Pooled Sequencing
After candidate genomic regions have been identified by GWAS or any other approaches, the next step is often to look for the actual genetic variation within those regions. To that end, we proudly offer a new service for ‘Pooled Sequencing’. With this technology we are able to pool 20-400 individual DNA samples and 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 cost and research time 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, would require less than 2ug genomic DNA per sample, and would take only 6 - 8 weeks to complete from date of DNA receipt at deCODE’s 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
Should representative pools of cases and controls be provided by our clients deCODE 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
Deep Sequencing
Addresses our clients need for detailed sequence information and genetic variation across large tracts of DNA from one or several individuals. These DNA samples might be representative ‘cases’ taken from a pooled sequencing experiment (above). deCODE’s indexed sequencing approach allows significant cost economies and increased speed whilst maintaining the very best in fidelity.
A typical deep sequencing experiment consisting of 12 individuals across 1 megabase of sequence at 25 fold redundancy of read would cost less than $25,000 and would take typically 8 weeks to perform after sample receipt.
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.
