Chad
Middle Name
A.
Shaw, Ph.D.
Middle Name
A.
Picture
Positions
- Professor
-
Mol. and Human Gen./Shaw
Baylor College of Medicine
Houston, TX US
- Sr. Director, BG Innovation Lab
-
Baylor Genetics
- Faculty Member
-
Stem Cells and Regenerative Medicine (STaR) Center
Baylor College of Medicine
- Adjunct Assistant Professor
-
Department of Statistics
Rice University
Houston, Texas United States
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
My main research interests are systems biology and the analysis of large scale genomic data. My laboratory has done extensive research in the use of genomic annotations to enhance analysis of microarray experiments. We have developed a variety of web-based software including tools for Gene Ontology analysis as well as an interactive system for exploration of protein-protein interaction networks. We have also developed tools for web-based visualization and sharing of gene expression data. We analyze primary microarray data sets from all array platforms including expression arrays, genome content arrays (aCGH), microRNA arrays, and chromatin arrays with an expertise in data pre-processing and normalization. Our methodological work involves statistical considerations for use of annotations in analysis of very large scale genomic data.Websites
Selected Publications
- 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 October 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 October ; 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 April ; 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 December 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 December ; 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 June 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 January ; 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 June 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 September ; 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 August 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 November ; 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 January 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
Log In to edit your profile
