Table 2 Fusion filtering and annotation criteria
Order | Description | Filtering type | Rationale | Output type | Filtering criteria |
|---|---|---|---|---|---|
1 | Artifact filtering for readthroughs (readthrough fusions in mittelman database are not filtered) | QC | To filter artifacts | All | General |
2 | Artifact filtering for fusions found in normal datasets and gene homologs (red flag database from FusionAnnotator) | QC | To filter artifacts | All | General |
3 | JunctionReadCount == 0 | QC | To filter out false calls | All | General |
4 | SpanningFragCount-JunctionReadCount >= 100 | QC | To filter false calls from low mapping | All | General |
5 | Both gene partners with FPKM < 1 | QC | To filter out not expressed fused genes | All | General |
6 | Fused genes with either gene in TSGs,Cosmic,Oncogenic,TCGA fusion list | Gene-list | To capture cancer-specific fusions | Putative-driver | Project-specific |
7 | Local Rearrangement | QC | To remove local rearrangement within neighbouring genes | Filtered-fusion | Project-specific |
8 | Fusion is called by both callers | QC | To filter out calls from only 1 caller | Filtered-fusion | Project-specific |
9 | Fusion is called in atleast 2 samples per histology | Recurrence | To gather recurrent fusion calls | Filtered-fusion | Project-specific |
10 | Fusion in Filtered-fusions found in more than 1 histology | QC | To remove fusions from Filered-fusion list that are found in more than1 histology | Filtered-fusion | Project-specific |
11 | Fused genes in Filtered-fusion fusions found to be multi-fused more than 5 times in a sample | QC | To remove fusions from Filtered-fusion list that are found to be multi-fused | Filtered-fusion | Project-specific |
12 | Add recurrent fusions that pass QC from steps 7–11 | Recurrence | To add non-oncogenic fusions to putative-driver fusion list | Putative-driver + recurrent non-oncogenic fusion | Project-specific |
Description | Annotation type | Rationale | Output type | Annotation source |
|---|---|---|---|---|
genelistreference.txt | Gene-list | To annotate filtered and unfiltered fusion calls with gene list of interest saved in reference folder | All | Oncogene, tsgs, kinase, cosmic census, curated tf and predicted tf |
fusionreference.txt | Gene-list | To annotate filtered and unfiltered fusion calls with fusion list of interest saved in reference folder | All | TCGA |
GTEx zscored comparison | Expression | To annotate filtered and unfiltered fusion calls zscore and comparison with GTEx | All | GTEx |
Cohort comparison | Expression | To annotate filtered and unfiltered fusion calls zscore and comparison with cohort level expression | All | Cohort |