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

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.; Hernandez, D. G.; Mok, K. Y.; Robak, L.; Campbell, R. H.; Rogaeva, E.; Traynor, B. J.; Chia, R.; Chung, S. J.; Hardy, J. A.; Brice, A.; Wood, N. W.; Houlden, H.; Shulman, J. M.; Morris, H. R.; Gasser, T.; Kruger, R.; Heutink, P.; Sharma, M.; Simon-Sanchez, J.; Nalls, M. A.; Singleton, A. B.; Scholz, S. W.; Noyce, A. J.; Brice, A.; Brice, A.; Brice, A.; Giri, A.; Oehmig, A.; Tucci, A.; Nicolas, A.; Schulte, C.; Cookson, M. R.; Blauwendraat, C.; Kia, D.; Danjou, F.; Danjou, F.; Danjou, F.; Faghri, F.; Faghri, F.; Charlesworth, G.; Gibbs, J. R.; Gibbs, J. R.; Morris, H. R.; Plun-Favreau, H.; Hernandez, D. G.; Hernandez, D. G.; Holmans, P.; Morris, H. R.; Jansen, I.; Hardy, J.; Simon-Sanchez, J.; Bras, J. M.; Shulman, J. M.; Quinn, J.; Botia, J. A.; Mok, K. Y.; Billingsley, K.; Pihlstrom, L.; R'Bibo, L.; Lungu, C.; Sharma, M.; Martinez, M.; Ryten, M.; Escott-Price, V.; Mencacci, N. E.; Nalls, M. A.; Nalls, M. A.; Wood, N. W.; Topley, Lewis; Denny, P.; Heutink, P.; Rizzu, P.; Taba, P.; Guerreiro, R.; Lovering, R.; Ogalla, R. D.; Foulger, R.; Robak, L.; Lubbe, S.; Finkbeiner, S.; Finkbeiner, S.; Sveinbjornsdottir, S.; Sveinbjornsdottir, S.; Sveinbjornsdottir, S.; Singleton, A. B.; Scholz, S.; Koks, S.; Lesage, S.; Lesage, S.; Lesage, S.; Corvol, J. -C.; Corvol, J. -C.; Corvol, J. -C.; Corvol, J. -C.; Foltynie, T.; Gasser, T.; Price, T. R.; Sheerin, U. -M.; Williams, N.; Reed, X.; Gasser, T.; Kruger, R.; Sharma, M.; Simon-Sanchez, J.; Schulte, C.; Heutink, P.; Wang, L.; Giri, A.; Brockmann, K.; Oertel, W.; Klein, C.; Mohamed, F.; Malard, L.; Elbaz, A.; Lesage, S.; Corti, O.; Drouet, V.; Corvol, J. -C.; Brice, A.; Goldwurm, S.; Tesei, S.; Canesi, M.; Valente, E. M.; Petrucci, S.; Petrucci, S.; Ginevrino, M.; Ginevrino, M.; Toft, M.; Pihlstrom, L.; Aasly, J.; Henriksen, S. P.; Saetehaug, C.; Wood, N. W.; Houlden, H.; Hardy, J.; Bras, J.; Orr-Urtreger, A.; Giladi, N.; Ferreira, J.; Guedes, L. C.; Guedes, L. C.; Bouca-Machado, R.; Coelho, M.; Coelho, M.; Rosa, M. M.; Rosa, M. M.; Tolosa, E.; Fernandez-Santiago, R.; Ezquerra, M.; Marti, M. J.; Kruger, R.; May, P.; Glaab, E.; Balling, R.; Heutink, P.; Chung, S. -J.

doi:10.1016/j.neurobiolaging.2017.05.009

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.

NeuroChip, an updated version of the NeuroX genotyping platform to rapidly screen for variants associated with neurological diseases / 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.; Hernandez, D. G.; Mok, K. Y.; Robak, L.; Campbell, R. H.; Rogaeva, E.; Traynor, B. J.; Chia, R.; Chung, S. J.; Hardy, J. A.; Brice, A.; Wood, N. W.; Houlden, H.; Shulman, J. M.; Morris, H. R.; Gasser, T.; Kruger, R.; Heutink, P.; Sharma, M.; Simon-Sanchez, J.; Nalls, M. A.; Singleton, A. B.; Scholz, S. W.; Noyce, A. J.; Brice, A.; Brice, A.; Brice, A.; Giri, A.; Oehmig, A.; Tucci, A.; Nicolas, A.; Schulte, C.; Cookson, M. R.; Blauwendraat, C.; Kia, D.; Danjou, F.; Danjou, F.; Danjou, F.; Faghri, F.; Faghri, F.; Charlesworth, G.; Gibbs, J. R.; Gibbs, J. R.; Morris, H. R.; Plun-Favreau, H.; Hernandez, D. G.; Hernandez, D. G.; Holmans, P.; Morris, H. R.; Jansen, I.; Hardy, J.; Simon-Sanchez, J.; Bras, J. M.; Shulman, J. M.; Quinn, J.; Botia, J. A.; Mok, K. Y.; Billingsley, K.; Pihlstrom, L.; R'Bibo, L.; Lungu, C.; Sharma, M.; Martinez, M.; Ryten, M.; Escott-Price, V.; Mencacci, N. E.; Nalls, M. A.; Nalls, M. A.; Wood, N. W.; Topley, Lewis; Denny, P.; Heutink, P.; Rizzu, P.; Taba, P.; Guerreiro, R.; Lovering, R.; Ogalla, R. D.; Foulger, R.; Robak, L.; Lubbe, S.; Finkbeiner, S.; Finkbeiner, S.; Sveinbjornsdottir, S.; Sveinbjornsdottir, S.; Sveinbjornsdottir, S.; Singleton, A. B.; Scholz, S.; Koks, S.; Lesage, S.; Lesage, S.; Lesage, S.; Corvol, J. -C.; Corvol, J. -C.; Corvol, J. -C.; Corvol, J. -C.; Foltynie, T.; Gasser, T.; Price, T. R.; Sheerin, U. -M.; Williams, N.; Reed, X.; Gasser, T.; Kruger, R.; Sharma, M.; Simon-Sanchez, J.; Schulte, C.; Heutink, P.; Wang, L.; Giri, A.; Brockmann, K.; Oertel, W.; Klein, C.; Mohamed, F.; Malard, L.; Elbaz, A.; Lesage, S.; Corti, O.; Drouet, V.; Corvol, J. -C.; Brice, A.; Goldwurm, S.; Tesei, S.; Canesi, M.; Valente, E. M.; Petrucci, S.; Petrucci, S.; Ginevrino, M.; Ginevrino, M.; Toft, M.; Pihlstrom, L.; Aasly, J.; Henriksen, S. P.; Saetehaug, C.; Wood, N. W.; Houlden, H.; Hardy, J.; Bras, J.; Orr-Urtreger, A.; Giladi, N.; Ferreira, J.; Guedes, L. C.; Guedes, L. C.; Bouca-Machado, R.; Coelho, M.; Coelho, M.; Rosa, M. M.; Rosa, M. M.; Tolosa, E.; Fernandez-Santiago, R.; Ezquerra, M.; Marti, M. J.; Kruger, R.; May, P.; Glaab, E.; Balling, R.; Heutink, P.; Chung, S. -J.. - In: NEUROBIOLOGY OF AGING. - ISSN 0197-4580. - 57:(2017), pp. 247e9-247e13. [10.1016/j.neurobiolaging.2017.05.009]