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

Background Short-read genome sequencing generates the signal necessary to detect balanced reciprocal translocations at single-nucleotide resolution, but standard structural variant callers represent them as breakend pairs. Structural variant callers produce thousands of breakend records per genome, the majority of which are false positives arising from segmental duplications, repetitive elements, and reference assembly artifacts. This specificity problem has prevented balanced translocation detection from entering routine genome sequencing workflows. We developed a highly specific pipeline to

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