Analysis of chromosomal structural variations in patients with recurrent spontaneous abortion using optical genome mapping

Huihua Rao; Haoyi Zhang; Yongyi Zou; Pengpeng Ma; Tingting Huang; Huizhen Yuan; Jihui Zhou; Wan Lu; Qiao Li; Shuhui Huang; Yanqiu Liu; Bicheng Yang

doi:10.3389/fgene.2023.1248755

Analysis of chromosomal structural variations in patients with recurrent spontaneous abortion using optical genome mapping

Front Genet. 2023 Sep 4:14:1248755. doi: 10.3389/fgene.2023.1248755. eCollection 2023.

Authors

Huihua Rao^{1

2}, Haoyi Zhang³, Yongyi Zou^{1

2}, Pengpeng Ma^{1

2}, Tingting Huang^{1

2}, Huizhen Yuan^{1

2}, Jihui Zhou^{1

2}, Wan Lu^{1

2}, Qiao Li^{1

2}, Shuhui Huang^{1

2}, Yanqiu Liu^{1

2}, Bicheng Yang^{1

2}

Affiliations

¹ Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China.
² Jiangxi Key Laboratory of Birth Defect Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, Jiangxi, China.
³ School of Public Health, Nanchang University, Nanchang, Jiangxi, China.

Abstract

Background and aims: Certain chromosomal structural variations (SVs) in biological parents can lead to recurrent spontaneous abortions (RSAs). Unequal crossing over during meiosis can result in the unbalanced rearrangement of gamete chromosomes such as duplication or deletion. Unfortunately, routine techniques such as karyotyping, fluorescence in situ hybridization (FISH), chromosomal microarray analysis (CMA), and copy number variation sequencing (CNV-seq) cannot detect all types of SVs. In this study, we show that optical genome mapping (OGM) quickly and accurately detects SVs for RSA patients with a high resolution and provides more information about the breakpoint regions at gene level. Methods: Seven couples who had suffered RSA with unbalanced chromosomal rearrangements of aborted embryos were recruited, and ultra-high molecular weight (UHMW) DNA was isolated from their peripheral blood. The consensus genome map was created by de novo assembly on the Bionano Solve data analysis software. SVs and breakpoints were identified via alignments of the reference genome GRCh38/hg38. The exact breakpoint sequences were verified using either Oxford Nanopore sequencing or Sanger sequencing. Results: Various SVs in the recruited couples were successfully detected by OGM. Also, additional complex chromosomal rearrangement (CCRs) and four cryptic balanced reciprocal translocations (BRTs) were revealed, further refining the underlying genetic causes of RSA. Two of the disrupted genes identified in this study, FOXK2 [46,XY,t(7; 17)(q31.3; q25)] and PLXDC2 [46,XX,t(10; 16)(p12.31; q23.1)], had been previously shown to be associated with male fertility and embryo transit. Conclusion: OGM accurately detects chromosomal SVs, especially cryptic BRTs and CCRs. It is a useful complement to routine human genetic diagnostics, such as karyotyping, and detects cryptic BRTs and CCRs more accurately than routine genetic diagnostics.

Keywords: Oxford Nanopore technology (ONT); balanced reciprocal translocation (BRT); complex chromosomal rearrangement (CCR); optical genome mapping (OGM); recurrent spontaneous abortion (RSA); structural variations (SVs).

Associated data

figshare/10.6084/m9.figshare.24046965

Grants and funding

This work was supported by Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control (No. 20202BCD42017 to YL). Jiangxi Provincial Clinical Research Center for Birth Defects (No. 20223BCG74002 to YL). Provincial Health Commission Program of Jiangxi (No. 202211162 to HR). Youth Science Foundation of Jiangxi Province (No. 20192BAB215010 to WL).