High Throughput SNP Genotyping
We have built a system that delivers high throughput SNP genotype data using FP-TDI technology. Our customized Laboratory Information Management System (LIMS)
coupled with the flexibility of FP-TDI means quick turnaround for large quantities of data. More importantly, we have extensive SNP genotyping and analysis experience from
collaborations such as the International HapMap Project. Our information system links directly with dbSNP and other resources, providing our customers with an
esoteric collection of information about SNPs, genes, and larger genomic regions.
What makes it high throughput?
Typically, customers provide us with DNA samples and a genomic region of interest; within one week we are able to select SNPs and order primers to begin genotyping. Using both
human and computer-based quality control, we can generate over 50,000 genotypes per week. A password-protected web interface lets our customers
track the progress of their projects, request new loci for analysis, and export genotype data. Upon request we can deliver customized reports such as case-versus-control
comparisons and minor allele frequency calculations.
Ensuring the quality of SNP genotype data
We take many steps to ensure the quality of our high throughput data. DNA samples are quantitated and assayed against a standard marker set before genotyping begins.
Our information system (recently featured in the BioInform newsletter) checks for mendelian consistencies, hardy-weinberg failures, and technician mistakes. Data
from an assay is not released until both technician and QC teams assess its quality and assign a passing score. Should an assay fail initial quality control assessment, we
can often use de-quenching, mop-up reactions, and other techniques to rescue the data.
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