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Gilles Maussion, Cristiana Cruceanu, Jill A Rosenfeld, Scott C Bell, Fabrice Jollant, Jin Szatkiewicz, Ryan L Collins, Carrie Hanscom, Ilaria Kolobova, Nicolas Menjot de Champfleur, Ian Blumenthal, Colby Chiang, Vanessa Ota, Christina Hultman, Colm O'Dushlaine, Steve McCarroll, Martin Alda, Sebastien Jacquemont, Zehra Ordulu, Christian R Marshall, Melissa T Carter, Lisa G Shaffer, Pamela Sklar, Santhosh Girirajan, Cynthia C Morton, James F Gusella, Gustavo Turecki, Dimitri J Stavropoulos, Patrick F Sullivan, Stephen W Scherer, Michael E Talkowski, Carl Ernst
The cover image, by Carl Ernst et al., is based on the Original Article Implication of LRRC4C and DPP6 in neurodevelopmental disorders, DOI: 10.1002/ajmg.a.38021.
February 2017: American Journal of Medical Genetics. Part A
Natalie D Shaw, Harrison Brand, Zachary A Kupchinsky, Hemant Bengani, Lacey Plummer, Takako I Jones, Serkan Erdin, Kathleen A Williamson, Joe Rainger, Alexei Stortchevoi, Kaitlin Samocha, Benjamin B Currall, Donncha S Dunican, Ryan L Collins, Jason R Willer, Angela Lek, Monkol Lek, Malik Nassan, Shahrin Pereira, Tammy Kammin, Diane Lucente, Alexandra Silva, Catarina M Seabra, Colby Chiang, Yu An, Morad Ansari, Jacqueline K Rainger, Shelagh Joss, Jill Clayton Smith, Margaret F Lippincott, Sylvia S Singh, Nirav Patel, Jenny W Jing, Jennifer R Law, Nalton Ferraro, Alain Verloes, Anita Rauch, Katharina Steindl, Markus Zweier, Ianina Scheer, Daisuke Sato, Nobuhiko Okamoto, Christina Jacobsen, Jeanie Tryggestad, Steven Chernausek, Lisa A Schimmenti, Benjamin Brasseur, Claudia Cesaretti, Jose E García-Ortiz, Tatiana Pineda Buitrago, Orlando Perez Silva, Jodi D Hoffman, Wolfgang Mühlbauer, Klaus W Ruprecht, Bart L Loeys, Masato Shino, Angela M Kaindl, Chie-Hee Cho, Cynthia C Morton, Richard R Meehan, Veronica van Heyningen, Eric C Liao, Ravikumar Balasubramanian, Janet E Hall, Stephanie B Seminara, Daniel Macarthur, Steven A Moore, Koh-Ichiro Yoshiura, James F Gusella, Joseph A Marsh, John M Graham, Angela E Lin, Nicholas Katsanis, Peter L Jones, William F Crowley, Erica E Davis, David R FitzPatrick, Michael E Talkowski
Arhinia, or absence of the nose, is a rare malformation of unknown etiology that is often accompanied by ocular and reproductive defects. Sequencing of 40 people with arhinia revealed that 84% of probands harbor a missense mutation localized to a constrained region of SMCHD1 encompassing the ATPase domain. SMCHD1 mutations cause facioscapulohumeral muscular dystrophy type 2 (FSHD2) via a trans-acting loss-of-function epigenetic mechanism. We discovered shared mutations and comparable DNA hypomethylation patterning between these distinct disorders...
January 9, 2017: Nature Genetics
Gilles Maussion, Cristiana Cruceanu, Jill A Rosenfeld, Scott C Bell, Fabrice Jollant, Jin Szatkiewicz, Ryan L Collins, Carrie Hanscom, Ilaria Kolobova, Nicolas Menjot de Champfleur, Ian Blumenthal, Colby Chiang, Vanessa Ota, Christina Hultman, Colm O'Dushlaine, Steve McCarroll, Martin Alda, Sebastien Jacquemont, Zehra Ordulu, Christian R Marshall, Melissa T Carter, Lisa G Shaffer, Pamela Sklar, Santhosh Girirajan, Cynthia C Morton, James F Gusella, Gustavo Turecki, Dimitri J Stavropoulos, Patrick F Sullivan, Stephen W Scherer, Michael E Talkowski, Carl Ernst
We performed whole-genome sequencing on an individual from a family with variable psychiatric phenotypes that had a sensory processing disorder, apraxia, and autism. The proband harbored a maternally inherited balanced translocation (46,XY,t(11;14)(p12;p12)mat) that disrupted LRRC4C, a member of the highly specialized netrin G family of axon guidance molecules. The proband also inherited a paternally derived chromosomal inversion that disrupted DPP6, a potassium channel interacting protein. Copy Number (CN) analysis in 14,077 cases with neurodevelopmental disorders and 8,960 control subjects revealed that 60% of cases with exonic deletions in LRRC4C had a second clinically recognizable syndrome associated with variable clinical phenotypes, including 16p11...
February 2017: American Journal of Medical Genetics. Part A
Zehra Ordulu, Tammy Kammin, Harrison Brand, Vamsee Pillalamarri, Claire E Redin, Ryan L Collins, Ian Blumenthal, Carrie Hanscom, Shahrin Pereira, India Bradley, Barbara F Crandall, Pamela Gerrol, Mark A Hayden, Naveed Hussain, Bibi Kanengisser-Pines, Sibel Kantarci, Brynn Levy, Michael J Macera, Fabiola Quintero-Rivera, Erica Spiegel, Blair Stevens, Janet E Ulm, Dorothy Warburton, Louise E Wilkins-Haug, Naomi Yachelevich, James F Gusella, Michael E Talkowski, Cynthia C Morton
In this exciting era of "next-gen cytogenetics," integrating genomic sequencing into the prenatal diagnostic setting is possible within an actionable time frame and can provide precise delineation of balanced chromosomal rearrangements at the nucleotide level. Given the increased risk of congenital abnormalities in newborns with de novo balanced chromosomal rearrangements, comprehensive interpretation of breakpoints could substantially improve prediction of phenotypic outcomes and support perinatal medical care...
November 3, 2016: American Journal of Human Genetics
Samantha Lp Schilit, Benjamin B Currall, Ruen Yao, Carrie Hanscom, Ryan L Collins, Vamsee Pillalamarri, Dong-Young Lee, Tammy Kammin, Cinthya J Zepeda-Mendoza, Tarja Mononen, Lisa S Nolan, James F Gusella, Michael E Talkowski, Jun Shen, Cynthia C Morton
Analysis of chromosomal rearrangements has been highly successful in identifying genes involved in many congenital abnormalities including hearing loss. Herein, we report a subject, designated DGAP242, with congenital hearing loss (HL) and a de novo balanced translocation 46,XX,t(1;5)(q32;q15)dn. Using multiple next-generation sequencing techniques, we obtained high resolution of the breakpoints. This revealed disruption of the orphan receptor ESRRG on chromosome 1, which is differentially expressed in inner ear hair cells and has previously been implicated in HL, and disruption of KIAA0825 on chromosome 5...
November 2016: European Journal of Human Genetics: EJHG
Monika Macakova, Bozena Bohuslavova, Petra Vochozkova, Antonin Pavlok, Miroslava Sedlackova, Daniela Vidinska, Klara Vochyanova, Irena Liskova, Ivona Valekova, Monika Baxa, Zdenka Ellederova, Jiri Klima, Stefan Juhas, Jana Juhasova, Jana Klouckova, Martin Haluzik, Jiri Klempir, Hana Hansikova, Jana Spacilova, Ryan Collins, Ian Blumenthal, Michael Talkowski, James F Gusella, David S Howland, Marian DiFiglia, Jan Motlik
BACKGROUND: Huntington's disease is induced by CAG expansion in a single gene coding the huntingtin protein. The mutated huntingtin (mtHtt) primarily causes degeneration of neurons in the brain, but it also affects peripheral tissues, including testes. OBJECTIVE: We studied sperm and testes of transgenic boars expressing the N-terminal region of human mtHtt. METHODS: In this study, measures of reproductive parameters and electron microscopy (EM) images of spermatozoa and testes of transgenic (TgHD) and wild-type (WT) boars of F1 (24-48 months old) and F2 (12-36 months old) generations were compared...
2016: Neuro-degenerative Diseases
Derek J C Tai, Ashok Ragavendran, Poornima Manavalan, Alexei Stortchevoi, Catarina M Seabra, Serkan Erdin, Ryan L Collins, Ian Blumenthal, Xiaoli Chen, Yiping Shen, Mustafa Sahin, Chengsheng Zhang, Charles Lee, James F Gusella, Michael E Talkowski
Recurrent, reciprocal genomic disorders resulting from non-allelic homologous recombination (NAHR) between near-identical segmental duplications (SDs) are a major cause of human disease, often producing phenotypically distinct syndromes. The genomic architecture of flanking SDs presents a challenge for modeling these syndromes; however, the capability to efficiently generate reciprocal copy number variants (CNVs) that mimic NAHR would represent a valuable modeling tool. We describe here a CRISPR/Cas9 genome engineering method, single-guide CRISPR/Cas targeting of repetitive elements (SCORE), to model reciprocal genomic disorders and demonstrate its capabilities by generating reciprocal CNVs of 16p11...
March 2016: Nature Neuroscience
Kusumika Mukherjee, Kana Ishii, Vamsee Pillalamarri, Tammy Kammin, Joan F Atkin, Scott E Hickey, Qiongchao J Xi, Cinthya J Zepeda, James F Gusella, Michael E Talkowski, Cynthia C Morton, Richard L Maas, Eric C Liao
CAPZB is an actin-capping protein that caps the growing end of F-actin and modulates the cytoskeleton and tethers actin filaments to the Z-line of the sarcomere in muscles. Whole-genome sequencing was performed on a subject with micrognathia, cleft palate and hypotonia that harbored a de novo, balanced chromosomal translocation that disrupts the CAPZB gene. The function of capzb was analyzed in the zebrafish model. capzb(-/-) mutants exhibit both craniofacial and muscle defects that recapitulate the phenotypes observed in the human subject...
April 1, 2016: Human Molecular Genetics
Harrison Brand, Ryan L Collins, Carrie Hanscom, Jill A Rosenfeld, Vamsee Pillalamarri, Matthew R Stone, Fontina Kelley, Tamara Mason, Lauren Margolin, Stacey Eggert, Elyse Mitchell, Jennelle C Hodge, James F Gusella, Stephan J Sanders, Michael E Talkowski
Copy-number variants (CNVs) have been the predominant focus of genetic studies of structural variation, and chromosomal microarray (CMA) for genome-wide CNV detection is the recommended first-tier genetic diagnostic screen in neurodevelopmental disorders. We compared CNVs observed by CMA to the structural variation detected by whole-genome large-insert sequencing in 259 individuals diagnosed with autism spectrum disorder (ASD) from the Simons Simplex Collection. These analyses revealed a diverse landscape of complex duplications in the human genome...
July 2, 2015: American Journal of Human Genetics
Eugenia Migliavacca, Christelle Golzio, Katrin Männik, Ian Blumenthal, Edwin C Oh, Louise Harewood, Jack A Kosmicki, Maria Nicla Loviglio, Giuliana Giannuzzi, Loyse Hippolyte, Anne M Maillard, Ali Abdullah Alfaiz, Mieke M van Haelst, Joris Andrieux, James F Gusella, Mark J Daly, Jacques S Beckmann, Sébastien Jacquemont, Michael E Talkowski, Nicholas Katsanis, Alexandre Reymond
The 16p11.2 600 kb copy-number variants (CNVs) are associated with mirror phenotypes on BMI, head circumference, and brain volume and represent frequent genetic lesions in autism spectrum disorders (ASDs) and schizophrenia. Here we interrogated the transcriptome of individuals carrying reciprocal 16p11.2 CNVs. Transcript perturbations correlated with clinical endophenotypes and were enriched for genes associated with ASDs, abnormalities of head size, and ciliopathies. Ciliary gene expression was also perturbed in orthologous mouse models, raising the possibility that ciliary dysfunction contributes to 16p11...
May 7, 2015: American Journal of Human Genetics
Lucie J Rochard, Edward Li, Christina Nguyen, James F Gusella, Richard Maas, Cynthia Morton, Michael Talkowski, Eric C Liao
No abstract text is available yet for this article.
May 2015: Plastic and Reconstructive Surgery
Kusumika Mukherjee, Kanaa Ishii, Michael J Grimaldi, Christina Nguyen, Michael Talkowski, James Gusella, Richard Maas, Cynthia C Morton, Eric C Liao
No abstract text is available yet for this article.
May 2015: Plastic and Reconstructive Surgery
Marta Biagioli, Francesco Ferrari, Eric M Mendenhall, Yijing Zhang, Serkan Erdin, Ravi Vijayvargia, Sonia M Vallabh, Nicole Solomos, Poornima Manavalan, Ashok Ragavendran, Fatih Ozsolak, Jong Min Lee, Michael E Talkowski, James F Gusella, Marcy E Macdonald, Peter J Park, Ihn Sik Seong
The CAG repeat expansion in the Huntington's disease gene HTT extends a polyglutamine tract in mutant huntingtin that enhances its ability to facilitate polycomb repressive complex 2 (PRC2). To gain insight into this dominant gain of function, we mapped histone modifications genome-wide across an isogenic panel of mouse embryonic stem cell (ESC) and neuronal progenitor cell (NPC) lines, comparing the effects of Htt null and different size Htt CAG mutations. We found that Htt is required in ESC for the proper deposition of histone H3K27me3 at a subset of 'bivalent' loci but in NPC it is needed at 'bivalent' loci for both the proper maintenance and the appropriate removal of this mark...
May 1, 2015: Human Molecular Genetics
Aarathi Sugathan, Marta Biagioli, Christelle Golzio, Serkan Erdin, Ian Blumenthal, Poornima Manavalan, Ashok Ragavendran, Harrison Brand, Diane Lucente, Judith Miles, Steven D Sheridan, Alexei Stortchevoi, Manolis Kellis, Stephen J Haggarty, Nicholas Katsanis, James F Gusella, Michael E Talkowski
Truncating mutations of chromodomain helicase DNA-binding protein 8 (CHD8), and of many other genes with diverse functions, are strong-effect risk factors for autism spectrum disorder (ASD), suggesting multiple mechanisms of pathogenesis. We explored the transcriptional networks that CHD8 regulates in neural progenitor cells (NPCs) by reducing its expression and then integrating transcriptome sequencing (RNA sequencing) with genome-wide CHD8 binding (ChIP sequencing). Suppressing CHD8 to levels comparable with the loss of a single allele caused altered expression of 1,756 genes, 64...
October 21, 2014: Proceedings of the National Academy of Sciences of the United States of America
Harrison Brand, Vamsee Pillalamarri, Ryan L Collins, Stacey Eggert, Colm O'Dushlaine, Ellen B Braaten, Matthew R Stone, Kimberly Chambert, Nathan D Doty, Carrie Hanscom, Jill A Rosenfeld, Hillary Ditmars, Jessica Blais, Ryan Mills, Charles Lee, James F Gusella, Steven McCarroll, Jordan W Smoller, Michael E Talkowski, Alysa E Doyle
Structural variation (SV) is a significant component of the genetic etiology of both neurodevelopmental and psychiatric disorders; however, routine guidelines for clinical genetic screening have been established only in the former category. Genome-wide chromosomal microarray (CMA) can detect genomic imbalances such as copy-number variants (CNVs), but balanced chromosomal abnormalities (BCAs) still require karyotyping for clinical detection. Moreover, submicroscopic BCAs and subarray threshold CNVs are intractable, or cryptic, to both CMA and karyotyping...
October 2, 2014: American Journal of Human Genetics
Ian Blumenthal, Ashok Ragavendran, Serkan Erdin, Lambertus Klei, Aarathi Sugathan, Jolene R Guide, Poornima Manavalan, Julian Q Zhou, Vanessa C Wheeler, Joshua Z Levin, Carl Ernst, Kathryn Roeder, Bernie Devlin, James F Gusella, Michael E Talkowski
Reciprocal copy-number variation (CNV) of a 593 kb region of 16p11.2 is a common genetic cause of autism spectrum disorder (ASD), yet it is not completely penetrant and can manifest in a wide array of phenotypes. To explore its molecular consequences, we performed RNA sequencing of cerebral cortex from mouse models with CNV of the syntenic 7qF3 region and lymphoblast lines from 34 members of 7 multiplex ASD-affected families harboring the 16p11.2 CNV. Expression of all genes in the CNV region correlated well with their DNA copy number, with no evidence of dosage compensation...
June 5, 2014: American Journal of Human Genetics
Zehra Ordulu, Kristen E Wong, Benjamin B Currall, Andrew R Ivanov, Shahrin Pereira, Sara Althari, James F Gusella, Michael E Talkowski, Cynthia C Morton
With recent rapid advances in genomic technologies, precise delineation of structural chromosome rearrangements at the nucleotide level is becoming increasingly feasible. In this era of "next-generation cytogenetics" (i.e., an integration of traditional cytogenetic techniques and next-generation sequencing), a consensus nomenclature is essential for accurate communication and data sharing. Currently, nomenclature for describing the sequencing data of these aberrations is lacking. Herein, we present a system called Next-Gen Cytogenetic Nomenclature, which is concordant with the International System for Human Cytogenetic Nomenclature (2013)...
May 1, 2014: American Journal of Human Genetics
Michael E Talkowski, Eric Vallabh Minikel, James F Gusella
The last several years have seen unprecedented advances in deciphering the genetic etiology of autism spectrum disorders (ASDs). Heritability studies have repeatedly affirmed a contribution of genetic factors to the overall disease risk. Technical breakthroughs have enabled the search for these genetic factors via genome-wide surveys of a spectrum of potential sequence variations, from common single-nucleotide polymorphisms to essentially private chromosomal abnormalities. Studies of copy-number variation have identified significant roles for both recurrent and nonrecurrent large dosage imbalances, although they have rarely revealed the individual genes responsible...
March 2014: Harvard Review of Psychiatry
Sureni V Mullegama, Jill A Rosenfeld, Carmen Orellana, Bregje W M van Bon, Sara Halbach, Elena A Repnikova, Lauren Brick, Chumei Li, Lucie Dupuis, Monica Rosello, Swaroop Aradhya, D James Stavropoulos, Kandamurugu Manickam, Elyse Mitchell, Jennelle C Hodge, Michael E Talkowski, James F Gusella, Kory Keller, Jonathan Zonana, Stuart Schwartz, Robert E Pyatt, Darrel J Waggoner, Lisa G Shaffer, Angela E Lin, Bert B A de Vries, Roberto Mendoza-Londono, Sarah H Elsea
Copy number variations associated with abnormal gene dosage have an important role in the genetic etiology of many neurodevelopmental disorders, including intellectual disability (ID) and autism. We hypothesize that the chromosome 2q23.1 region encompassing MBD5 is a dosage-dependent region, wherein deletion or duplication results in altered gene dosage. We previously established the 2q23.1 microdeletion syndrome and report herein 23 individuals with 2q23.1 duplications, thus establishing a complementary duplication syndrome...
January 2014: European Journal of Human Genetics: EJHG
J C Hodge, E Mitchell, V Pillalamarri, T L Toler, F Bartel, H M Kearney, Y S Zou, W H Tan, C Hanscom, S Kirmani, R R Hanson, S A Skinner, R C Rogers, D B Everman, E Boyd, C Tapp, S V Mullegama, D Keelean-Fuller, C M Powell, S H Elsea, C C Morton, J F Gusella, B DuPont, A Chaubey, A E Lin, M E Talkowski
Microdeletions of chromosomal region 2q23.1 that disrupt MBD5 (methyl-CpG-binding domain protein 5) contribute to a spectrum of neurodevelopmental phenotypes; however, the impact of this locus on human psychopathology has not been fully explored. To characterize the structural variation landscape of MBD5 disruptions and the associated human psychopathology, 22 individuals with genomic disruption of MBD5 (translocation, point mutation and deletion) were identified through whole-genome sequencing or cytogenomic microarray at 11 molecular diagnostic centers...
March 2014: Molecular Psychiatry
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