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An integrated personal and population-based Egyptian genome reference

Inken Wohlers, Axel Künstner, View ORCID ProfileMatthias Munz, Michael Olbrich, Anke Fähnrich, Verónica Calonga-Solís, Caixia Ma, Misa Hirose, Shaaban El-Mosallamy, Mohamed Salama, View ORCID ProfileHauke Busch, Saleh Ibrahim
doi: https://doi.org/10.1101/681254
Inken Wohlers
1Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
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Axel Künstner
1Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
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Matthias Munz
1Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
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  • ORCID record for Matthias Munz
Michael Olbrich
1Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
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Anke Fähnrich
1Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
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Verónica Calonga-Solís
1Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
2Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil
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Caixia Ma
3Novogene (UK) Company Limited, Babraham Research Campus, Cambridge, United Kingdom
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Misa Hirose
6Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
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Shaaban El-Mosallamy
4Medical Experimental Research Center (MERC), Mansoura University, Mansoura, Egypt
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Mohamed Salama
4Medical Experimental Research Center (MERC), Mansoura University, Mansoura, Egypt
5Institute of Global Health and Human Ecology, The American University in Cairo, Cairo, Egypt
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Hauke Busch
1Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
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Saleh Ibrahim
6Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
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  • For correspondence: saleh.ibrahim@uksh.de
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Abstract

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 1–3, and few have been complemented with population-based genetic variation 4, which is particularly important for North Africans who are not represented in current genome-wide data sets 5–7. Here, we combine long- and short-read whole-genome next-generation sequencing data with recent assembly approaches into the first de novo assembly 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.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • * Additional assembly QC * Identification of non-reference insertions commonly found in Egyptians by using the de novo assembly * Characterization of genetic components in the Egyptian population by an admixture analysis using genetic data from 143 additional populations from the Middle East, North Africa and the world

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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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, Saleh Ibrahim
bioRxiv 681254; doi: https://doi.org/10.1101/681254
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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, Saleh Ibrahim
bioRxiv 681254; doi: https://doi.org/10.1101/681254

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