Comparative analysis of somatic variant calling on matched FF and FFPE WGS samples

Study ID Alternative Stable ID Type
EGAS00001004456 Other

Study Description

This study aims at assessing whether FFPE material can be used for cohort analysis. To this end, we performed an in-depth comparison of somatic SNVs called on matching FF and FFPE whole genome sequences samples extracted from the same metastatic prostate tumor. Four variant callers were used to call somatic variants on both the FF and the FFPE samples. An heuristic was developed to maximize the overlap between the FF and its FFPE counterparts. Then, the extent to which intra-tumor heterogeneity explains discrepancies in variants called between the FF and the FFPE samples was assessed by comparing the clonal and subclonal somatic variants. This study illustrates that when using the correct variant calling strategy, the majority of clonal SNVs can be recovered in an FFPE sample with high precision and sensitivity. These results suggest that somatic variants derived from WGS of FFPE material can be used in cohort studies.

Study Datasets 1 dataset.

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
This dataset contains three bam files. One normal blood sample and two matched FF and FFPE samples from the same metastatic prostate tumor.
HiSeq X Ten 3

Who archives the data?