Background: Hypospadias is a common characteristic of Disorders of Sex Development (DSD). At the present time a molecular diagnosis is not reached in over 50% of cases. The DDD Study represents a useful resource of large molecular and phenotypic datasets obtained from individuals with an undiagnosed developmental abnormality including DSD.
Objective: To review associated features and identify likely pathogenic variants in previously undiagnosed DDD participants with hypospadias, cardiovascular and neurodevelopmental disorders.
Method: Retrospective review of anonymised phenotype data and bioinformatic analysis of variant call format (VCF) files of 33 DDD participants (22 family trios and 11 singleton cases) manifesting hypospadias, cardiovascular and neurodevelopmental abnormalities. A customised filter chain (using GoldenHelix, VarsDefault 1.4.4) specific to each inheritance pattern was created and searches were performed in databases (Online Mendelian Inheritance in Man, OMIM; PubMed and The Jackson Laboratory).
Results: Analysis was undertaken in 238 and 155 phenotype entries, recorded in 22 family trios and 11 singleton cases, respectively. Additional features included ophthalmic (34/393, 7%), skull (19/393, 5%), skeletal (18/393, 5%) and hand (17/393, 4%) abnormalities. The filter chain comprised the following criteria: read depth (DP≥20), genotype quality (GQ≥30), allele frequency (AF<0.01 or missing) and effect (loss of function) in both the trio and singleton analysis workflows. Additional filter cards specific to each inheritance pattern have been added to the trio analysis pipelines including Mendel error: de novo for the autosomal dominant, compound heterozygous: yes for the compound heterozygous, Mendel error: transmitted, Zygosity: homozygous, Mother: heterozygous, Father: heterozygous for the recessive homozygous and Heterozygous for the x-linked analysis pipeline. A final filter card entitled Extended DSD panel: true was added to each pipeline to identify variants in the 57 carefully curated DSD genes that are available on the NGS DSD panel locally. Six previously unidentified variants in five genes, including EPHB4, DGKK, and PIEZO1, in addition to the 9 variants in nine genes reported by the DDD study, are described in the family trios. Variant analysis of the singleton cases revealed five variants in five genes (e.g. KIF1A, FMN2) in addition to 10 reported variants in 10 genes of 6 DDD patients.
Conclusion: Exome sequencing has proven a powerful tool for the investigation of DSD with a diagnostic rate of up to 60%. Data from this study widen the phenotypic and genetic spectrum associated with DSD thus facilitating earlier recognition, improved diagnostic rates and management for affected families.
27 Sep 2018 - 29 Sep 2018