Copy Number Variation in Patients with Disorders of Sex Development Due to 46,XY Gonadal Dysgenesis

Abstract

Disorders of sex development (DSD), ranging in severity from mild genital abnormalities to complete sex reversal, represent a major concern for patients and their families. DSD are often due to disruption of the genetic programs that regulate gonad development. Although some genes have been identified in these developmental pathways, the causative mutations have not been identified in more than 50% 46,XY DSD cases. We used the Affymetrix Genome-Wide Human SNP Array 6.0 to analyse copy number variation in 23 individuals with unexplained 46,XY DSD due to gonadal dysgenesis (GD). Here we describe three discrete changes in copy number that are the likely cause of the GD. Firstly, we identified a large duplication on the X chromosome that included DAX1 (NR0B1). Secondly, we identified a rearrangement that appears to affect a novel gonad-specific regulatory region in a known testis gene, SOX9. Surprisingly this patient lacked any signs of campomelic dysplasia, suggesting that the deletion affected expression of SOX9 only in the gonad. Functional analysis of potential SRY binding sites within this deleted region identified five putative enhancers, suggesting that sequences additional to the known SRY-binding TES enhancer influence human testis-specific SOX9 expression. Thirdly, we identified a small deletion immediately downstream of GATA4, supporting a role for GATA4 in gonad development in humans. These CNV analyses give new insights into the pathways involved in human gonad development and dysfunction, and suggest that rearrangements of non-coding sequences disturbing gene regulation may account for significant proportion of DSD cases.

Genome-wide identification of regulatory elements in Sertoli cells

“…The inability to provide a genetic diagnosis for the majority of individuals with a DSD has led to the development of more robust diagnostic tests to screen large regions of the genome for potential disease-causing mutations, including exome sequencing and copy number variation arrays (White et al, 2011;Arboleda et al, 2013;Baxter et al, 2015). This approach has revealed non-coding mutations upstream of SOX9 that result in DSDs (Kim et al, 2015).…”

Disorders of sex development: advances in genetic diagnosis and challenges in management

“…7 In addition, a probable regulatory element lying downstream of the GATA4 gene was identified when a 35 kb deletion was detected in a person with 46,XY complete gonadal dysgenesis. 17 Similarly, in those with 46,XY DSD, microarray analysis detected an intragenic deletion of WWOX 18 and a deletion at least 42 kb upstream of the DMRT1 gene. 19 In fact, array analyses have now identified many DNA duplications and deletions in people with DSD, several of which are located close to known sex development genes and are suspected to have caused disruption of gene regulatory regions.…”

Regulation of Sex Determination in Mice by a Non-coding Genomic Region

“…Point mutations within the human syntenic region of the testis-specific enhancer located 59 to the Sox9 open reading frame, TESCO, have not been found (Sekido and Lovell-Badge 2008;Georg et al 2010). However, duplications and deletions limited to the SOX9 regulatory regions have recently been identified in several familial and isolated cases of 46,XY DSD or 46,XX DSD (Benko et al 2011;Cox et al 2011;White et al 2011). These deletions and duplications cause dysregulation of SOX9 expression with either loss of testis-specific SOX9 expression or abnormal ectopic expression in an XX individual resulting in either 46,XY gonadal dysgenesis or 46,XX testicular DSD, respectively.…”