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Evan Eichler

Tatsiana Aneichyk, William T Hendriks, Rachita Yadav, David Shin, Dadi Gao, Christine A Vaine, Ryan L Collins, Aloysius Domingo, Benjamin Currall, Alexei Stortchevoi, Trisha Multhaupt-Buell, Ellen B Penney, Lilian Cruz, Jyotsna Dhakal, Harrison Brand, Carrie Hanscom, Caroline Antolik, Marisela Dy, Ashok Ragavendran, Jason Underwood, Stuart Cantsilieris, Katherine M Munson, Evan E Eichler, Patrick Acuña, Criscely Go, R Dominic G Jamora, Raymond L Rosales, Deanna M Church, Stephen R Williams, Sarah Garcia, Christine Klein, Ulrich Müller, Kirk C Wilhelmsen, H T Marc Timmers, Yechiam Sapir, Brian J Wainger, Daniel Henderson, Naoto Ito, Neil Weisenfeld, David Jaffe, Nutan Sharma, Xandra O Breakefield, Laurie J Ozelius, D Cristopher Bragg, Michael E Talkowski
X-linked Dystonia-Parkinsonism (XDP) is a Mendelian neurodegenerative disease that is endemic to the Philippines and is associated with a founder haplotype. We integrated multiple genome and transcriptome assembly technologies to narrow the causal mutation to the TAF1 locus, which included a SINE-VNTR-Alu (SVA) retrotransposition into intron 32 of the gene. Transcriptome analyses identified decreased expression of the canonical cTAF1 transcript among XDP probands, and de novo assembly across multiple pluripotent stem-cell-derived neuronal lineages discovered aberrant TAF1 transcription that involved alternative splicing and intron retention (IR) in proximity to the SVA that was anti-correlated with overall TAF1 expression...
February 22, 2018: Cell
Arianne S Wallace, Caitlin M Hudac, Kyle J Steinman, Jessica L Peterson, Trent D DesChamps, Michael H Duyzend, Xander Nuttle, Evan E Eichler, Raphael A Bernier
16p11.2 deletions and duplications are commonly associated with autism spectrum disorder and linked to mirrored phenotypes of physical characteristics and higher penetrance for deletions. A male with a rare 16p11.2 triplication demonstrated a similar phenotypic presentation to deletion carriers with neurocognitive and adaptive skill deficits and above-average physical growth.
January 2018: Clinical Case Reports
Jeramiah J Smith, Nataliya Timoshevskaya, Chengxi Ye, Carson Holt, Melissa C Keinath, Hugo J Parker, Malcolm E Cook, Jon E Hess, Shawn R Narum, Francesco Lamanna, Henrik Kaessmann, Vladimir A Timoshevskiy, Courtney K M Waterbury, Cody Saraceno, Leanne M Wiedemann, Sofia M C Robb, Carl Baker, Evan E Eichler, Dorit Hockman, Tatjana Sauka-Spengler, Mark Yandell, Robb Krumlauf, Greg Elgar, Chris T Amemiya
The sea lamprey (Petromyzon marinus) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we developed a new assembly of the lamprey germline genome that integrates several complementary data sets. Analysis of this highly contiguous (chromosome-scale) assembly shows that both chromosomal and whole-genome duplications have played significant roles in the evolution of ancestral vertebrate and lamprey genomes, including chromosomes that carry the six lamprey HOX clusters...
January 22, 2018: Nature Genetics
John Huddleston, Mark J P Chaisson, Karyn Meltz Steinberg, Wes Warren, Kendra Hoekzema, David Gordon, Tina A Graves-Lindsay, Katherine M Munson, Zev N Kronenberg, Laura Vives, Paul Peluso, Matthew Boitano, Chen-Shin Chin, Jonas Korlach, Richard K Wilson, Evan E Eichler
No abstract text is available yet for this article.
January 2018: Genome Research
Kyleen Luhrs, Tracey Ward, Caitlin M Hudac, Jennifer Gerdts, Holly A F Stessman, Evan E Eichler, Raphael A Bernier
The purpose of this study was to examine the confluence of genetic and familial risk factors in children with Autism Spectrum Disorder (ASD) with distinct de novo genetic events. We hypothesized that gene-disrupting mutations would be associated with reduced rates of familial psychiatric disorders relative to structural mutations. Participants included families of children with ASD in four groups: de novo duplication copy number variations (DUP, n = 62), de novo deletion copy number variations (DEL, n = 74), de novo likely gene-disrupting mutations (LGDM, n = 267), and children without a known genetic etiology (NON, n = 2111)...
2017: Autism Research and Treatment
Sandra Jansen, Alexander Hoischen, Bradley P Coe, Gemma L Carvill, Hilde Van Esch, Daniëlle G M Bosch, Ulla A Andersen, Carl Baker, Marijke Bauters, Raphael A Bernier, Bregje W van Bon, Hedi L Claahsen-van der Grinten, Jozef Gecz, Christian Gilissen, Lucia Grillo, Anna Hackett, Tjitske Kleefstra, David Koolen, Malin Kvarnung, Martin J Larsen, Carlo Marcelis, Fiona McKenzie, Marie-Lorraine Monin, Caroline Nava, Janneke H Schuurs-Hoeijmakers, Rolph Pfundt, Marloes Steehouwer, Servi J C Stevens, Connie T Stumpel, Fleur Vansenne, Mirella Vinci, Maartje van de Vorst, Petra de Vries, Kali Witherspoon, Joris A Veltman, Han G Brunner, Heather C Mefford, Corrado Romano, Lisenka E L M Vissers, Evan E Eichler, Bert B A de Vries
Genotype-first combined with reverse phenotyping has shown to be a powerful tool in human genetics, especially in the era of next generation sequencing. This combines the identification of individuals with mutations in the same gene and linking these to consistent (endo)phenotypes to establish disease causality. We have performed a MIP (molecular inversion probe)-based targeted re-sequencing study in 3,275 individuals with intellectual disability (ID) to facilitate a genotype-first approach for 24 genes previously implicated in ID...
January 2018: European Journal of Human Genetics: EJHG
Amy B Wilfert, Arvis Sulovari, Tychele N Turner, Bradley P Coe, Evan E Eichler
Next-generation sequencing (NGS) is now more accessible to clinicians and researchers. As a result, our understanding of the genetics of neurodevelopmental disorders (NDDs) has rapidly advanced over the past few years. NGS has led to the discovery of new NDD genes with an excess of recurrent de novo mutations (DNMs) when compared to controls. Development of large-scale databases of normal and disease variation has given rise to metrics exploring the relative tolerance of individual genes to human mutation. Genetic etiology and diagnosis rates have improved, which have led to the discovery of new pathways and tissue types relevant to NDDs...
November 27, 2017: Genome Medicine
Sébastien Küry, Geeske M van Woerden, Thomas Besnard, Martina Proietti Onori, Xénia Latypova, Meghan C Towne, Megan T Cho, Trine E Prescott, Melissa A Ploeg, Stephan Sanders, Holly A F Stessman, Aurora Pujol, Ben Distel, Laurie A Robak, Jonathan A Bernstein, Anne-Sophie Denommé-Pichon, Gaëtan Lesca, Elizabeth A Sellars, Jonathan Berg, Wilfrid Carré, Øyvind Løvold Busk, Bregje W M van Bon, Jeff L Waugh, Matthew Deardorff, George E Hoganson, Katherine B Bosanko, Diana S Johnson, Tabib Dabir, Øystein Lunde Holla, Ajoy Sarkar, Kristian Tveten, Julitta de Bellescize, Geir J Braathen, Paulien A Terhal, Dorothy K Grange, Arie van Haeringen, Christina Lam, Ghayda Mirzaa, Jennifer Burton, Elizabeth J Bhoj, Jessica Douglas, Avni B Santani, Addie I Nesbitt, Katherine L Helbig, Marisa V Andrews, Amber Begtrup, Sha Tang, Koen L I van Gassen, Jane Juusola, Kimberly Foss, Gregory M Enns, Ute Moog, Katrin Hinderhofer, Nagarajan Paramasivam, Sharyn Lincoln, Brandon H Kusako, Pierre Lindenbaum, Eric Charpentier, Catherine B Nowak, Elouan Cherot, Thomas Simonet, Claudia A L Ruivenkamp, Sihoun Hahn, Catherine A Brownstein, Fan Xia, Sébastien Schmitt, Wallid Deb, Dominique Bonneau, Mathilde Nizon, Delphine Quinquis, Jamel Chelly, Gabrielle Rudolf, Damien Sanlaville, Philippe Parent, Brigitte Gilbert-Dussardier, Annick Toutain, Vernon R Sutton, Jenny Thies, Lisenka E L M Peart-Vissers, Pierre Boisseau, Marie Vincent, Andreas M Grabrucker, Christèle Dubourg, Wen-Hann Tan, Nienke E Verbeek, Martin Granzow, Gijs W E Santen, Jay Shendure, Bertrand Isidor, Laurent Pasquier, Richard Redon, Yaping Yang, Matthew W State, Tjitske Kleefstra, Benjamin Cogné, Slavé Petrovski, Kyle Retterer, Evan E Eichler, Jill A Rosenfeld, Pankaj B Agrawal, Stéphane Bézieau, Sylvie Odent, Ype Elgersma, Sandra Mercier
Calcium/calmodulin-dependent protein kinase II (CAMK2) is one of the first proteins shown to be essential for normal learning and synaptic plasticity in mice, but its requirement for human brain development has not yet been established. Through a multi-center collaborative study based on a whole-exome sequencing approach, we identified 19 exceedingly rare de novo CAMK2A or CAMK2B variants in 24 unrelated individuals with intellectual disability. Variants were assessed for their effect on CAMK2 function and on neuronal migration...
November 2, 2017: American Journal of Human Genetics
Lukas F K Kuderna, Chad Tomlinson, LaDeana W Hillier, Annabel Tran, Ian T Fiddes, Joel Armstrong, Hafid Laayouni, David Gordon, John Huddleston, Raquel Garcia Perez, Inna Povolotskaya, Aitor Serres Armero, Jèssica Gómez Garrido, Daniel Ho, Paolo Ribeca, Tyler Alioto, Richard E Green, Benedict Paten, Arcadi Navarro, Jaume Betranpetit, Javier Herrero, Evan E Eichler, Andrew J Sharp, Lars Feuk, Wesley C Warren, Tomas Marques-Bonet
The chimpanzee is arguably the most important species for the study of human origins. A key resource for these studies is a high-quality reference genome assembly; however, as with most mammalian genomes, the current iteration of the chimpanzee reference genome assembly is highly fragmented. In the current iteration of the chimpanzee reference genome assembly (Pan_tro_2.1.4), the sequence is scattered across more then 183 000 contigs, incorporating more than 159 000 gaps, with a genome-wide contig N50 of 51 Kbp...
November 1, 2017: GigaScience
Paige M Siper, Silvia De Rubeis, Maria Del Pilar Trelles, Allison Durkin, Daniele Di Marino, François Muratet, Yitzchak Frank, Reymundo Lozano, Evan E Eichler, Morgan Kelly, Jennifer Beighley, Jennifer Gerdts, Arianne S Wallace, Heather C Mefford, Raphael A Bernier, Alexander Kolevzon, Joseph D Buxbaum
BACKGROUND: Haploinsufficiency of the forkhead-box protein P1 (FOXP1) gene leads to a neurodevelopmental disorder termed FOXP1 syndrome. Previous studies in individuals carrying FOXP1 mutations and deletions have described the presence of autism spectrum disorder (ASD) traits, intellectual disability, language impairment, and psychiatric features. The goal of the present study was to comprehensively characterize the genetic and clinical spectrum of FOXP1 syndrome. This is the first study to prospectively examine the genotype-phenotype relationship in multiple individuals with FOXP1 syndrome, using a battery of standardized clinical assessments...
2017: Molecular Autism
Rachel K Earl, Tychele N Turner, Heather C Mefford, Caitlin M Hudac, Jennifer Gerdts, Evan E Eichler, Raphael A Bernier
BACKGROUND: DYRK1A is a gene recurrently disrupted in 0.1-0.5% of the ASD population. A growing number of case reports with DYRK1A haploinsufficiency exhibit common phenotypic features including microcephaly, intellectual disability, speech delay, and facial dysmorphisms. METHODS: Phenotypic information from previously published DYRK1A cases (n = 51) and participants in an ongoing study at the University of Washington (UW, n = 10) were compiled. Frequencies of recurrent phenotypic features in this population were compared to features observed in a large sample with idiopathic ASD from the Simons Simplex Collection (n = 1981)...
2017: Molecular Autism
Kay Prüfer, Cesare de Filippo, Steffi Grote, Fabrizio Mafessoni, Petra Korlević, Mateja Hajdinjak, Benjamin Vernot, Laurits Skov, Pinghsun Hsieh, Stéphane Peyrégne, David Reher, Charlotte Hopfe, Sarah Nagel, Tomislav Maricic, Qiaomei Fu, Christoph Theunert, Rebekah Rogers, Pontus Skoglund, Manjusha Chintalapati, Michael Dannemann, Bradley J Nelson, Felix M Key, Pavao Rudan, Željko Kućan, Ivan Gušić, Liubov V Golovanova, Vladimir B Doronichev, Nick Patterson, David Reich, Evan E Eichler, Montgomery Slatkin, Mikkel H Schierup, Aida M Andrés, Janet Kelso, Matthias Meyer, Svante Pääbo
To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases...
November 3, 2017: Science
Tychele N Turner, Bradley P Coe, Diane E Dickel, Kendra Hoekzema, Bradley J Nelson, Michael C Zody, Zev N Kronenberg, Fereydoun Hormozdiari, Archana Raja, Len A Pennacchio, Robert B Darnell, Evan E Eichler
To further our understanding of the genetic etiology of autism, we generated and analyzed genome sequence data from 516 idiopathic autism families (2,064 individuals). This resource includes >59 million single-nucleotide variants (SNVs) and 9,212 private copy number variants (CNVs), of which 133,992 and 88 are de novo mutations (DNMs), respectively. We estimate a mutation rate of ∼1.5 × 10-8 SNVs per site per generation with a significantly higher mutation rate in repetitive DNA. Comparing probands and unaffected siblings, we observe several DNM trends...
October 19, 2017: Cell
Anne B Arnett, Brianna E Cairney, Arianne S Wallace, Jennifer Gerdts, Tychele N Turner, Evan E Eichler, Raphael A Bernier
BACKGROUND: Symptoms of autism spectrum disorder (ASD) and inattention (IA) are highly comorbid and associated with deficits in executive cognition. Cognitive deficits have been posited as candidate endophenotypes of psychiatric traits, but few studies have conceptualized cognitive deficits as psychiatric comorbidities. The latter model is consistent with a latent factor reflecting broader liability to neuropsychological dysfunction, and explains heterogeneity in the cognitive profile of individuals with ASD and IA...
March 2018: Journal of Child Psychology and Psychiatry, and Allied Disciplines
Mario Ventura, Claudia R Catacchio, Saba Sajjadian, Laura Vives, Peter H Sudmant, Tomas Marques-Bonet, Tina A Graves, Richard K Wilson, Evan E Eichler
No abstract text is available yet for this article.
September 2017: Genome Research
Laura A Adang, Omar Sherbini, Laura Ball, Miriam Bloom, Anil Darbari, Hernan Amartino, Donna DiVito, Florian Eichler, Maria Escolar, Sarah H Evans, Ali Fatemi, Jamie Fraser, Leslie Hollowell, Nicole Jaffe, Christopher Joseph, Mary Karpinski, Stephanie Keller, Ryan Maddock, Edna Mancilla, Bruce McClary, Jana Mertz, Kiley Morgart, Thomas Langan, Richard Leventer, Sumit Parikh, Amy Pizzino, Erin Prange, Deborah L Renaud, William Rizzo, Jay Shapiro, Dean Suhr, Teryn Suhr, Davide Tonduti, Jacque Waggoner, Amy Waldman, Nicole I Wolf, Ayelet Zerem, Joshua L Bonkowsky, Genevieve Bernard, Keith van Haren, Adeline Vanderver
Leukodystrophies are a broad class of genetic disorders that result in disruption or destruction of central myelination. Although the mechanisms underlying these disorders are heterogeneous, there are many common symptoms that affect patients irrespective of the genetic diagnosis. The comfort and quality of life of these children is a primary goal that can complement efforts directed at curative therapies. Contained within this report is a systems-based approach to management of complications that result from leukodystrophies...
September 2017: Molecular Genetics and Metabolism
Megan Y Dennis, Lana Harshman, Bradley J Nelson, Osnat Penn, Stuart Cantsilieris, John Huddleston, Francesca Antonacci, Kelsi Penewit, Laura Denman, Archana Raja, Carl Baker, Kenneth Mark, Maika Malig, Nicolette Janke, Claudia Espinoza, Holly A F Stessman, Xander Nuttle, Kendra Hoekzema, Tina A Lindsay-Graves, Richard K Wilson, Evan E Eichler
Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (N = 80 genes from 33 gene families)...
February 17, 2017: Nature Ecology & Evolution
Mark J Chaisson, Sudipto Mukherjee, Sreeram Kannan, Evan E Eichler
While the rise of single-molecule sequencing systems has enabled an unprecedented rise in the ability to assemble complex regions of the genome, long segmental duplications in the genome still remain a challenging frontier in assembly. Segmental duplications are at the same time both gene rich and prone to large structural rearrangements, making the resolution of their sequences important in medical and evolutionary studies. Duplicated sequences that are collapsed in mammalian de novo assemblies are rarely identical; after a sequence is duplicated, it begins to acquire paralog specific variants...
May 2017: Research in Computational Molecular Biology: ... Annual International Conference, RECOMB ...: Proceedings
Madeleine R Geisheker, Gabriel Heymann, Tianyun Wang, Bradley P Coe, Tychele N Turner, Holly A F Stessman, Kendra Hoekzema, Malin Kvarnung, Marie Shaw, Kathryn Friend, Jan Liebelt, Christopher Barnett, Elizabeth M Thompson, Eric Haan, Hui Guo, Britt-Marie Anderlid, Ann Nordgren, Anna Lindstrand, Geert Vandeweyer, Antonino Alberti, Emanuela Avola, Mirella Vinci, Stefania Giusto, Tiziano Pramparo, Karen Pierce, Srinivasa Nalabolu, Jacob J Michaelson, Zdenek Sedlacek, Gijs W E Santen, Hilde Peeters, Hakon Hakonarson, Eric Courchesne, Corrado Romano, R Frank Kooy, Raphael A Bernier, Magnus Nordenskjöld, Jozef Gecz, Kun Xia, Larry S Zweifel, Evan E Eichler
Although de novo missense mutations have been predicted to account for more cases of autism than gene-truncating mutations, most research has focused on the latter. We identified the properties of de novo missense mutations in patients with neurodevelopmental disorders (NDDs) and highlight 35 genes with excess missense mutations. Additionally, 40 amino acid sites were recurrently mutated in 36 genes, and targeted sequencing of 20 sites in 17,688 patients with NDD identified 21 new patients with identical missense mutations...
August 2017: Nature Neuroscience
Megan Y Dennis, Lana Harshman, Bradley J Nelson, Osnat Penn, Stuart Cantsilieris, John Huddleston, Francesca Antonacci, Kelsi Penewit, Laura Denman, Archana Raja, Carl Baker, Kenneth Mark, Maika Malig, Nicolette Janke, Claudia Espinoza, Holly A F Stessman, Xander Nuttle, Kendra Hoekzema, Tina A Lindsay-Graves, Richard K Wilson, Evan E Eichler
Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (n=80 genes/33 gene families)...
2017: Nature Ecology & Evolution
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