Pooled DNA Sequencing
After candidate genomic regions have been identified by GWAS or other approaches, the next step is to drill down to search for additional signals and markers within those regions. To do this efficiently, we developed and offer our ‘Pooled Sequencing’ service.
With this technology we analyze together pooled batches of 20 to 400 individual DNA samples and can discover SNPs with a minor allele frequency as low as 1%. Novel SNPs can be discovered and confirmed, along with their frequency rates, as associating with a condition of interest by simply comparing the respective 'pool' sequences of affected individuals with controls. This approach offers real economy in terms of time and cost, while simultaneously providing detailed and accurate answers.
A typical pooled sequencing experiment, consisting of 400 individuals across a typical linkage disequilibrium block of 200Kb would cost less than $25,000; require less than 2ug genomic DNA per sample; and take only 6 - 8 weeks to complete from the arrival of samples at our laboratory.
Deliverables:
- FASTA files with quality metrics for each 36bp sequence
- Alignments (Ace files, usable by ‘Consed’, DNA sequence analysis software)
- Analyzed and filtered data
- List of putative SNPs over the 100 kb region with quality, SD, SNP frequency
If you provide us with representative pools of cases and controls, we will provide a comparison table of minor allele frequencies between these pools highlighting the significantly associating SNPs.
Example of SNP list
Comparison of cases vs controls MAFs
Getting a quote
The prices given above are indicators only as the final price is affected by the number of individuals included for study, the size and number of regions and the level of sequence read redundancy. It is important that interested clients contact deCODE directly to get an accurate cost of their prospective project.
For more information, please contact services@decode.com.
