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5. Integrated gene analyses of de novo variants from 46,612 trios with autism and developmental disorders

Author

Wang, Tianyun, Kim, Chang N, Bakken, Trygve E, Gillentine, Madelyn A, Henning, Barbara, Mao, Yafei, Gilissen, Christian, Consortium, The SPARK, Nowakowski, Tomasz J, Eichler, Evan E, Acampado, John, Ace, Andrea J, Amatya, Alpha, Astrovskaya, Irina, Bashar, Asif, Brooks, Elizabeth, Butler, Martin E, Cartner, Lindsey A, Chin, Wubin, Chung, Wendy K, Daniels, Amy M, Feliciano, Pamela, Fleisch, Chris, Ganesan, Jensen, William, Lash, Alex E, Marini, Richard, Myers, Vincent J, O'Connor, Eirene, Rigby, Chris, Robertson, Beverly E, Shah, Neelay, Shah, Swapnil, Singer, Emily, Snyder, LeeAnne G, Stephens, Alexandra N, Tjernagel, Jennifer, Vernoia, Brianna M, Volfovsky, Natalia, White, Loran Casey, Hsieh, Alexander, Shen, Yufeng, Zhou, Xueya, Turner, Tychele N, Bahl, Ethan, Thomas, Taylor R, Brueggeman, Leo, Koomar, Tanner, Michaelson, Jacob J, O'Roak, Brian J, Barnard, Rebecca A, Gibbs, Richard A, Muzny, Donna, Sabo, Aniko, Ahmed, Kelli L Baalman, Siegel, Matthew, Abbeduto, Leonard, Amaral, David G, Hilscher, Brittani A, Li, Deana, Smith, Kaitlin, Thompson, Samantha, Albright, Charles, Butter, Eric M, Eldred, Sara, Hanna, Nathan, Jones, Mark, Coury, Daniel Lee, Scherr, Jessica, Pifher, Taylor, Roby, Erin, Dennis, Brandy, Higgins, Lorrin, Brown, Melissa, Alessandri, Michael, Gutierrez, Anibal, Hale, Melissa N, Herbert, Lynette M, Schneider, Hoa Lam, David, Giancarla, Annett, Robert D, Sarver, Dustin E, Arriaga, Ivette, Camba, Alexies, Gulsrud, Amanda C, Haley, Monica, McCracken, James T, Sandhu, Sophia, Tafolla, Maira, Yang, Wha S, Carpenter, Laura A, Bradley, Catherine C, Gwynette, Frampton, Manning, Patricia, Shaffer, Rebecca, Thomas, Carrie, Bernier, Raphael A, Fox, Emily A, and Gerdts, Jennifer A

Subjects
Biological Sciences, Genetics, Mental Health, Intellectual and Developmental Disabilities (IDD), Biotechnology, Pediatric, Autism, Brain Disorders, Mental health, Child, Male, Female, Humans, Autistic Disorder, Autism Spectrum Disorder, Developmental Disabilities, Genetic Predisposition to Disease, Exome, Histone Deacetylases, Repressor Proteins, Carrier Proteins, de novo variants, neurodevelopmental disorder, protein-protein interaction, single-nuclei transcriptome, SPARK Consortium, protein–protein interaction
Abstract

Most genetic studies consider autism spectrum disorder (ASD) and developmental disorder (DD) separately despite overwhelming comorbidity and shared genetic etiology. Here, we analyzed de novo variants (DNVs) from 15,560 ASD (6,557 from SPARK) and 31,052 DD trios independently and also combined as broader neurodevelopmental disorders (NDDs) using three models. We identify 615 NDD candidate genes (false discovery rate [FDR] < 0.05) supported by ≥1 models, including 138 reaching Bonferroni exome-wide significance (P < 3.64e-7) in all models. The genes group into five functional networks associating with different brain developmental lineages based on single-cell nuclei transcriptomic data. We find no evidence for ASD-specific genes in contrast to 18 genes significantly enriched for DD. There are 53 genes that show mutational bias, including enrichments for missense (n = 41) or truncating (n = 12) DNVs. We also find 10 genes with evidence of male- or female-bias enrichment, including 4 X chromosome genes with significant female burden (DDX3X, MECP2, WDR45, and HDAC8). This large-scale integrative analysis identifies candidates and functional subsets of NDD genes.

Published
2022

6. Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes

Author

Zhou, Xueya, Feliciano, Pamela, Shu, Chang, Wang, Tianyun, Astrovskaya, Irina, Hall, Jacob B, Obiajulu, Joseph U, Wright, Jessica R, Murali, Shwetha C, Xu, Simon Xuming, Brueggeman, Leo, Thomas, Taylor R, Marchenko, Olena, Fleisch, Christopher, Barns, Sarah D, Snyder, LeeAnne Green, Han, Bing, Chang, Timothy S, Turner, Tychele N, Harvey, William T, Nishida, Andrew, O’Roak, Brian J, Geschwind, Daniel H, Michaelson, Jacob J, Volfovsky, Natalia, Eichler, Evan E, Shen, Yufeng, and Chung, Wendy K

Subjects
Pediatric Research Initiative, Genetics, Intellectual and Developmental Disabilities (IDD), Autism, Clinical Research, Genetic Testing, Pediatric, Mental Health, Brain Disorders, 2.1 Biological and endogenous factors, Aetiology, Autism Spectrum Disorder, Autistic Disorder, Exome, Forkhead Transcription Factors, Genetic Predisposition to Disease, Humans, Mutation, Repressor Proteins, Exome Sequencing, SPARK Consortium, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

To capture the full spectrum of genetic risk for autism, we performed a two-stage analysis of rare de novo and inherited coding variants in 42,607 autism cases, including 35,130 new cases recruited online by SPARK. We identified 60 genes with exome-wide significance (P

Published
2022

7. Return of genetic research results in 21,532 individuals with autism

Author

Aarrestad, Alexandria, Abbeduto, Leonard, Aberbach, Gabriella, Aberle, Shelley, Adegbite, Adediwura, Adeniji, Debbie, Aguilar, Maria, Ahlers, Kaitlyn, Albright, Charles, Alessandri, Michael, Algaze, Zach, Alkazi, Jasem, Amador, Raquel, Amaral, David, Amon, Logan, Amundsen, Leonor, Andrus, Alicia, Anglo, Claudine, Annett, Robert, Arar, Adam, Arnold, Jonathan, Arriaga, Ivette, Arzate, Eduardo, Ashley, Raven, Aslamy, Leilemah, Baalman, Kelli, Baer, Melissa, Bahi, Ethan, Bailey, Joshua, Baldlock, Zachary, Banks, Grabrielle, Baraghoshi, Gabriele, Bardett, Nicole, Barrett, Mallory, Bartholomew, Yan, Bates, Heidi, Beard, Katie, Becerra, Juana, Beckwith, Malia, Beechan, Paige, Beeson, Landon, Beeson, Josh, Bell, Brandi, Belli, Monica, Bentley, Dawn, Berger, Natalie, Berman, Anna, Bernier, Raphael, Berry-Kravis, Elizabeth, Berwanger, Mary, Birdwell, Shelby, Blank, Elizabeth, Bond, Rebecca, Booker, Stephanie, Bordofsky, Aniela, Bower, Erin, Bowers, Lukas, Bradley, Catherine, Brayer, Heather, Brewster, Stephanie, Brown, Hallie, Brown, Alison, Brown, Melissa, Buck, Catherine, Buescher, Cate, Bullon, Kayleigh, Buraima, Joy, Butter, Eric, Caamano, Amalia, Cacciato, Nicole, CaI, Wenteng, Calderon, Norma, Callahan, Kristen, Camba, Alexies, Campo-Soria, Claudia, Caprara, Giuliana, Carbone, Paul, Carpenter, Laura, Carpenter, Sarah, Casseus, Myriam, Casten, Lucas, Catherine, Sullivan, Chappo, Ashley, Chavez, Kimberly, Cheathem-Johnson, Randi, Chen, Tia, Chintalapalli, Sharmista, Cho, Daniel, Choi, Y.B., Clark, Nia, Clark, Renee, Coffman, Marika, Coleman, Laura, Coleman, Kendra, Collins, Alister, Columbi, Costanza, Comitre, Joaquin, Constant, Stephanie, Contra, Arin, Conyers, Sarah, Cooper, Lindsey, Cooper, Cameron, Coppola, Leigh, Corlett, Allison, Corrales, Lady, Correa, Dahriana, Cottrell, Hannah, Coughlin, Michelle, Courchesne, Eric, Coury, Dan, Crocetti, Deana, Croson, Carrie, Crowell, Judith, Cubells, Joseph, Cunningham, Sean, Currin, Mary, Cutri, Michele, D'Ambrosi, Sophia, David, Giancarla, Davis, Ayana, Davis, Sabrina, Decius, Nickelle, Delaporte, Jennifer, DeMarco, Lindsey, Dennis, Brandy, Deronda, Alyssa, Dhawan, Esha, Dichter, Gabriel, Doan, Ryan, Dominick, Kelli, Ortega, Leonardo Dominquez, Doyle, Erin, Drayton, Andrea, DuBois, Megan, Dudley, Johnny, Duhon, Gabrielle, Duncan, Grabrielle, Duncan, Amie, Dunlevy, Megan, Dyer, Meaghan, Earl, Rachel, Edmonson, Catherine, Eldred, Sara, Elliott, Nelita, Emery, Brooke, Enright, Barbara, Erb, Sarah, Erickson, Craig, Esler, Amy, Estevez, Liza, Fanta, Anne, Fassler, Carrie, Fatemi, Ali, Fazal, Faris, Featherston, Marilyn, Ferguson, Jonathan, Fish, Angela, Fitzgerald, Kate, Flores, Kathleen, Fombonne, Eric, Foster, Margaret, Fowler, Tiffany, Fox, Emma, Fox, Emily, Francis, Sunday, Frayne, Margot, Froman, Sierra, Fuller, Laura, Galbraith, Virginia, Gallimore, Dakota, Gambrell, Ariana, Gazestani, Vahid, Geisheker, Madeleine R., Gerdts, Jennifer, Geschwind, Daniel, Ghaziuddin, Mohammad, Ghina, Haidar, Given, Erin, Goetz, Mykayla, Gong, Jared, Gonring, Kelsey, Gonzalez, Natalia, Gonzalez, Antonio, Goodwill, Ellie, Gordon, Rachel, Graham, Carter, Gray, Catherine, Grimes, Ellen, Griswold, Anthony, Gu, Pan, Guilfoyle, Janna, Gulsrud, Amanda, Gunderson, Jaclyn, Gunter, Chris, Gupta, Sanya, Gupta, Abha, Gutierrez, Anibal, Gwynette, Frampton, Haidar, Ghina, Hale, Melissa, Haley, Monica, Hall, Lauren K., Hamer, Kira, Hamilton, Piper, Hanna, Nathan, Hardan, Antonio, Harkins, Christina, Harrell, Eldric, Harris, Jill, Harris, Nina, Hayes, Caitlin, Hayse, Braden, Heckers, Teryn, Heerwagen, Kathryn, Hennelly, Daniela, Herbert, Lynette, Hermle, Luke, Hernandez, Briana, Herrera, Clara, Hess, Amy, Heyman, Michelle, Higgins, Lorrin, Phillips, Brittani Hilscher, Hirst, Kathy, Ho, Theodore, Hoffman, Emily, Hojlo, Margaret, Honaker, Makayla, Hong, Michael, Hooks, Gregory, Horner, Susannah, Horton, Danielle, Hounchell, Melanie, Howes, Dain, Huang-Storm, Lark, Hunter, Samantha, Hutter, Hanna, Hyde, Emily, Ibanez, Teresa, Ingram, Kelly, Istephanous, Dalia, Jacob, Suma, Jarratt, Andrea, Jelinek, Anna, Johnson, Mary, Jones, Mya, Jones, Garland, Jones, Mark, Jorgenson, Alissa, Judge, Jessyca, Kalb, Luther, Kalmus, Taylor, Kang, Sungeun, Kangas, Elizabeth, Kanne, Stephen, Kaplan, Hannah, Khan, Sara, Kim, Sophy, Kim, Annes, Kitaygordsky, Alex, Klaiman, Cheryl, Klever, Adam, Koene, Hope, Koomar, Tanner, Koza, Melinda, Kramer, Sydney, Krushena, Meghan, Kurtz-Nelson, Eva, Lamarche, Elena, Lampert, Erica, Lamy, Martine, Landa, Rebecca, Lebron-Cruz, Alexa, Lechniak, Holly, Lee, Soo, Leight, Bruce, Lerner, Matthew, Lesher, Laurie, Lewis, Courtney, Li, Hai, Li, Deana, Libove, Robin, Lillie, Natasha, Limon, Danica, Limpoco, Desi, Lin, Melody, Littlefield, Sandy, Lobisi, Brandon, Locarno, Laura, Long, Nancy, Long, Bailey, Long, Kennadie, Lopez, Marilyn, Lovering, Taylor, Lozano, Ivana, Lucio, Daniella, Luo, Addie, Luu, My-Linh, Lyon, Audrey, Ma, Julia, Madi, Natalie, Malloch, Lacy, Mankaryous, Reanna, Manning, Patricia, Mantey, Alvin, Marini, Richard, Marsden, Alexandra, Marwali, Clarissa, Marzano, Gabriela, Mason, Andrew, Mastel, Sarah, Mathai, Sheena, Matthews, Emily, Matusoff, Emma, Maxim, Clara, McCarthy, Caitlin, McClellen, Lynn, Mccoy, Nicole, McCullough, Kaylen, McDonald, Brooke, McGalliard, Julie, McIntyre, Anne-Marie, McKenna, Brooke, McKenzie, Alexander, McTaggart, Megan, Meinen, Hannah, Melnyk, Sophia, Miceli, Alexandra, Michaels, Sarah, Michaelson, Jacob, Milan, Estefania, Miller, Melissa, Milliken, Anna, Minton, Kyla, Mitchell, Terry, Gunn, Amanda Moffitt, Mohiuddin, Sarah, Money, Gina, Montezuma, Jessie, Mooney, Lindsey, Moore, Margo, Morales-Lara, Amy, Morgan, Kelly, Morotti, Hadley, Morrier, Michael, Munoz, Maria, Lavanderos, Ambar Munoz, Murali, Shwetha, Murillo, Karla, Murray, Kailey, Myhre, Erin, Neely, Jason, Neuhaus, Emily, Newman, Olivia, Nguyen, Richard, Nguyen, Victoria, Nichols, Evelyn, Nicholson, Amy, Niederhauser, Melanie, Norris, Megan, Norton, Shai, Nowell, Kerri, O’Brien, Kaela, O’Meara, Mitchell, O’Neil, Molly, O'Roak, Brian, Ocampo, Edith, Ochoa-Lubinoff, Cesar, Oft, Anna, Orobio, Jessica, Ortiz, Crissy, Ousley, Opal, Oyeyemi, Motunrayo, Pacheco, Lillian, Palacios, Valeria, Palmer, Samiza, Palmeri, Isabella, Pama, Katrina, Pandey, Juhi, Paolicelli, Anna Marie, Parker, Jaylaan, Patterson, Morgan, Pawlowski, Katherine, Pedapati, Ernest, Pepper, Michah, Perrin, Jeremy, Peura, Christine, Phillips, Diamond, Pierce, Karen, Piven, Joseph, Plate, Juhi, Polanco, Jose, Pott-Schmidt, Natalie, Pramparo, Tiziano, Pratt, Taleen, Prock, Lisa, White, Stormi Pulver, Qi, Hongjian, Qiu, Shanping, Queen, Eva, Questel, Marcia, Quinones, Ashley, Rambeck, Desiree, Randall, Shelley, Ranganathan, Vaikunt, Raymond, Laurie, Rayos, Madelyn, Real, Kelly, Rhea, Anna, Rice, Catherine, Richardson, Harper, Riffle, Stacy, Robertson, Tracy, Roby, Erin, Rocha, Ana, Roche, Casey, Rodriguez, Nicki, Rodriguez, Bianca, Roeder, Katherine, Rojas, Daniela, Rosewater, Jacob, Rosselott, Hilary, Runyan, Payton, Russo, Nicole, Rutter, Tara, Ruzzo, Elizabeth, Sahin, Mustafa, Salem, Fatima, Sanchez, Rebecca, Sanders, Muave, Sanderson, Tayler, Sandhu, Sophie, Sanford, Katelyn, Santangelo, Susan, Santulli, Madeline, Sarver, Dustin, Savage, Madeline, Scherr, Jessica, Schneider, Hoa, Schools, Hayley, Schoonover, Gregory, Schultz, Robert, Sebolt, Cheyanne, Shaffer, Rebecca, Shameen, Sana, Sherard, Curry, Shikov, Roman, Shillington, Amelle, Shir, Mojeeb, Shocklee, Amanda, Shrier, Clara, Shulman, Lisa, Siegel, Matt, Simon, Andrea, Simon, Laura, Singh, Arushi, Singh, Vini, Smalley, Devin, Smith, Kaitlin, Smith, Chris, Smith, Ashlyn, Soorya, Latha, Soscia, Julia, Soucy, Aubrie, Stchur, Laura, Steele, Morgan, Srishyla, Diksha, Stamps, Danielle, Sussman, Nicole, Swanson, Amy, Sweeney, Megan, Sziklay, Anthony, Tafolla, Maira, Taiba, Jabeen, Takahashi, Nicole, Terroso, Sydney, Strathearn, Camilla, Thomas, Taylor, Thompson, Samantha, Touchette, Ellyn, Townsend, Laina, Trog, Madison, Tsai, Katherine, Tseng, Angela, Tshering, Paullani, Tso, Ivy, Valicenti-Mcdermott, Maria, VanMetre, Bonnie, VanWade, Candace, Turecki, Samuel, Vargo, Kerrigan, Vattuone, Cristiana, Veenstra-Vanderweele, Jeremy, Vehorn, Alison, Benitez Velazquez, Alan Jesus, Verdi, Mary, Villalobos, Michele, Vrittamani, Lakshmi, Wainer, Allison, Wallace, Jermel, Walston, Corrie, Wang, Jiayaho, Ward, Audrey, Warren, Zachary, Washington, Katherine, Westerkamp, Grace, White, Sabrina, Wink, Logan, Winoto, Fiona, Winters, Sarah, Wodka, Ericka, Xavier, Samantha, Xu, Sidi, Yang, Yi, Yang, WhaJames, Yang, Amy, Yinger, Meredith, Yu, Timothy, Zaro, Christopher, Zha, Cindy, Zhang, Haicang, Zhao, Haoquan, Zick, Allyson, Salmon, Lauren Ziegelmayer, Wright, Jessica R., Astrovskaya, Irina, Barns, Sarah D., Goler, Alexandra, Zhou, Xueya, Shu, Chang, Snyder, LeeAnne Green, Han, Bing, Shen, Yufeng, Volfovsky, Natalia, Hall, Jacob B., Feliciano, Pamela, and Chung, Wendy K.

Published
2024
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8. Rare and de novo variants in 827 congenital diaphragmatic hernia probands implicate LONP1 as candidate risk gene

Author

Qiao, Lu, Xu, Le, Yu, Lan, Wynn, Julia, Hernan, Rebecca, Zhou, Xueya, Farkouh-Karoleski, Christiana, Krishnan, Usha S, Khlevner, Julie, De, Aliva, Zygmunt, Annette, Crombleholme, Timothy, Lim, Foong-Yen, Needelman, Howard, Cusick, Robert A, Mychaliska, George B, Warner, Brad W, Wagner, Amy J, Danko, Melissa E, Chung, Dai, Potoka, Douglas, Kosiński, Przemyslaw, McCulley, David J, Elfiky, Mahmoud, Azarow, Kenneth, Fialkowski, Elizabeth, Schindel, David, Soffer, Samuel Z, Lyon, Jane B, Zalieckas, Jill M, Vardarajan, Badri N, Aspelund, Gudrun, Duron, Vincent P, High, Frances A, Sun, Xin, Donahoe, Patricia K, Shen, Yufeng, and Chung, Wendy K

Subjects
Congenital Structural Anomalies, Perinatal Period - Conditions Originating in Perinatal Period, Pediatric, Lung, Clinical Research, Genetics, Human Genome, Infant Mortality, Rare Diseases, Digestive Diseases, Aetiology, 2.1 Biological and endogenous factors, Good Health and Well Being, ATP-Dependent Proteases, Animals, Case-Control Studies, Cohort Studies, Craniofacial Abnormalities, DNA Copy Number Variations, Eye Abnormalities, Female, Growth Disorders, Hernias, Diaphragmatic, Congenital, Hip Dislocation, Congenital, Humans, Male, Mice, Mice, Inbred C57BL, Mice, Knockout, Mitochondrial Proteins, Mutation, Missense, Osteochondrodysplasias, Pedigree, Tooth Abnormalities, ALYREF, LONP1, congenital diaphragmatic hernia, de novo variants, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly that is often accompanied by other anomalies. Although the role of genetics in the pathogenesis of CDH has been established, only a small number of disease-associated genes have been identified. To further investigate the genetics of CDH, we analyzed de novo coding variants in 827 proband-parent trios and confirmed an overall significant enrichment of damaging de novo variants, especially in constrained genes. We identified LONP1 (lon peptidase 1, mitochondrial) and ALYREF (Aly/REF export factor) as candidate CDH-associated genes on the basis of de novo variants at a false discovery rate below 0.05. We also performed ultra-rare variant association analyses in 748 affected individuals and 11,220 ancestry-matched population control individuals and identified LONP1 as a risk gene contributing to CDH through both de novo and ultra-rare inherited largely heterozygous variants clustered in the core of the domains and segregating with CDH in affected familial individuals. Approximately 3% of our CDH cohort who are heterozygous with ultra-rare predicted damaging variants in LONP1 have a range of clinical phenotypes, including other anomalies in some individuals and higher mortality and requirement for extracorporeal membrane oxygenation. Mice with lung epithelium-specific deletion of Lonp1 die immediately after birth, most likely because of the observed severe reduction of lung growth, a known contributor to the high mortality in humans. Our findings of both de novo and inherited rare variants in the same gene may have implications in the design and analysis for other genetic studies of congenital anomalies.

Published
2021

10. Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes

Author

Feliciano, Pamela, Zhou, Xueya, Astrovskaya, Irina, Turner, Tychele N, Wang, Tianyun, Brueggeman, Leo, Barnard, Rebecca, Hsieh, Alexander, Snyder, LeeAnne Green, Muzny, Donna M, Sabo, Aniko, Gibbs, Richard A, Eichler, Evan E, O’Roak, Brian J, Michaelson, Jacob J, Volfovsky, Natalia, Shen, Yufeng, and Chung, Wendy K

Subjects
Biotechnology, Genetic Testing, Genetics, Prevention, Pediatric, Human Genome, Intellectual and Developmental Disabilities (IDD), Brain Disorders, Clinical Research, Autism, Mental Health, 2.1 Biological and endogenous factors, Aetiology, Mental health, SPARK Consortium, Autism spectrum disorders, Behavioural genetics, Medical genomics
Abstract

Autism spectrum disorder (ASD) is a genetically heterogeneous condition, caused by a combination of rare de novo and inherited variants as well as common variants in at least several hundred genes. However, significantly larger sample sizes are needed to identify the complete set of genetic risk factors. We conducted a pilot study for SPARK (SPARKForAutism.org) of 457 families with ASD, all consented online. Whole exome sequencing (WES) and genotyping data were generated for each family using DNA from saliva. We identified variants in genes and loci that are clinically recognized causes or significant contributors to ASD in 10.4% of families without previous genetic findings. In addition, we identified variants that are possibly associated with ASD in an additional 3.4% of families. A meta-analysis using the TADA framework at a false discovery rate (FDR) of 0.1 provides statistical support for 26 ASD risk genes. While most of these genes are already known ASD risk genes, BRSK2 has the strongest statistical support and reaches genome-wide significance as a risk gene for ASD (p-value = 2.3e-06). Future studies leveraging the thousands of individuals with ASD who have enrolled in SPARK are likely to further clarify the genetic risk factors associated with ASD as well as allow accelerate ASD research that incorporates genetic etiology.

Published
2019

11. Mutations in Hnrnpa1 cause congenital heart defects.

Author

Yu, Zhe, Tang, Paul Lf, Wang, Jing, Bao, Suying, Shieh, Joseph T, Leung, Alan Wl, Zhang, Zhao, Gao, Fei, Wong, Sandra Yy, Hui, Andy Lc, Gao, Yuan, Dung, Nelson, Zhang, Zhi-Gang, Fan, Yanhui, Zhou, Xueya, Zhang, Yalun, Wong, Dana Sm, Sham, Pak C, Azhar, Abid, Kwok, Pui-Yan, Tam, Patrick Pl, Lian, Qizhou, Cheah, Kathryn Se, Wang, Binbin, and Song, You-Qiang

Subjects
Myocardium, Heart, Myocytes, Cardiac, Animals, Mice, Transgenic, Humans, Mice, Heart Defects, Congenital, Disease Models, Animal, DNA Mutational Analysis, Signal Transduction, Organogenesis, Homozygote, Frameshift Mutation, Infant, Female, Male, Embryo, Mammalian, Gene Knockout Techniques, Heterogeneous Nuclear Ribonucleoprotein A1, Cardiovascular disease, Development, Genetics, Heart failure, Disease Models, Animal, Embryo, Mammalian, Heart Defects, Congenital, Transgenic, Myocytes, Cardiac
Abstract

Incomplete penetrance of congenital heart defects (CHDs) was observed in a mouse model. We hypothesized that the contribution of a major genetic locus modulates the manifestation of the CHDs. After genome-wide linkage mapping, fine mapping, and high-throughput targeted sequencing, a recessive frameshift mutation of the heterogeneous nuclear ribonucleoprotein A1 (Hnrnpa1) gene was confirmed (Hnrnpa1ct). Hnrnpa1 was expressed in both the first heart field (FHF) and second heart field (SHF) at the cardiac crescent stage but was only maintained in SHF progenitors after heart tube formation. Hnrnpa1ct/ct homozygous mutants displayed complete CHD penetrance, including truncated and incomplete looped heart tube at E9.5, ventricular septal defect (VSD) and persistent truncus arteriosus (PTA) at E13.5, and VSD and double outlet right ventricle at P0. Impaired development of the dorsal mesocardium and sinoatrial node progenitors was also observed. Loss of Hnrnpa1 expression leads to dysregulation of cardiac transcription networks and multiple signaling pathways, including BMP, FGF, and Notch in the SHF. Finally, two rare heterozygous mutations of HNRNPA1 were detected in human CHDs. These findings suggest a role of Hnrnpa1 in embryonic heart development in mice and humans.

Published
2018

12. Likely damaging de novo variants in congenital diaphragmatic hernia patients are associated with worse clinical outcomes

Author

Qiao, Lu, Wynn, Julia, Yu, Lan, Hernan, Rebecca, Zhou, Xueya, Duron, Vincent, Aspelund, Gudrun, Farkouh-Karoleski, Christiana, Zygumunt, Annette, Krishnan, Usha S., Nees, Shannon, Khlevner, Julie, Lim, Foong Yen, Crombleholme, Timothy, Cusick, Robert, Azarow, Kenneth, Danko, Melissa Ellen, Chung, Dai, Warner, Brad W., Mychaliska, George B., Potoka, Douglas, Wagner, Amy J., Soffer, Samuel, Schindel, David, McCulley, David J., Shen, Yufeng, and Chung, Wendy K.

Published
2020
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13. Meta-analysis of genome-wide association studies in East Asian-ancestry populations identifies four new loci for body mass index

Author

Wen, Wanqing, Zheng, Wei, Okada, Yukinori, Takeuchi, Fumihiko, Tabara, Yasuharu, Hwang, Joo-Yeon, Dorajoo, Rajkumar, Li, Huaixing, Tsai, Fuu-Jen, Yang, Xiaobo, He, Jiang, Wu, Ying, He, Meian, Zhang, Yi, Liang, Jun, Guo, Xiuqing, Sheu, Wayne Huey-Herng, Delahanty, Ryan, Guo, Xingyi, Kubo, Michiaki, Yamamoto, Ken, Ohkubo, Takayoshi, Go, Min Jin, Liu, Jian Jun, Gan, Wei, Chen, Ching-Chu, Gao, Yong, Li, Shengxu, Lee, Nanette R, Wu, Chen, Zhou, Xueya, Song, Huaidong, Yao, Jie, Lee, I-Te, Long, Jirong, Tsunoda, Tatsuhiko, Akiyama, Koichi, Takashima, Naoyuki, Cho, Yoon Shin, Ong, Rick TH, Lu, Ling, Chen, Chien-Hsiun, Tan, Aihua, Rice, Treva K, Adair, Linda S, Gui, Lixuan, Allison, Matthew, Lee, Wen-Jane, Cai, Qiuyin, Isomura, Minoru, Umemura, Satoshi, Kim, Young Jin, Seielstad, Mark, Hixson, James, Xiang, Yong-Bing, Isono, Masato, Kim, Bong-Jo, Sim, Xueling, Lu, Wei, Nabika, Toru, Lee, Juyoung, Lim, Wei-Yen, Gao, Yu-Tang, Takayanagi, Ryoichi, Kang, Dae-Hee, Wong, Tien Yin, Hsiung, Chao Agnes, Wu, I-Chien, Juang, Jyh-Ming Jimmy, Shi, Jiajun, Choi, Bo Youl, Aung, Tin, Hu, Frank, Kim, Mi Kyung, Lim, Wei Yen, Wang, Tzung-Dao, Shin, Min-Ho, Lee, Jeannette, Ji, Bu-Tian, Lee, Young-Hoon, Young, Terri L, Shin, Dong Hoon, Chun, Byung-Yeol, Cho, Myeong-Chan, Han, Bok-Ghee, Hwu, Chii-Min, Assimes, Themistocles L, Absher, Devin, Yan, Xiaofei, Kim, Eric, Kuo, Jane Z, Kwon, Soonil, Taylor, Kent D, Chen, Yii-Der I, Rotter, Jerome I, Qi, Lu, Zhu, Dingliang, Wu, Tangchun, Mohlke, Karen L, and Gu, Dongfeng

Subjects
Biological Sciences, Genetics, Obesity, Human Genome, Nutrition, Women's Health, 1.1 Normal biological development and functioning, Stroke, 5'-Nucleotidase, Aldehyde Dehydrogenase, Aldehyde Dehydrogenase, Mitochondrial, Asian People, Blood Proteins, Body Mass Index, Cardiac Myosins, Asia, Eastern, Female, Genetic Predisposition to Disease, Genome-Wide Association Study, Glycoproteins, Humans, KCNQ1 Potassium Channel, Male, Myosin Light Chains, Polymorphism, Single Nucleotide, Proteinase Inhibitory Proteins, Secretory, Medical and Health Sciences, Genetics & Heredity
Abstract

Recent genetic association studies have identified 55 genetic loci associated with obesity or body mass index (BMI). The vast majority, 51 loci, however, were identified in European-ancestry populations. We conducted a meta-analysis of associations between BMI and ∼2.5 million genotyped or imputed single nucleotide polymorphisms among 86 757 individuals of Asian ancestry, followed by in silico and de novo replication among 7488-47 352 additional Asian-ancestry individuals. We identified four novel BMI-associated loci near the KCNQ1 (rs2237892, P = 9.29 × 10(-13)), ALDH2/MYL2 (rs671, P = 3.40 × 10(-11); rs12229654, P = 4.56 × 10(-9)), ITIH4 (rs2535633, P = 1.77 × 10(-10)) and NT5C2 (rs11191580, P = 3.83 × 10(-8)) genes. The association of BMI with rs2237892, rs671 and rs12229654 was significantly stronger among men than among women. Of the 51 BMI-associated loci initially identified in European-ancestry populations, we confirmed eight loci at the genome-wide significance level (P < 5.0 × 10(-8)) and an additional 14 at P < 1.0 × 10(-3) with the same direction of effect as reported previously. Findings from this analysis expand our knowledge of the genetic basis of obesity.

Published
2014

17. A rare variant in MLKL confers susceptibility to ApoE ɛ4-negative Alzheimer's disease in Hong Kong Chinese population

Author

Wang, Binbin, Bao, Suying, Zhang, Zhigang, Zhou, Xueya, Wang, Jing, Fan, Yanhui, Zhang, Yan, Li, Yan, Chen, Luhua, Jia, Yizhen, Li, Jiang, Li, Miaoxin, Zheng, Wenhua, Mu, Nan, Wang, Liqiu, Yu, Zhe, Wong, Dana S.M., Zhang, Yalun, Kwan, Joseph, Ka-Fung Mak, Henry, Ambalavanan, Amirthagowri, Zhou, Sirui, Cai, Wangwei, Zheng, Jin, Huang, Shishu, Rouleau, Guy A., Yang, Wanling, Rogaeva, Ekaterina, Ma, Xu, St George-Hyslop, Peter, Chu, Leung Wing, and Song, You-Qiang

Published
2018
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20. eP121: Integrating de novo and inherited variants in over 42,607 autism cases identifies variants in new moderate risk genes

Author

Feliciano, Pamela, primary, Zhou, Xueya, additional, Wang, Tianyun, additional, Astrovskaya, Irina, additional, Shu, Chang, additional, Hall, Jacob, additional, Obiajulu, Joseph, additional, Wright, Jessica, additional, Murali, Schwetha, additional, Xu, Simon, additional, Brueggeman, Leo, additional, Thomas, Taylor, additional, Marchenko, Olena, additional, Fleisch, Christopher, additional, Barns, Sarah, additional, Snyder, LeeAnne Green, additional, Han, Bing, additional, Chang, Timothy, additional, Turner, Tychele, additional, Harvey, William, additional, Nishida, Andrew, additional, O'Roak, Brian, additional, Geschwind, Daniel, additional, Consortium, The SPARK., additional, Michaelson, Jacob, additional, Volfovsky, Natalia, additional, Eichler, Evan, additional, Shen, Yufeng, additional, and Chung, Wendy, additional

Published
2022
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25. Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH

Author

Zhu, Na, Swietlik, Emilia M., Welch, Carrie L., Pauciulo, Michael W., Hagen, Jacob J., Zhou, Xueya, Guo, Yicheng, Karten, Johannes, Pandya, Divya, Tilly, Tobias, Lutz, Katie A., Martin, Jennifer M., Treacy, Carmen M., Rosenzweig, Erika B., Krishnan, Usha, Coleman, Anna W., Gonzaga-Jauregui, Claudia, Lawrie, Allan, Trembath, Richard C., Wilkins, Martin R., Morrell, Nicholas W., Shen, Yufeng, Gräf, Stefan, Nichols, William C., Chung, Wendy K., Hirsch, Russel, White, R. James, Simon, Marc, Badesch, David, Rosenzweig, Erika, Burger, Charles, Chakinala, Murali, Thenappan, Thenappan, Elliott, Greg, Simms, Robert, Farber, Harrison, Frantz, Robert, Elwing, Jean, Hill, Nicholas, Ivy, Dunbar, Klinger, James, Nathan, Steven, Oudiz, Ronald, Robbins, Ivan, Schilz, Robert, Fortin, Terry, Wilt, Jeffrey, Yung, Delphine, Austin, Eric, Ahmad, Ferhaan, Bhatt, Nitin, Lahm, Tim, Frost, Adaani, Safdar, Zeenat, Rehman, Zia, Walter, Robert, Torres, Fernando, Bakshi, Sahil, Archer, Stephen, Argula, Rahul, Barnett, Christopher, Benza, Raymond, Desai, Ankit, Maddipati, Veeranna, Bogaard, Harm J., Church, Colin, Coghlin, Gerry, Condliffe, Robin, Eyries, Mélanie, Gall, Henning, Ghio, Stefano, Girerd, Barbara, Holden, Simon, Howard, Luke, Humbert, Marc, Kiely, David G., Kovacs, Gabor, Lordan, Jim, Machado, Rajiv D., MacKenzie Ross, Robert V., McCabe, Colm, Moledina, Shahin, Montani, David, Olschewski, Horst, Penkett, Christopher J., Pepke-Zaba, Joanna, Price, Laura, Rhodes, Christopher J., Seeger, Werner, Soubrier, Florent, Southgate, Laura, Suntharalingam, Jay, Swift, Andrew J., Toshner, Mark R., Noordegraaf, Anton Vonk, Wharton, John, Wild, Jim, Wort, Stephen John, and Apollo - University of Cambridge Repository

Subjects
Exome sequencing, Case-control association testing, Research, FOS: Biological sciences, Genetics, De novo variant analysis, Pulmonary arterial hypertension, Genome sequencing
Abstract

Background: Pulmonary arterial hypertension (PAH) is a lethal vasculopathy characterized by pathogenic remodeling of pulmonary arterioles leading to increased pulmonary pressures, right ventricular hypertrophy, and heart failure. PAH can be associated with other diseases (APAH: connective tissue diseases, congenital heart disease, and others) but often the etiology is idiopathic (IPAH). Mutations in bone morphogenetic protein receptor 2 (BMPR2) are the cause of most heritable cases but the vast majority of other cases are genetically undefined. Methods: To identify new risk genes, we utilized an international consortium of 4241 PAH cases with exome or genome sequencing data from the National Biological Sample and Data Repository for PAH, Columbia University Irving Medical Center, and the UK NIHR BioResource – Rare Diseases Study. The strength of this combined cohort is a doubling of the number of IPAH cases compared to either national cohort alone. We identified protein-coding variants and performed rare variant association analyses in unrelated participants of European ancestry, including 1647 IPAH cases and 18,819 controls. We also analyzed de novo variants in 124 pediatric trios enriched for IPAH and APAH-CHD. Results: Seven genes with rare deleterious variants were associated with IPAH with false discovery rate smaller than 0.1: three known genes (BMPR2, GDF2, and TBX4), two recently identified candidate genes (SOX17, KDR), and two new candidate genes (fibulin 2, FBLN2; platelet-derived growth factor D, PDGFD). The new genes were identified based solely on rare deleterious missense variants, a variant type that could not be adequately assessed in either cohort alone. The candidate genes exhibit expression patterns in lung and heart similar to that of known PAH risk genes, and most variants occur in conserved protein domains. For pediatric PAH, predicted deleterious de novo variants exhibited a significant burden compared to the background mutation rate (2.45×, p = 2.5e−5). At least eight novel pediatric candidate genes carrying de novo variants have plausible roles in lung/heart development. Conclusions: Rare variant analysis of a large international consortium identified two new candidate genes—FBLN2 and PDGFD. The new genes have known functions in vasculogenesis and remodeling. Trio analysis predicted that ~ 15% of pediatric IPAH may be explained by de novo variants.

Published
2021
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26. Erratum

Author

Zhang, Xuegong, Zhou, Xueya, Wang, Xiaowo, Jiang, Rui, editor, Zhang, Xuegong, editor, and Zhang, Michael Q., editor

Published
2013
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32. Rare and de novo variants in 827 congenital diaphragmatic hernia probands implicate LONP1 and ALYREF as new candidate risk genes

Author

Qiao, Lu, primary, Xu, Le, additional, Yu, Lan, additional, Wynn, Julia, additional, Hernan, Rebecca, additional, Zhou, Xueya, additional, Farkouh-Karoleski, Christiana, additional, Krishnan, Usha S., additional, Khlevner, Julie, additional, De, Aliva, additional, Zygmunt, Annette, additional, Crombleholme, Timothy, additional, Lim, Foong-Yen, additional, Needelman, Howard, additional, Cusick, Robert A., additional, Mychaliska, George B., additional, Warner, Brad W., additional, Wagner, Amy J., additional, Danko, Melissa E., additional, Chung, Dai, additional, Potoka, Douglas, additional, Kosiński, Przemyslaw, additional, McCulley, David J., additional, Elfiky, Mahmoud, additional, Azarow, Kenneth, additional, Fialkowski, Elizabeth, additional, Schindel, David, additional, Soffer, Samuel Z., additional, Lyon, Jane B., additional, Zalieckas, Jill M., additional, Vardarajan, Badri N., additional, Aspelund, Gudrun, additional, Duron, Vincent P., additional, High, Frances A., additional, Sun, Xin, additional, Donahoe, Patricia K., additional, Shen, Yufeng, additional, and Chung, Wendy K., additional

Published
2021
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36. Return of genetic research results in 21,532 individuals with autism

Author

Wright, Jessica R., Astrovskaya, Irina, Barns, Sarah D., Goler, Alexandra, Zhou, Xueya, Shu, Chang, Snyder, LeeAnne Green, Han, Bing, Aarrestad, Alexandria, Abbeduto, Leonard, Aberbach, Gabriella, Aberle, Shelley, Adegbite, Adediwura, Adeniji, Debbie, Aguilar, Maria, Ahlers, Kaitlyn, Albright, Charles, Alessandri, Michael, Algaze, Zach, Alkazi, Jasem, Amador, Raquel, Amaral, David, Amon, Logan, Amundsen, Leonor, Andrus, Alicia, Anglo, Claudine, Annett, Robert, Arar, Adam, Arnold, Jonathan, Arriaga, Ivette, Arzate, Eduardo, Ashley, Raven, Aslamy, Leilemah, Baalman, Kelli, Baer, Melissa, Bahi, Ethan, Bailey, Joshua, Baldlock, Zachary, Banks, Grabrielle, Baraghoshi, Gabriele, Bardett, Nicole, Barrett, Mallory, Bartholomew, Yan, Bates, Heidi, Beard, Katie, Becerra, Juana, Beckwith, Malia, Beechan, Paige, Beeson, Landon, Beeson, Josh, Bell, Brandi, Belli, Monica, Bentley, Dawn, Berger, Natalie, Berman, Anna, Bernier, Raphael, Berry-Kravis, Elizabeth, Berwanger, Mary, Birdwell, Shelby, Blank, Elizabeth, Bond, Rebecca, Booker, Stephanie, Bordofsky, Aniela, Bower, Erin, Bowers, Lukas, Bradley, Catherine, Brayer, Heather, Brewster, Stephanie, Brown, Hallie, Brown, Alison, Brown, Melissa, Buck, Catherine, Buescher, Cate, Bullon, Kayleigh, Buraima, Joy, Butter, Eric, Caamano, Amalia, Cacciato, Nicole, CaI, Wenteng, Calderon, Norma, Callahan, Kristen, Camba, Alexies, Campo-Soria, Claudia, Caprara, Giuliana, Carbone, Paul, Carpenter, Laura, Carpenter, Sarah, Casseus, Myriam, Casten, Lucas, Catherine, Sullivan, Chappo, Ashley, Chavez, Kimberly, Cheathem-Johnson, Randi, Chen, Tia, Chintalapalli, Sharmista, Cho, Daniel, Choi, Y.B., Clark, Nia, Clark, Renee, Coffman, Marika, Coleman, Laura, Coleman, Kendra, Collins, Alister, Columbi, Costanza, Comitre, Joaquin, Constant, Stephanie, Contra, Arin, Conyers, Sarah, Cooper, Lindsey, Cooper, Cameron, Coppola, Leigh, Corlett, Allison, Corrales, Lady, Correa, Dahriana, Cottrell, Hannah, Coughlin, Michelle, Courchesne, Eric, Coury, Dan, Crocetti, Deana, Croson, Carrie, Crowell, Judith, Cubells, Joseph, Cunningham, Sean, Currin, Mary, Cutri, Michele, D'Ambrosi, Sophia, David, Giancarla, Davis, Ayana, Davis, Sabrina, Decius, Nickelle, Delaporte, Jennifer, DeMarco, Lindsey, Dennis, Brandy, Deronda, Alyssa, Dhawan, Esha, Dichter, Gabriel, Doan, Ryan, Dominick, Kelli, Ortega, Leonardo Dominquez, Doyle, Erin, Drayton, Andrea, DuBois, Megan, Dudley, Johnny, Duhon, Gabrielle, Duncan, Grabrielle, Duncan, Amie, Dunlevy, Megan, Dyer, Meaghan, Earl, Rachel, Edmonson, Catherine, Eldred, Sara, Elliott, Nelita, Emery, Brooke, Enright, Barbara, Erb, Sarah, Erickson, Craig, Esler, Amy, Estevez, Liza, Fanta, Anne, Fassler, Carrie, Fatemi, Ali, Fazal, Faris, Featherston, Marilyn, Ferguson, Jonathan, Fish, Angela, Fitzgerald, Kate, Flores, Kathleen, Fombonne, Eric, Foster, Margaret, Fowler, Tiffany, Fox, Emma, Fox, Emily, Francis, Sunday, Frayne, Margot, Froman, Sierra, Fuller, Laura, Galbraith, Virginia, Gallimore, Dakota, Gambrell, Ariana, Gazestani, Vahid, Geisheker, Madeleine R., Gerdts, Jennifer, Geschwind, Daniel, Ghaziuddin, Mohammad, Ghina, Haidar, Given, Erin, Goetz, Mykayla, Gong, Jared, Gonring, Kelsey, Gonzalez, Natalia, Gonzalez, Antonio, Goodwill, Ellie, Gordon, Rachel, Graham, Carter, Gray, Catherine, Grimes, Ellen, Griswold, Anthony, Gu, Pan, Guilfoyle, Janna, Gulsrud, Amanda, Gunderson, Jaclyn, Gunter, Chris, Gupta, Sanya, Gupta, Abha, Gutierrez, Anibal, Gwynette, Frampton, Haidar, Ghina, Hale, Melissa, Haley, Monica, Hall, Lauren K., Hamer, Kira, Hamilton, Piper, Hanna, Nathan, Hardan, Antonio, Harkins, Christina, Harrell, Eldric, Harris, Jill, Harris, Nina, Hayes, Caitlin, Hayse, Braden, Heckers, Teryn, Heerwagen, Kathryn, Hennelly, Daniela, Herbert, Lynette, Hermle, Luke, Hernandez, Briana, Herrera, Clara, Hess, Amy, Heyman, Michelle, Higgins, Lorrin, Phillips, Brittani Hilscher, Hirst, Kathy, Ho, Theodore, Hoffman, Emily, Hojlo, Margaret, Honaker, Makayla, Hong, Michael, Hooks, Gregory, Horner, Susannah, Horton, Danielle, Hounchell, Melanie, Howes, Dain, Huang-Storm, Lark, Hunter, Samantha, Hutter, Hanna, Hyde, Emily, Ibanez, Teresa, Ingram, Kelly, Istephanous, Dalia, Jacob, Suma, Jarratt, Andrea, Jelinek, Anna, Johnson, Mary, Jones, Mya, Jones, Garland, Jones, Mark, Jorgenson, Alissa, Judge, Jessyca, Kalb, Luther, Kalmus, Taylor, Kang, Sungeun, Kangas, Elizabeth, Kanne, Stephen, Kaplan, Hannah, Khan, Sara, Kim, Sophy, Kim, Annes, Kitaygordsky, Alex, Klaiman, Cheryl, Klever, Adam, Koene, Hope, Koomar, Tanner, Koza, Melinda, Kramer, Sydney, Krushena, Meghan, Kurtz-Nelson, Eva, Lamarche, Elena, Lampert, Erica, Lamy, Martine, Landa, Rebecca, Lebron-Cruz, Alexa, Lechniak, Holly, Lee, Soo, Leight, Bruce, Lerner, Matthew, Lesher, Laurie, Lewis, Courtney, Li, Hai, Li, Deana, Libove, Robin, Lillie, Natasha, Limon, Danica, Limpoco, Desi, Lin, Melody, Littlefield, Sandy, Lobisi, Brandon, Locarno, Laura, Long, Nancy, Long, Bailey, Long, Kennadie, Lopez, Marilyn, Lovering, Taylor, Lozano, Ivana, Lucio, Daniella, Luo, Addie, Luu, My-Linh, Lyon, Audrey, Ma, Julia, Madi, Natalie, Malloch, Lacy, Mankaryous, Reanna, Manning, Patricia, Mantey, Alvin, Marini, Richard, Marsden, Alexandra, Marwali, Clarissa, Marzano, Gabriela, Mason, Andrew, Mastel, Sarah, Mathai, Sheena, Matthews, Emily, Matusoff, Emma, Maxim, Clara, McCarthy, Caitlin, McClellen, Lynn, Mccoy, Nicole, McCullough, Kaylen, McDonald, Brooke, McGalliard, Julie, McIntyre, Anne-Marie, McKenna, Brooke, McKenzie, Alexander, McTaggart, Megan, Meinen, Hannah, Melnyk, Sophia, Miceli, Alexandra, Michaels, Sarah, Michaelson, Jacob, Milan, Estefania, Miller, Melissa, Milliken, Anna, Minton, Kyla, Mitchell, Terry, Gunn, Amanda Moffitt, Mohiuddin, Sarah, Money, Gina, Montezuma, Jessie, Mooney, Lindsey, Moore, Margo, Morales-Lara, Amy, Morgan, Kelly, Morotti, Hadley, Morrier, Michael, Munoz, Maria, Lavanderos, Ambar Munoz, Murali, Shwetha, Murillo, Karla, Murray, Kailey, Myhre, Erin, Neely, Jason, Neuhaus, Emily, Newman, Olivia, Nguyen, Richard, Nguyen, Victoria, Nichols, Evelyn, Nicholson, Amy, Niederhauser, Melanie, Norris, Megan, Norton, Shai, Nowell, Kerri, O’Brien, Kaela, O’Meara, Mitchell, O’Neil, Molly, O'Roak, Brian, Ocampo, Edith, Ochoa-Lubinoff, Cesar, Oft, Anna, Orobio, Jessica, Ortiz, Crissy, Ousley, Opal, Oyeyemi, Motunrayo, Pacheco, Lillian, Palacios, Valeria, Palmer, Samiza, Palmeri, Isabella, Pama, Katrina, Pandey, Juhi, Paolicelli, Anna Marie, Parker, Jaylaan, Patterson, Morgan, Pawlowski, Katherine, Pedapati, Ernest, Pepper, Michah, Perrin, Jeremy, Peura, Christine, Phillips, Diamond, Pierce, Karen, Piven, Joseph, Plate, Juhi, Polanco, Jose, Pott-Schmidt, Natalie, Pramparo, Tiziano, Pratt, Taleen, Prock, Lisa, White, Stormi Pulver, Qi, Hongjian, Qiu, Shanping, Queen, Eva, Questel, Marcia, Quinones, Ashley, Rambeck, Desiree, Randall, Shelley, Ranganathan, Vaikunt, Raymond, Laurie, Rayos, Madelyn, Real, Kelly, Rhea, Anna, Rice, Catherine, Richardson, Harper, Riffle, Stacy, Robertson, Tracy, Roby, Erin, Rocha, Ana, Roche, Casey, Rodriguez, Nicki, Rodriguez, Bianca, Roeder, Katherine, Rojas, Daniela, Rosewater, Jacob, Rosselott, Hilary, Runyan, Payton, Russo, Nicole, Rutter, Tara, Ruzzo, Elizabeth, Sahin, Mustafa, Salem, Fatima, Sanchez, Rebecca, Sanders, Muave, Sanderson, Tayler, Sandhu, Sophie, Sanford, Katelyn, Santangelo, Susan, Santulli, Madeline, Sarver, Dustin, Savage, Madeline, Scherr, Jessica, Schneider, Hoa, Schools, Hayley, Schoonover, Gregory, Schultz, Robert, Sebolt, Cheyanne, Shaffer, Rebecca, Shameen, Sana, Sherard, Curry, Shikov, Roman, Shillington, Amelle, Shir, Mojeeb, Shocklee, Amanda, Shrier, Clara, Shulman, Lisa, Siegel, Matt, Simon, Andrea, Simon, Laura, Singh, Arushi, Singh, Vini, Smalley, Devin, Smith, Kaitlin, Smith, Chris, Smith, Ashlyn, Soorya, Latha, Soscia, Julia, Soucy, Aubrie, Stchur, Laura, Steele, Morgan, Srishyla, Diksha, Stamps, Danielle, Sussman, Nicole, Swanson, Amy, Sweeney, Megan, Sziklay, Anthony, Tafolla, Maira, Taiba, Jabeen, Takahashi, Nicole, Terroso, Sydney, Strathearn, Camilla, Thomas, Taylor, Thompson, Samantha, Touchette, Ellyn, Townsend, Laina, Trog, Madison, Tsai, Katherine, Tseng, Angela, Tshering, Paullani, Tso, Ivy, Valicenti-Mcdermott, Maria, VanMetre, Bonnie, VanWade, Candace, Turecki, Samuel, Vargo, Kerrigan, Vattuone, Cristiana, Veenstra-Vanderweele, Jeremy, Vehorn, Alison, Benitez Velazquez, Alan Jesus, Verdi, Mary, Villalobos, Michele, Vrittamani, Lakshmi, Wainer, Allison, Wallace, Jermel, Walston, Corrie, Wang, Jiayaho, Ward, Audrey, Warren, Zachary, Washington, Katherine, Westerkamp, Grace, White, Sabrina, Wink, Logan, Winoto, Fiona, Winters, Sarah, Wodka, Ericka, Xavier, Samantha, Xu, Sidi, Yang, Yi, Yang, WhaJames, Yang, Amy, Yinger, Meredith, Yu, Timothy, Zaro, Christopher, Zha, Cindy, Zhang, Haicang, Zhao, Haoquan, Zick, Allyson, Salmon, Lauren Ziegelmayer, Shen, Yufeng, Volfovsky, Natalia, Hall, Jacob B., Feliciano, Pamela, and Chung, Wendy K.

Abstract

The aim of this study is to identify likely pathogenic (LP) and pathogenic (P) genetic results for autism that can be returned to participants in SPARK (SPARKforAutism.org): a large recontactable cohort of people with autism in the United States. We also describe the process to return these clinically confirmed genetic findings.

Published
2024
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37. Beliefs in vaccine as causes of autism among SPARK cohort caregivers

Author

Fombonne, Eric, primary, Goin-Kochel, Robin P., additional, O'Roak, Brian J., additional, Abbeduto, Leonard, additional, Aberbach, Gabriella, additional, Acampado, John, additional, Ace, Andrea J., additional, Albright, Charles, additional, Alessandri, Michael, additional, Amaral, David G., additional, Amatya, Alpha, additional, Anglo, Claudine, additional, Annett, Robert D., additional, Arriaga, Ivette, additional, Ashley, Raven, additional, Astrovskaya, Irina, additional, Baalman, Kelly, additional, Baer, Melissa, additional, Bahl, Ethan, additional, Balasubramanian, Adithya, additional, Baraghoshi, Gabrielle, additional, Bardett, Nicole, additional, Barnard, Rebecca A., additional, Bashar, Asif, additional, Beaudet, Arthur, additional, Beckwith, Malia, additional, Beeson, Landon, additional, Bentley, Dawn, additional, Bernier, Raphael A., additional, Berry-Kravis, Elizabeth, additional, Boland, Sarah, additional, Booker, Stephanie, additional, Bradley, Catherine, additional, Brewster, Stephanie J., additional, Brooks, Elizabeth, additional, Brown, Melissa, additional, Brueggeman, Leo, additional, Butler, Martin E., additional, Butter, Eric M., additional, Callahan, Kristen, additional, Camba, Alexies, additional, Carbone, Paul, additional, Carpenter, Laura, additional, Carpenter, Sarah, additional, Carriero, Nicholas, additional, Cartner, Lindsey A., additional, Casten, Lucas, additional, Chatha, Ahmad S., additional, Chin, Wubin, additional, Chintalapalli, Sharmista, additional, Cho, Daniel, additional, Chung, Wendy K., additional, Clark, Renee D., additional, Cohen, Cheryl, additional, Coleman, Kendra, additional, Columbi, Costanza, additional, Coppola, Leigh, additional, Courchesne, Eric, additional, Cubells, Joseph F., additional, Hannah Currin, Mary, additional, Daniels, Amy M., additional, David, Giancarla, additional, DeMarco, Lindsey, additional, Dennis, Megan Y., additional, Dent, Kate, additional, Dichter, Gabriel S., additional, Ding, Yan, additional, Dinh, Huyen, additional, Doan, Ryan, additional, Doddapaneni, HarshaVardhan, additional, Eichler, Evan E., additional, Eldred, Sara, additional, Eng, Christine, additional, Erickson, Craig A., additional, Esler, Amy, additional, Fatemi, Ali, additional, Feliciano, Pamela, additional, Fischer, Gregory, additional, Fish, Angela, additional, Fisk, Ian, additional, Fombonne, Eric J., additional, Foster, Margaret, additional, Fox, Emily A., additional, Francis, Sunday, additional, Friedman, Sandra L., additional, Ganesan, Swami, additional, Garrett, Michael, additional, Gazestani, Vahid, additional, Geisheker, Madeleine R., additional, Gerdts, Jennifer A., additional, Geschwind, Daniel H., additional, Ghaziuddin, Mohammad, additional, Gibbs, Richard A., additional, Gonzalez, Natalia, additional, Goudreau, Lindsey, additional, Griswold, Anthony J., additional, Grosvenor, Luke P., additional, Gruber, Angela J., additional, Gulsrud, Amanda C., additional, Gunderson, Jaclyn, additional, Gunter, Chris, additional, Gupta, Abha, additional, Gutierrez, Anibal, additional, Hale, Melissa N., additional, Haley, Monica, additional, Hall, Jacob B., additional, Hamer, Kira E., additional, Han, Bing, additional, Hanna, Nathan, additional, Hardan, Antonio, additional, Harkins, Christina, additional, Harrington, Gloria, additional, Harris, Jill, additional, Harris, Nina, additional, Hauf, Brenda, additional, Hayes, Caitlin, additional, Heerwagen, Kathryn, additional, Hepburn, Susan L., additional, Herbert, Lynette M., additional, Heyman, Michelle, additional, Higgins, Lorrin, additional, Hilscher, Brittani A., additional, Hofammann, Eugenia, additional, Hojlo, Margaret, additional, Horner, Susannah, additional, Hsieh, Alexander, additional, Hu, Jianhong, additional, Huang-Storms, Lark Y., additional, Hunter, Samantha, additional, Hutter, Hanna, additional, Istephanous, Dalia, additional, Jacob, Suma, additional, Jaramillo, Nancy, additional, Jelinek, Anna, additional, Jensen, William, additional, Jones, Mark, additional, Jordy, Michelle, additional, Jorgenson, Alissa, additional, Jou, Roger, additional, Pablo Juarez, A., additional, Judge, Jessyca, additional, Jurayj, Jane, additional, Kalmus, Taylor, additional, Kanne, Stephen, additional, Kaplan, Hannah E., additional, Kasparson, Lauren, additional, Kent, Matt, additional, Hyun Kim, So, additional, Kitaygorodsky, Alex, additional, Koene, Hope, additional, Koomar, Tanner, additional, Korchina, Viktoriya, additional, Krentz, Anthony D., additional, Lam Schneider, Hoa, additional, Lamarche, Elena, additional, Lampert, Erica, additional, Landa, Rebecca J., additional, Lash, Alex E., additional, Kiely Law, J., additional, Lawson, Noah, additional, Layman, Kevin, additional, Lechniak, Holly, additional, Lee, Sandra, additional, Lee, Soo J., additional, Lee Coury, Daniel, additional, Lese Martin, Christa, additional, Lesher, Laurie, additional, Li, Hai, additional, Li, Deana, additional, Lillie, Natasha, additional, Liu, Xiuping, additional, Lopez, Marilyn, additional, Lord, Catherine, additional, Lowe, Kathryn, additional, Mallardi, Malcolm D., additional, Manning, Patricia, additional, Manoharan, Julie, additional, Marini, Richard, additional, Martin, Christa, additional, Marzano, Gabriela, additional, Mason, Andrew, additional, Mastel, Sarah, additional, Matthews, Emily T., additional, McCracken, James T., additional, McKenzie, Alexander P., additional, Miceli, Alexandra, additional, Michaelson, Jacob J., additional, Milliken, Anna, additional, Mohiuddin, Sarah, additional, Momin, Zeineen, additional, Morrier, Michael J., additional, Mostofsky, Stewart, additional, Murali, Shwetha, additional, Muzny, Donna, additional, Myers, Vincent J., additional, Neely, Jason, additional, Nessner, Caitlin, additional, Nicholson, Amy, additional, Niederhouser, Melanie, additional, O'Brien, Kaela, additional, O'Connor, Eirene, additional, O'Neil, Molly, additional, Ochoa-Lubinoff, Cesar, additional, Orobio, Jessica, additional, Orrick, Libby, additional, Ortiz, Crissy, additional, Ousley, Opal Y., additional, Pacheco, Lillian D., additional, Palmer, Samiza, additional, Pandey, Juhi, additional, Marie Paolicelli, Anna, additional, Pawlowski, Katherine G., additional, Pierce, Karen L., additional, Piven, Joseph, additional, Plate, Samantha, additional, Polanco, Jose, additional, Popp, Marc, additional, Pottschmidt, Natalie, additional, Pramparo, Tiziano, additional, Prock, Lisa M., additional, Qi, Hongjian, additional, Qiu, Shanping, additional, Rachubinski, Angela L., additional, Rajbhandari, Kshitij, additional, Rana, Rishiraj, additional, Ranganathan, Vai, additional, Raymond, Laurie, additional, Remington, Rick, additional, Rice, Catherine E., additional, Rigby, Chris, additional, Robertson, Beverly E., additional, Rodriguez, Nicki, additional, Rodriguez, Barbara, additional, Roeder, Katherine, additional, Rosenberg, Cordelia R., additional, Russo-Ponsaran, Nicole, additional, Ruzzo, Elizabeth, additional, Sabo, Aniko, additional, Sahin, Mustafa, additional, Salomatov, Andrei, additional, Sandhu, Sophia, additional, Santangelo, Susan, additional, Sarver, Dustin E., additional, Scherr, Jessica, additional, Schultz, Robert T., additional, Schweers, Kathryn A., additional, Shaffer, Rebecca, additional, Shah, Swapnil, additional, Shaikh, Tamim, additional, Shen, Yufeng, additional, Shocklee, Amanda D., additional, Shulman, Lisa, additional, Siegel, Matthew, additional, Simon, Andrea R., additional, Simon, Laura, additional, Singh, Vini, additional, Skinner, Steve, additional, Smith, Christopher J., additional, Smith, Kaitlin, additional, Snyder, LeeAnne G., additional, Soorya, Latha V., additional, Soucy, Aubrie, additional, Stamps, Danielle, additional, Steele, Morgan, additional, Stephens, Alexandra N., additional, Stock, Colleen M., additional, Sullivan, Catherine, additional, Sutcliffe, James S., additional, Swanson, Amy, additional, Tafolla, Maira, additional, Takahashi, Nicole, additional, Taylor, Cora, additional, Thomas, Carrie, additional, Thomas, Taylor, additional, Thompson, Samantha, additional, Tjernagel, Jennifer, additional, Turner, Tychele N., additional, Valicenti-McDermott, Maria, additional, Van Metre, Bonnie, additional, Van Wade, Candace, additional, Veenstra-Vanderweele, Jeremy, additional, Verdi, Mary, additional, Vernoia, Brianna M., additional, Volfovsky, Natalia, additional, Wallace, Jermel, additional, Walston, Corrie H., additional, Wang, Jiayao, additional, Wang, Tianyun, additional, Warren, Zachary, additional, Wasserburg, Lucy, additional, White, Sabrina, additional, Casey White-Lehman, L., additional, Wodka, Ericka L., additional, Xu, Simon, additional, Yang, Wha S., additional, Yinger, Meredith, additional, Youngkin, Sarah, additional, Yu, Timothy, additional, Zang, Lan, additional, Zaydens, Hana, additional, Zhang, Haicang, additional, Zhao, Haoquan, additional, Zhou, Xueya, additional, and Zick, Allyson, additional

Published
2020
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40. De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders

Author

Qi, Hongjian, primary, Yu, Lan, additional, Zhou, Xueya, additional, Wynn, Julia, additional, Zhao, Haoquan, additional, Guo, Yicheng, additional, Zhu, Na, additional, Kitaygorodsky, Alexander, additional, Hernan, Rebecca, additional, Aspelund, Gudrun, additional, Lim, Foong-Yen, additional, Crombleholme, Timothy, additional, Cusick, Robert, additional, Azarow, Kenneth, additional, Danko, Melissa E., additional, Chung, Dai, additional, Warner, Brad W., additional, Mychaliska, George B., additional, Potoka, Douglas, additional, Wagner, Amy J., additional, ElFiky, Mahmoud, additional, Wilson, Jay M., additional, Nickerson, Debbie, additional, Bamshad, Michael, additional, High, Frances A., additional, Longoni, Mauro, additional, Donahoe, Patricia K., additional, Chung, Wendy K., additional, and Shen, Yufeng, additional

Published
2018
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41. Trans-Ethnic Polygenic Analysis Supports Genetic Overlaps of Lumbar Disc Degeneration With Height, Body Mass Index, and Bone Mineral Density

Author

Zhou, Xueya, primary, Cheung, Ching-Lung, additional, Karasugi, Tatsuki, additional, Karppinen, Jaro, additional, Samartzis, Dino, additional, Hsu, Yi-Hsiang, additional, Mak, Timothy Shin-Heng, additional, Song, You-Qiang, additional, Chiba, Kazuhiro, additional, Kawaguchi, Yoshiharu, additional, Li, Yan, additional, Chan, Danny, additional, Cheung, Kenneth Man-Chee, additional, Ikegawa, Shiro, additional, Cheah, Kathryn Song-Eng, additional, and Sham, Pak Chung, additional

Published
2018
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42. Genetic analysis ofde novovariants reveals sex differences in complex and isolated congenital diaphragmatic hernia and indicatesMYRFas a candidate gene

Author

Qi, Hongjian, primary, Yu, Lan, additional, Zhou, Xueya, additional, Kitaygorodsky, Alexander, additional, Wynn, Julia, additional, Zhu, Na, additional, Aspelund, Gudrun, additional, Lim, Foong Yen, additional, Crombleholme, Timothy, additional, Cusick, Robert, additional, Azarow, Kenneth, additional, Danko, Melissa Ellen, additional, Chung, Dai, additional, Warner, Brad W., additional, Mychaliska, George B., additional, Potoka, Douglas, additional, Wagner, Amy J., additional, ElFiky, Mahmoud, additional, Nickerson, Deborah A., additional, Bamshad, Michael J., additional, Wilson, Jay M., additional, High, Frances A., additional, Longoni, Mauro, additional, Donahoe, Patricia, additional, Chung, Wendy K., additional, and Shen, Yufeng, additional

Published
2017
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47. Genome-wide Association Analysis of Blood-Pressure Traits in African-Ancestry Individuals Reveals Common Associated Genes in African and Non-African Populations

Author

Go, Min Jin, Kim, Young Jin, Lee, Jong-Young, Jeon, Jae-Pil, Kim, Sung Soo, Han, Bok-Ghee, Cho, Yoon Shin, Sim, Xueling, Tay, Wan Ting, Ong, Rick Twee Hee, Seielstad, Mark, Liu, Jian Jun, Aung, Tin, Wong, Tien Yin, Teo, Yik Ying, Tai, E. Shyong, Chen, Chien-Hsiun, Chang, Li-ching, Chen, Yuan-Tsong, Wu, Jer-Yuarn, Kelly, Tanika N., Gu, Dongfeng, Hixson, James E., Sung, Yun Ju, He, Jiang, Tabara, Yasuharu, Kokubo, Yoshihiro, Miki, Tetsuro, Iwai, Naoharu, Kato, Norihiro, Takeuchi, Fumihiko, Katsuya, Tomohiro, Nabika, Toru, Sugiyama, Takao, Zhang, Yi, Huang, Wei, Zhang, Xuegong, Zhou, Xueya, Jin, Li, Zhu, Dingliang, Franceschini, Nora, Fox, Ervin, Zhang, Zhaogong, Edwards, Todd L., Nalls, Michael A., Tayo, Bamidele O., Sun, Yan V., Gottesman, Omri, Adeyemo, Adebawole, Johnson, Andrew D., Young, J. Hunter, Rice, Ken, Duan, Qing, Chen, Fang, Li, Yun, Tang, Hua, Fornage, Myriam, Keene, Keith L., Andrews, Jeanette S., Smith, Jennifer A., Faul, Jessica D., Guangfa, Zhang, Guo, Wei, Liu, Yu, Murray, Sarah S., Musani, Solomon K., Srinivasan, Sathanur, Velez Edwards, Digna R., Wang, Heming, Becker, Lewis C., Bovet, Pascal, Bochud, Murielle, Broeckel, Ulrich, Burnier, Michel, Carty, Cara, Chasman, Daniel I., Ehret, Georg, Chen, Wei-Min, Chen, Guanjie, Chen, Wei, Ding, Jingzhong, Dreisbach, Albert W., Evans, Michele K., Guo, Xiuqing, Garcia, Melissa E., Jensen, Rich, Keller, Margaux F., Lettre, Guillaume, Lotay, Vaneet, Martin, Lisa W., Moore, Jason H., Morrison, Alanna C., Mosley, Thomas H., Ogunniyi, Adesola, Palmas, Walter, Papanicolaou, George, Penman, Alan, Polak, Joseph F., Ridker, Paul M., Salako, Babatunde, Singleton, Andrew B., Shriner, Daniel, Taylor, Kent D., Vasan, Ramachandran, Wiggins, Kerri, Williams, Scott M., Yanek, Lisa R., Zhao, Wei, Zonderman, Alan B., Becker, Diane M., Berenson, Gerald, Boerwinkle, Eric, Bottinger, Erwin, Cushman, Mary, Eaton, Charles, Nyberg, Fredrik, Heiss, Gerardo, Hirschhron, Joel N., Howard, Virginia J., Karczewsk, Konrad J., Lanktree, Matthew B., Liu, Kiang, Liu, Yongmei, Loos, Ruth, Margolis, Karen, Snyder, Michael, Psaty, Bruce M., Schork, Nicholas J., Weir, David R., Rotimi, Charles N., Sale, Michele M., Harris, Tamara, Kardia, Sharon L.R., Hunt, Steven C., Arnett, Donna, Redline, Susan, Cooper, Richard S., Risch, Neil J., Rao, D.C., Rotter, Jerome I., Chakravarti, Aravinda, Reiner, Alex P., Levy, Daniel, Keating, Brendan J., and Zhu, Xiaofeng

Published
2013
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50. CNV analysis in Chinese children of mental retardation highlights a sex differentiation in parental contribution to de novo and inherited mutational burdens

Author

Wang, Binbin, primary, Ji, Taoyun, additional, Zhou, Xueya, additional, Wang, Jing, additional, Wang, Xi, additional, Wang, Jingmin, additional, Zhu, Dingliang, additional, Zhang, Xuejun, additional, Sham, Pak Chung, additional, Zhang, Xuegong, additional, Ma, Xu, additional, and Jiang, Yuwu, additional

Published
2016
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