genetic-technology

Advances in Genomics – Embracing Newer Technologies and More Data

The Future is Here. Or something like that.

Genomics is exciting right now. The sci-fi movies I watched growing up have somehow become not just feasible, but reality. We’ve successfully determined most of the 6 billion bases that makes a human. Our brilliant scientists and researchers are starting to piece together the massive amounts of data that might describe how our genes interact. Genetics is digital.

One of the major forces behind recent advances has been hard technology. Illumina, Ion Torrent, Affymetrix, Pacific Biosciences, Complete Genomics, and Oxford Nanopore are companies developing new and exciting sequencing technologies, vastly expanding our ability to sequence a whole genome, in a cost-effective and time-effective manner.

Clinical Diagnostics: making genomics accessibly to the everyday person

Right now at Recombine, we work on the clinical spectrum of genomics. Not rare or complex diseases. Every day diagnostics. Despite the hype, the research, and the advances in technology, the every day person has not been greatly affected by this revolution in a very meaningful way. My aunt hasn’t benefitted from 2×300 read lengths. My next door neighbor doesn’t really see a difference in her life because we are ‘bending the laws of physics’. These advances will pay off in a research setting, and will lead to great discoveries. But they’ve yet to have a significant marginal impact on healthcare. Yet.

CarrierMap is our test developed a test on Illumina’s Infinium Assay. This test screens for over 300 single gene diseases that a child might inherit from parents. The test is robust, accurate, comprehensive, and cost-effective. Genetic counselors, Ob/Gyn’s, and fertility specialists all gave input into the development of the assay. It was geared towards the clinic: genetic testing for every day individuals. We focused on assay quality and platform stability. This makes most sense. We also wanted it to be affordable. It is.

When and how we update our technology

sample-carriermap-reportThis year, we launched a version of our CarrierMap running on illumina’s Next Generation Sequencing (NGS) platform. This
tecnology has been around for just a few years now, and we’ve reached the point where it is now ready for the clinic. One of the challenges with NGS is that you get data about mutations with unknown significance – Variants of Unknown Significance (VUS). In developing our technology and our protocol for the NGS version of our CarrierMap test, we had to consider that our network of physicians deal with many patients everyday in primary care, Ob/Gyn, and infertility settings. Dealing with ‘extra’ information from sequencing would possibly be more disruptive in providing care than the benefit it providers.

To deal with all of this information, at Recombine we have developed a protocol for classifying and curating all variants. Moreover, all annotation data is provided to a team of Board Certified Genetic Counselors who speak with each patient to help provide the information on what the mutation means and how it may or may not affect their child. Information management and communication is essential in delivering genetic test results.

Still just the tip of the iceberg

Right now, when we use our NGS technology at Recombine we sequence roughly 60 Million bases for each individual. Inevitably, every person carries hundreds to thousands of mutations. We’re able to predict the outcome for most of the mutations, but ultimately, the art & science of curating variants is one we have thought about a lot and will be the subject of a future post. And remember: that’s 60 million out of > 3 billion bases. There is still much more to discover.

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