A DNA resequencing array for genes involved in Parkinson’s disease

Abstract Parkinson’s disease (PD) is aetiologically complex with both familial and sporadic forms. Familial PD results from rare, highly penetrant pathogenic mutations whereas multiple variants of low penetrance may contribute to the risk of sporadic PD. Common variants implicated in PD risk appear...

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Published in:	Parkinsonism & related disorders Vol. 18; no. 4; pp. 386 - 390
Main Authors:	Wilkins, E.J, Rubio, J.P, Kotschet, K.E, Cowie, T.F, Boon, W.C, O’Hely, M, Burfoot, R, Wang, W, Sue, C.M, Speed, T.P, Stankovitch, J, Horne, M.K
Format:	Journal Article
Language:	English
Published:	England Elsevier Ltd 01-05-2012
Subjects:	Adult Affymetrix resequencing array Aged alpha-Synuclein - genetics DNA resequencing Female Gene Expression Profiling Genetic Predisposition to Disease Genotype Humans Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 Male Middle Aged Neurology Oligonucleotide Array Sequence Analysis Parkinson Disease - genetics Parkinsons disease Phenotype Polymorphism, Single Nucleotide - genetics Protein Kinases - genetics Protein Serine-Threonine Kinases - genetics Reproducibility of Results Ubiquitin-Protein Ligases - genetics Affymetrix resequencing array DNA resequencing Parkinsons disease
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Summary:	Abstract Parkinson’s disease (PD) is aetiologically complex with both familial and sporadic forms. Familial PD results from rare, highly penetrant pathogenic mutations whereas multiple variants of low penetrance may contribute to the risk of sporadic PD. Common variants implicated in PD risk appear to explain only a minor proportion of the familial clustering observed in sporadic PD. It is therefore plausible that combinations of rare and/or common variants in genes already implicated in disease pathogenesis may help to explain the genetic basis of PD. We have developed a CustomSeq Affymetrix resequencing array to enable high-throughput sequencing of 13 genes (44 kb) implicated in the pathogenesis of PD. Using the array we sequenced 269 individuals, including 186 PD patients and 75 controls, achieving an overall call rate of 96.5% and 93.6%, for two respective versions of the array, and >99.9% accuracy for five samples sequenced by capillary sequencing in parallel. We identified modest associations with common variants in SNCA and LRRK2 and a trend suggestive of an overrepresentation of rare variants in cases compared to controls for several genes. We propose that this technology offers a robust and cost-effective alternative to targeted sequencing using traditional sequencing methods, and here we demonstrate the potential of this approach for either routine clinical investigation or for research studies aimed at understanding the genetic aetiology of PD.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1353-8020 1873-5126
DOI:	10.1016/j.parkreldis.2011.12.012