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Next generation sequencing of CLU, PICALM and CR1: pitfalls and potential solutions

Lord, Jenny; Turton, James; Medway, Christopher; Shi, Hui; Brown, Kristelle; Lowe, James; Mann, David; Pickering-Brown, Stuart; Kalsheker, Noor; Passmore, Peter; Morgan, Kevin

Authors

Jenny Lord

James Turton

Christopher Medway

Hui Shi

James Lowe

David Mann

Stuart Pickering-Brown

Noor Kalsheker

Peter Passmore

KEVIN MORGAN kevin.morgan@nottingham.ac.uk
Professor of Human Genomics and Molecular Genetics



Abstract

CLU, PICALM and CR1 were identified as genetic risk factors for late onset Alzheimer’s disease (AD) in two large genome wide association studies (GWAS) published in 2009, but the variants that convey this alteration in disease risk, and how the genes relate to AD pathology is yet to be discovered. A next generation sequencing (NGS) project was conducted targeting CLU, CR1 and PICALM, in 96 AD samples (8 pools of 12), in an attempt to discover rare variants within these AD associated genes. Inclusion of repetitive regions in the design of the SureSelect capture lead to significant issues in alignment of the data, leading to poor specificity and a lower than expected depth of coverage. A strong positive correlation (0.964, p

Citation

Lord, J., Turton, J., Medway, C., Shi, H., Brown, K., Lowe, J., …Morgan, K. (2012). Next generation sequencing of CLU, PICALM and CR1: pitfalls and potential solutions. International Journal of Molecular Epidemiology and Genetics, IJMEG, 3(4),

Journal Article Type Article
Publication Date Nov 15, 2012
Deposit Date Apr 25, 2014
Publicly Available Date Apr 25, 2014
Journal International Journal of Molecular Epidemiology and Genetics
Electronic ISSN 1948-1756
Publisher e-Century Publishing
Peer Reviewed Peer Reviewed
Volume 3
Issue 4
Public URL http://eprints.nottingham.ac.uk/id/eprint/2696
Publisher URL http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3508540/
Copyright Statement Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by-nc/4.0

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Copyright Statement
Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by-nc/4.0



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