Arab gene geography: From population diversities to personalized medical genomics

Exploring Public Knowledge, Attitudes, and Barriers to Using Genetic Services in Damanhur City and Beni-Suef City, Egypt: A Cross-Sectional Study

BACKGROUND

Advancements in genetic disorder management mark a transformative era in healthcare. This study aimed to assess knowledge, attitudes, and barriers to using genetic services among the Egyptian population.

METHODS

A cross-sectional study was used to achieve the aim of the study. A convenient sample was used to involve 385 residents of Damanhur City and Beni-Suef City to represent Upper and Lower Egypt. A validated questionnaire covering socio-demographic details, genetic knowledge, attitudes, and perceived barriers to using genetic services was used.

RESULTS

Regarding genetic knowledge, 70.9% of the participants reported an unsatisfactory level of knowledge about genetics. Furthermore, 67.6% expressed a negative attitude toward genetic services. Concerns about whether the test result is positive were the most common obstacle, cited by 64.94% of participants, followed by cost, which 60.78% of people found to be a major barrier. Significant associations emerge between socio-demographic factors and awareness levels.

CONCLUSION

The findings illuminate significant gaps in knowledge and attitude levels where less than a third of the participants had a satisfactory level of knowledge and about one-third had a positive attitude regarding genetic testing. Barriers such as concerns about treatment strategies, financial constraints, and conflict with personal beliefs emerge as critical obstacles. The identified associations between socio-demographic factors and awareness levels underscore the need for targeted interventions tailored to specific demographic groups.

RECOMMENDATIONS

This study recommends developing and implementing culturally sensitive awareness campaigns about genetics tailored to the specific demographic characteristics of the Egyptian population.

Arginase 1 Deficiency: using genetic databases as a tool to establish global prevalence

BACKGROUND/OBJECTIVE

Arginase 1 Deficiency (ARG1-D) is a rare inherited metabolic disease with progressive, devastating neurological manifestations with early mortality and high unmet need. Information on prevalence is scarce and highly variable due to limited newborn screening (NBS) availability, variability of arginine levels in the first days of life, and high rates of misdiagnosis. US birth prevalence was recently estimated via indirect methods at 1.1 cases per million live births. Due to the autosomal recessive nature of ARG1-D we hypothesize that the global prevalence may be more accurately estimated using genetic population databases.

METHODS

MEDLINE and EMBASE were systematically searched for previously reported disease variants. Disease variants in ARG1-D were annotated wherever possible with allele frequencies from gnomAD. Ethnicity-specific prevalence was calculated using the Hardy-Weinberg equation and applied to generate country-specific carrier frequencies for 38 countries. Finally, documented consanguinity rates were applied to establish a birth prevalence for each country.

RESULTS

133 of 228 (58%) known causative alleles were annotated with ethnic-specific frequencies. Global birth prevalence for ARG1-D was estimated at 2.8 cases per million live births (country-specific estimates ranged from 0.92 to 17.5) and population prevalence to be 1.4 cases per million people (approximately 1/726,000 people). Birth prevalence estimates were dependent on population demographics and consanguinity rate.

CONCLUSION

Birth prevalence of ARG1-D based on genetic database analysis was estimated to be more frequent than previous NBS studies have indicated. There was a higher degree of confidence in North American and European countries due to availability of genetic databases and mutational analysis versus other regions. These findings suggest the need for greater disease education around signs and manifestations of ARG1-D, as well as more widespread testing and standardization of screening for this severe disease in order to appropriately identify patients prior to disease progression.

Molecular Spectra and Frequency Patterns of Somatic Mutations in Arab Women with Breast Cancer

BACKGROUND

The role of somatic mutations in breast cancer prognosis and management continues to be recognized. However, data on the molecular profiles of Arab women are limited.

MATERIALS AND METHODS

This was a cross-sectional study based on medical chart review of all Arab women diagnosed with breast cancer at a single institution between 2010 and 2018 who underwent next-generation sequencing with Ampliseq 46-Gene or 50-Gene.

RESULTS

A total of 78 Arab women were identified, with a median age at diagnosis of 52.3 years (range: 37-82 years; 38.5% ≤50 years). The majority of patients had stage III or IV disease (74.4%). Next-generation sequencing revealed the following somatic mutation rates: TP53, 23.1%; ATM, 2.6%; IDH1, 2.6%; IDH2, 3.8%; PTEN, 7.7%; PIK3CA, 15.4%; APC, 7.7%; NPM1, 2.5%; MPL, 1.3%; JAK2, 2.5%; KIT, 7.7%; KRAS, 3.8%; and NRAS, 3.8%.

CONCLUSION

Our study illustrates frequencies of somatic mutations in Arab women with breast cancer and suggests potential variations from estimates reported in the Western population. These data calls for larger epidemiologic studies considering the evolving role of such mutations in prognostication and personalized management.

HER2 overexpression is a putative diagnostic and prognostic biomarker for late-stage colorectal cancer in North African patients

Aim: Colorectal cancer (CRC) is one of the leading cancers in the world. Even though its mortality and pathophysiology are well documented in the US and the European countries, it is seldom studied in North African population. Recent studies have shown link of HER2 overexpression in oesophageal and gastric cancers. The aim of this study is to assess the HER2 protein and mRNA expression and its correlation with tumor pathogenesis in Libyan CRC patients.

Methodology: A total of 17 FFPE tissue blocks were collected from patients with primary CRC. The HER2 protein expression was assessed by immunohistochemistry and the mRNA expression was assessed using qRT-PCR. Survival analysis of the role of HER2 overexpression on rectal adenocarcinoma was carried out on additional 165 patients.

Results: From the CRC cohort, adenocarcinoma was found to be more frequent accounting for 88.2%, and 11.8% for mucinous adenocarcinomas. Almost 47% of the cases were positive for HER2 (score ≥ 2+) and about 50% adenocarcinoma cases with tumor grade II were positive for HER2. Moreover, 57.4% adenocarcinoma patients with grade-II tumor had undergone right hemicolectomy. Furthermore, significant correlation (p = 0.03) between the HER2 mRNA expression with the tumor grade was observed. In addition, poor overall all survival was observed with high HER2 expression in rectum adenocarcinoma.

Conclusion: To our knowledge, this is the first study that HER2 overexpression correlates with more aggressive colorectal cancer in North African population. Our study shows that HER2 overexpression associates with right colon surgeries. Also, the correlation of mRNA and protein expression could warrant the implementation of a nationwide screening program for HER2 positivity in CRC patients. Taken together, stratifying patients according to HER2 expression can help in the diagnosis and prognosis of CRC patients from North African origin.

Unraveling a fine-scale high genetic heterogeneity and recent continental connections of an Arabian Peninsula population

Recent studies have showed the diverse genetic architecture of the highly consanguineous populations inhabiting the Arabian Peninsula. Consanguinity coupled with heterogeneity is complex and makes it difficult to understand the bases of population-specific genetic diseases in the region. Therefore, comprehensive genetic characterization of the populations at the finest scale is warranted. Here, we revisit the genetic structure of the Kuwait population by analyzing genome-wide single nucleotide polymorphisms data from 583 Kuwaiti individuals sorted into three subgroups. We envisage a diverse demographic genetic history among the three subgroups based on drift and allelic sharing with modern and ancient individuals. Furthermore, our comprehensive haplotype-based analyses disclose a high genetic heterogeneity among the Kuwaiti populations. We infer the major sources of ancestry within the newly defined groups; one with an obvious predominance of sub-Saharan/Western Africa mostly comprising Kuwait-B individuals, and other with West Eurasia including Kuwait-P and Kuwait-S individuals. Overall, our results recapitulate the historical population movements and reaffirm the genetic imprints of the legacy of continental trading in the region. Such deciphering of fine-scale population structure and their regional genetic heterogeneity would provide clues to the uncharted areas of disease-gene discovery and related associations in populations inhabiting the Arabian Peninsula.

DALIA- a comprehensive resource of Disease Alleles in Arab population

The Arab population encompasses over 420 million people characterized by genetic admixture and a consequent rich genetic diversity. A number of genetic diseases have been reported for the first time from the population. Additionally a high prevalence of some genetic diseases including autosomal recessive disorders such as hemoglobinopathies and familial mediterranean fever have been found in the population and across the region. There is a paucity of databases cataloguing genetic variants of clinical relevance from the population. The availability of such a catalog could have implications in precise diagnosis, genetic epidemiology and prevention of disease. To fill in the gap, we have compiled DALIA, a comprehensive compendium of genetic variants reported in literature and implicated in genetic diseases reported from the Arab population. The database aims to act as an effective resource for population-scale and sub-population specific variant analyses, enabling a ready reference aiding clinical interpretation of genetic variants, genetic epidemiology, as well as facilitating rapid screening and a quick reference for evaluating evidence on genetic diseases.

Clinicopathological characteristics of gene-positive breast cancer in the United Arab Emirates

Introduction

Breast cancer is the most prevalent cancer in the United Arab Emirates (UAE). This is the first study to provide data on predisposition of breast cancer susceptibility genes with associated clinical and pathological aspects in the UAE.

Material & methods

A retrospective chart review for breast cancer patients undergoing genetic testing from 2016 to 2018. According to National Comprehensive Cancer Network (NCCN) guidelines genetic testing was offered. The analyzed data included; age, ethnicity, family cancer history, pathogenic variant, histopathology, stage, molecular subtype and proliferation.

Results

309 patients underwent genetic testing with a positive result in 130 patients (11.9%) over a period of 36 months. In 34.6% pathogenic and likely pathogenic variants were identified. BRCA2 was the most common gene identified. The mean age was 42.9 years (±9.01). Positive family history was identified in 66 patients (50.7%). Majority had stage 1 or 2 disease (66.2%), invasive ductal carcinoma (81.5%) and hormone receptor positive cancer (45.3%).

Conclusions

This is the first study in the UAE to describe the clinical and pathological characteristics of hereditary breast cancer in a mixed ethnic group with dominant Arabic population. Further genetic studies will be required in the UAE population, as the prevalence of breast cancer continues to rise.

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First study about breast cancer genetics in the United Arab Emirates with a mixed ethnic population.

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BRCA2 is the most common mutation detected.

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Most hereditary breast cancers with a dominant Arabic ethnic group is diagnosed at a lower stage.

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Most hereditary breast cancers diagnosed a decade earlier compared to western population.

Genome-Wide Selection Scan in an Arabian Peninsula Population Identifies a TNKS Haplotype Linked to Metabolic Traits and Hypertension

Despite the extreme and varying environmental conditions prevalent in the Arabian Peninsula, it has experienced several waves of human migrations following the out-of-Africa diaspora. Eventually, the inhabitants of the peninsula region adapted to the hot and dry environment. The adaptation and natural selection that shaped the extant human populations of the Arabian Peninsula region have been scarcely studied. In an attempt to explore natural selection in the region, we analyzed 662,750 variants in 583 Kuwaiti individuals. We searched for regions in the genome that display signatures of positive selection in the Kuwaiti population using an integrative approach in a conservative manner. We highlight a haplotype overlapping TNKS that showed strong signals of positive selection based on the results of the multiple selection tests conducted (integrated Haplotype Score, Cross Population Extended Haplotype Homozygosity, Population Branch Statistics, and log-likelihood ratio scores). Notably, the TNKS haplotype under selection potentially conferred a fitness advantage to the Kuwaiti ancestors for surviving in the harsh environment while posing a major health risk to present-day Kuwaitis.

Discovering Novel Biochemical and Genetic Markers for Coronary Heart Disease in Qatari Individuals: The Initiative Qatar Cardiovascular Biorepository

Background:

We aimed to describe the creation and challenge of a DNA and plasma biorepository (Qatar Cardiovascular Biorepository) with linkage to the electronic health record of cardiovascular risk factors to facilitate discovery of novel genetic and proteomic biomarkers for coronary heart disease in Qatari individuals.

Methods:

A prospective case–control study was conducted between October 2013 and February 2018. CHD was defined as a history of an acute coronary syndrome (myocardial infarction [MI]/unstable angina) or coronary revascularization. Controls were identified from blood donors who had no history of coronary heart diesase. After informed consent, blood samples were obtained for DNA and plasma. Demographic, laboratory, and clinical variables were derived from the electronic medical record, and information regarding history of cardiovascular diseases and risk factors was collected from surveys. Challenges in establishing the biorepository were noted, and processes to promote use of the biorepository by Qatari investigators were put in place.

Results:

During the study period, 2671 individuals were approached; of them, 2087 participants were recruited (1029 patients and 1058 controls). Relevant risk factors were ascertained from the electronic health record and surveys. The mean age was 49 ± 16 years, with 61% males. Challenges included setting up the infrastructure for qatar cardiovascular biorepository, developing an informed consent document in Arabic/English, and meeting target recruitment goals. The prevalence of diabetes mellitus, hypertension, dyslipidemia, and smoking was 41%, 44.5%, 40%, and 19%, respectively. History of myocardial infarction, percutaneous coronary intervention, and coronary artery bypass surgery was 55%, 68%, and 17%, respectively, among patients.

Conclusions:

This study addresses the challenges in setting up qatar cardiovascular biorepository, the first cardiovascular genomics biorepository in the Arab Middle Eastern region. QCBio is a unique resource for identifying genetic susceptibility variants and novel circulating markers for coronary heart disease in Qatari adults and enables individualized assessment of risk for coronary heart disease.

Parkinson's Disease in the Middle East, North Africa, and South Asia: Consensus from the International Parkinson and Movement Disorder Society Task Force for the Middle East

BACKGROUND

Understanding the regional needs and available healthcare resources to treat Parkinson's disease (PD) is essential to plan appropriate future priorities. The International Parkinson and Movement Disorder Society (MDS) Task Force for the Middle East was established to raise awareness and promote education across the region on PD and other movement disorders. Broadly, the task force encompasses the countries of the Middle East but has included North Africa and South Asia as well (MENASA).

OBJECTIVE

To create a list of needs and priorities in the advancement of PD in MENASA countries based on consensuses generated by the MDS task force for the Middle East.

METHODS

A Strengths Weaknesses-Opportunities-Threats (SWOT) analysis was conducted by the task force members to generate consensus about PD care this region.

RESULTS

Eight overarching principles emerged for the consensus statement on current needs: more movement disorders specialists, multidisciplinary care, accurate epidemiologic data, educational programs, availability of drugs, and availability of more advanced therapy, enhanced health care resources and infrastructure, and greater levels of awareness within the general population and among health care professionals.

CONCLUSION

This pilot study sheds light on unmet needs for providing care to people with PD in the MENASA region. These data offer directions on priorities to increase awareness of PD, to develop better infrastructure for research and management of PD, to foster healthcare policy discussions for PD and to provide educational opportunities within these countries.

Association between ESR1, ESR2, HER2, UGT1A4, and UGT2B7 polymorphisms and breast Cancer in Jordan: a case-control study

BACKGROUND

Breast cancer risk, development, and treatment are influenced by genetic variation in certain genes, namely those involved in cell proliferation, tumor suppression, and drug metabolism. In turn, the relevance of the aforementioned genetic variation to cancer depends on the ethnic group in question, highlighting the need for population-specific association studies. Therefore, the objective of the present study was to investigate the association between certain ESR1, ESR2, HER2, UGT1A4, and UGT2B7 single nucleotide polymorphisms and breast cancer.

METHODS

Blood samples were collected from 437 Jordanian-Arab breast cancer patients and healthy volunteers and subject to genotyping using the Sequenom MassARRAY® system (iPLEX GOLD).

RESULTS

Our findings show a significant association between breast cancer and the allelic (P = 0.02486879) and genotypic (P = 0.04793066) frequencies of the ESR1 polymorphism rs3798577, a result which was confirmed in different genetic models. No other investigated polymorphism showed a significant association with breast cancer itself in Jordanian Arabs, but the Rare Hz (GG) vs Het (AG) genetic model revealed an association of the disease with the ESR1 polymorphism rs3798577. However, several associations were found between certain polymorphisms and breast cancer's prognostic factors.

CONCLUSION

This study suggests that certain polymorphisms may increase the risk of breast cancer in the Jordanian-Arab population. Future research and clinical translation could incorporate the current results in preventative breast cancer approaches tailored for Jordanian-Arab patients.

Characterization of BRCA1 and BRCA2 genetic variants in a cohort of Bahraini breast cancer patients using next-generation sequencing

Background

Breast cancer is the most common malignancy in women worldwide. About 5%–10% are due to hereditary predisposition. The contribution of BRCA1/2 mutations to familial breast cancer in Bahrain has not been explored. The objective of this study was to investigate the spectrum of BRCA1/2 genetic variants and estimate their frequencies in familial breast cancer. We also aim to test the efficiency of the next‐generation sequencing (NGS) as a powerful tool for detecting genetic variation within BRCA1/2 genes.

Methods

Twenty‐five unrelated female patients diagnosed with familial breast cancer were screened for BRCA1/2 variants. All targeted coding exons and exon–intron boundaries of BRCA1/2 genes were amplified with 167 pairs of primers by NGS.

Results

We have identified two deleterious BRCA1/2 variants in two patients, one in BRCA1 gene (c.4850C>A) and other in BRCA2 gene (c.67+2T>C). In addition to the deleterious variants, we identified 24 distinct missense variants of uncertain significance, 10 of them are seen to confer minor but cumulatively significant risk of breast cancer.

Conclusion

Our data suggest that BRCA1/2 variants may contribute to the pathogenesis of familial breast cancer in Bahrain. It also shows that NGS is useful tool for screening BRCA1/2 genetic variants of probands and unaffected relatives.

HLA class I allele lineages and haplotype frequencies in Arabs of the United Arab Emirates

The high degree of polymorphism of the HLA system provides suitable genetic markers to study the diversity and migration of different world populations and is beneficial for forensic identification, anthropology, transplantation and disease associations. Although the United Arab Emirates (UAE) population of about nine million people is heterogeneous, information is limited for the HLA class I allele and haplotype frequencies of the Bedouin ethnic group. We performed low-resolution PCR-SSP genotyping of three HLA class I loci at HLA-A, -B and -C for 95 unrelated healthy Bedouins from the cities of Al Ain and Abu Dhabi in the UAE. A total of 54 HLA allele lineages were detected; the most frequent low-resolution allele lineages at each HLA locus were A*02 (0.268), B*51 (0.163) and C*07 (0.216). The inferred estimates for the two most frequent HLA-A and HLA-B haplotypes were HLA-A*02 ~ HLA-B*50 (0.070) and HLA-A*02 ~ HLA-B*51 (0.051), and the most frequent 3-locus haplotype was HLA-A*02 ~ HLA-B*50 ~ HLA-C*06 (0.068). The HLA allele lineage frequencies of the UAE Arabs were compared to those previously reported for 70 other world populations, and a strong genetic similarity was detected between the UAE Arabs and the Saudi Arabians from the west with evidence of a limited gene flow between the UAE Arabs and Pakistani across the Gulf from the east, and the UAE Arabs and Omani from the south of the Gulf Peninsula.

Genetics and genomic medicine in Tunisia

Genetics and genomic medicine in Tunisia.

Genetic risk variants for metabolic traits in Arab populations

Despite a high prevalence of metabolic trait related diseases in Arabian Peninsula, there is a lack of convincingly identified genetic determinants for metabolic traits in this population. Arab populations are underrepresented in global genome-wide association studies. We genotyped 1965 unrelated Arab individuals from Kuwait using Cardio-MetaboChip, and tested SNP associations with 13 metabolic traits. Models based on recessive mode of inheritance identified Chr15:40531386-rs12440118/ZNF106/W->R as a risk variant associated with glycated-hemoglobin at close to ‘genome-wide significant’ p-value and five other risk variants ‘nominally’ associated (p-value ≤ 5.45E-07) with fasting plasma glucose (rs7144734/[OTX2-AS1,RPL3P3]) and triglyceride (rs17501809/PLGRKT; rs11143005/LOC105376072; rs900543/[THSD4,NR2E3]; and Chr12:101494770/IGF1). Furthermore, we identified 33 associations (30 SNPs with 12 traits) with ‘suggestive’ evidence of association (p-value < 1.0E-05); 20 of these operate under recessive mode of inheritance. Two of these ‘suggestive’ associations (rs1800775-CETP/HDL; and rs9326246-BUD13/TGL) showed evidence at genome-wide significance in previous studies on Euro-centric populations. Involvement of many of the identified loci in mediating metabolic traits was supported by literature evidences. The identified loci participate in critical metabolic pathways (such as Ceramide signaling, and Mitogen-Activated Protein Kinase/Extracellular Signal Regulated Kinase signaling). Data from Genotype-Tissue Expression database affirmed that 7 of the identified variants differentially regulate the up/downstream genes that mediate metabolic traits.

Mapping genetic research in non-communicable disease publications in selected Arab countries: first step towards a guided research agenda

Background

In the Arab world, intervention and policy response to non-communicable diseases (NCD) has been weak despite extensive epidemiological evidence highlighting the alarmingly increased prevalence of chronic diseases. Generating genetic information is one key component to promote efficient disease management strategies. This study undertook a scoping review to generate the profile of the undertaken research on genetics of NCD publications in selected Arab countries. An analysis of the research produced examined the extent, range, nature, topic and methods of published research. The study aimed at identifying the gaps in genetic NCD research to inform policy action for NCD prevention and control.

Methods

The scoping review was conducted based on the five-stage methodological framework and included countries in Arab region selected to represent various economies and epidemiological transitions.

Results

The search identified 555 articles that focus on genetics-NCD research in the selected Arab countries over the duration of this study (January 2000 to December 2013). The most commonly conducted research was descriptive and clinically focused, rather than etiologically focused. Country-specific carrier and risk screening studies were not among the top research designs. The genetic component of certain highly heritable diseases, as well as diabetes, obesity, hypertension, chronic lung dysfunction and metabolic syndrome were all under investigated.

Conclusions

This scoping review identified gaps for further research in the context of bioinformatics and genome-wide association studies. Genetic research in the Arab region has to be redirected towards NCDs with the highest morbidity, heritability and health burden within each country. A focused research plan to include community genetics is required for its proper integration in the Arab community.

Different Resting State EEG Features in Children from Switzerland and Saudi Arabia

Background: Cultural neuroscience is an emerging research field concerned with studying the influences of different cultures on brain anatomy and function. In this study, we examined whether different cultural or genetic influences might influence the resting state electroencephalogram (EEG) in young children (mean age 10 years) from Switzerland and Saudi Arabia.

Methods: Resting state EEG recordings were obtained from relatively large groups of healthy children (95 healthy Swiss children and 102 Saudi Arabian children). These EEG data were analyzed using group independent components analyses (gICA) and conventional analyses of spectral data, together with estimations of the underlying intracortical sources, using LORETA software.

Results: We identified many similarities, but also some substantial differences with respect to the resting state EEG data. For Swiss children, we found stronger delta band power values in mesial frontal areas and stronger power values in three out of four frequency bands in occipital areas. For Saudi Arabian children, we uncovered stronger alpha band power over the sensorimotor cortex. The additionally measured theta/beta ratio (TBR) was similar for Swiss and Saudi Arabian children.

Conclusions: The different EEG resting state features identified, are discussed in the context of different cultural experiences and possible genetic influences. In addition, we emphasize the importance of using appropriate EEG databases when comparing resting state EEG features between groups.