Description
Somatic single nucleotide variants (SNVs) in cancer genome affect gene expression through various mechanisms depending on their genomic location. In this study, we found that somatic SNVs near splice site are associated with abnormal intronic polyadenylation (IPA) . Here we give examples to show how to detect SNV-associated IPA events and SNV-associated intron retention (IR) events.
RNAseq density plots and IGV browser screenshots showing that somatic variant could cause intronic polyadenylation in GRHL2 (A) and intron retention in TP53 (B).
Detect SNV-associated IPA event in GRHL2
python Detect_SNV_IPA.py -bam GRHL2_TCGA-95-7043_test.bam -anno_txt hg38_annotation.txt -snv_file GRHL2_SNV_information.txt -output GRHL2_SNV_IPA.txt
GRHL2_TCGA-95-7043_test.bam: a bamfile extracted reads mapping the gene GRHL2 from RNAseq bamfile of patient TCGA-95-7043
hg38_annotation.txt: a file contains all information of introns and exons annotated by Refseq
GRHL2_SNV_information.txt: a file contains information about somatic variants of GRHL2 in patient TCGA-95-7043
Detect SNV-associated IR event in TP53
python Detect_SNV_IR.py -bam TP53_TCGA-LA-A446_test.bam -anno_txt hg38_annotation.txt -snv_file TP53_SNV_information.txt -output TP53_SNV_IR.txt
TP53_TCGA-LA-A446_test.bam: a bamfile extracted reads mapping the gene TP53 from RNAseq bamfile of patient TCGA-LA-A446
GRHL2_SNV_information.txt: a file contains information about somatic variants of GRHL2 in patient TCGA-95-7043
Statement: The Cancer Genome Atlas (TCGA) characterizes a comprehensive list of genomic, epigenomic, and transcriptomic features in thousands of tumor samples. Here we give the examples to show how to perform SNV-associated IPA analysis and SNV-associated IR analysis. One can utilize our code functions in the python script file to further perform SNV-associated IPA analysis and SNV-associated IR analysis by intergrating more whole-exome sequencing and RNAseq datasets.
The following python packages are necessary:
HTSeq、itertools、numpy、collections、multiprocessing、scipy、argparse、re、os
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