Three Small Steps Toward Genomically Sensible Healthcare

Nathan Pearson, Principal Genome Scientist

Nathan Pearson, Principal Genome Scientist

Nathan Pearson, Principal Genome Scientist here at Ingenuity, spoke at the Clinical Genome Conference and recently posted the first of three follow-on articles about his presentation, “Three Small Steps Toward Genomically Sensible Healthcare.”

In a sea of talks about the big “conference bingo-card” challenges to making genomes useful in healthcare, he focused on clear steps the community can take to correct ways in which “current convention, rooted in sparse data, will fail for millions of whole human genomes.” In this series of articles, he will detail these “three small but concrete ways to help put genome-informed healthcare on firmer footing”:

  1. Use different reference genomes to align a person’s raw data (pick reference(s) most like her/him), and then write the finished genome against the human ancestral reference.
  2. Clinically classify genotypes, not variants.
  3. Filter a genome against other individuated genomes, not allele frequency tables.

These are “early course tweaks that can save bigger tacks later,” Nathan says.

The first article takes a deep dive into reference genomes, starting with a thought-provoking perspective that “the current single reference is arbitrary and ethnocentric; inevitably misaligns most people’s raw data; and is poor for writing and interpreting genomes afterward, because it includes rare and risky variants, and muddles summary insights on data quality and evolution.”

What do you think?

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