Application of rare variant transmission disequilibrium tests to epileptic encephalopathy trio sequence data

European Journal of Human Genetics

Volumn 25, Issue 7, 2017, Pages 894-899

  Allen, Andrew S ^a   Berkovic, Samuel F ^b   Bridgers, Joshua ^c   Cossette, Patrick ^d   Dlugos, Dennis ^e   Epstein, Michael P ^f   Glauser, Tracy ^g   Goldstein, David B ^c   Heinzen, Erin L ^c   Jiang, Yu ^a   Johnson, Michael R ^h   Kuzniecky, Ruben ⁱ   Lowenstein, Daniel H ^j   Marson, Anthony G ^k   Mefford, Heather C ^l   O'Brien, Terence J ^m   Ottman, Ruth ^n,o   Petrou, Steven ^b,m   Petrovski, Slavé ^b,c,n   Poduri, Annapurna ^p   Ren, Zhong ^c   Scheffer, Ingrid E ^b   Sherr, Elliott ^j   Wang, Quanli ^c   Balling, Rudi ^q   Barisic, Nina ^r   Baulac, Stéphanie ^s,t,u,v,w   Caglayan, Hande ^x   Craiu, Dana ^y,z   De Jonghe, Peter ^aa,ab   Depienne, Christel ^ac,ad   Guerrini, Renzo ^ae   Helbig, Ingo ^af,ag   Hjalgrim, Helle ^ah,ai   Hoffman Zacharska, Dorota ^aj   Jähn, Johanna ^af   Klein, Karl Martin ^ak,al   Koeleman, Bobby ^am   Komarek, Vladimir ^an   Krause, Roland ^q   Leguern, Eric ^s,t,u,v,w   Lehesjoki, Anna Elina ^ao   Lemke, Johannes R ^ap   Lerche, Holger ^aq   Linnankivi, Tarja ^ao   Marini, Carla ^ae   May, Patrick ^q   Møller, Rikke S ^ah,ai   Muhle, Hiltrud ^af   Pal, Deb ^ar   Palotie, Aarno ^ao,as,at   Rosenow, Felix ^ak,al   Selmer, Kaja ^au   Serratosa, Jose M ^av   Sisodiya, Sanjay ^aw,ax   Stephani, Ulrich ^af   Sterbova, Katalin ^an   Striano, Pasquale ^ay   Suls, Arvid ^aa,ab,az   Talvik, Tiina ^ba,bb   Von Spiczak, Sarah ^af   Weber, Yvonne ^aq   Weckhuysen, Sarah ^aa,ab   Zara, Federico ^ay   Abou Khalil, Bassel ^bc   Alldredge, Brian K ^j,bd   Amrom, Dina ^be,bf   Andermann, Eva ^be,bf   Andermann, Frederick ^be,bf   Bautista, Jocelyn F ^bg   Bluvstein, Judith ⁱ   Cascino, Gregory D ^bh   Consalvo, Damian ^bi   Crumrine, Patricia ^bj   Devinsky, Orrin ⁱ   Fiol, Miguel E ^bk   Fountain, Nathan B ^bl   French, Jacqueline ^bm   Friedman, Daniel ⁱ   Haas, Kevin ^bc   Haut, Sheryl R ^bn   Hayward, Jean ^bo   Joshi, Sucheta ^bp   Kanner, Andres ^bq   Kirsch, Heidi E ^br   Kossoff, Eric H ^bs   Kuperman, Rachel ^bt   McGuire, Shannon M ^bu   Motika, Paul V ^bv   Novotny, Edward J ^l   Paolicchi, Juliann M ^bw   Parent, Jack ^bx,by   Park, Kristen ^bz,ca   Shellhaas, Renée A ^bp   Sirven, Joseph ^cb   Smith, Michael C ^cc   Sullivan, Joseph ^j   Thio, Liu Lin ^cd   Venkat, Anu ^ce   Vining, Eileen P G ^bs   Von Allmen, Gretchen K ^cf   Weisenberg, Judith L ^cd   Widdess Walsh, Peter ^cg   Winawer, Melodie R ⁿ   more..

^a DUKE CLINICAL RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c NewYork Presbyterian Hospital   (United States)

^d CENTRE HOSPITALIER DE L UNIVERSITÉ DE MONTRÉAL   (Canada)

^e UNIVERSITY OF PENNSYLVANIA   (United States)

^f EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^g CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

^h IMPERIAL COLLEGE LONDON   (United Kingdom)

ⁱ NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^j UNIVERSITY OF CALIFORNIA   (United States)

^k UNIVERSITY OF LIVERPOOL   (United Kingdom)

^l UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^m ROYAL MELBOURNE HOSPITAL   (Australia)

ⁿ Taub Institute for Research on Alzheimer's Disease and the Aging Brain and the Gertrude H Sergievsky Center   (United States)

^o NEW YORK STATE PSYCHIATRIC INSTITUTE   (United States)

^p BOSTON CHILDREN S HOSPITAL   (United States)

^q UNIVERSITY OF LUXEMBOURG   (Luxembourg)

^r UNIVERSITY OF ZAGREB   (Croatia)

^s SORBONNE UNIVERSITÉ   (France)

^t INSERM   (France)

^u CNRS   (France)

^v ICM   (France)

^w PITIÉ SALPÊTRIÈRE HOSPITAL   (France)

^x BOGAZICI UNIVERSITY   (Turkey)

^y CAROL DAVILA UNIVERSITY OF MEDICINE AND PHARMACY   (Romania)

^z Al Obregia Clinical Hospital   (Romania)

^aa DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^ab UNIVERSITY OF ANTWERP   (Belgium)

^ac UNIVERSITÉ DE STRASBOURG   (France)

^ad UNIVERSITY HOSPITAL OF STRASBOURG   (France)

^ae UNIVERSITY OF FLORENCE   (Italy)

^af UNIVERSITY OF KIEL   (Germany)

^ag CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

^ah DANISH EPILEPSY CENTRE   (Denmark)

^ai UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^aj INSTITUTE OF MOTHER AND CHILD   (Poland)

^ak GOETHE UNIVERSITY   (Germany)

^al PHILIPPS UNIVERSITY MARBURG   (Germany)

^am UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^an UNIVERSITY HOSPITAL MOTOL   (Czech Republic)

^ao UNIVERSITY OF HELSINKI   (Finland)

^ap UNIVERSITY OF LEIPZIG   (Germany)

^aq UNIVERSITY OF TÜBINGEN   (Germany)

^ar KING'S COLLEGE LONDON   (United Kingdom)

^as WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^at BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^au OSLO UNIVERSITY HOSPITAL   (Norway)

^av HOSPITAL UNIVERSITARIO FUNDACIÓN JIMÉNEZ DÍAZ   (Spain)

^aw UNIVERSITY COLLEGE LONDON   (United Kingdom)

^ax EPILEPSY SOCIETY   (United Kingdom)

^ay UNIVERSITY OF GENOA   (Italy)

^az UNIVERSITY OF ANTWERP   (Belgium)

^ba UNIVERSITY OF TARTU   (Estonia)

^bb TARTU UNIVERSITY HOSPITAL   (Estonia)

^bc VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^bd UCSF Medical Center and Associate Clinical UCSF School of Pharmacy   (United States)

^be MCGILL UNIVERSITY   (Canada)

^bf MCGILL UNIVERSITY   (Canada)

^bg LERNER RESEARCH INSTITUTE   (United States)

^bh MAYO CLINIC   (United States)

^bi HOSPITAL RAMOS MEJÍA   (Argentina)

^bj CHILDREN S HOSPITAL OF PITTSBURGH   (United States)

^bk UNIVERSITY OF MINNESOTA MEDICAL SCHOOL   (United States)

^bl UNIVERSITY OF VIRGINIA   (United States)

^bm NEW YORK UNIVERSITY MEDICAL CENTER   (United States)

^bn MONTEFIORE MEDICAL CENTER   (United States)

^bo KAISER PERMANENTE   (United States)

^bp UNIVERSITY OF MICHIGAN   (United States)

^bq UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

^br UNIVERSITY OF CALIFORNIA   (United States)

^bs JOHNS HOPKINS HOSPITAL   (United States)

^bt CHILDREN S HOSPITAL OAKLAND   (United States)

^bu CHILDREN S HOSPITAL   (United States)

^bv OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^bw WEILL CORNELL MEDICAL CENTER   (United States)

^bx UNIVERSITY OF MICHIGAN HEALTH SYSTEM   (United States)

^by Veterans Administration Ann Arbor Healthcare Systems   (United States)

^bz UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^ca CHILDREN S HOSPITAL COLORADO   (United States)

^cb MAYO CLINIC   (United States)

^cc RUSH UNIVERSITY MEDICAL CENTER   (United States)

^cd WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^ce SAINT PETER S UNIVERSITY HOSPITAL   (United States)

^cf UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

^cg BEAUMONT HOSPITAL   (Ireland)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER A13; ANKZF1 PROTEIN; C14ORF177 PROTEIN; CENPO PROTEIN; CEP120 PROTEIN; CNTRL PROTEIN; CR1 PROTEIN; DACT1 PROTEIN; DST PROTEIN; IPPK PROTEIN; KATNB1 PROTEIN; KIAA1614 PROTEIN; OR2B2 PROTEIN; PCF11 PROTEIN; PGM2L1 PROTEIN; PROTEIN; SAP130 PROTEIN; SBSN PROTEIN; SCAPER PROTEIN; SCARF1 PROTEIN; SLC46A3 PROTEIN; STEAP4 PROTEIN; SYNJ1 PROTEIN; TRAF3IP1 PROTEIN; UNCLASSIFIED DRUG; ZNF677 PROTEIN; ZNF878 PROTEIN;

ARTICLE; AUTOSOMAL RECESSIVE INHERITANCE; CLINICAL ASSESSMENT; CLINICAL EFFECTIVENESS; GENE LINKAGE DISEQUILIBRIUM; GENETIC SCREENING; GENETIC VARIABILITY; GENETIC VARIATION; HUMAN; INFANTILE SPASM; LENNOX GASTAUT SYNDROME; MAJOR CLINICAL STUDY; METABOLIC DISORDER; PRIORITY JOURNAL; TRANSMISSION DISEQUILIBRIUM TEST; CLINICAL TRIAL; GENE FREQUENCY; GENETIC POLYMORPHISM; GENETIC PREDISPOSITION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; INFANT; MULTICENTER STUDY; PROCEDURES;

GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; INFANT; LENNOX GASTAUT SYNDROME; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, GENETIC; SPASMS, INFANTILE;

EID: 85019562360     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2017.61     Document Type: Article

References (14)

1. Epi4K Consortium. Epilepsy Phenome/Genome Project, Allen AS et al: De novo mutations in epileptic encephalopathies. Nature 2013; 501: 217-221.
2. EuroEPINOMICS-RES Consortium. Epilepsy Phenome/Genome Project. Epi4K Consortium: De novo mutations in synaptic transmission genes including DNM1 cause epileptic encephalopathies. Am J Hum Genet 2014; 95: 360-370.
3. Harkin LA, McMahon JM, Iona X et al: The spectrum of SCN1A-related infantile epileptic encephalopathies. Brain 2007; 130 (Pt 3): 843-852.
4. Epilepsy Phenome/Genome Project Epi4K Consortium: Copy number variant analysis from exome data in 349 patients with epileptic encephalopathy. Ann Neurol 2015; 78: 323-328.
5. Purcell S, Neale B, Todd-Brown K et al: PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81: 559-575.
6. Jiang Y, Satten GA, Han Y et al: Utilizing population controls in rare-variant case-parent association tests. Am J Hum Genet 2014; 94: 845-853.
7. Jiang Y, McCarthy JM, Allen AS: Testing the effect of rare compound-heterozygous and recessive mutations in case-parent sequencing studies. Genet Epidemiol 2015; 39: 166-172.
8. Adzhubei IA, Schmidt S, Peshkin L et al: A method and server for predicting damaging missense mutations. Nat Methods 2010; 7: 248-249.
9. van Karnebeek CD, Shevell M, Zschocke J, Moeschler JB, Stockler S: The metabolic evaluation of the child with an intellectual developmental disorder: diagnostic algorithm for identification of treatable causes and new digital resource. Mol Genet Metab 2014; 111: 428-438.
10. Exome Variant Server (EVS), NHLBI GO Exome Sequencing Project (ESP), Seattle, WA, USA.
11. Zhu X, Petrovski S, Xie P et al: Whole-exome sequencing in undiagnosed genetic diseases: interpreting 119 trios. Genet Med 2015; 17: 774-781.
12. Need AC, Shashi V, Hitomi Y et al: Clinical application of exome sequencing in undiagnosed genetic conditions. J Med Genet 2012; 49: 353-361.
13. Tanaka AJ, Cho MT, Millan F et al: Mutations in SPATA5 are associated with microcephaly, intellectual disability, seizures, and hearing loss. Am J Hum Genet 2015; 97: 457-464.
14. Akawi N, McRae J, Ansari M et al: Discovery of four recessive developmental disorders using probabilistic genotype and phenotype matching among 4,125 families. Nat Genet 2015; 47: 1363-1369.