Low-pass Whole-genome Sequencing in Recurrent Miscarriage Couples
Background of recurrent miscarriage:
In Hong Kong, 1 in 6 couples are infertile. Recurrent miscarriage (RM_) is one of the major causes of infertility adversely affecting 1-2% of couples, and it can be physically and emotionally taxing for couples, particularly for the maternal healthcare. Genetic factors and antiphospholipid syndrome are the most commonly recognized etiologies for RM_. Chromosomal abnormalities (i.e., mainly balanced rearrangements) are the major recognized genetic causes for RM_ with a prevalence in couples of approximately 5%, which is significantly higher than that reported in the general population (~1 in 500). Couples in whom one partner carries a balanced translocation may have an overall miscarriage rate as high as 49%. Recently, studies on the RM_ couples with/without their abortus show some of the single-nucleotide variants (SNVs) might contribute to the RM_ outcome or lethal disorder. However, the related testing is not yet recognized and recommended by the society. The etiology of RM_ in 40-60% of couples remains idiopathic; thus, it is challenging to provide appropriate therapy recommendations. Therefore, new technologies to increase the diagnostic yield for this patient group would be called for to address this need.
Low-pass whole-genome sequencing:
Starting from 2008, there were several groups leading projects for delineation of breakpoints of balanced chromosomal rearrangements in disease groups using state-of-the-art next-generation sequencing with whole-genome or capture based assays. These studies revealed the advantages of using next-generation sequencing to identify disease-causing genes by definition of breakpoints to single-nucleotide resolution. However, due to the algorithms used in these analyses, all studies were performed based on prior knowledge of the rearranged chromosome bands reported from cytogenetic studies.
We expanded the analysis to low-pass (or low-coverage) whole-genome sequencing (WGS) by establishing a pipeline with a dataset of systematic errors generated from library construction, sequencing and reads alignment, for identification of balanced chromosomal rearrangements and CNVs independent of prior chromosome analysis. We further tested its sensitivity in an existing dataset from the 1000 Genomes Project without knowledge on the potential inclusion of subjects with apparent balanced translocations akin to those traditionally detected in diagnostic cytogenetics laboratories. The incidence of balanced translocations detected was higher (~1 in 291) than reported by routine chromosome analysis (~1 in 500); and one of the translocations was cryptic to traditional cytogenetic analysis due to similarity of the banding pattern and size of exchanged segments. In addition, compared to chromosomal microarray analysis, our study in early abortus, prenatal and postnatal samples demonstrated the power of low-pass WGS for identifying additional CNVs likely to be causing the diseases. Therefore, in this study, we aim to conduct low-pass WGS in identification of chromosomal abnormalities etiologic to RM_ couple.
This study has been approved by the Institutional Review Boards of Shandong University and The Chinese University of Hong Kong.
Each couple will be subjected to multiple tests and those diagnosed with the established causes as defined by guidelines of the American Society of Human Reproductive (ASRM) will be excluded.
A 1-ml peripheral blood sample will be collected into an EDTA tube, buffy coat of which will be separated and stored frozen at -80 ºC for DNA extraction. After DNA extraction, a total of 1·5 μg genomic DNA (OD260/OD280 > 1.8; OD260/OD230 > 1.5) will be subjected to DNA fragmentation and low-pass WGS. Detection of chromosomal rearrangement and CNVs will be performed in parallel and report of chromosomal abnormalities will be generated following interpretation of all detection results.
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Project leader and enquiry:
Dr. Richard KW Choy,
Dept of Obstetrics and Gynaecology, The Chinese University of Hong Kong
Phone-enquiry: 3505 2810