Whole-genome mate-pair sequencing of apparently balanced chromosome rearrangements reveals complex structural variations: two case studies

Abstract BACKGROUND: Apparently balanced chromosome rearrangements (ABCRs) in non-affected individuals are well-known to have high reproductive risks such as infertility, abnormal offspring, and pregnancy loss. However, caution should be exercised in genetic counseling and reproductive intervention because cryptic unbalanced defects and genome structural variations beyond the resolution of routine cytogenetics may get omitted.CASE PRESENTATION: Two cases of ABCRs were recruited in this study. In family 1, the couple suffered two terminated pregnancies and underwent labor induction. Single nucleotide polymorphism (SNP) array analysis of the aborted sample from the second pregnancy showed a 10.8 Mb heterozygous deletion at 10q26.13q26.3 and a 5.5 Mb duplication at 19q13.41-q13.43. The non-affected father was diagnosed as a carrier of three-way complex chromosomal rearrangement [t(6;10;19)(p22;q26;q13)] by karyotyping. Whole-genome mate-pair sequencing revealed a cryptic breakpoint on derivative (der) chromosome 19 indicating that the karyotype was a more complex structural rearrangement including four breakpoints. Three genes, FAM24B, CACNG8, and KIAA0556, were disrupted without causing any abnormal phenotype in the carrier. In family 2, the couple suffered from a spontaneous miscarriage. They had an affected child with multiple congenital malformations and an unbalanced karyotype, 46,XY,der(11)t(6;11)(q13;p11.2). The female partner was considered a balanced translocation carrier with the karyotype 46,XX,t(6;11)(q13;p11.2)dn. Further SNP array and fluorescent in situ hybridization (FISH) indicated a cryptic insertion between chromosome 6 and chromosome 11. Finally, whole-genome mate-pair sequencing revealed an extremely complex genomic structural variation, including a cryptic deletion and 12 breakpoints on derivative chromosome 11[der(11)], and 1 breakpoint on derivative chromosome 6 [der(6)].CONCLUSIONS: Our study investigated two rare cases of ABCRs and demonstrated that whole-genome mate-pair sequencing is a powerful approach to analyze the genome complex structural variation. In case of ABCRs detected by conventional cytogenetic techniques, whole genome sequencing (WGS) based approaches should be considered for accurate diagnosis, effective genetic counseling, and correct reproductive intervention to avoid recurrence risks.