Compilation of copy number variants identified in phenotypically normal and parous Japanese women

Analysis of chromosome microstructures in products of conception associated with recurrent miscarriage

RESEARCH QUESTION

The causes of almost half of all miscarriages are unknown. Genetic alterations undetectable by conventional methods may cause some cases of recurrent miscarriage. The study aimed to identify candidate genetic alterations associated with recurrent miscarriage.

DESIGN

Twenty-nine Japanese women with a history of recurrent miscarriage without any known underlying anatomical or medical causes were recruited. The products of conception were collected after miscarriage and showed either a normal karyotype or a failure of complete chromosomal Giemsa banding. Genomic DNA from the chorionic villi of the conception products was analysed using genome-wide single-nucleotide polymorphism (SNP) arrays.

RESULTS

In four cases, the products could not be analysed because of contaminating maternal-origin DNA, and chromosomal aneuploidies were observed in 10 cases. Thirty-three copy-number variations (CNV) were identified from the array data of 15 diploid cases. Causative CNV were identified by comparison with CNV observed in healthy, parous Japanese women. Twenty-four chromosomal regions with 26 CNV were identified as strong candidates for causing recurrent miscarriage, and these were all too small to detect by conventional chromosome analysis banding. Moreover, one novel CNV that caused complete deletion of a microRNA cluster region was detected.

CONCLUSIONS

High-resolution genome-wide SNP arrays are effective for detecting novel genetic factors causing recurrent miscarriage. A more appropriate reference CNV list may be necessary to more effectively enrich for CNV likely to cause recurrent miscarriage. The findings confirmed one non-coding RNA cluster as a strong candidate that may contribute to unexplained miscarriages. Gene expression-regulatory mechanisms may play important roles in the pathogenesis of miscarriages.

Genomic characteristics of miscarriage copy number variants

Studies of copy number variants (CNVs) in miscarriages are rare in comparison to post-natal cases with developmental abnormalities. The overall characteristics of miscarriage CNVs (size, gene content and function) are therefore largely unexplored. Our goal was to assess and compare the characteristics of CNVs identified in 101 euploid miscarriages from four high-resolution array studies that documented both common miscarriage CNVs (i.e. CNVs found in controls from the Database of Genomic Variants, DGV) and rare miscarriage CNVs (not reported in DGV). Our miscarriage analysis included 24 rare CNVs with 93 genes, and 372 common CNVs (merged into 119 common CNV regions; CNVRs) with 354 genes. The rare and common CNVs were comparable in size (median size of ∼ 0.16 and 0.14 Mb, respectively); however, rare CNVs showed a significantly higher gene density, with 56 genes/Mb in rare and 24 genes/Mb in common CNVs (P = 0.03). Rare CNVs also had two times more genes with mouse knock-out models which were reported for 42% of rare and 19% of common CNV genes. No specific pathway enrichment was noted for 24 rare CNV genes, but common CNV genes showed significant enrichment in genes from immune-response related pathways and pregnancy/reproduction-related biological processes. Our analysis of CNVs from euploid miscarriages suggests that both rare and common CNVs could have a role in miscarriage by impacting pregnancy-related genes or pathways. Cataloguing of all CNVs and detailed description of their characteristics (e.g. gene content, genomic breakpoints) is desirable in the future for better understanding of their relevance to pregnancy loss.