Semiconductor Sequencing Analysis of Chromosomal Copy Number Variations in Spontaneous Miscarriage

Area of Science:

• Genetics
• Reproductive Biology
• Genomic Technology

Background:

• Array comparative genomic hybridization (CGH) is the standard for copy number variation (CNV) detection but is limited by DNA quality requirements and high costs.
• These limitations hinder its widespread use in developing countries' hospitals for genetic diagnostics.
• Spontaneous miscarriage analysis requires accessible and reliable methods for identifying chromosomal abnormalities.

Purpose of the Study:

• To evaluate the semiconductor sequencing platform (SSP) as a potential alternative for CNV detection in spontaneous miscarriage cases.
• To compare the efficacy of SSP with array CGH and MLPA (Multiplex Ligation-dependent Probe Amplification) for CNV and mosaicism identification.

Main Methods:

• Low-coverage (0.1X) whole-genome analysis using SSP was performed on 443 spontaneous miscarriage samples.
• Array CGH was used for verification of samples analyzed by SSP.
• Eight low-quality DNA samples were analyzed by SSP and validated using MLPA.

Main Results:

• SSP identified 195 chromosomal numerical abnormalities, 74 CNVs, and 9 mosaicisms in 435 samples.
• SSP showed equivalent performance to array CGH for CNVs >1 Mb (56 cases each) but missed more CNVs <1 Mb (18 vs. 12).
• SSP detected more mosaicisms (9 vs. 7) and identified a case with 8% X monosomy, which was below array CGH's detection limit.

Conclusions:

• SSP is as effective as array CGH for detecting CNVs larger than 1 Mb and superior for identifying mosaicism.
• SSP's lower cost and reduced DNA input requirements make it a viable alternative for genetic diagnosis in spontaneous miscarriages.
• The findings support SSP as a practical tool for genetic testing in resource-limited settings.