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2. Considerations for reporting variants in novel candidate genes identified during clinical genomic testing

Author

Abouhala, Siwaar, Albert, Jessica, Almalvez, Miguel, Alvarez, Raquel, Amin, Mutaz, Anderson, Peter, Aradhya, Swaroop, Ashley, Euan, Assimes, Themistocles, Auriga, Light, Austin-Tse, Christina, Bamshad, Mike, Barseghyan, Hayk, Baxter, Samantha, Behera, Sairam, Beheshti, Shaghayegh, Bejerano, Gill, Berger, Seth, Bernstein, Jon, Best, Sabrina, Blankenmeister, Benjamin, Blue, Elizabeth, Boerwinkle, Eric, Bonkowski, Emily, Bonner, Devon, Boone, Philip, Bornhorst, Miriam, Brand, Harrison, Buckingham, Kati, Calame, Daniel, Carter, Jennefer, Casadei, Silvia, Chadwick, Lisa, Chavez, Clarisa, Chen, Ziwei, Chinn, Ivan, Chong, Jessica, Coban-Akdemir, Zeynep, Cohen, Andrea J., Conner, Sarah, Conomos, Matthew, Coveler, Karen, Cui, Ya Allen, Currin, Sara, Daber, Robert, Dardas, Zain, Davis, Colleen, Dawood, Moez, de Dios, Ivan, de Esch, Celine, Delaney, Meghan, Delot, Emmanuele, DiTroia, Stephanie, Doddapaneni, Harsha, Du, Haowei, Duan, Ruizhi, Dugan-Perez, Shannon, Duong, Nhat, Duyzend, Michael, Eichler, Evan, Emami, Sara, Fraser, Jamie, Fusaro, Vincent, Galey, Miranda, Ganesh, Vijay, Garcia, Brandon, Garimella, Kiran, Gibbs, Richard, Gifford, Casey, Ginsburg, Amy, Goddard, Page, Gogarten, Stephanie, Gogate, Nikhita, Gordon, William, Gorzynski, John E., Greenleaf, William, Grochowski, Christopher, Groopman, Emily, Sousa, Rodrigo Guarischi, Gudmundsson, Sanna, Gulati, Ashima, Hall, Stacey, Harvey, William, Hawley, Megan, Heavner, Ben, Horike-Pyne, Martha, Hu, Jianhong, Huang, Yongqing, Hwang, James, Jarvik, Gail, Jensen, Tanner, Jhangiani, Shalini, Jimenez-Morales, David, Jin, Christopher, Saad, Ahmed K., Kahn-Kirby, Amanda, Kain, Jessica, Kaur, Parneet, Keehan, Laura, Knoblach, Susan, Ko, Arthur, Kundaje, Anshul, Kundu, Soumya, Lancaster, Samuel M., Larsson, Katie, Lee, Arthur, Lemire, Gabrielle, Lewis, Richard, Li, Wei, Li, Yidan, Liu, Pengfei, LoTempio, Jonathan, Lupski, James (Jim), Ma, Jialan, MacArthur, Daniel, Mahmoud, Medhat, Malani, Nirav, Mangilog, Brian, Marafi, Dana, Marmolejos, Sofia, Marten, Daniel, Martinez, Eva, Marvin, Colby, Marwaha, Shruti, Mastrorosa, Francesco Kumara, Matalon, Dena, May, Susanne, McGee, Sean, Meador, Lauren, Mefford, Heather, Mendez, Hector Rodrigo, Miller, Alexander, Miller, Danny E., Mitani, Tadahiro, Montgomery, Stephen, Moyses, Mariana, Munderloh, Chloe, Muzny, Donna, Nelson, Sarah, Nguyen, Thuy-mi P., Nguyen, Jonathan, Nussbaum, Robert, Nykamp, Keith, O'Callaghan, William, O'Heir, Emily, O'Leary, Melanie, Olsen, Jeren, Osei-Owusu, Ikeoluwa, O'Donnell-Luria, Anne, Padhi, Evin, Pais, Lynn, Pan, Miao, Panchal, Piyush, Patterson, Karynne, Payne, Sheryl, Pehlivan, Davut, Petrowski, Paul, Pham, Alicia, Pitsava, Georgia, Podesta, Astaria`Sara, Ponce, Sarah, Porter, Elizabeth, Posey, Jennifer, Prosser, Jaime, Quertermous, Thomas, Rai, Archana, Ramani, Arun, Rehm, Heidi, Reuter, Chloe, Reuter, Jason, Richardson, Matthew, Rivera-Munoz, Andres, Rubio, Oriane, Sabo, Aniko, Salani, Monica, Samocha, Kaitlin, Sanchis-Juan, Alba, Savage, Sarah, Scott, Evette, Scott, Stuart, Sedlazeck, Fritz, Shah, Gulalai, Shojaie, Ali, Singh, Mugdha, Smith, Kevin, Smith, Josh, Snow, Hana, Snyder, Michael, Socarras, Kayla, Starita, Lea, Stark, Brigitte, Stenton, Sarah, Stergachis, Andrew, Stilp, Adrienne, Sutton, V. Reid, Tai, Jui-Cheng, Talkowski, Michael (Mike), Tise, Christina, Tong, Catherine (Cat), Tsao, Philip, Ungar, Rachel, VanNoy, Grace, Vilain, Eric, Voutos, Isabella, Walker, Kim, Wei, Chia-Lin, Weisburd, Ben, Weiss, Jeff, Wellington, Chris, Weng, Ziming, Westheimer, Emily, Wheeler, Marsha, Wheeler, Matthew, Wiel, Laurens, Wilson, Michael, Wojcik, Monica, Wong, Quenna, Xiao, Changrui, Yadav, Rachita, Yi, Qian, Yuan, Bo, Zhao, Jianhua, Zhen, Jimmy, Zhou, Harry, Chong, Jessica X., Berger, Seth I., Smith, Erica, Calame, Daniel G., Hawley, Megan H., Rivera-Munoz, E. Andres, Bamshad, Michael J., and Rehm, Heidi L.

Published
2024
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3. Exome sequencing identifies genetic variants in anophthalmia and microphthalmia

Author

Li, Jingjing, Yang, Wei, Wang, Yuejun Jessie, Ma, Chen, Curry, Cynthia J, McGoldrick, Daniel, Nickerson, Deborah A, Chong, Jessica X, Blue, Elizabeth E, Mullikin, James C, Reefhuis, Jennita, Nembhard, Wendy N, Romitti, Paul A, Werler, Martha M, Browne, Marilyn L, Olshan, Andrew F, Finnell, Richard H, Feldkamp, Marcia L, Pangilinan, Faith, Almli, Lynn M, Bamshad, Mike J, Brody, Lawrence C, Jenkins, Mary M, Shaw, Gary M, Program, NISC Comparative Sequencing, Genomics, University of Washington Center for Mendelian, and Study, Birth Defects Prevention

Subjects
Eye Disease and Disorders of Vision, Genetics, Prevention, Pediatric, Human Genome, Clinical Research, Congenital Structural Anomalies, Aetiology, 2.1 Biological and endogenous factors, Anophthalmos, Exome, Humans, Infant, Microphthalmos, Mutation, Missense, Exome Sequencing, congenital abnormalities, genetic epidemiology, newborn eye abnormalities, NISC Comparative Sequencing Program, University of Washington Center for Mendelian Genomics, National Birth Defects Prevention Study, Clinical Sciences
Abstract

Anophthalmia and microphthalmia (A/M) are rare birth defects affecting up to 2 per 10,000 live births. These conditions are manifested by the absence of an eye or reduced eye volumes within the orbit leading to vision loss. Although clinical case series suggest a strong genetic component in A/M, few systematic investigations have been conducted on potential genetic contributions owing to low population prevalence. To overcome this challenge, we utilized DNA samples and data collected as part of the National Birth Defects Prevention Study (NBDPS). The NBDPS employed multi-center ascertainment of infants affected by A/M. We performed exome sequencing on 67 family trios and identified numerous genes affected by rare deleterious nonsense and missense variants in this cohort, including de novo variants. We identified 9 nonsense changes and 86 missense variants that are absent from the reference human population (Genome Aggregation Database), and we suggest that these are high priority candidate genes for A/M. We also performed literature curation, single cell transcriptome comparisons, and molecular pathway analysis on the candidate genes and performed protein structure modeling to determine the potential pathogenic variant consequences on PAX6 in this disease.

Published
2022

4. Beyond the exome: What’s next in diagnostic testing for Mendelian conditions

Author

Abouhala, Siwaar, Albert, Jessica, Almalvez, Miguel, Alvarez, Raquel, Amin, Mutaz, Anderson, Peter, Aradhya, Swaroop, Ashley, Euan, Assimes, Themistocles, Auriga, Light, Austin-Tse, Christina, Bamshad, Mike, Barseghyan, Hayk, Baxter, Samantha, Behera, Sairam, Beheshti, Shaghayegh, Bejerano, Gill, Berger, Seth, Bernstein, Jon, Best, Sabrina, Blankenmeister, Benjamin, Blue, Elizabeth, Boerwinkle, Eric, Bonkowski, Emily, Bonner, Devon, Boone, Philip, Bornhorst, Miriam, Bozkurt-Yozgatli, Tugce, Brand, Harrison, Buckingham, Kati, Calame, Daniel, Casadei, Silvia, Chadwick, Lisa, Chavez, Clarisa, Chen, Ziwei, Chinn, Ivan, Chong, Jessica, Coban-Akdemir, Zeynep, Cohen, Andrea J., Conner, Sarah, Conomos, Matthew, Coveler, Karen, Cui, Ya Allen, Currin, Sara, Daber, Robert, Dardas, Zain, Davis, Colleen, Dawood, Moez, de Dios, Ivan, de Esch, Celine, Delaney, Meghan, Délot, Emmanuèle, DiTroia, Stephanie, Doddapaneni, Harsha, Du, Haowei, Duan, Ruizhi, Dugan-Perez, Shannon, Duong, Nhat, Duyzend, Michael, Eichler, Evan, Emami, Sara, Fatih, Jawid, Fraser, Jamie, Fusaro, Vincent, Galey, Miranda, Ganesh, Vijay, Garimella, Kiran, Gibbs, Richard, Gifford, Casey, Ginsburg, Amy, Goddard, Pagé, Gogarten, Stephanie, Gogate, Nikhita, Gordon, William, Gorzynski, John E., Greenleaf, William, Grochowski, Christopher, Groopman, Emily, Guarischi Sousa, Rodrigo, Gudmundsson, Sanna, Gulati, Ashima, Guo, Daniel, Hale, Walker, Hall, Stacey, Harvey, William, Hawley, Megan, Heavner, Ben, Herman, Isabella, Horike-Pyne, Martha, Hu, Jianhong, Huang, Yongqing, Hwang, James, Jarvik, Gail, Jensen, Tanner, Jhangiani, Shalini, Jimenez-Morales, David, Jin, Christopher, Saad, Ahmed K., Kahn-Kirby, Amanda, Kain, Jessica, Kaur, Parneet, Keehan, Laura, Knoblach, Susan, Ko, Arthur, Kohler, Jennefer, Kundaje, Anshul, Kundu, Soumya, Lancaster, Samuel M., Larsson, Katie, Lemire, Gabrielle, Lewis, Richard, Li, Wei, Li, Yidan, Liu, Pengfei, LoTempio, Jonathan, Lupski, James, Ma, Jialan, MacArthur, Daniel, Mahmoud, Medhat, Malani, Nirav, Mangilog, Brian, Marafi, Dana, Marmolejos, Sofia, Marten, Daniel, Martinez, Eva, Marvin, Colby, Marwaha, Shruti, Kumara Mastrorosa, Francesco, Matalon, Dena, May, Susanne, McGee, Sean, Meador, Lauren, Mefford, Heather, Rodrigo Mendez, Hector, Miller, Alexander, Miller, Danny E., Mitani, Tadahiro, Montgomery, Stephen, Moussa, Hala Mohamed, Moyses, Mariana, Munderloh, Chloe, Muzny, Donna, Nelson, Sarah, Neu, Matthew B., Nguyen, Jonathan, Nguyen, Thuy-mi P., Nussbaum, Robert, Nykamp, Keith, O'Callaghan, William, O'Heir, Emily, O'Leary, Melanie, Olsen, Jeren, Osei-Owusu, Ikeoluwa, O'Donnell-Luria, Anne, Padhi, Evin, Pais, Lynn, Pan, Miao, Panchal, Piyush, Patterson, Karynne, Payne, Sheryl, Pehlivan, Davut, Petrowski, Paul, Pham, Alicia, Pitsava, Georgia, Podesta, Astaria, Ponce, Sarah, Posey, Jennifer, Prosser, Jaime, Quertermous, Thomas, Rai, Archana, Ramani, Arun, Rehm, Heidi, Reuter, Chloe, Reuter, Jason, Richardson, Matthew, Rivera-Munoz, Andres, Rubio, Oriane, Sabo, Aniko, Salani, Monica, Samocha, Kaitlin, Sanchis-Juan, Alba, Savage, Sarah, Scott, Stuart, Scott, Evette, Sedlazeck, Fritz, Shah, Gulalai, Shojaie, Ali, Singh, Mugdha, Smith, Josh, Smith, Kevin, Snow, Hana, Snyder, Michael, Socarras, Kayla, Starita, Lea, Stark, Brigitte, Stenton, Sarah, Stergachis, Andrew, Stilp, Adrienne, Sundaram, Laksshman, Sutton, V. Reid, Tai, Jui-Cheng, Talkowski, Michael, Tise, Christina, Tong, Catherine, Tsao, Philip, Ungar, Rachel, VanNoy, Grace, Vilain, Eric, Voutos, Isabella, Walker, Kim, Weisburd, Ben, Weiss, Jeff, Wellington, Chris, Weng, Ziming, Westheimer, Emily, Wheeler, Marsha, Wheeler, Matthew, Wiel, Laurens, Wilson, Michael, Wojcik, Monica, Wong, Quenna, Wong, Issac, Xiao, Changrui, Yadav, Rachita, Yi, Qian, Yuan, Bo, Zhao, Jianhua, Zhen, Jimmy, Zhou, Harry, Wojcik, Monica H., Reuter, Chloe M., Duyzend, Michael H., Boone, Philip M., Groopman, Emily E., Délot, Emmanuèle C., Jain, Deepti, Starita, Lea M., Montgomery, Stephen B., Bamshad, Michael J., Chong, Jessica X., Wheeler, Matthew T., Berger, Seth I., and Sedlazeck, Fritz J.

Published
2023
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6. Race-Specific HIV-1 Disease-Modifying Effects Associated with CCR5 Haplotypes

Author

Gonzalez, Enrique, Bamshad, Mike, Sato, Naoko, Mummidi, Srinivas, Dhanda, Rahul, Catano, Gabriel, Cabrera, Sonia, McBride, Megan, Cao, Xuan-Hien, Merrill, Gerald, O'Connell, Peter, Bowden, Donald W., Freedman, Barry I., Anderson, Stephanie A., Walter, Elizabeth A., Evans, James S., Stephan, Kevin T., Clark, Robert A., Tyagi, Sanjay, Ahuja, Seema S., Dolan, Matthew J., and Ahuja, Sunil K.

Published
1999

8. Letters to the Editor [with Response]

Author

SPURDLE, AMANDA, MITCHELL, JOHN, JENKINS, TREFOR, BAMSHAD, MIKE, RAO, B. BHASKARA, NAIDU, J.M., PRASAD, B.V.R., WATKINS, SCOTT, and JORDE, LYNN

Published
1997

9. Functional characterization vs in silicoprediction for TBX5missense and splice variants in Holt-Oram syndrome

Author

Vanlerberghe, Clémence, Jourdain, Anne Sophie, Frenois, Frédéric, Ait-Yahya, Emilie, Bamshad, Mike, Dieux, Anne, Dufour, William, Leduc, Fiona, Manouvrier-Hanu, Sylvie, Patterson, Karynne, Ghoumid, Jamal, Escande, Fabienne, Smol, Thomas, Brunelle, Perrine, and Petit, Florence

Abstract

Predicting effects of genomic variants has become a real challenge in the diagnosis of rare human diseases. Holt-Oram syndrome is an autosomal condition characterized by the association of radial and heart defects, due to variants in TBX5. Most variants are predicted to be truncating and result in haploinsufficiency. The pathogenicity of missense or splice variants is harder to demonstrate.

Published
2024
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10. Considerations for reporting variants in novel candidate genes identified during clinical genomic testing

Author

Chong, Jessica X., Berger, Seth I., Baxter, Samantha, Smith, Erica, Xiao, Changrui, Calame, Daniel G., Hawley, Megan H., Rivera-Munoz, E. Andres, DiTroia, Stephanie, Abouhala, Siwaar, Albert, Jessica, Almalvez, Miguel, Alvarez, Raquel, Amin, Mutaz, Anderson, Peter, Aradhya, Swaroop, Ashley, Euan, Assimes, Themistocles, Auriga, Light, Austin-Tse, Christina, Bamshad, Mike, Barseghyan, Hayk, Baxter, Samantha, Behera, Sairam, Beheshti, Shaghayegh, Bejerano, Gill, Berger, Seth, Bernstein, Jon, Best, Sabrina, Blankenmeister, Benjamin, Blue, Elizabeth, Boerwinkle, Eric, Bonkowski, Emily, Bonner, Devon, Boone, Philip, Bornhorst, Miriam, Brand, Harrison, Buckingham, Kati, Calame, Daniel, Carter, Jennefer, Casadei, Silvia, Chadwick, Lisa, Chavez, Clarisa, Chen, Ziwei, Chinn, Ivan, Chong, Jessica, Coban-Akdemir, Zeynep, Cohen, Andrea J., Conner, Sarah, Conomos, Matthew, Coveler, Karen, Cui, Ya Allen, Currin, Sara, Daber, Robert, Dardas, Zain, Davis, Colleen, Dawood, Moez, de Dios, Ivan, de Esch, Celine, Delaney, Meghan, Delot, Emmanuele, DiTroia, Stephanie, Doddapaneni, Harsha, Du, Haowei, Duan, Ruizhi, Dugan-Perez, Shannon, Duong, Nhat, Duyzend, Michael, Eichler, Evan, Emami, Sara, Fraser, Jamie, Fusaro, Vincent, Galey, Miranda, Ganesh, Vijay, Garcia, Brandon, Garimella, Kiran, Gibbs, Richard, Gifford, Casey, Ginsburg, Amy, Goddard, Page, Gogarten, Stephanie, Gogate, Nikhita, Gordon, William, Gorzynski, John E., Greenleaf, William, Grochowski, Christopher, Groopman, Emily, Sousa, Rodrigo Guarischi, Gudmundsson, Sanna, Gulati, Ashima, Hall, Stacey, Harvey, William, Hawley, Megan, Heavner, Ben, Horike-Pyne, Martha, Hu, Jianhong, Huang, Yongqing, Hwang, James, Jarvik, Gail, Jensen, Tanner, Jhangiani, Shalini, Jimenez-Morales, David, Jin, Christopher, Saad, Ahmed K., Kahn-Kirby, Amanda, Kain, Jessica, Kaur, Parneet, Keehan, Laura, Knoblach, Susan, Ko, Arthur, Kundaje, Anshul, Kundu, Soumya, Lancaster, Samuel M., Larsson, Katie, Lee, Arthur, Lemire, Gabrielle, Lewis, Richard, Li, Wei, Li, Yidan, Liu, Pengfei, LoTempio, Jonathan, Lupski, James (Jim), Ma, Jialan, MacArthur, Daniel, Mahmoud, Medhat, Malani, Nirav, Mangilog, Brian, Marafi, Dana, Marmolejos, Sofia, Marten, Daniel, Martinez, Eva, Marvin, Colby, Marwaha, Shruti, Mastrorosa, Francesco Kumara, Matalon, Dena, May, Susanne, McGee, Sean, Meador, Lauren, Mefford, Heather, Mendez, Hector Rodrigo, Miller, Alexander, Miller, Danny E., Mitani, Tadahiro, Montgomery, Stephen, Moyses, Mariana, Munderloh, Chloe, Muzny, Donna, Nelson, Sarah, Nguyen, Thuy-mi P., Nguyen, Jonathan, Nussbaum, Robert, Nykamp, Keith, O'Callaghan, William, O'Heir, Emily, O'Leary, Melanie, Olsen, Jeren, Osei-Owusu, Ikeoluwa, O'Donnell-Luria, Anne, Padhi, Evin, Pais, Lynn, Pan, Miao, Panchal, Piyush, Patterson, Karynne, Payne, Sheryl, Pehlivan, Davut, Petrowski, Paul, Pham, Alicia, Pitsava, Georgia, Podesta, Astaria`Sara, Ponce, Sarah, Porter, Elizabeth, Posey, Jennifer, Prosser, Jaime, Quertermous, Thomas, Rai, Archana, Ramani, Arun, Rehm, Heidi, Reuter, Chloe, Reuter, Jason, Richardson, Matthew, Rivera-Munoz, Andres, Rubio, Oriane, Sabo, Aniko, Salani, Monica, Samocha, Kaitlin, Sanchis-Juan, Alba, Savage, Sarah, Scott, Evette, Scott, Stuart, Sedlazeck, Fritz, Shah, Gulalai, Shojaie, Ali, Singh, Mugdha, Smith, Kevin, Smith, Josh, Snow, Hana, Snyder, Michael, Socarras, Kayla, Starita, Lea, Stark, Brigitte, Stenton, Sarah, Stergachis, Andrew, Stilp, Adrienne, Sutton, V. Reid, Tai, Jui-Cheng, Talkowski, Michael (Mike), Tise, Christina, Tong, Catherine (Cat), Tsao, Philip, Ungar, Rachel, VanNoy, Grace, Vilain, Eric, Voutos, Isabella, Walker, Kim, Wei, Chia-Lin, Weisburd, Ben, Weiss, Jeff, Wellington, Chris, Weng, Ziming, Westheimer, Emily, Wheeler, Marsha, Wheeler, Matthew, Wiel, Laurens, Wilson, Michael, Wojcik, Monica, Wong, Quenna, Xiao, Changrui, Yadav, Rachita, Yi, Qian, Yuan, Bo, Zhao, Jianhua, Zhen, Jimmy, Zhou, Harry, Bamshad, Michael J., and Rehm, Heidi L.

Abstract

Since the first novel gene discovery for a Mendelian condition was made via exome sequencing, the rapid increase in the number of genes known to underlie Mendelian conditions coupled with the adoption of exome (and more recently, genome) sequencing by diagnostic testing labs has changed the landscape of genomic testing for rare diseases. Specifically, many individuals suspected to have a Mendelian condition are now routinely offered clinical ES. This commonly results in a precise genetic diagnosis but frequently overlooks the identification of novel candidate genes. Such candidates are also less likely to be identified in the absence of large-scale gene discovery research programs. Accordingly, clinical laboratories have both the opportunity, and some might argue a responsibility, to contribute to novel gene discovery, which should, in turn, increase the diagnostic yield for many conditions. However, clinical diagnostic laboratories must necessarily balance priorities for throughput, turnaround time, cost efficiency, clinician preferences, and regulatory constraints and often do not have the infrastructure or resources to effectively participate in either clinical translational or basic genome science research efforts. For these and other reasons, many laboratories have historically refrained from broadly sharing potentially pathogenic variants in novel genes via networks such as Matchmaker Exchange, much less reporting such results to ordering providers. Efforts to report such results are further complicated by a lack of guidelines for clinical reporting and interpretation of variants in novel candidate genes. Nevertheless, there are myriad benefits for many stakeholders, including patients/families, clinicians, and researchers, if clinical laboratories systematically and routinely identify, share, and report novel candidate genes. To facilitate this change in practice, we developed criteria for triaging, sharing, and reporting novel candidate genes that are most likely to be promptly validated as underlying a Mendelian condition and translated to use in clinical settings.

Published
2024
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12. Genetic influences on health: Does race matter?

Author

Bamshad, Mike

Subjects
Genetic variation -- Research, Genetic disorders -- Research, Genetic disorders -- Influence, Physical fitness -- Influence
Abstract

New studies of human genetic variation show that while genetic ancestry is highly correlated with geographic ancestry, its correlation with race is modest. Therefore, geographic ancestry and explicit genetic information are alternatives to race that appear to be more accurate predictors of genetic risk factors that influence health.

Published
2005

15. Exome sequencing of child–parent trios with bladder exstrophy: Findings in 26 children.

Author

Pitsava, Georgia, Feldkamp, Marcia L., Pankratz, Nathan, Lane, John, Kay, Denise M., Conway, Kristin M., Shaw, Gary M., Reefhuis, Jennita, Jenkins, Mary M., Almli, Lynn M., Olshan, Andrew F., Pangilinan, Faith, Brody, Lawrence C., Sicko, Robert J., Hobbs, Charlotte A., Bamshad, Mike, McGoldrick, Daniel, Nickerson, Deborah A., Finnell, Richard H., and Mullikin, James

Abstract

Bladder exstrophy (BE) is a rare, lower ventral midline defect with the bladder and part of the urethra exposed. The etiology of BE is unknown but thought to be influenced by genetic variation with more recent studies suggesting a role for rare variants. As such, we conducted paired‐end exome sequencing in 26 child/mother/father trios. Three children had rare (allele frequency ≤ 0.0001 in several public databases) inherited variants in TSPAN4, one with a loss‐of‐function variant and two with missense variants. Two children had loss‐of‐function variants in TUBE1. Four children had rare missense or nonsense variants (one per child) in WNT3, CRKL, MYH9, or LZTR1, genes previously associated with BE. We detected 17 de novo missense variants in 13 children and three de novo loss‐of‐function variants (AKR1C2, PRRX1, PPM1D) in three children (one per child). We also detected rare compound heterozygous loss‐of‐function variants in PLCH2 and CLEC4M and rare inherited missense or loss‐of‐function variants in additional genes applying autosomal recessive (three genes) and X‐linked recessive inheritance models (13 genes). Variants in two genes identified may implicate disruption in cell migration (TUBE1) and adhesion (TSPAN4) processes, mechanisms proposed for BE, and provide additional evidence for rare variants in the development of this defect. [ABSTRACT FROM AUTHOR]

Published
2021
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17. p63 Gene Mutations in EEC Syndrome, Limb-Mammary Syndrome, and Isolated Split Hand–Split Foot Malformation Suggest a Genotype-Phenotype Correlation

Author

van Bokhoven, Hans, Hamel, Ben C.J., Bamshad, Mike, Sangiorgi, Eugenio, Gurrieri, Fiorella, Duijf, Pascal H.G., Vanmolkot, Kaate R.J., van Beusekom, Ellen, van Beersum, Sylvia E.C., Celli, Jacopo, Merkx, Gerard F.M., Tenconi, Romano, Fryns, Jean Pierre, Verloes, Alain, Newbury-Ecob, Ruth A., Raas-Rotschild, Annick, Majewski, Frank, Beemer, Frits A., Janecke, Andreas, Chitayat, David, Crisponi, Giangiorgio, Kayserili, Hülya, Yates, John R.W., Neri, Giovanni, and Brunner, Han G.

Published
2001
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18. Evolution of Human and Non-human Primate CC Chemokine Receptor 5 Gene and mRNA: POTENTIAL ROLES FOR HAPLOTYPE AND mRNA DIVERSITY, DIFFERENTIAL HAPLOTYPE-SPECIFIC TRANSCRIPTIONAL ACTIVITY, AND ALTERED TRANSCRIPTION FACTOR BINDING TO POLYMORPHIC NUCLEOTIDES IN THE PATHOGENESIS OF HIV-1 AND SIMIAN IMMUNODEFICIENCY VIRUS

Author

Mummidi, Srinivas, Bamshad, Mike, Ahuja, Seema S., Gonzalez, Enrique, Feuillet, Pablo M., Begum, Kazi, Galvis, M.Cristina, Kostecki, Vannessa, Valente, Anthony J., Murthy, Krishna K., Haro, Luis, Dolan, Matthew J., Allan, Jonathan S., and Ahuja, Sunil K.

Published
2000
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19. Novel Mutations in Neurogenic Chronic Intestinal Pseudo-Obstruction Identified by High-Throughput Sequencing

Author

Bonora, Elena, primary, Bianco, Francesca, additional, Agnese, Stanzani, additional, Diquigiovanni, Chiara, additional, Rinaldi, Rita, additional, D'Angelo, Roberto, additional, Cogliandro, Rosanna, additional, Smith, Joshua D., additional, Nickerson, Deborah, additional, Bamshad, Mike, additional, Assadi, Ghazaleh, additional, Clavenzani, Paolo, additional, Lindberg, Greger, additional, D'Amato, Mauro, additional, Graziano, Claudio, additional, Stanghellini, Vincenzo, additional, Seri, Marco, additional, and De Giorgio, Roberto, additional

Published
2017
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20. 591 - Novel Mutations in Neurogenic Chronic Intestinal Pseudo-Obstruction Identified by High-Throughput Sequencing

Author

Bonora, Elena, Bianco, Francesca, Agnese, Stanzani, Diquigiovanni, Chiara, Rinaldi, Rita, D'Angelo, Roberto, Cogliandro, Rosanna, Smith, Joshua D., Nickerson, Deborah, Bamshad, Mike, Assadi, Ghazaleh, Clavenzani, Paolo, Lindberg, Greger, D'Amato, Mauro, Graziano, Claudio, Stanghellini, Vincenzo, Seri, Marco, and De Giorgio, Roberto

Published
2017
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21. Su2019 Functional Characterization of a Novel RAD21 Mutation in Familial Chronic Intestinal Pseudo-Obstruction (CIPO)

Author

Bonora, Elena, primary, Bianco, Francesca, additional, Bamshad, Mike, additional, Dowless, Dustin, additional, Francescatto, Ludmila, additional, Katsanis, Nicholas, additional, Cooper, Gregory, additional, Savic, Daniel, additional, Stanghellini, Vincenzo, additional, Mungan, Zeynel, additional, Cefle, Kivanc, additional, Cogliandro, Rosanna, additional, Boschetti, Elisa, additional, Graziano, Claudio, additional, Seri, Marco, additional, Romeo, Giovanni, additional, and De Giorgio, Roberto, additional

Published
2014
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25. Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes

Author

Wood, Elizabeth T, primary, Stover, Daryn A, additional, Ehret, Christopher, additional, Destro-Bisol, Giovanni, additional, Spedini, Gabriella, additional, McLeod, Howard, additional, Louie, Leslie, additional, Bamshad, Mike, additional, Strassmann, Beverly I, additional, Soodyall, Himla, additional, and Hammer, Michael F, additional

Published
2005
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26. Global survey of genetic variation in CCR5 , RANTES , and MIP-1 α: Impact on the epidemiology of the HIV-1 pandemic

Author

Gonzalez, Enrique, primary, Dhanda, Rahul, additional, Bamshad, Mike, additional, Mummidi, Srinivas, additional, Geevarghese, Reni, additional, Catano, Gabriel, additional, Anderson, Stephanie A., additional, Walter, Elizabeth A., additional, Stephan, Kevin T., additional, Hammer, Michael F., additional, Mangano, Andrea, additional, Sen, Luisa, additional, Clark, Robert A., additional, Ahuja, Seema S., additional, Dolan, Matthew J., additional, and Ahuja, Sunil K., additional

Published
2001
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28. Novel Mutations in Neurogenic Chronic Intestinal Pseudo-Obstruction Identified by High-Throughput Sequencing

Author

Chiara Diquigiovanni, Mauro D'Amato, Marco Seri, Paolo Clavenzani, Elena Bonora, Rita Rinaldi, Joshua D. Smith, Ghazaleh Assadi, Roberto D'Angelo, Roberto De Giorgio, Rosanna Cogliandro, Francesca Bianco, Michael J. Bamshad, Stanzani Agnese, Greger Lindberg, Claudio Graziano, Deborah A. Nickerson, Vincenzo Stanghellini, Bonora, Elena, Bianco, Francesca, Stanzani, Agnese, Diquigiovanni, Chiara, Rinaldi, Rita, D'Angelo, Roberto, Cogliandro, ROSANNA FRANCESCA, Smith, Joshua D., Nickerson, Deborah, Bamshad, Mike, Assadi, Ghazaleh, Clavenzani, Paolo, Lindberg, Greger, D'Amato, Mauro, Graziano, Claudio, Stanghellini, Vincenzo, Seri, Marco, and DE GIORGIO, Roberto

Subjects
Intestinal pseudo-obstruction, Hepatology, Gastroenterology, medicine, Computational biology, Biology, medicine.disease, Chronic Intestinal Pseudo-Obstruction, DNA sequencing
Published
2017

29. Assessing human variation data for signatures of natural selection.

Author

Bamshad M and Stephens JC

Subjects
Genome, Human genetics, Humans, Genetic Techniques, Genetic Variation, Selection, Genetic genetics
Abstract

In this article, we highlight some of the different types of natural selection, their effects on patterns of DNA variation, and some of the statistical tests that are commonly used to detect such effects. We also explain some of the relative strengths and weaknesses of different strategies that can be used to detect signatures of natural selection at individual loci. These strategies are illustrated by their application to empirical data from gene variants that are often associated with differences in disease susceptibility. We briefly outline some of the methods proposed to scan the genome for evidence of selection. Finally, we discuss some of the problems associated with identifying signatures of selection and with making inferences about the nature of the selective process.

Published
2009
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