By Diagnostics World Staff
December 9, 2015 | In a paper published last week in Genetics in Medicine, GeneDx reported the results of whole exome sequence analysis for 3,040 cases the company sequenced over three years. Based on their experiences, the researchers recommend that whole exome sequencing increasingly be considered as a first-line diagnostic test.
GeneDx is a commercial laboratory specializing in genetic diagnostic tests. The company offers a large menu of tests, but in this study (doi:10.1038/gim.2015.148) looked back at whole exome sequencing (WES) tests performed between January 2012 and October 2014. The study did not compare WES methods to other tests, but reported historic diagnostic rates.
The study revealed the power of trios to reveal diagnoses, said Marc Grodman, CEO of BioReference Laboratories, the parent company of GeneDx.
Including tested family members, the 3,040 cases represented more over 10,000 samples, Grodman said. Primary clinical diagnoses and phenotype were provided by referring physicians, and DNA was isolated from whole blood samples and sequenced on either the Illumina HiSeq 2000 or HiSeq 2500 system. Sequence was aligned with BWA and variants were called with SAMtools. All WES data were analyzed using the GeneDx XomeAnalyzer tool. The pipeline generated an average of 11 GB of data per sample.
Variants were interpreted using guidelines similar to those published by the American College of Medical Genetics and Genomics, the authors wrote. The Xome Analyzer tool limited variants to those within regions of interest and filtered out common SNPs arriving at about 5,000 variants for each case. The median number of variants requiring human evaluation ranged from 5 to 70 per sample.
3,040 cases were tested over that time period for patients with 23 primary phenotypes. Researchers found that overall 28.8% of cases received a definitive diagnosis. A possible or probable result was provided in 51.8% of cases, a candidate gene was suggested in 7.6% of cases and for 11.8% of cases a negative result was returned.
As expected, rate of diagnosis increased when multiple family members were tested. Of the 3,040 total cases, 532 submitted only proband samples, and 2,308 submitted at least two additional family members. For cases with samples only from the proband, the diagnostic yield was 23.6%; for cases in which at least three related samples were tested, 31% received diagnoses.
Rate of diagnosis also varied by indication. Though sample size was small, whole exome sequencing most successfully suggested diagnoses for patients with problems with hearing (55%, N=11), vision (47%, N=60), the skeletal muscle system (40%, N=43), the skeletal system (39%, N=54), multiple congenital anomalies (36%, N=729), the skin (32%, N=31), and the central nervous system (31%, N=1,082).
Of the 3,040 cases, twenty-five revealed two genetic diagnoses and for three cases, three diagnoses were revealed.
The authors also emphasized that candidate genes discovered in whole exome sequencing should be shared in databases such as GeneMatcher so that clinicians, researchers, and labs have access to the latest research.
With such positive results from whole exome sequencing, Grodman believes it’s clear that the diagnostics industry will move in that direction. “Whole exome [sequencing] can go in and be an answer to a lot of different questions. I think in the future more testing will migrate there. I truly believe that it’s a process that will go on, but it’s not going to happen all at once.”