Targeting the Non-Coding Genome for the Diagnosis of Disorders of Sex Development

Abstract

Disorders of sex development (DSD) are a complex group of conditions with highly variable clinical phenotypes, most often caused by failure of gonadal development. DSD are estimated to occur in around 1.7% of all live births. Whilst the understanding of genes involved in gonad development has increased exponentially, approximately 50% of patients with a DSD remain without a genetic diagnosis, possibly implicating non-coding genomic regions instead. Here, we review how variants in the non-coding genome of DSD patients can be identified using techniques such as array comparative genomic hybridization (CGH) to detect copy number variants (CNVs), and more recently, whole genome sequencing (WGS). Once a CNV in a patient’s non-coding genome is identified, putative regulatory elements such as enhancers need to be determined within these vast genomic regions. We will review the available online tools and databases that can be used to refine regions with potential enhancer activity based on chromosomal accessibility, histone modifications, transcription factor binding site analysis, chromatin conformation, and disease association. We will also review the current in vitro and in vivo techniques available to demonstrate the functionality of the identified enhancers. The review concludes with a clinical update on the enhancers linked to DSD.

Tenuous Transcriptional Threshold of Human Sex Determination. I. SRY and Swyer Syndrome at the Edge of Ambiguity

“…PCR and quantitative reverse-transcriptase-PCR (qPCR) protocols were as described ( 31 ). The pairs of forward (F) and reverse (R) DNA oligonucleotide primers employed to probe embryonic testis-specific enhancer elements ( TESCO ( 16 ); mouse and human Enh13 ( 17 – 19 )).…”

“…A downstream gene-regulatory network (GRN) has been investigated in mouse models (12)(13)(14)(15), identifying autosomal gene Sox9 as the principal target of Sry in embryonic pre-Sertoli cells (15). Sry binds to specific regulatory DNA sites in the upstream region of Sox9 (or human SOX9), functioning as testis-specific enhancers (designated TES and Enh13) (16)(17)(18)(19). Whereas Sry/SRY represents an evolutionary innovation in therian mammals, Sox9 is broadly conserved among vertebrate sex-determining (VSD) pathways: an example of such pathways "growing backwards" in evolution (20,21).…”

Genomic instability in patients with sex determination defects and germ cell cancer

“…Given that genetic causes for DSD remain unknown for about half of the patients, it’s likely that polygenic mutations or even noncoding regions of genome could be involved( 48 ). This supports our idea that a state of genome integrity is behind DSD-phenotypes.…”

The Use of Genetics for Reaching a Diagnosis in XY DSD

“…Others may be discovered by overlapping WES results with animal model experiments [Barseghayn et al, 2018]. The moderate diagnostic success of WES in DSD patients may be explained by limitations of the technique itself (Table 2) or by the increasing belief that other genetic mechanisms exist within the subset of non-coding DNA that may be involved in the regulation of sex development [Atlas et al, 2021]. The viability of the latter is supported by discoveries in the field of androgen insensitivity syndrome (AIS).…”