RETRACTED ARTICLE: Mutation pattern is an influential factor on functional mutation rates in cancer

To investigate the mutation pattern and what factors influence mutation rates in cancers, we obtained 71,424 somatic mutations from 14 paired ccRCC and normal samples [12], 2,011,261 variants from 25 melanoma patients [13], 1,845,976 from 24 lung adenocarcinoma patients, and 881,136 from 88 liver cancer patients [6] (see “Methods” section). We also took 38,248,779 SNPs (single nucleotide polymorphism) from the 1000 genomes project pilot one [14] as a comparison. We intersected somatic mutations and SNPs with a wide range of genomic features, epigenetic properties and computed the average mutation densities of somatic mutations and SNPs for each feature type. Figure 1 and Additional file 1: Figure S1–S4 showed the somatic mutation and SNP densities associated to various features. We found functionally important regions, such as CDS, promoter, UTR and ncExons are relatively low mutated compared to introns of lncRNAs (P value <0.05 in most cases except for promoter in kidney cancer and ncExon in melanoma and CDS, UTR for SNPs, Wilcoxon rank sum test). Furthermore, we obtained 5 cancer driver genes in ccRCC, VHL, PBRM1, TCEB1, BAP1 and SETD2, from Sato’s study [12], we found only two mutations, one in the CDS and another in the promoter of PBRM1, suggesting the CDS, promoters and UTR of these cancer-driving genes are mainly protected from mutations in ccRCC. Exons of either protein coding genes or lncRNAs showed lower somatic mutation rates relative to their introns respectively (P value <0.05 for lncRNAs in all cases, P value <0.05 for protein coding genes in liver and lung cancer, Wilcoxon rank sum test). However, no significant difference was observed on the SNP density between exons and introns of either protein coding genes or lncRNAs (P value >0.05 in all cases, Wilcoxon rank sum test). Expression level and replication time are two important factors affecting cancer mutation and SNP rates, as evidenced by consistently lower mutation and SNP rates in high expressed and early replicated genes versus low expressed and late replicated ones (P value <0.05 in all cases with a range from 0.008 to 2.429e-13, Wilcoxon rank sum test). Repressive histone marks, such as H3K9me1, H3K9me2, H3K9me3, H3K27me2 and H3K27me3 are largely over-mutated in comparison with active histone marks, such as H3K4me1, H3K4me2, H3K79me1,H3K79me2,H3K79me3, and H4K20me1 (P values range from 0.3482 to 2.429e-13 and are less than 0.05 in 95.83 % of cases for cancer somatic mutations, P values range from 0.8618 to 3.5742e-09 and are less than 0.05 in 73.33 % of cases for SNPs, Wilcoxon rank sum test). Furthermore, in order to further characterize the relation between somatic mutation, SNP rates and each feature, we constructed 2856 1-Mb windows, in which each row (1-Mb window) contains somatic mutation, SNP densities and 54 feature vectors (see “Methods” section). Correlation analyses were conducted between cancer somatic mutation, SNP densities and each feature vector. Features such as promoter, replication time, CDS, UTR are most negatively correlated with both somatic mutation and SNP densities (r = −0.3036 to −0.6178, P value <1.5233e-61 for somatic mutations; r = −0.0264 to −0.1219, P value = 1.6048e-01–7.2937e-11 for SNPs). Repressive histone marks, such as H3K9me1, H3K9me2, H3K9me3, H4K20me3, H3K27me2 show high positive correlations with both somatic mutation and SNP densities (r = 0.1336–0.6044, P value <1.1440e-12 for somatic mutations; r = 0.3393–0.5178, P value = 0 for SNPs) (Fig. 2). In general, SNP rates exhibit a large difference with somatic mutations, such as conserved regions and cTFBS (conserved transcription factor binding sites). These two regions are over-mutated in somatic mutations but protected from SNPs (Fig. 1). Recombination rates show strong positive correlation with SNPs but a relatively weak correlation with somatic mutations (r = −0.1210–0.0499, P value <7.8871e-03 for somatic mutations; r = 0.5015, P value = 0 for SNPs). Moreover, multiple features have contrasting correlations with somatic mutation and SNP rates, such as H3K4ac, H4K5ac, H3K4me1, H3K4me2, H4K20me1 and ncExon (Fig. 2), suggesting distinct mutation patterns of somatic mutations and SNPs in cancer genome.

Given the sparse number of cancer mutations, we built two random forest models, referred to as the CSM and SNP models, with 2856 1-Mb windows constructed above in order to analyze mutation distribution in more detail. %IncMSE is computed from permuting a predictor’s values over the original dataset, if a predictor is important in the model, the prediction error on the out-of-bag portion of the data (MSE for regression) will be increased [15]. We used %IncMSE to measure feature importance in the random Forest. In the CSM model, repressive histone marks such as H3K9me1, H3K9me2, H3K27me3, H3K27me2 and H4K20me3, replication time and promoter are among the most informative factors, which corresponds to the findings in the correlation analyses (Fig. 3a; Additional file 1: Figure S5). However, features such as CDS, UTR have medium importance in the CSM model, a possible explanation is these regions are relatively small in the genome and have little impact on genome-wide mutation rates, supporting that repressive histone marks, replication time and promoter contribute most to the CSM models. In the SNP model, the most important features are recombination rate, H4R3me2, H4K20me3, ECS, H3R3me2 and H3K27me2, which is in line with the correlation analyses above (Fig. 3b).

Next, we asked whether mutation frequencies are associated to functionality and distribution of functional mutations. In order to examine this hypothesis, firstly, we constructed annotation data which are overlapping 1-Mb windows with a step size 1 Kb using all 54 features, CSM and SNP densities (CSM and SNP scores) were predicted with the CSM and SNP random models for each 1 Mb-window and cancer type and averaged on a 1 Kb scale (see “Methods” section). We applied SIFT and Mutation Assessor to predict damaging coding mutations for all cancer types. In total, 10,572, 1208,1625, 2519, and 7745, 1924,3009,3579 mutations were predicted as deleterious by SIFT and Mutation Assessor in ccRCC, liver cancer, lung cancer and melanoma respectively. We found markedly higher densities of deleterious mutations in the low CSM and SNP scoring regions as compared with those in the high CSM and SNP scoring ones. Moreover, negative correlations of average CSM and SNP scores were observed with densities of damaging mutations (r = −0.6034 to −0.9060 for CSM scores, r = −0.4721 for SNP scores, p value <0.05 in all cases), suggesting strong enrichment of deleterious mutations in the low mutated regions (Fig. 4a, b; Additional file 1: Figure S6). On the other hand, we computed functional scores for all non-coding mutations with FunSeq 2 and GWAVA and analyzed their distributions with respect to mutation rates. We observed that hypomutated regions with low CSM and SNP scores have higher average FunSeq 2 and GWAVA scores than hypermutated ones. Take the 200 Mb intervals with the highest and lowest CSM and SNP scores as examples, the 200 Mb interval with the lowest average CSM score has higher average GWAVA and FunSeq 2 scores than that with highest CSM score (P value <2.2e-16 in all cases, Wilcoxon rank sum test); The differences of average GWAVA and FunSeq 2 scores are relatively weak between the 200 Mb intervals with lowest SNP score and highest SNP score (P value = 0.0090 for GWAVA, P value = 0.161 for FunSeq 2, Wilcoxon rank sum test) (Fig. 4c, d; Additional file 1: Figure S7). Furthermore, we took 100 Mb lowest and highest scoring CSM, SNP regions respectively and analyzed their distributions across various genetic features. As expected, functionally important regions, such as CDS, exons, UTR, splicing sites of protein coding genes and miRNAs, have 2–48-fold higher enrichment of low CSM and SNP scoring regions than high CSM and SNP scoring regions (P value <2.2e-16 for all cases, Chi squared test), however, nearly functionally neutral regions, such as lncRNAs and intron of lncRNAs are 1.5–2-fold more enriched with high CSM and SNP scoring regions relative to low CSM and SNP scoring ones (P value <2.2e-16 for all cases, Chi squared test). Strikingly, fractions of low CSM and SNP scoring regions are 7~ times higher than those of high CSM and SNP scoring regions in cancer-related miRNAs and genes (P value <2.2e-16 in all cases, Chi squared test) (Fig. 5a; Additional file 1: Figure S8). In addition, ccRCC driver genes, VHL, PBRM1, TCEB1, BAP1 and SETD2, are all located in the low scoring 1-Kb windows, their average CSM scores are 21.436, 20.7088, 25.043, 20.7625 and 20.3447 respectively, which are less than the average (25.0582) in ccRCC. Lastly, we obtained non-coding disease-causing variants from HGMD and ClinVar databases and analyzed their distributions with regards to mutation rates. Disease-associated variants have lower average SNP and CSM scores than random SNPs (P value <2.2e-16 in all cases, Wilcoxon rank sum test) (Fig. 5b; Additional file 1: Figure S9). Low CSM and SNP scoring regions have higher enrichment of disease-causing variants than high CSM and SNP scoring ones. Take the lowest and highest CSM and SNP scoring 200-Mb intervals as examples, the former has an 14–117 times higher average densities of disease-causing variants than the latter (P value <2.2e-16 in all cases, Chi squared test). Significant negative correlations were observed between average CSM and SNP scores and densities of disease-associated variants (r = −0.6593 to −0.7790 for CSM scores,−0.5718 for SNP scores, P values <0.05 in all cases) (Fig. 5c, d; Additional file 1: Figure S10). All these findings support the fact that mutation rate is an important indicator of function and an influential factor on the distribution of functional mutations in cancer genome.

Somatic variants were generated by whole genome sequencing of paired cancer and normal tissues and obtained from three studies: 2,011,261 variants from 25 melanoma patients [13], 1,845,976 variants from 24 lung adenocarcinoma patients, and 881,136 variants from 88 liver cancer patients [6] and 71,424 variants from 14 paired ccRCC and normal samples [12].Variants described as “substitution” or “indel” were both collected and are referred to collectively as mutations in the text. Germ line mutation data including 38,248,779 SNPs (single nucleotide polymorphism) were obtained from the 1000 genomes project [14] ⁠ (http://​www.​1000genomes.​org). Disease-associated variants data come from ClinVar (Version 2014/03/03, 55,689 variants) [23] and HGMD [24] (Version 2014/04/14, 166,768 variants) databases which are two common curations of variants related to human inherited diseases, coding variants were removed in this study, forming 6045 and 13,108 disease-implicated variants in the non-coding genome.

Human genome annotation were obtained from Gencode V21, including protein coding genes, exons, introns, UTR, non-coding exons (ncExon) ect [25]. Evolutionarily conserved bases with phast Cons score greater than 117 were identified through alignment of 46 mammalian genomes with human [26]. Evolutionarily conserved structures (ECS) are RNA secondary structures predicted with a nouvel pipeline based on RNAz and SISSIz in Smith MA’ study [27]. Promoters generated by the Gerstein lab are regulatory regions 2.5 Kb from transcription start sites (TSS) [28]. Genome-wide mapping of histone acetylation and methylation data of CD4+ T cell line were produced by ChIP-seq in Wang’s [29] and Barski’s study [30] respectively, all coordinates conversion from hg18 assembly to hg19 was performed with the UCSC Lift Over program [26]. Conserved TFBS (conserved transcription factor binding sites, cTFBS) were generated through aligning mouse and rat genomes with human [31]. Replication time data were obtained from Hepg2, Imr90, K562 and Bg02 cell lines for liver cancer, lung cancer, ccRCC and melanoma respectively (http://​genome.​ucsc.​edu/​) ENCODE, ‘Repli-seq track’ [31]. Genome-wide replication timing was mapped to protein coding genes and lncRNAs, the (G1b + S1)/(S4 + G2) ratio, early-to-late ratio, was determined for each protein coding gene and lncRNA. Genes that have a ratio greater than 1 or less than 1 were defined as early or late replicated genes respectively. Recombination rates (RR) were obtained from International HapMap Project (http://​hapmap.​ncbi.​nlm.​nih.​gov/​) and averaged over successive 1-Kb windows in human genome [32]. 1-Kb windows that have an average RR above 4.0 were regarded as high RR regions (RRH), while low RR regions are 1-Kb windows with recombination rate less than 0.5 (RRL). GC content denotes the percentage of G or C nucleotides per 1-Kb window. 1-Kb windows that have greater than 50 % or less than 30 % GC coverage are considered as high (GCH) or low GC regions (GCL) respectively [26].

RNA-seq data in sra format generated by sequencing 6 Hek293T cell lines were downloaded from NCBI (GSE55572) [33] for expression analysis in ccRCC. Read alignment was conducted with TopHat2 release 2.0.13 [34]. As for other cancer types, RNA-seq data in bam format were acquired from Hepg2, A549 and Nhek cell lines for liver cancer, lung cancer and melanoma respectively [31]. Read coverage was determined with bedtools v2.22.1 for lncRNAs and protein coding genes [35]. The number of reads per Kilobase per million reads (RPKM) was computed and averaged from three cell samples for each protein coding gene and lncRNA. Genes whose RPKM >20 or <0.25 were defined as high and low expressed respectively.

Cancer micro RNAs are a manual curation of mammalian miRNAs that have been experimentally characterized and actively involved in various cancers [36]. Cancer census genes are 547 cancer-driving genes annotated in COSMIC v71 (catalogue of somatic mutations in cancer) [37].

We used 1-Mb window strategy to construct 1-Mb windows for correlation analyses between SNP, cancer somatic mutation densities and genetic features as well as fitting Random forest models. Non-overlapping 1-Mb windows were formed across human genome, cancer mutations and SNPs were mapped into them and the number of somatic mutations and SNPs were counted for each 1-Mb window. Genome-wide replication timing was mapped into 1-Mb windows and the (G1b+S1)/(S4+G2) ratio was computed for each 1-Mb window. Read coverage was determined with bedtools v2.22.1 for each 1-Mb window, exons from Gencode V21 were intersected with 1-Mb windows and the length of exons was then calculated for each 1-Mb window. The number of reads per Kilobase per million reads (RPKM) was computed and averaged from three cell samples for each 1-Mb window. Recombination rates (RR) were averaged over successive 1-Mb windows in the human genome. Regarding other features, the number of bases covered by each feature was calculated for each 1-Mb window. As a number of 1-Mb windows are lack of coverage of features and mutation information, partial 1-Mb windows were discarded, including 1-Mb windows defined as telomere, centromere, stalk, pericentromere, 1-Mb windows which are all undefined bases. The whole chromosome Y was ruled out from this study too, due to its consistently low mutation rates caused by gender bias. In total, 224.3 Mb regions were abandoned in this study, forming 2856 1-Mb windows and 56 columns corresponding to cancer somatic mutation density, SNP density and 54 features ranging from conserved regions, promoters to histone modifications. Correlation analyses between SNP, cancer somatic mutation densities and each feature were performed in R.

The SNP and cancer somatic mutation (CSM) random forest (RF) models were constructed with the R random Forest package [15]. In the RF models, we used 2856 1-Mb windows constructed above and cancer mutation density (CSM model), SNP density (SNP model) as response variables and 54 genomic features as predictor variables to build two RF models, CSM and SNP models. All predictor values were plus one and log scaled to reduce the great variation of vectors. The number of trees was set to 500, mtry was set to 20 for CSM model and 15 for SNP model, all other parameters were set to default values. Model calibration and validation were described in the Additional file 2.

For CSM and SNP score prediction, we used the same 1-Mb window strategy as in the model building, however, the 1 Mb-window was slided across the human genome with a step size of 1 Kb. 1 Mb windows overlapping telomere, centromere, stalk or pericentromere regions, 1 Mb windows which are all undefined bases and chromosome Y were removed from the annotation data, resulting in 2,832,687 row annotations. The CSM and SNP scores were predicted using the two RF models for each 1 Mb window and averaged on a 1-Kb window scale.

Coding mutations mainly came from two sources for ccRCC: whole genome sequencing of 14 paired ccRCC samples and exome sequencing of 325 paired ccRCC samples from TCGA [38]. The coding mutations of other cancer types were obtained from the same sources as described in the section of “Mutation data”. Their functional impacts were predicted by SIFT [39], and Mutation assessor [40] respectively, variants were regarded as deleterious based on the following criteria: SIFT score <0.05, and Mutation Assessor socre >1.9. 70,659 ccRCC, 881,130 liver cancer, 1,623,242 lung cancer and 2,011,261 melanoma non-coding variants were scored with FunSeq 2 [41] (http://​funseq2.​gersteinlab.​org/​) and GWAVA [42] (https://​www.​sanger.​ac.​uk/​sanger/​StatGen_​Gwava) respectively, all the parameters were set to default. Deleterious coding mutations, non-coding variants with GWAVA and FunSeq 2 scores and disease-causing variants from HGMD and ClinVar databases were mapped into 1-Kb windows which have average CSM and SNP scores. 1-Kb windows were then sorted based on SNP and CSM scores and divided into non-overlapping 200-Mb intervals respectively. For each 200-Mb interval, the following values were computed, including the average densities of deleterious coding mutations, disease-causing variants, average GWAVA and FunSeq 2 scores, average CSM and SNP scores. Correlation analyses were conducted in R between densities of deleterious coding mutations, disease-causing variants and average CSM and SNP scores.