An integrated personal and population-based Egyptian genome reference

Inken Wohlers, Axel Künstner, Matthias Munz, Michael Olbrich, Anke Fähnrich, Verónica Calonga-Solís, Caixia Ma, Misa Hirose, Shaaban El-Mosallamy, Mohamed Salama, Hauke Busch () and Saleh Ibrahim ()
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Inken Wohlers: University of Lübeck
Axel Künstner: University of Lübeck
Matthias Munz: University of Lübeck
Michael Olbrich: University of Lübeck
Anke Fähnrich: University of Lübeck
Verónica Calonga-Solís: University of Lübeck
Caixia Ma: 25 Cambridge Science Park
Misa Hirose: University of Lübeck
Shaaban El-Mosallamy: Mansoura University
Mohamed Salama: Mansoura University
Hauke Busch: University of Lübeck
Saleh Ibrahim: University of Lübeck

Nature Communications, 2020, vol. 11, issue 1, 1-10

Abstract: Abstract 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 Africa, a region underrepresented in current genome-wide references. Here, we combine long- and short-read whole-genome sequencing data with recent assembly approaches into a de novo assembly of an Egyptian genome. The assembly demonstrates well-balanced quality metrics and is complemented with variant phasing via linked reads into haploblocks, which we associate with gene expression changes in blood. To construct an Egyptian genome reference, we identify genome-wide genetic variation within a 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 genome references. Thus, the Egyptian genome reference will be a valuable resource for precision medicine.

Date: 2020
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DOI: 10.1038/s41467-020-17964-1

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