An integrated personal and population-based Egyptian genome reference

0
329
views

The human genome is composed of chromosomal DNA sequences consisting of bases A, C, G and T – the blueprint to implement the molecular functions that are the basis of every individual’s life. Deciphering the first human genome was a consortium effort that took more than a decade and considerable cost. With the latest technological advances, determining an individual’s entire personal genome with manageable cost and effort has come within reach. Although the benefits of the all-encompassing genetic information that entire genomes provide are manifold, only a small number of de novo assembled human genomes have been reported to date, and few have been complemented with population-based genetic variation, which is particularly important for North Africans who are not represented in current genome-wide data sets. Here, we combine long- and short-read whole-genome next-generation sequencing data with recent assembly approaches into the first de novoassembly of the genome of an Egyptian individual.

The resulting assembly demonstrates well-balanced quality metrics and is complemented with high-quality variant phasing via linked reads into haploblocks, which we can associate with gene expression changes in blood. To construct an Egyptian genome reference, we further assayed genome-wide genetic variation occurring in the Egyptian population within a representative cohort of 110 Egyptian individuals. We show that differences in allele frequencies and linkage disequilibrium between Egyptians and Europeans may compromise the transferability of European ancestry-based genetic disease risk and polygenic scores, substantiating the need for multi-ethnic genetic studies and corresponding genome references.

The Egyptian genome reference represents a comprehensive population data set based on a high-quality personal genome. It is a proof of concept to be considered by the many national and international genome initiatives underway. More importantly, we anticipate that the Egyptian genome reference will be a valuable resource for precision medicine targeting the Egyptian population and beyond.

Reference:

Inken Wohlers, Axel Künstner, Matthias Munz, Michael Olbrich, Anke Fähnrich, Caixia Ma, Misa Hirose, Shaaban El-Mosallamy, Mohamed Salama, Hauke Busch, Saleh Ibrahim (2020). An integrated personal and population-based Egyptian genome reference. 

Image credit: National Cancer Institute- unsplash.com

+ posts

Institute of Global Health and Human Ecology, American University in Cairo, Egypt

Dr Mohamed Salama established the first Translational Neuroscience Unit in Egypt. Mohamed’s collaborative research led to establishing the Egyptian Network for Neurodegenerative Disorders (ENND). Mohamed was selected as a SOT Global Senior Scholar in 2013 and Translational/bridging awardee in 2016. He was awarded by Parkinson’s and Movement Disorders Foundation (PMDF) for his continuing research in the field of neurodegeneration.

Recently, Mohamed and his colleagues succeeded to draft the first Reference Egyptian Genome and collaborating with other colleagues to start a national cohort (A Longitudinal Study of Egyptian Health Aging [AL-SEHA]). Currently, Mohamed is Atlantic senior fellow for Equity in brain health at the Global Brain Health Institute (GBHI) and Associate professor at the Institute of Global Health and Human Ecology at the American University in Cairo (AUC).