FarGen: Elucidating the distribution of coding variants in the isolated population of the Faroe Islands

Egypt Genome: Towards an African new genomic era

BACKGROUND

Studying the human genome is crucial to embrace precision medicine through tailoring treatment and prevention strategies to the unique genetic makeup and molecular information of individuals. After human genome project (1990-2003) generated the first full sequence of a human genome, there have been concerns towards Northern bias due to underrepresentation of other populations. Multiple countries have now established national genome projects aiming at the genomic knowledge that can be harnessed from their populations, which in turn can serve as a basis for their health care policies in the near future.

AIM OF REVIEW

The intention is to introduce the recently established Egypt Genome (EG) to delineate the genomics and genetics of both the modern and Ancient Egyptian populations. Leveraging genomic medicine to improve precision medicine strategies while building a solid foundation for large-scale genomic research capacity is the fundamental focus of EG.

KEY SCIENTIFIC CONCEPTS

EG generated genomic knowledge is predicted to enrich the existing human genome and to expand its diversity by studying the underrepresented African/Middle Eastern populations. The insightful impact of EG goes beyond Egypt and Africa as it fills the knowledge gaps in health and disease genomics towards improved and sustainable genomic-driven healthcare systems for better outcomes. Promoting the integration of genomics into clinical practice and spearheading the implementation of genomic-driven healthcare and precision medicine is therefore a key focus of EG. Mining into the wealth of Ancient Egyptian Genomics to delineate the genetic bridge between the contemporary and Ancient Egyptian populations is another excitingly unique area of EG to realize the global vision of human genome.

High prevalence of patellar dislocation and trochlear dysplasia in a geographically and genetically isolated society: an observational national cohort study from the Faroese Knee Cohort

BACKGROUND AND PURPOSE

We aimed to calculate the prevalence of patellar dislocation (PD) and trochlear dysplasia (TD) in a national cohort aged 15-19 years in the Faroe Island.

PATIENTS AND METHODS

All inhabitants in the Faroe Islands aged 15-19 years were invited to answer an online survey, including demographics and questions regarding prior PD. Participants with prior PD were invited for radiographs and MRI of both knees to be taken. Trochlear dysplasia was defined as one of the following: Dejour type A-D on radiographs, lateral trochlear inclination angle (LTI) < 11°, or trochlear depth < 3 mm on MRI.

RESULTS

3,749 individuals were contacted, 41 were excluded, and 1,638 (44%) completed the survey. 146 reported a prior PD (the PD cohort) and 100 accepted to participate and have radiographs and MRI taken of both knees (the clinical PD cohort), 76 of whom were diagnosed with TD. The national prevalence of PD was 8.9%. The national prevalence of symptomatic TD was 6.8%. The prevalence of TD in the clinical PD cohort was 76%. TD was bilateral in 78% of TD patients, but only 27% of patients with bilateral TD had PD in both knees.

CONCLUSION

The prevalence of PD in the Faroe Islands is found to be very high. The national prevalence of TD and the prevalence of TD in participants with prior PD is high, indicating a potential genetic influence.

SNP heterozygosity, relatedness and inbreeding of whole genomes from the isolated population of the Faroe Islands

BACKGROUND

The population of the Faroe Islands is an isolated population but very little is known about it from whole genome sequencing. The population of about 50000 people has a high incidence of rare diseases e.g., 1:300 for Primary Carnitine Deficiency. A screening programme was implemented, and eleven persons were also whole genome sequenced at x37 coverage for diagnostic purposes of those cases that were not affected by the known mutations. The purpose of our study is to utilize the high coverage data to explore the genomic variation and the ancestral history of the population. We study the SNP heterozygosity, the pairwise relatedness from kinship, the inbreeding from runs of homozygosity ROH, and we find the minor allele frequency distribution. We estimate the population ancestry and the timing of the founding event by using the whole genomes from eight consenting individuals.

RESULTS

We find the number of SNPs and the heterozygosity for the eight individual samples, and for merged samples, for which we also study the relatedness. We find close relatedness between the supposedly unrelated individuals. From ROH, we interpret the high relatedness as an ancient property of the isolated population. A bottleneck event is estimated starting between years [Formula: see text] with a maximum consanguineous population in year [Formula: see text] and similarly consanguineous between years [Formula: see text]. The ancestry analysis shows the population descends from founders of [Formula: see text] European and [Formula: see text] Admixed American ancestry. A distinct clustering near the central European and British populations of the 1000 Genome Project is likely the result of the population isolation and genetic drift. The minor allele frequency distribution suggests many rare variants.

CONCLUSIONS

The ancestry is mainly European while the inbreeding is higher compared to European populations and population isolates. The Faroese population has inbreeding more like ancient Europeans. We discovered a bottlenecked and consanguineous population event and estimated it starting in the 1st-4th century as compared to the oldest archaeological findings from the 4th-6th century.