Translating genomics to the clinical diagnosis of disorders/differences of sex development

Abstract

The medical and psychosocial challenges faced by patients living with Disorders/Differences of Sex Development (DSD) and their families can be alleviated by a rapid and accurate diagnostic process. Clinical diagnosis of DSD is limited by a lack of standardization of anatomical and endocrine phenotyping and genetic testing, as well as poor genotype/phenotype correlation. Historically, DSD genes have been identified through positional cloning of disease-associated variants segregating in families and validation of candidates in animal and in vitro modeling of variant pathogenicity. Owing to the complexity of conditions grouped under DSD, genome-wide scanning methods are better suited for identifying disease causing gene variant(s) and providing a clinical diagnosis. Here, we review a number of established genomic tools (karyotyping, chromosomal microarrays and exome sequencing) used in clinic for DSD diagnosis, as well as emerging genomic technologies such as whole-genome (short-read) sequencing, long-read sequencing, and optical mapping used for novel DSD gene discovery. These, together with gene expression and epigenetic studies can potentiate the clinical diagnosis of DSD diagnostic rates and enhance the outcomes for patients and families.

Keywords: Disorders/differences of sex development; Exome sequencing; Genetic diagnosis; Long-read sequencing; Next-generation sequencing; Optical genome mapping; Sexual development; Structural variants; Whole genome sequencing.

Figure 1:. Simplified overview of sex determination and sex differentiation in humans

(The figure has been modified from (Arbodela and Vilain, 2009) using Barseghyan et al., 2015; Biason-Lauber, 2012; Croft et al., 2016; Kyriakou et al., 2015; Ohnesorg et al., 2014; Makoto Ono and Harley, 2013; Zhao et al., 2017) and references therein.

Figure 2:. Preparation of long DNA molecules for optical mapping:

High molecular weight DNA is incubated with fluorescent labels and Direct Labeling Enzyme 1 (DLE1). The enzyme recognizes CTTAAG sequences throughout the genome and covalently attaches a fluorescent label (green). Subsequently, the DNA backbone is stained overnight and loaded onto the Bionano Genomics Chips containing millions of nanochannels for imaging. The green fluorescent labels are used to map DLE1 enzyme recognition patterns, whereas the blue staining of the DNA backbone is used to identify molecule sizes. Both are used for de novo genome assembly.