Neurox

Manufactured by Illumina

The NeuroX is a high-throughput, targeted next-generation sequencing (NGS) panel designed for comprehensive genomic profiling of neurological disorders. It covers over 1,700 genes associated with a wide range of neurological conditions, including neurodegenerative diseases, neuromuscular disorders, and developmental and epileptic encephalopathies. The NeuroX panel enables researchers to efficiently analyze multiple genes simultaneously, facilitating the identification of genetic variations that may contribute to neurological disorders.

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Lab products found in correlation

Neuro consortium array, by Illumina (3 mentions) Genomestudio v2, by Illumina (2 mentions) Immunochip, by Illumina (1 mentions) Neurox array, by Illumina (1 mentions)

4 protocols using neurox

Genotyping Patients for Parkinson's Disease

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Initial genotyping in patients without a known mutation was performed using a genome-wide coverage array (NeuroX or Neuro Consortium Array, Illumina, Inc., San Diego, CA),^{19 , 20} whole-genome sequencing, Sanger sequencing, or commercial next-generation sequencing of a panel of PD-related genes (GeneDx Pakinson Disease Panel; Gaithersburg, MD). All genotypes were confirmed with CLIA-certified testing performed by GeneDx (Gaithersburg, MD), with the exception of one patient with a GBA mutation and an unaffected Gaucher patient, both of whom were genotyped by Sanger sequencing in the laboratory of Dr. Ellen Sidransky at NHGRI (Bethesda, MD).

Isonaka R., Goldstein D.S., Zhu W., Yoon E., Ehrlich D., Schindler A.B., Kokkinis A.D., Sabir M.S., Scholz S.W., Bandres-Ciga S., Blauwendraat C., Gonzalez-Alegre P., Lopez G., Sidransky E, & Narendra D.P. (2021). α-Synuclein deposition in sympathetic nerve fibers in genetic forms of Parkinson’s Disease. Movement disorders : official journal of the Movement Disorder Society, 36(10), 2346-2357.

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PPMI Genotyping and Quality Control

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All PPMI samples were genotyped using the Illumina Immunochip and NeuroX. Before association analyses. All samples and genotypes underwent stringent quality controls (QC). The NeuroX array underwent the same QC steps as the Immunochip but removed variants based on the Minor Allele Frequency (MAF)¹¹. For SNP selection, we extracted GCH1 RS026 genotype data (C/C, C/T, T/T).

Webb J, & Willette A.A. (2016). Aging Modifies the Effect of GCH1 RS11158026 on DAT Uptake and Parkinson's Disease Clinical Severity. Neurobiology of aging, 50, 39-46.

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Genetic analysis of PD patients

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A total of 5 GBA+DBS+ subjects with clinical and genetic data were available in the NIH Parkinson’s Clinic database (2012–2019). Genotyping was performed using a genotyping array (NeuroX or Neuro Consortium Array, Illumina, Inc., San Diego, CA) with custom content covering neurodegenerative disease-related variants. To identify SNPs from the genotyping array, Illumina GenomeStudio (v.2.0) was used cluster genotypes. After quality control, subjects with pathogenic GBA variants were included while VUS were excluded.

Pal G., Mangone G., Hill E.J., Ouyang B., Liu Y., Lythe V., Ehrlich D., Saunders-Pullman R., Shanker V., Bressman S., Alcalay R.N., Garcia P., Marder K.S., Aasly J., Mouradian M.M., Link S., Rosenbaum M., Anderson S., Bernard B., Wilson R., Stebbins G., Nichols W.C., Welter M.L., Sani S., Afshari M., Verhagen L., de Bie R.M., Foltynie T., Hall D., Corvol J.C, & Goetz C.G. (2022). Parkinson disease and STN-DBS: cognitive effects in GBA mutation carriers. Annals of neurology, 91(3), 424-435.

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Genotyping of Parkinson's Disease Cohort

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Genotyping of the NIH-PD cohort was performed using a genome-wide coverage genotyping array (NeuroX or Neuro Consortium Array, Illumina, Inc., San Diego, CA) and/or WGS. The NeuroX array is based on the Illumina HumanExome array v1.1 and the NeuroChip array is based on the Infinium HumanCore-24 c1.0 array 23, (link)24 (link) . Both have additional custom content covering neurodegenerative disease-related variants. To identify SNPs from the genotyping array, Illumina GenomeStudio (v.2.0) was used cluster genotypes. Quality-Control measured included limiting to samples with call rates of >95%, excluding samples with excess heterogeneity (F statistic > ± 0.25), and excluding samples whose genotyped sex did not match the sample demographics. CNVs were identified by manual inspection of the B Allele Frequency and Log R Ratio for the PRKN gene region (Chr6: 161770811 -163140694, hg19), using the gglot2 visualization package for R (https://www.r-project.org/), as described previously 25 (link) .
for use under a CC0 license.

Zhu W., Huang X., Yoon E., Bandrés‐Ciga S., Blauwendraat C., Cade J.H., Wu B.P., Williams V.H., Schindler A.B., Brooks J., Gibbs J.R., Hernández D., Ehrlich D., Singleton A., & Narendra D.P. (2021). Heterozygous PRKN mutations are common but do not increase the risk of Parkinson’s disease.

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