Distinct genetic variation and heterogeneity of the Iranian population

Identification of novel and known genetic variants associated with hereditary hearing loss in iranian families using whole exome sequencing

BACKGROUND

Hearing loss (HL) is a common sensory impairment worldwide, with genetic and environmental factors contributing to its occurrence. Next Generation Sequencing (NGS) plays a crucial role in identifying the genetic factors involved in this heterogeneous disorder.

METHODS AND RESULTS

In this study, a total of 9 unrelated Iranian families, each having at least one affected individual who tested negative for mutations in GJB2, underwent screening using whole exome sequencing (WES). The pathogenicity and novelty of the identified variant was checked using various databases. Co-segregation study was also performed to confirm the presence of the candidate variants in parents. Plus, The pathogenicity of the detected variant was assessed through in silico analysis using a number of mutation prediction software tools. Among the 9 investigated families, hearing loss-causing genes were identified in 6 families. the mutations were observed in USH2A, CLRN1, BSND, SLC26A4, and MITF, with two of the identified mutations being novel.

CONCLUSION

Discovering additional variants and broadening the range of mutations associated with hearing impairment has the potential to enhance the diagnostic effectiveness of molecular testing in patient screening, and can also lead to improved counseling aimed at reducing the risk of affected offspring for high-risk couples.

Haplotype diversity of 17 Y-STR in the Iranian population

The current study aimed to evaluate Y chromosome haplotypes obtained from 1353 unrelated Iranian males using the AmpFlSTRTM YfilerTM kit; 1353 out of the 1353 identified haplotypes were unique. The haplotype diversity (HD) and discriminating capacity (DC) values were 1.00000 and 0.997, respectively. Analysis of genetic distance was performed using molecular variance (AMOVA) and multidimensional scaling plots (MDS), revealing a statistically significant difference between the study population and previous data reported for other Iranian populations and other neighboring countries. The present findings are likely to be useful for forensic casework analyses and kinship investigations.

A national registry-based study of ethnic differences in people with multiple sclerosis in Iran

OBJECTIVE

The relationship between MS and ethnicity has been understudied in the Middle East compared to the United States and Europe. As Iran as the highest prevalence of MS in the Middle East, we decided to investigate the demographic and clinical differences in people with MS (pwMS) from major ethnicities Iran.

METHODS

In a cross-sectional study using data from National Multiple Sclerosis Registry in Iran. PwMS from six provinces were chosen and interviewed for determining their ethnicity. Persians (Fars), Kurds, Lurs, Azeris and Arabs with a clear ethnic background were included. Recorded data from the registry was used to compare the demographic and clinical features.

RESULTS

A total of 4015 pwMS (74.2% female) were included in the study with an average age of 36.76 ± 9.68 years. Persians and Kurds had the highest percentage of pwMS in youngest and oldest age groups, respectively, with 2.9% and 5.7% (p<0.01). The highest average age of onset was seen in Persians (29.47 ± 8.89) and the lowest observed in Mazandaranis (26.82 ± 7.68, p<0.01). Azeris and Kurds had the highest proportions of pwMS diagnosed <18 and >55, at rates of 12% and 1.6%, respectively (p<0.01). There were statistically significant differences in distribution of phenotypes (p<0.01) and time to progression to secondary progressive MS (p<0.01) such that Persians had the highest rate of clinically isolated syndrome (CIS) at 19.3% and Arabs had highest rates of relapsing-remitting MS (86.2%) and secondary progressive MS (16.4%). Lurs, Azeris and Mazandaranis had significantly more patients progressing to secondary-progressive MS <5 years from diagnosis (p<0.01). There was a significant difference in number of relapses between the ethnicities (p<0.01) with Lurs having the highest proportion of participants reporting >4 relapses with 23.0% and Azeris having the highest percentage of pwMS reporting no relapse (53.0%). Kurds had the highest Expanded Disability Status Scale (EDSS) average at 2.93 ± 1.99 and Lurs had the lowest with 1.28 ± 1.25 (p<0.01). The differences in prevalence of positive family history for the whole cohort between ethnicities were significant (P=0.02), ranging from 12.8% in Kurds to 19.6% in Persians.

CONCLUSION

We found Persians to have higher rates of pediatric MS and higher rates of CIS. Kurds and Lurs had higher and lower EDSS scores, respectively. Lurs and Persian had higher annual relapse rates. We also found lower rates of SPMS among Arabs and earlier progression to SPMS in Lurs, Azeris and Mazandaranis. Such differences highlight the importance of the potential role of ethnicities in diagnosis and prognosis of MS, especially considering their observation within the geographical limits of a single country.

Predictors of Recurrent Urolithiasis in Iran: Findings from a Nationwide Study

BACKGROUND

Prevention of urinary stone recurrence is the ultimate goal in urolithiasis patients. In this study, we aimed to investigate the national prevalence rate and possible determinants of increased urolithiasis recurrence risk in a nationwide study in Iran.

METHODS

All data regarding stone occurrence and recurrence episodes were extracted from the cross-sectional Iran National Stone Survey (INSS) study, and the possible determinants of recurrence were evaluated in the subset of 2913 patients who had a positive history of at least one episode of urolithiasis.

RESULTS

The national prevalence rate of recurrent urolithiasis was 2.6% (95% CI: 2.5, 2.8) in Iran. Moreover, the relative ratio of recurrent stone formers to all stone formers was 39.8% (95% CI: 38.0, 41.6). Our univariable truncated negative binomial regressions suggested that a positive history of urolithiasis in the patient's father (prevalence ratio [PR] [95% CI]=1.83 [1.39, 2.41], P<0.001), mother (PR [95% CI]=1.92 [1.39, 2.66], P<0.001) or brother (PR [95% CI]=1.32 [1.03, 1.69], P=0.026); and residence in urban areas (PR [95% CI]=1.27 [1.04, 1.55], P=0.016) were significant predictors of repetitive recurrence episodes. However, when incorporated into a multivariable truncated negative binomial regression model, the only significant predictors of more frequent recurrence episodes were a positive history in father (PR [95% CI]=1.66 [1.24, 2.22], P<0.001) and mother (PR [95% CI]=1.68 [1.20, 2.36], P=0.002); and urban residence (PR [95% CI]=1.24 [1.01, 1.51], P=0.031).

CONCLUSION

Our results indicate that a positive family history of urolithiasis in mother and father and residence in urban areas are the significant predictors of recurrence risk in urolithiasis patients in Iran.

The Tehran longitudinal family-based cardiometabolic cohort study sheds new light on dyslipidemia transmission patterns

Dyslipidemia, as a metabolic risk factor, with the strongest and most heritable independent cause of cardiovascular diseases worldwide. We investigated the familial transmission patterns of dyslipidemia through a longitudinal family-based cohort, the Tehran Cardiometabolic Genetic Study (TCGS) in Iran. We enrolled 18,729 individuals (45% were males) aged > 18 years (mean: 38.15 (15.82)) and observed them over five 3-year follow-up periods. We evaluated the serum concentrations of total cholesterol, triglyceride, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol with the first measurement among longitudinal measures and the average measurements (AM) of the five periods. Heritability analysis was conducted using a mixed-effect framework with likelihood-based and Bayesian approaches. The periodic prevalence and heritability of dyslipidemia were estimated to be 65.7 and 42%, respectively. The likelihood of an individual having at least one dyslipidemic parent reveals an OR = 6.94 (CI 5.28-9.30) compared to those who do not have dyslipidemic parents. The most considerable intraclass correlation of family members was for the same-sex siblings, with ICC ~ 25.5%. For serum concentrations, heritability ranged from 33.64 to 60.95%. Taken together, these findings demonstrate that familial transmission of dyslipidemia in the Tehran population is strong, especially within the same-gender siblings. According to previous reports, the heritability of dyslipidemia in this population is considerably higher than the global average.

Genetic Analysis of 27 Y-STR Haplotypes in 11 Iranian Ethnic Groups

BACKGROUND

The study of Y-chromosomal variations provides valuable insights into male susceptibility in certain diseases like cardiovascular disease (CVD). In this study, we analyzed paternal lineage in different Iranian ethnic groups, not only to identify developing medical etiology, but also to pave the way for gender-specific targeted strategies and personalized medicine in medical genetic research studies.

METHODS

The diversity of eleven Iranian ethnic groups was studied using 27 Y-chromosomal short tandem repeat (Y-STR) haplotypes from Y-filer® Plus kit. Analysis of molecular variance (AMOVA) based on pair-wise RST along with multidimensional scaling (MDS) calculation and Network phylogenic analysis was employed to quantify the differences between 503 unrelated individuals from each ethnicity.

RESULTS

Results from AMOVA calculation confirmed that Gilaks and Azeris showed the largest genetic distance (RST=0.35434); however, Sistanis and Lurs had the smallest considerable genetic distance (RST=0.00483) compared to other ethnicities. Although Azeris had a considerable distance from other ethnicities, they were still close to Turkmens. MDS analysis of ethnic groups gave the indication of lack of similarity between different ethnicities. Besides, network phylogenic analysis demonstrated insignificant clustering between samples.

CONCLUSION

The AMOVA analysis results explain that the close distance of Azeris and Turkmens may be the effect of male-dominant expansions across Central Asia that contributed to historical and demographics of populations in the region. Insignificant differences in network analysis could be the consequence of high mutation events that happened in the Y-STR regions over the years. Considering the ethnic group affiliations in medical research, our results provided an understanding and characterization of Iranian male population for future medical and population genetics studies.

Evaluation of miR-let-7f, miR-125a, and miR-125b expression levels in sputum and serum samples of Iranians and Afghans with pulmonary tuberculosis

Background and Objectives

The role of microRNAs (miRNAs) in tuberculosis infection is well established. As microRNAs are able to change expression profiles according to different conditions, they can be useful biomarkers. Iranians and Afghans with tuberculosis were studied for three immune-related miRNAs (miR-let-7f, miR-125a, and miR-125b).

Materials and Methods

A total of 60 Iranian and Afghan patients with active pulmonary TB were enrolled in the Pulmonary Department of the Pasteur Institute of Iran. Serum and sputum samples were collected simultaneously from all participants. A Real-time PCR was conducted to detect differentially expressed miRNAs.

Results

Iranian (P<0.0001) and Afghan (P<0.0001) serum samples and Afghan (P<0.0001) sputum samples overexpressed miR-125a, whereas Iranian sputum samples showed downregulation (P=0.0039). In both Iranian (P<0.0001; P=0.0007) and Afghan (P<0.0001; P<0.0001) serum and sputum samples, miR-125b was overexpressed. Furthermore, miR-let-7f down-regulation was observed in serum and sputum samples (P<0.0001), whereas Iranian sputum samples had no statistically significant differences (P=0.348).

Conclusion

Overexpression of miR-125a and miR-125b has been detected in Iranian and Afghan samples. In both races, miR-let-7f downregulation has been confirmed. Identification of miRNA profiles under different conditions opens the door to evaluating potential new biomarkers for diagnosis, disease monitoring, and therapeutic markers in TB infection.

Spatiotemporal variations in childhood lymphoma cancer incidence and its survival rate in Iran, 2005-2015: a cross-sectional study

BACKGROUND

Childhood lymphoma is the second leading cause of cancer in children under 15 years of age in Iran. The aim of this study was to investigate the spatial and time variations in lymphoma incidence as well as the children's survival time in Iran.

METHOD

This cross-sectional study was conducted using lymphoma cases (children under 14 years of age) from 2005 to 2015, and the data were obtained from the National Cancer Registry Center. The frequency, age-standardised incidence rate (ASIR), spatial clustering in national level and the survival rate (1 year and 5 years) using Kaplan-Meier method were evaluated. We used Spatial and Temporal Scan statistics software in order to detect statistically significant clusters in spatial analysis.

RESULTS

A total number of 746 girls and 1610 boys were diagnosed with lymphoma during a 10-year period. ASIRs (per 100 000 people) for girls ranged from 0 in Ilam to 3.47 in Yasuj, and it ranged from 0.19 in Ilam to 5.91 in Yazd for boys from 2005 to 2015. Spatial analysis result showed a large statistically significant cluster (the most likely cluster) for both boys (relative risk (RR)=2.37) and girls (RR=2.49) located in the northwest of Iran. Fortunately, survival rate for both boys and girls was over 95.5%.

CONCLUSION

Lymphoma incidence rates had heterogeneous geographical distribution, and some significant clusters were identified which strengthens the role of possible aetiological factors, and further studies are needed to clarify this ambiguity. Fortunately, the survival rate of this cancer in Iran was good and it was similar to the high-income countries.

Genetic attributes of Iranian cystic fibrosis patients: the diagnostic efficiency of CFTR mutations in over a decade

Objectives: Cystic fibrosis (CF) is the most prevalent autosomal recessive disorder among Caucasians. Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause this pathology. We, therefore, aimed to describe the CFTR mutations and their geographical distribution in Iran. Method: The mutation spectrum for 87 families from all Iranian ethnicities was collected using ARMS PCR, Sanger sequencing, and MLPA. Results: Mutations were identified in 95.8% of cases. This dataset revealed that the most frequent mutations in the Iranian population were F508del, c.1000C>T, c.1397C>G, c.1911delG, and c.1393-1G>A. In addition, we found weak evidence for Turkey being the possible geographical pathway for introducing CFTR mutations into Iran by mapping the frequency of CFTR mutations. Conclusion: Our descriptive results will facilitate the genetic detection and prenatal diagnosis of cystic fibrosis within the Iranian population.

Evaluation of a warfarin dosing algorithm including CYP2C9, VKORC1, and CYP4F2 polymorphisms and non-genetic determinants for the Iranian population

BACKGROUND

The response to warfarin, as an oral anticoagulant agent, varies widely among patients from different ethnic groups. In this study, we tried to ascertain and determine the relationship between non-genetic factors and genetic polymorphisms with warfarin therapy; we then proposed a new warfarin dosing prediction algorithm for the estimation of drug sensitivity and resistance in the Iranian population.

METHODS

Overall, 200 warfarin-treated patients with stable doses were recruited, the demographic and clinical characteristics were documented, and genotyping was done using a sequencing assay.

RESULTS

The outcomes of our investigation showed that the genetic polymorphisms of VKORC1(-1639 G > A), CYP2C9*3, CYP2C9*2, amiodarone use, and increasing age were found to be related to a significantly lower mean daily warfarin dose. In contrast, the CYP4F2*3 variant and increased body surface area were linked with an increased dose of warfarin in the Iranians. Our descriptive model could describe 56.5% of the variability in response to warfarin. This population-specific dosing model performed slightly better than other previously published warfarin algorithms for our patient's series. Furthermore, our findings provided the suggestion that incorporating the CYP4F2*3 variant into the dosing algorithm could result in a more precise calculation of warfarin dose requirements in the Iranian population.

CONCLUSIONS

We proposed and validated a population-specific dosing algorithm based on genetic and non-genetic determinants for Iranian patients and evaluated its performance. Accordingly, by using this newly developed algorithm, prescribers could make more informed decisions regarding the treatment of Iranian patients with warfarin.

Allelic and Genotype Frequencies of CYP2B6∗2 (64C > T) and CYP2B6∗3 (777C > A) in Three Dominant Ethnicities of the Iranian Population

Background

Cytochrome P450 complex plays a key role in drug metabolism. CYP2B6 has an essential part in Cytochrome P450 complex metabolism. This study aims to determine the allelic distribution of CYP2B6^∗2 and CYP2B6^∗3 in three main Iranian ethnicities: Fars, Turk, and Kurd.

Methods

The study was conducted on 174 unrelated healthy volunteers from three main Iranian ethnicities. After DNA extraction from peripheral blood samples, genotyping of CYP2B6^∗2 and ^∗3 was performed using tetra ARMS and ARMS PCR, respectively.

Results

The average age of 174 cases was 40.69 ± 11.87 (mean ± SD) and 39.06 ± 11.63 (mean ± SD) for males and females. In the CYP2B6^∗2 variant, the genotyping frequency of wild type (C/C), heterozygous (C/T), and homozygous mutant (T/T) was 8.7%, 86%, and 5.2%, respectively. The CYP2B6^∗2 (c.64C > T) allele frequency was 48.2% (95% CI: (37.8-58.6)). In the CYP2B6^∗3 variant, the frequency of wild type (C/C), heterozygous (C/T), and homozygous mutant (T/T) was 75.3%, 11%, and 13.6%, respectively. The CYP2B6^∗3 (c.777C > A) allelic frequency was 19.1% (95% CI: (17.5-20.7)).

Conclusion

Allelic distribution in three main Iranian ethnicities, i.e., Turk, Kurd, and Fars, is remarkably higher than that in other populations, even that in Southern Iran. High frequencies of CYP2B6^∗2 and ^∗3 in the Iranian population highly affect drug responsiveness. Understanding such variability could help to increase drug efficacy and reduce its toxicity.

Aesthetic considerations for treating the Middle Eastern patient: Thriving in Diversity international roundtable series

BACKGROUND

The Middle East has a significant influence on the global aesthetic market. Within the United States and globally, patients with Middle Eastern heritage have a wide range of ethnic and cultural backgrounds that affect their perceptions of beauty and motivations to seek cosmetic treatment.

AIMS

The aim of this roundtable was to discuss similarities and differences in anatomy and treatment preferences of Middle Eastern patients and explore how these differences may influence aesthetic practices.

PATIENTS/METHODS

In support of clinicians who wish to serve a diverse patient population, a 6-part international roundtable series focused on diversity in aesthetics was conducted from August 24, 2021, to May 16, 2022.

RESULTS

The results of the fourth roundtable in the series, the Middle Eastern Patient, are described here. A discussion of treatment preferences is included, and specific procedural information is provided for  commonly treated areas in this population (forehead, infraorbital area, and jawline).

CONCLUSIONS

Middle Eastern patients have a variety of aesthetic preferences, which are influenced by a wide range of cultural backgrounds, making it difficult to develop general statements about this demographic. There is an unmet need for research into this diverse group of patients to help physicians understand and incorporate their unique needs and desires into clinical practice.

Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean

We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term "the expanding mobility model." Interestingly, this increase in inter-regional divergence can be captured by outgroup-f₃-based genetic distances, but not by the commonly used F_ST statistic, due to the sensitivity of F_ST, but not outgroup-f₃, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.

Reporting Two Novel Mutations in Two Iranian Families with Cystic Fibrosis, Molecular and Bioinformatic Analysis

Background

Cystic fibrosis (CF) is the most common heredity disease among the Caucasian population. More than 350 known pathogenic variations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene (NM_000492.4) cause CF. Herein, we report the outcome of our investigation in two unrelated Iranian families with CF patients.

Methods

We conducted phenotypic examination, segregation, linkage analysis, and CFTR gene sequencing to define causative mutations.

Results

We found two novel mutations in the present study. The first one was a deletion causing frameshift, c.299delT p.(Leu100Profs*7), and the second one was a missense mutation, c.1857G>T, at nucleotide binding domain 1 of the CFTR protein. Haplotype segregation data supported our new mutation findings.

Conclusion

Findings of this study expand the spectrum of CFTR pathogenic variations and can improve prenatal diagnosis and genetic counseling for CF.

Development and pilot implementation of Iranian Hemolytic Uremic Syndrome Registry

Background

Patients with Hemolytic Uremic Syndrome (HUS) face late diagnosis and lack of appropriate treatment because of a lack of knowledge and experience in this field. A prerequisite for such knowledge is the development of research infrastructures such as a registry system. Therefore, this study aimed to develop and describe the HUS registry in accordance with the Iranian health system and implement its software system.

Methods

We first interviewed 10 pediatric nephrologists and after analyzing the interviews, we identified the features and requirements and the data related to HUS. Then, during two rounds of the Delphi technique (the first round with 23 participants and the second round with 18 participants), the model of this registry was finalized based on the agreement of at least 75% of specialists. At the next step, based on the agreed requirements, IRI.HUS.Reg (Iranian Hemolytic Uremic Syndrome Registry) software was developed and implemented in a pediatric hospital.

Results

We classified 369 meaning units of interviews in 41 codes and 7 final themes including purposes of the registry (10 codes), inclusion criteria (7 codes), data collection method (4 codes), data quality control (6 codes), data sources (4 codes), data analysis (3 codes) and software features (7 codes). These 7 feature groups (67 subgroups) and 12 data classes (138 data elements) include demographic data, referrals, examinations, clinical signs, causes, laboratory tests, medical histories, paraclinical measures, treatments, outcomes, patient’s status at discharge, and follow-up data were reviewed by the Delphi panelists, and finally, 64 features and 131 data elements were accepted by at least 78% agreement. Then, we developed and implemented a registry software system in a hospital.

Conclusion

We implemented IRI.HUS.Reg based on related features, 12 data classes agreed by specialists, literature review, and comparison with other existing registries. Therefore, the data collected in this registry can be compared with other data from existing registries in other countries.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13023-022-02376-9.

Genetic continuity of Indo-Iranian speakers since the Iron Age in southern Central Asia

Since prehistoric times, southern Central Asia has been at the crossroads of the movement of people, culture, and goods. Today, the Central Asian populations are divided into two cultural and linguistic groups: the Indo-Iranian and the Turko-Mongolian groups. Previous genetic studies unveiled that migrations from East Asia contributed to the spread of Turko-Mongolian populations in Central Asia and the partial replacement of the Indo-Iranian populations. However, little is known about the origin of the latters. To shed light on this, we compare the genetic data on two current-day Indo-Iranian populations — Yaghnobis and Tajiks — with genome-wide data from published ancient individuals. The present Indo-Iranian populations from Central Asia display a strong genetic continuity with Iron Age samples from Turkmenistan and Tajikistan. We model Yaghnobis as a mixture of 93% Iron Age individual from Turkmenistan and 7% from Baikal. For the Tajiks, we observe a higher Baikal ancestry and an additional admixture event with a South Asian population. Our results, therefore, suggest that in addition to a complex history, Central Asia shows a remarkable genetic continuity since the Iron Age, with only limited gene flow.

The significant role of a functional polymorphism in the NF-κB1 gene in breast cancer: evidence from an Iranian cohort

Aims: Breast cancer (BC) is one of the most common cancers among women. The influence of genetic variations on BC risk has been thus far assessed via genome-wide association studies. NF-κB has been recognized as a major player in BC progression. In this study, the association between rs28362491 and BC was evaluated in a population from northeastern Iran. Materials & methods: This study was conducted on 476 patients with BC and 524 healthy controls. The genotyping method used was an amplification-refractory mutation system. Results: The INS/DEL genotype conferred a statistically significant increased risk in patients in comparison with controls. Additionally, in the recessive model, INS/INS + INS/DEL versus DEL/DEL was statistically significant (OR = 0.34; 95% CI: 0.12-0.96; p = 0.042). Conclusion: This study found that rs28362491, as a susceptibility genetic factor, may affect BC risk in the Iranian population.

The genetic structure of the Turkish population reveals high levels of variation and admixture

The construction of population-based variomes has contributed substantially to our understanding of the genetic basis of human inherited disease. Here, we investigated the genetic structure of Turkey from 3,362 unrelated subjects whose whole exomes (n = 2,589) or whole genomes (n = 773) were sequenced to generate a Turkish (TR) Variome that should serve to facilitate disease gene discovery in Turkey. Consistent with the history of present-day Turkey as a crossroads between Europe and Asia, we found extensive admixture between Balkan, Caucasus, Middle Eastern, and European populations with a closer genetic relationship of the TR population to Europeans than hitherto appreciated. We determined that 50% of TR individuals had high inbreeding coefficients (≥0.0156) with runs of homozygosity longer than 4 Mb being found exclusively in the TR population when compared to 1000 Genomes Project populations. We also found that 28% of exome and 49% of genome variants in the very rare range (allele frequency < 0.005) are unique to the modern TR population. We annotated these variants based on their functional consequences to establish a TR Variome containing alleles of potential medical relevance, a repository of homozygous loss-of-function variants and a TR reference panel for genotype imputation using high-quality haplotypes, to facilitate genome-wide association studies. In addition to providing information on the genetic structure of the modern TR population, these data provide an invaluable resource for future studies to identify variants that are associated with specific phenotypes as well as establishing the phenotypic consequences of mutations in specific genes.

Exome sequencing utility in defining the genetic landscape of hearing loss and novel-gene discovery in Iran

Hearing loss (HL) is one of the most common sensory defects affecting more than 466 million individuals worldwide. It is clinically and genetically heterogeneous with over 120 genes causing non-syndromic HL identified to date. Here, we performed exome sequencing (ES) on a cohort of Iranian families with no disease-causing variants in known deafness-associated genes after screening with a targeted gene panel. We identified likely causal variants in 20 out of 71 families screened. Fifteen families segregated variants in known deafness-associated genes. Eight families segregated variants in novel candidate genes for HL: DBH, TOP3A, COX18, USP31, TCF19, SCP2, TENM1, and CARMIL1. In the three of these families, intrafamilial locus heterogeneity was observed with variants in both known and novel candidate genes. In aggregate, we were able to identify the underlying genetic cause of HL in nearly 30% of our study cohort using ES. This study corroborates the observation that high-throughput DNA sequencing in populations with high rates of consanguineous marriages represents a more appropriate strategy to elucidate the genetic etiology of heterogeneous conditions such as HL.

Long term prognostic implication of newly detected abnormal glucose tolerance among patients with stable cardiovascular disease: a population-based cohort study

Background

Fasting plasma glucose (FPG) and 2-h post challenge plasma glucose (2 h-PCPG), whether as continuous or categorical variables, are associated with incident cardiovascular disease (CVD) and diabetes; however, their role among patients with existing CVD is a matter of debate. We aimed to evaluate associations of different glucose intolerance states with recurrent CVD and incident diabetes among subjects with previous CVD.

Methods

From a prospective population-based cohort, 408 Iranians aged  ≥  30 years, with history of CVD and without known diabetes were included. Associations of impaired fasting glucose (IFG) according to the American Diabetes Association (ADA) and World Health Organization (WHO) criteria, impaired glucose tolerance (IGT), newly diagnosed diabetes (NDM) with outcomes of interest were determined by multivariable Cox proportional hazard models after adjustment for traditional risk factors. Furthermore, FPG and 2 h-PCPG were entered as continuous variables.

Results

Over a decade of follow-up, 220 CVD events including 89 hard events (death, myocardial infarction and stroke) occurred. Regarding prediabetes, only IFG-ADA was associated with increased risk of hard CVD [hazard ratio(HR), 95%CI: 1.62,1.03–2.57] in the age-sex adjusted model. In patients with NDM, those with FPG ≥ 7 mmol/L were at higher risk of incident CVD/coronary heart disease(CHD) and their related hard outcomes (HR ranged from 1.89 to 2.84, all P < 0.05). Moreover, those with 2 h-PCPG ≥ 11.1 mmol/L had significant higher risk of CVD (1.46,1.02–2.11), CHD (1.46,1.00–2.15) and hard CHD (1.95:0.99–3.85, P = 0.05). In the fully adjusted model, each 1 SD increase in FPG was associated with 20, 27, 15 and 25% higher risk of CVD, hard CVD, CHD and hard CHD, respectively; moreover each 1 SD higher 2 h-PCPG was associated with 21% and 16% higher risk of CVD, and CHD, respectively. Among individuals free of diabetes at baseline (n = 361), IFG-ADA, IFG-WHO and IGT were significantly associated with incident diabetes (all P < 0.05); significant associations were also found for FPG and 2 h-PCPG as continuous variables (all HRs for 1-SD increase > 2, P < 0.05).

Conclusions

Among subjects with stable CVD, NDM whether as high FPG or 2 h-PCPG, but not pre-diabetes status was significantly associated with CVD/CHD and related hard outcomes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-021-02950-y.

Clinical characteristics, gastrointestinal manifestations and outcomes of COVID-19 patients in Iran; does the location matters?

BACKGROUND

Coronavirus disease 2019 (COVID-19) started in Asia, and Iran was one of its first epicenters.

AIM

To study the gastrointestinal (GI) symptoms and comorbidities associated with this pandemic in four different regions of Iran.

METHODS

We analyzed data from severe acute respiratory syndrome coronavirus 2 positive patients evaluated at four hospitals of Iran (n = 91), including South (Shiraz), Southeast (Dezful), Rasht (North), and Northwest (Mashhad) between April and September 2020. Demographics, comorbidities and clinical findings including GI symptoms were collected. Statistical descriptive analysis and correlation analyses of symptoms, comorbidities, and mortality were performed.

RESULTS

The average age of COVID-19 patients was 51.1 years, and 56% were male. Mortality rate was 17%. Cough with 84.6%, shortness of breath with 71.4%, fever with 52.7%, and loss of appetite with 43.9% were the main symptoms. Overall cardiac disease was the most common comorbidity with an average of 28.5% followed by hypertension (28.5%) and diabetes (25.2%). The highest comorbidity in North (Rasht) was diabetes (30%) and in South (Dezful) hypertension (37%). Shiraz leads cardiac disease with 43.4%. The most reported GI symptoms included nausea, diarrhea, vomiting, and abdominal pain, with 42.8%, 31.8%, 26.8%, and 12% prevalence, respectively. In addition, albumin, alkaline phosphatase, aspartate aminotransferase, and alanine aminotransferase were elevated in 26.3%.

CONCLUSION

Our results show hypertension and diabetes as the most common comorbidities, but their distribution was different in COVID-19 patients in the four studied regions of Iran. Nausea, diarrhea, and elevated liver enzymes were the most common GI symptoms. There was also a high mortality rate that was associated with high infection rates in Iran at the beginning of the pandemic.

Exome sequencing reveals novel rare variants in Iranian familial multiple sclerosis: The importance of POLD2 in the disease pathogenesis

The prevalence of familial multiple sclerosis (FMS) is increasing worldwide which endorses the heritability of the disease. Given that many genome variations are ethnicity-specific and consanguineous marriage could affect genetic diseases, hereditary disease gene analysis among FMS patients from Iran, a country with high rates of parental consanguinity, could be highly effective in finding mutations underlying disease pathogenesis. To examine rare genetic mutations, we selected three Iranian FMS cases with ≥3 MS patients in more than one generation and performed whole exome sequencing. We identified a homozygous rare missense variant in POLD2 (p. Arg141Cys; rs372336011). Molecular dynamics analysis showed reduced polar dehydration energy and conformational changes in POLD2 mutant. Further, we found a heterozygote rare missense variant in NBFP1 (p. Gly487Asp; rs778806175). Our study revealed the possible role of novel rare variants in FMS. Molecular dynamic simulation provided the initial evidence of the structural changes behind POLD2 mutant.

Cigarette Smoking Behavior a Gateway to Opium Use Disorder: A Mendelian Randomization Analysis

Gateway hypothesis presumes that using a psychotropic drug can increase the probability of using another drug. The study was to assess whether cigarette smoking is a gateway drug for subsequent opium use. Mendelian randomization (MR) analysis was applied to test and estimate the size of causal effect of cigarette smoking on opium use. The CHRNA3 rs1051730 polymorphism was used as an instrumental variable. A population-based case control study in the setting of Fasa Cohort Study was carried out using 477 cases and 531 controls based on their opium use status at the baseline of cohort study. The logistic two stage estimator method was applied. The Number of cigarettes smoked per day was associated with opium use (OR 1.17, 95% CI 1.15-1.19). In the MR analysis, rs1051730 T alleles were associated with increased risk of opium use among ever smokers (OR 5.73, 95% CI 1.72-19.07) however there found no evidence of association among never smokers. In instrumental variable analysis, showed that on average smoking every 1 more cigarette per day increases the odds of opium use by 1.17 (OR 1.17, 95%CI:1.14-1.19). The MR analysis found a positive finding on the relationship between cigarette smoking and opium use which supports the gateway hypothesis. It adds new information to the gateway theory regarding the relation of cigarette smoking and drug use, and increases our understanding of the importance of tobacco control for prevention of opium addiction.

Human genetic admixture

Throughout human history, large-scale migrations have facilitated the formation of populations with ancestry from multiple previously separated populations. This process leads to subsequent shuffling of genetic ancestry through recombination, producing variation in ancestry between populations, among individuals in a population, and along the genome within an individual. Recent methodological and empirical developments have elucidated the genomic signatures of this admixture process, bringing previously understudied admixed populations to the forefront of population and medical genetics. Under this theme, we present a collection of recent PLOS Genetics publications that exemplify recent progress in human genetic admixture studies, and we discuss potential areas for future work.

Pharmacogenomics Implementation and Hurdles to Overcome; In the Context of a Developing Country

Having multiple dimensions, uncertainties and several stakeholders, the costly pharmacogenomics (PGx) is associated with dynamic implementation complexities. Identification of these challenges is critical to harness its full potential, especially in developing countries with fragile healthcare systems and scarce resources. This is the first study aimed to identify most salient challenges related to PGx implementation, with respect to the experiences of early-adopters and local experts' prospects, in the context of a developing country in the Middle East. To perform a comprehensive reconnaissance on PGx adoption challenges a scoping literature review was conducted based on national drug policy components: efficacy/safety, access, affordability and rational use of medicine (RUM). Strategic option development and analysis workshop method with cognitive mapping as the technique was used to evaluate challenges in the context of Iran. The cognitive maps were face-validated and analyzed via Decision Explorer XML. The findings indicated a complex network of issues relative to PGx adoption, categorized in national drug policy indicators. In the rational use of medicine category, ethics, education, bench -to- bedside strategies, guidelines, compliance, and health system issues were found. Clinical trial issues, test's utility, and biomarker validation were identified in the efficacy group. Affordability included pricing, reimbursement, and value assessment issues. Finally, access category included regulation, availability, and stakeholder management challenges. The current study identified the most significant challenges ahead of clinical implementation of PGx in a developing country. This could be the basis of a policy-note development in future work, which may consolidate vital communication among stakeholders and accelerate the efficient implementation in developing new-comer countries.

Studying the Effects of ACE2 Mutations on the Stability, Dynamics, and Dissociation Process of SARS-CoV-2 S1/hACE2 Complexes

A highly infectious coronavirus, SARS-CoV-2, has spread in many countries. This virus recognizes its receptor, angiotensin-converting enzyme 2 (ACE2), using the receptor binding domain of its spike protein subunit S1. Many missense mutations are reported in various human populations for the ACE2 gene. In the current study, we predict the affinity of many ACE2 variants for binding to S1 protein using different computational approaches. The dissociation process of S1 from some variants of ACE2 is studied in the current work by molecular dynamics approaches. We study the relation between structural dynamics of ACE2 in closed and open states and its affinity for S1 protein of SARS-CoV-2.

A Rare Mutation in the MARVELD2 Gene Can Cause Nonsyndromic Hearing Loss

The MARVELD2 gene which is located on the 5q13.2 may cause nonsyndromic hearing loss (NSHL) with autosomal recessive inherited pattern. So far c.1331+1G>A (IVS4+1G>A); NM_001038603.3, variant in deafness, has only reported previously in one Pakistani family in 2008 and it is reported for the first time in Iran and second time in the world. The case is a 21-year-old Iranian woman who has NSHL referred for genetic consultation, and her parents had a consanguineous marriage. To study the responsible genes for the mentioned disorder, whole exome sequencing (WES) was performed for the case. The result of WES analysis revealed a transition at the splice donor variant site of the MARVELD2 gene. The NGS result was confirmed by Sanger sequencing.

High genetic burden of type 2 diabetes can promote the high prevalence of disease: a longitudinal cohort study in Iran

Type 2 diabetes (T2D) is emerging as one of the serious public health issues in both developed and developing counties. Here, we surveyed the worldwide population differentiation in T2D-associated variants and assessed the genetic burden of the disease in an ongoing Tehran Cardio-Metabolic Genetic Study (TCGS) cohort represented the Iranian population. We found multiple SNPs that were significantly depleted or enriched in at least one of the five populations of 1,000 Genome Project (African, American, East Asian, European, and South Asian) as well as the Iranian population. Interestingly, TCF7L2, a well-known associated gene with T2D, harbors the highest number of enriched risk alleles almost in all populations except for East Asian, where this gene embraces the largest number of significantly depleted risk alleles. The polygenic risk score (PRS) of the enriched risk alleles was calculated for 1,867 diabetic and 2,855 non-diabetic participants in the TCGS cohort, interestingly demonstrating that the risk of developing T2D was almost two times higher in top PRS quintile compared with the lowest quintile after adjusting for other known risk factors.

KIR Variation in Iranians Combines High Haplotype and Allotype Diversity With an Abundance of Functional Inhibitory Receptors

Natural killer (NK) cells are innate lymphocytes that eliminate infected and transformed cells. They discriminate healthy from diseased tissue through killer cell Ig-like receptor (KIR) recognition of HLA class I ligands. Directly impacting NK cell function, KIR polymorphism associates with infection control and multiple autoimmune and pregnancy syndromes. Here we analyze KIR diversity of 241 individuals from five groups of Iranians. These five populations represent Baloch, Kurd, and Lur, together comprising 15% of the ethnically diverse Iranian population. We identified 159 KIR alleles, including 11 not previously characterized. We also identified 170 centromeric and 94 telomeric haplotypes, and 15 different KIR haplotypes carrying either a deletion or duplication encompassing one or more complete KIR genes. As expected, comparing our data with those representing major worldwide populations revealed the greatest similarity between Iranians and Europeans. Despite this similarity we observed higher frequencies of KIR3DL1^*001 in Iran than any other population, and the highest frequency of HLA-B^*51, a Bw4-containing allotype that acts as a strong educator of KIR3DL1^*001⁺ NK cells. Compared to Europeans, the Iranians we studied also have a reduced frequency of 3DL1^*004, which encodes an allotype that is not expressed at the NK cell surface. Concurrent with the resulting high frequency of strong viable interactions between inhibitory KIR and polymorphic HLA class I, the majority of KIR-A haplotypes characterized do not express a functional activating receptor. By contrast, the most frequent KIR-B haplotype in Iran expresses only one functional inhibitory KIR and the maximum number of activating KIR. This first complete, high-resolution, characterization of the KIR locus of Iranians will form a valuable reference for future clinical and population studies.

Prevalence of CCR5delta32 in Northeastern Iran

Background

A 32-base pair deletion (∆32) in the open reading frame (ORF) of C-C motif chemokine receptor 5 (CCR5) seems to be a protective variant against immune system diseases, especially human immunodeficiency virus type 1 (HIV-1). We aimed to assess the frequency of CCR5∆32 in the healthy Iranian population.

Methods

In this study, 400 normal samples from Khorasan, northeastern Iran, were randomly selected. The frequency of CCR5∆32 carriers was investigated using PCR analysis. Allele prevalence and the fit to the Hardy-Weinberg equilibrium were analyzed.

Results

The prevalence of CCR5∆32 in the northeastern population of Iran was 0.016. Four hundred samples were studied, among which one with CCR5^∆32/∆32 and 11 with CCR5^Wild/∆32 genotype were detected.

Conclusion

This study was the first investigation for an assessment of the prevalence of CCR5∆32 in northeastern Iran. The low prevalence of CCR5∆32 allele in the Iranian population may result in the increased susceptibility to HIV-1. In addition, this prevalence is the same as that of reported in East Asia, while is lower than that in the Europeans.