Chad A. Shaw

PhD
Sr. Director, Data Innovation

Chad A. Shaw is trained as a mathematical statistician and has worked in genomics and bioinformatics for approximately 20 years. He is currently Senior Director of Data Innovation at Baylor Genetics. In addition, Chad is a Professor at Baylor College Medicine in the Department of Molecular and Human Genetics as well as Adjunct Professor in the Department of Statistics at Rice University. 

Chad 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.  He has worked in the area of mechanistic studies of structural variation with a focus on the role of repetitive elements on new structural mutations.   

Chad led the development and analysis of an applied probability model for origin and transmission of new mutations in the context of human genetic disease.  This modeling led to the discovery of parent of origin, parental somatic mosaicism, and paternal age as drivers of recurrence risk for de novo variants within families. This fundamental contribution to human genetics was featured in many reviews and in the New York Times.   

Chad is an author for approximately 200 peer-reviewed publications, and his work has been cited over 20,000 times. 

Position

Professor
Molecular and Human Genetics
Baylor College of Medicine
Houston, TX, United States

Adjunct Professor
Statistics
Rice University
Houston, TX, United States

Sr. Director, Data Innovation
Baylor Genetics
Houston, TX, United States

Education

Ph.D. from Rice University
Houston, TX, United States

BS from Duke University
Durham, NC, United States

Publications
Sequencing individual genomes with recurrent deletions reveals allelic architecture and disease loci for autosomal recessive traits

Sequencing individual genomes with recurrent deletions reveals allelic architecture and disease loci for autosomal recessive traits. Bo Yuan, Katharina Schulze, Nurit Assia Batzir, Jefferson Sinson, Hongzheng Dai, Wenmiao Zhu, Francia Bocanegra, Chin-To Fong, Jimmy Holder, Joanne Nguyen, Christian Schaaf, Yaping Yang, Weimin Bi, Christine Eng, Chad Shaw, James R Lupski, Pengfei Liu. medRxiv. 2021 Jan 1. https://doi.org/10.1101/2021.02.16.21251842.

Consultagene: Pre-and Post-Pandemic Experience with a Web-based Platform and Remote Delivery of Genetic Services

Consultagene: Pre-and Post-Pandemic Experience with a Web-based Platform and Remote Delivery of Genetic Services. Kim C Worley, Daniel Lee Riconda, Amy M Wallis, Chad A Shaw, Chris M Holder, Salma A Nassef, Sandra A Darilek, Seema R Lalani, Pilar L Magoulas, Sarah M Huguenard, Brendan HL Lee. medRxiv. 2021 Jan 1. https://doi.org/10.1101/2021.02.16.21251842.

Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions
Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions. Tomasz Gambin, Qian Liu, Justyna A Karolak, Christopher M Grochowski, Nina G Xie, Lucia R Wu, Yan Helen Yan, Ye Cao, Zeynep H Coban Akdemir, Theresa A Wilson, Shalini N Jhangiani, Ed Chen, Christine M Eng, Donna Muzny, Jennifer E Posey, Yaping Yang, David Y Zhang, Chad Shaw, Pengfei Liu, James R Lupski, Paweł Stankiewicz. Genet Med. 2020 Nov;22(11):1768-1776. PMID: 32655138
CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels
CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels. Bo Yuan, Lei Wang, Pengfei Liu, Chad Shaw, Hongzheng Dai, Lance Cooper, Wenmiao Zhu, Stephanie A Anderson, Linyan Meng, Xia Wang, Yue Wang, Fan Xia, Rui Xiao, Alicia Braxton, Sandra Peacock, Eric Schmitt, Patricia A Ward, Francesco Vetrini, Weimin He, Theodore Chiang, Donna Muzny, Richard A Gibbs, Arthur L Beaudet, Amy M Breman, Janice Smith, Sau Wai Cheung, Carlos A Bacino, Christine M Eng, Yaping Yang, James R Lupski, Weimin Bi. Genet Med
. 2020 Oct;22(10):1633-1641. PMID: 32576985
Integrated sequencing and array comparative genomic hybridization in familial Parkinson disease
Integrated sequencing and array comparative genomic hybridization in familial Parkinson disease. Laurie A Robak, Renqian Du, Bo Yuan, Shen Gu, Isabel Alfradique-Dunham, Vismaya Kondapalli, Evelyn Hinojosa, Amanda Stillwell, Emily Young, Chaofan Zhang, Xiaofei Song, Haowei Du, Tomasz Gambin, Shalini N Jhangiani, Zeynep Coban Akdemir, Donna M Muzny, Anusha Tejomurtula, Owen A Ross, Chad Shaw, Joseph Jankovic, Weimin Bi, Jennifer E Posey, James R Lupski, Joshua M Shulman. Neurol Genet. 2020 Jul 28;6(5):e498. PMID: 32802956
Bayesian modelling of high-throughput sequencing assays with malacoda
Bayesian modelling of high-throughput sequencing assays with malacoda. Andrew R Ghazi, Xianguo Kong, Ed S Chen, Leonard C Edelstein, Chad A Shaw. PLoS Comput Biol. 2020 Jul; 16(7): e1007504. PMID: 32692749
Increased Moraxella and Streptococcus species abundance after severe bronchiolitis is associated with recurrent wheezing
Increased Moraxella and Streptococcus species abundance after severe bronchiolitis is associated with recurrent wheezing. Jonathan M Mansbach, Pamela N Luna, Chad A Shaw, Kohei Hasegawa, Joseph F Petrosino, Pedro A Piedra, Ashley F Sullivan, Janice A Espinola, Christopher J Stewart, Carlos A Camargo Jr.  2020 Feb; 145(2): 518–527.e8. PMID: 31738994
De novo mutation in ancestral generations evolves haplotypes contributing to disease
De novo mutation in ancestral generations evolves haplotypes contributing to disease. Zeynep Coban Akdemir, Xiaofei Song, Davut Pehlivan, Ender Karaca, Yavuz Bayram, Tomasz Lech Gambin, Shalini Jhangiani, Richard Lewis, Pengfei Liu, Eric Boerwinkle, Ada Hamosh, Richard A Gibbs, Reid Sutton, Nara Sobreira, Claudia MB Carvalho, Jennifer Posey, Chad A Shaw, David Valle, James R Lupski. Biorxiv. 2020 Apr; DOI: https://doi.org/10.1101/2020.04.27.064824
Validation studies for single circulating trophoblast genetic testing as a form of noninvasive prenatal diagnosis
Validation studies for single circulating trophoblast genetic testing as a form of noninvasive prenatal diagnosis. Liesbeth Vossaert, Qun Wang, Roseen Salman, Anne K McCombs, Vipulkumar Patel, Chunjing Qu, Michael A Mancini, Dean P Edwards, Anna Malovannaya, Pengfei Liu, Chad A Shaw, Brynn Levy, Ronald J Wapner, Weimin Bi, Amy M Breman, Ignatia B Van den Veyver, Arthur L Beaudet. Am J Hum Genet. 2019 Dec 5;105(6):1262-1273. PMID: 31785788
A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencingx
A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencing. Ye Cao, Mari J Tokita, Edward S Chen, Rajarshi Ghosh, Tiansheng Chen, Yanming Feng, Elizabeth Gorman, Federica Gibellini, Patricia A Ward, Alicia Braxton, Xia Wang, Linyan Meng, Rui Xiao, Weimin Bi, Fan Xia, Christine M Eng, Yaping Yang, Tomasz Gambin, Chad Shaw, Pengfei Liu, Pawel Stankiewicz. Genome Med. 2019 Jul 26;11(1):48. PMID:  31349857
Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases
Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases. Avinash V Dharmadhikari, Rajarshi Ghosh, Bo Yuan, Pengfei Liu, Hongzheng Dai, Sami Al Masri, Jennifer Scull, Jennifer E Posey, Allen H Jiang, Weimin He, Francesco Vetrini, Alicia A Braxton, Patricia Ward, Theodore Chiang, Chunjing Qu, Shen Gu, Chad A Shaw, Janice L Smith, Seema Lalani, Pawel Stankiewicz, Sau-Wai Cheung, Carlos A Bacino, Ankita Patel, Amy M Breman, Xia Wang, Linyan Meng, Rui Xiao, Fan Xia, Donna Muzny, Richard A Gibbs, Arthur L Beaudet, Christine M Eng, James R Lupski, Yaping Yang, Weimin Bi. Genome Med. 2019 May 17;11(1):30. PMID: 31101064
Interchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome
Interchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome. Claudia MB Carvalho, Zeynep Coban-Akdemir, Hadia Hijazi, Bo Yuan, Matthew Pendleton, Eoghan Harrington, John Beaulaurier, Sissel Juul, Daniel J Turner, Rupa S Kanchi, Shalini N Jhangiani, Donna M Muzny, Richard A Gibbs, Pawel Stankiewicz, John W Belmont, Chad A Shaw, Sau Wai Cheung, Neil A Hanchard, V Reid Sutton, Patricia I Bader, James R Lupski. Genome Med. 2019 Apr 23;11(1):25. . PMID: 31014393
Targeting the mevalonate pathway to overcome acquired anti-HER2 treatment resistance in breast cancer
Targeting the mevalonate pathway to overcome acquired anti-HER2 treatment resistance in breast cancer. Vidyalakshmi Sethunath, Huizhong Hu, Carmine De Angelis, Jamunarani Veeraraghavan, Lanfang Qin, Nicholas Wang, Lukas M Simon, Tao Wang, Xiaoyong Fu, Agostina Nardone, Resel Pereira, Sarmistha Nanda, Obi L Griffith, Anna Tsimelzon, Chad Shaw, Gary C Chamness, Jorge S Reis-Filho, Britta Weigelt, Laura M Heiser, Susan G Hilsenbeck, Shixia Huang, Mothaffar F Rimawi, Joe W Gray, C Kent Osborne, Rachel Schiff. Genome Med. 2019 Apr 23;11(1):25. . PMID: 31014393
Phasing of complex genomic rearrangements reveal involvement of both homologous chromosomes in pre-and post-zigotic events
Phasing of complex genomic rearrangements reveal involvement of both homologous chromosomes in pre-and post-zigotic events. CM Carvalho, C Beck, Z Akdemir, F Sedlazeck, Q Meng, J Hu, H Doddapaneni, E Chen, S Jhangiani, A English, D Muzni, R Gibbs, C Shaw, P Hastings, JR Lupski. 2019 Oct; 27(Suppl 2): 1043–1173. PMID: 6876491
Small structural differences between two ferrocenyl diphenols determine large discrepancies of reactivity and biological effects
Small structural differences between two ferrocenyl diphenols determine large discrepancies of reactivity and biological effects.Federica Tonolo, Michèle Salmain, Valeria Scalcon, Siden Top, Pascal Pigeon, Alessandra Folda, Benoit Caron, Michael Mcglinchey, Robert-Alain Toillon, Alberto Bindoli, Gérard Jaouen, Anne Vessières, Maria Pia Rigobello. ChemMedChem, Wiley-VCH Verlag, 2019, 14 (19), pp.1717-1726. PMID: 31483560
Reanalysis of Clinical Exome Sequencing Data

Liu, P., Meng, L., Normand, E.A., Xia, F., Song, X., Ghazi, A., Rosenfeld, J., Magoulas, P.L., Braxton, A., Ward, P., Dai, H., Yuan, B., Bi, W., Xiao, R., Wang, X., Chiang, T., Vetrini, F., He, W., Cheng, H., Dong, J., Gijavanekar, C., Benke, P.J., Bernstein, J.A., Eble, T., Eroglu, Y., Erwin, D., Escobar, L., Gibson, J.B., Gripp, K., Kleppe, S., Koenig, M.K., Lewis, A.M., Natowicz, M., Mancias, P., Minor, L., Scaglia, F., Schaaf, C.P., Streff, H., Vernon, H., Uhles, C.L., Zackai, E.H., Wu, N., Sutton, V.R., Beaudet, A.L., Muzny, D., Gibbs, R.A., Posey, J.E., Lalani, S., Shaw, C., Eng, C.M., Lupski, J.R., and Yang, Y. (2019). Reanalysis of Clinical Exome Sequencing Data. N Engl J Med 380, 2478-2480. PMID: 31216405

Publisher Correction: Non-invasive prenatal sequencing for multiple Mendelian monogenic disorders using circulating cell-free fetal DNA.
Publisher Correction: Non-invasive prenatal sequencing for multiple Mendelian monogenic disorders using circulating cell-free fetal DNA.. Jinglan Zhang, Jianli Li, Jennifer B Saucier, Yanming Feng, Yanjun Jiang, Jefferson Sinson, Anne K McCombs, Eric S Schmitt, Sandra Peacock, Stella Chen, Hongzheng Dai, Xiaoyan Ge, Guoli Wang, Chad A Shaw, Hui Mei, Amy Breman. Nat Med. 2019 Apr;25(4):701-702 PMID: 30787481
Megabase length hypermutation accompanies human structural variation at 17p11. 2
Megabase length hypermutation accompanies human structural variation at 17p11. 2. Jinglan Zhang, Jianli Li, Jennifer B Saucier, Yanming Feng, Yanjun Jiang, Jefferson Sinson, Anne K McCombs, Eric S Schmitt, Sandra Peacock, Stella Chen, Hongzheng Dai, Xiaoyan Ge, Guoli Wang, Chad A Shaw, Hui Mei, Amy Breman. Cell. 2019 Mar 7;176(6):1310-1324.e10. PMID: 30827684
Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies

Yuan, B., Neira, J., Pehlivan, D., Santiago-Sim, T., Song, X., Rosenfeld, J., Posey, J.E., Patel, V., Jin, W., Adam, M.P., Baple, E.L., Dean, J., Fong, C.T., Hickey, S.E., Hudgins, L., Leon, E., Madan-Khetarpal, S., Rawlins, L., Rustad, C.F., Stray-Pedersen, A., Tveten, K., Wenger, O., Diaz, J., Jenkins, L., Martin, L., McGuire, M., Pietryga, M., Ramsdell, L., Slattery, L., Study, D.D.D., Abid, F., Bertuch, A.A., Grange, D., Immken, L., Schaaf, C.P., Van Esch, H., Bi, W., Cheung, S.W., Breman, A.M., Smith, J.L., Shaw, C., Crosby, A.H., Eng, C., Yang, Y., Lupski, J.R., Xiao, R., and Liu, P. (2019). Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies. Genet Med 21, 663-675. PMID: 30158690

900: A pilot validation study for cell-based noninvasive prenatal testing (NIPT) in 42 cases

900: A pilot validation study for cell-based noninvasive prenatal testing (NIPT) in 42 cases. Liesbeth Vossaert, Qun Wang, Roseen Salman, Anne McCombs, David Henke, Chunjing Qu, Weimin Bi, Brynn Levy, Yaping Yang, Chad Shaw, Ronald Wapner, Amy Breman, Ignatia Van den Veyver, Arthur Beaudet.  Amer. Jour. of Obstetrics & Gynecology. V.220 Issue 1 Pgs S582-S583 Jan 2019. DOI: https://doi.org/10.1016/j.ajog.2018.11.924

Non-invasive prenatal sequencing for multiple Mendelian monogenic disorders using circulating cell-free fetal DNA

Zhang J, Li J, Saucier JB, Feng Y, Jiang Y, Sinson J, McCombs AK, Schmitt ES, Peacock S, Chen S, Dai H, Ge X, Wang G, Shaw CA, Mei H, Breman A, Xia F, Yang Y, Purgason A2, Pourpak A, Chen Z, Wang X, Wang Y, Kulkarni S, Choy KW, Wapner RJ, Van den Veyver IB, Beaudet A, Parmar S, Wong LJ, Eng CM (2019). Non-invasive prenatal sequencing for multiple Mendelian monogenic disorders using circulating cell-free fetal DNA. Nat. Med. PMID: 30692697

Chad A. Shaw

PhD
Sr. Director, Data Innovation

Chad A. Shaw is trained as a mathematical statistician and has worked in genomics and bioinformatics for approximately 20 years. He is currently Senior Director of Data Innovation at Baylor Genetics. In addition, Chad is a Professor at Baylor College Medicine in the Department of Molecular and Human Genetics as well as Adjunct Professor in the Department of Statistics at Rice University. 

Chad 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.  He has worked in the area of mechanistic studies of structural variation with a focus on the role of repetitive elements on new structural mutations.   

Chad led the development and analysis of an applied probability model for origin and transmission of new mutations in the context of human genetic disease.  This modeling led to the discovery of parent of origin, parental somatic mosaicism, and paternal age as drivers of recurrence risk for de novo variants within families. This fundamental contribution to human genetics was featured in many reviews and in the New York Times.   

Chad is an author for approximately 200 peer-reviewed publications, and his work has been cited over 20,000 times. 

Position

Professor
Molecular and Human Genetics
Baylor College of Medicine
Houston, TX, United States

Adjunct Professor
Statistics
Rice University
Houston, TX, United States

Sr. Director, Data Innovation
Baylor Genetics
Houston, TX, United States

Education

Ph.D. from Rice University
Houston, TX, United States

BS from Duke University
Durham, NC, United States

Publications
Sequencing individual genomes with recurrent deletions reveals allelic architecture and disease loci for autosomal recessive traits

Sequencing individual genomes with recurrent deletions reveals allelic architecture and disease loci for autosomal recessive traits. Bo Yuan, Katharina Schulze, Nurit Assia Batzir, Jefferson Sinson, Hongzheng Dai, Wenmiao Zhu, Francia Bocanegra, Chin-To Fong, Jimmy Holder, Joanne Nguyen, Christian Schaaf, Yaping Yang, Weimin Bi, Christine Eng, Chad Shaw, James R Lupski, Pengfei Liu. medRxiv. 2021 Jan 1. https://doi.org/10.1101/2021.02.16.21251842.

Consultagene: Pre-and Post-Pandemic Experience with a Web-based Platform and Remote Delivery of Genetic Services

Consultagene: Pre-and Post-Pandemic Experience with a Web-based Platform and Remote Delivery of Genetic Services. Kim C Worley, Daniel Lee Riconda, Amy M Wallis, Chad A Shaw, Chris M Holder, Salma A Nassef, Sandra A Darilek, Seema R Lalani, Pilar L Magoulas, Sarah M Huguenard, Brendan HL Lee. medRxiv. 2021 Jan 1. https://doi.org/10.1101/2021.02.16.21251842.

Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions
Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions. Tomasz Gambin, Qian Liu, Justyna A Karolak, Christopher M Grochowski, Nina G Xie, Lucia R Wu, Yan Helen Yan, Ye Cao, Zeynep H Coban Akdemir, Theresa A Wilson, Shalini N Jhangiani, Ed Chen, Christine M Eng, Donna Muzny, Jennifer E Posey, Yaping Yang, David Y Zhang, Chad Shaw, Pengfei Liu, James R Lupski, Paweł Stankiewicz. Genet Med. 2020 Nov;22(11):1768-1776. PMID: 32655138
CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels
CNVs cause autosomal recessive genetic diseases with or without involvement of SNV/indels. Bo Yuan, Lei Wang, Pengfei Liu, Chad Shaw, Hongzheng Dai, Lance Cooper, Wenmiao Zhu, Stephanie A Anderson, Linyan Meng, Xia Wang, Yue Wang, Fan Xia, Rui Xiao, Alicia Braxton, Sandra Peacock, Eric Schmitt, Patricia A Ward, Francesco Vetrini, Weimin He, Theodore Chiang, Donna Muzny, Richard A Gibbs, Arthur L Beaudet, Amy M Breman, Janice Smith, Sau Wai Cheung, Carlos A Bacino, Christine M Eng, Yaping Yang, James R Lupski, Weimin Bi. Genet Med
. 2020 Oct;22(10):1633-1641. PMID: 32576985
Integrated sequencing and array comparative genomic hybridization in familial Parkinson disease
Integrated sequencing and array comparative genomic hybridization in familial Parkinson disease. Laurie A Robak, Renqian Du, Bo Yuan, Shen Gu, Isabel Alfradique-Dunham, Vismaya Kondapalli, Evelyn Hinojosa, Amanda Stillwell, Emily Young, Chaofan Zhang, Xiaofei Song, Haowei Du, Tomasz Gambin, Shalini N Jhangiani, Zeynep Coban Akdemir, Donna M Muzny, Anusha Tejomurtula, Owen A Ross, Chad Shaw, Joseph Jankovic, Weimin Bi, Jennifer E Posey, James R Lupski, Joshua M Shulman. Neurol Genet. 2020 Jul 28;6(5):e498. PMID: 32802956
Bayesian modelling of high-throughput sequencing assays with malacoda
Bayesian modelling of high-throughput sequencing assays with malacoda. Andrew R Ghazi, Xianguo Kong, Ed S Chen, Leonard C Edelstein, Chad A Shaw. PLoS Comput Biol. 2020 Jul; 16(7): e1007504. PMID: 32692749
Increased Moraxella and Streptococcus species abundance after severe bronchiolitis is associated with recurrent wheezing
Increased Moraxella and Streptococcus species abundance after severe bronchiolitis is associated with recurrent wheezing. Jonathan M Mansbach, Pamela N Luna, Chad A Shaw, Kohei Hasegawa, Joseph F Petrosino, Pedro A Piedra, Ashley F Sullivan, Janice A Espinola, Christopher J Stewart, Carlos A Camargo Jr.  2020 Feb; 145(2): 518–527.e8. PMID: 31738994
De novo mutation in ancestral generations evolves haplotypes contributing to disease
De novo mutation in ancestral generations evolves haplotypes contributing to disease. Zeynep Coban Akdemir, Xiaofei Song, Davut Pehlivan, Ender Karaca, Yavuz Bayram, Tomasz Lech Gambin, Shalini Jhangiani, Richard Lewis, Pengfei Liu, Eric Boerwinkle, Ada Hamosh, Richard A Gibbs, Reid Sutton, Nara Sobreira, Claudia MB Carvalho, Jennifer Posey, Chad A Shaw, David Valle, James R Lupski. Biorxiv. 2020 Apr; DOI: https://doi.org/10.1101/2020.04.27.064824
Validation studies for single circulating trophoblast genetic testing as a form of noninvasive prenatal diagnosis
Validation studies for single circulating trophoblast genetic testing as a form of noninvasive prenatal diagnosis. Liesbeth Vossaert, Qun Wang, Roseen Salman, Anne K McCombs, Vipulkumar Patel, Chunjing Qu, Michael A Mancini, Dean P Edwards, Anna Malovannaya, Pengfei Liu, Chad A Shaw, Brynn Levy, Ronald J Wapner, Weimin Bi, Amy M Breman, Ignatia B Van den Veyver, Arthur L Beaudet. Am J Hum Genet. 2019 Dec 5;105(6):1262-1273. PMID: 31785788
A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencingx
A clinical survey of mosaic single nucleotide variants in disease-causing genes detected by exome sequencing. Ye Cao, Mari J Tokita, Edward S Chen, Rajarshi Ghosh, Tiansheng Chen, Yanming Feng, Elizabeth Gorman, Federica Gibellini, Patricia A Ward, Alicia Braxton, Xia Wang, Linyan Meng, Rui Xiao, Weimin Bi, Fan Xia, Christine M Eng, Yaping Yang, Tomasz Gambin, Chad Shaw, Pengfei Liu, Pawel Stankiewicz. Genome Med. 2019 Jul 26;11(1):48. PMID:  31349857
Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases
Copy number variant and runs of homozygosity detection by microarrays enabled more precise molecular diagnoses in 11,020 clinical exome cases. Avinash V Dharmadhikari, Rajarshi Ghosh, Bo Yuan, Pengfei Liu, Hongzheng Dai, Sami Al Masri, Jennifer Scull, Jennifer E Posey, Allen H Jiang, Weimin He, Francesco Vetrini, Alicia A Braxton, Patricia Ward, Theodore Chiang, Chunjing Qu, Shen Gu, Chad A Shaw, Janice L Smith, Seema Lalani, Pawel Stankiewicz, Sau-Wai Cheung, Carlos A Bacino, Ankita Patel, Amy M Breman, Xia Wang, Linyan Meng, Rui Xiao, Fan Xia, Donna Muzny, Richard A Gibbs, Arthur L Beaudet, Christine M Eng, James R Lupski, Yaping Yang, Weimin Bi. Genome Med. 2019 May 17;11(1):30. PMID: 31101064
Interchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome
Interchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome. Claudia MB Carvalho, Zeynep Coban-Akdemir, Hadia Hijazi, Bo Yuan, Matthew Pendleton, Eoghan Harrington, John Beaulaurier, Sissel Juul, Daniel J Turner, Rupa S Kanchi, Shalini N Jhangiani, Donna M Muzny, Richard A Gibbs, Pawel Stankiewicz, John W Belmont, Chad A Shaw, Sau Wai Cheung, Neil A Hanchard, V Reid Sutton, Patricia I Bader, James R Lupski. Genome Med. 2019 Apr 23;11(1):25. . PMID: 31014393
Targeting the mevalonate pathway to overcome acquired anti-HER2 treatment resistance in breast cancer
Targeting the mevalonate pathway to overcome acquired anti-HER2 treatment resistance in breast cancer. Vidyalakshmi Sethunath, Huizhong Hu, Carmine De Angelis, Jamunarani Veeraraghavan, Lanfang Qin, Nicholas Wang, Lukas M Simon, Tao Wang, Xiaoyong Fu, Agostina Nardone, Resel Pereira, Sarmistha Nanda, Obi L Griffith, Anna Tsimelzon, Chad Shaw, Gary C Chamness, Jorge S Reis-Filho, Britta Weigelt, Laura M Heiser, Susan G Hilsenbeck, Shixia Huang, Mothaffar F Rimawi, Joe W Gray, C Kent Osborne, Rachel Schiff. Genome Med. 2019 Apr 23;11(1):25. . PMID: 31014393
Phasing of complex genomic rearrangements reveal involvement of both homologous chromosomes in pre-and post-zigotic events
Phasing of complex genomic rearrangements reveal involvement of both homologous chromosomes in pre-and post-zigotic events. CM Carvalho, C Beck, Z Akdemir, F Sedlazeck, Q Meng, J Hu, H Doddapaneni, E Chen, S Jhangiani, A English, D Muzni, R Gibbs, C Shaw, P Hastings, JR Lupski. 2019 Oct; 27(Suppl 2): 1043–1173. PMID: 6876491
Small structural differences between two ferrocenyl diphenols determine large discrepancies of reactivity and biological effects
Small structural differences between two ferrocenyl diphenols determine large discrepancies of reactivity and biological effects.Federica Tonolo, Michèle Salmain, Valeria Scalcon, Siden Top, Pascal Pigeon, Alessandra Folda, Benoit Caron, Michael Mcglinchey, Robert-Alain Toillon, Alberto Bindoli, Gérard Jaouen, Anne Vessières, Maria Pia Rigobello. ChemMedChem, Wiley-VCH Verlag, 2019, 14 (19), pp.1717-1726. PMID: 31483560
Reanalysis of Clinical Exome Sequencing Data

Liu, P., Meng, L., Normand, E.A., Xia, F., Song, X., Ghazi, A., Rosenfeld, J., Magoulas, P.L., Braxton, A., Ward, P., Dai, H., Yuan, B., Bi, W., Xiao, R., Wang, X., Chiang, T., Vetrini, F., He, W., Cheng, H., Dong, J., Gijavanekar, C., Benke, P.J., Bernstein, J.A., Eble, T., Eroglu, Y., Erwin, D., Escobar, L., Gibson, J.B., Gripp, K., Kleppe, S., Koenig, M.K., Lewis, A.M., Natowicz, M., Mancias, P., Minor, L., Scaglia, F., Schaaf, C.P., Streff, H., Vernon, H., Uhles, C.L., Zackai, E.H., Wu, N., Sutton, V.R., Beaudet, A.L., Muzny, D., Gibbs, R.A., Posey, J.E., Lalani, S., Shaw, C., Eng, C.M., Lupski, J.R., and Yang, Y. (2019). Reanalysis of Clinical Exome Sequencing Data. N Engl J Med 380, 2478-2480. PMID: 31216405

Publisher Correction: Non-invasive prenatal sequencing for multiple Mendelian monogenic disorders using circulating cell-free fetal DNA.
Publisher Correction: Non-invasive prenatal sequencing for multiple Mendelian monogenic disorders using circulating cell-free fetal DNA.. Jinglan Zhang, Jianli Li, Jennifer B Saucier, Yanming Feng, Yanjun Jiang, Jefferson Sinson, Anne K McCombs, Eric S Schmitt, Sandra Peacock, Stella Chen, Hongzheng Dai, Xiaoyan Ge, Guoli Wang, Chad A Shaw, Hui Mei, Amy Breman. Nat Med. 2019 Apr;25(4):701-702 PMID: 30787481
Megabase length hypermutation accompanies human structural variation at 17p11. 2
Megabase length hypermutation accompanies human structural variation at 17p11. 2. Jinglan Zhang, Jianli Li, Jennifer B Saucier, Yanming Feng, Yanjun Jiang, Jefferson Sinson, Anne K McCombs, Eric S Schmitt, Sandra Peacock, Stella Chen, Hongzheng Dai, Xiaoyan Ge, Guoli Wang, Chad A Shaw, Hui Mei, Amy Breman. Cell. 2019 Mar 7;176(6):1310-1324.e10. PMID: 30827684
Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies

Yuan, B., Neira, J., Pehlivan, D., Santiago-Sim, T., Song, X., Rosenfeld, J., Posey, J.E., Patel, V., Jin, W., Adam, M.P., Baple, E.L., Dean, J., Fong, C.T., Hickey, S.E., Hudgins, L., Leon, E., Madan-Khetarpal, S., Rawlins, L., Rustad, C.F., Stray-Pedersen, A., Tveten, K., Wenger, O., Diaz, J., Jenkins, L., Martin, L., McGuire, M., Pietryga, M., Ramsdell, L., Slattery, L., Study, D.D.D., Abid, F., Bertuch, A.A., Grange, D., Immken, L., Schaaf, C.P., Van Esch, H., Bi, W., Cheung, S.W., Breman, A.M., Smith, J.L., Shaw, C., Crosby, A.H., Eng, C., Yang, Y., Lupski, J.R., Xiao, R., and Liu, P. (2019). Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies. Genet Med 21, 663-675. PMID: 30158690

900: A pilot validation study for cell-based noninvasive prenatal testing (NIPT) in 42 cases

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