Literature DB >> 23368808

Next-generation sequencing in understanding complex neurological disease.

Adam E Handel1, Giulio Disanto, Sreeram V Ramagopalan.   

Abstract

Next-generation sequencing techniques have made vast quantities of data on human genomes and transcriptomes available to researchers. Huge progress has been made towards understanding the basis of many Mendelian neurological conditions, but progress has been considerably slower in complex neurological diseases (multiple sclerosis, migraine, Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and so on). The authors review current next-generation sequencing methodologies and present selected studies illustrating how these have been used to cast light on the genetic etiology of complex neurological diseases with specific focus on multiple sclerosis. The authors highlight particular pitfalls in next-generation sequencing experiments and speculate on both clinical and research applications of these sequencing platforms for complex neurological disorders in the future.

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Year:  2013        PMID: 23368808      PMCID: PMC3836167          DOI: 10.1586/ern.12.165

Source DB:  PubMed          Journal:  Expert Rev Neurother        ISSN: 1473-7175            Impact factor:   4.618


  171 in total

1.  CASK aberrations in male patients with Ohtahara syndrome and cerebellar hypoplasia.

Authors:  Hirotomo Saitsu; Mitsuhiro Kato; Hitoshi Osaka; Nobuko Moriyama; Hideki Horita; Kiyomi Nishiyama; Yuriko Yoneda; Yukiko Kondo; Yoshinori Tsurusaki; Hiroshi Doi; Noriko Miyake; Kiyoshi Hayasaka; Naomichi Matsumoto
Journal:  Epilepsia       Date:  2012-06-18       Impact factor: 5.864

Review 2.  Statistical analysis of rare sequence variants: an overview of collapsing methods.

Authors:  Carmen Dering; Claudia Hemmelmann; Elizabeth Pugh; Andreas Ziegler
Journal:  Genet Epidemiol       Date:  2011       Impact factor: 2.135

3.  A compound heterozygous missense mutation and a large deletion in the KCTD7 gene presenting as an opsoclonus-myoclonus ataxia-like syndrome.

Authors:  Lubov Blumkin; Sara Kivity; Dorit Lev; Sarit Cohen; Ruth Shomrat; Tally Lerman-Sagie; Esther Leshinsky-Silver
Journal:  J Neurol       Date:  2012-05-26       Impact factor: 4.849

Review 4.  RNA-Seq: a revolutionary tool for transcriptomics.

Authors:  Zhong Wang; Mark Gerstein; Michael Snyder
Journal:  Nat Rev Genet       Date:  2009-01       Impact factor: 53.242

5.  Heterozygous de-novo mutations in ATP1A3 in patients with alternating hemiplegia of childhood: a whole-exome sequencing gene-identification study.

Authors:  Hendrik Rosewich; Holger Thiele; Andreas Ohlenbusch; Ulrike Maschke; Janine Altmüller; Peter Frommolt; Birgit Zirn; Friedrich Ebinger; Hartmut Siemes; Peter Nürnberg; Knut Brockmann; Jutta Gärtner
Journal:  Lancet Neurol       Date:  2012-07-30       Impact factor: 44.182

6.  Identification of a novel Cys146X mutation of SOD1 in familial amyotrophic lateral sclerosis by whole-exome sequencing.

Authors:  Jinyu Wu; Enjian Shen; Dashuang Shi; ZhongSheng Sun; Tao Cai
Journal:  Genet Med       Date:  2012-05-17       Impact factor: 8.822

7.  Patterns and rates of exonic de novo mutations in autism spectrum disorders.

Authors:  Benjamin M Neale; Yan Kou; Li Liu; Avi Ma'ayan; Kaitlin E Samocha; Aniko Sabo; Chiao-Feng Lin; Christine Stevens; Li-San Wang; Vladimir Makarov; Paz Polak; Seungtai Yoon; Jared Maguire; Emily L Crawford; Nicholas G Campbell; Evan T Geller; Otto Valladares; Chad Schafer; Han Liu; Tuo Zhao; Guiqing Cai; Jayon Lihm; Ruth Dannenfelser; Omar Jabado; Zuleyma Peralta; Uma Nagaswamy; Donna Muzny; Jeffrey G Reid; Irene Newsham; Yuanqing Wu; Lora Lewis; Yi Han; Benjamin F Voight; Elaine Lim; Elizabeth Rossin; Andrew Kirby; Jason Flannick; Menachem Fromer; Khalid Shakir; Tim Fennell; Kiran Garimella; Eric Banks; Ryan Poplin; Stacey Gabriel; Mark DePristo; Jack R Wimbish; Braden E Boone; Shawn E Levy; Catalina Betancur; Shamil Sunyaev; Eric Boerwinkle; Joseph D Buxbaum; Edwin H Cook; Bernie Devlin; Richard A Gibbs; Kathryn Roeder; Gerard D Schellenberg; James S Sutcliffe; Mark J Daly
Journal:  Nature       Date:  2012-04-04       Impact factor: 49.962

8.  Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease.

Authors:  Adam C Naj; Gyungah Jun; Gary W Beecham; Li-San Wang; Badri Narayan Vardarajan; Jacqueline Buros; Paul J Gallins; Joseph D Buxbaum; Gail P Jarvik; Paul K Crane; Eric B Larson; Thomas D Bird; Bradley F Boeve; Neill R Graff-Radford; Philip L De Jager; Denis Evans; Julie A Schneider; Minerva M Carrasquillo; Nilufer Ertekin-Taner; Steven G Younkin; Carlos Cruchaga; John S K Kauwe; Petra Nowotny; Patricia Kramer; John Hardy; Matthew J Huentelman; Amanda J Myers; Michael M Barmada; F Yesim Demirci; Clinton T Baldwin; Robert C Green; Ekaterina Rogaeva; Peter St George-Hyslop; Steven E Arnold; Robert Barber; Thomas Beach; Eileen H Bigio; James D Bowen; Adam Boxer; James R Burke; Nigel J Cairns; Chris S Carlson; Regina M Carney; Steven L Carroll; Helena C Chui; David G Clark; Jason Corneveaux; Carl W Cotman; Jeffrey L Cummings; Charles DeCarli; Steven T DeKosky; Ramon Diaz-Arrastia; Malcolm Dick; Dennis W Dickson; William G Ellis; Kelley M Faber; Kenneth B Fallon; Martin R Farlow; Steven Ferris; Matthew P Frosch; Douglas R Galasko; Mary Ganguli; Marla Gearing; Daniel H Geschwind; Bernardino Ghetti; John R Gilbert; Sid Gilman; Bruno Giordani; Jonathan D Glass; John H Growdon; Ronald L Hamilton; Lindy E Harrell; Elizabeth Head; Lawrence S Honig; Christine M Hulette; Bradley T Hyman; Gregory A Jicha; Lee-Way Jin; Nancy Johnson; Jason Karlawish; Anna Karydas; Jeffrey A Kaye; Ronald Kim; Edward H Koo; Neil W Kowall; James J Lah; Allan I Levey; Andrew P Lieberman; Oscar L Lopez; Wendy J Mack; Daniel C Marson; Frank Martiniuk; Deborah C Mash; Eliezer Masliah; Wayne C McCormick; Susan M McCurry; Andrew N McDavid; Ann C McKee; Marsel Mesulam; Bruce L Miller; Carol A Miller; Joshua W Miller; Joseph E Parisi; Daniel P Perl; Elaine Peskind; Ronald C Petersen; Wayne W Poon; Joseph F Quinn; Ruchita A Rajbhandary; Murray Raskind; Barry Reisberg; John M Ringman; Erik D Roberson; Roger N Rosenberg; Mary Sano; Lon S Schneider; William Seeley; Michael L Shelanski; Michael A Slifer; Charles D Smith; Joshua A Sonnen; Salvatore Spina; Robert A Stern; Rudolph E Tanzi; John Q Trojanowski; Juan C Troncoso; Vivianna M Van Deerlin; Harry V Vinters; Jean Paul Vonsattel; Sandra Weintraub; Kathleen A Welsh-Bohmer; Jennifer Williamson; Randall L Woltjer; Laura B Cantwell; Beth A Dombroski; Duane Beekly; Kathryn L Lunetta; Eden R Martin; M Ilyas Kamboh; Andrew J Saykin; Eric M Reiman; David A Bennett; John C Morris; Thomas J Montine; Alison M Goate; Deborah Blacker; Debby W Tsuang; Hakon Hakonarson; Walter A Kukull; Tatiana M Foroud; Jonathan L Haines; Richard Mayeux; Margaret A Pericak-Vance; Lindsay A Farrer; Gerard D Schellenberg
Journal:  Nat Genet       Date:  2011-04-03       Impact factor: 38.330

9.  Whole-genome sequencing reveals a coding non-pathogenic variant tagging a non-coding pathogenic hexanucleotide repeat expansion in C9orf72 as cause of amyotrophic lateral sclerosis.

Authors:  Sarah Herdewyn; Hui Zhao; Matthieu Moisse; Valérie Race; Gert Matthijs; Joke Reumers; Benno Kusters; Helenius J Schelhaas; Leonard H van den Berg; An Goris; Wim Robberecht; Diether Lambrechts; Philip Van Damme
Journal:  Hum Mol Genet       Date:  2012-02-17       Impact factor: 6.150

10.  Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility.

Authors:  Margaret Wrensch; Robert B Jenkins; Jeffrey S Chang; Ru-Fang Yeh; Yuanyuan Xiao; Paul A Decker; Karla V Ballman; Mitchel Berger; Jan C Buckner; Susan Chang; Caterina Giannini; Chandralekha Halder; Thomas M Kollmeyer; Matthew L Kosel; Daniel H LaChance; Lucie McCoy; Brian P O'Neill; Joe Patoka; Alexander R Pico; Michael Prados; Charles Quesenberry; Terri Rice; Amanda L Rynearson; Ivan Smirnov; Tarik Tihan; Joe Wiemels; Ping Yang; John K Wiencke
Journal:  Nat Genet       Date:  2009-07-05       Impact factor: 38.330

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  8 in total

Review 1.  Review of alignment and SNP calling algorithms for next-generation sequencing data.

Authors:  M Mielczarek; J Szyda
Journal:  J Appl Genet       Date:  2015-06-09       Impact factor: 3.240

Review 2.  Application of next-generation sequencing technologies in Neurology.

Authors:  Teng Jiang; Meng-Shan Tan; Lan Tan; Jin-Tai Yu
Journal:  Ann Transl Med       Date:  2014-12

Review 3.  Advances in reprogramming-based study of neurologic disorders.

Authors:  Anjana Nityanandam; Kristin K Baldwin
Journal:  Stem Cells Dev       Date:  2015-04-06       Impact factor: 3.272

4.  Development of the variant calling algorithm, ADIScan, and its use to estimate discordant sequences between monozygotic twins.

Authors:  Yangrae Cho; Sunho Lee; Jong Hui Hong; Byong Joon Kim; Woon-Young Hong; Jongcheol Jung; Hyang Burm Lee; Joohon Sung; Han-Na Kim; Hyung-Lae Kim; Jongsun Jung
Journal:  Nucleic Acids Res       Date:  2018-09-06       Impact factor: 16.971

Review 5.  Genetic forms of epilepsies and other paroxysmal disorders.

Authors:  Heather E Olson; Annapurna Poduri; Phillip L Pearl
Journal:  Semin Neurol       Date:  2014-09-05       Impact factor: 3.420

6.  Detection of genomic rearrangements from targeted resequencing data in Parkinson's disease patients.

Authors:  Nino Spataro; Ana Roca-Umbert; Laura Cervera-Carles; Mònica Vallès; Roger Anglada; Javier Pagonabarraga; Berta Pascual-Sedano; Antònia Campolongo; Jaime Kulisevsky; Ferran Casals; Jordi Clarimón; Elena Bosch
Journal:  Mov Disord       Date:  2016-11-07       Impact factor: 10.338

7.  Transcriptomics Profiling of Alzheimer's Disease Reveal Neurovascular Defects, Altered Amyloid-β Homeostasis, and Deregulated Expression of Long Noncoding RNAs.

Authors:  Marco Magistri; Dmitry Velmeshev; Madina Makhmutova; Mohammad Ali Faghihi
Journal:  J Alzheimers Dis       Date:  2015       Impact factor: 4.472

8.  Bioinformatics Analysis of Estrogen-Responsive Genes.

Authors:  Adam E Handel
Journal:  Methods Mol Biol       Date:  2016
  8 in total

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