Services: Targeted Resequencing of Genomic DNA
Targeted resequencing of genomic DNA offers a focused, cost-effective approach to identifying and genotyping polymorphisms in candidate genes. Informatics pipelines
such as ours automated the processes of target identification, primer design, SNP discovery, and genotype extraction.
High-Throughput Resequencing Protocol
In the past, we provided complete DNA sequencing services to researchers at Washington University and elsewhere. The sequencing was done using our "ten to one" resequencing
protocol (Vieux et al, 2002) and
an ABI 3700 sequencer. Unfortunately, there was a problem with the 3700 machine in which the laser went bad (a.k.a. "caught on fire") and ABI wanted $15,000 to
repair it. We decided not to spend that kind of money on an outdated machine.
Instead, we now collaborate with the
Protein and Nucleic Acid Chemistry Laboratory
(PNACL) for resequencing projects. We provide high-throughput informatics assistance with target selection and primer design
(see informatics services). Your wet lab orders the primers and does the PCR
according to our protocol for resequencing genomic DNA. Then, the PNACL adds big-dye and runs the sequencing reaction.
SNP Discovery and Analysis Pipeline
One reason to collaborate with us on your resequencing project is our pipeline for analysis that combines SSAHA-SNP, Polyphred, and other tools
for polymorphism detection. We can download and manage the sequence traces directly from PNACL's secure server and provide you with a list of
the identified polymorphisms
cross-referenced with public databases such as dbSNP and the International HapMap Project.
For more information, please contact us.
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