Analysis of balanced reciprocal translocations in patients with subfertility using single-molecule optical mapping

• Published in: Journal of assisted reproduction and genetics Vol. 37; no. 3; pp. 509 - 516
• Main Authors: Wang, Hui, Jia, Zhengjun, Mao, Aiping, Xu, Bing, Wang, Shuling, Wang, Li, Liu, Sai, Zhang, Haiman, Zhang, Xiaojie, Yu, Tao, Mu, Ting, Xu, Mengnan, Cram, David S., Yao, Yuanqing
• Format: Journal Article
• Language: English
• Published: New York Springer US 01-03-2020; Springer Nature B.V
• Subjects: Adult; Breakpoints; Chromosome translocations; Cytogenetics; Female; Fertility; Fertilization in Vitro; Gene mapping; Gynecology; Human Genetics; Humans; In Situ Hybridization, Fluorescence - methods; In vitro fertilization; Infertility; Infertility - genetics; Infertility - pathology; Infertility, Male - diagnosis; Infertility, Male - genetics; Infertility, Male - pathology; Karyotyping; Male; Medicine; Medicine & Public Health; Methyltransferase; Middle Aged; Reproductive Medicine; Single Molecule Imaging - methods; Technological Innovations; Translocation, Genetic - genetics; Single-molecule optical mapping; Mate-pair sequencing; Balanced reciprocal translocation (BRT); Infertility
• ISSN: 1058-0468; 1573-7330
• DOI: 10.1007/s10815-020-01702-z

Purpose
Approximately 1% of individuals who carry a balanced reciprocal translocation (BRT) are subfertile. Current karyotyping does not have the resolution to determine whether the breakpoints of the involved chromosomes perturb genes important for fertility. The aim of this study was to apply single-molecule optical mapping (SMOM) to patients presenting for IVF (in vitro fertilization) to ascertain whether the BRT disrupted any genes associated with normal fertility.
Methods
Nine subfertile patients with different BRTs were recruited for the study. Methyltransferase enzyme DLE1 was used to fluorescently label their genomic DNA samples at the recognition motif CTTAAG. The SMOM was performed on the Bionano platform, and long molecules aligned against the reference genome hg19 to identify the breakpoint regions. Mate-pair and PCR-Sanger sequencing were used to confirm the precise breakpoint sequences.
Results
Both breakpoint regions in each of the nine BRTs were finely mapped to small regions of approximately 10 Kb, and their positions were consistent with original cytogenetic banding patterns determined by karyotyping. In three BRTs, breakpoints disrupted genes known to be associated with male infertility, namely
NUP155
and
FNDC3A
[46,XY,t(5;13)(p15;q22)],
DPY19L1
[46,XY,t(1;7)(p36.3;p15), and
BAI3
[46,XY,t(3;6)(p21;q16)].
Conclusions
The SMOM has potential clinical application as a rapid tool to screen patients with BRTs for underlying genetic causes of infertility and other diseases.