has trained 5 Ph.D. students in his own laboratory and over 10 students as a thesis committee member. He serves as chairman of the qualifying exam committee for the Quantitative and Computational Biosciences program. His students have performed methodologic research in high dimensional sparse regression, statistical methods for high throughput NGS screens approaches to modifiers of Mendelian disease, eQTL analyses and software tools for variant prioritization in rare disease diagnostics.
Websites
Selected Publications
- Ghazi AR, Kong X, Chen ES, Edelstein LC, Shaw CA "Bayesian modelling of high-throughput sequencing assays with malacoda.." PLoS Comput Biol.. 2020;16:e1007504. Pubmed PMID: 32692749
- Yuan, B., Wang, L., Liu, P. et al "CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels.." Genet Med.. 2020;22:1633–1641.
- Beck CR, Carvalho CMB, Akdemir ZC, Sedlazeck FJ, Song X, (...), Shaw CA, Gibbs RA, Hastings PJ, Lupski JR "Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2.." Cell. 2019;176:1310-1324.e10..
- Cao Y, Tokita MJ, Chen ES, et al. "A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencing." Genome Med. 2019;11:12. Pubmed PMID: 31349857
- Liu P, Meng L, Normand EA, Xia F, Song X, et al. "Reanalysis of Clinical Exome Sequencing Data.." N Engl J Med. 2019;380:2478-2480. Pubmed PMID: 31216405
- Yuan B, Neira J, Pehlivan D, Santiago-Sim T, Song X, et al. "Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies.." Genet Med. 2019;21:663-675. Pubmed PMID: 30158690
- Posey JE, Harel T, Liu P, Rosenfeld JA, James RA, et al. "Dissection of Disease Phenotypes of Multiple Genetic Causes.." N Engl J Med.. 2017;376:21-31. Pubmed PMID: 27959697
- Liu P, Yuan B, Carvalho CM, Wuster A, Walter K, et al. "An Organismal CNV Mutator Phenotype Restricted to Early Human Development.." Cell. 2017;168:830. Pubmed PMID: 28235197
- Breman AM, Chow JC, U'Ren L, et al. "Evidence for feasibility of fetal trophoblastic cell-based noninvasive prenatal testing.." Prenat Diagn.. 2016;36:1009‐1019. Pubmed PMID: 27616633
- Kølvraa S, Singh R, Normand EA, Qdaisat S, Van denVeyver IB, Jackson L, Hatt L, Schelde P, Uldbjerg N, Vestergaard EM, Zhao L, Chen R, Shaw CA, Breman AM, Beaudet AL. "Genome-wide copy number analysis on DNA from fetal cells isolated from the blood of pregnant women.." Prenat Diagn.. 2016; Pubmed PMID: 27761919
- Normand, E., Qdaisat, S., Bi, W., Shaw, C., Van den Veyver, I., Beaudet, A., Breman, A. "Comparison of three whole genome amplification methods for detection of genomic aberrations in single cells.." Prenat Diagn.. 2016;36:823-30. Pubmed PMID: 27368744
- Simon LM, Chen ES, Edelstein LC, Kong X, Bhatlekar S, Rigoutsos I, Bray PF, Shaw CA "Integrative Multi-omic Analysis of Human Platelet eQTLs Reveals Alternative Start Site in Mitofusin 2.." Am J Hum Genet. 2016;98:883-97. Pubmed PMID: 27132591
- Hsu TY, Simon LM, Neill NJ; Marcotte R, Sayad A, et al. "The spliceosome is a therapeutic vulnerability in MYC-driven cancer.." Nature. 2015;525:384-8. Pubmed PMID: 26331541
- Startek M, Szafranski P, Gambin T, Campbell IM, Hixson P, Shaw CA, Stankiewicz P, Gambin A. "Genome-wide analyses of LINE-LINE-mediated nonallelic homologous recombination.." Nucleic Acids Res.. 2015;43:2188-98. Pubmed PMID: 25613453
- James RA, Campbell IM, Chen ES, Boone PM, Rao MA, Bainbridge MN, Lupski JR, Yang Y, Eng CM, Posey JE, Shaw CA. "A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics.." Nucleic Acids Res.. 2015;43:2188-98. Pubmed PMID: 25613453
- Campbell, Stewart JR, James RA, Lupski JR, Stankiewicz P, Olofsson LP, Shaw CA "Parent of origin, mosaicism, and recurrence risk: probabilistic modeling explains the broken symmetry of transmission genetics.." 2014 Oct 2;95(4):345-359. Pubmed PMID: 25242496
- Boone PM, Yuan B, Campbell IM, Scull JC, Withers MA, et al. "The Alu-rich genomic architecture of SPAST predisposes to diverse and functionally distinct disease-associated CNV alleles.." Am J Hum Genet. 2014;95:143-61. Pubmed PMID: 25065914
- Campbell IM, Yuan B, Robberecht C, Pfundt R, Szafranski P, …, Cheung SW, Shaw CA, Vissers LE, Vermeesch JR, Lupski JR, Stankiewicz P. "Parental Somatic Mosaicism Is Underrecognized and Influences Recurrence Risk of Genomic Disorders.." Am J Hum Genet. 2014;95:173-82. Pubmed PMID: 25087610
- Venezia TA, Merchant AA, Ramos CA, Whitehouse NL, Young AS, Shaw CA, Goodell MA "Molecular signatures of proliferation and quiescence in hematopoietic stem cells.." PLoS Biol.. 2004 Oct;2(10):e301. Pubmed PMID: 15459755
- Dittwald P, Gambin T, Szafranski P, Li J, Amato S, Divon MY, Kang SH, Breman A, Lalani SR, Bacino CA, Bi W, Milosavljevic A, Beaudet AL, Patel A, Shaw CA, Lupski JR, Gambin A, Cheung SW, Stankiewicz P. "NAHR-mediated copy-number variants in a clinical population: Mechanistic insights into both genomic disorders and Mendelizing traits.." Genome Res.. 2013;23:1395-409. Pubmed PMID: 23657883
- Breman A, Pursley AN, Hixson P, Bi W, Ward P, Bacino CA, Shaw C, Lupski JR, Beaudet A, Patel A, Cheung SW, Van den Veyver I "Prenatal chromosomal microarray analysis in a diagnostic laboratory; experience with >1000 cases and review of the literature.." Prenat. Diagn.. 2012 Apr;32(4):351-61. Pubmed PMID: 22467166
- Ramocki MB, Bartnik M, Szafranski P, Kolodziejska KE, Xia Z, Bravo J, Miller GS, Rodriguez DL, Williams CA, Bader PI, Szczepanik E, Mazurczak T, Antczak-Marach D, Coldwell JG, Akman CI, McAlmon K, Cohen MP, McGrath J, Roeder E, Mueller J, Kang SH, Bacino "Recurrent Distal 7q11.23 Deletion Including HIP1 and YWHAG Identified in Patients with Intellectual Disabilities, Epilepsy, and Neurobehavioral Problems.." Am. J. Hum. Genet.. 2010 Dec 10;87(6):857-65. Pubmed PMID: 21109226
- Boone PM, Bacino CA, Shaw CA, Eng PA, Hixson PM, Pursley AN, Kang SH, Yang Y, Wiszniewska J, Nowakowska BA, del Gaudio D, Xia Z, Simpson-Patel G, Immken LL, Gibson JB, Tsai AC, Bowers JA, Reimschisel TE, Schaaf CP, Potocki L, Scaglia F, Gambin T, Sykulski "Detection of clinically relevant exonic copy-number changes by array CGH.." Hum. Mutat.. 2010 Dec;31(12):1326-42. Pubmed PMID: 20848651
- Carvalho CM, Zhang F, Liu P, Patel A, Sahoo T, Bacino CA, Shaw C, Peacock S, Pursley A, Tavyev YJ, Ramocki MB, Nawara M, Obersztyn E, Vianna-Morgante AM, Stankiewicz P, Zoghbi HY, Cheung SW, Lupski JR "Complex rearrangements in patients with duplications of MECP2 can occur by fork stalling and template switching.." Hum. Mol. Genet.. 2009 Jun 15;18(12):2188-203. Pubmed PMID: 19324899
- Van den Veyver IB, Patel A, Shaw CA, Pursley AN, Kang SH, Simovich MJ, Ward PA, Darilek S, Johnson A, Neill SE, Bi W, White LD, Eng CM, Lupski JR, Cheung SW, Beaudet AL "Clinical use of array comparative genomic hybridization (aCGH) for prenatal diagnosis in 300 cases.." Prenat. Diagn.. 2009 Jan;29(1):29-39. Pubmed PMID: 19012303
- Probst FJ, Roeder ER, Enciso VB, Ou Z, Cooper ML, Eng P, Li J, Gu Y, Stratton RF, Chinault AC, Shaw CA, Sutton VR, Cheung SW, Nelson DL "Chromosomal microarray analysis (CMA) detects a large X chromosome deletion including FMR1, FMR2, and IDS in a female patient with mental retardation.." Am. J. Med. Genet. A. 2007 Jun 15;143(12):1358-65. Pubmed PMID: 17506108
- Sahoo T, Bacino CA, German JR, Shaw CA, Bird LM, Kimonis V, Anselm I, Waisbren S, Beaudet AL, Peters SU "Identification of novel deletions of 15q11q13 in Angelman syndrome by array-CGH: molecular characterization and genotype-phenotype correlations.." Eur. J. Hum. Genet.. 2007 Sep;15(9):943-9. Pubmed PMID: 17522620
- Lu X, Shaw CA, Patel A, Li J, Cooper ML, Wells WR, Sullivan CM, Sahoo T, Yatsenko SA, Bacino CA, Stankiewicz P, Ou Z, Chinault AC, Beaudet AL, Lupski JR, Cheung SW, Ward PA "Clinical implementation of chromosomal microarray analysis: summary of 2513 postnatal cases.." PLoS ONE. 2007;2(3):e327. Pubmed PMID: 17389918
- Cheung SW, Shaw CA, Scott DA, Patel A, Sahoo T, Bacino CA, Pursley A, Li J, Erickson R, Gropman AL, Miller DT, Seashore MR, Summers AM, Stankiewicz P, Chinault AC, Lupski JR, Beaudet AL, Sutton VR "Microarray-based CGH detects chromosomal mosaicism not revealed by conventional cytogenetics.." Am. J. Med. Genet. A. 2007 Aug 1;143(15):1679-86. Pubmed PMID: 17607705
- Sahoo T, Cheung SW, Ward P, Darilek S, Patel A, del Gaudio D, Kang SH, Lalani SR, Li J, McAdoo S, Burke A, Shaw CA, Stankiewicz P, Chinault AC, Van den Veyver IB, Roa BB, Beaudet AL, Eng CM "Prenatal diagnosis of chromosomal abnormalities using array-based comparative genomic hybridization.." Genet. Med.. 2006 Nov;8(11):719-27. Pubmed PMID: 17108764
- Lim J, Hao T, Shaw C, Patel AJ, Szabó G, Rual JF, Fisk CJ, Li N, Smolyar A, Hill DE, Barabási AL, Vidal M, Zoghbi HY "A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration.." Cell. 2006 May 19;125(4):801-14. Pubmed PMID: 16713569
- Young A, Whitehouse N, Cho J, Shaw C "OntologyTraverser: an R package for GO analysis.." Bioinformatics. 2005 Jan 15;21(2):275-6. Pubmed PMID: 15333457
- Shaw CJ, Shaw CA, Yu W, Stankiewicz P, White LD, Beaudet AL, Lupski JR "Comparative genomic hybridisation using a proximal 17p BAC/PAC array detects rearrangements responsible for four genomic disorders.." J Med Genet.. 2004;41(2):113-9. Pubmed PMID: 14757858
- Cheung SW, Shaw CA, Yu W, Li J, Ou Z, Patel A, Yatsenko SA, Cooper ML, Furman P, Stankiewicz P, Stankiewicz P, Lupski JR, Chinault AC, Beaudet AL "Development and validation of a CGH microarray for clinical cytogenetic diagnosis.." Genet. Med..;7(6):422-32. Pubmed PMID: 16024975
Memberships
- American Society of Human Genetics
- member
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