GREGoR: Accelerating Genomics for Rare Diseases

Authors: Dawood, Moez, Heavner, Ben, Wheeler, Marsha M., Ungar, Rachel A., LoTempio, Jonathan, Wiel, Laurens, Berger, Seth, Bernstein, Jonathan A., Chong, Jessica X., Délot, Emmanuèle C., Eichler, Evan E., Gibbs, Richard A., Lupski, James R., Shojaie, Ali, Talkowski, Michael E., Wagner, Alex H., Wei, Chia-Lin, Wellington, Christopher, Wheeler, Matthew T., Members, GREGoR Partner, Carvalho, Claudia M. B., Gifford, Casey A., May, Susanne, Miller, Danny E., Rehm, Heidi L., Sedlazeck, Fritz J., Vilain, Eric, O'Donnell-Luria, Anne, Posey, Jennifer E., Chadwick, Lisa H., Bamshad, Michael J., Montgomery, Stephen B., Diseases, Genomics Research to Elucidate the Genetics of Rare, Consortium

Subject Terms: Quantitative Biology - Other Quantitative Biology

Access URL: http://arxiv.org/abs/2412.14338

CFAP47 is Implicated in X-Linked Polycystic Kidney Disease

Authors: Wei, Chia-Lin, Bamshad, Michael J., Eichler, Evan E., Anderson, Kailyn, Anderson, Peter, Bacus, Tamara J., Best, Sabrina, Blue, Elizabeth E., Brower, Katherine, Buckingham, Kati J., Carroll, Brianne, Casadei, Silvia, Chong, Jessica X., Damaraju, Nikhita, Davis, Colleen P., Frazar, Christian D., Gibson, Sophia, Goffena, Joy, Gordon, William W., Gustafson, Jonas A., Harvey, William T., Horike-Pyne, Martha, Hurless, Jameson R., Jacques, Caitlin, Jarvik, Gail P., Johanson, Eric, Thomas Kolar, J., Liu, Xiaomeng, Marvin, Colby T., McGee, Sean, Meyers, Holli, Miller, Danny E., Nielsen, Patrick M., Patterson, Karynne, Radhakrishnan, Aparna, Richardson, Matthew A., Ryke, Erica L., Sarkytbayeva, Aliya, Shaffer, Tristan, Shively, Kathryn M., Sommers, Olivia M., Storz, Sophie H.R., Smith, Joshua D., Starita, Lea M., Tackettl, Monica, Ward, Sydney A., Weiss, Jeffrey M., Yi, Qian, Zalusky, Miranda P.G., Mefford, Heather, Mori, Takayasu, Fujimaru, Takuya, Liu, Chunyu, Yamamoto, Kouhei, Suzuki, Takefumi, Chiga, Motoko, Sekine, Akinari, Ubara, Yoshifumi, Mandai, Shintaro, Ando, Fumiaki, Mori, Yutaro, Kikuchi, Hiroaki, Susa, Koichiro, Tan, Yue-Qiu, Zhang, Feng, Uchida, Shinichi, Sohara, Eisei

Source: In Kidney International Reports December 2024 9(12):3580-3591

Structural and genetic diversity in the secreted mucins MUC5AC and MUC5B

Authors: Plender, Elizabeth G., Prodanov, Timofey, Hsieh, PingHsun, Nizamis, Evangelos, Harvey, William T., Sulovari, Arvis, Munson, Katherine M., Kaufman, Eli J., O’Neal, Wanda K., Valdmanis, Paul N., Marschall, Tobias, Bloom, Jesse D., Eichler, Evan E.

Source: In The American Journal of Human Genetics 8 August 2024 111(8):1700-1716

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

Authors: The SPARK Consortium, Wang, Tianyun, Kim, Chang N., Bakken, Trygve E., Gillentine, Madelyn A., Henning, Barbara, Mao, Yafei, Gilissen, Christian, Nowakowski, Tomasz J., Eichler, Evan E.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2022 Nov . 119(46), 1-12.

Access URL: https://www.jstor.org/stable/27209374

Structurally divergent and recurrently mutated regions of primate genomes

Authors: Mao, Yafei, Harvey, William T., Porubsky, David, Munson, Katherine M., Hoekzema, Kendra, Lewis, Alexandra P., Audano, Peter A., Rozanski, Allison, Yang, Xiangyu, Zhang, Shilong, Yoo, DongAhn, Gordon, David S., Fair, Tyler, Wei, Xiaoxi, Logsdon, Glennis A., Haukness, Marina, Dishuck, Philip C., Jeong, Hyeonsoo, del Rosario, Ricardo, Bauer, Vanessa L., Fattor, Will T., Wilkerson, Gregory K., Mao, Yuxiang, Shi, Yongyong, Sun, Qiang, Lu, Qing, Paten, Benedict, Bakken, Trygve E., Pollen, Alex A., Feng, Guoping, Sawyer, Sara L., Warren, Wesley C., Carbone, Lucia, Eichler, Evan E.

Source: In Cell 14 March 2024 187(6):1547-1562

A 25-year odyssey of genomic technology advances and structural variant discovery

Authors: Porubsky, David, Eichler, Evan E.

Source: In Cell 29 February 2024 187(5):1024-1037

3-hour genome sequencing and targeted analysis to rapidly assess genetic risk

Authors: Zalusky, Miranda P.G., Gustafson, Jonas A., Bohaczuk, Stephanie C., Mallory, Ben, Reed, Paxton, Wenger, Tara, Beckman, Erika, Chang, Irene J., Paschal, Cate R., Buchan, Jillian G., Lockwood, Christina M., Puia-Dumitrescu, Mihai, Garalde, Daniel R., Guillory, Joseph, Markham, Androo J., Bamshad, Michael J., Eichler, Evan E., Stergachis, Andrew B., Miller, Danny E.

Source: In Genetics in Medicine Open 2024 2

Characterizing the autism spectrum phenotype in DYRK1A‐related syndrome

Authors: Kurtz‐Nelson, Evangeline C., Rea, Hannah M., Petriceks, Aiva C., Hudac, Caitlin M., Wang, Tianyun, Earl, Rachel K., Bernier, Raphael A., Eichler, Evan E., Neuhaus, Emily

Source: Autism research. 16(8):1488-1500

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190862437.0x000001&indx=1&recIds=ETOCvdc_100190862437.0x000001

Genetic Ablation of GIGYF1, Associated With Autism, Causes Behavioral and Neurodevelopmental Defects in Zebrafish and Mice

Authors: Ding, Zijiao, Huang, Guiyang, Wang, Tianyun, Duan, Weicheng, Li, Hua, Wang, Yirong, Jia, Huiting, Yang, Ziqian, Wang, Kang, Chu, Xufeng, Kurtz-Nelson, Evangeline C., Ahlers, Kaitlyn, Earl, Rachel K., Han, Yunyun, Feliciano, Pamela, Chung, Wendy K., Eichler, Evan E., Jiang, Man, Xiong, Bo

Source: In Biological Psychiatry 15 November 2023 94(10):769-779

Envisioning a new era: Complete genetic information from routine, telomere-to-telomere genomes

Authors: Miga, Karen H., Eichler, Evan E.

Source: In The American Journal of Human Genetics 2 November 2023 110(11):1832-1840

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Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome

Authors: Liao, Wen-Wei, Asri, Mobin, Ebler, Jana, Doerr, Daniel, Haukness, Marina, Hickey, Glenn, Lu, Shuangjia, Lucas, Julian K., Monlong, Jean, Abel, Haley J., Buonaiuto, Silvia, Chang, Xian H., Cheng, Haoyu, Chu, Justin, Colonna, Vincenza, Eizenga, Jordan M., Feng, Xiaowen, Fischer, Christian, Fulton, Robert S., Garg, Shilpa, Groza, Cristian, Guarracino, Andrea, Harvey, William T., Heumos, Simon, Howe, Kerstin, Jain, Miten, Lu, Tsung-Yu, Markello, Charles, Martin, Fergal J., Mitchell, Matthew W., Munson, Katherine M., Mwaniki, Moses Njagi, Novak, Adam M., Olsen, Hugh E., Pesout, Trevor, Porubsky, David, Prins, Pjotr, Sibbesen, Jonas A., Tomlinson, Chad, Villani, Flavia, Vollger, Mitchell R., Antonacci-Fulton, Lucinda L., Baid, Gunjan, Baker, Carl A., Belyaeva, Anastasiya, Billis, Konstantinos, Carroll, Andrew, Chang, Pi-Chuan, Cody, Sarah, Cook, Daniel E., Cornejo, Omar E., Diekhans, Mark, Ebert, Peter, Fairley, Susan, Fedrigo, Olivier, Felsenfeld, Adam L., Formenti, Giulio, Frankish, Adam, Gao, Yan, Giron, Carlos Garcia, Green, Richard E., Haggerty, Leanne, Hoekzema, Kendra, Hourlier, Thibaut, Ji, Hanlee P., Kolesnikov, Alexey, Korbel, Jan O., Kordosky, Jennifer, Lee, HoJoon, Lewis, Alexandra P., Magalhães, Hugo, Marco-Sola, Santiago, Marijon, Pierre, McDaniel, Jennifer, Mountcastle, Jacquelyn, Nattestad, Maria, Olson, Nathan D., Puiu, Daniela, Regier, Allison A., Rhie, Arang, Sacco, Samuel, Sanders, Ashley D., Schneider, Valerie A., Schultz, Baergen I., Shafin, Kishwar, Sirén, Jouni, Smith, Michael W., Sofia, Heidi J., Abou Tayoun, Ahmad N., Thibaud-Nissen, Françoise, Tricomi, Francesca Floriana, Wagner, Justin, Wood, Jonathan M.D., Zimin, Aleksey V., Popejoy, Alice B., Bourque, Guillaume, Chaisson, Mark J.P., Flicek, Paul, Phillippy, Adam M., Zook, Justin M., Eichler, Evan E., Haussler, David, Jarvis, Erich D., Miga, Karen H., Wang, Ting, Garrison, Erik, Marschall, Tobias, Hall, Ira, Li, Heng, Paten, Benedict, Greer, Stephanie U., Pavlichin, Dmitri S., Zhou, Bo, Urban, Alexander E., Weissman, Tsachy

Source: In Cell Reports Methods 28 August 2023 3(8)

Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements

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

Source: In Cell Genomics 10 May 2023 3(5)

Brief Report: Associations between Self-Injurious Behaviors and Abdominal Pain among Individuals with ASD-Associated Disruptive Mutations

Authors: Kurtz-Nelson, Evangeline C., Tham, See Wan, Ahlers, Kaitlyn, Cho, Daniel, Wallace, Arianne S., Eichler, Evan E., Bernier, Raphael A., Earl, Rachel K.

Source: Journal of Autism and Developmental Disorders. Sep 2021 51(9):3365-3373.

Peer Reviewed: Y

Page Count: 9

Sponsoring Agency: National Institute of Mental Health (NIMH) (DHHS/NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) (DHHS/NIH)

Descriptors: Self Destructive Behavior, Injuries, Autism, Pervasive Developmental Disorders, Genetic Disorders, Incidence, Predictor Variables, Behavior Problems, Pain, Severity (of Disability), Age Differences, Correlation

Quantitative assessment reveals the dominance of duplicated sequences in germline-derived extrachromosomal circular DNA

Authors: Mouakkad-Montoya, Lila, Murata, Michael M., Sulovari, Arvis, Suzuki, Ryusuke, Osia, Beth, Malkova, Anna, Katsumata, Makoto, Giuliano, Armando E., Eichler, Evan E., Tanaka, Hisashi

Source: Proceedings of the National Academy of Sciences of the United States of America, 2021 Nov . 118(47), 1-10.

Access URL: https://www.jstor.org/stable/27093998

A family study implicates GBE1 in the etiology of autism spectrum disorder

Authors: Fanjul‐Fernández, Miriam, Brown, Natasha J., Hickey, Peter, Diakumis, Peter, Rafehi, Haloom, Bozaoglu, Kiymet, Green, Cherie C., Rattray, Audrey, Young, Savannah, Alhuzaimi, Dana, Mountford, Hayley S., Gillies, Greta, Lukic, Vesna, Vick, Tanya, Finlay, Keri, Coe, Bradley P., Eichler, Evan E., Delatycki, Martin B., Wilson, Sarah J., Bahlo, Melanie, Scheffer, Ingrid E., Lockhart, Paul J.

Source: Human mutation. 43(1):16-29

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100140073175.0x000001&indx=1&recIds=ETOCvdc_100140073175.0x000001

Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants

Authors: Lin, Jiadong, Yang, Xiaofei, Kosters, Walter, Xu, Tun, Jia, Yanyan, Wang, Songbo, Zhu, Qihui, Ryan, Mallory, Guo, Li, Zhang, Chengsheng, Lee, Charles, Devine, Scott E., Eichler, Evan E., Ye, Kai

Source: Genomics proteomics & bioinformatics. 20(1):205-218

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100173453094.0x000001&indx=1&recIds=ETOCvdc_100173453094.0x000001

Rare variants and the oligogenic architecture of autism

Authors: Wang, Tianyun, Zhao, Peiyao A., Eichler, Evan E.

Source: Trends in genetics. 38(9):895-903

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100168419720.0x000001&indx=1&recIds=ETOCvdc_100168419720.0x000001

Targeted Long‐Read Sequencing Identifies a Retrotransposon Insertion as a Cause of Altered GNAS Exon A/B Methylation in a Family With Autosomal Dominant Pseudohypoparathyroidism Type 1b (PHP1B)

Authors: Miller, Danny E, Hanna, Patrick, Galey, Miranda, Reyes, Monica, Linglart, Agnès, Eichler, Evan E, Jüppner, Harald

Source: Journal of bone and mineral research. 37(9):1711-1719

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100162723539.0x000001&indx=1&recIds=ETOCvdc_100162723539.0x000001

Familial long-read sequencing increases yield of de novo mutations

Authors: Noyes, Michelle D., Harvey, William T., Porubsky, David, Sulovari, Arvis, Li, Ruiyang, Rose, Nicholas R., Audano, Peter A., Munson, Katherine M., Lewis, Alexandra P., Hoekzema, Kendra, Mantere, Tuomo, Graves-Lindsay, Tina A., Sanders, Ashley D., Goodwin, Sara, Kramer, Melissa, Mokrab, Younes, Zody, Michael C., Hoischen, Alexander, Korbel, Jan O., McCombie, W. Richard, Eichler, Evan E.

Source: American journal of human genetics. 109(4):631-646

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100161231951.0x000001&indx=1&recIds=ETOCvdc_100161231951.0x000001