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SNP Resequencing

Figure: The top pane shows the hetero-indel sequence trace. An AAG indel causes the frameshift. The bottom 3 panes show the deconvoluted peak profiles of the conserved and mutant forms. The deconvoluted profiles can be clearly seen as overlapping peaks in the pane 1 unanalyzed hetero-indel profile. Picture was taken using Mutation Surveyor™ from SoftGenetics.

 

SNP Resequencing

Description of Services

  • Assay development and validation with many pre-validated genes already available.
  • PCR amplification and product purification
  • Bi-directional DNA sequencing on ABI 3730xl DNA sequencers
  • Mutation profiling & sequence variation reporting
  • Geospiza Finch® Suite sample tracking
  • Automated calling & manual curation of heterozygotes
  • Optional 2 assay-platform packages for strong validation of any SNPs
  • ASSAY TESTING AGAINST THE HAP-MAP SAMPLES
  • Experienced with tumor sample and working with parrafin-embedded tissues
  • dbSNP submission available

2-Platform, Mutation-Validation Assay Packages
For highly reliable confirmation of novel SNPs, it is recommended that a second assay-platform be used to validate the mutation. Following mutation discovery by sequencing, the most common secondary method is a SNP genotyping/allelic discrimination assay. SeqWright offers this 2-assay approach as an integrated package for high-confidence data suitable for any publication.

Assay Testing Against the HapMap Samples
If a new mutation has been discovered in a patient panel, a valuable next step approach is to screen the mutation against the HapMap samples, available from the Coriell Institute, for any positive haplotype associations that may contribute to a particular disease or drug response. The HapMap panels are commercially available. SeqWright will provide consultation about which HapMap panel is most appropriate for a particular study and will screen the set for the new mutation.

Tumor Samples & Heterogeneous Mixtures
SeqWright is experienced detecting low-frequency mutations in uneven mixtures, such as tumor samples and pooled DNA, as low as 10% using standard PCR and sequencing. Mixtures with mutations below 10% can be detected using a subcloning strategy.

Heterozygote insertion-deletions (indels) are detected by the frameshift in data and the loss of signal quality at the boundary. Again, the 10% threshold applies. The deconvoluted hetero-indel peak profiles are included in the final report.

  • DNA extraction from paraffin-embedded tissue
  • Detection of low-frequency mutations as low as 10% without subcloning
  • Detection and deconvolution of hetero-indel profiles
  • Whole Genome Amplification (WGA) for low sample quantities
  • CLIA certified for handling patient samples
  • 21 CFR 58 and 21 CFR 11 compliant

**Not for diagnostic purposes.

DNA Amplification (EBV Transformation and WGA)
Whether limited by very small sample amounts or needing to maintain a perpetual supply of DNA belonging to a specific genotype, SeqWright offers services for both increasing and preserving critical DNA samples for future studies. Methods have been validated for both STR and SNP genotyping.

Additional Resources