Whole exome sequencing and trio analysis to broaden the variant spectrum of genes in idiopathic hypogonadotropic hypogonadism

Digenic CHD7 and SMCHD1 inheritance Unveils phenotypic variability in a family mainly presenting with hypogonadotropic hypogonadism

Objectives

CHARGE syndrome is a congenital hereditary condition involving multiple systems. Patients are easily misdiagnosed with idiopathic hypogonadotropic hypogonadism (IHH) due to the overlap of clinical manifestations. An accurate clinical diagnosis remains challenging when the predominant clinical manifestation resembles hypogonadotropic hypogonadism.

Methods

This original research is conducted based on the genetic finding and analysis of clinical cases. Whole-exome sequencing (WES) and in-silico analyse were performed on two sisters to investigate the pathogenesis in this family. Homology modelling was conducted to evaluate structural changes in the variants.

Results

WES and Sanger sequencing revealed two siblings carrying a nonsense mutation (NM_017780.4: c.115C > T) in exon 2 of CHD7 inherited from a mildly affected mother and a missense mutation (NM_015295.3: c.2582T > C) in exon 20 of SMCHD1 inherited from an asymptomatic father. The nonsense mutation in CHD7 was predicted to generate nonsense-mediated decay, whereas the missense mutation in SMCHD1 decreased protein stability.

Conclusions

We identified digenic CHD7 and SMCHD1 mutations in IHH-associated diseases for the first time and verified the synergistic role of oligogenic inheritance. It was also determined that WES is an effective tool for distinguishing diseases with overlapping features and establishing a molecular diagnosis for cases with digenic or oligogenic hereditary disorders, which is beneficial for timely treatment, and family genetic counseling.

Genetic architecture of DCC and influence on psychological, psychiatric and cardiometabolic traits in multiple ancestry groups in UK Biobank

BACKGROUND

People with severe mental illness have a higher risk of cardiometabolic disease than the general population. Traditionally attributed to sociodemographic, behavioural factors and medication effects, recent genetic studies have provided evidence of shared biological mechanisms underlying mental illness and cardiometabolic disease. We aimed to determine whether signals in the DCC locus, implicated in psychiatric and cardiometabolic traits, were shared or distinct.

METHODS

In UK Biobank, we systematically assessed genetic variation in the DCC locus for association with metabolic, cardiovascular and psychiatric-related traits in unrelated "white British" participants (N = 402,837). Logistic or linear regression were applied assuming an additive genetic model and adjusting for age, sex, genotyping chip and population structure. Bonferroni correction for the number of independent variants was applied. Conditional analyses (including lead variants as covariates) and trans-ancestry analyses were used to investigate linkage disequilibrium between signals.

RESULTS

Significant associations were observed between DCC variants and smoking, anhedonia, body mass index (BMI), neuroticism and mood instability. Conditional analyses and linkage disequilibrium structure suggested signals for smoking and BMI were distinct from each other and the mood traits, whilst individual mood traits were inter-related in a complex manner.

LIMITATIONS

Restricting analyses in non-"white British" individuals to the phenotypes significant in the "white British" sample is not ideal, but the smaller samples sizes restricted the phenotypes possible to analyse.

CONCLUSIONS

Genetic variation in the DCC locus had distinct effects on BMI, smoking and mood traits, and therefore is unlikely to contribute to shared mechanisms underpinning mental and cardiometabolic traits.

Whole Exome-Trio Analysis Reveals Rare Variants Associated with Congenital Pouch Colon

Anorectal malformations (ARM) are individually common, but Congenital Pouch Colon (CPC) is a rare anorectal anomaly that causes a dilated pouch and communication with the genitourinary tract. In this work, we attempted to identify de novo heterozygous missense variants, and further discovered variants of unknown significance (VUS) which could provide insights into CPC manifestation. From whole exome sequencing (WES) performed earlier, the trio exomes were analyzed from those who were admitted to J.K. Lon Hospital, SMS Medical College, Jaipur, India, between 2011 and 2017. The proband exomes were compared with the unaffected sibling/family members, and we sought to ask whether any variants of significant interest were associated with the CPC manifestation. The WES data from a total of 64 samples including 16 affected neonates (11 male and 5 female) with their parents and unaffected siblings were used for the study. We examined the role of rare allelic variation associated with CPC in a 16 proband/parent trio family, comparing the mutations to those of their unaffected parents/siblings. We also performed RNA-Seq as a pilot to find whether or not the genes harboring these mutations were differentially expressed. Our study revealed extremely rare variants, viz., TAF1B, MUC5B and FRG1, which were further validated for disease-causing mutations associated with CPC, further closing the gaps of surgery by bringing intervention in therapies.

Phenotypic and genotypic landscape of PROKR2 in neuroendocrine disorders

Prokineticin receptor 2 (PROKR2) encodes for a G-protein-coupled receptor that can bind PROK1 and PROK2. Mice lacking Prokr2 have been shown to present abnormal olfactory bulb formation as well as defects in GnRH neuron migration. Patients carrying mutations in PROKR2 typically present hypogonadotropic hypogonadism, anosmia/hyposmia or Kallmann Syndrome. More recently variants in PROKR2 have been linked to several other endocrine disorders. In particular, several patients with pituitary disorders have been reported, ranging from mild phenotypes, such as isolated growth hormone deficiency, to more severe ones, such as septo-optic dysplasia. Here we summarize the changing landscape of PROKR2-related disease, the variants reported to date, and discuss their origin, classification and functional assessment.