Increased diagnostic yield from negative whole genome-slice panels using automated reanalysis

Abstract

We evaluated the diagnostic yield using genome-slice panel reanalysis in the clinical setting using an automated phenotype/gene ranking system. We analyzed whole genome sequencing (WGS) data produced from clinically ordered panels built as bioinformatic slices for 16 clinically diverse, undiagnosed cases referred to the Pediatric Mendelian Genomics Research Center, an NHGRI-funded GREGoR Consortium site. Genome-wide reanalysis was performed using Moon™, a machine-learning-based tool for variant prioritization. In five out of 16 cases, we discovered a potentially clinically significant variant. In four of these cases, the variant was found in a gene not included in the original panel due to phenotypic expansion of a disorder or incomplete initial phenotyping of the patient. In the fifth case, the gene containing the variant was included in the original panel, but being a complex structural rearrangement with intronic breakpoints outside the clinically analyzed regions, it was not initially identified. Automated genome-wide reanalysis of clinical WGS data generated during targeted panels testing yielded a 25% increase in diagnostic findings and a possibly clinically relevant finding in one additional case, underscoring the added value of analyses versus those routinely performed in the clinical setting.

Keywords: panel testing; whole genome sequencing.

Figure 1.

A) Magnetic Resonance Spectroscopy over the basal ganglia in case 3 demonstrates markedly decreased creatine peak at 3 ppm (arrow) compared to the expected height labeled with an asterisk(*) pathognomonic for a cerebral creatine deficiency. B) Outlier expression analysis show significant decreased expression of SLC6A8 in case 3 compared to control panel. C) Sashimi plot demonstrating skipping of exon 9 and 10-fold decreased expression of SLC6A8 compared to counts from panel of 11 male controls.

Figure 2.

In case 4, a complex rearrangement of OCA2, with multiple deep intronic breakpoints, was found in trans with a clinically reported pathogenic missense variant diagnostic for oculocutaneous albinism. 348 kb region of chr15 (hg19:chr15:27,998,021–28,346,461) is visualized in IGV, with schematic arrows showing the pattern of the rearrangement and dashed lines connecting split reads. Diagram below shows inversion of the segment containing exons 3–19 followed by subsequent insertion within the first intron.