Optical mapping of the 22q11.2DS region reveals complex repeat structures and preferred locations for non-allelic homologous recombination (NAHR)

Abstract

The most prevalent microdeletion in humans occurs at 22q11.2, a region rich in chromosome-specific low copy repeats (LCR22s). The structure of this region has defied elucidation due to its size, regional complexity, and haplotype diversity, and is not well represented in the human genome reference. Most individuals with 22q11.2 deletion syndrome (22q11.2DS) carry a de novo hemizygous deletion of ~ 3 Mbp occurring by non-allelic homologous recombination (NAHR) mediated by LCR22s. In this study, optical mapping has been used to elucidate LCR22 structure and variation in 88 individuals in thirty 22q11.2DS families to uncover potential risk factors for germline rearrangements leading to 22q11.2DS offspring. Families were optically mapped to characterize LCR22 structures, NAHR locations, and genomic signatures associated with the deletion. Bioinformatics analyses revealed clear delineations between LCR22 structures in normal and deletion-containing haplotypes. Despite no explicit whole-haplotype predisposing configurations being identified, all NAHR events contain a segmental duplication encompassing FAM230 gene members suggesting preferred recombination sequences. Analysis of deletion breakpoints indicates that preferred recombinations occur between FAM230 and specific segmental duplication orientations within LCR22A and LCR22D, ultimately leading to NAHR. This work represents the most comprehensive analysis of 22q11.2DS NAHR events demonstrating completely contiguous LCR22 structures surrounding and within deletion breakpoints. The 22q11.2 Deletion Syndrome (22q11.2DS) is a congenital malformation disorder and the most frequent microdeletion syndrome in humans 1. It has a prevalence of about one in every 3,000 live births 1,2 and one in every 1,000 pregnancies 3. Significant medical issues present in affected individuals may include: congenital cardiac defects (~ 75%), immune deficiencies, speech/language defects, intellectual disabilities, and a 25-30% risk for developing schizophrenia in adolescence or adulthood 2. The causative deletion usually occurs as a de novo event in meiosis in one of the parents. Ninety percent of affected individuals have a hemizygous ~ 3 million base pair (Mbp) deletion in chromosome 22q11.2 2,4. The mechanism responsible for the deletion is non-allelic homologous recombination (NAHR) between surrounding chromosome 22-specific low copy repeats (LCR22s) 5,6. There are eight LCR22s, labeled alphabetically as LCRA to LCRH from centromere to telomere on 22q 6. The LCR22s are comprised of sequence modules of varying lengths containing interspersed genes and pseudogenes.

Consequences of 22q11.2 Microdeletion on the Genome, Individual and Population Levels

“…Specific NAHR (non-allelic homologous recombination) locations and a genomic signature associated with the deletion were detected. After an analysis of the potential deletion breakpoints in 30 22q11.2DS families, the results show that, for a group of 88 people, favored recombination happens between FAM230 gene members and segmental duplication orientations within LCR22A and LCR22D [35]. Well-characterized genes that play a role in the 22q11.…”

Human-specific expansion of 22q11.2 low copy repeats

“…This locus is not present in any of the LCR22 blocks of the Pan genus. Pastor et al [22] narrowed this region to SD22-6, the duplicon encompassing the FAM230 gene member. Guo et al [29] predicted the rearrangement breakpoint was located in the BCR (Breakpoint Cluster Region) locus, present in the distal part of SD22-4 (end of arrow).…”

“…By combining fiber-FISH and Bionano optical mapping we assembled the LCR22s de novo and uncovered over 30 haplotypes of LCR22-A, with alleles ranging in size from 250 kb to 2000 kb within 169 normal diploid individuals [21]. Pastor et al recently expanded the LCR22-A catalogue by haplotyping the complete alleles of 30 22q11.2DS families [22]. To determine whether this extreme haplotype variability is human-specific, we set out to chart the inter- and intra-species variability of these LCR22s in non-human primates (S1 Table).…”

Optical Genome Mapping as a Next-Generation Cytogenomic Tool for Detection of Structural and Copy Number Variations for Prenatal Genomic Analyses

“…Other useful filtration criteria include SV confidence, size and SV supporting molecule cutoffs (i.e., number of molecules confirming the identified SV). This process generally results in a small list of SVs requiring an additional review for pathogenicity classification [ 11 , 12 , 13 , 14 ].…”