Cytogenomic Characterization of a Novel de novo Balanced Reciprocal Translocation t(1;12) by Genome Sequencing Leading to Fusion Gene Formation of <b><i>EYA3/EFCAB4b</i></b>

Abstract

<b><i>Introduction:</i></b> The accurate detection of breakpoint regions of disease-associated chromosomal rearrangements helps understand the molecular mechanisms and identify the risks involved with disrupted genes. <b><i>Methods:</i></b> In this study, a girl with growth retardation is characterized using positional cloning and genome sequencing. The techniques include fluorescence in situ hybridization (FISH) with paint (WCP) and bacterial-artificial chromosomes (BAC) probes, PCR, real-time PCR, and short and long-read sequencing. <b><i>Results:</i></b> The translocation was identified by GTG banding and confirmed by WCP FISH. Microarray ruled out the involvement of other copy number variations except for 6 homozygous regions which are not disease-causing variants. Fine mapping with FISH showed split signals with BAC clone RP11-312A3. Genome sequencing of short-read with an average 30× depth and long-read sequencing technology with a 3.8× coverage identified both breakpoints, confirmed by Sanger sequencing, that showed microhomology. The breakpoint at 1p and 12p regions disrupted <i>EYA3</i> and <i>EFCAB4B</i> genes. Expression analysis of <i>EYA3</i> showed a 7-fold increase, suggesting the formation of a fusion gene with <i>EFCAB4B</i>. <i>EYA3</i> is involved in skeleton development, and <i>EFCAB4B</i> plays a role in calcium metabolism, which may be relevant for the patient’s phenotype. <b><i>Conclusion:</i></b> The systematic application of genome techniques to translocations and their advantages is discussed.