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Gene. 2018 Aug 20;668:129-134. doi: 10.1016/j.gene.2018.05.048. Epub 2018 May 25.

Whole genome sequencing and bioinformatics analysis of two Egyptian genomes.

Author information

1
Biomedical Informatics and Chemo-Informatics Group, Centre of Excellence for Advanced Sciences (CEAS), and Informatics and Systems Department, National Research Centre, Cairo 12622, Egypt. Electronic address: mahef@aucegypt.edu.
2
Korean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
3
Biomedical Informatics and Chemo-Informatics Group, Centre of Excellence for Advanced Sciences (CEAS), and Informatics and Systems Department, National Research Centre, Cairo 12622, Egypt; Environmental and Occupational Medicine Department, National Research Centre, Cairo 12622, Egypt.
4
Biomedical Informatics and Chemo-Informatics Group, Centre of Excellence for Advanced Sciences (CEAS), and Informatics and Systems Department, National Research Centre, Cairo 12622, Egypt.
5
Personal Genomics Institute, Genome Research Foundation, Cheongju 28160, Republic of Korea; Geromics, Ulsan 44919, Republic of Korea.
6
Geromics, Ulsan 44919, Republic of Korea.
7
Korean Genomics Industrialization and Commercialization Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.; Personal Genomics Institute, Genome Research Foundation, Cheongju 28160, Republic of Korea; Geromics, Ulsan 44919, Republic of Korea.. Electronic address: jongbhak@genomics.org.

Abstract

We report two Egyptian male genomes (EGP1 and EGP2) sequenced at ~ 30× sequencing depths. EGP1 had 4.7 million variants, where 198,877 were novel variants while EGP2 had 209,109 novel variants out of 4.8 million variants. The mitochondrial haplogroup of the two individuals were identified to be H7b1 and L2a1c, respectively. We also identified the Y haplogroup of EGP1 (R1b) and EGP2 (J1a2a1a2 > P58 > FGC11). EGP1 had a mutation in the NADH gene of the mitochondrial genome ND4 (m.11778 G > A) that causes Leber's hereditary optic neuropathy. Some SNPs shared by the two genomes were associated with an increased level of cholesterol and triglycerides, probably related with Egyptians obesity. Comparison of these genomes with African and Western-Asian genomes can provide insights on Egyptian ancestry and genetic history. This resource can be used to further understand genomic diversity and functional classification of variants as well as human migration and evolution across Africa and Western-Asia.

KEYWORDS:

Bioinformatics; Egyptian; Human migration; Variants; Whole-genome sequencing

PMID:
29775755
DOI:
10.1016/j.gene.2018.05.048
[Indexed for MEDLINE]

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