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As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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Samples linked to the study "Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples"

We generated 42 human whole-exome sequencing data sets from fresh-frozen (FF) and FFPE samples. These samples include normal and tumor tissues from two different organs (liver and colon), that we extracted with three different FFPE extraction kits (QIAamp DNA FFPE Tissue kit and GeneRead DNA FFPE kit from Qiagen, Maxwell\textsuperscript{TM} RSC DNA FFPE Kit from Promega). Variant calling analysis shows a very high rate of concordance between matched FF / FFPE pairs and equivalent performance for the three kits we analyzed. We find a significant variation in the difference of total number of variants called between FF and FFPE samples for the three different FFPE DNA extraction kits. Coverage analysis shows that FFPE samples have less good indicators than FF samples, yet the coverage quality remains above accepted thresholds. We detect limited but significant variations in coverage indicator values between the three FFPE extraction kits. Globally, the GeneRead and QIAamp kits have better variant calling and coverage indicators than the Maxwell kit on the samples used in this study, although this kit performs better on some indicators and has advantages in terms of practical usage. Taken together, our results confirm the potential of FFPE samples analysis for clinical genomic studies, but also indicate that the choice of a FFPE DNA extraction kit should be done with careful testing and analysis beforehand in order to maximize the accuracy of the results.

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These terms and conditions govern access to the managed access datasets to which the User Institution has requested access. These datasets are managed by the french Centre National de Recherche en Génomique Humaine (CNRGH, National Center for Human Genomics Research).

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001002631 Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Quality Report
Located in
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EGAF00001766094 fastq.gz 5.0 GB Report
EGAF00001766095 fastq.gz 5.1 GB Report
EGAF00001767987 fastq.gz 5.5 GB Report
EGAF00001767988 fastq.gz 5.5 GB Report
EGAF00001767989 fastq.gz 5.0 GB Report
EGAF00001767990 fastq.gz 5.0 GB Report
EGAF00001767991 fastq.gz 6.3 GB Report
EGAF00001767992 fastq.gz 6.5 GB Report
EGAF00001767993 fastq.gz 5.7 GB Report
EGAF00001767994 fastq.gz 5.9 GB Report
EGAF00001767995 fastq.gz 6.3 GB Report
EGAF00001767996 fastq.gz 6.5 GB Report
EGAF00001767997 fastq.gz 5.8 GB Report
EGAF00001767998 fastq.gz 6.0 GB Report
EGAF00001767999 fastq.gz 5.1 GB Report
EGAF00001768000 fastq.gz 5.2 GB Report
EGAF00001768001 fastq.gz 6.4 GB Report
EGAF00001768002 fastq.gz 6.5 GB Report
EGAF00001768003 fastq.gz 5.6 GB Report
EGAF00001768004 fastq.gz 5.8 GB Report
EGAF00001768005 fastq.gz 4.2 GB Report
EGAF00001768006 fastq.gz 4.2 GB Report
EGAF00001768007 fastq.gz 4.5 GB Report
EGAF00001768008 fastq.gz 4.5 GB Report
EGAF00001768009 fastq.gz 4.9 GB Report
EGAF00001768010 fastq.gz 4.9 GB Report
EGAF00001768011 fastq.gz 5.8 GB Report
EGAF00001768012 fastq.gz 5.9 GB Report
EGAF00001768013 fastq.gz 5.5 GB Report
EGAF00001768014 fastq.gz 5.5 GB Report
EGAF00001768015 fastq.gz 5.6 GB Report
EGAF00001768016 fastq.gz 5.7 GB Report
EGAF00001768017 fastq.gz 4.9 GB Report
EGAF00001768018 fastq.gz 4.9 GB Report
EGAF00001768019 fastq.gz 5.6 GB Report
EGAF00001768020 fastq.gz 5.8 GB Report
EGAF00001768021 fastq.gz 6.0 GB Report
EGAF00001768022 fastq.gz 6.2 GB Report
EGAF00001768023 fastq.gz 6.4 GB Report
EGAF00001768024 fastq.gz 6.5 GB Report
EGAF00001768025 fastq.gz 6.1 GB Report
EGAF00001768026 fastq.gz 6.3 GB Report
EGAF00001768027 fastq.gz 5.9 GB Report
EGAF00001768028 fastq.gz 6.0 GB Report
EGAF00001768029 fastq.gz 5.0 GB Report
EGAF00001768030 fastq.gz 5.1 GB Report
EGAF00001768031 fastq.gz 5.9 GB Report
EGAF00001768032 fastq.gz 6.0 GB Report
EGAF00001768033 fastq.gz 5.3 GB Report
EGAF00001768034 fastq.gz 5.4 GB Report
EGAF00001768035 fastq.gz 4.1 GB Report
EGAF00001768036 fastq.gz 4.1 GB Report
EGAF00001768037 fastq.gz 4.1 GB Report
EGAF00001768038 fastq.gz 4.1 GB Report
EGAF00001768039 fastq.gz 3.7 GB Report
EGAF00001768040 fastq.gz 3.8 GB Report
EGAF00001768041 fastq.gz 6.0 GB Report
EGAF00001768042 fastq.gz 6.0 GB Report
EGAF00001768043 fastq.gz 7.6 GB Report
EGAF00001768044 fastq.gz 7.6 GB Report
EGAF00001768045 fastq.gz 5.5 GB Report
EGAF00001768046 fastq.gz 5.5 GB Report
EGAF00001768047 fastq.gz 3.7 GB Report
EGAF00001768048 fastq.gz 3.8 GB Report
EGAF00001768049 fastq.gz 3.4 GB Report
EGAF00001768050 fastq.gz 3.5 GB Report
EGAF00001768051 fastq.gz 2.7 GB Report
EGAF00001768052 fastq.gz 2.7 GB Report
EGAF00001768053 fastq.gz 3.8 GB Report
EGAF00001768054 fastq.gz 3.9 GB Report
EGAF00001768055 fastq.gz 4.5 GB Report
EGAF00001768056 fastq.gz 4.6 GB Report
EGAF00001768057 fastq.gz 4.8 GB Report
EGAF00001768058 fastq.gz 4.9 GB Report
EGAF00001768059 fastq.gz 4.4 GB Report
EGAF00001768060 fastq.gz 4.5 GB Report
EGAF00001768061 fastq.gz 4.2 GB Report
EGAF00001768062 fastq.gz 4.3 GB Report
EGAF00001768063 fastq.gz 3.1 GB Report
EGAF00001768064 fastq.gz 3.1 GB Report
EGAF00001768065 fastq.gz 4.3 GB Report
EGAF00001768066 fastq.gz 4.4 GB Report
EGAF00001768067 fastq.gz 4.5 GB Report
EGAF00001768068 fastq.gz 4.6 GB Report
84 Files (428.8 GB)