Hereditary Cancer Diagnostics with I2HCP gene panel

This dataset contains targetted DNA sequencing data generated in the context of genetic diagnostics of hereditary cancer. Target enrichment was performed with the I2HCP, a custom hereditary cancer gene panel based in Agilent SureSelect and developed by the Germans Trias i Pujol Research Institute (IGTP, Badalona, Catalonia, Spain) and the Catalan Institute of Oncology (ICO, L'Hospitalet de Llobregat, Catalonia, Spain). After the enrichment, 108 samples were sequenced in Illumina HiSeq machines and 130 in MiSeq machines. Some of the samples were sequenced on both platforms. The dataset also includes MLPA validation data for all identified copy-number alterations, annotated with exon resolution and information about negative MLPA results. All this data was generated in the context of routine diagnostics and compiled together with MPLA validation data for a genetic diagnostics oriented benchmark of germline CNV calling tools.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 4 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
EGAD00001006171	Germline blood DNA sequencing data generated in routine diagnostics of hereditary cancer using the I2HCP gene panel (~135 genes). There are 130 samples sequenced in a MiSeq machine and 108 sequenced in a HiSeq machine. There is a partial overlap between those two sets, meaning that some samples were sequenced in both machines. There is a strong enrichment in samples with copy-number variants (CNV), both single- and multi-exon, since this dataset was compiled for a benchmarking effort of CNV calling tools for genetic diagnostics.	Illumina HiSeq 2500 Illumina MiSeq	188

Publications	Citations
Benchmarking of Whole Exome Sequencing and Ad Hoc Designed Panels for Genetic Testing of Hereditary Cancer. Feliubadaló L, Tonda R, Gausachs M, Trotta JR, Castellanos E, López-Doriga A, Teulé À, Tornero E, Del Valle J, Gel B, Gut M, Pineda M, González S, Menéndez M, Navarro M, Capellá G, Gut I, Serra E, Brunet J, Beltran S, Lázaro C. Sci Rep 7: 2017 37984	25
A comprehensive custom panel design for routine hereditary cancer testing: preserving control, improving diagnostics and revealing a complex variation landscape. Castellanos E, Gel B, Rosas I, Tornero E, Santín S, Pluvinet R, Velasco J, Sumoy L, Del Valle J, Perucho M, Blanco I, Navarro M, Brunet J, Pineda M, Feliubadaló L, Capellá G, Lázaro C, Serra E. Sci Rep 7: 2017 39348	22
Evaluation of CNV detection tools for NGS panel data in genetic diagnostics. Moreno-Cabrera JM, Del Valle J, Castellanos E, Feliubadaló L, Pineda M, Brunet J, Serra E, Capellà G, Lázaro C, Gel B. Eur J Hum Genet 28: 2020 1645-1655	50
Detection of germline CNVs from gene panel data: benchmarking the state of the art. Munté E, Roca C, Del Valle J, Feliubadaló L, Pineda M, Gel B, Castellanos E, Rivera B, Cordero D, Moreno V, Lázaro C, Moreno-Cabrera JM. Brief Bioinform 26: 2024 bbae645	0