Characterizing Homozygous Variants in Bardet-Biedl Syndrome-Associated Genes Within Iranian Families: Unveiling a Founder Variant in BBS2, c.471G>A.

Bardet-Biedl syndrome (BBS) is a rare inherited ciliopathy disorder characterized by a broad spectrum of clinical symptoms such as retinal dystrophy, obesity, polydactyly, genitourinary and kidney anomalies, learning disability, and hypogonadism. The understanding of the variants involved in BBS-causing genes remains incomplete, highlighting the need for further research to develop a molecular diagnostic strategy for this syndrome. Singleton whole-exome sequencing (WES) was performed on sixteen patients. Our study revealed (1) nine patients carried eight homozygous pathogenic variants with four of them being novel (2) Specifically, a synonymous splicing variant (c.471G > A) in BBS2 gene in six patients with Baloch ethnicity. The identification of runs of homozygosity (ROH) calling was performed using the BCFtools/RoH software on WES data of patients harboring c.471G > A variant. The presence of shared homozygous regions containing the identified variant was confirmed in these patients. In-silico analysis predicted the effect of the c.471G > A variants on BBS2 mRNA splicing. This variant results in disrupted wild-type donor site and intron retention in the mature mRNA. (3) And a deletion of exons 14 to 17 in the BBS1 gene was identified in one patient by Copy-Number Variation (CNV) analysis using the ExomeDepth pipeline. Our results identified the founder variant c.471G > A in the BBS2 gene in the Baloch ethnicity of the Iranian population. This finding can guide the diagnostic approach of this syndrome in future studies.

BMP2 and BMP4 variations and risk of non-syndromic cleft lip and palate.

OBJECTIVE: Non-syndromic cleft lip with or without cleft palate (CL/P) is one of the most common congenital anomalies and arises from the interaction of environmental and genetic factors. The objective of this study was to investigate the association between the BMP2 (bone morphogenetic protein 2) and BMP4 (bone morphogenetic protein 4) polymorphisms with non-syndromic CL/P to clarify the potential role of these genes in the etiology of CL/P in Iranian population. DESIGN: The allelic and genotypic frequencies of BMP2 rs235768 A>T and BMP4 rs17563 T>C polymorphisms were determined in 107 unrelated Iranian subjects with non-syndromic CL/P and 186 control subjects using PCR and RFLP methods, and the results were compared with healthy controls. A p-value of <0.05 was considered statistically significant. RESULTS: The BMP2 rs235768 AT genotype was significantly higher (P=0.009, OR=3, 95% CI=1.3-7.0) in the CL/P (59.8%) than the control group (33.3%). Similarly, the BMP4 rs17563 TC genotype were significantly higher (P=0.008, OR=3.7, 95% CI=1.4-9.9) in the CL/P (70.0%) than the control group (44.6%). CONCLUSION: The BMP2 rs235768 A>T and BMP4 rs17563 T>C polymorphisms could be considered as the risk factor for non-syndromic CL/P in Iranian population.

Association of common variations of the E-cadherin with endometriosis.

Endometriosis is a polygenic and multifactorial disease. E-cadherin (CDH1) gene encodes an epithelial cell-cell adhesion glycoprotein that modulates a wide variety of processes, including cell polarization, migration and cancer metastasis. Decreased expression of CDH1 in epithelial cells in peritoneal endometriosis has been reported in advanced stages of endometriotic lesions. We investigated the CDH1 -160C/A and +54C/T variations with susceptibility to endometriosis in an Iranian population. In this case-control study, 149 patients with endometriosis (stages I-IV) and 151 healthy women as controls were included. Genotyping was performed using PCR-RFLP method. A p value of <0.05 was considered statistically significant. The CDH1 + 54TT genotype was significantly lower (p = 0.012; OR = 0.30, 95% CI: 0.12-0.77) in the patients (11.6%) than the control group (26.7%). The CDH1 + 54T allele was significantly lower (p = 0.001; OR = 0.55, 95% CI: 0.38-0.77) in the cases (35.7%) compared with the control group (50.3%). No association was found between CDH1 - 160C/A polymorphism and endometriosis. The CDH1 +54C/T was associated with susceptibility to endometriosis in Iranian population, and +54T allele may have a protective role in progression of endometriosis.

DNA repair gene XRCC1 and XRCC4 variations and risk of endometriosis: an association study.

BACKGROUND: Endometriosis is a polygenic and multifactorial disease. DNA damage plays a major role in mutagenesis, carcinogenesis and aging and is usually repaired by the action of several DNA repair enzymes. We investigated the association of the common variations of the DNA repair genes XRCC1 and XRCC4 with susceptibility to endometriosis in an Iranian population. METHODS: In total, 160 patients with endometriosis (stages I-IV) and 174 healthy women were included in this case-control study. Genotyping of XRCC1 codon 399 as well as of XRCC4 -1394T/G, codon 247 and intron 3 insertion/deletion variations was performed using restriction fragment length polymorphism analysis of PCR-amplified fragments. RESULTS: The XRCC4 -1394TG genotype frequency was significantly lower (p = 0.005) in the patients (9.4%) than in the controls (21.1%). The frequency of the -1394G allele was significantly lower (p < 0.0001) in the patients (6.6%) than in the controls (19.0%). There were no statistically significant differences in the genotype and allele frequencies of the XRCC1 codon 399, XRCC4 codon 247 and XRCC4 intron 3 insertion/deletion polymorphisms between the cases and controls. CONCLUSIONS: The XRCC4 -1394T/G polymorphism was associated with susceptibility to endometriosis in an Iranian population.