What's Next in Cytogenetics: Molecular Characterization of De Novo Apparently Balanced Chromosomal Rearrangements to Assess Pathogenicity by Whole Genome Mate Pair Sequencing

In circumstances where chromosome analysis reveals a karyotype with an apparently balanced rearrangement, we routinely reflex to parental studies to determine if the rearrangement is inherited or de novo to help assess pathogenicity. However, previous studies investigating the pathogenicity of de novo rearrangements suggest that these events are pathogenic only 6.7% of the time; hence, a de novo balanced rearrangement is still of uncertain clinical significance. Until recently, a method to determine pathogenicity of balanced rearrangements was not available. We report 14 patients with de novo balanced rearrangements referred to the Mayo Clinic Cytogenetics Laboratory for which we performed whole genome mate pair sequencing, a next-generation sequencing technique that allows for the characterization of structural rearrangements, to further assess pathogenicity. Samples were library-prepped using the Illumina Nextera Mate Pair Kit and sequenced on the Illumina HiSeq2000. BIMA and SVAtools, an in-house bioinformatics mapping algorithm and a post-processing visualization tool respectively, were used for analysis and characterization of the breakpoints. We found 3/14 (21.4%) samples had disruption of a known pathogenic gene, 6/14 (42.9%) had disruption of at least one gene of uncertain significance, and 5/14 (35.7%) had breakpoints in intergenic regions on both derivative chromosomes, providing evidence that de novo balanced rearrangements have a higher likelihood of being pathogenic than previously thought. Our results provide additional evidence to the contributory nature of apparently balanced rearrangements to abnormal phenotypes and highlight the clinical utility of mate pair sequencing to characterize cytogenetically balanced rearrangements.