PPLine: An Automated Pipeline for SNP, SAP, and Splice Variant Detection in the Context of Proteogenomics

Abstract

The fundamental mission of the Chromosome-Centric Human Proteome Project (C-HPP) is the research of human proteome diversity, including rare variants. Liver tissues, HepG2 cells, and plasma were selected as one of the major objects for C-HPP studies. The proteogenomic approach, a recently introduced technique, is a powerful method for predicting and validating proteoforms coming from alternative splicing, mutations, and transcript editing. We developed PPLine, a Python-based proteogenomic pipeline providing automated single-amino-acid polymorphism (SAP), indel, and alternative-spliced-variants discovery based on raw transcriptome and exome sequence data, single-nucleotide polymorphism (SNP) annotation and filtration, and the prediction of proteotypic peptides (available at https://sourceforge.net/projects/ppline). In this work, we performed deep transcriptome sequencing of HepG2 cells and liver tissues using two platforms: Illumina HiSeq and Applied Biosystems SOLiD. Using PPLine, we revealed 7756 SAP and indels for HepG2 cells and liver (including 659 variants nonannotated in dbSNP). We found 17 indels in transcripts associated with the translation of alternate reading frames (ARF) longer than 300 bp. The ARF products of two genes, SLMO1 and TMEM8A, demonstrate signatures of caspase-binding domain and Gcn5-related N-acetyltransferase. Alternative splicing analysis predicted novel proteoforms encoded by 203 (liver) and 475 (HepG2) genes according to both Illumina and SOLiD data. The results of the present work represent a basis for subsequent proteomic studies by the C-HPP consortium.

The influence of pro-longevity gene Gclc overexpression on the age-dependent changes in Drosophila transcriptome and biological functions

“…Processing of transcriptomic data was performed using PPLine toolkit [8] including read preprocessing (trimmomatic), mapping (STAR) and counting (HTSeq-count). The further analysis was done with R programming language (R core Team).…”

Connecting Proteomics to Next‐Generation Sequencing: Proteogenomics and Its Current Applications in Biology

“…The results revealed 2172 and 149 differentially expressed splicesoforms respectively including RAC1, OSBPL3, MKI67, and SYK . PPLine is a python‐based proteogenomic pipeline assisting discovery of SAPs, INDELs, and ASVs from transcriptome and exome sequence data, besides facilitating the annotation and filtration of SNPs and the prediction of proteotypic peptides …”

The Gene-Centric Content Management System and Its Application for Cognitive Proteomics

“… Datasets to map the canonical and spliced forms of missing proteins of Chr18 in the liver tissue ( a ) and in the HepG2 cell line ( b ). PE: protein evidence according to neXtProt; DB: information from several mass-spectrometry databases on protein detection in the biosample; Chr18 HPP transcriptomic data [ 19 , 20 , 26 ]; CF: level of expression of canonical form; S2–S7: levels of expression of the splice forms. Colored boxes represent the quantitative value assigned to the descriptor.…”