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Egyptref: An integrated personal and population-based Egyptian genome reference

North African individuals are not represented in current genetic data sets. To address this issue, we generated an integrated personal and population-based Egyptian genome reference called Egyptref. Towards this end, we performed a human de novo assembly of an Egyptian individual using long PacBio reads (99x genome coverage) and polished it using Illumina short reads (90x). Variants were phased using 10x Genomics linked reads (80x). This personal genome was complemented with whole genome sequencing-based variant data of 109 further Egyptians and mitochondrial haplogroups from mtDNA sequencing of 326 further Egyptians (of which 100 individuals from EGAD00001001372/EGAD00001001380) to obtain a population-based genome. We used Egyptref for assessing the impact of genetic variation, e.g. by integration of blood RNA sequencing data of the assembly individual.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001006034 Sequel 1
EGAD00001006035 HiSeq X Ten 1
EGAD00001006036 Illumina NovaSeq 6000 1
EGAD00001006037 HiSeq X Ten 9
EGAD00001006038 HiSeq X Ten 10
EGAD00001006039 10
EGAD00001006040 Illumina MiSeq 217
Publications Citations
An integrated personal and population-based Egyptian genome reference.
Nat Commun 11: 2020 4719
14
Genetic analysis of CFH and MCP in Egyptian patients with immune-complex proliferative glomerulonephritis.
Front Immunol 13: 2022 960068
0