IntSplice2: Prediction of the Splicing Effects of Intronic Single-Nucleotide Variants Using LightGBM Modeling

Abstract

Prediction of the effect of a single-nucleotide variant (SNV) in an intronic region on aberrant pre-mRNA splicing is challenging except for an SNV affecting the canonical GU/AG splice sites (ss). To predict pathogenicity of SNVs at intronic positions -50 (Int-50) to -3 (Int-3) close to the 3' ss, we developed light gradient boosting machine (LightGBM)-based IntSplice2 models using pathogenic SNVs in the human gene mutation database (HGMD) and ClinVar and common SNVs in dbSNP with 0.01 ≤ minor allelic frequency (MAF) < 0.50. The LightGBM models were generated using features representing splicing cis-elements. The average recall/sensitivity and specificity of IntSplice2 by fivefold cross-validation (CV) of the training dataset were 0.764 and 0.884, respectively. The recall/sensitivity of IntSplice2 was lower than the average recall/sensitivity of 0.800 of IntSplice that we previously made with support vector machine (SVM) modeling for the same intronic positions. In contrast, the specificity of IntSplice2 was higher than the average specificity of 0.849 of IntSplice. For benchmarking (BM) of IntSplice2 with IntSplice, we made a test dataset that was not used to train IntSplice. After excluding the test dataset from the training dataset, we generated IntSplice2-BM and compared it with IntSplice using the test dataset. IntSplice2-BM was superior to IntSplice in all of the seven statistical measures of accuracy, precision, recall/sensitivity, specificity, F1 score, negative predictive value (NPV), and matthews correlation coefficient (MCC). We made the IntSplice2 web service at https://www.med.nagoya-u.ac.jp/neurogenetics/IntSplice2.

Keywords: LightGBM; aberrant splicing; intronic mutations; single nucleotide variations; splice acceptor site.

FIGURE 1

Evaluation of IntSplice2 by fivefold CV. (A) Five iterated and mean ROC curves with AUROCs. (B) Five iterated and mean PR curves with AUPRs.

FIGURE 2

The top 10 important features of IntSplice2 in 110 features.

FIGURE 3

A representative screenshot of the output of IntSplice2 web service. As previously reported, g.73550880G > A on chromosome 10 (GRCh37/hg19) identified in a patient with Usher syndrome is at the ninth nucleotide from the 3’ end of intron 45 of CDH23. When a user chooses “GRCh37/hg19” and enters the chromosome number “10” and the genomic coordinate “73550880,” the IntSplice2 web service returns the result on the same window on a browser.