Integrated small copy number variations and epigenome maps of disorders of sex development

Abstract

Small copy number variations (CNVs) have typically not been analyzed or reported in clinical settings and hence have remained underrepresented in databases and the literature. Here, we focused our investigations on these small CNVs using chromosome microarray analysis (CMA) data previously obtained from patients with atypical characteristics or disorders of sex development (DSD). Using our customized CMA track targeting 334 genes involved in the development of urogenital and reproductive structures and a less stringent analysis filter, we uncovered small genes with recurrent and overlapping CNVs as small as 1 kb, and small regions of homozygosity (ROHs), imprinting and position effects. Detailed analysis of these high-resolution data revealed CNVs and ROHs involving structural and functional domains, repeat elements, active transcription sites and regulatory regions. Integration of these genomic data with DNA methylation, histone modification and predicted RNA expression profiles in normal testes and ovaries suggested spatiotemporal and tissue-specific gene regulation. This study emphasized a DSD-specific and gene-targeted CMA approach that uncovered previously unanalyzed or unreported small genes and CNVs, contributing to the growing resources on small CNVs and facilitating the narrowing of the genomic gap for identifying candidate genes or regions. This high-resolution analysis tool could improve the diagnostic utility of CMA, not only in patients with DSD but also in other clinical populations. These integrated data provided a better genomic-epigenomic landscape of DSD and greater opportunities for downstream research.

Genetics of Disorders of Sex Development

“…5,27–30 Genome-wide maps of CNVs of known pathogenicity as well as of uncertain clinical significance will continue to support clinical diagnosis and drive research for new etiologies. 31 The advent of next-generation sequencing in the realm of clinical diagnosis in the past 4 to 5 years is now allowing providers to rethink the diagnostic process.…”

Corrigendum: Corrigendum for: Disorders of sex development: The evolving role of genomics in diagnosis and gene discovery, 108:337–350 (10.1002/bdrc.21148)

“…Another large cohort of eighty‐seven 46,XY GD patients was screened with a diagnostic hit rate of 30% (Ledig et al, ), while a smaller screen of 46,XY DSD patients found CNVs in 23.8% of cases by jointly utilizing a CGH microarray, as well as Multiplex ligation‐dependant Probe Amplification (MPLA) for validation (White et al, ). More recently these technologies have been combined with epigenomic studies using a retrospective analysis to create a high‐density gene specific CNV and epigenomic maps from patients with DSD, in an effort to improve the diagnostic potential of CNV screening (Amarillo et al, ).…”

Under-reported aspects of diagnosis and treatment addressed in the Dutch-Flemish guideline for comprehensive diagnostics in disorders/differences of sex development

“…NGS-based techniques have also now made their appearance in prenatal diagnosis of congenital anomalies 29 30. Panels using these techniques can be specific for genes involved in DSD, or be larger panels covering multiple congenital anomalies, and are usually employed with trio-analysis to compare variants identified in the child with the parents’ genetics 29–31. Finding a genetic cause before delivery can help reduce parental stress in the neonatal period and speed up decisions regarding gender assignment.…”

“…Very recently, a European position paper has been published focusing on the genetic workup of DSD 16. It highlights the limitations and drawbacks of NGS-based tests, which include the chance of missing subtle structural variants such as CNVs and mosaicism and the fact that NGS cannot detect methylation defects or other epigenetic changes 16 28 31. Targeted DNA analysis is preferred in cases where hormonal investigations suggest a block in steroidogenesis (eg, 11-β-hydroxylase deficiency, 21-hydroxylase deficiency), or in the context of a specific clinical constellation such as the often coincidental finding of Müllerian structures in a boy with normal external genitalia or cryptorchidism, that is, persistent Müllerian duct syndrome 33 34.…”