Whole exome sequencing (WES) uses hybridization capture to enrich genomic samples for coding regions before performing next generation sequencing experiments. This versatile technique enables investigators to identify not only known, common or expected variants, but also novel, rare, or otherwise unexpected variants. WES is thus a practical strategy for identifying candidate variants less expensively than with whole genome sequencing.
Here, Fomchenko et al. used the xGen Exome Research Panel and Illumina WES sequencing to identify both a rare missense mutation of Myosin heavy chain 9 (MYH9) and a novel association of that mutation with congenital hemangioma (CH).
Congenital hemangiomas are challenging because their genetic and phenotypic heterogeneity have obscured an understanding of disease pathogenesis. However, there is evidence of genetic origins, somatic and germline, for CH pathogenesis. CH is known to be associated with several hereditary syndromes, including hereditary hemorrhagic telangiectasia (HTT) and CLOVES syndrome; previous sequencing studies have also identified several somatic mutations in CHs. In this study, a neonatal patient required surgical removal of a congenital scalp hemangioma 1 day following birth. WES of the patient’s hemangioma and germline DNA, as well as parental germline DNA, was performed to identify CH-associated genomic variants.
The investigators extracted genomic DNA (gDNA) from tissue and germline samples from the patient and parents. The gDNA samples then underwent target enrichment with the xGen Exome Research Panel and were sequenced with Illumina whole exome sequencing. The resulting sequences were interrogated for known causal mutations associated with CH and other vascular anomalies, as well as for de novo mutations. Finally, the investigators confirmed candidate calls with PCR amplification and Sanger sequencing.
Fomchenko et al. identified a rare, missense de novo germline mutation in MYH9 resulting in an Arg to Cys transition (c.5308C>T, p.[Arg1770Cys]). The location of this missense mutation in the highly conserved tail domain, and the fact that an Arg to Cys substitution is likely damaging because it can cause increased disulfide bonding between related proteins strongly suggested that this was the causative mutation. In addition, WES did not detect the presence of any mutations that previously have been described as causal for CH or other vascular malformations.
These findings are of particular interest because MYH9 is a known regulator of multiple processes, including cytokinesis, VEGF-regulated angiogenesis, and p53-dependent tumorigenesis, but it had not previously been associated with CH. The results of this study therefore suggest that MYH9 is an additional candidate gene for future investigations into CH pathogenesis, and demonstrate the utility of the xGen Exome Research Panel as an ideal tool for WES studies, including identification of rare variants.