Frontiers of clinical genomics

I got my genome sequenced a few years back. It cost me $199 for the sequencing (30-50 fold coverage) and an initial report. I paid an additional $100 for my variant call file, which is now annotated so I can look for any newly discovered risk alleles.

Of course, most single-gene genetic disorders already evidence themselves clinically by the seventh decade. Indeed, most become symptomatic within the first two decades. I was mainly interested in risk alleles for dementia (e.g., ApoE4), thrombotic disorders or cancer, since my parents had one or another of these conditions.

A major promise for the clinical application of genomics was the “thousand dollar genome.” We’re pretty much there, now, and yet genomic sequencing for neonates isn’t routine. Why not?

“About one in five extremely ill infants lacking a clear diagnosis benefited from whole genome sequencing, researchers found in a randomized trial.

Clinical management shifted for 34 of 161 evaluable patients whose full genomic sequences were obtained (20.1%), compared with 17 of 165 (10.3%) in an unsequenced control group 60 days after enrollment, according to Ryan Taft, PhD, of the sequencing company Illumina, and colleagues.

In addition, twice as many infants undergoing sequencing received a molecular diagnosis compared with controls (31% vs 15%), the researchers reported in JAMA Pediatrics.”

*snip*

“The NICU-Seq investigators didn't give cost figures for their sequencing. But if the $1,000 figure is a reasonable approximation, $488,000 was spent to change treatment plans for 34 infants -- including the sequencing performed in family members -- or about $14,400 per patient. That's almost pocket change for infants whose average stay in intensive care is 1 month. Yet in the last line of their paper, Taft and colleagues suggested that would still be much too expensive as an everyday tool.

"The cost of [whole genome sequencing] may be a barrier to implementation in some environments, but this may be ameliorated by 2030 if recent projections of a $20 [sequence] are correct," they wrote.””

*snip*

“In addition to the primary outcome assessment at day 60, Taft and colleagues were able to follow almost all the sample out to day 90, by which point the control group had also undergone sequencing. At that point, another four infants in the original intervention group had a change in management; in the control group, meanwhile, another 28 infants had a new care plan -- presumably based on the sequencing results for most of them.” https://www.medpagetoday.com/genetics/genetictesting/94721?xid=nl_mpt_DHE_2021-09-28&eun=g1700464d0r&utm_source=Sailthru&utm_medium=email&utm_campaign=Daily%20Headlines%20Top%20Cat%20HeC%20%202021-09-28&utm_term=NL_Daily_DHE_dual-gmail-definition