Illumina CEO sees bioinformatics as key to completing sequencing puzzle

Illumina CEO Jay Flatley

The expansion of whole-genome sequencing into clinical care has intensified discussions about the limitations of the technology. Illumina ($ILMN) CEO Jay Flatley this week acknowledged that sequencing still has some weaknesses and identified what he sees as the solution--improved bioinformatics.

Flatley made the comments in an interview with tech publication Re/code, which asked the Illumina CEO for his take on a paper published in The New England Journal of Medicine this month. The NEJM paper looked at results generated by sequencers from Illumina and Complete Genomics--now part of BGI--and found several weaknesses. For the authors, these flaws--which include incomplete coverage of inherited genes and low reproducibility of detection of genetic variation--suggest sequencing must improve before it is clinical grade.

While noting that the study only gathered data from 12 people and used sequencing technology that is now at least two years old, Flatley acknowledged that the software component of the workflow can improve. "What's hard is to determine whether there's a base inserted or deleted. That's a bioinformatics problem, not a sequencing problem. That's a software issue that we and others and the whole world is trying to work on," Flatley said.

The technical limitations are likely a temporary drag on the entry of sequencing into medicine, but in some areas ethical concerns could create a more permanent barrier. Prenatal testing, for example, can detect Down syndrome from fetal DNA in the mother's blood, but may also reveal characteristics like height and hair color. Illumina won't disclose what traits are decipherable, but couldn't stop users of its machines from doing so. Flatley expects lawmakers will step in. "This isn't something we think we can arbitrate," he said.

- here's the Re/code interview
- and the NEJM abstract

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