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1. SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing

Author

Danis, Daniel, Jacobsen, Julius OB, Balachandran, Parithi, Zhu, Qihui, Yilmaz, Feyza, Reese, Justin, Haimel, Matthias, Lyon, Gholson J, Helbig, Ingo, Mungall, Christopher J, Beck, Christine R, Lee, Charles, Smedley, Damian, and Robinson, Peter N

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Generic health relevance, Good Health and Well Being, Base Sequence, Chromosome Mapping, Genomics, Humans, Sequence Analysis, DNA, Virulence, Long-read sequencing, Structural variant, Whole genome sequencing, Clinical Sciences
Abstract

Structural variants (SVs) are implicated in the etiology of Mendelian diseases but have been systematically underascertained owing to sequencing technology limitations. Long-read sequencing enables comprehensive detection of SVs, but approaches for prioritization of candidate SVs are needed. Structural variant Annotation and analysis (SvAnna) assesses all classes of SVs and their intersection with transcripts and regulatory sequences, relating predicted effects on gene function with clinical phenotype data. SvAnna places 87% of deleterious SVs in the top ten ranks. The interpretable prioritizations offered by SvAnna will facilitate the widespread adoption of long-read sequencing in diagnostic genomics. SvAnna is available at https://github.com/TheJacksonLaboratory/SvAnn a .

Published
2022

2. Assembly of 43 human Y chromosomes reveals extensive complexity and variation

Author

Hallast, Pille, Ebert, Peter, Loftus, Mark, Yilmaz, Feyza, Audano, Peter A., Logsdon, Glennis A., Bonder, Marc Jan, Zhou, Weichen, Höps, Wolfram, Kim, Kwondo, Li, Chong, Hoyt, Savannah J., Dishuck, Philip C., Porubsky, David, Tsetsos, Fotios, Kwon, Jee Young, Zhu, Qihui, Munson, Katherine M., Hasenfeld, Patrick, Harvey, William T., Lewis, Alexandra P., Kordosky, Jennifer, Hoekzema, Kendra, O’Neill, Rachel J., Korbel, Jan O., Tyler-Smith, Chris, Eichler, Evan E., Shi, Xinghua, Beck, Christine R., Marschall, Tobias, Konkel, Miriam K., and Lee, Charles

Published
2023
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3. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers

Author

Kim, Hoon, Nguyen, Nam-Phuong, Turner, Kristen, Wu, Sihan, Gujar, Amit D, Luebeck, Jens, Liu, Jihe, Deshpande, Viraj, Rajkumar, Utkrisht, Namburi, Sandeep, Amin, Samirkumar B, Yi, Eunhee, Menghi, Francesca, Schulte, Johannes H, Henssen, Anton G, Chang, Howard Y, Beck, Christine R, Mischel, Paul S, Bafna, Vineet, and Verhaak, Roel GW

Subjects
Biological Sciences, Genetics, Cancer, Cancer Genomics, Biotechnology, Human Genome, Rare Diseases, Women's Health, Breast Cancer, 2.1 Biological and endogenous factors, Cell Line, Tumor, Chromatin, Chromosomes, DNA, Gene Amplification, Humans, Neoplasms, Oncogenes, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Extrachromosomal DNA (ecDNA) amplification promotes intratumoral genetic heterogeneity and accelerated tumor evolution1-3; however, its frequency and clinical impact are unclear. Using computational analysis of whole-genome sequencing data from 3,212 cancer patients, we show that ecDNA amplification frequently occurs in most cancer types but not in blood or normal tissue. Oncogenes were highly enriched on amplified ecDNA, and the most common recurrent oncogene amplifications arose on ecDNA. EcDNA amplifications resulted in higher levels of oncogene transcription compared to copy number-matched linear DNA, coupled with enhanced chromatin accessibility, and more frequently resulted in transcript fusions. Patients whose cancers carried ecDNA had significantly shorter survival, even when controlled for tissue type, than patients whose cancers were not driven by ecDNA-based oncogene amplification. The results presented here demonstrate that ecDNA-based oncogene amplification is common in cancer, is different from chromosomal amplification and drives poor outcome for patients across many cancer types.

Published
2020

7. Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders

Author

Porubsky, David, Höps, Wolfram, Ashraf, Hufsah, Hsieh, PingHsun, Rodriguez-Martin, Bernardo, Yilmaz, Feyza, Ebler, Jana, Hallast, Pille, Maria Maggiolini, Flavia Angela, Harvey, William T., Henning, Barbara, Audano, Peter A., Gordon, David S., Ebert, Peter, Hasenfeld, Patrick, Benito, Eva, Zhu, Qihui, Lee, Charles, Antonacci, Francesca, Steinrücken, Matthias, Beck, Christine R., Sanders, Ashley D., Marschall, Tobias, Eichler, Evan E., and Korbel, Jan O.

Published
2022
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8. Centers for Mendelian Genomics: A decade of facilitating gene discovery

Author

Adams, Marcia, Aguet, François, Akay, Gulsen, Anderson, Peter, Antonescu, Corina, Arachchi, Harindra M., Atik, Mehmed M., Austin-Tse, Christina A., Babb, Larry, Bacus, Tamara J., Bahrambeigi, Vahid, Balasubramanian, Suganthi, Bayram, Yavuz, Beaudet, Arthur L., Beck, Christine R., Belmont, John W., Below, Jennifer E., Bilguvar, Kaya, Boehm, Corinne D., Boerwinkle, Eric, Boone, Philip M., Bowne, Sara J., Brand, Harrison, Buckingham, Kati J., Byrne, Alicia B., Calame, Daniel, Campbell, Ian M., Cao, Xiaolong, Carvalho, Claudia, Chander, Varuna, Chang, Jaime, Chao, Katherine R., Chinn, Ivan K., Clarke, Declan, Collins, Ryan L., Cummings, Beryl, Dardas, Zain, Dawood, Moez, Delano, Kayla, DiTroia, Stephanie P., Doddapaneni, Harshavardhan, Du, Haowei, Du, Renqian, Duan, Ruizhi, Eldomery, Mohammad, Eng, Christine M., England, Eleina, Evangelista, Emily, Everett, Selin, Fatih, Jawid, Felsenfeld, Adam, Francioli, Laurent C., Frazar, Christian D., Fu, Jack, Gamarra, Emmanuel, Gambin, Tomasz, Gan, Weiniu, Gandhi, Mira, Ganesh, Vijay S., Garimella, Kiran V., Gauthier, Laura D., Giroux, Danielle, Gonzaga-Jauregui, Claudia, Goodrich, Julia K., Gordon, William W., Griffith, Sean, Grochowski, Christopher M., Gu, Shen, Gudmundsson, Sanna, Hall, Stacey J., Hansen, Adam, Harel, Tamar, Harmanci, Arif O., Herman, Isabella, Hetrick, Kurt, Hijazi, Hadia, Horike-Pyne, Martha, Hsu, Elvin, Hu, Jianhong, Huang, Yongqing, Hurless, Jameson R., Jahl, Steve, Jarvik, Gail P., Jiang, Yunyun, Johanson, Eric, Jolly, Angad, Karaca, Ender, Khayat, Michael, Knight, James, Kolar, J. Thomas, Kumar, Sushant, Lalani, Seema, Laricchia, Kristen M., Larkin, Kathryn E., Leal, Suzanne M., Lemire, Gabrielle, Lewis, Richard A., Li, He, Ling, Hua, Lipson, Rachel B., Liu, Pengfei, Lovgren, Alysia Kern, López-Giráldez, Francesc, MacMillan, Melissa P., Mangilog, Brian E., Mano, Stacy, Marafi, Dana, Marosy, Beth, Marshall, Jamie L., Martin, Renan, Marvin, Colby T., Mawhinney, Michelle, McGee, Sean, McGoldrick, Daniel J., Mehaffey, Michelle, Mekonnen, Betselote, Meng, Xiaolu, Mitani, Tadahiro, Miyake, Christina Y., Mohr, David, Morris, Shaine, Mullen, Thomas E., Murdock, David R., Murugan, Mullai, Muzny, Donna M., Myers, Ben, Neira, Juanita, Nguyen, Kevin K., Nielsen, Patrick M., Nudelman, Natalie, O’Heir, Emily, O’Leary, Melanie C., Ongaco, Chrissie, Orange, Jordan, Osei-Owusu, Ikeoluwa A., Paine, Ingrid S., Pais, Lynn S., Paschall, Justin, Patterson, Karynne, Pehlivan, Davut, Pelle, Benjamin, Penney, Samantha, Perez de Acha Chavez, Jorge, Pierce-Hoffman, Emma, Poli, Cecilia M., Punetha, Jaya, Radhakrishnan, Aparna, Richardson, Matthew A., Rodrigues, Eliete, Roote, Gwendolin T., Rosenfeld, Jill A., Ryke, Erica L., Sabo, Aniko, Sanchez, Alice, Schrauwen, Isabelle, Scott, Daryl A., Sedlazeck, Fritz, Serrano, Jillian, Shaw, Chad A., Shelford, Tameka, Shively, Kathryn M., Singer-Berk, Moriel, Smith, Joshua D., Snow, Hana, Snyder, Grace, Solomonson, Matthew, Son, Rachel G., Song, Xiaofei, Stankiewicz, Pawel, Stephan, Taylorlyn, Sutton, V. Reid, Sveden, Abigail, Sánchez, Diana Cornejo, Tackett, Monica, Talkowski, Michael, Threlkeld, Machiko S., Tiao, Grace, Udler, Miriam S., Vail, Laura, Valivullah, Zaheer, Valkanas, Elise, VanNoy, Grace E., Wang, Qingbo S., Wang, Gao, Wang, Lu, Wangler, Michael F., Watts, Nicholas A., Weisburd, Ben, Weiss, Jeffrey M., Wheeler, Marsha M., White, Janson J., Williamson, Clara E., Wilson, Michael W., Wiszniewski, Wojciech, Withers, Marjorie A., Witmer, Dane, Witzgall, Lauren, Wohler, Elizabeth, Wojcik, Monica H., Wong, Isaac, Wood, Jordan C., Wu, Nan, Xing, Jinchuan, Yang, Yaping, Yi, Qian, Yuan, Bo, Zeiger, Jordan E., Zhang, Chaofan, Zhang, Peng, Zhang, Yan, Zhang, Xiaohong, Zhang, Yeting, Zhang, Shifa, Zoghbi, Huda, van den Veyver, Igna, Baxter, Samantha M., Posey, Jennifer E., Lake, Nicole J., Sobreira, Nara, Chong, Jessica X., Buyske, Steven, Blue, Elizabeth E., Chadwick, Lisa H., Coban-Akdemir, Zeynep H., Doheny, Kimberly F., Davis, Colleen P., Lek, Monkol, Wellington, Christopher, Jhangiani, Shalini N., Gerstein, Mark, Gibbs, Richard A., Lifton, Richard P., MacArthur, Daniel G., Matise, Tara C., Lupski, James R., Valle, David, Bamshad, Michael J., Hamosh, Ada, Mane, Shrikant, Nickerson, Deborah A., Rehm, Heidi L., and O’Donnell-Luria, Anne

Published
2022
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11. Impact and characterization of serial structural variations across humans and great apes.

Author

Höps, Wolfram, Rausch, Tobias, Jendrusch, Michael, Human Genome Structural Variation Consortium (HGSVC), Ashraf, Hufsah, Audano, Peter A., Austine, Ola, Basile, Anna O., Beck, Christine R., Jan Bonder, Marc, Byrska-Bishop, Marta, Chaisson, Mark J. P., Chong, Zechen, Corvelo, André, Devine, Scott E., Ebert, Peter, Ebler, Jana, Eichler, Evan E., Gerstein, Mark B., and Hallast, Pille

Subjects
GENE rearrangement, HOMOLOGOUS recombination, HOMINIDS, GENOMES, ALLELES
Abstract

Modern sequencing technology enables the systematic detection of complex structural variation (SV) across genomes. However, extensive DNA rearrangements arising through a series of mutations, a phenomenon we refer to as serial SV (sSV), remain underexplored, posing a challenge for SV discovery. Here, we present NAHRwhals (https://github.com/WHops/NAHRwhals), a method to infer repeat-mediated series of SVs in long-read genomic assemblies. Applying NAHRwhals to haplotype-resolved human genomes from 28 individuals reveals 37 sSV loci of various length and complexity. These sSVs explain otherwise cryptic variation in medically relevant regions such as the TPSAB1 gene, 8p23.1, 22q11 and Sotos syndrome regions. Comparisons with great ape assemblies indicate that most human sSVs formed recently, after the human-ape split, and involved non-repeat-mediated processes in addition to non-allelic homologous recombination. NAHRwhals reliably discovers and characterizes sSVs at scale and independent of species, uncovering their genomic abundance and suggesting broader implications for disease. Structural variants (SV) can accumulate in repeat-rich parts of the genome and transform them in unexpected ways. Here, with their new assembly-based genotyper (NAHRwhals), the authors verify multi-step SVs in 37 human loci and identify alleles at risk for copy-number variation. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Primary immunodeficiency diseases: Genomic approaches delineate heterogeneous Mendelian disorders

Author

Stray-Pedersen, Asbjørg, Sorte, Hanne Sørmo, Samarakoon, Pubudu, Gambin, Tomasz, Chinn, Ivan K, Akdemir, Zeynep H Coban, Erichsen, Hans Christian, Forbes, Lisa R, Gu, Shen, Yuan, Bo, Jhangiani, Shalini N, Muzny, Donna M, Rødningen, Olaug Kristin, Sheng, Ying, Nicholas, Sarah K, Noroski, Lenora M, Seeborg, Filiz O, Davis, Carla M, Canter, Debra L, Mace, Emily M, Vece, Timothy J, Allen, Carl E, Abhyankar, Harshal A, Boone, Philip M, Beck, Christine R, Wiszniewski, Wojciech, Fevang, Børre, Aukrust, Pål, Tjønnfjord, Geir E, Gedde-Dahl, Tobias, Hjorth-Hansen, Henrik, Dybedal, Ingunn, Nordøy, Ingvild, Jørgensen, Silje F, Abrahamsen, Tore G, Øverland, Torstein, Bechensteen, Anne Grete, Skogen, Vegard, Osnes, Liv TN, Kulseth, Mari Ann, Prescott, Trine E, Rustad, Cecilie F, Heimdal, Ketil R, Belmont, John W, Rider, Nicholas L, Chinen, Javier, Cao, Tram N, Smith, Eric A, Caldirola, Maria Soledad, Bezrodnik, Liliana, Reyes, Saul Oswaldo Lugo, Rosales, Francisco J Espinosa, Guerrero-Cursaru, Nina Denisse, Pedroza, Luis Alberto, Poli, Cecilia M, Franco, Jose L, Vargas, Claudia M Trujillo, Becerra, Juan Carlos Aldave, Wright, Nicola, Issekutz, Thomas B, Issekutz, Andrew C, Abbott, Jordan, Caldwell, Jason W, Bayer, Diana K, Chan, Alice Y, Aiuti, Alessandro, Cancrini, Caterina, Holmberg, Eva, West, Christina, Burstedt, Magnus, Karaca, Ender, Yesil, Gözde, Artac, Hasibe, Bayram, Yavuz, Atik, Mehmed Musa, Eldomery, Mohammad K, Ehlayel, Mohammad S, Jolles, Stephen, Flatø, Berit, Bertuch, Alison A, Hanson, I Celine, Zhang, Victor W, Wong, Lee-Jun, Hu, Jianhong, Walkiewicz, Magdalena, Yang, Yaping, Eng, Christine M, Boerwinkle, Eric, Gibbs, Richard A, Shearer, William T, Lyle, Robert, Orange, Jordan S, and Lupski, James R

Subjects
Biomedical and Clinical Sciences, Immunology, Human Genome, Prevention, Clinical Research, Genetic Testing, Genetics, Rare Diseases, 2.1 Biological and endogenous factors, Detection, screening and diagnosis, 4.1 Discovery and preclinical testing of markers and technologies, Aetiology, Good Health and Well Being, Adolescent, Adult, Aged, Child, Child, Preschool, DNA Copy Number Variations, Female, Genomics, High-Throughput Nucleotide Sequencing, Humans, Immunologic Deficiency Syndromes, Infant, Male, Middle Aged, Young Adult, Primary immunodeficiency disease, whole-exome sequencing, copy number variants, Allergy
Abstract

BackgroundPrimary immunodeficiency diseases (PIDDs) are clinically and genetically heterogeneous disorders thus far associated with mutations in more than 300 genes. The clinical phenotypes derived from distinct genotypes can overlap. Genetic etiology can be a prognostic indicator of disease severity and can influence treatment decisions.ObjectiveWe sought to investigate the ability of whole-exome screening methods to detect disease-causing variants in patients with PIDDs.MethodsPatients with PIDDs from 278 families from 22 countries were investigated by using whole-exome sequencing. Computational copy number variant (CNV) prediction pipelines and an exome-tiling chromosomal microarray were also applied to identify intragenic CNVs. Analytic approaches initially focused on 475 known or candidate PIDD genes but were nonexclusive and further tailored based on clinical data, family history, and immunophenotyping.ResultsA likely molecular diagnosis was achieved in 110 (40%) unrelated probands. Clinical diagnosis was revised in about half (60/110) and management was directly altered in nearly a quarter (26/110) of families based on molecular findings. Twelve PIDD-causing CNVs were detected, including 7 smaller than 30 Kb that would not have been detected with conventional diagnostic CNV arrays.ConclusionThis high-throughput genomic approach enabled detection of disease-related variants in unexpected genes; permitted detection of low-grade constitutional, somatic, and revertant mosaicism; and provided evidence of a mutational burden in mixed PIDD immunophenotypes.

Published
2017

13. Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2

Author

Beck, Christine R., Carvalho, Claudia M.B., Akdemir, Zeynep C., Sedlazeck, Fritz J., Song, Xiaofei, Meng, Qingchang, Hu, Jianhong, Doddapaneni, Harsha, Chong, Zechen, Chen, Edward S., Thornton, Philip C., Liu, Pengfei, Yuan, Bo, Withers, Marjorie, Jhangiani, Shalini N., Kalra, Divya, Walker, Kimberly, English, Adam C., Han, Yi, Chen, Ken, Muzny, Donna M., Ira, Grzegorz, Shaw, Chad A., Gibbs, Richard A., Hastings, P.J., and Lupski, James R.

Published
2019
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25. The Alu-Rich Genomic Architecture of SPAST Predisposes to Diverse and Functionally Distinct Disease-Associated CNV Alleles

Author

Boone, Philip M., Yuan, Bo, Campbell, Ian M., Scull, Jennifer C., Withers, Marjorie A., Baggett, Brett C., Beck, Christine R., Shaw, Christine J., Stankiewicz, Pawel, Moretti, Paolo, Goodwin, Wendy E., Hein, Nichole, Fink, John K., Seong, Moon-Woo, Seo, Soo Hyun, Park, Sung Sup, Karbassi, Izabela D., Batish, Sat Dev, Ordóñez-Ugalde, Andrés, Quintáns, Beatriz, Sobrido, María-Jesús, Stemmler, Susanne, and Lupski, James R.

Published
2014
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27. Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements

Author

Ferraj, Ardian, primary, Audano, Peter A., additional, Balachandran, Parithi, additional, Czechanski, Anne, additional, Flores, Jacob I., additional, Radecki, Alexander A., additional, Mosur, Varun, additional, Gordon, David S., additional, Walawalkar, Isha A., additional, Eichler, Evan E., additional, Reinholdt, Laura G., additional, and Beck, Christine R., additional

Published
2022
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29. Centers for Mendelian Genomics: A decade of facilitating gene discovery

Author

Baxter, Samantha M., primary, Posey, Jennifer E., additional, Lake, Nicole J., additional, Sobreira, Nara, additional, Chong, Jessica X., additional, Buyske, Steven, additional, Blue, Elizabeth E., additional, Chadwick, Lisa H., additional, Coban-Akdemir, Zeynep H., additional, Doheny, Kimberly F., additional, Davis, Colleen P., additional, Lek, Monkol, additional, Wellington, Christopher, additional, Jhangiani, Shalini N., additional, Gerstein, Mark, additional, Gibbs, Richard A., additional, Lifton, Richard P., additional, MacArthur, Daniel G., additional, Matise, Tara C., additional, Lupski, James R., additional, Valle, David, additional, Bamshad, Michael J., additional, Hamosh, Ada, additional, Mane, Shrikant, additional, Nickerson, Deborah A., additional, Rehm, Heidi L., additional, O’Donnell-Luria, Anne, additional, Adams, Marcia, additional, Aguet, François, additional, Akay, Gulsen, additional, Anderson, Peter, additional, Antonescu, Corina, additional, Arachchi, Harindra M., additional, Atik, Mehmed M., additional, Austin-Tse, Christina A., additional, Babb, Larry, additional, Bacus, Tamara J., additional, Bahrambeigi, Vahid, additional, Balasubramanian, Suganthi, additional, Bayram, Yavuz, additional, Beaudet, Arthur L., additional, Beck, Christine R., additional, Belmont, John W., additional, Below, Jennifer E., additional, Bilguvar, Kaya, additional, Boehm, Corinne D., additional, Boerwinkle, Eric, additional, Boone, Philip M., additional, Bowne, Sara J., additional, Brand, Harrison, additional, Buckingham, Kati J., additional, Byrne, Alicia B., additional, Calame, Daniel, additional, Campbell, Ian M., additional, Cao, Xiaolong, additional, Carvalho, Claudia, additional, Chander, Varuna, additional, Chang, Jaime, additional, Chao, Katherine R., additional, Chinn, Ivan K., additional, Clarke, Declan, additional, Collins, Ryan L., additional, Cummings, Beryl, additional, Dardas, Zain, additional, Dawood, Moez, additional, Delano, Kayla, additional, DiTroia, Stephanie P., additional, Doddapaneni, Harshavardhan, additional, Du, Haowei, additional, Du, Renqian, additional, Duan, Ruizhi, additional, Eldomery, Mohammad, additional, Eng, Christine M., additional, England, Eleina, additional, Evangelista, Emily, additional, Everett, Selin, additional, Fatih, Jawid, additional, Felsenfeld, Adam, additional, Francioli, Laurent C., additional, Frazar, Christian D., additional, Fu, Jack, additional, Gamarra, Emmanuel, additional, Gambin, Tomasz, additional, Gan, Weiniu, additional, Gandhi, Mira, additional, Ganesh, Vijay S., additional, Garimella, Kiran V., additional, Gauthier, Laura D., additional, Giroux, Danielle, additional, Gonzaga-Jauregui, Claudia, additional, Goodrich, Julia K., additional, Gordon, William W., additional, Griffith, Sean, additional, Grochowski, Christopher M., additional, Gu, Shen, additional, Gudmundsson, Sanna, additional, Hall, Stacey J., additional, Hansen, Adam, additional, Harel, Tamar, additional, Harmanci, Arif O., additional, Herman, Isabella, additional, Hetrick, Kurt, additional, Hijazi, Hadia, additional, Horike-Pyne, Martha, additional, Hsu, Elvin, additional, Hu, Jianhong, additional, Huang, Yongqing, additional, Hurless, Jameson R., additional, Jahl, Steve, additional, Jarvik, Gail P., additional, Jiang, Yunyun, additional, Johanson, Eric, additional, Jolly, Angad, additional, Karaca, Ender, additional, Khayat, Michael, additional, Knight, James, additional, Kolar, J. Thomas, additional, Kumar, Sushant, additional, Lalani, Seema, additional, Laricchia, Kristen M., additional, Larkin, Kathryn E., additional, Leal, Suzanne M., additional, Lemire, Gabrielle, additional, Lewis, Richard A., additional, Li, He, additional, Ling, Hua, additional, Lipson, Rachel B., additional, Liu, Pengfei, additional, Lovgren, Alysia Kern, additional, López-Giráldez, Francesc, additional, MacMillan, Melissa P., additional, Mangilog, Brian E., additional, Mano, Stacy, additional, Marafi, Dana, additional, Marosy, Beth, additional, Marshall, Jamie L., additional, Martin, Renan, additional, Marvin, Colby T., additional, Mawhinney, Michelle, additional, McGee, Sean, additional, McGoldrick, Daniel J., additional, Mehaffey, Michelle, additional, Mekonnen, Betselote, additional, Meng, Xiaolu, additional, Mitani, Tadahiro, additional, Miyake, Christina Y., additional, Mohr, David, additional, Morris, Shaine, additional, Mullen, Thomas E., additional, Murdock, David R., additional, Murugan, Mullai, additional, Muzny, Donna M., additional, Myers, Ben, additional, Neira, Juanita, additional, Nguyen, Kevin K., additional, Nielsen, Patrick M., additional, Nudelman, Natalie, additional, O’Heir, Emily, additional, O’Leary, Melanie C., additional, Ongaco, Chrissie, additional, Orange, Jordan, additional, Osei-Owusu, Ikeoluwa A., additional, Paine, Ingrid S., additional, Pais, Lynn S., additional, Paschall, Justin, additional, Patterson, Karynne, additional, Pehlivan, Davut, additional, Pelle, Benjamin, additional, Penney, Samantha, additional, Perez de Acha Chavez, Jorge, additional, Pierce-Hoffman, Emma, additional, Poli, Cecilia M., additional, Punetha, Jaya, additional, Radhakrishnan, Aparna, additional, Richardson, Matthew A., additional, Rodrigues, Eliete, additional, Roote, Gwendolin T., additional, Rosenfeld, Jill A., additional, Ryke, Erica L., additional, Sabo, Aniko, additional, Sanchez, Alice, additional, Schrauwen, Isabelle, additional, Scott, Daryl A., additional, Sedlazeck, Fritz, additional, Serrano, Jillian, additional, Shaw, Chad A., additional, Shelford, Tameka, additional, Shively, Kathryn M., additional, Singer-Berk, Moriel, additional, Smith, Joshua D., additional, Snow, Hana, additional, Snyder, Grace, additional, Solomonson, Matthew, additional, Son, Rachel G., additional, Song, Xiaofei, additional, Stankiewicz, Pawel, additional, Stephan, Taylorlyn, additional, Sutton, V. Reid, additional, Sveden, Abigail, additional, Sánchez, Diana Cornejo, additional, Tackett, Monica, additional, Talkowski, Michael, additional, Threlkeld, Machiko S., additional, Tiao, Grace, additional, Udler, Miriam S., additional, Vail, Laura, additional, Valivullah, Zaheer, additional, Valkanas, Elise, additional, VanNoy, Grace E., additional, Wang, Qingbo S., additional, Wang, Gao, additional, Wang, Lu, additional, Wangler, Michael F., additional, Watts, Nicholas A., additional, Weisburd, Ben, additional, Weiss, Jeffrey M., additional, Wheeler, Marsha M., additional, White, Janson J., additional, Williamson, Clara E., additional, Wilson, Michael W., additional, Wiszniewski, Wojciech, additional, Withers, Marjorie A., additional, Witmer, Dane, additional, Witzgall, Lauren, additional, Wohler, Elizabeth, additional, Wojcik, Monica H., additional, Wong, Isaac, additional, Wood, Jordan C., additional, Wu, Nan, additional, Xing, Jinchuan, additional, Yang, Yaping, additional, Yi, Qian, additional, Yuan, Bo, additional, Zeiger, Jordan E., additional, Zhang, Chaofan, additional, Zhang, Peng, additional, Zhang, Yan, additional, Zhang, Xiaohong, additional, Zhang, Yeting, additional, Zhang, Shifa, additional, Zoghbi, Huda, additional, and van den Veyver, Igna, additional

Published
2022
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30. Additional file 1 of SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing

Author

Danis, Daniel, Jacobsen, Julius O. B., Balachandran, Parithi, Zhu, Qihui, Yilmaz, Feyza, Reese, Justin, Haimel, Matthias, Lyon, Gholson J., Helbig, Ingo, Mungall, Christopher J., Beck, Christine R., Lee, Charles, Smedley, Damian, and Robinson, Peter N.

Abstract

Additional file 1: Table S1. Summary of VCF fields used to report depth of coverage. Fig. S1. Distribution of lengths of the curated structural variants. Figs. S2-S9. Examples of graphical displays generated for different types of structural variants. Fig. S10. Mean variant rank depending on the number of phenotype terms. Fig. S11. Screenshot of tabular and graphical summary generated for structural variants.

Published
2022
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31. Global transcriptional disturbances underlie Cornelia de Lange syndrome and related phenotypes

Author

Yuan, Bo, Pehlivan, Davut, Karaca, Ender, Patel, Nisha, Charng, Wu-Lin, Gambin, Tomasz, Gonzaga-Jauregui, Claudia, Sutton, V. Reid, Yesil, Gozde, Bozdogan, Sevcan Tug, Tos, Tulay, Koparir, Asuman, Koparir, Erkan, Beck, Christine R., Gu, Shen, Aslan, Huseyin, Yuregir, Ozge Ozalp, Rubeaan, Khalid Al, Alnaqeb, Dhekra, Alshammari, Muneera J., Bayram, Yavuz, Atik, Mehmed M., Aydin, Hatip, Geckinli, B. Bilge, Seven, Mehmet, Ulucan, Hakan, Fenercioglu, Elif, Ozen, Mustafa, Jhangiani, Shalini, Muzny, Donna M., Boerwinkle, Eric, Tuysuz, Beyhan, Alkuraya, Fowzan S., Gibbs, Richard A., and Lupski, James R.

Subjects
Identification and classification, Diagnosis, Development and progression, Research, Methods, Genetic research, Exome sequencing -- Methods, De Lange syndrome -- Diagnosis -- Development and progression, Gene mutation -- Identification and classification, Transcription (Genetics) -- Research, Gene mutations -- Identification and classification, Genetic transcription -- Research
Abstract

Introduction Cornelia de Lange syndrome (CdLS, MIM # 122470, MIM # 300590, MIM # 610759, MIM # 614701, and MIM # 300882) was initially described by Brachmann in 1916 and [...], Cornelia de Lange syndrome (CdLS) is a genetically heterogeneous disorder that presents with extensive phenotypic variability, including facial dysmorphism, developmental delay/intellectual disability (DD/ID), abnormal extremities, and hirsutism. About 65% of patients harbor mutations in genes that encode subunits or regulators of the cohesin complex, including NIPBL, SMC1A, SMC3, RAD21, and HDAC8. Wiedemann-Steiner syndrome (WDSTS), which shares CdLS phenotypic features, is caused by mutations in lysine-specific methyltransferase 2A (KMT2A). Here, we performed whole-exome sequencing (WES) of 2 male siblings clinically diagnosed with WDSTS; this revealed a hemizygous, missense mutation in SMC1A that was predicted to be deleterious. Extensive clinical evaluation and WES of 32 Turkish patients clinically diagnosed with CdLS revealed the presence of a de novo heterozygous nonsense KMT2A mutation in 1 patient without characteristic WDSTS features. We also identified de novo heterozygous mutations in SMC3 or SMC1A that affected RNA splicing in 2 independent patients with combined CdLS and WDSTS features. Furthermore, in families from 2 separate world populations segregating an autosomal-recessive disorder with CdLS-like features, we identified homozygous mutations in TAF6, which encodes a core transcriptional regulatory pathway component. Together, our data, along with recent transcriptome studies, suggest that CdLS and related phenotypes may be 'transcriptomopathies' rather than cohesinopathies.

Published
2015
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34. Chapter Contributors

Author

Abecasis, Gonçalo R., Applegate, Carolyn Dinsmore, Arbour, Laura, Beck, Christine R., Cohn, Iris, Cohn, Ronald Doron, Costain, Gregory, Cytrynbaum, Cheryl, Deng, Wei Q., Goodman, Sarah, Hamosh, Ada, Sutland, Dr. Frank V., Jelin, Angie Child, Klein, Ophir, Knoppers, Bartha Maria, Lee, Charles, Marshall, Christian R., Maass, Philipp G., Popejoy, Alice B., Scherer, Stephen W., Sondheimer, Neal, Stavropoulos, Dimitri J., Sun, Lei, Van den Veyver, Ignatia B., Vento, Jodie Marie, Walsh, Michael F., Weksberg, Rosanna, Willer, Cristen J., Wynshaw-Boris, Anthony, Yilmaz, Feyza, Yuen, Ryan, and Zawati, Ma'n H.

Published
2024
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38. Recurrent HERV-H-Mediated 3q13.2–q13.31 Deletions Cause a Syndrome of Hypotonia and Motor, Language, and Cognitive Delays

Author

Shuvarikov, Andrey, Campbell, Ian M., Dittwald, Piotr, Neill, Nicholas J., Bialer, Martin G., Moore, Christine, Wheeler, Patricia G., Wallace, Stephanie E., Hannibal, Mark C., Murray, Michael F., Giovanni, Monica A., Terespolsky, Deborah, Sodhi, Sandi, Cassina, Matteo, Viskochil, David, Moghaddam, Billur, Herman, Kristin, Brown, Chester W., Beck, Christine R., Gambin, Anna, Cheung, Sau Wai, Patel, Ankita, Lamb, Allen N., Shaffer, Lisa G., Ellison, Jay W., Ravnan, Britt J., Stankiewicz, Paweł, and Rosenfeld, Jill A.

Published
2013
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46. PGM3 Mutations Cause a Congenital Disorder of Glycosylation with Severe Immunodeficiency and Skeletal Dysplasia

Author

Stray-Pedersen, Asbjørg, Backe, Paul H., Sorte, Hanne S., Mørkrid, Lars, Chokshi, Niti Y., Erichsen, Hans Christian, Gambin, Tomasz, Elgstøen, Katja B.P., Bjørås, Magnar, Wlodarski, Marcin W., Krüger, Marcus, Jhangiani, Shalini N., Muzny, Donna M., Patel, Ankita, Raymond, Kimiyo M., Sasa, Ghadir S., Krance, Robert A., Martinez, Caridad A., Abraham, Shirley M., Speckmann, Carsten, Ehl, Stephan, Hall, Patricia, Forbes, Lisa R., Merckoll, Else, Westvik, Jostein, Nishimura, Gen, Rustad, Cecilie F., Abrahamsen, Tore G., Rønnestad, Arild, Osnes, Liv T., Egeland, Torstein, Rødningen, Olaug K., Beck, Christine R., Boerwinkle, Eric A., Gibbs, Richard A., Lupski, James R., Orange, Jordan S., Lausch, Ekkehart, and Hanson, I. Celine

Published
2014
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47. Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics

Author

Loviglio, Maria Nicla, primary, Beck, Christine R., additional, White, Janson J., additional, Leleu, Marion, additional, Harel, Tamar, additional, Guex, Nicolas, additional, Niknejad, Anne, additional, Bi, Weimin, additional, Chen, Edward S., additional, Crespo, Isaac, additional, Yan, Jiong, additional, Charng, Wu-Lin, additional, Gu, Shen, additional, Fang, Ping, additional, Coban-Akdemir, Zeynep, additional, Shaw, Chad A., additional, Jhangiani, Shalini N., additional, Muzny, Donna M., additional, Gibbs, Richard A., additional, Rougemont, Jacques, additional, Xenarios, Ioannis, additional, Lupski, James R., additional, and Reymond, Alexandre, additional

Published
2016
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48. POGZ truncating alleles cause syndromic intellectual disability

Author

White, Janson, primary, Beck, Christine R., additional, Harel, Tamar, additional, Posey, Jennifer E., additional, Jhangiani, Shalini N., additional, Tang, Sha, additional, Farwell, Kelly D., additional, Powis, Zöe, additional, Mendelsohn, Nancy J., additional, Baker, Janice A., additional, Pollack, Lynda, additional, Mason, Kati J., additional, Wierenga, Klaas J., additional, Arrington, Daniel K., additional, Hall, Melissa, additional, Psychogios, Apostolos, additional, Fairbrother, Laura, additional, Walkiewicz, Magdalena, additional, Person, Richard E., additional, Niu, Zhiyv, additional, Zhang, Jing, additional, Rosenfeld, Jill A., additional, Muzny, Donna M., additional, Eng, Christine, additional, Beaudet, Arthur L., additional, Lupski, James R., additional, Boerwinkle, Eric, additional, Gibbs, Richard A., additional, Yang, Yaping, additional, Xia, Fan, additional, and Sutton, V. Reid, additional

Published
2016
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49. Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates

Author

Yuan, Bo, primary, Liu, Pengfei, additional, Gupta, Aditya, additional, Beck, Christine R., additional, Tejomurtula, Anusha, additional, Campbell, Ian M., additional, Gambin, Tomasz, additional, Simmons, Alexandra D., additional, Withers, Marjorie A., additional, Harris, R. Alan, additional, Rogers, Jeffrey, additional, Schwartz, David C., additional, and Lupski, James R., additional

Published
2015
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50. Assessing structural variation in a personal genome—towards a human reference diploid genome

Author

English, Adam C, primary, Salerno, William J, additional, Hampton, Oliver A, additional, Gonzaga-Jauregui, Claudia, additional, Ambreth, Shruthi, additional, Ritter, Deborah I, additional, Beck, Christine R, additional, Davis, Caleb F, additional, Dahdouli, Mahmoud, additional, Ma, Singer, additional, Carroll, Andrew, additional, Veeraraghavan, Narayanan, additional, Bruestle, Jeremy, additional, Drees, Becky, additional, Hastie, Alex, additional, Lam, Ernest T, additional, White, Simon, additional, Mishra, Pamela, additional, Wang, Min, additional, Han, Yi, additional, Zhang, Feng, additional, Stankiewicz, Pawel, additional, Wheeler, David A, additional, Reid, Jeffrey G, additional, Muzny, Donna M, additional, Rogers, Jeffrey, additional, Sabo, Aniko, additional, Worley, Kim C, additional, Lupski, James R, additional, Boerwinkle, Eric, additional, and Gibbs, Richard A, additional

Published
2015
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