Overcoming a diagnostic blindspot: Identifying balanced translocations in Mendelian rare disease cohorts

Short-read genome sequencing has the signal needed to detect balanced reciprocal translocations at single-nucleotide resolution, but standard structural variant callers report them as breakend pairs. These callers produce thousands of breakend records per genome, with most false positives arising from segmental duplications, repetitive elements, and reference assembly artifacts. That specificity problem has kept balanced translocation detection out of routine genome sequencing workflows, so the authors built a highly specific pipeline to resolve balanced reciprocal translocations and applied it across five clinically distinct cohorts to assess prevalence and diagnostic contribution.

They analyzed short-read genome sequencing data from 16,131 individuals in five cohorts: 3,202 healthy participants from the 1000 Genomes Project; 2,875 probands with structural birth defects and family members from the CHOP BDB cohort, including 1,017 probands; 3,574 probands from the GREGoR consortium; 6,071 probands with undiagnosed disease and family members from the Undiagnosed Diseases Network, including 2,027 probands; and 409 neonates who underwent rapid genome sequencing in the CHOP Baby Eagle cohort. The computational pipeline characterizes breakend events from standard structural variant callers and converts them into high-confidence balanced translocation calls by exploiting well-characterized properties of true balanced translocation signatures in short-read data. Breakpoints were resolved to single-nucleotide precision and interrogated for disruption of known disease genes or potential regulatory consequences, and a subset was confirmed with Sanger sequencing.

Balanced reciprocal translocations were identified in 0.196% of structural birth defect probands (2/1,017), 0.25% of GREGoR probands (9/3,574), 0.39% of UDN probands (8/2,027), and 0.24% of neonates who underwent rapid genome sequencing (1/409). Parental carrier frequency was 0.269% in the birth defects cohort (5/1,858), consistent with previous estimates in similarly ascertained families, and 0.098% in the UDN cohort (3/3,040). All six translocations found in the birth defects cohort were orthogonally validated by Sanger sequencing, confirming the pipeline's specificity.