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Genomic sequencing of HG001 sample

This study is for testing purposes. We will use only chromosome 22 alignment BAM file and a complete variant calling VCF file to illustrate the technical compliancy with FEGA processes.

Type: Whole Genome Sequencing
Archive: Federated EGA France Federated EGA Node

1 Dataset 2 Publications

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
EGAD50000000558	The following dataset contains chromosome 22 alignment file and whole genome variant calls for sample HG001 from 1KGP. Analyses were performed using GRCh38 reference genome. BWA was used for the genomic alignment. GATK4 for variant calling	Illumina NovaSeq 6000	1

Publications	Citations
Epigenetic landscape reorganisation and reactivation of embryonic development genes are associated with malignancy in IDH-mutant astrocytoma. Ghisai SA, van Hijfte L, Vallentgoed WR, Tesileanu CMS, de Heer I, Kros JM, Sanson M, Gorlia T, Wick W, Vogelbaum MA, Brandes AA, Franceschi E, Clement PM, Nowak AK, Golfinopoulos V, van den Bent MJ, French PJ, Hoogstrate Y. Acta Neuropathol 148: 2024 50	18
Gemistocytic tumor cells programmed for glial scarring characterize T cell confinement in IDH-mutant astrocytoma. van Hijfte L, Geurts M, de Heer I, Ghisai SA, Balcioglu HE, Hoogstrate Y, Vallentgoed WR, Head R, Luning R, van den Bosch T, Westerman B, Wesseling P, Joyce JA, French P, Debets R. Nat Commun 16: 2025 1156	7

Publications

Citations

Epigenetic landscape reorganisation and reactivation of embryonic development genes are associated with malignancy in IDH-mutant astrocytoma.
Ghisai SA, van Hijfte L, Vallentgoed WR, Tesileanu CMS, de Heer I, Kros JM, Sanson M, Gorlia T, Wick W, Vogelbaum MA, Brandes AA, Franceschi E, Clement PM, Nowak AK, Golfinopoulos V, van den Bent MJ, French PJ, Hoogstrate Y. Acta Neuropathol 148: 2024 50

Gemistocytic tumor cells programmed for glial scarring characterize T cell confinement in IDH-mutant astrocytoma.
van Hijfte L, Geurts M, de Heer I, Ghisai SA, Balcioglu HE, Hoogstrate Y, Vallentgoed WR, Head R, Luning R, van den Bosch T, Westerman B, Wesseling P, Joyce JA, French P, Debets R. Nat Commun 16: 2025 1156