TY - JOUR
T1 - NeuroX, a fast and efficient genotyping platform for investigation of neurodegenerative diseases
AU - International Parkinson's Disease Genomics Consortium (IPDGC)
AU - Nalls, Mike A
AU - Bras, Jose
AU - Hernandez, Dena G
AU - Keller, Margaux F
AU - Majounie, Elisa
AU - Renton, Alan E
AU - Saad, Mohamad
AU - Jansen, Iris
AU - Guerreiro, Rita
AU - Lubbe, Steven
AU - Plagnol, Vincent
AU - Gibbs, J Raphael
AU - Schulte, Claudia
AU - Pankratz, Nathan
AU - Sutherland, Margaret
AU - Bertram, Lars
AU - Lill, Christina M
AU - DeStefano, Anita L
AU - Faroud, Tatiana
AU - Eriksson, Nicholas
AU - Tung, Joyce Y
AU - Edsall, Connor
AU - Nichols, Noah
AU - Brooks, Janet
AU - Arepalli, Sampath
AU - Pliner, Hannah
AU - Letson, Chris
AU - Heutink, Peter
AU - Martinez, Maria
AU - Gasser, Thomas
AU - Traynor, Bryan J
AU - Wood, Nick
AU - Hardy, John
AU - Singleton, Andrew B
N1 - Published by Elsevier Inc.
PY - 2015
Y1 - 2015
N2 - 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.
AB - 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.
U2 - 10.1016/j.neurobiolaging.2014.07.028
DO - 10.1016/j.neurobiolaging.2014.07.028
M3 - Journal articles
C2 - 25444595
SN - 0197-4580
VL - 36
SP - 1605.e7-12
JO - Neurobiology of Aging
JF - Neurobiology of Aging
IS - 3
ER -