Biomedical Genomics Center of Excellence

Egyptian Human Genome Sequencing Project

Providing the necessary infrastructure for genome sequencing based on Next Generation Sequencing and the related data analysis.

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A biomedical genomics center of excellence based on Next Generation Sequencing technology (NGS), focusing on whole genome sequencing and its applications in identifying (individual) structural genomic variations, gene expression, epigenetics, and meta-genomics. The center includes the necessary bioinformatics infrastructure and expertise to analyze the produced datasets.

NGS Sequencing
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The center includes the Ion Proton as well as the Ion PGM Sequencing Platforms, with equipment for high throughput DNA extraction, DNA processing, Read More ...

Sequencing Options
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The center can run whole genome sequencing, exome sequencing, as well as sequencing of gene panels. It can also run RNAseq sequencing experiments Read More ...

Sequencing Applications
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The sequencing experiments can be used to identify point mutations and larger structural variations against a reference genome. It can also be used to Read More ...


Variant Analysis

Identification of different variants compared to a reference genome. It includes the steps of read mapping, variant analysis, and variant annotation. Large indels can also be detected using CNV algorithms.


Analysis of a sample, including mix of micro-organisms: The analysis workflow includes the steps of read assembly, read alignment to nucleotide databases, and taxa identification and quantization.

Transcriptome Analysis

Analysis of mRNA data: The analysis workflow includes the steps of aligning the reads to a reference genome, assembly of mapped reads into transcripts, and measuring relative expression levels.

Hepatitis diseases and its progression into hepatocellular carcinoma (HCC) show the highest incidence rate in Egyptian population compared to other countries world-wide. The project aims at determining the genetic background responsible for the manifestation and progression of the hepatocellular carcinoma (HCC) as well as response to drugs. The use of NGS technology for analyzing the whole genomes of Egyptian patients will bring more insight into the problem and will help in discovering the key genomic features and mechanisms associated with the disease. Our methodology includes the sequencing of the genomes of hundreds of patients at different disease stages (from HCV to HCC) and the included viruses as well as genomes of control persons. The genomes will be analyzed for identifying genomic variations and for associating these variations to disease stages and other clinical features.

Team & Funding


A group of scientists from National Cancer Institute (NCI) and Nile University


The Center and the research project is funded by the Science and Technology Development Fund (STDF), Egypt.