Sanger Medical Resequencing Technology

Graphic by NCBI

Medical Resequencing requires that specific fragmets of genome are sequenced. The BCM-HGSC has developed a specialized bioinformatics pipeline to accomplish this goal.

The MedRS pipeline uses locus-specific primers tailed with standard sequencing primers enabling integration into the existing production sequencing infrastructure. A balance has been obtained between robust PCR and sequencing needs with respect to the amount of product that is optimal for sequencing reactions.

The laboratory and informatics pipeline comprises selection of equencing primer binding sites, testing of the primers against a series of standard human genomic DNA samples, QC testing of DNA samples, PCR amplification and tracking of amplicons throughout the process, bidirectional sequencing of amplicons, informatics-based mapping of the resulting sequence reads to the reference genome, and identification and annotation of any resulting nucleotide or structural variants.

The new MedRS LIMS system is now well integrated with the main BCM-HGSC production sequencing database and with the SNPdetector software. This LIMS tracks the thousands of primer sequences and DNA samples with the required precision and fidelity needed for MedRS projects. Extensive barcoding at all transfer steps ensures sample and data connectivity throughout the process. Strict quality assurance measures have been implemented including daily monitoring of PCR and sequence success via automated reports and manual review of select gels and traces.