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 language | English (US) |
|---|---|
| Pages (from-to) | 247.e9-247.e13 |
| Journal | Neurobiology of Aging |
| Volume | 57 |
| DOIs | |
| State | Published - Sep 1 2017 |
Keywords
- Genetic screening
- Genotyping
- NeuroChip
- NeuroX
- Neurodegeneration
ASJC Scopus subject areas
- Neuroscience(all)
- Aging
- Clinical Neurology
- Developmental Biology
- Geriatrics and Gerontology
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NeuroChip, an updated version of the NeuroX genotyping platform to rapidly screen for variants associated with neurological diseases. / Blauwendraat, Cornelis; Faghri, Faraz; Pihlstrom, Lasse; Geiger, Joshua T.; Elbaz, Alexis; Lesage, Suzanne; Corvol, Jean Christophe; May, Patrick; Nicolas, Aude; Abramzon, Yevgeniya; Murphy, Natalie A.; Gibbs, J. Raphael; Ryten, Mina; Ferrari, Raffaele; Bras, Jose; Guerreiro, Rita; Williams, Julie; Sims, Rebecca; Lubbe, Steven; Hernandez, Dena G.; Mok, Kin Y.; Robak, Laurie; Campbell, Roy H.; Rogaeva, Ekaterina; Traynor, Bryan J.; Chia, Ruth; Chung, Sun Ju; Hardy, John A.; Brice, Alexis; Wood, Nicholas W.; Houlden, Henry; Shulman, Joshua M.; Morris, Huw R.; Gasser, Thomas; Krüger, Rejko; Heutink, Peter; Sharma, Manu; Simón-Sánchez, Javier; Nalls, Mike A.; Singleton, Andrew B.; Scholz, Sonja W.; Noyce, Alastair J.; Brice, Alexis; Brice, Alexis; Brice, Alexis; Giri, Anamika; Oehmig, Angelika; Tucci, Arianna; Nicolas, Aude; Schulte, Claudia; Cookson, Mark R.; Blauwendraat, Cornelis; Kia, Demis; Danjou, Fabrice; Danjou, Fabrice; Danjou, Fabrice; Faghri, Faraz; Faghri, Faraz; Charlesworth, Gavin; Gibbs, J. Raphael; Gibbs, J. Raphael; Morris, Huw R.; Plun-Favreau, Helene; Hernandez, Dena G.; Hernandez, Dena G.; Holmans, Peter; Morris, Huw R.; Jansen, Iris; Hardy, John; Simón-Sánchez, Javier; Bras, Jose M.; Shulman, Joshua M.; Quinn, John; Botía, Juan A.; Mok, Kin Y.; Billingsley, Kimberley; Pihlstrom, Lasse; R’bibo, Lea; Lungu, Codrin; Sharma, Manu; Martinez, Maria; Ryten, Mina; Escott-Price, Valentina; Mencacci, Niccolo E.; Nalls, Mike A.; Nalls, Mike A.; Wood, Nicholas W.; Lewis, Patrick; Denny, Paul; Heutink, Peter; Rizzu, Patrizia; Taba, Pille; Guerreiro, Rita; Lovering, Ruth; Ogalla, Raquel Duran; Foulger, Rebecca; Robak, Laurie; Lubbe, Steven; Finkbeiner, Steven; Finkbeiner, Steven; Sveinbjörnsdóttir, Sigurlaug; Sveinbjörnsdóttir, Sigurlaug; Sveinbjörnsdóttir, Sigurlaug; Singleton, Andrew B.; Scholz, Sonja; Koks, Sulev; Lesage, Suzanne; Lesage, Suzanne; Lesage, Suzanne; Corvol, Jean Christophe; Corvol, Jean Christophe; Corvol, Jean Christophe; Corvol, Jean Christophe; Foltynie, Thomas; Gasser, Thomas; Price, T. Ryan; Sheerin, Una Marie; Williams, Nigel; Reed, Xylena; Gasser, Thomas; Krüger, Rejko; Sharma, Manu; Simón-Sánchez, Javier; Schulte, Claudia; Heutink, Peter; Wang, Lisa; Giri, Anamika; Brockmann, Kathrin; Oertel, Wolfgang; Klein, Christine; Mohamed, Fatima; Malard, Lucile; Elbaz, Alexis; Lesage, Suzanne; Corti, Olga; Drouet, Valérie; Corvol, Jean Christophe; Brice, Alexis; Goldwurm, Stefano; Tesei, Silvana; Canesi, Margherita; Valente, Enza Maria; Petrucci, Simona; Petrucci, Simona; Ginevrino, Monia; Ginevrino, Monia; Toft, Mathias; Pihlstrøm, Lasse; Aasly, Jan; Henriksen, Sandra Pilar; Sætehaug, Camilla; Wood, Nicholas W.; Houlden, Henry; Hardy, John; Bras, Jose; Orr-Urtreger, Avi; Giladi, Nir; Ferreira, Joaquim; Guedes, Leonor Correia; Guedes, Leonor Correia; Bouça-Machado, Raquel; Coelho, Miguel; Coelho, Miguel; Rosa, Mário Miguel; Rosa, Mário Miguel; Tolosa, Eduardo; Fernández-Santiago, Ruben; Ezquerra, Mario; Marti, Maria Jose; Krüger, Rejko; May, Patrick; Glaab, Enrico; Balling, Rudi; Heutink, Peter; Chung, Sun Ju.
In: Neurobiology of Aging, Vol. 57, 01.09.2017, p. 247.e9-247.e13.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - NeuroChip, an updated version of the NeuroX genotyping platform to rapidly screen for variants associated with neurological diseases
AU - Blauwendraat, Cornelis
AU - Faghri, Faraz
AU - Pihlstrom, Lasse
AU - Geiger, Joshua T.
AU - Elbaz, Alexis
AU - Lesage, Suzanne
AU - Corvol, Jean Christophe
AU - May, Patrick
AU - Nicolas, Aude
AU - Abramzon, Yevgeniya
AU - Murphy, Natalie A.
AU - Gibbs, J. Raphael
AU - Ryten, Mina
AU - Ferrari, Raffaele
AU - Bras, Jose
AU - Guerreiro, Rita
AU - Williams, Julie
AU - Sims, Rebecca
AU - Lubbe, Steven
AU - Hernandez, Dena G.
AU - Mok, Kin Y.
AU - Robak, Laurie
AU - Campbell, Roy H.
AU - Rogaeva, Ekaterina
AU - Traynor, Bryan J.
AU - Chia, Ruth
AU - Chung, Sun Ju
AU - Hardy, John A.
AU - Brice, Alexis
AU - Wood, Nicholas W.
AU - Houlden, Henry
AU - Shulman, Joshua M.
AU - Morris, Huw R.
AU - Gasser, Thomas
AU - Krüger, Rejko
AU - Heutink, Peter
AU - Sharma, Manu
AU - Simón-Sánchez, Javier
AU - Nalls, Mike A.
AU - Singleton, Andrew B.
AU - Scholz, Sonja W.
AU - Noyce, Alastair J.
AU - Brice, Alexis
AU - Brice, Alexis
AU - Brice, Alexis
AU - Giri, Anamika
AU - Oehmig, Angelika
AU - Tucci, Arianna
AU - Nicolas, Aude
AU - Schulte, Claudia
AU - Cookson, Mark R.
AU - Blauwendraat, Cornelis
AU - Kia, Demis
AU - Danjou, Fabrice
AU - Danjou, Fabrice
AU - Danjou, Fabrice
AU - Faghri, Faraz
AU - Faghri, Faraz
AU - Charlesworth, Gavin
AU - Gibbs, J. Raphael
AU - Gibbs, J. Raphael
AU - Morris, Huw R.
AU - Plun-Favreau, Helene
AU - Hernandez, Dena G.
AU - Hernandez, Dena G.
AU - Holmans, Peter
AU - Morris, Huw R.
AU - Jansen, Iris
AU - Hardy, John
AU - Simón-Sánchez, Javier
AU - Bras, Jose M.
AU - Shulman, Joshua M.
AU - Quinn, John
AU - Botía, Juan A.
AU - Mok, Kin Y.
AU - Billingsley, Kimberley
AU - Pihlstrom, Lasse
AU - R’bibo, Lea
AU - Lungu, Codrin
AU - Sharma, Manu
AU - Martinez, Maria
AU - Ryten, Mina
AU - Escott-Price, Valentina
AU - Mencacci, Niccolo E.
AU - Nalls, Mike A.
AU - Nalls, Mike A.
AU - Wood, Nicholas W.
AU - Lewis, Patrick
AU - Denny, Paul
AU - Heutink, Peter
AU - Rizzu, Patrizia
AU - Taba, Pille
AU - Guerreiro, Rita
AU - Lovering, Ruth
AU - Ogalla, Raquel Duran
AU - Foulger, Rebecca
AU - Robak, Laurie
AU - Lubbe, Steven
AU - Finkbeiner, Steven
AU - Finkbeiner, Steven
AU - Sveinbjörnsdóttir, Sigurlaug
AU - Sveinbjörnsdóttir, Sigurlaug
AU - Sveinbjörnsdóttir, Sigurlaug
AU - Singleton, Andrew B.
AU - Scholz, Sonja
AU - Koks, Sulev
AU - Lesage, Suzanne
AU - Lesage, Suzanne
AU - Lesage, Suzanne
AU - Corvol, Jean Christophe
AU - Corvol, Jean Christophe
AU - Corvol, Jean Christophe
AU - Corvol, Jean Christophe
AU - Foltynie, Thomas
AU - Gasser, Thomas
AU - Price, T. Ryan
AU - Sheerin, Una Marie
AU - Williams, Nigel
AU - Reed, Xylena
AU - Gasser, Thomas
AU - Krüger, Rejko
AU - Sharma, Manu
AU - Simón-Sánchez, Javier
AU - Schulte, Claudia
AU - Heutink, Peter
AU - Wang, Lisa
AU - Giri, Anamika
AU - Brockmann, Kathrin
AU - Oertel, Wolfgang
AU - Klein, Christine
AU - Mohamed, Fatima
AU - Malard, Lucile
AU - Elbaz, Alexis
AU - Lesage, Suzanne
AU - Corti, Olga
AU - Drouet, Valérie
AU - Corvol, Jean Christophe
AU - Brice, Alexis
AU - Goldwurm, Stefano
AU - Tesei, Silvana
AU - Canesi, Margherita
AU - Valente, Enza Maria
AU - Petrucci, Simona
AU - Petrucci, Simona
AU - Ginevrino, Monia
AU - Ginevrino, Monia
AU - Toft, Mathias
AU - Pihlstrøm, Lasse
AU - Aasly, Jan
AU - Henriksen, Sandra Pilar
AU - Sætehaug, Camilla
AU - Wood, Nicholas W.
AU - Houlden, Henry
AU - Hardy, John
AU - Bras, Jose
AU - Orr-Urtreger, Avi
AU - Giladi, Nir
AU - Ferreira, Joaquim
AU - Guedes, Leonor Correia
AU - Guedes, Leonor Correia
AU - Bouça-Machado, Raquel
AU - Coelho, Miguel
AU - Coelho, Miguel
AU - Rosa, Mário Miguel
AU - Rosa, Mário Miguel
AU - Tolosa, Eduardo
AU - Fernández-Santiago, Ruben
AU - Ezquerra, Mario
AU - Marti, Maria Jose
AU - Krüger, Rejko
AU - May, Patrick
AU - Glaab, Enrico
AU - Balling, Rudi
AU - Heutink, Peter
AU - Chung, Sun Ju
N1 - Funding Information: The authors would like to thank all of the subjects who donated their time and biological samples to be a part of this study. NABEC control brain tissues were obtained from the Baltimore Longitudinal Study on Aging at the Johns Hopkins School of Medicine, and from the NICHD Brain and Tissue Bank for Developmental Disorders at the University of Maryland, Baltimore, MD. This work was supported in part by the Intramural Research Programs of the National Institute of Neurological Disorders and Stroke (NINDS), the National Institute on Aging (NIA), and the National Institute of Environmental Health Sciences both part of the National Institutes of Health, Department of Health and Human Services; project numbers Z01-AG000949-02, Z01-ES101986, 1ZIANS003154. Faraz Faghri's contribution to this work has been supported in part through the grant 1U54GM114838 awarded by NIGMS through funds provided by the trans-NIH big data to Knowledge (BD2K) initiative (www.bd2k.nih.gov/). The project underlying this publication was funded by the German Federal Ministry of Education and Research under the support code 031 A 430 A. Responsibility for the content lies with the authors. The project was also supported through the following funding organizations under the aegis of the EU Joint Programme for Neurodegenerative Disease Research (JPND; www.jpnd.eu). This study was also supported by Parkinson's UK (grants 8047 and J-0804) and the Medical Research Council (G0700943 and G1100643). Joshua M. Shulman is supported by the Huffington Foundation and a Career Award for Medical Scientists from the Burroughs Wellcome Fund.
PY - 2017/9/1
Y1 - 2017/9/1
N2 - 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.
AB - 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.
KW - Genetic screening
KW - Genotyping
KW - NeuroChip
KW - NeuroX
KW - Neurodegeneration
UR - http://www.scopus.com/inward/record.url?scp=85020407918&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85020407918&partnerID=8YFLogxK
U2 - 10.1016/j.neurobiolaging.2017.05.009
DO - 10.1016/j.neurobiolaging.2017.05.009
M3 - Article
C2 - 28602509
AN - SCOPUS:85020407918
VL - 57
SP - 247.e9-247.e13
JO - Neurobiology of Aging
JF - Neurobiology of Aging
SN - 0197-4580
ER -