The latest advancement in Blueprint Genetics’ production environment involves customized sequencing solutions for difficult-to-sequence genes, designed to maximize detection of clinically relevant variants. Currently, the most extensive developments are in genes SMN1/SMN2, PKD1 and RPGR (ORF15), associated with spinal muscular atrophy, autosomal dominant polycystic kidney disease and X-linked retinitis pigmentosa, respectively.
“Leaps in DNA technology and in the ability to interpret genomic sequences has prompted the buildup of tailored treatments and precision medicine for individual patients based on their genetic makeup. The power of targeted treatments and gene therapies is in their specificity. That is why an in-depth knowledge of the architecture of individual genes is so extremely important”, says the founder of Blueprint Genetics, Chief Operating Officer Samuel Myllykangas (PhD).
The need for a customized confirmation strategy arises when a low-quality variant is detected in a difficult-to-sequence gene or segmentally duplicated region, when unusual SNP clusters are observed or when other quality control steps, such as coverage analysis, detects an event deviating from normal.
Developing new methods to analyze clinically important but technically challenging genes involves both innovations in bioinformatic data analysis as well as laboratory protocols tailored to a particular genetic region. For each of the SMN1/SMN2, PKD1 and RPGR (ORF15) genes, we have developed a custom method to increase our clinical sensitivity, where most other NGS-derived solutions have had limited sensitivity to detect clinically relevant variants in these genes/regions.
In PKD1, associated with autosomal dominant polycystic kidney disease, variants are confirmed with Sanger sequencing that uses primers manually designed to maximize their PKD1 specificity over several highly homologous pseudogenes. In RPGR, associated with X-linked retinitis pigmentosa, variants detected in the ORF15 region, consisting of technically challenging GA-rich repetitive sequence, are confirmed with custom Sanger sequencing.
“When standard Sanger sequencing cannot be applied in confirmation of a variant, our team sets up custom laboratory methods that are usually based on either long-range PCR-based sequencing or quantitative PCR. These methods involve specialized primer and probe designs as well as protocols optimized for the specific region of interest”, Myllykangas concludes.
Examples of customized methods include analyses which confirm variants in autosomal dominant polycystic kidney disease associated PKD1 gene, which harbors six highly homologous genetic regions, as well as Alu element insertions that are generally challenging to detect using standard protocols.
The improvements in clinical sensitivity were enabled by a technological transition earlier this year, when a whole exome sequencing (WES) based platform was introduced. Since then, all panels are sliced from high-quality WES data and include a higher number of relevant genes and ~1,500 disease-causing deep intronic variants.
As part of our commitment to transparency in genetic testing, Blueprint Genetics has authored a detailed document to share with the rare disease community, including information about our Clinical R&D pathways, anonymized patient cases, and what are the next areas of interest in our R&D pipeline.
Chief Operating Officer, founder Samuel Myllykangas, firstname.lastname@example.org
Communication Manager Juulia Simonen, tel. +35850 305 9018, email@example.com
Head of Clinical R&D Johanna Sistonen, firstname.lastname@example.org