Detection of cryptic balanced chromosomal rearrangements using high-resolution optical genome mapping

Abstract

BackgroundChromosomal rearrangements have profound consequences in diverse human genetic diseases. Currently, the detection of balanced chromosomal rearrangements (BCRs) mainly relies on routine cytogenetic G-banded karyotyping. However, cryptic BCRs are hard to detect by karyotyping, and the risk of miscarriage or delivering abnormal offspring with congenital malformations in carrier couples is significantly increased. In the present study, we aimed to investigate the potential of single-molecule optical genome mapping (OGM) in unravelling cryptic chromosomal rearrangements.MethodsEleven couples with normal karyotypes that had abortions/affected offspring with unbalanced rearrangements were enrolled. Ultra-high-molecular-weight DNA was isolated from peripheral blood cells and processed via OGM. The genome assembly was performed followed by variant calling and annotation. Meanwhile, multiple detection strategies, including FISH, long-range-PCR amplicon-based next-generation sequencing and Sanger sequencing were implemented to confirm the results obtained from OGM.ResultsHigh-resolution OGM successfully detected cryptic reciprocal translocation in all recruited couples, which was consistent with the results of FISH and sequencing. All high-confidence cryptic chromosomal translocations detected by OGM were confirmed by sequencing analysis of rearrangement breakpoints. Moreover, OGM revealed additional complex rearrangement events such as inverted aberrations, further refining potential genetic interpretation.ConclusionTo the best of our knowledge, this is the first study wherein OGM facilitate the rapid and robust detection of cryptic chromosomal reciprocal translocations in clinical practice. With the excellent performance, our findings suggest that OGM is well qualified as an accurate, comprehensive and first-line method for detecting cryptic BCRs in routine clinical testing.

Case report: Optical genome mapping revealed double rearrangements in a male undergoing preimplantation genetic testing

“…However, molecular genetic techniques, such as chromosomal microarray and CNV-Seq, can only detect unbalanced translocations, although their resolution is greatly improved (Giardino et al, 2006). FISH technology has difficulty detecting balanced translocations of the whole chromosome set due to the restriction of the number of probes and the necessity of knowing loci a priori (Zhang et al, 2022). In recent years, OGM has become a very promising method to detect large-scale structural variations in the human genome (Dremsek et al, 2021).…”

Identification of complex and cryptic chromosomal rearrangements by optical genome mapping

“…Unbalanced SVs refer to insertions, deletions, duplications, complex rearrangements and other events, while balanced SVs refer to copy-neutral variations with changes in the positioning or direction of the chromosome fragments but without gain or loss of chromosome fragments, such as balanced translocations and inversions [ 1 , 3 , 4 ]. Among the various SVs, complex chromosomal rearrangements (CCRs) and cryptic chromosomal rearrangements have received particular attention because they are difficult to identify with routine cytogenetic techniques [ 5 – 8 ].…”

Identification of a familial complex chromosomal rearrangement by optical genome mapping

“…With the development of cytogenetic and molecular techniques, more complex and cryptic chromosomal imbalances have been revealed [ 6 – 9 ]. Optical genome mapping (OGM) has been proven to show efficacy in detecting complex chromosomal structural aberrations [ 10 , 11 ]. Here, we present a familial CCR identified by OGM.…”