AMD: Whole Genome Sequencing
Background[edit]
Age related macular degeneration is the most common cause of blindness in the elderly. Very strong genetic susceptibility factors have been identified, particularly common variants in and around CFH, ARMS2 (a gene of poorly understood function on chromosome 10), C3, CFB and C2 and CFI.
Proposed Experiment[edit]
We are considered low pass whole genome sequencing (with 6-12 GB of data per individual, corresponding to 2-4x coverage). The coverage could be used to recapitulate whole genome association study results by studying randomly selected cases and controls or, alternatively, to identify causes of disease in individuals who don't carry the common risk alleles. The second experiment would sequence only cases or controls who are known to carry none (or very few) of the common risk alleles.
Status[edit]
Conversations ongoing with Anand Swaroop about potential for funding.
LifeTechnologies (also known as ABI) is very interested in collaborating on this project. They estimate that their platform could deliver 60GB of sequence per run, with 2 runs per instrument per month. With 300 individuals sequenced at 2x, the project could be completed in 7-8 months. The key contacts there are:
- Jay Therrien (VP Sales, formerly at Illumina)
- David Miller (local sales)
- Karen Bray
