Correction: Multilocus pathogenic variants contribute to intrafamilial clinical heterogeneity: a retrospective study of sibling pairs with neurodevelopmental disorders

Authors: Tugce Bozkurt‑Yozgatli, Davut Pehlivan, Richard A. Gibbs, Ugur Sezerman, Jennifer E. Posey, James R. Lupski, Zeynep Coban‑Akdemir

Source: BMC Medical Genomics, Vol 17, Iss 1, Pp 1-6 (2024)

Subject Terms: Internal medicine, RC31-1245, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1755-8794

Access URL: https://doaj.org/article/7c2f8ce730c04c82bbae724581e6bcc6

Multilocus pathogenic variants contribute to intrafamilial clinical heterogeneity: a retrospective study of sibling pairs with neurodevelopmental disorders

Authors: Tugce Bozkurt-Yozgatli, Davut Pehlivan, Richard A. Gibbs, Ugur Sezerman, Jennifer E. Posey, James R. Lupski, Zeynep Coban-Akdemir

Source: BMC Medical Genomics, Vol 17, Iss 1, Pp 1-9 (2024)

Subject Terms: Exome sequencing, Runs-of-homozygosity, Multilocus pathogenic variation, Neurodevelopmental disorders, Internal medicine, RC31-1245, Genetics, QH426-470

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Relation: https://doaj.org/toc/1755-8794

Access URL: https://doaj.org/article/51d450bce538427a9c0786a16cce4ff7

NODAL variants are associated with a continuum of laterality defects from simple D-transposition of the great arteries to heterotaxy

Authors: Zain Dardas, Jawid M. Fatih, Angad Jolly, Moez Dawood, Haowei Du, Christopher M. Grochowski, Edward G. Jones, Shalini N. Jhangiani, Xander H. T. Wehrens, Pengfei Liu, Weimin Bi, Eric Boerwinkle, Jennifer E. Posey, Donna M. Muzny, Richard A. Gibbs, James R. Lupski, Zeynep Coban-Akdemir, Shaine A. Morris

Source: Genome Medicine, Vol 16, Iss 1, Pp 1-20 (2024)

Subject Terms: Congenital heart disease, NODAL, Laterality defects, Heterotaxy, Transposition, Single ventricle, Medicine, Genetics, QH426-470

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Relation: https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/732bd51decf14dba8374c1b62dec21e8

The impact of the Turkish population variome on the genomic architecture of rare disease traits

Authors: Zeynep Coban-Akdemir, Xiaofei Song, Francisco C. Ceballos, Davut Pehlivan, Ender Karaca, Yavuz Bayram, Tadahiro Mitani, Tomasz Gambin, Tugce Bozkurt-Yozgatli, Shalini N. Jhangiani, Donna M. Muzny, Richard A. Lewis, Pengfei Liu, Eric Boerwinkle, Ada Hamosh, Richard A. Gibbs, V. Reid Sutton, Nara Sobreira, Claudia M.B. Carvalho, Chad A. Shaw, Jennifer E. Posey, David Valle, James R. Lupski

Source: Genetics in Medicine Open, Vol 2, Iss , Pp 101830- (2024)

Subject Terms: Admixture, Consanguinity, Genomic architecture of rare disease traits, Runs of homozygosity, Turkish population, Genetics, QH426-470, Medicine

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2949774424009762; https://doaj.org/toc/2949-7744

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The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation

Authors: Haowei Du, Angad Jolly, Christopher M. Grochowski, Bo Yuan, Moez Dawood, Shalini N. Jhangiani, He Li, Donna Muzny, Jawid M. Fatih, Zeynep Coban-Akdemir, Mary Esther Carlin, Angela E. Scheuerle, Karin Witzl, Jennifer E. Posey, Matthew Pendleton, Eoghan Harrington, Sissel Juul, P. J. Hastings, Weimin Bi, Richard A. Gibbs, Fritz J. Sedlazeck, James R. Lupski, Claudia M. B. Carvalho, Pengfei Liu

Source: Genome Medicine, Vol 14, Iss 1, Pp 1-21 (2022)

Subject Terms: Long-read sequencing, Genomic data integration, Genomic data visualization, MMBIR, Genomic instability, Tandem duplication, De novo CNV, De novo SNV, Human Phenotype Ontology, Structural variation, Medicine, Genetics, QH426-470

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Relation: https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/fea7d8f692a64a578e2bc6531220b304

P669: VariantMatcher: A tool to enable connections amongst individuals with interest in a specific variant

Authors: Nara Sobreira, Sean Griffith, Corina Antonescu, Laura Vail, Jennifer Posey, Zeynep Coban-Akdemir, Shalini Jhangiani, Kimberly Doheny, James Lupski, David Valle, Ada Hamosh, Renan Martin

Source: Genetics in Medicine Open, Vol 1, Iss 1, Pp 100734- (2023)

Subject Terms: Genetics, QH426-470, Medicine

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2949774423007343; https://doaj.org/toc/2949-7744

Access URL: https://doaj.org/article/e1a01f486f2c4397ad554b19f25e1d15

Deep clinicopathological phenotyping identifies a previously unrecognized pathogenic EMD splice variant

Authors: Daniel G. Calame, Jawid M. Fatih, Isabella Herman, Zeynep Coban‐Akdemir, Haowei Du, Tadahiro Mitani, Shalini N. Jhangiani, Dana Marafi, Richard A. Gibbs, Jennifer E. Posey, Vidya P. Mehta, Carrie A. Mohila, Farida Abid, Timothy E. Lotze, Davut Pehlivan, Adekunle M. Adesina, James R. Lupski

Source: Annals of Clinical and Translational Neurology, Vol 8, Iss 10, Pp 2052-2058 (2021)

Subject Terms: Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571, Neurology. Diseases of the nervous system, RC346-429

File Description: electronic resource

Relation: https://doaj.org/toc/2328-9503

Access URL: https://doaj.org/article/cb34fe521e7d4c82ae7f6de309954374

Developmental genomics of limb malformations: Allelic series in association with gene dosage effects contribute to the clinical variability

Authors: Ruizhi Duan, Hadia Hijazi, Elif Yilmaz Gulec, Hatice Koçak Eker, Silvia R. Costa, Yavuz Sahin, Zeynep Ocak, Sedat Isikay, Ozge Ozalp, Sevcan Bozdogan, Huseyin Aslan, Nursel Elcioglu, Débora R. Bertola, Alper Gezdirici, Haowei Du, Jawid M. Fatih, Christopher M. Grochowski, Gulsen Akay, Shalini N. Jhangiani, Ender Karaca, Shen Gu, Zeynep Coban-Akdemir, Jennifer E. Posey, Yavuz Bayram, V. Reid Sutton, Claudia M.B. Carvalho, Davut Pehlivan, Richard A. Gibbs, James R. Lupski

Source: HGG Advances, Vol 3, Iss 4, Pp 100132- (2022)

Subject Terms: allelic series, Alu/Alu-mediated rearrangement, birth defect, clinical genomics, congenital limb malformation, developmental genomics, Genetics, QH426-470

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666247722000483; https://doaj.org/toc/2666-2477

Access URL: https://doaj.org/article/335675b4b479443ca3e74cb451032f99

PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data

Authors: Elizabeth Wohler, Renan Martin, Sean Griffith, Eliete da S. Rodrigues, Corina Antonescu, Jennifer E. Posey, Zeynep Coban-Akdemir, Shalini N. Jhangiani, Kimberly F. Doheny, James R. Lupski, David Valle, Ada Hamosh, Nara Sobreira

Source: Orphanet Journal of Rare Diseases, Vol 16, Iss 1, Pp 1-10 (2021)

Subject Terms: PhenoDB, GeneMatcher, VariantMatcher, Data sharing, Genomic data, Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/1750-1172

Access URL: https://doaj.org/article/4318a9ec0d084d8d8a388f43495e19c1

Novel pathogenic variants and quantitative phenotypic analyses of Robinow syndrome: WNT signaling perturbation and phenotypic variability

Authors: Chaofan Zhang, Angad Jolly, Brian J. Shayota, Juliana F. Mazzeu, Haowei Du, Moez Dawood, Patricia Celestino Soper, Ariadne Ramalho de Lima, Bárbara Merfort Ferreira, Zeynep Coban-Akdemir, Janson White, Deborah Shears, Fraser Robert Thomson, Sarah Louise Douglas, Andrew Wainwright, Kathryn Bailey, Paul Wordsworth, Mike Oldridge, Tracy Lester, Alistair D. Calder, Katja Dumic, Siddharth Banka, Dian Donnai, Shalini N. Jhangiani, Lorraine Potocki, Wendy K. Chung, Sara Mora, Hope Northrup, Myla Ashfaq, Jill A. Rosenfeld, Kati Mason, Lynda C. Pollack, Allyn McConkie-Rosell, Wei Kelly, Marie McDonald, Natalie S. Hauser, Peter Leahy, Cynthia M. Powell, Raquel Boy, Rachel Sayuri Honjo, Fernando Kok, Lucia R. Martelli, Vicente Odone Filho, Genomics England Research Consortium, Donna M. Muzny, Richard A. Gibbs, Jennifer E. Posey, Pengfei Liu, James R. Lupski, V. Reid Sutton, Claudia M.B. Carvalho

Source: HGG Advances, Vol 3, Iss 1, Pp 100074- (2022)

Subject Terms: genotype-phenotype correlation, skeletal dysplasia, HPO terms, quantitative phenotyping cluster heatmap, molecular diagnosis, traits and OMIM clinical synopsis, Genetics, QH426-470

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666247721000555; https://doaj.org/toc/2666-2477

Access URL: https://doaj.org/article/111938d44884445f92d7831c96a453cf

Interchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome

Authors: Claudia M. B. Carvalho, Zeynep Coban-Akdemir, Hadia Hijazi, Bo Yuan, Matthew Pendleton, Eoghan Harrington, John Beaulaurier, Sissel Juul, Daniel J. Turner, Rupa S. Kanchi, Shalini N. Jhangiani, Donna M. Muzny, Richard A. Gibbs, Baylor-Hopkins Center for Mendelian Genomics, Pawel Stankiewicz, John W. Belmont, Chad A. Shaw, Sau Wai Cheung, Neil A. Hanchard, V. Reid Sutton, Patricia I. Bader, James R. Lupski

Source: Genome Medicine, Vol 11, Iss 1, Pp 1-14 (2019)

Subject Terms: Triplication, DUP-TRP/INV-DUP, Complex genomic rearrangement, MMBIR, Replicative-based mechanism, Inter-homologous chromosomal template switch, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13073-019-0633-y; https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/9879805980e143e1af4e72fdff58ff03

Immune Dysregulation Mimicking Systemic Lupus Erythematosus in a Patient With Lysinuric Protein Intolerance: Case Report and Review of the Literature

Authors: Josefina Longeri Contreras, Mabel A. Ladino, Katherine Aránguiz, Gonzalo P. Mendez, Zeynep Coban-Akdemir, Bo Yuan, Richard A. Gibbs, Lindsay C. Burrage, James R. Lupski, Ivan K. Chinn, Tiphanie P. Vogel, Jordan S. Orange, M. Cecilia Poli

Source: Frontiers in Pediatrics, Vol 9 (2021)

Subject Terms: lysinuric protein intolerance, systemic lupus erythematosus, hemophagocytic lymphohistiocytosis, immune mediated glomerulonephritis, case report, systemic lupus–erythematosus, Pediatrics, RJ1-570

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fped.2021.673957/full; https://doaj.org/toc/2296-2360

Access URL: https://doaj.org/article/7f674538bee04d729f9bb565e0c6aa14

Identification of novel candidate disease genes from de novo exonic copy number variants

Authors: Tomasz Gambin, Bo Yuan, Weimin Bi, Pengfei Liu, Jill A. Rosenfeld, Zeynep Coban-Akdemir, Amber N. Pursley, Sandesh C. S. Nagamani, Ronit Marom, Sailaja Golla, Lauren Dengle, Heather G. Petrie, Reuben Matalon, Lisa Emrick, Monica B. Proud, Diane Treadwell-Deering, Hsiao-Tuan Chao, Hannele Koillinen, Chester Brown, Nora Urraca, Roya Mostafavi, Saunder Bernes, Elizabeth R. Roeder, Kimberly M. Nugent, Patricia I. Bader, Gary Bellus, Michael Cummings, Hope Northrup, Myla Ashfaq, Rachel Westman, Robert Wildin, Anita E. Beck, LaDonna Immken, Lindsay Elton, Shaun Varghese, Edward Buchanan, Laurence Faivre, Mathilde Lefebvre, Christian P. Schaaf, Magdalena Walkiewicz, Yaping Yang, Sung-Hae L. Kang, Seema R. Lalani, Carlos A. Bacino, Arthur L. Beaudet, Amy M. Breman, Janice L. Smith, Sau Wai Cheung, James R. Lupski, Ankita Patel, Chad A. Shaw, Paweł Stankiewicz

Source: Genome Medicine, Vol 9, Iss 1, Pp 1-15 (2017)

Subject Terms: Exon targeted array CGH, Intragenic copy number variants, CNVs, de novo variants, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13073-017-0472-7; https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/e6f31aabb43544b3bfd37c91bba99006

Phenotypic and molecular characterisation of CDK13-related congenital heart defects, dysmorphic facial features and intellectual developmental disorders

Authors: Bret L. Bostwick, Scott McLean, Jennifer E. Posey, Haley E. Streff, Karen W. Gripp, Alyssa Blesson, Nina Powell-Hamilton, Jessica Tusi, David A. Stevenson, Ellyn Farrelly, Louanne Hudgins, Yaping Yang, Fan Xia, Xia Wang, Pengfei Liu, Magdalena Walkiewicz, Marianne McGuire, Dorothy K. Grange, Marisa V. Andrews, Marybeth Hummel, Suneeta Madan-Khetarpal, Elena Infante, Zeynep Coban-Akdemir, Karol Miszalski-Jamka, John L. Jefferies, Members of the Undiagnosed Diseases Network, Jill A. Rosenfeld, Lisa Emrick, Kimberly M. Nugent, James R. Lupski, John W. Belmont, Brendan Lee, Seema R. Lalani

Source: Genome Medicine, Vol 9, Iss 1, Pp 1-9 (2017)

Subject Terms: CDK13, CHDFIDD, De novo variant, Neurodevelopmental disorders, Agenesis of the corpus callosum, Hypertelorism, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13073-017-0463-8; https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/9e8b3e6b6e104c55b95b2eb2877f0f28

Novel Heterozygous Mutation in NFKB2 Is Associated With Early Onset CVID and a Functional Defect in NK Cells Complicated by Disseminated CMV Infection and Severe Nephrotic Syndrome

Authors: Alejandra Aird, Macarena Lagos, Alexander Vargas-Hernández, Jennifer E. Posey, Zeynep Coban-Akdemir, Shalini Jhangiani, Emily M. Mace, Anaid Reyes, Alejandra King, Felipe Cavagnaro, Lisa R. Forbes, Ivan K. Chinn, James R. Lupski, Jordan S. Orange, Maria Cecilia Poli

Source: Frontiers in Pediatrics, Vol 7 (2019)

Subject Terms: primary immunodeficiency, NF-κB2, common variable immunodeficiency (CVID), nephrotic syndrome, systemic cytomegalovirus, pituitary deficiency, Pediatrics, RJ1-570

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fped.2019.00303/full; https://doaj.org/toc/2296-2360

Access URL: https://doaj.org/article/1eab47348551429cb8c5a97383b3954c

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

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

Source: Genome Medicine, Vol 8, Iss 1, Pp 1-15 (2016)

Subject Terms: Diagnostic, Intellectual disability, Chromatin conformation, Text mining, Disease network, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13073-016-0359-z; https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/b944a7ab8a69489a919bdf59be14b60a

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Genetic and molecular mechanism for distinct clinical phenotypes conveyed by allelic truncating mutations implicated in FBN1

Authors: Mao Lin, Zhenlei Liu, Gang Liu, Sen Zhao, Chao Li, Weisheng Chen, Zeynep Coban Akdemir, Jiachen Lin, Xiaofei Song, Shengru Wang, Qiming Xu, Yanxue Zhao, Lianlei Wang, Yuanqiang Zhang, Zihui Yan, Sen Liu, Jiaqi Liu, Yixin Chen, Yuzhi Zuo, Xu Yang, Tianshu Sun, Xin‐Zhuang Yang, Yuchen Niu, Xiaoxin Li, Wesley You, Bintao Qiu, Chen Ding, Pengfei Liu, Shuyang Zhang, Claudia M. B. Carvalho, Jennifer E. Posey, Guixing Qiu, Deciphering Disorders Involving Scoliosis and COmorbidities (DISCO) study, James R. Lupski, Zhihong Wu, Jianguo Zhang, Nan Wu

Source: Molecular Genetics & Genomic Medicine, Vol 8, Iss 1, Pp n/a-n/a (2020)

Subject Terms: dominant‐negative mechanism, FBN1, Marfan syndrome, Marfanoid–progeroid–lipodystrophy syndrome, targeted next generation sequencing, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/2324-9269

Access URL: https://doaj.org/article/5cbefdd21f0a45fc98c8888556471ceb

Clinically severe CACNA1A alleles affect synaptic function and neurodegeneration differentially.

Authors: Xi Luo, Jill A Rosenfeld, Shinya Yamamoto, Tamar Harel, Zhongyuan Zuo, Melissa Hall, Klaas J Wierenga, Matthew T Pastore, Dennis Bartholomew, Mauricio R Delgado, Joshua Rotenberg, Richard Alan Lewis, Lisa Emrick, Carlos A Bacino, Mohammad K Eldomery, Zeynep Coban Akdemir, Fan Xia, Yaping Yang, Seema R Lalani, Timothy Lotze, James R Lupski, Brendan Lee, Hugo J Bellen, Michael F Wangler, Members of the UDN

Source: PLoS Genetics, Vol 13, Iss 7, p e1006905 (2017)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC5557584?pdf=render; https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

Access URL: https://doaj.org/article/56bd9b19ccf04563bd8e2253cc607059

Mechanisms for Complex Chromosomal Insertions.

Authors: Shen Gu, Przemyslaw Szafranski, Zeynep Coban Akdemir, Bo Yuan, Mitchell L Cooper, Maria A Magriñá, Carlos A Bacino, Seema R Lalani, Amy M Breman, Janice L Smith, Ankita Patel, Rodger H Song, Weimin Bi, Sau Wai Cheung, Claudia M B Carvalho, Paweł Stankiewicz, James R Lupski

Source: PLoS Genetics, Vol 12, Iss 11, p e1006446 (2016)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC5120786?pdf=render; https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

Access URL: https://doaj.org/article/f2390e2325234092888cd316fbc87b0d