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

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. and Horne, M.K. 2012, A DNA resequencing array for genes involved in Parkinson's disease, Parkinsonism and related disorders, vol. 18, no. 4, pp. 386-390, doi: 10.1016/j.parkreldis.2011.12.012.

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Title A DNA resequencing array for genes involved in Parkinson's disease
Author(s) 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.
Journal name Parkinsonism and related disorders
Volume number 18
Issue number 4
Start page 386
End page 390
Total pages 5
Publisher Elsevier
Place of publication London, Eng.
Publication date 2012-05
ISSN 1353-8020
1873-5126
Keyword(s) parkinsons disease
Affymetrix resequencing array
DNA resequencing
Adult
Aged
Female
Gene Expression Profiling
Genetic Predisposition to Disease
Genotype
Humans
Leucine-Rich Repeat Serine-Threonine Protein Kinase-2
Male
Middle Aged
Oligonucleotide Array Sequence Analysis
Phenotype
Polymorphism, Single Nucleotide
Protein Kinases
Protein-Serine-Threonine Kinases
Reproducibility of Results
Ubiquitin-Protein Ligases
alpha-Synuclein
Science & Technology
Life Sciences & Biomedicine
Clinical Neurology
Neurosciences & Neurology
WHOLE-GENOME ASSOCIATION
MUTATIONS
SUSCEPTIBILITY
VARIANTS
RISK
Summary 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.
Language eng
DOI 10.1016/j.parkreldis.2011.12.012
Field of Research 110399 Clinical Sciences not elsewhere classified
1103 Clinical Sciences
1702 Cognitive Science
Socio Economic Objective 970111 Expanding Knowledge in the Medical and Health Sciences
HERDC Research category C1.1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2011, Crown Copyright
Persistent URL http://hdl.handle.net/10536/DRO/DU:30087909

Document type: Journal Article
Collections: Faculty of Health
School of Medicine
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