Human diversity in Jordan: polymorphic Alu insertions in general Jordanian and Bedouin groups

Tau (MAPT) haplotypes in Jordan: new evidence on the Middle East as a melting-pot predating Neolithic migration

Frequencies of H1 and H2 haplotypes of the microtubule-associated protein tau (MAPT) gene were examined in two Jordanian samples. The criterion for haplotype assignment was the presence/absence of the intronic 238-bp deletion, located between exons 9 and 10 of the MAPT genomic region. We further compiled MAPT haplotype frequencies in Middle Eastern, South Asian, and European populations to widen the scope of analyses. Jordan MAPT*H2 haplotype frequencies peaked among worldwide samples analysed to date, with the Jordan general population featuring the top value (0.386). AMOVA tests results indicated spatial genetic structuring, as they unveiled significant differences in H2 frequencies between South Asia and Europe, with a hypothetical contact zone in the Middle East. The southeastern region of the Middle East shares low H2 frequencies with South Asia, while the northwestern area shows high H2 frequencies, similar to and even higher than observed in Europe. We suggest that high H2 frequencies could have originated at the beginning of the Neolithic in the western region of the Middle East, most likely through genetic drift episodes associated with founding events. Subsequently, the arrival of Neolithic farmers boosted the H2 haplotype spreading throughout Europe.

Unique Variant Spectrum in a Jordanian Cohort with Inherited Retinal Dystrophies

Whole Exome Sequencing (WES) is a powerful approach for detecting sequence variations in the human genome. The aim of this study was to investigate the genetic defects in Jordanian patients with inherited retinal dystrophies (IRDs) using WES. WES was performed on proband patients' DNA samples from 55 Jordanian families. Sanger sequencing was used for validation and segregation analysis of the detected, potential disease-causing variants (DCVs). Thirty-five putatively causative variants (6 novel and 29 known) in 21 IRD-associated genes were identified in 71% of probands (39 of the 55 families). Three families showed phenotypes different from the typically reported clinical findings associated with the causative genes. To our knowledge, this is the largest genetic analysis of IRDs in the Jordanian population to date. Our study also confirms that WES is a powerful tool for the molecular diagnosis of IRDs in large patient cohorts.

Informed Consent Form Challenges for Genetic Research in Jordan

Background

Informed consent is an obligatory requirement for research engaging human subjects. Informed consent form (ICF) should be provided for human subjects to confirm their willingness for voluntary participation in a study. Ethical and legal obligations necessitate the presence of informed consent essential items to be built into the ICF.

Objective

To evaluate the content of ICFs obtained from different genetic studies accomplished in Jordan and their adherence to ethical guidelines proposed by the International Conference on Harmonization—Good Clinical Practice (ICHGCP).

Methods and Measures

A total of 44 ICFs obtained from master theses and grant proposals at two major universities in Jordan were analyzed according to the good clinical practice criteria proposed by ICHGCP. ICFs were scored for the presence or absence of ICF main items/categories.

Results

Results show inadequate information present in the examined ICFs. The highest information score was 17 out of 20, while the lowest score was one out of 20. The average score for all studied ICFs was 6.18±3.65. Among essential items/categories that were absent from the majority of studied ICFs were a statement about voluntary participation, confidentiality of data, compensation to study participants, risk/benefits of the study, and researchers’ contact information.

Conclusion

The ICFs were missing a number of required items. This could reflect inadequate knowledge about minimal informed consent requirements among Jordanian investigators highlighting the need for research ethical training in the country.

Y-Chromosome haplotypes reveal relationships between populations of the Arabian Peninsula, North Africa and South Asia

BACKGROUND

The United Arab Emirates (UAE) is positioned at the crossroads of human migration out of Africa and through to Asia and Europe.

AIM

To compare the degree of genetic diversity of the Arabian UAE population with populations in other countries from the Middle East, South Asia and North Africa.

SUBJECTS AND METHODS

Twenty-seven Y-STR were analysed in 217 individuals. Y-STR haplotypes from this study were compared to population data stored in YHRD, using MDS and AMOVA.

RESULTS

Two hundred and twelve haplotypes were observed in the 217 individuals studied. Although the reduction in Y-STR loci from 27 to 17 resulted in a decrease in discriminatory power, comparisons of populations were possible. The UAE population clustered closer with other populations of the Middle East. The South Asian and North African populations were separated by Middle Eastern populations in between both clusters.

CONCLUSION

This is the first study to report the diversity of a population of the Arabian Peninsula using 27 Y-STR. MDS plots show that Middle Eastern populations are positioned in the centre, with African, Asian and European populations around the Arab population cluster. The findings of this study are consistent with this region being at the epicentre of human migration between continents.

Potential Signals of Natural Selection in the Top Risk Loci for Coronary Artery Disease: 9p21 and 10q11

BACKGROUND

Coronary artery disease (CAD) is a complex disease and the leading cause of death in the world. Populations of different ancestry do not always share the same risk markers. Natural selective processes may be the cause of some of the population differences detected for specific risk mutations.

OBJECTIVE

In this study, 384 single nucleotide polymorphisms (SNPs) located in four genomic regions associated with CAD (1p13, 1q41, 9p21 and 10q11) are analysed in a set of 19 populations from Europe, Middle East and North Africa and also in Asian and African samples from the 1000 Genomes Project. The aim of this survey is to explore for the first time whether the genetic variability in these genomic regions is better explained by demography or by natural selection.

RESULTS

The results indicate significant differences in the structure of genetic variation and in the LD patterns among populations that probably explain the population disparities found in markers of susceptibility to CAD.

CONCLUSIONS

The results are consistent with potential signature of positive selection in the 9p21 region and of balancing selection in the 9p21 and 10q11. Specifically, in Europe three CAD risk markers in the 9p21 region (rs9632884, rs1537371 and rs1333042) show consistent signals of positive selection. The results of this study are consistent with a potential selective role of CAD in the configuration of genetic diversity in current human populations.