Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 Sep;57:247.e9-247.e13.
doi: 10.1016/j.neurobiolaging.2017.05.009. Epub 2017 May 17.

NeuroChip, an Updated Version of the NeuroX Genotyping Platform to Rapidly Screen for Variants Associated With Neurological Diseases

Affiliations
Free PMC article

NeuroChip, an Updated Version of the NeuroX Genotyping Platform to Rapidly Screen for Variants Associated With Neurological Diseases

Cornelis Blauwendraat et al. Neurobiol Aging. .
Free PMC article

Abstract

Genetics has proven to be a powerful approach in neurodegenerative diseases research, resulting in the identification of numerous causal and risk variants. Previously, we introduced the NeuroX Illumina genotyping array, a fast and efficient genotyping platform designed for the investigation of genetic variation in neurodegenerative diseases. Here, we present its updated version, named NeuroChip. The NeuroChip is a low-cost, custom-designed array containing a tagging variant backbone of about 306,670 variants complemented with a manually curated custom content comprised of 179,467 variants implicated in diverse neurological diseases, including Alzheimer's disease, Parkinson's disease, Lewy body dementia, amyotrophic lateral sclerosis, frontotemporal dementia, progressive supranuclear palsy, corticobasal degeneration, and multiple system atrophy. The tagging backbone was chosen because of the low cost and good genome-wide resolution; the custom content can be combined with other backbones, like population or drug development arrays. Using the NeuroChip, we can accurately identify rare variants and impute over 5.3 million common SNPs from the latest release of the Haplotype Reference Consortium. In summary, we describe the design and usage of the NeuroChip array and show its capability for detecting rare pathogenic variants in numerous neurodegenerative diseases. The NeuroChip has a more comprehensive and improved content, which makes it a reliable, high-throughput, cost-effective screening tool for genetic research and molecular diagnostics in neurodegenerative diseases.

Keywords: Genetic screening; Genotyping; NeuroChip; NeuroX; Neurodegeneration.

Figures

Figure 1
Figure 1. Overview of the number of HGMD disease associated variants that are present on the NeuroChip
AD = Alzheimer's disease, ALS = amyotrophic lateral sclerosis, FTD = frontotemporal dementia, and PD = Parkinson's disease

Similar articles

  • NeuroX, a fast and efficient genotyping platform for investigation of neurodegenerative diseases.
    Nalls MA, Bras J, Hernandez DG, Keller MF, Majounie E, Renton AE, Saad M, Jansen I, Guerreiro R, Lubbe S, Plagnol V, Gibbs JR, Schulte C, Pankratz N, Sutherland M, Bertram L, Lill CM, DeStefano AL, Faroud T, Eriksson N, Tung JY, Edsall C, Nichols N, Brooks J, Arepalli S, Pliner H, Letson C, Heutink P, Martinez M, Gasser T, Traynor BJ, Wood N, Hardy J, Singleton AB; International Parkinson's Disease Genomics Consortium (IPDGC); Parkinson's Disease meta-analysis consortium. Nalls MA, et al. Neurobiol Aging. 2015 Mar;36(3):1605.e7-12. doi: 10.1016/j.neurobiolaging.2014.07.028. Epub 2014 Aug 4. Neurobiol Aging. 2015. PMID: 25444595 Free PMC article.
  • Mutation analysis of patients with neurodegenerative disorders using NeuroX array.
    Ghani M, Lang AE, Zinman L, Nacmias B, Sorbi S, Bessi V, Tedde A, Tartaglia MC, Surace EI, Sato C, Moreno D, Xi Z, Hung R, Nalls MA, Singleton A, St George-Hyslop P, Rogaeva E. Ghani M, et al. Neurobiol Aging. 2015 Jan;36(1):545.e9-14. doi: 10.1016/j.neurobiolaging.2014.07.038. Epub 2014 Aug 1. Neurobiol Aging. 2015. PMID: 25174650 Free PMC article.
  • Genetic analysis of neurodegenerative diseases in a pathology cohort.
    Blauwendraat C, Pletnikova O, Geiger JT, Murphy NA, Abramzon Y, Rudow G, Mamais A, Sabir MS, Crain B, Ahmed S, Rosenthal LS, Bakker CC, Faghri F, Chia R, Ding J, Dawson TM, Pantelyat A, Albert MS, Nalls MA, Resnick SM, Ferrucci L, Cookson MR, Hillis AE, Troncoso JC, Scholz SW. Blauwendraat C, et al. Neurobiol Aging. 2019 Apr;76:214.e1-214.e9. doi: 10.1016/j.neurobiolaging.2018.11.007. Epub 2018 Nov 17. Neurobiol Aging. 2019. PMID: 30528841 Free PMC article.
  • Meta-analysis of the association between variants in MAPT and neurodegenerative diseases.
    Zhang CC, Zhu JX, Wan Y, Tan L, Wang HF, Yu JT, Tan L. Zhang CC, et al. Oncotarget. 2017 Jul 4;8(27):44994-45007. doi: 10.18632/oncotarget.16690. Oncotarget. 2017. PMID: 28402959 Free PMC article. Review.
  • [Proteins and mutations: a new vision (molecular) of neurodegenerative diseases].
    Christen Y. Christen Y. J Soc Biol. 2002;196(1):85-94. J Soc Biol. 2002. PMID: 12134639 Review. French.
See all similar articles

Cited by 17 articles

See all "Cited by" articles

Publication types

Substances

Feedback