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Evan Eichler

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https://www.readbyqxmd.com/read/29295848/corrigendum-discovery-and-genotyping-of-structural-variation-from-long-read-haploid-genome-sequence-data
#1
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
https://www.readbyqxmd.com/read/29250444/associations-between-familial-rates-of-psychiatric-disorders-and-de-novo-genetic-mutations-in-autism
#2
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
https://www.readbyqxmd.com/read/29209020/a-genotype-first-approach-identifies-an-intellectual-disability-overweight-syndrome-caused-by-phip-haploinsufficiency
#3
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...
December 5, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29179772/recurrent-de-novo-mutations-in-neurodevelopmental-disorders-properties-and-clinical-implications
#4
REVIEW
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
https://www.readbyqxmd.com/read/29100089/de-novo-mutations-in-protein-kinase-genes-camk2a-and-camk2b-cause-intellectual-disability
#5
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
https://www.readbyqxmd.com/read/29092041/a-3-way-hybrid-approach-to-generate-a-new-high-quality-chimpanzee-reference-genome-pan_tro_3-0
#6
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
https://www.readbyqxmd.com/read/29090079/prospective-investigation-of-foxp1-syndrome
#7
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
https://www.readbyqxmd.com/read/29034068/clinical-phenotype-of-asd-associated-dyrk1a-haploinsufficiency
#8
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
https://www.readbyqxmd.com/read/28982794/a-high-coverage-neandertal-genome-from-vindija-cave-in-croatia
#9
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
https://www.readbyqxmd.com/read/28965761/genomic-patterns-of-de-novo-mutation-in-simplex-autism
#10
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
https://www.readbyqxmd.com/read/28921525/comorbid-symptoms-of-inattention-autism-and-executive-cognition-in-youth-with-putative-genetic-risk
#11
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...
September 18, 2017: Journal of Child Psychology and Psychiatry, and Allied Disciplines
https://www.readbyqxmd.com/read/28864551/corrigendum-the-evolution-of-african-great-ape-subtelomeric-heterochromatin-and-the-fusion-of-human-chromosome-2
#12
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
https://www.readbyqxmd.com/read/28863857/revised-consensus-statement-on-the-preventive-and-symptomatic-care-of-patients-with-leukodystrophies
#13
REVIEW
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
https://www.readbyqxmd.com/read/28812736/the-evolution-and-population-diversity-of-human-specific-segmental-duplications
#14
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
https://www.readbyqxmd.com/read/28808695/resolving-multicopy-duplications-de-novo-using-polyploid-phasing
#15
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
https://www.readbyqxmd.com/read/28628100/hotspots-of-missense-mutation-identify-neurodevelopmental-disorder-genes-and-functional-domains
#16
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
https://www.readbyqxmd.com/read/28580430/the-evolution-and-population-diversity-of-human-specific-segmental-duplications
#17
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
https://www.readbyqxmd.com/read/28559932/exploring-the-heterogeneity-of-neural-social-indices-for-genetically-distinct-etiologies-of-autism
#18
Caitlin M Hudac, Holly A F Stessman, Trent D DesChamps, Anna Kresse, Susan Faja, Emily Neuhaus, Sara Jane Webb, Evan E Eichler, Raphael A Bernier
BACKGROUND: Autism spectrum disorder (ASD) is a genetically and phenotypically heterogeneous disorder. Promising initiatives utilizing interdisciplinary characterization of ASD suggest phenotypic subtypes related to specific likely gene-disrupting mutations (LGDMs). However, the role of functionally associated LGDMs in the neural social phenotype is unknown. METHODS: In this study of 26 children with ASD (n = 13 with an LGDM) and 13 control children, we characterized patterns of mu attenuation and habituation as children watched videos containing social and nonsocial motions during electroencephalography acquisition...
2017: Journal of Neurodevelopmental Disorders
https://www.readbyqxmd.com/read/28496210/the-caterpillar-fungus-ophiocordyceps-sinensis-genome-provides-insights-into-highland-adaptation-of-fungal-pathogenicity
#19
En-Hua Xia, Da-Rong Yang, Jian-Jun Jiang, Qun-Jie Zhang, Yuan Liu, Yun-Long Liu, Yun Zhang, Hai-Bin Zhang, Cong Shi, Yan Tong, Changhoon Kim, Hua Chen, Yan-Qiong Peng, Yue Yu, Wei Zhang, Evan E Eichler, Li-Zhi Gao
To understand the potential genetic basis of highland adaptation of fungal pathogenicity, we present here the ~116 Mb de novo assembled high-quality genome of Ophiocordyceps sinensis endemic to the Qinghai-Tibetan Plateau. Compared with other plain-dwelling fungi, we find about 3.4-fold inflation of the O. sinensis genome due to a rapid amplification of long terminal repeat retrotransposons that occurred ~38 million years ago in concert with the uplift of the plateau. We also observe massive removal of thousands of genes related to the transport process and energy metabolism...
May 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28473262/the-tea-tree-genome-provides-insights-into-tea-flavor-and-independent-evolution-of-caffeine-biosynthesis
#20
En-Hua Xia, Hai-Bin Zhang, Jun Sheng, Kui Li, Qun-Jie Zhang, Changhoon Kim, Yun Zhang, Yuan Liu, Ting Zhu, Wei Li, Hui Huang, Yan Tong, Hong Nan, Cong Shi, Chao Shi, Jian-Jun Jiang, Shu-Yan Mao, Jun-Ying Jiao, Dan Zhang, Yuan Zhao, You-Jie Zhao, Li-Ping Zhang, Yun-Long Liu, Ben-Ying Liu, Yue Yu, Sheng-Fu Shao, De-Jiang Ni, Evan E Eichler, Li-Zhi Gao
Tea is the world's oldest and most popular caffeine-containing beverage with immense economic, medicinal, and cultural importance. Here, we present the first high-quality nucleotide sequence of the repeat-rich (80.9%), 3.02-Gb genome of the cultivated tea tree Camellia sinensis. We show that an extraordinarily large genome size of tea tree is resulted from the slow, steady, and long-term amplification of a few LTR retrotransposon families. In addition to a recent whole-genome duplication event, lineage-specific expansions of genes associated with flavonoid metabolic biosynthesis were discovered, which enhance catechin production, terpene enzyme activation, and stress tolerance, important features for tea flavor and adaptation...
June 5, 2017: Molecular Plant
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