The FHIR & Genomics Newsletter

Happy National DNA Day!

Yes, there really is a National DNA Day 🙂 On this day we commemorate the successful completion of the Human Genome Project in 2003 as well as the discovery of the double helix in 1953. It’s a day to learn, celebrate, and spread the ATCG love around.

Advancements in Genomic Medicine

It’s nearly impossible to keep track of the tremendous number of significant advances in genomic medicine this past year. In the spirit of National DNA Day, we’d like to acknowledge five advances that have been of particular interest (in no specific order):

  1. January 2019 FHIR Genomics guide: If you are interested in Genomics-EHR integration, this guide is a must-read. Once ballot comments have been resolved and applied (by summer 2019), we will have a remarkably useful resource for semantic interoperability of genomic findings and interpretations, that supports pharmacogenomics (PGx), variant reanalysis, patient-facing apps, and a host of additional scenarios.
  2. NCBI Variation Services: This is the best resource we have seen, for determining whether two genetic variants are the same. Variant catalogs such as ClinVar and dbSNP rely on these services to harmonize variant submissions from different contributors. Services enable interconversions between VCF, HGVS, and SPDI formats. Given the vast amount of data flowing around in each of these formats, it’s hard to imagine a clinical genomics scenario where you DON’T benefit from the use of these services.
  3. Database of structural variants: Ryan Collins and colleagues have developed the largest collection of structural variants, making them publicly available through the gnomAD browser. The data make a significant contribution to understanding the profound consequences that structural variants have on human disease and the high frequency at which they occur.
  4. Enhanced copy number variant (CNV) detection: Rebecca Truty and colleagues report on evolving technology that can dramatically enhance our ability to detect CNVs from next-generation sequencing testing. This is substantial given the high frequency of structural variants (including CNVs) we now know to be causative in human disease. As the 6 Million Dollar Man would say, when it comes to detecting pathogenic CNVs, ‘we have the technology’.
  5. Variant Interpretation for Cancer Consortium (VICC) Meta-Knowledgebase: Andrew Tanenbaum is quoted as saying ‘The nice thing about standards is that you have so many to choose from’. We can say the same thing about genomic knowledge bases… Many robust somatic variant resources have emerged. These resources provide variant catalogues, interpretations, treatment recommendations, and more, but often have differences in internal knowledge representation that affect data sharing. VICC’s key objective is to enable data sharing amongst these resources, and in so doing, enable common public access methods. We strongly encourage any group with an interest in interpreting the clinical significance of cancer variants to take a close look at VICC.

Our Contribution to Genomics-EHR Integration

We have been busy staying abreast of this amazing field, developing clinical genomics applications, and doing our part to advance genomics-EHR integration capabilities. Some of our own contributions include:

  1. Introduction to Human Genomics for Clinical Informaticists: We found that our team benefited from some baseline genetics education, but we couldn’t find just the right program, that had the right blend of genomics biology, bioinformatics, and clinical informatics, so we created our own.
  2. Cloud-based genomics clinical decision support (CDS): Our prototype applications cover PGx and variant reanalysis scenarios. We will soon be embarking on live clinical trials. We are always on the lookout for new partners!
  3. VCF-to-FHIR converter: The converter takes variants identified via next-generation sequencing and stored in a VCF file and translates them into FHIR Genomics format, so as to be more easily consumable by an EHR or CDS engine. VCF-2-FHIR conversion is a component of a broader project, a FHIR-enabled genomic data server, that we are collaborating in. This latter project is being explored as a novel solution for making a person’s full genomic data accessible for precision health care.
  4. Structural variants in PGx CDS: Our preliminary (unpublished) findings, coupled with important advances called out above, suggest that technical innovations in structural variant identification coupled with enhanced analytic variant calling pipelines will soon allow us to reliably factor structural variants into our PGx CDS.

Now, can we be a little reflective, here on National DNA Day? What is it that draws us to this field? As trained clinicians, we are motivated to do something useful, to open the flood-gates and enable the onslaught of ‘omic’ data to be leverageable by EHRs and CDS. As biologists and scientists and informaticists, we find that no field provides the same challenging complexity at the intersection of biology, technology, and computer science. But perhaps more than anything, as just humans, we are drawn to the field out of sheer wonder.

And, in the spirit of advancing the world’s understanding of DNA, we will continue our quest to clarify that DNA is a right-handed spiral, and NOT the left-handed spiral so often portrayed in pictures ;-). Or, as so eloquently stated many years ago by Dr. Christopher Welch after seeing yet another misrepresented drawing of a DNA molecule:

 

On your cover a very rare sight,

a helix that gave me a fright.

Did you forget that this spiral

called DNA is chiral,

and it normally twists to the right?

 

May you have a happy and healthy DNA Day!

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