Additional file 3 of Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

Additional file 3. List of exonic genetic variants called by Proton™ VC for the eleven tumor samples. All variants are annotated with the gene ID and locus RefSeq, and the mutation nomenclature is based on the convention recommended by the Human Genome Variation Society ( http://www.hgvs.org/mutnomen/ ) other than the variant allele and the nature of the allele call (heterozygous or homozygous). Frequency data indicate the percentage of the variant allele detected by Proton VC. Moreover, they are annotated for dbSNP (rs number) or COSMIC v86 database, together with FATHMM score. The FATHMM is a functional score for individual mutations from FATHMM-MKL are in the form of a single p-value, ranging from 0 to 1. Scores above 0.5 are deleterious, but in order to highlight the most significant data in COSMIC, only scores ≥0.7 are classified as ‘Pathogenic’ whereas mutations are classed as ‘Neutral’ if the score is ≤0.5 [47]. The “Effect” column reports the effect of nucleotide change on the protein. The last three columns of the table report the GnomAD Frequency, the predictive effect on the protein based on SIFT, and the conservation score, namely GERP. Converted rankscore is reported for SIFT. To obtain the rankscore, Sorting Intolerant from Tolerant (SIFT) scores were first converted to SIFTnew = (1-SIFTori), then ranked among all SIFTnew scores in dbNSFP. The rankscore is the ratio of the rank the SIFT new score over the total number of SIFTnew scores in dbNSFP. If there are multiple scores, only the largest (most damaging) rankscore is presented. Rank scores range from 0.02654 to 0.87932. Genomic Evolutionary Rate Profiling (GERP) is a conservation score calculated by quantifying substitution deficits across multiple alignments of orthologues using the genomes of 35 mammals. It ranges from − 12.3 to 6.17, with 6.17 being the most conserved [48]. Abbreviations: VC: Variant Caller; −: no available data; GERP: Genomic Evolutionary Rate Profiling. SIFT: Sorts Intolerant From Tolerant. GnomAD: Genome Aggregation Database.

附加文件3：11份肿瘤样本经Proton™变异检测工具（Variant Caller，VC）鉴定得到的外显子区遗传变异列表。所有变异均已注释基因ID与RefSeq基因座信息，变异命名规则遵循人类基因组变异学会（Human Genome Variation Society, HGVS）推荐的规范（http://www.hgvs.org/mutnomen/），仅变异等位基因及等位基因分型（杂合或纯合）除外。频率数据代表经Proton VC检测到的变异等位基因占比。此外，每条变异还注释了dbSNP（rs编号）或COSMIC v86数据库信息，以及FATHMM评分。FATHMM评分源自FATHMM-MKL工具，是针对单个突变的功能预测分值，以单一p值形式呈现，取值范围为0至1。评分高于0.5即具有有害性；为突出COSMIC数据库中具有显著意义的数据，本研究将评分≥0.7的变异归类为"致病（Pathogenic）"，评分≤0.5的变异则归类为"中性（Neutral）"[47]。"Effect"（变异效应）列标注了核苷酸改变对蛋白质产生的影响。表格最后三列依次为GnomAD频率、基于SIFT的蛋白质预测效应值，以及保守性评分GERP（Genomic Evolutionary Rate Profiling，基因组进化速率谱）。其中SIFT的转换秩评分（rankscore）已一并给出。秩评分的计算方式为：首先将Sorting Intolerant from Tolerant（SIFT，错义突变功能预测工具）的原始得分转换为SIFTnew = (1 - SIFTori)，随后在dbNSFP数据库的所有SIFTnew得分中进行排序；秩评分为该SIFTnew得分的排名与dbNSFP中总SIFTnew得分数量的比值。若存在多个得分，仅保留最大（即损伤性最强）的秩评分。秩评分的取值范围为0.02654至0.87932。基因组进化速率谱（Genomic Evolutionary Rate Profiling, GERP）是一种保守性评分，通过比对35种哺乳动物的同源基因序列、量化直系同源序列间的替换缺失情况计算得到，其取值范围为-12.3至6.17，其中6.17代表最高保守性[48]。缩写说明：VC：Variant Caller（变异检测工具）；−：无可用数据；GERP：Genomic Evolutionary Rate Profiling（基因组进化速率谱）；SIFT：Sorting Intolerant From Tolerant（错义突变功能预测工具）；GnomAD：Genome Aggregation Database（基因组聚合数据库）。