title: NeuroX, a fast and efficient genotyping platform for investigation of neurodegenerative diseases.
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.
authors.forename: Mike A
authors.initials: MA
authors.lastname: Nalls
authors.forename: Jose
authors.initials: J
authors.lastname: Bras
authors.forename: Dena G
authors.initials: DG
authors.lastname: Hernandez
authors.forename: Margaux F
authors.initials: MF
authors.lastname: Keller
authors.forename: Elisa
authors.initials: E
authors.lastname: Majounie
authors.forename: Alan E
authors.initials: AE
authors.lastname: Renton
authors.forename: Mohamad
authors.initials: M
authors.lastname: Saad
authors.forename: Iris
authors.initials: I
authors.lastname: Jansen
authors.forename: Rita
authors.initials: R
authors.lastname: Guerreiro
authors.forename: Steven
authors.initials: S
authors.lastname: Lubbe
authors.forename: Vincent
authors.initials: V
authors.lastname: Plagnol
authors.forename: J Raphael
authors.initials: JR
authors.lastname: Gibbs
authors.forename: Claudia
authors.initials: C
authors.lastname: Schulte
authors.forename: Nathan
authors.initials: N
authors.lastname: Pankratz
authors.forename: Margaret
authors.initials: M
authors.lastname: Sutherland
authors.forename: Lars
authors.initials: L
authors.lastname: Bertram
authors.forename: Christina M
authors.initials: CM
authors.lastname: Lill
authors.forename: Anita L
authors.initials: AL
authors.lastname: DeStefano
authors.forename: Tatiana
authors.initials: T
authors.lastname: Faroud
authors.forename: Nicholas
authors.initials: N
authors.lastname: Eriksson
authors.forename: Joyce Y
authors.initials: JY
authors.lastname: Tung
authors.forename: Connor
authors.initials: C
authors.lastname: Edsall
authors.forename: Noah
authors.initials: N
authors.lastname: Nichols
authors.forename: Janet
authors.initials: J
authors.lastname: Brooks
authors.forename: Sampath
authors.initials: S
authors.lastname: Arepalli
authors.forename: Hannah
authors.initials: H
authors.lastname: Pliner
authors.forename: Chris
authors.initials: C
authors.lastname: Letson
authors.forename: Peter
authors.initials: P
authors.lastname: Heutink
authors.forename: Maria
authors.initials: M
authors.lastname: Martinez
authors.forename: Thomas
authors.initials: T
authors.lastname: Gasser
authors.forename: Bryan J
authors.initials: BJ
authors.lastname: Traynor
authors.forename: Nick
authors.initials: N
authors.lastname: Wood
authors.forename: John
authors.initials: J
authors.lastname: Hardy
authors.forename: Andrew B
authors.initials: AB
authors.lastname: Singleton
mesh_terms: D000483:Alleles; D003365:Costs and Cost Analysis; D056726:Genetic Association Studies / Q000379:methods*; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D014644:Genetic Variation; D060005:Genotyping Techniques / Q000191:economics / Q000379:methods*; D019636:Neurodegenerative Diseases / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*
keywords: Genetics; Genotyping; Imputation; Meta-analysis; Methods; Neurodegeneration; Parkinson's