The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape

Bi-allelic PRRT2 variants may predispose to Self-limited Familial Infantile Epilepsy

Heterozygous PRRT2 variants are frequently implicated in Self-limited Infantile Epilepsy, whereas homozygous variants are so far linked to severe presentations including developmental and epileptic encephalopathy, movement disorders, and intellectual disability. In a study aiming to explore the genetics of epilepsy in the Sudanese population, we investigated several families including a consanguineous family with three siblings diagnosed with self-limited infantile epilepsy. We evaluated both dominant and recessive inheritance using whole exome sequencing and genomic arrays. We identified a pathogenic homozygous splice-site variant in the first intron of PRRT2 [NC_000016.10(NM_145239.3):c.-65-1G > A] that segregated with the phenotype in this family. This work taps into the genetics of epilepsy in an underrepresented African population and suggests that the phenotypes of homozygous PRRT2 variants may include milder epilepsy presentations without movement disorders.

Clinical phenotyping and genetic diagnosis of a large cohort of Sudanese families with hereditary spinocerebellar degenerations

Hereditary spinocerebellar degenerations (SCDs) is an umbrella term that covers a group of monogenic conditions that share common pathogenic mechanisms and include hereditary spastic paraplegia (HSP), cerebellar ataxia, and spinocerebellar ataxia. They are often complicated with axonal neuropathy and/or intellectual impairment and overlap with many neurological conditions, including neurodevelopmental disorders. More than 200 genes and loci inherited through all modes of Mendelian inheritance are known. Autosomal recessive inheritance predominates in consanguineous communities; however, autosomal dominant and X-linked inheritance can also occur. Sudan is inhabited by genetically diverse populations, yet it has high consanguinity rates. We used next-generation sequencing, genotyping, bioinformatics analysis, and candidate gene approaches to study 90 affected patients from 38 unrelated Sudanese families segregating multiple forms of SCDs. The age-at-onset in our cohort ranged from birth to 35 years; however, most patients manifested childhood-onset diseases (the mean and median ages at onset were 7.5 and 3 years, respectively). We reached the genetic diagnosis in 63% and possibly up to 73% of the studied families when considering variants of unknown significance. Combining the present data with our previous analysis of 25 Sudanese HSP families, the success rate reached 52-59% (31-35/59 families). In this article we report candidate variants in genes previously known to be associated with SCDs or other phenotypically related monogenic disorders. We also highlight the genetic and clinical heterogeneity of SCDs in Sudan, as we did not identify a major causative gene in our cohort, and the potential for discovering novel SCD genes in this population.

Factors associated with completeness in documentation of diagnostic work-up and treatment in patients with breast cancer in Sudan

Purpose

This study evaluates the relationship between geography and ethnicity on the completeness of documentation of diagnostic work-up and treatment modalities in Sudan for patients with breast cancer.

Methods

This retrospective study used data abstracted from patients with breast cancer receiving cancer care at Sudan's largest cancer centre (Radiation and Isotopes Center Khartoum) in 2017. Patient demographic and clinical characteristics were abstracted from paper medical records. Odds ratios and 95% confidence intervals were estimated to evaluate complete diagnostic work-up on ethnic group, origin and residence using binomial logistic regression models.

Results

Of 237 patients, the median age was 52 (interquartile range 43-61). Most often patients identified as Arab (68%), originated from Central, Northeastern and Khartoum regions (all 28%) and lived in the Khartoum region (52%). Overall, 49% had incomplete diagnostic work-up, with modest differences by ethnicity and geography. In adjusted analyses, non-statistical differences were found between the ethnic group, geographic origin and residence and having complete diagnostic work-up. For treatment modality, significant differences were observed between receptor status and receiving hormone therapy (p = 0.004). Only 28% of patients with HR+ breast cancer received hormonal therapy. For those with HR- or undocumented breast cancer subtype, 36% and 17% received hormone therapy, respectively.

Conclusion

Approximately half of Sudanese patients with breast cancer had incomplete diagnostic work-up, irrespective of ethnicity and geography. Moreover, a high proportion of patients received inappropriate treatment. This underlines a considerable systems-based quality gap in care delivery, demanding efforts to improve diagnostic work-up for all patients with breast cancer in Sudan.

Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia

Relatively little is known about Nubia's genetic landscape prior to the influence of the Islamic migrations that began in the late 1st millennium CE. Here, we increase the number of ancient individuals with genome-level data from the Nile Valley from three to 69, reporting data for 66 individuals from two cemeteries at the Christian Period (~650-1000 CE) site of Kulubnarti, where multiple lines of evidence suggest social stratification. The Kulubnarti Nubians had ~43% Nilotic-related ancestry (individual variation between ~36-54%) with the remaining ancestry consistent with being  introduced through Egypt and ultimately deriving from an ancestry pool like that found in the Bronze and Iron Age Levant. The Kulubnarti gene pool - shaped over a millennium - harbors disproportionately female-associated West Eurasian-related ancestry. Genetic similarity among individuals from the two cemeteries supports a hypothesis of social division without genetic distinction. Seven pairs of inter-cemetery relatives suggest fluidity between cemetery groups. Present-day Nubians are not directly descended from the Kulubnarti Nubians, attesting to additional genetic input since the Christian Period.

Analysis of HLA gene polymorphisms in East Africans reveals evidence of gene flow in two Semitic populations from Sudan

Sudan, a northeastern African country, is characterized by high levels of cultural, linguistic, and genetic diversity, which is believed to be affected by continuous migration from neighboring countries. Consistent with such demographic effect, genome-wide SNP data revealed a shared ancestral component among Sudanese Afro-Asiatic speaking groups and non-African populations, mainly from West Asia. Although this component is shared among all Afro-Asiatic speaking groups, the extent of this sharing in Semitic groups, such as Sudanese Arab, is still unknown. Using genotypes of six polymorphic human leukocyte antigen (HLA) genes (i.e., HLA-A, -C, -B, -DRB1, -DQB1, and -DPB1), we examined the genetic structure of eight East African ethnic groups with origins in Sudan, South Sudan, and Ethiopia. We identified informative HLA alleles using principal component analysis, which revealed that the two Semitic groups (Gaalien and Shokrya) constituted a distinct cluster from the other Afro-Asiatic speaking groups in this study. The HLA alleles that distinguished Semitic Arabs co-exist in the same extended HLA haplotype, and those alleles are in strong linkage disequilibrium. Interestingly, we find the four-locus haplotype "C*12:02-B*52:01-DRB1*15:02-DQB1*06:01" exclusively in non-African populations and it is widely spread across Asia. The identification of this haplotype suggests a gene flow from Asia, and likely these haplotypes were brought to Africa through back migration from the Near East. These findings will be of interest to biomedical and anthropological studies that examine the demographic history of northeast Africa.

Vitamin D receptor gene polymorphisms in Sudanese children with type 1 diabetes

Type 1 diabetes mellitus (T1DM) is a T cell mediated autoimmune disease. Vitamin D was found to suppress the incidence of diabetes when bind to its receptor (VDR), probably by suppressing T cell activations. Thus the VDR gene polymorphism may have an impact on pathophysiology of this disease. Since there was no consistent association between VDR polymorphisms and the risk of T1DM, this study aimed to investigate a VDR gene polymorphism in Sudanese children with T1DM. We examined the VDR gene Bsm1 (rs1544410), Apa1 (rs7975232), and Taq1 (rs731236) single nucleotide polymorphisms in 174 children with T1DM, and 56 children as control, and the association of these polymorphisms with the diabetic control. Among study patients, the majority (85.63%) of diabetic patients reported metabolically poor controlled (HbA1c > 8%). As compared with the control, patients with T1DM presented more commonly with Bsm1 B allele (p = 0.001; OR 0.283; 95% CI 0.131–0.609) and Taq1 T allele (p = 0.05; OR 2.429; 95% CI 1.073–5.496). Apa1 A allele was less common in patients with T1DM without statistical difference (p = 0.862; OR 1.085; 95% CI 0.546–2.156). Our study suggests that, Bsm1 and Taq1 polymorphisms of the VDR gene associated with the prevalence of T1DM.

Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples

As the field of forensic DNA analysis has started to transition from genetics to genomics, new methods to aid in crime scene investigations have arisen. The development of informative single nucleotide polymorphism (SNP) markers has led the forensic community to question if DNA can be a reliable "eye-witness" and whether the data it provides can shed light on unknown perpetrators. We have developed an assay called the Ion AmpliSeq™ PhenoTrivium Panel, which combines three groups of markers: 41 phenotype- and 163 ancestry-informative autosomal SNPs together with 120 lineage-specific Y-SNPs. Here, we report the results of testing the assay's sensitivity and the predictions obtained for known reference samples. Moreover, we present the outcome of a blind study performed on real casework samples in order to understand the value and reliability of the information that would be provided to police investigators. Furthermore, we evaluated the accuracy of admixture prediction in Converge™ Software. The results show the panel to be a robust and sensitive assay which can be used to analyze casework samples. We conclude that the combination of the obtained predictions of phenotype, biogeographical ancestry, and male lineage can serve as a potential lead in challenging police investigations such as cold cases or cases with no suspect.

Positive selection in admixed populations from Ethiopia

BACKGROUND

In the process of adaptation of humans to their environment, positive or adaptive selection has played a main role. Positive selection has, however, been under-studied in African populations, despite their diversity and importance for understanding human history.

RESULTS

Here, we have used 119 available whole-genome sequences from five Ethiopian populations (Amhara, Oromo, Somali, Wolayta and Gumuz) to investigate the modes and targets of positive selection in this part of the world. The site frequency spectrum-based test SFselect was applied to idfentify a wide range of events of selection (old and recent), and the haplotype-based statistic integrated haplotype score to detect more recent events, in each case with evaluation of the significance of candidate signals by extensive simulations. Additional insights were provided by considering admixture proportions and functional categories of genes. We identified both individual loci that are likely targets of classic sweeps and groups of genes that may have experienced polygenic adaptation. We found population-specific as well as shared signals of selection, with folate metabolism and the related ultraviolet response and skin pigmentation standing out as a shared pathway, perhaps as a response to the high levels of ultraviolet irradiation, and in addition strong signals in genes such as IFNA, MRC1, immunoglobulins and T-cell receptors which contribute to defend against pathogens.

CONCLUSIONS

Signals of positive selection were detected in Ethiopian populations revealing novel adaptations in East Africa, and abundant targets for functional follow-up.

The shaping of immunological responses through natural selection after the Roma Diaspora

The Roma people are the largest transnational ethnic minority in Europe and can be considered the last human migration of South Asian origin into the continent. They left Northwest India approximately 1,000 years ago, reaching the Balkan Peninsula around the twelfth century and Romania in the fourteenth century. Here, we analyze whole-genome sequencing data of 40 Roma and 40 non-Roma individuals from Romania. We performed a genome-wide scan of selection comparing Roma, their local host population, and a Northwestern Indian population, to identify the selective pressures faced by the Roma mainly after they settled in Europe. We identify under recent selection several pathways implicated in immune responses, among them cellular metabolism pathways known to be rewired after immune stimulation. We validated the interaction between PIK3-mTOR-HIF-1α and cytokine response influenced by bacterial and fungal infections. Our results point to a significant role of these pathways for host defense against the most prevalent pathogens in Europe during the last millennium.

Breast cancer in Tanzanian, black American, and white American women: An assessment of prognostic and predictive features, including tumor infiltrating lymphocytes

Introduction

Breast cancer is a major cause of morbidity and mortality for women in Sub-Saharan Africa and for black American women. There is evidence that the pathologic characteristics of breast cancers in both African women and black American women may differ from their counterparts of European ancestry. However, despite the great burden of disease, data on pathologic features of breast carcinoma in Sub-Saharan Africa is limited and often contradictory. This lack of information makes it difficult to prioritize resource use in efforts to improve breast cancer outcomes in the region.

Methods

We examined consecutive cases of breast cancer in Tanzanian women (n = 83), black American women (n = 120), and white American women (n = 120). Each case was assessed for tumor type, grade, mitotic count, ER and HER2 status, and tumor infiltrating lymphocyte involvement.

Results

The Tanzanian subjects were younger and had higher stage tumors than the subjects in either American group. Breast cancers in the Tanzanian and black American groups were more likely to be high grade (p = 0.008), to have a high mitotic rate (p<0.0001), and to be ER-negative (p<0.001) than the tumors in the white American group. Higher levels of tumor infiltrating lymphocyte involvement were seen among Tanzanian and black American subjects compared to white American subjects (p = 0.0001). Among all subjects, tumor infiltrating lymphocyte levels were higher in tumors with a high mitotic rate. Among Tanzanian and black American subjects, tumor infiltrating lymphocyte levels were higher in ER-negative tumors. These findings have implications for treatment priorities for breast cancer in Tanzania and other Sub-Saharan African countries.

African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations

BACKGROUND

Africa is the origin of modern humans within the past 300 thousand years. To infer the complex demographic history of African populations and adaptation to diverse environments, we sequenced the genomes of 92 individuals from 44 indigenous African populations.

RESULTS

Genetic structure analyses indicate that among Africans, genetic ancestry is largely partitioned by geography and language, though we observe mixed ancestry in many individuals, consistent with both short- and long-range migration events followed by admixture. Phylogenetic analysis indicates that the San genetic lineage is basal to all modern human lineages. The San and Niger-Congo, Afroasiatic, and Nilo-Saharan lineages were substantially diverged by 160 kya (thousand years ago). In contrast, the San and Central African rainforest hunter-gatherer (CRHG), Hadza hunter-gatherer, and Sandawe hunter-gatherer lineages were diverged by ~ 120-100 kya. Niger-Congo, Nilo-Saharan, and Afroasiatic lineages diverged more recently by ~ 54-16 kya. Eastern and western CRHG lineages diverged by ~ 50-31 kya, and the western CRHG lineages diverged by ~ 18-12 kya. The San and CRHG populations maintained the largest effective population size compared to other populations prior to 60 kya. Further, we observed signatures of positive selection at genes involved in muscle development, bone synthesis, reproduction, immune function, energy metabolism, and cell signaling, which may contribute to local adaptation of African populations.

CONCLUSIONS

We observe high levels of genomic variation between ethnically diverse Africans which is largely correlated with geography and language. Our study indicates ancient population substructure and local adaptation of Africans.

Genetic signatures of gene flow and malaria-driven natural selection in sub-Saharan populations of the "endemic Burkitt Lymphoma belt"

Populations in sub-Saharan Africa have historically been exposed to intense selection from chronic infection with falciparum malaria. Interestingly, populations with the highest malaria intensity can be identified by the increased occurrence of endemic Burkitt Lymphoma (eBL), a pediatric cancer that affects populations with intense malaria exposure, in the so called "eBL belt" in sub-Saharan Africa. However, the effects of intense malaria exposure and sub-Saharan populations' genetic histories remain poorly explored. To determine if historical migrations and intense malaria exposure have shaped the genetic composition of the eBL belt populations, we genotyped ~4.3 million SNPs in 1,708 individuals from Ghana and Northern Uganda, located on opposite sides of eBL belt and with ≥ 7 months/year of intense malaria exposure and published evidence of high incidence of BL. Among 35 Ghanaian tribes, we showed a predominantly West-Central African ancestry and genomic footprints of gene flow from Gambian and East African populations. In Uganda, the North West population showed a predominantly Nilotic ancestry, and the North Central population was a mixture of Nilotic and Southern Bantu ancestry, while the Southwest Ugandan population showed a predominant Southern Bantu ancestry. Our results support the hypothesis of diverse ancestral origins of the Ugandan, Kenyan and Tanzanian Great Lakes African populations, reflecting a confluence of Nilotic, Cushitic and Bantu migrations in the last 3000 years. Natural selection analyses suggest, for the first time, a strong positive selection signal in the ATP2B4 gene (rs10900588) in Northern Ugandan populations. These findings provide important baseline genomic data to facilitate disease association studies, including of eBL, in eBL belt populations.

Ethnicity and diabetes complications in Sudanese population: The need for further genetic population testing

BACKGROUND

The aim of the present study was to assess whether there is an association between ethnicity and the high prevalence of diabetes complications in Sudan.

METHODS

This was cross-sectional hospital-based study with 316 individuals with diabetes conducted in Khartoum state, Sudan. A questionnaire was used to collect demographic information. In addition to measurements of blood pressure, lipid profile and HbA1c, weight and height measurement were also performed for calculation of body mass index.

RESULTS

The study included individuals recruited from 62 tribes across Sudan. The effect of ethnicity on diabetic septic foot (DSF) was not statistically significant across different tribes (X-squared = 2.6098, df = 4, p-value = 0.6251). The effect of ethnicity on Albuminuria was also not statistically significant across different tribes recruited for this study (X-squared = 4.3787, df = 4, p-value = 0.3572). The Northern group carried a significantly higher unadjusted risk for development of retinopathy (OR = 1.8471, p-value = 0.04603). The Southern group was significantly different from the others regarding the effect of ethnicity on neuropathy, compared to the 'West' group (OR = 0.1905, p-value = 0.0345). The unadjusted effect for the Southern group was also significant (OR = 0.2933, p-value = 0.0320).

CONCLUSION

There was no role of ethnicity in term of DSF and albuminuria complications. However, retinopathy likely to be seen in tribes originally from north of Sudan, while neuropathy is more likely to be found in tribes originally from the south of Sudan. Further focus genetic population testing is needed.

Trends and patterns in leprosy in nine states of the Republic of the Sudan 7 years after the introduction of routine contact screening

Background

This paper analyzes the trends of key indicators reflecting the epidemiological situation of leprosy in nine different states of the Republic of the Sudan after the introduction of a systematic contact screening in 2010.

Methods

The routinely assessed data from the leprosy control program from 2010 to 2016 were analyzed.

Results

Despite, intense contact screening, the overall number of new cases detected showed a decreasing trend. The female:male ratio among new cases was constantly low. The overall average number of contacts needed to screen in order to detect a new case among contacts was 64. However, this number varied significantly in the nine states under investigation, with the best yield being observed in the state with the lowest case detection rate.

Conclusions

The total number of new cases of leprosy in nine states of the Republic of the Sudan has shown declining tendencies since 2010. Our data are not suggestive of a significant impact of contact screening on the trends of leprosy key indicators. Overall, contact screening proved to be efficient in most states, including those that exhibited very low annual new case detection rates (ANCDRs). Sensitization of personnel undergoing training and measures improving access of females to leprosy services are urgently needed.

Genetic history of Chad

OBJECTIVES

The Sahel is a semi-arid zone stretching from the Atlantic Ocean in the west to the Red Sea in the east and from the Sahara in the north to the Sudanian Savanna in the south. Here, we investigated the genetic history of the spread of Northern African ancestry common among Berbers, the Y DNA haplogroup R1b-V88, and Chadic languages throughout the Sahel, with a focus on Chad.

MATERIALS AND METHODS

We integrated and analyzed genotype data from 751 individuals from Chad, Burkina Faso, Mali, South Sudan, and Sudan in the context of a global reference panel of 5,966 individuals.

RESULTS

We found that genetic diversity in Chad was broadly divided by a north-south axis. The core ancestry of Southern Chadians was Central African, most closely related to Pygmies. Southern Chadians then experienced four waves of gene flow over the last 3,000 years from West-Central Africans, Eastern Africans, West-Central Africans again, and then Arabians. In contrast, Northern Chadians did not share Central African ancestry and were not influenced by the first wave of West-Central Africans but were influenced by Northern African ancestry.

DISCUSSION

We found that Y DNA haplogroup R1b entered the Chadian gene pool during Baggarization. Baggara Arabs spoke Arabic, not Chadic, implying that people carrying R1b-V88 were not responsible for the spread of Chadic languages, which may have spread approximately 3,700 years ago. We found no evidence for migration of Near Eastern farmers or any ancient episodes involving Eurasian backflow.

African genetic diversity provides novel insights into evolutionary history and local adaptations

Genetic variation and susceptibility to disease are shaped by human demographic history and adaptation. We can now study the genomes of extant Africans and uncover traces of population migration, admixture, assimilation and selection by applying sophisticated computational algorithms. There are four major ethnolinguistic divisions among present day Africans: Hunter-gatherer populations in southern and central Africa; Nilo-Saharan speakers from north and northeast Africa; Afro-Asiatic speakers from north and east Africa; and Niger-Congo speakers who are the predominant ethnolinguistic group spread across most of sub-Saharan Africa. The enormous ethnolinguistic diversity in sub-Saharan African populations is largely paralleled by extensive genetic diversity and until a decade ago, little was known about detailed origins and divergence of these groups. Results from large-scale population genetic studies, and more recently whole genome sequence data, are unravelling the critical role of events like migration and admixture and environmental factors including diet, infectious diseases and climatic conditions in shaping current population diversity. It is now possible to start providing quantitative estimates of divergence times, population size and dynamic processes that have affected populations and their genetic risk for disease. Finally, the availability of ancient genomes from Africa provides historical insights of unprecedented depth. In this review, we highlight some key interpretations that have emerged from recent African genome studies.

A novel mutation in the TG gene (G2322S) causing congenital hypothyroidism in a Sudanese family: a case report

Background

Congenital hypothyroidism (CH) has an incidence of approximately 1:3000, but only 15% have mutations in the thyroid hormone synthesis pathways. Genetic analysis allows for the precise diagnosis.

Case presentation

A 3-week old girl presented with a large goiter, serum TSH > 100 mIU/L (reference range: 0.7–5.9 mIU/L); free T₄ < 3.2 pmol/L (reference range: 8.7–16 pmol/L); thyroglobulin (TG) 101 μg/L. Thyroid Tc-99 m scan showed increased radiotracer uptake. One brother had CH and both affected siblings have been clinically and biochemically euthyroid on levothyroxine replacement. Another sibling had normal thyroid function. Both Sudanese parents reported non-consanguinity. Peripheral blood DNA from the proposita was subjected to whole exome sequencing (WES). WES identified a novel homozygous missense mutation of the TG gene: c.7021G > A, p.Gly2322Ser, which was subsequently confirmed by Sanger sequencing and present in one allele of both parents. DNA samples from 354 alleles in four Sudanese ethnic groups (Nilotes, Darfurians, Nuba, and Halfawien) failed to demonstrate the presence of the mutant allele. Haplotyping showed a 1.71 centiMorgans stretch of homozygosity in the TG locus suggesting that this mutation occurred identical by descent and the possibility of common ancestry of the parents. The mutation is located in the cholinesterase-like (ChEL) domain of TG.

Conclusions

A novel rare missense mutation in the TG gene was identified. The ChEL domain is critical for protein folding and patients with CH due to misfolded TG may present without low serum TG despite the TG gene mutations.

Electronic supplementary material

The online version of this article (10.1186/s12881-018-0588-7) contains supplementary material, which is available to authorized users.

Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations

Northeast Africa has a long history of human habitation, with fossil-finds from the earliest anatomically modern humans, and housing ancient civilizations. The region is also the gate-way out of Africa, as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula. We investigate the population history of northeast Africa by genotyping ~3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400–200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa.

Northeast Africa has geographic and historical links to Eurasia via the Middle East and the Arabian Peninsula, but the demographic history of the region itself has been more elusive. We investigate genomic diversity of northeast African populations and found a clear bimodal distribution of variation, correlated with geography, and likely driven by Eurasian admixture in the wake of migrations along the Nile. This admixture process largely coincides with the time of the Arab conquest, spreading in a southbound direction along the Nile and the Blue Nile. Nilotic populations occupying the region around the White Nile show long-term continuity, genetic isolation and genetic links to ancestral East African people. Compared to current times, groups that are ancestral to the current-day Nilotes likely inhabited a larger area of northeast Africa prior to the migration from the Middle East as their ancestry component can still be found in a large area. Our findings reveal the genetic history of Sudanese and South Sudanese people, broaden our knowledge on demographic history of humans, and quantify the impact of large-scale historic migration events in northeast Africa.

Pathological outcomes and agressiveness of low-risk prostate cancer in Northern African men

BACKGROUND

Northern African (NAf) men show a high incidence of advanced prostate cancer (PCa) at diagnosis. Several studies suggested the existence of ethnic differences in the PCa aggressiveness and this has led to some concerns related to the inclusion of some ethnic groups into active surveillance protocols.

OBJECTIVE

To evaluate pathological outcomes and aggressiveness of low risk PCa treated by radical prostatectomy in a NAf ethnic group.

SUBJECTS AND METHODS

Data of 147 NAfs, who underwent radical prostatectomy for low risk PCa diagnosed via a 12-core biopsy in 2 academic centers between 2011 and 2015, were reviewed retrospectively to assess rates of worse pathological outcomes defined as: Gleason score upgrade to at least 3+4, upstage to pT3a or higher or pN1, and positive surgical margins.

RESULTS

Overall significant upstage and/or upgrade occurred in 20.2% and positive surgical margins occured in18.3%. In multivariate logistic regression analysis, independent variables that predicted for upstage and/or upgrade or positive surgical margins in the entire cohort were: NCCN risk group (low risk>very low risk), advanced age>60 years, PSA>6ng/ml, PSA density≥0.15, more than 2 positive cores in biopsy, more than 50% cancer involvement in positive cores, clinical stage (T2a>T1c) and UCSF-CAPRA-S score>3.

CONCLUSIONS

Our study found that, at least pathologically, NAf men do not have more aggressive disease than Caucasians and African Americans in both low and very low risk PCa. Thus, we think that active surveillance is a suitable approach for selected patients since there is no definitive data that show a more aggressive natural history of PCa in NAf men.