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How often does the GDC update the workflow/reference genome? If the GDC updates the workflow/reference genome, does the GDC re-process all data sets?

Submitted by Anonymous on

For the reference genome, the GDC has been using an augmented version of GRCh38.p2 (with additional decoy sequences and virus sequences) since inception. The GDC does not use alternative contigs, and only derives high-level data from the major chromosomes, so the same reference genome is used for both gene model GENCODE v22 (from Data Release 1 to 31) and GENCODE v36 (from Data Release 32). As future versions of the reference genome are released, e.g., GRCh39, the GDC will evaluate the benefits of updating data to utilize the new version.

Does the GDC use common exomes across all whole exome platforms?

Submitted by Anonymous on

There is a variety of target capture kits used by different sequencing centers. Most of the whole exome capture kits share many common genomic regions, especially for cancer related genes; However, which exons are included is totally dependent on the vendor's library preparation kit. There are often more differences among capture regions from different Targeted-Sequencing/Panel data.

What considerations should be taken when comparing samples with different target capture kits?

Submitted by Anonymous on

Target capture kits are used to "target" specific regions of a given genome for the Whole Exome Sequencing (WXS) and Targeted Sequencing experimental strategies. Users should therefore take care when comparing data from different target capture kits for the WXS and Targeted Sequencing experimental strategies because of potential differences in genomic regions targeted, variant filtering, and subsequent variants recovered.

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