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36 results on '"Jain, Preti"'

1. Autosomal-Dominant Multiple Pterygium Syndrome Is Caused by Mutations in MYH3

Author

Chong, Jessica X, Burrage, Lindsay C, Beck, Anita E, Marvin, Colby T, McMillin, Margaret J, Shively, Kathryn M, Harrell, Tanya M, Buckingham, Kati J, Bacino, Carlos A, Jain, Mahim, Alanay, Yasemin, Berry, Susan A, Carey, John C, Gibbs, Richard A, Lee, Brendan H, Krakow, Deborah, Shendure, Jay, Nickerson, Deborah A, Genomics, University of Washington Center for Mendelian, Bamshad, Michael J, Abecasis, Gonçalo R, Anderson, Peter, Blue, Elizabeth Marchani, Annable, Marcus, Browning, Brian L, Chen, Christina, Chin, Jennifer, Cooper, Gregory M, Davis, Colleen P, Frazar, Christopher, He, Zongxiao, Jain, Preti, Jarvik, Gail P, Jimenez, Guillaume, Johanson, Eric, Jun, Goo, Kircher, Martin, Kolar, Tom, Krauter, Stephanie A, Krumm, Niklas, Leal, Suzanne M, Luksic, Daniel, McGee, Sean, O’Reilly, Patrick, Paeper, Bryan, Patterson, Karynne, Perez, Marcos, Phillips, Sam W, Pijoan, Jessica, Poel, Christa, Reinier, Frederic, Robertson, Peggy D, Santos-Cortez, Regie, Shaffer, Tristan, Shephard, Cindy, Siegel, Deborah L, Smith, Joshua D, Staples, Jeffrey C, Tabor, Holly K, Tackett, Monica, Underwood, Jason G, Wegener, Marc, Wang, Gao, Wheeler, Marsha M, and Yi, Qian

Subjects
Biological Sciences, Genetics, Brain Disorders, Intellectual and Developmental Disabilities (IDD), Clinical Research, Congenital Structural Anomalies, Rare Diseases, Pediatric, Arthrogryposis, Cytoskeletal Proteins, Exome, Genetic Predisposition to Disease, High-Throughput Nucleotide Sequencing, Humans, Mutation, Myosins, Osteogenesis, University of Washington Center for Mendelian Genomics, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Multiple pterygium syndrome (MPS) is a phenotypically and genetically heterogeneous group of rare Mendelian conditions characterized by multiple pterygia, scoliosis, and congenital contractures of the limbs. MPS typically segregates as an autosomal-recessive disorder, but rare instances of autosomal-dominant transmission have been reported. Whereas several mutations causing recessive MPS have been identified, the genetic basis of dominant MPS remains unknown. We identified four families affected by dominantly transmitted MPS characterized by pterygia, camptodactyly of the hands, vertebral fusions, and scoliosis. Exome sequencing identified predicted protein-altering mutations in embryonic myosin heavy chain (MYH3) in three families. MYH3 mutations underlie distal arthrogryposis types 1, 2A, and 2B, but all mutations reported to date occur in the head and neck domains. In contrast, two of the mutations found to cause MPS in this study occurred in the tail domain. The phenotypic overlap among persons with MPS, coupled with physical findings distinct from other conditions caused by mutations in MYH3, suggests that the developmental mechanism underlying MPS differs from that of other conditions and/or that certain functions of embryonic myosin might be perturbed by disruption of specific residues and/or domains. Moreover, the vertebral fusions in persons with MPS, coupled with evidence of MYH3 expression in bone, suggest that embryonic myosin plays a role in skeletal development.

Published
2015

2. De Novo Mutations in NALCN Cause a Syndrome Characterized by Congenital Contractures of the Limbs and Face, Hypotonia, and Developmental Delay

Author

Chong, Jessica X, McMillin, Margaret J, Shively, Kathryn M, Beck, Anita E, Marvin, Colby T, Armenteros, Jose R, Buckingham, Kati J, Nkinsi, Naomi T, Boyle, Evan A, Berry, Margaret N, Bocian, Maureen, Foulds, Nicola, Uzielli, Maria Luisa Giovannucci, Haldeman-Englert, Chad, Hennekam, Raoul CM, Kaplan, Paige, Kline, Antonie D, Mercer, Catherine L, Nowaczyk, Malgorzata JM, Wassink-Ruiter, Jolien S Klein, McPherson, Elizabeth W, Moreno, Regina A, Scheuerle, Angela E, Shashi, Vandana, Stevens, Cathy A, Carey, John C, Monteil, Arnaud, Lory, Philippe, Tabor, Holly K, Smith, Joshua D, Shendure, Jay, Nickerson, Deborah A, Genomics, University of Washington Center for Mendelian, Bamshad, Michael J, Abecasis, Gonçalo R, Anderson, Peter, Blue, Elizabeth Marchani, Annable, Marcus, Browning, Brian L, Chen, Christina, Chin, Jennifer, Cooper, Gregory M, Davis, Colleen P, Frazar, Christopher, Harrell, Tanya M, He, Zongxiao, Jain, Preti, Jarvik, Gail P, Jimenez, Guillaume, Johanson, Eric, Jun, Goo, Kircher, Martin, Kolar, Tom, Krauter, Stephanie A, Krumm, Niklas, Leal, Suzanne M, Luksic, Daniel, McGee, Sean, O’Reilly, Patrick, Paeper, Bryan, Patterson, Karynne, Perez, Marcos, Phillips, Sam W, Pijoan, Jessica, Poel, Christa, Reinier, Frederic, Robertson, Peggy D, Santos-Cortez, Regie, Shaffer, Tristan, Shephard, Cindy, Siegel, Deborah L, Staples, Jeffrey C, Tackett, Monica, Underwood, Jason G, Wegener, Marc, Wang, Gao, Wheeler, Marsha M, and Yi, Qian

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Rare Diseases, Congenital Structural Anomalies, Pediatric, Clinical Research, Aetiology, 2.1 Biological and endogenous factors, Congenital, Arthrogryposis, Contracture, Craniofacial Dysostosis, Cytoskeletal Proteins, Exome, Extremities, Face, Female, Gene Frequency, High-Throughput Nucleotide Sequencing, Homozygote, Humans, Infant, Ion Channels, Male, Membrane Proteins, Muscle Hypotonia, Mutation, Missense, Sodium Channels, University of Washington Center for Mendelian Genomics, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Freeman-Sheldon syndrome, or distal arthrogryposis type 2A (DA2A), is an autosomal-dominant condition caused by mutations in MYH3 and characterized by multiple congenital contractures of the face and limbs and normal cognitive development. We identified a subset of five individuals who had been putatively diagnosed with "DA2A with severe neurological abnormalities" and for whom congenital contractures of the limbs and face, hypotonia, and global developmental delay had resulted in early death in three cases; this is a unique condition that we now refer to as CLIFAHDD syndrome. Exome sequencing identified missense mutations in the sodium leak channel, non-selective (NALCN) in four families affected by CLIFAHDD syndrome. We used molecular-inversion probes to screen for NALCN in a cohort of 202 distal arthrogryposis (DA)-affected individuals as well as concurrent exome sequencing of six other DA-affected individuals, thus revealing NALCN mutations in ten additional families with "atypical" forms of DA. All 14 mutations were missense variants predicted to alter amino acid residues in or near the S5 and S6 pore-forming segments of NALCN, highlighting the functional importance of these segments. In vitro functional studies demonstrated that NALCN alterations nearly abolished the expression of wild-type NALCN, suggesting that alterations that cause CLIFAHDD syndrome have a dominant-negative effect. In contrast, homozygosity for mutations in other regions of NALCN has been reported in three families affected by an autosomal-recessive condition characterized mainly by hypotonia and severe intellectual disability. Accordingly, mutations in NALCN can cause either a recessive or dominant condition characterized by varied though overlapping phenotypic features, perhaps based on the type of mutation and affected protein domain(s).

Published
2015

4. Genes that Affect Brain Structure and Function Identified by Rare Variant Analyses of Mendelian Neurologic Disease

Author

Karaca, Ender, Harel, Tamar, Pehlivan, Davut, Jhangiani, Shalini N., Gambin, Tomasz, Coban Akdemir, Zeynep, Gonzaga-Jauregui, Claudia, Erdin, Serkan, Bayram, Yavuz, Campbell, Ian M., Hunter, Jill V., Atik, Mehmed M., Van Esch, Hilde, Yuan, Bo, Wiszniewski, Wojciech, Isikay, Sedat, Yesil, Gozde, Yuregir, Ozge O., Tug Bozdogan, Sevcan, Aslan, Huseyin, Aydin, Hatip, Tos, Tulay, Aksoy, Ayse, De Vivo, Darryl C., Jain, Preti, Geckinli, B. Bilge, Sezer, Ozlem, Gul, Davut, Durmaz, Burak, Cogulu, Ozgur, Ozkinay, Ferda, Topcu, Vehap, Candan, Sukru, Cebi, Alper Han, Ikbal, Mevlit, Yilmaz Gulec, Elif, Gezdirici, Alper, Koparir, Erkan, Ekici, Fatma, Coskun, Salih, Cicek, Salih, Karaer, Kadri, Koparir, Asuman, Duz, Mehmet Bugrahan, Kirat, Emre, Fenercioglu, Elif, Ulucan, Hakan, Seven, Mehmet, Guran, Tulay, Elcioglu, Nursel, Yildirim, Mahmut Selman, Aktas, Dilek, Alikaşifoğlu, Mehmet, Ture, Mehmet, Yakut, Tahsin, Overton, John D., Yuksel, Adnan, Ozen, Mustafa, Muzny, Donna M., Adams, David R., Boerwinkle, Eric, Chung, Wendy K., Gibbs, Richard A., and Lupski, James R.

Published
2015
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7. A Validated Regulatory Network for Th17 Cell Specification

Author

Ciofani, Maria, Madar, Aviv, Galan, Carolina, Sellars, MacLean, Mace, Kieran, Pauli, Florencia, Agarwal, Ashish, Huang, Wendy, Parkurst, Christopher N., Muratet, Michael, Newberry, Kim M., Meadows, Sarah, Greenfield, Alex, Yang, Yi, Jain, Preti, Kirigin, Francis K., Birchmeier, Carmen, Wagner, Erwin F., Murphy, Kenneth M., Myers, Richard M., Bonneau, Richard, and Littman, Dan R.

Published
2012
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8. Whole-Exome Sequencing in Familial Parkinson Disease

Author

Farlow, Janice L., Robak, Laurie A., Hetrick, Kurt, Bowling, Kevin, Boerwinkle, Eric, Coban-Akdemir, Zeynep H., Gambin, Tomasz, Gibbs, Richard A., Gu, Shen, Jain, Preti, Jankovic, Joseph, Jhangiani, Shalini, Kaw, Kaveeta, Lai, Dongbing, Lin, Hai, Ling, Hua, Liu, Yunlong, Lupski, James R., Muzny, Donna, Porter, Paula, Pugh, Elizabeth, White, Janson, Doheny, Kimberly, Myers, Richard M., Shulman, Joshua M., and Foroud, Tatiana

Published
2016
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9. D‐bifunctional protein deficiency caused by splicing variants in a neonate with severe peroxisomal dysfunction and persistent hypoglycemia

Author

Werner, Kelly M., primary, Cox, Allison J., additional, Qian, Emily, additional, Jain, Preti, additional, Ji, Weizhen, additional, Tikhonova, Irina, additional, Castaldi, Christopher, additional, Bilguvar, Kaya, additional, Knight, James, additional, Ferdinandusse, Sacha, additional, Fawaz, Rima, additional, Jiang, Yong‐Hui, additional, Gallagher, Patrick G., additional, Bizzarro, Matthew, additional, Gruen, Jeffrey R., additional, Bale, Allen, additional, and Zhang, Hui, additional

Published
2021
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10. An integrated encyclopedia of DNA elements in the human genome

Author

Dunham, Ian, Kundaje, Anshul, Aldred, Shelley F., Collins, Patrick J., Davis, Carrie A., Doyle, Francis, Epstein, Charles B., Frietze, Seth, Harrow, Jennifer, Kaul, Rajinder, Khatun, Jainab, Lajoie, Bryan R., Landt, Stephen G., Lee, Bum-Kyu, Pauli, Florencia, Rosenbloom, Kate R., Sabo, Peter, Safi, Alexias, Sanyal, Amartya, Shoresh, Noam, Simon, Jeremy M., Song, Lingyun, Trinklein, Nathan D., Altshuler, Robert C., Birney, Ewan, Brown, James B., Cheng, Chao, Djebali, Sarah, Dong, Xianjun, Ernst, Jason, Furey, Terrence S., Gerstein, Mark, Giardine, Belinda, Greven, Melissa, Hardison, Ross C., Harris, Robert S., Herrero, Javier, Hoffman, Michael M., Iyer, Sowmya, Kellis, Manolis, Kheradpour, Pouya, Lassmann, Timo, Li, Qunhua, Lin, Xinying, Marinov, Georgi K., Merkel, Angelika, Mortazavi, Ali, Parker, Stephen C. J., Reddy, Timothy E., Rozowsky, Joel, Schlesinger, Felix, Thurman, Robert E., Wang, Jie, Ward, Lucas D., Whitfield, Troy W., Wilder, Steven P., Wu, Weisheng, Xi, Hualin S., Yip, Kevin Y., Zhuang, Jiali, Bernstein, Bradley E., Green, Eric D., Gunter, Chris, Snyder, Michael, Pazin, Michael J., Lowdon, Rebecca F., Dillon, Laura A. L., Adams, Leslie B., Kelly, Caroline J., Zhang, Julia, Wexler, Judith R., Good, Peter J., Feingold, Elise A., Crawford, Gregory E., Dekker, Job, Elnitski, Laura, Farnham, Peggy J., Giddings, Morgan C., Gingeras, Thomas R., Guigo, Roderic, Hubbard, Timothy J., Kent, W. James, Lieb, Jason D., Margulies, Elliott H., Myers, Richard M., Stamatoyannopoulos, John A., Tenenbaum, Scott A., Weng, Zhiping, White, Kevin P., Wold, Barbara, Yu, Yanbao, Wrobel, John, Risk, Brian A., Gunawardena, Harsha P., Kuiper, Heather C., Maier, Christopher W., Xie, Ling, Chen, Xian, Mikkelsen, Tarjei S., Gillespie, Shawn, Goren, Alon, Ram, Oren, Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael J., Durham, Timothy, Ku, Manching, Truong, Thanh, Eaton, Matthew L., Dobin, Alex, Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Xue, Chenghai, Williams, Brian A., Zaleski, Chris, Roder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F., Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T., Batut, Philippe, Bell, Ian, Bell, Kimberly, Chakrabortty, Sudipto, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jackie, Duttagupta, Radha, Fastuca, Megan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J., Gao, Hui, Gonzalez, David, Gordon, Assaf, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Li, Guoliang, Luo, Oscar J., Park, Eddie, Preall, Jonathan B., Presaud, Kimberly, Ribeca, Paolo, Robyr, Daniel, Ruan, Xiaoan, Sammeth, Michael, Sandhu, Kuljeet Singh, Schaeffer, Lorain, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Hayashizaki, Yoshihide, Reymond, Alexandre, Antonarakis, Stylianos E., Hannon, Gregory J., Ruan, Yijun, Carninci, Piero, Sloan, Cricket A., Learned, Katrina, Malladi, Venkat S., Wong, Matthew C., Barber, Galt P., Cline, Melissa S., Dreszer, Timothy R., Heitner, Steven G., Karolchik, Donna, Kirkup, Vanessa M., Meyer, Laurence R., Long, Jeffrey C., Maddren, Morgan, Raney, Brian J., Grasfeder, Linda L., Giresi, Paul G., Battenhouse, Anna, Sheffield, Nathan C., Showers, Kimberly A., London, Darin, Bhinge, Akshay A., Shestak, Christopher, Schaner, Matthew R., Ki Kim, Seul, Zhang, Zhuzhu Z., Mieczkowski, Piotr A., Mieczkowska, Joanna O., Liu, Zheng, McDaniell, Ryan M., Ni, Yunyun, Rashid, Naim U., Kim, Min Jae, Adar, Sheera, Zhang, Zhancheng, Wang, Tianyuan, Winter, Deborah, Keefe, Damian, Iyer, Vishwanath R., Zheng, Meizhen, Wang, Ping, Gertz, Jason, Vielmetter, Jost, Partridge, E., Varley, Katherine E., Gasper, Clarke, Bansal, Anita, Pepke, Shirley, Jain, Preti, Amrhein, Henry, Bowling, Kevin M., Anaya, Michael, Cross, Marie K., Muratet, Michael A., Newberry, Kimberly M., McCue, Kenneth, Nesmith, Amy S., Fisher-Aylor, Katherine I., Pusey, Barbara, DeSalvo, Gilberto, Parker, Stephanie L., Balasubramanian, Sreeram, Davis, Nicholas S., Meadows, Sarah K., Eggleston, Tracy, Newberry, J. Scott, Levy, Shawn E., Absher, Devin M., Wong, Wing H., Blow, Matthew J., Visel, Axel, Pennachio, Len A., Petrykowska, Hanna M., Abyzov, Alexej, Aken, Bronwen, Barrell, Daniel, Barson, Gemma, Berry, Andrew, Bignell, Alexandra, Boychenko, Veronika, Bussotti, Giovanni, Davidson, Claire, Despacio-Reyes, Gloria, Diekhans, Mark, Ezkurdia, Iakes, Frankish, Adam, Gilbert, James, Gonzalez, Jose Manuel, Griffiths, Ed, Harte, Rachel, Hendrix, David A., Hunt, Toby, Jungreis, Irwin, Kay, Mike, Khurana, Ekta, Leng, Jing, Lin, Michael F., Loveland, Jane, Lu, Zhi, Manthravadi, Deepa, Mariotti, Marco, Mudge, Jonathan, Mukherjee, Gaurab, Notredame, Cedric, Pei, Baikang, Rodriguez, Jose Manuel, Saunders, Gary, Sboner, Andrea, Searle, Stephen, Sisu, Cristina, Snow, Catherine, Steward, Charlie, Tapanari, Electra, Tress, Michael L., van Baren, Marijke J., Washietl, Stefan, Wilming, Laurens, Zadissa, Amonida, Zhang, Zhengdong, Brent, Michael, Haussler, David, Valencia, Alfonso, Addleman, Nick, Alexander, Roger P., Auerbach, Raymond K., Balasubramanian, Suganthi, Bettinger, Keith, Bhardwaj, Nitin, Boyle, Alan P., Cao, Alina R., Cayting, Philip, Charos, Alexandra, Cheng, Yong, Eastman, Catharine, Euskirchen, Ghia, Fleming, Joseph D., Grubert, Fabian, Habegger, Lukas, Hariharan, Manoj, Harmanci, Arif, Iyengar, Sushma, Jin, Victor X., Karczewski, Konrad J., Kasowski, Maya, Lacroute, Phil, Lam, Hugo, Lamarre-Vincent, Nathan, Lian, Jin, Lindahl-Allen, Marianne, Min, Renqiang, Miotto, Benoit, Monahan, Hannah, Moqtaderi, Zarmik, Mu, Xinmeng J., Ouyang, Zhengqing, Patacsil, Dorrelyn, Raha, Debasish, Ramirez, Lucia, Reed, Brian, Shi, Minyi, Slifer, Teri, Witt, Heather, Wu, Linfeng, Xu, Xiaoqin, Yan, Koon-Kiu, Yang, Xinqiong, Struhl, Kevin, Weissman, Sherman M., Penalva, Luiz O., Karmakar, Subhradip, Bhanvadia, Raj R., Choudhury, Alina, Domanus, Marc, Ma, Lijia, Moran, Jennifer, Victorsen, Alec, Auer, Thomas, Centanin, Lazaro, Eichenlaub, Michael, Gruhl, Franziska, Heermann, Stephan, Hoeckendorf, Burkhard, Inoue, Daigo, Kellner, Tanja, Kirchmaier, Stephan, Mueller, Claudia, Reinhardt, Robert, Schertel, Lea, Schneider, Stephanie, Sinn, Rebecca, Wittbrodt, Beate, Wittbrodt, Jochen, Partridge, E. Christopher, Jain, Gaurav, Balasundaram, Gayathri, Bates, Daniel L., Byron, Rachel, Canfield, Theresa K., Diegel, Morgan J., Dunn, Douglas, Ebersol, Abigail K., Frum, Tristan, Garg, Kavita, Gist, Erica, Hansen, R. Scott, Boatman, Lisa, Haugen, Eric, Humbert, Richard, Johnson, Audra K., Johnson, Ericka M., Kutyavin, Tattyana V., Lee, Kristen, Lotakis, Dimitra, Maurano, Matthew T., Neph, Shane J., Neri, Fiedencio V., Nguyen, Eric D., Qu, Hongzhu, Reynolds, Alex P., Roach, Vaughn, Rynes, Eric, Sanchez, Minerva E., Sandstrom, Richard S., Shafer, Anthony O., Stergachis, Andrew B., Thomas, Sean, Vernot, Benjamin, Vierstra, Jeff, Vong, Shinny, Weaver, Molly A., Yan, Yongqi, Zhang, Miaohua, Akey, Joshua M., Bender, Michael, Dorschner, Michael O., Groudine, Mark, MacCoss, Michael J., Navas, Patrick, Stamatoyannopoulos, George, Beal, Kathryn, Brazma, Alvis, Flicek, Paul, Johnson, Nathan, Lukk, Margus, Luscombe, Nicholas M., Sobral, Daniel, Vaquerizas, Juan M., Batzoglou, Serafim, Sidow, Arend, Hussami, Nadine, Kyriazopoulou-Panagiotopoulou, Sofia, Libbrecht, Max W., Schaub, Marc A., Miller, Webb, Bickel, Peter J., Banfai, Balazs, Boley, Nathan P., Huang, Haiyan, Li, Jingyi Jessica, Noble, William Stafford, Bilmes, Jeffrey A., Buske, Orion J., Sahu, Avinash D., Kharchenko, Peter V., Park, Peter J., Baker, Dannon, Taylor, James, and Lochovsky, Lucas

Subjects
Research, Genetic research, Transcription (Genetics) -- Research, Human genome -- Research, Genetic transcription -- Research
Abstract

Author(s): The ENCODE Project Consortium; Overall coordination (data analysis coordination); Ian Dunham [2]; Anshul Kundaje [3, 82]; Data production leads (data production); Shelley F. Aldred [4]; Patrick J. Collins [4]; [...], The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.

Published
2012
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11. Architecture of the human regulatory network derived from ENCODE data

Author

Gerstein, Mark B., Kundaje, Anshul, Hariharan, Manoj, Landt, Stephen G., Yan, Koon-Kiu, Cheng, Chao, Mu, Xinmeng Jasmine, Khurana, Ekta, Rozowsky, Joel, Alexander, Roger, Min, Renqiang, Alves, Pedro, Abyzov, Alexej, Addleman, Nick, Bhardwaj, Nitin, Boyle, Alan P., Cayting, Philip, Charos, Alexandra, Chen, David Z., Cheng, Yong, Clarke, Declan, Eastman, Catharine, Euskirchen, Ghia, Frietze, Seth, Fu, Yao, Gertz, Jason, Grubert, Fabian, Harmanci, Arif, Jain, Preti, Kasowski, Maya, Lacroute, Phil, Leng, Jing, Lian, Jin, Monahan, Hannah, O'Geen, Henriette, Ouyang, Zhengqing, Partridge, E. Christopher, Patacsil, Dorrelyn, Pauli, Florencia, Raha, Debasish, Ramirez, Lucia, Reddy, Timothy E., Reed, Brian, Shi, Minyi, Slifer, Teri, Wang, Jing, Wu, Linfeng, Yang, Xinqiong, Yip, Kevin Y., Zilberman-Schapira, Gili, Batzoglou, Serafim, Sidow, Arend, Farnham, Peggy J., Myers, Richard M., Weissman, Sherman M., and Snyder, Michael

Subjects
Research, Genetic aspects, Protein-protein interactions -- Genetic aspects -- Research, Alleles -- Research, Transcription factors -- Research, DNA binding proteins -- Research, Genetic regulation -- Research, Allelomorphism -- Research
Abstract

Author(s): Mark B. Gerstein (corresponding author) [1, 2, 3, 15]; Anshul Kundaje [4, 15]; Manoj Hariharan [5, 15]; Stephen G. Landt [5, 15]; Koon-Kiu Yan [1, 2, 15]; Chao Cheng [...], Transcription factors bind in a combinatorial fashion to specify the on-and-off states of genes; the ensemble of these binding events forms a regulatory network, constituting the wiring diagram for a cell. To examine the principles of the human transcriptional regulatory network, we determined the genomic binding information of 119 transcription-related factors in over 450 distinct experiments. We found the combinatorial, co-association of transcription factors to be highly context specific: distinct combinations of factors bind at specific genomic locations. In particular, there are significant differences in the binding proximal and distal to genes. We organized all the transcription factor binding into a hierarchy and integrated it with other genomic information (for example, microRNA regulation), forming a dense meta-network. Factors at different levels have different properties; for instance, top-level transcription factors more strongly influence expression and middle-level ones co-regulate targets to mitigate information-flow bottlenecks. Moreover, these co-regulations give rise to many enriched network motifs (for example, noise-buffering feed-forward loops). Finally, more connected network components are under stronger selection and exhibit a greater degree of allele-specific activity (that is, differential binding to the two parental alleles). The regulatory information obtained in this study will be crucial for interpreting personal genome sequences and understanding basic principles of human biology and disease.

Published
2012
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13. Variants in STXBP3 are Associated with Very Early Onset Inflammatory Bowel Disease, Bilateral Sensorineural Hearing Loss and Immune Dysregulation

Author

Ouahed, Jodie, primary, Kelsen, Judith R, additional, Spessott, Waldo A, additional, Kooshesh, Kameron, additional, Sanmillan, Maria L, additional, Dawany, Noor, additional, Sullivan, Kathleen E, additional, Hamilton, Kathryn E, additional, Slowik, Voytek, additional, Nejentsev, Sergey, additional, Neves, João Farela, additional, Flores, Helena, additional, Chung, Wendy K, additional, Wilson, Ashley, additional, Anyane-Yeboa, Kwame, additional, Wou, Karen, additional, Jain, Preti, additional, Field, Michael, additional, Tollefson, Sophia, additional, Dent, Maiah H, additional, Li, Dalin, additional, Naito, Takeo, additional, McGovern, Dermot P B, additional, Kwong, Andrew C, additional, Taliaferro, Faith, additional, Ordovas-Montanes, Jose, additional, Horwitz, Bruce H, additional, Kotlarz, Daniel, additional, Klein, Christoph, additional, Evans, Jonathan, additional, Dorsey, Jill, additional, Warner, Neil, additional, Elkadri, Abdul, additional, Muise, Aleixo M, additional, Goldsmith, Jeffrey, additional, Thompson, Benjamin, additional, Engelhardt, Karin R, additional, Cant, Andrew J, additional, Hambleton, Sophie, additional, Barclay, Andrew, additional, Toth-Petroczy, Agnes, additional, Vuzman, Dana, additional, Carmichael, Nikkola, additional, Bodea, Corneliu, additional, Cassa, Christopher A, additional, Devoto, Marcella, additional, Maas, Richard L, additional, Behrens, Edward M, additional, Giraudo, Claudio G, additional, and Snapper, Scott B, additional

Published
2021
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16. D‐bifunctional protein deficiency caused by splicing variants in a neonate with severe peroxisomal dysfunction and persistent hypoglycemia.

Author

Werner, Kelly M., Cox, Allison J., Qian, Emily, Jain, Preti, Ji, Weizhen, Tikhonova, Irina, Castaldi, Christopher, Bilguvar, Kaya, Knight, James, Ferdinandusse, Sacha, Fawaz, Rima, Jiang, Yong‐Hui, Gallagher, Patrick G., Bizzarro, Matthew, Gruen, Jeffrey R., Bale, Allen, and Zhang, Hui

Abstract

D‐bifunctional protein (DBP) deficiency is a rare, autosomal recessive peroxisomal enzyme deficiency resulting in a high burden of morbidity and early mortality. Patients with DBP deficiency resemble those with a severe Zellweger phenotype, with neonatal hypotonia, seizures, craniofacial dysmorphisms, psychomotor delay, deafness, blindness, and death typically within the first 2 years of life, although patients with residual enzyme function can survive longer. The clinical severity of the disease depends on the degree of enzyme deficiency. Loss‐of‐function variants typically result in no residual enzyme activity; however, splice variants may result in protein with residual function. We describe a full‐term newborn presenting with hypotonia, seizures, and unexplained hypoglycemia, who was later found to have rickets at follow up. Rapid whole genome sequencing identified two HSD17B4 variants in trans; one likely pathogenic variant and one variant of uncertain significance (VUS) located in the polypyrimidine tract of intron 13. To determine the functional consequence of the VUS, we analyzed RNA from the patient's father with RNA‐seq which showed skipping of Exon 14, resulting in a frameshift mutation three amino acids from the new reading frame. This RNA‐seq analysis was correlated with virtually absent enzyme activity, elevated very‐long‐chain fatty acids in fibroblasts, and a clinically severe phenotype. Both variants are reclassified as pathogenic. Due to the clinical spectrum of DBP deficiency, this provides important prognostic information, including early mortality. Furthermore, we add persistent hypoglycemia to the clinical spectrum of the disease, and advocate for the early management of fat‐soluble vitamin deficiencies to reduce complications. [ABSTRACT FROM AUTHOR]

Published
2022
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17. Impact of Receiving Secondary Results from Genomic Research: A 12‐Month Longitudinal Study

Author

Jain Preti, Abby Fyer, Josue Natanael Martinez, Paul S. Appelbaum, Yiying Zhang, Wendy K. Chung, Julia Wynn, Maria L. Cremona, Codruta Chiuzan, Robert L. Klitzman, Vaidehi Jobanputra, Jessica Bulafka, and Jimmy Duong

Subjects
Adult, Heart Defects, Congenital, Male, 0301 basic medicine, Longitudinal study, medicine.medical_specialty, Genetic counseling, Genomic research, Breast Neoplasms, 030105 genetics & heredity, Article, 03 medical and health sciences, medicine, Humans, Longitudinal Studies, Clinical care, Genetics (clinical), Hernia, Diaphragmatic, business.industry, Public health, Genomics, Middle Aged, Bioethics, Disease risk, Female, business, Clinical psychology
Abstract

The impact of returning secondary results from exome sequencing (ES) on patients/participants is important to understand as ES is increasingly utilized in clinical care and research. Participants were recruited from studies using ES and were separated into two arms: 107 who had ES and were offered the choice to learn secondary results (ES group) and 85 who had not yet had ES (No ES group). Questionnaires were administered at baseline and 1 and 12 months, following results disclosure (ES group) or enrollment (No ES group). While the majority (65%) elected to learn all results following pre-test counseling, it was reduced from the 76% who indicated a desire for all results at baseline. Thirty-seven percent received results associated with an increased personal disease risk. There were no differences in changes in any of the psychological and social measures from baseline to post-results disclosure between the ES and No ES groups. Receiving a wide range of secondary findings appeared to have little measurable impact on most participants. The experience of learning secondary results may be related to participants’ previous experiences with genetics, as well as the genetic counseling provided. Future research with a more diverse, genetically naïve group, as well as scalable methods of delivery, is needed.

Published
2018
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18. Sa2008 - Mutations in Stxbp3 Contribute to Very Early Onset of IBD Immunodeficieny and Hearing Loss

Author

Kelsen, Judith R., primary, Ouahed, Jodie, additional, Spessott, Waldo, additional, Kooshesh, Kameron, additional, Sanmillan, Maria, additional, Dawany, Noor, additional, Sullivan, Kathleen E., additional, Hamilton, Kathryn E., additional, Slowik, Voyteck, additional, Nejentsev, Sergey, additional, Neves, João Farela, additional, Flores, Helena, additional, Chung, Wendy, additional, Wilson, Ashley, additional, Yeboa, Kwame Anyane, additional, Wou, Karen, additional, Jain, Preti, additional, Tollefson, Sophia, additional, Evans, Jonathan S., additional, Warner, Neil E., additional, Muise, Aleixo, additional, Toth-Petroczy, Agnes, additional, Vuzman, Dana, additional, Carmichael, Nikkola, additional, Bodea, Corneliu, additional, Cassa, Christopher, additional, Devoto, Marcella, additional, Mass, Richard, additional, Behrens, Edward, additional, Snapper, Scott B., additional, and Giraudo, Claudio, additional

Published
2018
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19. Autosomal-Dominant Multiple Pterygium Syndrome Is Caused by Mutations in MYH3

Author

Bamshad, Michael J., Shendure, Jay, Nickerson, Deborah A., Abecasis, Gonçalo R., Anderson, Peter, Blue, Elizabeth Marchani, Annable, Marcus, Browning, Brian L., Buckingham, Kati J., Chen, Christina, Chin, Jennifer, Chong, Jessica X., Cooper, Gregory M., Davis, Colleen P., Frazar, Christopher, Harrell, Tanya M., He, Zongxiao, Jain, Preti, Jarvik, Gail P., Jimenez, Guillaume, Johanson, Eric, Jun, Goo, Kircher, Martin, Kolar, Tom, Krauter, Stephanie A., Krumm, Niklas, Leal, Suzanne M., Luksic, Daniel, Marvin, Colby T., McMillin, Margaret J., McGee, Sean, O’Reilly, Patrick, Paeper, Bryan, Patterson, Karynne, Perez, Marcos, Phillips, Sam W., Pijoan, Jessica, Poel, Christa, Reinier, Frederic, Robertson, Peggy D., Santos-Cortez, Regie, Shaffer, Tristan, Shephard, Cindy, Shively, Kathryn M., Siegel, Deborah L., Smith, Joshua D., Staples, Jeffrey C., Tabor, Holly K., Tackett, Monica, Underwood, Jason G., Wegener, Marc, Wang, Gao, Wheeler, Marsha M., Yi, Qian, Burrage, Lindsay C., Beck, Anita E., Bacino, Carlos A., Jain, Mahim, Alanay, Yasemin, Berry, Susan A., Carey, John C., Gibbs, Richard A., Lee, Brendan H., and Krakow, Deborah

Published
2015
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20. De Novo Mutations in NALCN Cause a Syndrome Characterized by Congenital Contractures of the Limbs and Face, Hypotonia, and Developmental Delay

Author

Bamshad, Michael J., Shendure, Jay, Nickerson, Deborah A., Abecasis, Gonçalo R., Anderson, Peter, Blue, Elizabeth Marchani, Annable, Marcus, Browning, Brian L., Buckingham, Kati J., Chen, Christina, Chin, Jennifer, Chong, Jessica X., Cooper, Gregory M., Davis, Colleen P., Frazar, Christopher, Harrell, Tanya M., He, Zongxiao, Jain, Preti, Jarvik, Gail P., Jimenez, Guillaume, Johanson, Eric, Jun, Goo, Kircher, Martin, Kolar, Tom, Krauter, Stephanie A., Krumm, Niklas, Leal, Suzanne M., Luksic, Daniel, Marvin, Colby T., McMillin, Margaret J., McGee, Sean, O’Reilly, Patrick, Paeper, Bryan, Patterson, Karynne, Perez, Marcos, Phillips, Sam W., Pijoan, Jessica, Poel, Christa, Reinier, Frederic, Robertson, Peggy D., Santos-Cortez, Regie, Shaffer, Tristan, Shephard, Cindy, Shively, Kathryn M., Siegel, Deborah L., Smith, Joshua D., Staples, Jeffrey C., Tabor, Holly K., Tackett, Monica, Underwood, Jason G., Wegener, Marc, Wang, Gao, Wheeler, Marsha M., Yi, Qian, Beck, Anita E., Armenteros, Jose R., Nkinsi, Naomi T., Boyle, Evan A., Berry, Margaret N., Bocian, Maureen, Foulds, Nicola, Uzielli, Maria Luisa Giovannucci, Haldeman-Englert, Chad, Hennekam, Raoul C.M., Kaplan, Paige, Kline, Antonie D., Mercer, Catherine L., Nowaczyk, Malgorzata J.M., Klein Wassink-Ruiter, Jolien S., McPherson, Elizabeth W., Moreno, Regina A., Scheuerle, Angela E., Shashi, Vandana, Stevens, Cathy A., Carey, John C., Monteil, Arnaud, and Lory, Philippe

Published
2015
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21. 25 MUTATIONS IN STXBP3 CONTRIBUTE TO VERY EARLY ONSET OF IBD, IMMUNODEFICIENCY AND HEARING LOSS

Author

Kelsen, Judith R, primary, Ouahed, Jodie, additional, Spessott, Waldo A, additional, Kooshesh, Kameron, additional, Sanmillan, Maria L, additional, Dawany, Noor, additional, Sullivan, Kathleen E, additional, Hamilton, Kathryn, additional, Slowik, Voytek, additional, Nejentsev, Sergey, additional, Neves, João Farela, additional, Flores, Helena, additional, Chung, Wendy K, additional, Wilson, Ashley, additional, Yeboa, Kwame Anyane, additional, Wou, Karen, additional, Jain, Preti, additional, Tollefson, Sophia, additional, Evans, Jonathan, additional, Warner, Neil, additional, Muise, Alexio, additional, Goldsmith, Jeffrey, additional, Toth-Petroczy, Agnes, additional, Vuzman, Dana, additional, Carmichael, Nikkola, additional, Bodea, Corneliu, additional, Cassa, Christopher, additional, Devoto, Marcella, additional, Maas, Richard L, additional, Behrens, Edward M, additional, Snapper, Scott B, additional, and Giraudo, Claudio G, additional

Published
2018
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22. 25 MUTATIONS IN STXBP3 CONTRIBUTE TO VERY EARLY ONSET OF IBD, IMMUNODEFICIENCY AND HEARING LOSS

Author

Kelsen, Judith R., primary, Ouahed, Jodie, additional, Spessott, Waldo A., additional, Kooshesh, Kameron, additional, Sanmillan, Maria L., additional, Dawany, Noor, additional, Sullivan, Kathleen E., additional, Hamilton, Kathryn, additional, Slowik, Voytek, additional, Nejentsev, Sergey, additional, Farela Neves, João, additional, Flores, Helena, additional, Chung, Wendy K., additional, Wilson, Ashley, additional, Yeboa, Kwame Anyane, additional, Wou, Karen, additional, Jain, Preti, additional, Tollefson, Sophia, additional, Evans, Jonathan, additional, Warner, Neil, additional, Muise, Alexio, additional, Goldsmith, Jeffrey, additional, Toth-Petroczy, Agnes, additional, Vuzman, Dana, additional, Carmichael, Nikkola, additional, Bodea, Corneliu, additional, Cassa, Christopher, additional, Devoto, Marcella, additional, Maas, Richard L., additional, Behrens, Edward M., additional, Snapper, Scott B., additional, and Giraudo, Claudio G., additional

Published
2018
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23. The Human Blood-Nerve Barrier Transcriptome

Author

Palladino, Steven P., primary, Helton, E. Scott, additional, Jain, Preti, additional, Dong, Chaoling, additional, Crowley, Michael R., additional, Crossman, David K., additional, and Ubogu, Eroboghene E., additional

Published
2017
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24. Targeted next generation sequencing of breast implant‐associated anaplastic large cell lymphoma reveals mutations in JAK/STAT signalling pathway genes, TP53 and DNMT3A

Author

Di Napoli, Arianna, primary, Jain, Preti, additional, Duranti, Enrico, additional, Margolskee, Elizabeth, additional, Arancio, Walter, additional, Facchetti, Fabio, additional, Alobeid, Bachir, additional, Santanelli di Pompeo, Fabio, additional, Mansukhani, Mahesh, additional, and Bhagat, Govind, additional

Published
2016
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26. Genetic landscape of T- and NK-cell post-transplant lymphoproliferative disorders

Author

Margolskee, Elizabeth, primary, Jobanputra, Vaidehi, additional, Jain, Preti, additional, Chen, Jinli, additional, Ganapathi, Karthik, additional, Nahum, Odelia, additional, Levy, Brynn, additional, Morscio, Julie, additional, Murty, Vundavalli, additional, Tousseyn, Thomas, additional, Alobeid, Bachir, additional, Mansukhani, Mahesh, additional, and Bhagat, Govind, additional

Published
2016
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27. The genetic landscape of dural marginal zone lymphomas

Author

Ganapathi, Karthik A., primary, Jobanputra, Vaidehi, additional, Iwamoto, Fabio, additional, Jain, Preti, additional, Chen, Jinli, additional, Cascione, Luciano, additional, Nahum, Odelia, additional, Levy, Brynn, additional, Xie, Yi, additional, Khattar, Pallavi, additional, Hoehn, Daniela, additional, Bertoni, Francesco, additional, Murty, Vundavalli V., additional, Pittaluga, Stefania, additional, Jaffe, Elaine S., additional, Alobeid, Bachir, additional, Mansukhani, Mahesh M., additional, and Bhagat, Govind, additional

Published
2016
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28. You have free access to this contentTargeted next generation sequencing of breast implant-associated anaplastic large cell lymphoma reveals mutations in JAK/STAT signalling pathway genes, TP53 and DNMT3A.

Author

Di Napoli, Arianna, Jain, Preti, Duranti, Enrico, Margolskee, Elizabeth, Arancio, Walter, Facchetti, Fabio, Alobeid, Bachir, Santanelli di Pompeo, Fabio, Mansukhani, Mahesh, and Bhagat, Govind

Subjects
*BREAST implants, *ANAPLASTIC lymphoma kinase, *LYMPHOCYTES, *BIOMARKERS, *GENETIC mutation
Abstract

The article focuses on next generation sequencing of breast implant associated anaplastic large cell lymphoma (BI-ALCL) which reveals mutations in JAK/STAT signalling pathway genes, TP53 and DNMT3A. It mentions BI-ALCL is characterized by the presence of CD30 with atypical lymphocytes frequently confined to the peri-implant seroma fluid. It also mentions identification of biomarkers that enable disease prognostication and optimal treatment.

Published
2018
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29. Genomic and Targeted Mutational Analysis of T/NK-Cell Post-Transplant Lymphoproliferative Disorders Provides Insight into Disease Biology

Author

Margolskee, Elizabeth Michelle, primary, Jobanputra, Vaidehi, additional, Jain, Preti, additional, Chen, Jinli, additional, Nahum, Odelia, additional, Levy, Brynn, additional, Ganapathi, Karthik A, additional, Murty, Vundavalli, additional, Tousseyn, Thomas, additional, Alobeid, Bachir, additional, Manuskhani, Mahesh, additional, and Bhagat, Govind, additional

Published
2015
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35. Phenotypic Heterogeneity of Neutropenia and Gastrointestinal Illness Associated with G6PC3Founder Mutation

Author

Glasser, Chana L., Picoraro, Joseph A., Jain, Preti, Kinberg, Sivan, Rustia, Evelyn, Gross Margolis, Kara, Anyane-Yeboa, Kwame, Iglesias, Alejandro D., and Green, Nancy S.

Abstract

Severe congenital neutropenia type IV (SCN IV) is a syndrome of severe neutropenia, cardiac and urogenital defects, prominent superficial veins, facial dysmorphism, failure to thrive (FTT), and intermittent thrombocytopenia, caused by a glucose-6-phosphatase catalytic subunit 3 (G6PC3) gene mutation. SCN IV has been linked to glycogen storage disease type 1b as both disorders involve disruption of the glucose-6-phosphatase/glucose-6-phosphate transporter complex, leading to arrested neutrophil maturation. Emerging evidence suggests that neutrophil function plays an important role in intestinal integrity, evidenced by inflammatory bowel disease in certain neutropenic patients. Here, we report 3 unrelated Hispanic males from the Dominican Republic with classic features of SCN IV found to share an identical inherited canonical splice-site mutation of the G6PC3gene (c.218+1G>A). All 3 patients presented with severe FTT and gastrointestinal manifestations. Two of the patients had significant improvement in growth and resolution of gastrointestional symptoms with initiation of granulocyte colony-stimulating factor. We hypothesize that the gene variant described represents a founder mutation in the Dominican Republic, the first to be described in this geographical region. We discuss the potential associations between neutropenia and gastrointestinal disease with FTT and the role of granulocyte colony-stimulating factor in improving neutrophil count and intestinal integrity and growth.

Published
2016
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36. Vector-G: Multi-Modular SVM-Based Heterotrimeric G Protein Prediction.

Author

Jain, Preti, Wadhwa, Puneet, Aygun, Ramazan, and Podila, Gopi

Subjects
*G proteins, *MEMBRANE proteins, *NEUROTRANSMITTERS, *CHEMOKINES, *CARDIOVASCULAR diseases, *RAS proteins
Abstract

Heterotrimeric G proteins interact with G protein-coupled receptors in response to stimulation by hormones, neurotransmitters, chemokines, and sensory signals to intracellular signaling cascades. Recently reported studies indicate that G protein subunits play a significant role in different eukaryotic diseases including inflammation, neurological diseases, cardiovascular diseases, endocrine disorders as well as plant pathogen response, infectious hyphae growth, differentiation and virulence of pathogenic fungi. Thus a study of their functions, signaling pathways, and protein interactions may lead to the development of various preventive approaches. The diversity of α, β and γ subunits of G proteins necessitates a prediction algorithm that helps in the identification of new proteins such as Gβ where WD-40 repeats are not well characterized. The currently available techniques for finding G proteins are homology based search analyses and wet lab experiments, which are not very effective in finding new classes of proteins. We present here a robust computational method for finding new G proteins and their homologs using a SVM based pattern recognition algorithm. Several physicochemical and compositional properties including dipeptide, tripeptide and hydrophobicity composition are used for generating the SVM classifiers. This method has 96.17%, 95.38%, 97.6% sensitivity and 99.45%, 100%, 100% specificity on test sets for G protein α, β, and γ subunits, respectively. This algorithm correctly predicts the known α, β and γ subunits reported in literature. One important contribution of this algorithm is that it helps in improving genome annotation of several proteins as G proteins and serves as a useful tool for comparative genomic analysis of G proteins. Using this method, novel G protein subunits are predicted in 31 genomes covering plant, fungi and animal kingdom. The software is available at the website http://biomine.cs.uah.edu/bioinformatics/svm_prog/scripts/GProteins/vectorg.html. Supplementary files: The supplementary files are available on http://www.bioinfo.de/isb/2008/08/0013/supplementary_material/. [ABSTRACT FROM AUTHOR]

Published
2008
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