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.
- 42 samples
- DAC: EGAC00001000723
- Technology: Illumina HiSeq 2000
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 |
|---|---|---|
| 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 | Located in | |
|---|---|---|---|---|
| EGAF00001766094 | fastq.gz | 5.0 GB | ||
| EGAF00001766095 | fastq.gz | 5.1 GB | ||
| EGAF00001767987 | fastq.gz | 5.5 GB | ||
| EGAF00001767988 | fastq.gz | 5.5 GB | ||
| EGAF00001767989 | fastq.gz | 5.0 GB | ||
| EGAF00001767990 | fastq.gz | 5.0 GB | ||
| EGAF00001767991 | fastq.gz | 6.3 GB | ||
| EGAF00001767992 | fastq.gz | 6.5 GB | ||
| EGAF00001767993 | fastq.gz | 5.7 GB | ||
| EGAF00001767994 | fastq.gz | 5.9 GB | ||
| EGAF00001767995 | fastq.gz | 6.3 GB | ||
| EGAF00001767996 | fastq.gz | 6.5 GB | ||
| EGAF00001767997 | fastq.gz | 5.8 GB | ||
| EGAF00001767998 | fastq.gz | 6.0 GB | ||
| EGAF00001767999 | fastq.gz | 5.1 GB | ||
| EGAF00001768000 | fastq.gz | 5.2 GB | ||
| EGAF00001768001 | fastq.gz | 6.4 GB | ||
| EGAF00001768002 | fastq.gz | 6.5 GB | ||
| EGAF00001768003 | fastq.gz | 5.6 GB | ||
| EGAF00001768004 | fastq.gz | 5.8 GB | ||
| EGAF00001768005 | fastq.gz | 4.2 GB | ||
| EGAF00001768006 | fastq.gz | 4.2 GB | ||
| EGAF00001768007 | fastq.gz | 4.5 GB | ||
| EGAF00001768008 | fastq.gz | 4.5 GB | ||
| EGAF00001768009 | fastq.gz | 4.9 GB | ||
| EGAF00001768010 | fastq.gz | 4.9 GB | ||
| EGAF00001768011 | fastq.gz | 5.8 GB | ||
| EGAF00001768012 | fastq.gz | 5.9 GB | ||
| EGAF00001768013 | fastq.gz | 5.5 GB | ||
| EGAF00001768014 | fastq.gz | 5.5 GB | ||
| EGAF00001768015 | fastq.gz | 5.6 GB | ||
| EGAF00001768016 | fastq.gz | 5.7 GB | ||
| EGAF00001768017 | fastq.gz | 4.9 GB | ||
| EGAF00001768018 | fastq.gz | 4.9 GB | ||
| EGAF00001768019 | fastq.gz | 5.6 GB | ||
| EGAF00001768020 | fastq.gz | 5.8 GB | ||
| EGAF00001768021 | fastq.gz | 6.0 GB | ||
| EGAF00001768022 | fastq.gz | 6.2 GB | ||
| EGAF00001768023 | fastq.gz | 6.4 GB | ||
| EGAF00001768024 | fastq.gz | 6.5 GB | ||
| EGAF00001768025 | fastq.gz | 6.1 GB | ||
| EGAF00001768026 | fastq.gz | 6.3 GB | ||
| EGAF00001768027 | fastq.gz | 5.9 GB | ||
| EGAF00001768028 | fastq.gz | 6.0 GB | ||
| EGAF00001768029 | fastq.gz | 5.0 GB | ||
| EGAF00001768030 | fastq.gz | 5.1 GB | ||
| EGAF00001768031 | fastq.gz | 5.9 GB | ||
| EGAF00001768032 | fastq.gz | 6.0 GB | ||
| EGAF00001768033 | fastq.gz | 5.3 GB | ||
| EGAF00001768034 | fastq.gz | 5.4 GB | ||
| EGAF00001768035 | fastq.gz | 4.1 GB | ||
| EGAF00001768036 | fastq.gz | 4.1 GB | ||
| EGAF00001768037 | fastq.gz | 4.1 GB | ||
| EGAF00001768038 | fastq.gz | 4.1 GB | ||
| EGAF00001768039 | fastq.gz | 3.7 GB | ||
| EGAF00001768040 | fastq.gz | 3.8 GB | ||
| EGAF00001768041 | fastq.gz | 6.0 GB | ||
| EGAF00001768042 | fastq.gz | 6.0 GB | ||
| EGAF00001768043 | fastq.gz | 7.6 GB | ||
| EGAF00001768044 | fastq.gz | 7.6 GB | ||
| EGAF00001768045 | fastq.gz | 5.5 GB | ||
| EGAF00001768046 | fastq.gz | 5.5 GB | ||
| EGAF00001768047 | fastq.gz | 3.7 GB | ||
| EGAF00001768048 | fastq.gz | 3.8 GB | ||
| EGAF00001768049 | fastq.gz | 3.4 GB | ||
| EGAF00001768050 | fastq.gz | 3.5 GB | ||
| EGAF00001768051 | fastq.gz | 2.7 GB | ||
| EGAF00001768052 | fastq.gz | 2.7 GB | ||
| EGAF00001768053 | fastq.gz | 3.8 GB | ||
| EGAF00001768054 | fastq.gz | 3.9 GB | ||
| EGAF00001768055 | fastq.gz | 4.5 GB | ||
| EGAF00001768056 | fastq.gz | 4.6 GB | ||
| EGAF00001768057 | fastq.gz | 4.8 GB | ||
| EGAF00001768058 | fastq.gz | 4.9 GB | ||
| EGAF00001768059 | fastq.gz | 4.4 GB | ||
| EGAF00001768060 | fastq.gz | 4.5 GB | ||
| EGAF00001768061 | fastq.gz | 4.2 GB | ||
| EGAF00001768062 | fastq.gz | 4.3 GB | ||
| EGAF00001768063 | fastq.gz | 3.1 GB | ||
| EGAF00001768064 | fastq.gz | 3.1 GB | ||
| EGAF00001768065 | fastq.gz | 4.3 GB | ||
| EGAF00001768066 | fastq.gz | 4.4 GB | ||
| EGAF00001768067 | fastq.gz | 4.5 GB | ||
| EGAF00001768068 | fastq.gz | 4.6 GB | ||
| 84 Files (428.8 GB) | ||||