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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.

SUBMITTER: Nalls MA 

PROVIDER: S-EPMC4317375 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature

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

Nalls Mike A MA   Bras Jose J   Hernandez Dena G DG   Keller Margaux F MF   Majounie Elisa E   Renton Alan E AE   Saad Mohamad M   Jansen Iris I   Guerreiro Rita R   Lubbe Steven S   Plagnol Vincent V   Gibbs J Raphael JR   Schulte Claudia C   Pankratz Nathan N   Sutherland Margaret M   Bertram Lars L   Lill Christina M CM   DeStefano Anita L AL   Faroud Tatiana T   Eriksson Nicholas N   Tung Joyce Y JY   Edsall Connor C   Nichols Noah N   Brooks Janet J   Arepalli Sampath S   Pliner Hannah H   Letson Chris C   Heutink Peter P   Martinez Maria M   Gasser Thomas T   Traynor Bryan J BJ   Wood Nick N   Hardy John J   Singleton Andrew B AB  

Neurobiology of aging 20140804 3


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  ...[more]

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