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Neurobiol Aging. 2015 Mar;36(3):1605.e7-12. doi: 10.1016/j.neurobiolaging.2014.07.028. Epub 2014 Aug 4.

NeuroX, a fast and efficient genotyping platform for investigation of neurodegenerative diseases.

Collaborators (459)

Nalls MA, Plagnol V, Hernandez DG, Edsall C, Nichols N, Sharma M, Sheerin UM, Saad M, Simón-Sánchez J, Schulte C, Lesage S, Sveinbjörnsdóttir S, Arepalli S, Barker R, Ben-Shlomo Y, Berendse HW, Berg D, Bhatia K, de Bie RM, Biffi A, Bloem B, Bochdanovits Z, Bonin M, Bras JM, Brockmann K, Brooks J, Burn DJ, Charlesworth G, Chen H, Chinnery PF, Chong S, Clarke CE, Cookson MR, Cooper JM, Corvol JC, Counsell C, Damier P, Dartigues JF, Deloukas P, Deuschl G, Dexter DT, van Dijk KD, Dillman A, Durif F, Dürr A, Edkins S, Evans JR, Foltynie T, Dong J, Gardner M, Gibbs JR, Goate A, Gray E, Guerreiro R, Harris C, van Hilten JJ, Hofman A, Hollenbeck A, Holton J, Hu M, Huang X, Wurster I, Mätzler W, Hudson G, Hunt SE, Huttenlocher J, Illig T, Jónsson PV, Lambert JC, Langford C, Lees A, Lichtner P, Limousin P, Lopez G, Lorenz D, Lubbe S, McNeill A, Moorby C, Moore M, Morris HR, Morrison KE, O'Sullivan SS, Pearson J, Perlmutter JS, Pétursson H, Pollak P, Post B, Potter S, Ravina B, Revesz T, Riess O, Rivadeneira F, Rizzu P, Ryten M, Sawcer S, Schapira A, Scheffer H, Shaw K, Shoulson I, Sidransky E, Smith C, Spencer CC, Stefánsson H, Bettella F, Stockton JD, Strange A, Talbot K, Tanner CM, Tashakkori-Ghanbaria A, Tison F, Trabzuni D, Traynor BJ, Uitterlinden AG, Velseboer D, Vidailhet M, Walker R, van de Warrenburg B, Wickremaratchi M, Williams N, Williams-Gray CH, Winder-Rhodes S, Stefánsson K, Martinez M, Wood NW, Hardy J, Heutink P, Brice A, Gasser T, Singleton AB, Renton AE, Nichols N, Brooks J, Arepalli S, Pilner H, Letson C, Traynor BJ, Factor S, Higgins D, Evans S, Shill H, Stacy M, Danielson J, Marlor L, Williamson K, Jankovic J, Hunter C, Simon D, Ryan P, Scollins L, Saunders-Pullman R, Boyar K, Costan-Toth C, Ohmann E, Sudarsky L, Joubert C, Friedman J, Chou K, Fernandez H, Lannon M, Galvez-Jimenez N, Podichetty A, Thompson K, Lewitt P, DeAngelis M, O'Brien C, Seeberger L, Dingmann C, Judd D, Marder K, Fraser J, Harris J, Bertoni J, Peterson C, Rezak M, Medalle G, Chouinard S, Panisset M, Hall J, Poiffaut H, Calabrese V, Roberge P, Wojcieszek J, Belden J, Jennings D, Marek K, Mendick S, Reich S, Dunlop B, Jog M, Horn C, Uitti R, Turk M, Ajax T, Mannetter J, Sethi K, Carpenter J, Dill B, Hatch L, Ligon K, Narayan S, Blindauer K, Abou-Samra K, Petit J, Elmer L, Aiken E, Davis K, Schell C, Wilson S, Velickovic M, Koller W, Phipps S, Feigin A, Gordon M, Hamann J, Licari E, Marotta-Kollarus M, Shannon B, Winnick R, Simuni T, Videnovic A, Kaczmarek A, Williams K, Wolff M, Rao J, Cook M, Fernandez M, Kostyk S, Hubble J, Campbell A, Reider C, Seward A, Camicioli R, Carter J, Nutt J, Andrews P, Morehouse S, Stone C, Mendis T, Grimes D, Alcorn-Costa C, Gray P, Haas K, Vendette J, Sutton J, Hutchinson B, Young J, Rajput A, Rajput A, Klassen L, Shirley T, Manyam B, Simpson P, Whetteckey J, Wulbrecht B, Truong D, Pathak M, Frei K, Luong N, Tra T, Tran A, Vo J, Lang A, Kleiner-Fisman G, Nieves A, Johnston L, So J, Podskalny G, Giffin L, Atchison P, Allen C, Martin W, Wieler M, Suchowersky O, Furtado S, Klimek M, Hermanowicz N, Niswonger S, Shults C, Fontaine D, Aminoff M, Christine C, Diminno M, Hevezi J, Dalvi A, Kang U, Richman J, Uy S, Young J, Dalvi A, Sahay A, Gartner M, Schwieterman D, Hall D, Leehey M, Culver S, Derian T, Demarcaida T, Thurlow S, Rodnitzky R, Dobson J, Lyons K, Pahwa R, Gales T, Thomas S, Shulman L, Reich S, Weiner W, Dustin K, Lyons K, Singer C, Koller W, Weiner W, Zelaya L, Tuite P, Hagen V, Rolandelli S, Schacherer R, Kosowicz J, Gordon P, Werner J, Serrano C, Roque S, Kurlan R, Berry D, Gardiner I, Hauser R, Sanchez-Ramos J, Zesiewicz T, Delgado H, Price K, Rodriguez P, Wolfrath S, Pfeiffer R, Davis L, Pfeiffer B, Dewey R, Hayward B, Johnson A, Meacham M, Estes B, Walker F, Hunt V, O'Neill C, Racette B, Swisher L, Eriksson N, Dijamco C, Drabant EM, Dorfman E, Tung JY, Hinds DA, Mountain JL, Wojcicki A, Lill C, Bertram L, Lew M, Suchowersky O, Klein C, Golbe L, Mark MH, Growdon J, Huggins N, Wooten GF, Watts R, Guttman M, Racette B, Perlmutter J, Marlor L, Shill H, Singer C, Goldwurm S, Pezzoli G, Saint-Hilaire MH, Massood T, Baker K, Itin I, Litvan I, Nicholson G, Corbett A, Nance M, Drasby E, Isaacson S, Burn D, Chinnery P, Pramstaller P, Al-hinti J, Moller A, Ostergaard K, Sherman S, Roxburgh R, Snow B, Slevin J, Cambi F, Kay D, Montimurro J, Kusel V, Samii A, Martinez E, Yearout D, Nutt J, Agarwal P, Griffith A, Roberts JW, Higgins DS, Molho E, Rosen A, Clark LN, Liu X, Lee JH, Cheng R, Marder K, Louis ED, Cote LJ, Waters C, Ford B, Fahn S, Vance JM, Beecham GW, Martin ER, Nuytemans K, Pericak-Vance MA, Haines JL, DeStefano A, Seshadri S, Choi SH, Frank S, Bis JC, Psaty BM, Rice K, Longstreth WT Jr, Ton TG, Jain S, Ikram MA, van Duijn CM, Hofman A, Uitterlinden A, Verlinden V, Koudstaal PJ, Kara E, Xiromerisiou G, Dardiotis E, Tsimourtou V, Spanaki C, Plaitakis A, Bozi M, Stefanis L, Vassilatis D, Koutsis G, Panas M, Houlden H, Hadjigeorgiou GM, Guerreiro R, Bras J, Lunnon K, Lupton M, Powell J, Parkkinen L, Ansorge O, Hardy J.

Abstract

Our objective was to design a genotyping platform that would allow rapid genetic characterization of samples in the context of genetic mutations and risk factors associated with common neurodegenerative diseases. The platform needed to be relatively affordable, rapid to deploy, and use a common and accessible technology. Central to this project, we wanted to make the content of the platform open to any investigator without restriction. In designing this array we prioritized a number of types of genetic variability for inclusion, such as known risk alleles, disease-causing mutations, putative risk alleles, and other functionally important variants. The array was primarily designed to allow rapid screening of samples for disease-causing mutations and large population studies of risk factors. Notably, an explicit aim was to make this array widely available to facilitate data sharing across and within diseases. The resulting array, NeuroX, is a remarkably cost and time effective solution for high-quality genotyping. NeuroX comprises a backbone of standard Illumina exome content of approximately 240,000 variants, and over 24,000 custom content variants focusing on neurologic diseases. Data are generated at approximately $50-$60 per sample using a 12-sample format chip and regular Infinium infrastructure; thus, genotyping is rapid and accessible to many investigators. Here, we describe the design of NeuroX, discuss the utility of NeuroX in the analyses of rare and common risk variants, and present quality control metrics and a brief primer for the analysis of NeuroX derived data.

Published by Elsevier Inc.

KEYWORDS:

Genetics; Genotyping; Imputation; Meta-analysis; Methods; Neurodegeneration; Parkinson's

PMID:
25444595
[PubMed - indexed for MEDLINE]
PMCID:
PMC4317375
Free PMC Article
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