Study

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

Study ID Alternative Stable ID Type
EGAS00001004303 Other

Study Description

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.

Study Datasets 7 datasets.

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
This is the PacBio long read data used for performing de novo assembly of the EGYPT individual (mapped against GRCh38).
Sequel 1
EGAD00001006035
10x Genomics linked read data used in variant phasing and de novo assembly scaffolding for the EGYPT individual (mapped against GRCh38).
HiSeq X Ten 1
EGAD00001006036
This is the blood RNA-Seq read data used for expression analysis such as haplotypic expression (mapped against GRCh38).
Illumina NovaSeq 6000 1
EGAD00001006037
High-coverage WGS
HiSeq X Ten 9
EGAD00001006038
This data set contains for 10 Egyptian individuals the WGS reads mapping to chrM. These were subsequently used for haplogroup assignment.
HiSeq X Ten 10
EGAD00001006039
This data set comprises WGS small variants and structural variants called in a cohort of 110 Egyptian individuals (10 individuals have been sequenced as part of this study and 100 are from EGAD00001001372/EGAD00001001380).
10
EGAD00001006040
This data set contains for 217 Egyptian individuals the amplicon sequencing reads mapping to chrM. These were subsequently used for haplogroup assignment.
Illumina MiSeq 217

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