Combining cytogenetic and genomic technologies for deciphering challenging complex chromosomal rearrangements

Area of Science:

• Genetics
• Genomics
• Molecular Biology

Background:

• Complex chromosomal rearrangements (CCRs) are structural variants involving multiple chromosome breaks.
• CCRs were once considered rare but are increasingly recognized as significant causes of genetic disorders.
• Understanding the mechanisms underlying CCRs is crucial for genetic diagnostics and counseling.

Purpose of the Study:

• To investigate the mechanism of a challenging CCR involving repetitive sequences.
• To precisely identify sequence-level changes and their order in complex structural variants.
• To develop and apply an integrated approach for deciphering CCRs and enabling family risk assessment.

Main Methods:

• Whole exome sequencing (WES) for initial detection of structural variants (SVs).
• Chromosomal microarray (CMA) and FISH analyses for SV interpretation.
• Nanopore long-read sequencing for nucleotide-level breakpoint junction analysis.

Main Results:

• A large deletion in the FOXF1 enhancer, identified by WES, caused alveolar capillary dysplasia and perinatal death.
• CMA revealed duplications in the mother, suggesting her CCR as the source of the proband's deletion.
• Nanopore sequencing elucidated the CCR mechanism as a result of meiotic double-strand breaks and intra-chromosomal homologous recombination.

Conclusions:

• An integrated approach combining cytogenetics and long-read sequencing can delineate breakpoints in challenging CCRs.
• The study proposed a specific mechanism for the arising of the observed CCR.
• This integrative strategy is recommended for future CCR deciphering and family risk assessment.