NeuroChip, an updated version of the NeuroX genotyping platform to rapidly screen for variants associated with neurological diseases

Cornelis Blauwendraat, Faraz Faghri, Lasse Pihlstrom, Joshua T. Geiger, Alexis Elbaz, Suzanne Lesage, Jean Christophe Corvol, Patrick May, Aude Nicolas, Yevgeniya Abramzon, Natalie A. Murphy, J. Raphael Gibbs, Mina Ryten, Raffaele Ferrari, Jose Bras, Rita Guerreiro, Julie Williams, Rebecca Sims, Steven Lubbe, Dena G. HernandezKin Y. Mok, Laurie Robak, Roy H. Campbell, Ekaterina Rogaeva, Bryan J. Traynor, Ruth Chia, Sun Ju Chung, John A. Hardy, Alexis Brice, Nicholas W. Wood, Henry Houlden, Joshua M. Shulman, Huw R. Morris, Thomas Gasser, Rejko Krüger, Peter Heutink, Manu Sharma, Javier Simón-Sánchez, Mike A. Nalls, Andrew B. Singleton, Sonja W. Scholz, Alastair J. Noyce, Alexis Brice, Alexis Brice, Alexis Brice, Anamika Giri, Angelika Oehmig, Arianna Tucci, Aude Nicolas, Claudia Schulte, Mark R. Cookson, Cornelis Blauwendraat, Demis Kia, Fabrice Danjou, Fabrice Danjou, Fabrice Danjou, Faraz Faghri, Faraz Faghri, Gavin Charlesworth, J. Raphael Gibbs, J. Raphael Gibbs, Huw R. Morris, Helene Plun-Favreau, Dena G. Hernandez, Dena G. Hernandez, Peter Holmans, Huw R. Morris, Iris Jansen, John Hardy, Javier Simón-Sánchez, Jose M. Bras, Joshua M. Shulman, John Quinn, Juan A. Botía, Kin Y. Mok, Kimberley Billingsley, Lasse Pihlstrom, Lea R’bibo, Codrin Lungu, Manu Sharma, Maria Martinez, Mina Ryten, Valentina Escott-Price, Niccolo E. Mencacci, Mike A. Nalls, Mike A. Nalls, Nicholas W. Wood, Patrick Lewis, Paul Denny, Peter Heutink, Patrizia Rizzu, Pille Taba, Rita Guerreiro, Ruth Lovering, Raquel Duran Ogalla, Rebecca Foulger, Laurie Robak, Steven Lubbe, Steven Finkbeiner, Steven Finkbeiner, Sigurlaug Sveinbjörnsdóttir, Sigurlaug Sveinbjörnsdóttir, Sigurlaug Sveinbjörnsdóttir, Andrew B. Singleton, Sonja Scholz, Sulev Koks, Suzanne Lesage, Suzanne Lesage, Suzanne Lesage, Jean Christophe Corvol, Jean Christophe Corvol, Jean Christophe Corvol, Jean Christophe Corvol, Thomas Foltynie, Thomas Gasser, T. Ryan Price, Una Marie Sheerin, Nigel Williams, Xylena Reed, Thomas Gasser, Rejko Krüger, Manu Sharma, Javier Simón-Sánchez, Claudia Schulte, Peter Heutink, Lisa Wang, Anamika Giri, Kathrin Brockmann, Wolfgang Oertel, Christine Klein, Fatima Mohamed, Lucile Malard, Alexis Elbaz, Suzanne Lesage, Olga Corti, Valérie Drouet, Jean Christophe Corvol, Alexis Brice, Stefano Goldwurm, Silvana Tesei, Margherita Canesi, Enza Maria Valente, Simona Petrucci, Simona Petrucci, Monia Ginevrino, Monia Ginevrino, Mathias Toft, Lasse Pihlstrøm, Jan Aasly, Sandra Pilar Henriksen, Camilla Sætehaug, Nicholas W. Wood, Henry Houlden, John Hardy, Jose Bras, Avi Orr-Urtreger, Nir Giladi, Joaquim Ferreira, Leonor Correia Guedes, Leonor Correia Guedes, Raquel Bouça-Machado, Miguel Coelho, Miguel Coelho, Mário Miguel Rosa, Mário Miguel Rosa, Eduardo Tolosa, Ruben Fernández-Santiago, Mario Ezquerra, Maria Jose Marti, Rejko Krüger, Patrick May, Enrico Glaab, Rudi Balling, Peter Heutink, Sun Ju Chung

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)247.e9-247.e13
JournalNeurobiology of Aging
Volume57
DOIs
StatePublished - Sep 1 2017

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Keywords

  • Genetic screening
  • Genotyping
  • NeuroChip
  • NeuroX
  • Neurodegeneration

ASJC Scopus subject areas

  • Neuroscience(all)
  • Aging
  • Clinical Neurology
  • Developmental Biology
  • Geriatrics and Gerontology

Cite this

Blauwendraat, C., Faghri, F., Pihlstrom, L., Geiger, J. T., Elbaz, A., Lesage, S., Corvol, J. C., May, P., Nicolas, A., Abramzon, Y., Murphy, N. A., Gibbs, J. R., Ryten, M., Ferrari, R., Bras, J., Guerreiro, R., Williams, J., Sims, R., Lubbe, S., ... Chung, S. J. (2017). NeuroChip, an updated version of the NeuroX genotyping platform to rapidly screen for variants associated with neurological diseases. Neurobiology of Aging, 57, 247.e9-247.e13. https://doi.org/10.1016/j.neurobiolaging.2017.05.009