Population Genomics

Malaria and Visceral Leishmaniasis

Overdominance Effects between Malaria and Visceral Leishmaniasis in the 5q31 Region



A group of SNPs in 5q31, genotyped from Hausa tribe of Koka village in eastern Sudan; an area endemic with malaria and visceral leishmaniasis, were analyzed by The Leishmaniasis research group and found to have significant excess of heterozygosis level and departure from HWE and assumed to be due to natural selection resulting from notorious deadly outbreaks since various ethnic groups from western Sudan settled the area although sequence information in the 5q31 region did not detect functional SNPs that could be associated with such drastic phenotypes. Malaria was thought to inflict inferior selective pressure due to the mild clinical phenotype observed. Taking advantage of follow up phenotype data sets available from the Malaria Gen study we re-analyzed these genotypes using different bioinformatics software to determine their effect on the regulation, function and expression of interleukins, miRNA binding and splicing mechanism. The SNPs were found to potentially affect the binding of many transcription factors that regulate the expression of IL-4 and IL-13 and stability of IL-5 mRNA. Association of haplotypes susceptibility revealed that the haplotype of low cytokine TH2 profile is associated with higher risk of malaria infection (P-value = 0.02). Through modulating TH2 cytokine response; the excess heterozygosity in 5q31 is explained with the phenomenon of overdominance between malaria and visceral leishmaniasis, acted by natural selection and driving the locus towards optimum response


Ancestral Genomes and the History of Adaptation

Ancestral Genomes and the History of Adaptation

Maha M Osman1, 2, Rayan S Ali1, Mahmoud Koko1, Muntaser E Ibrahim1*

1 Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan.

2 Commission for Biotechnology and Genetic Engineering, National Center for Research, Sudan.

*Corresponding author: Prof. Muntaser E Ibrahim, mibrahim@iend.org


The evolutionary history of a species is best seen from the summation of genetic variation across its genome. Genomes of African populations are believed to have retained some of the ancestral states of their genetic variation based on autosomes and sex specific chromosomes as well. In order to understand the evolutionary history of human populations in relation to other hominines, including the Neanderthal as a close species, and in attempt to gain insights to mechanisms of human adaptation, genomic data in different classes of adaptive traits were compared. Sudanese samples were sequenced on IlluminaHiSeq2000 platform. Sequences were compared to Neanderthal and global samples collected from 1000 Genomes and UCSC browsers.  Genes of adaptive traits and whole mitochondrial genomes and genes were extracted using Linux commands and Bioinformatics tools. Different software programs and statistical methods were used include; population differentiation test (FST), principal component analyses (PCA), Tajima Test for selective neutrality, phylogenetic trees were constructed using BEAST and MEGA7. Whole mitogenomes produced robust phylogenies that were greatly concordant with available HVRI, indicating that the HVRI has the upper hand in depicting the overall information content of the mtDNA sequence variation. Skyline plots based on HVRI show expansion dates to alter when the north eastern sequences are used compared to the plot of the world population, indicating the pivotal contribution of east Africans to human key evolutionary events. The results indicate that although Neanderthal and humans are adequately divergent in terms of speciation and genetic distance, ample variations are retained more pronouncedly in the biological class of variations.  Interestingly and as manifestation of the peculiarity of cultural variations to humans there was an observed divergence between humans and Neanderthal, manifested in reduced clustering and higher distance metrics, indicating the effect of cultural evolutionary forces.




Fatima A Elmugadam1, Liena ELsayed3, Haytham M Gorshi2, Almigdad HMohammed1, Murad Almak1, IsraaH Hussain1 Mohammed A.Farag1, Mohammed S.Tawar1, Elhami A Ahmed4, Almegdad S A1, Wadah O Awad1, Ahmed M Musa


1- Khartoum University, Faculty of Medicine, Sudan

2- Institute of Endemic Diseases, Faculty of medicine, University of Khartoum, Sudan.

 3- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Sudan.

4- UNESCO chair in Bioethics, Faculty of Medicine, University of Khartoum, Sudan.

Aim: The study aimed to assess the knowledge, attitude and practice aspects on the relationship of consanguinity to negative health outcomes. Also, to explore the attitude towards premarital genetic testing.


Background: Consanguinity (intra-familial marriage) is a global health problem with various adverse health outcomes. As this practice increases homozygosity of recessive alleles, it results in higher risk of early mortality and morbidity. Although, Sudan has one of the highest rates of consanguinity exceeding 40-50%.

Methodology: Data was collected from 1089 participants. Study was conducted in 13 urban and semi urban areas from 8 different states, using convenience sampling, trained interviewers paid house visits. Sudanese residents, 18 years and above, irrespective of their socio-economic status, were interviewed based on a locally generated and tested questionnaire. Analysis was done using descriptive and inferential statistics.

Results: 518 (48%) of participants were females, 571(52%) were males. about 800(73%) were among 18-40 years’ age group. The majority of respondents 437(39%) were college graduates. 803(74%) agreed on the negative health consequences of consanguinity, while 150(14%) opposed and 136 (12%) said “I do not know”. Among the respondents, 696(64%) showed non-preference for consanguineous marriage, Most frequently due to the possible transmission of genetic diseases. Of the 393 (36%) that showed preference the most frequent reason was its contribution to the stability of marriage.  When asked if they were willing to undergo premarital genetic testing, 908(83%) of respondents agreed to take it.

Conclusion: in our study, the overall awareness towards the issue was moderately high. But the practice still persists also in high rates.  It is not a revolution needed against consanguineous marriage in Sudan, rather, we need more investigation and integration of public health genomics sector to build efficient community-based awareness programs.

Keywords: Consanguinity; awareness; attitude; Sudan.


Presenter: Fatima Abdelhakam Abdellatif, MBBS, Faculty of Medicine University of Khartoum.




Haplotype Diversity

Haplotype Diversity and Structure of Y Chromosome STR and SNPs of East Africans: further evidence to the antiquity of its populations


East Africa has been in the spotlight of palaeoanthropological investigation for its role as a potential cradle of humanity and as a gateway out of Africa Since the discovery of the first hominin fossils. A Y chromosome SNP and mitochondrial genotyping on east African populations complement this notion and demonstrated the high effective population size and diversity of its populations attesting to the antiquity of the populations of the region. As Y chromosome STRs analysis has become increasingly important for forensic and human population genetics study; in this study Y-chromosome specific STRs (Y-STRs) and SNPs genotyping are used to study the recent population histories and their role in paternity testing and forensic applications in east African populations. To answer these pertinent questions a total of 562 unrelated male samples (94 from this study) from different east African populations were analysed for their 17- loci Y-STR distribution. Moreover, a Phylogenetic and population differentiation analysis of 17-loci Y-STR were carried out on the east African and global samples to see the contribution of east Africans to the global genetic landscape.

The 17 loci Y-STR loci analysis allowed a total of 451 (395 unique and 56 shared) haplotypes to be defined.  SNP defined haplogroups identified and subsequent phylogenetic and population differentiation analyses done in the studied populations once more attesting to the long existence of the east African populations and their contribution to the out-of-Africa scenario. Haplotypes differences between individuals from east Africa also conforms to the relatively larger male effective size and emphasize the necessity of including Ne measures in population and forensic studies. Joint Y-SNP and Y-STR data on more individuals and populations will help to clarify the association between the two Y-chromosome markers and their implication to forensics and better understanding of human evolutionary history in the region.

Key words: Y chromosome, Short tandem repeats, Y-STR, SNPs, East Africa


Thomas Krahn



Thomas Krahn (YSEQ, Germany)
Bonnie Schrack (A00-Cameroon Research Project, USA)
Forka Leypey Mathew Fomine (University of Buea, Cameroon)

Gregory Magoon (Aerodyne Research Inc, USA)
Astrid-Maria Krahn (YSEQ, Germany)


In 2012 we discovered an African American customer sample that didn’t match any known Y haplogroup. Our further investigation showed that he represented a new Y branch (A00) predating all other known haplogroups by at least 70,000 years. Research in public Y-STR databases indicated that the haplotype of the A00 sample was found in Cameroon.



We sequenced the Y chromosome of this sample with classical Sanger technology (ABI3730XL, ~400,000 bases) to identify the general structure of the new branch and established SNP typing assays for a selection of key markers that could be used to screen a wider population.  We collected 950 male cheek swab samples in different regions of Cameroon and intensified the sampling density in regions where A00 was found. Later we sequenced four A00 samples with NGS technology (Illumina HiSeq X Ten) to elaborate 3 distinct branches within A00.



We found 5018 novel Y-SNPs on the A00 branch, 1455 Y-SNPs on the A0-T branch. The screening identified 83 samples that we confirmed to belong to haplogroup A00-L1086. Every confirmed A00 sample could be assigned to one of the 3 branches A00a A00b and A00c defined by the markers FGC25576, A4985 and A12222 respectively.



We observed a very restricted regional distribution of the A00 population and a very young TMRCA of 700 ybp despite the extremely deep split from all other known Y haplogroups of more than 200,000 ybp. A00 is significantly older than the previously oldest branch A0-V148. And the A00 population is tightly concentrated in the mountains of West Cameroon. The highest A00 frequency is observed among the Bangwa and Mbo while we didn’t observe any A00 samples among the Baka people who were suspected to be distinct from their visual appearance and language.



Dipl.-Ing. Thomas Krahn (YSEQ, Germany)



Geza Ephifania

Authors and Affiliations Ephifania Geza1,2*, Nicola. Mulder2, Emile R. Chimusa3, and Gaston K. Mazandu1,2,3*

1Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Health Sciences Campus. Anzio Rd, Observatory, 7925, South Africa,

2African Institute for Mathematical Sciences Melrose Rd, Muizenberg, 7945, Cape Town, South Africa, and

3Division of Human genetics, Department of Pathology, University of Cape Town Health Sciences Campus. Anzio Rd, Observatory, 7925, South Africa

Content Aim

To integrate existing state-of-the-art local ancestry inference methods within a unified framework.


The inference of ancestry at every chromosomal site of individuals that resulted from the mixing of two or more genetically distinct populations (local ancestry inference) have found applications in several biomedical studies.  Such studies include understanding complex diseases, population history and demographics and personalizing medicines. Although several local ancestry inference methods exist, they are available as individual scripts requiring unique inputs and producing unique outputs. As a result, existing methods do not facilitate the local ancestry inference process and its applications. Thus, local ancestry inference is challenging to researchers with limited programming language.


We use python scripts, PLINK and EAGLE softwares to manipulate tool-specific inputs, deconvolve and standardize local ancestry inference results.


We introduce a unified framework for multi-way local ancestry inference, FRANC, integrating nine state-of-the-art local ancestry deconvolution tools. FRANC is adaptable, expandable and a portable tool that manipulates tool-specific inputs, deconvolves ancestry and standardizes tool-specific results.

Conclusions FRANC is a single piece of python portable application integrating nine state-of-the-art local ancestry deconvolution models filling the bioinformatics needs of facilitating the local ancestry estimate process in an admixed individual. It provides an easy-to-use and flexible tool, enabling different admixture scenario

analysis within the same framework and the assessment of local ancestry deconvolution models, helping users to select an appropriate tool based on data and application under consideration.