Detection of chromosomal abnormalities in spontaneous miscarriage by low‑coverage next‑generation sequencing

Area of Science:

• Genetics
• Reproductive Medicine
• Genomic Analysis

Background:

• Chromosomal abnormalities (CAs) are a significant cause of spontaneous miscarriage and subsequent pregnancy complications.
• Current detection methods like array comparative genomic hybridization (CGH) and single nucleotide polymorphism microarrays are established but can be costly and require substantial DNA input.
• Developing more accessible and efficient methods for CA detection in miscarriage is crucial for reproductive health management.

Purpose of the Study:

• To develop and evaluate a low-coverage next-generation sequencing (NGS) method for detecting chromosomal abnormalities in spontaneous miscarriage samples.
• To assess the clinical performance and cost-effectiveness of this novel NGS method compared to existing techniques.
• To analyze the spectrum of chromosomal abnormalities identified in a large cohort of miscarriage cases.

Main Methods:

• A low-coverage NGS method was established using a semiconductor sequencing platform on 437 previously array CGH-validated miscarriage samples (Group I).
• The method was applied to 964 unverified samples (Group II), with copy number variant (CNV)-positive and euploidy samples further validated by array CGH and short tandem repeat profiling.
• The NGS method was optimized to detect CNVs greater than 1 Mb, analyzing a total of 3.5 million unique reads.

Main Results:

• The low-coverage NGS method demonstrated results comparable to array CGH in Group I, with minor discrepancies for CNVs less than 1 Mb.
• In Group II, the method identified 341 aneuploidies, 195 CNVs, and 25 mosaicisms among 964 samples.
• Across all 1,401 samples, a total of 536 aneuploidies, 263 CNVs, and 34 mosaicisms were detected, with trisomies occurring across all autosomal chromosomes. Common aneuploidies included T16, monosomy X, T22, T15, T21, and T13. Rare cases like tetrasomy 21 and syndromes (Wolf-Hirschhorn, DiGeorge, Prader-Willi/Angelman) were confirmed.

Conclusions:

• The developed low-coverage NGS method is effective for detecting chromosomal abnormalities, including copy number variants greater than 1 Mb, in spontaneous miscarriage.
• This NGS approach offers comparable efficacy to array CGH for clinically significant CNVs while requiring less input DNA and incurring lower costs.
• The study highlights the utility of NGS in identifying a wide spectrum of chromosomal abnormalities in miscarriage, providing valuable insights for reproductive genetics and patient management.