Establishing DNA analysis methods for GBA mutations in Parkinson’s disease

Project brief

Introduction

Mutations in a gene called GBA cause Gaucher disease, a rare lysosomal storage disorder with autosomal recessive inheritance patterns [1]. Over the past decade, however, it has become abundantly clear that people who carry a single GBA mutation are at greatly elevated risk of Parkinson’s disease (PD) compared with non-carriers [2]. Large studies have shown that up to 7% of people with PD will carry GBA mutations, and that a single mutation in GBA increases risk of PD by ~7-fold [3, 4].

Prof Tim Anderson and colleagues at the NZ Brain Research Institute (NZBRI), Christchurch, have developed a longitudinal cohort of PD patients in which they are studying progression of disease and particularly cognitive decline, using a wide variety of assessments. It is important to identify which of the patients in this cohort carry GBA mutations, because of the impact of such variants on clinical features of the disease [3, 5, 6].

Aim

The aim of this project is to establish analytical procedures to detect mutations in GBA, a complex gene which requires very specific methods for successful genotyping. The specific goals are:

1. Carry out a literature review of existing methods for GBA analysis and the range of mutations now known
2. Establish long and accurate PCR amplification methods for the complete GBA gene
3. Apply this method to positive control DNA samples from Coriell Institute, which contain known GBA mutations
4. Carry out Sanger sequencing on the long PCR amplicons to confirm the presence of these known mutations
5. Should time permit, begin applying these methods to DNA samples from the NZ Parkinson’s Disease (NZPD) cohort

Method

Analysis of GBA is not straightforward. Two closely related pseudogenes of GBA exist, and care must be taken to amplify only the true GBA gene [1, 7]. In addition, many GBA mutations result from structural rearrangements, including gene conversions, gene fusions, and duplications [7], and these require more complex analyses.  The project will begin by carrying out initial PCR experiments to obtain an ~9kb amplicon encompassing the entire GBA gene [8], with analysis of amplicons by agarose gel electrophoresis. Once successful, this will be optimized, then applied to a range of DNA samples including several controls carrying different GBA mutations (purchased from Coriell Institute, USA). Targeted PCRs followed by Sanger DNA sequencing will then be carried out on these long amplicons to confirm the presence of mutations in the control samples. If time allows, the method would be applied to a subset of NZPD participants to begin screening for GBA mutations in these cases.

Student researcher’s component of the study:

The student will be trained to carry out all laboratory procedures, and will perform and document all aspects of this project. This will involve developing and optimizing the long PCR method, applying it to control DNA with different GBA mutations, and carrying out Sanger sequencing to confirm the mutations, then analyzing the data and documenting the results.

References

1. Hruska, K.S., et al., Gaucher disease: mutation and polymorphism spectrum in the glucocerebrosidase gene (GBA). Hum Mutat, 2008. 29(5): p. 567-83.
2. Halperin, A., D. Elstein, and A. Zimran, Increased incidence of Parkinson disease among relatives of patients with Gaucher disease. Blood Cells Mol Dis, 2006. 36(3): p. 426-8.
3. Lesage, S., et al., Large-scale screening of the Gaucher's disease-related glucocerebrosidase gene in Europeans with Parkinson's disease. Hum Mol Genet, 2011. 20(1): p. 202-10.
4. Lill, C.M., et al., Comprehensive research synopsis and systematic meta-analyses in Parkinson's disease genetics: The PDGene database. PLoS Genet, 2012. 8(3): p. e1002548.
5. Gan-Or, Z., et al., Genotype-phenotype correlations between GBA mutations and Parkinson disease risk and onset. Neurology, 2008. 70(24): p. 2277-83.
6. Nichols, W.C., et al., Mutations in GBA are associated with familial Parkinson disease susceptibility and age at onset. Neurology, 2009. 72(4): p. 310-6.
7. Tayebi, N., et al., Reciprocal and nonreciprocal recombination at the glucocerebrosidase gene region: implications for complexity in Gaucher disease. Am J Hum Genet, 2003. 72(3): p. 519-34.
8. Tayebi, N., S. Cushner, and E. Sidransky, Differentiation of the glucocerebrosidase gene from pseudogene by long-template PCR: implications for Gaucher disease. Am J Hum Genet, 1996. 59(3): p. 740-1.