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Genome-wide analyses disclose the distinctive HLA architecture and the pharmacogenetic landscape of the Somali population.

ABSTRACT: African populations are underrepresented in medical genomics studies. For the Somali population, there is virtually no information on genomic markers with significance to precision medicine. Here, we analyzed nearly 900,000 genomic markers in samples collected from 95 unrelated individuals in the North Eastern Somalia. ADMIXTURE program for estimation of individual ancestries revealed a homogenous Somali population. Principal component analysis with PLINK software showed approximately 60% East African and 40% West Eurasian genes in the Somali population, with a close relation to the Cushitic and Semitic speaking Ethiopian populations. We report the unique features of human leukocyte antigens (HLA) in the Somali population, which seem to differentiate from all other neighboring regions compared. Current study identified high prevalence of the diabetes type 1 (T1D) predisposing HLA DR-DQ haplotypes in Somalia. This finding may explain the increased T1D risk observed among Somali children. In addition, ethnic Somalis were found to host the highest frequencies observed thus far for several pharmacogenetic variants, including UGT1A4*2. In conclusion, we report that the Somali population displays genetic traits of significance to health and disease. The Somali dataset is publicly available and will add more information to the few genomic datasets available for African populations.

SUBMITTER: Ali AA

PROVIDER: S-EPMC7101338 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Genome-wide analyses disclose the distinctive HLA architecture and the pharmacogenetic landscape of the Somali population.

Ali Abshir A AA Aalto Mikko M Jonasson Jon J Osman Abdimajid A

Scientific reports 20200327 1

African populations are underrepresented in medical genomics studies. For the Somali population, there is virtually no information on genomic markers with significance to precision medicine. Here, we analyzed nearly 900,000 genomic markers in samples collected from 95 unrelated individuals in the North Eastern Somalia. ADMIXTURE program for estimation of individual ancestries revealed a homogenous Somali population. Principal component analysis with PLINK software showed approximately 60% East A ...[more]

PMID: 32221414

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Project description:BackgroundAccurate assessment of fetal size is essential in providing optimal prenatal care. National Institute of Child Health and Human Development (NICHD) study from 2015 demonstrated that estimated fetal weight (EFW) differed significantly by race/ethnicity after 20 weeks. There is a large Somali population residing in Minnesota, many of whom are cared for at our maternal fetal medicine practice at the University of Minnesota. Anecdotally, we noticed an increased proportion of small-for-gestational age diagnoses within this population. We sought to use our ultrasound data to create a reference standard specific for this population and compare to currently applied references.PurposeWe aimed to model fetal growth standards within a healthy Somali population between 16 and 40 weeks gestation, and address possible differences in the growth patterns compared with standards for non-Hispanic White, non-Hispanic Black, Hispanic, and Asian singleton fetuses published by the NICHD in the Fetal Growth Study.Materials and methodsThis is a retrospective cohort study using ultrasound data from 527 low risk pregnancies of Somali ethnicity at single tertiary care center between 2011 and 2017. A total of 1107 scans were identified for these pregnancies and maternal and obstetrical data were reviewed. Women 18-40 years of age with low-risk pregnancies and established dating consistent with first trimester ultrasound scan were included. Exclusion criteria were any maternal, fetal or obstetrical conditions known to affect fetal growth.ResultsEstimated fetal weight among Somali pregnancies differed significantly at some time points from the NICHD four ethnic groups, but generally the EFW graph curves crossed over at most time points between the study groups. At week 18, EFW was significantly larger than all other four ethnic groups (all p<.001), it was also significantly larger from the Hispanic, Black, and Asian ethnic groups at some time points between 18 and 27 weeks gestation (p < .05). Additionally, EFW among Somali pregnancies was significantly smaller than the Black and Asian ethnicity at 32 and 35-36 weeks and smaller than the White ethnicity at 30 and 38-39 weeks (p < .05). Abdominal circumference (AC) for the Somali population was significantly smaller than the other ethnic groups, especially than the White ethnicity at various time points across 16-40 weeks (p < .05). Femur and humerus length were significantly longer when compared to all other ethnic groups at most time points from 16 to 40 weeks of gestation (p < .05). Biparietal diameter (BPD) was significantly smaller than all other ethnic groups specifically at time of fetal survey (18 weeks) and at time of fetal growth assessment (32 weeks) (p < .05).ConclusionsSignificant differences in fetal growth standards were found between the Somali ethnicity and other ethnic groups (White, Black, Asian, and Hispanic) at various time points from 16 to 40 weeks of gestation. Racial/ethnic-specific standards improve the precision for evaluating fetal growth and may decrease the proportion of fetuses of Somali ethnicity labeled as small-for-gestational age.

Dataset Information

Genome-wide analyses disclose the distinctive HLA architecture and the pharmacogenetic landscape of the Somali population.

Publications

Genome-wide analyses disclose the distinctive HLA architecture and the pharmacogenetic landscape of the Somali population.

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