Whole genome sequencing not yet practical for the clinical setting

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1. Between 10% to 19% of genes associated with inherited disease were not covered at a minimum standard for genetic variant discovery. 

2. Follow up referrals and diagnostic tests cost $351-$776 per person. 

Evidence Rating Level: 2 (Good)           

Study Rundown: Over the past decade, whole genome sequencing (WGS) technology has been advancing at an accelerated pace. As opposed to whole exome sequencing (WES), WGS allows us to analyze parts of the genome both inside and outside the exome, the part of the genome which encodes proteins. Just as the advent of proper hygiene ushered in a new era of medicine, WGS is set to transform clinical practices for the better. With decreasing costs and improved accuracy, WGS will one day be able to provide clinicians with ability to cater treatment plans to individual patients at a molecular level.

This study demonstrates that this day may not be as close as researchers have hoped for. Major findings of this study include a moderate amount of inheritable diseases not being discovered during sequencing with insertion/deletion mutations being most difficult to discover. A major weakness of the study is the small sample size of twelve adults, hence limiting its reproducibility. However, the results do highlight the importance of questioning our increasing reliance on WGS to aid clinical decision making. Future research will be needed in order to reliably confirm the results. Further, we must continue to educate clinicians on both the capabilities and deficits of WGS being used in the clinical setting.

Click to read the study in JAMA

Click to read an accompanying editorial in JAMA

Relevant Reading: Clinical assessment incorporating a personal genome

In-Depth [observational cohort]: This study recruited 12 adults between November 2011 and March 2012 who had their genome sequenced, interpreted, and acted on by physicians. A median of 10% to 19% of genes associated with inherited disease were not covered at a minimum threshold for genetic variant discovery. Genotype concordance was high for single nucleotide variants in protein coding regions of the genome, and among candidate variants for inherited disease risk (99%-100%). However, concordance for small insertion and deletion variants was moderate (53%-59%). This was even lower among genetic variants that were candidates for inherited disease risk (10%- 75%). A median of 1-3 follow up referrals and tests were prompted following physician review of the genomics reports, costing a median of $351-$776 per person.

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