Additional file 4 of Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

Additional file 4. List of exonic genetic variants called by MiSeq™ Illumina Variant interpreter 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 Illumina. 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 SIFTnew score over the total number of SIFTnew scores in dbNSFP. If there are multiple scores, only the largest (most damaging) rankscore is presented. Rankscores 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.

补充文件4。针对11份肿瘤样本，由MiSeq™ 因美纳（Illumina）变异解读器（Variant Interpreter）所检出的外显子区域遗传变异列表。所有变异均已注释基因ID与RefSeq参考序列基因座，突变命名规范遵循人类基因组变异学会（Human Genome Variation Society, HGVS）推荐的惯例（http://www.hgvs.org/mutnomen/），但未包含变异等位基因及等位基因分型（杂合或纯合）信息。频率数据表示因美纳（Illumina）测序检测到的变异等位基因在总等位基因中的占比。此外，本列表还针对变异注释了单核苷酸多态性数据库（dbSNP，rs编号）或癌症体细胞突变目录（COSMIC）v86版本的相关信息，以及FATHMM功能评分。FATHMM评分源自FATHMM-MKL工具，为针对单个突变的功能评分，形式为取值0~1的单值p值。评分高于0.5的突变具有有害功能；为突出COSMIC数据库中最具显著性的数据，仅将评分≥0.7的变异归类为“致病（Pathogenic）”，而评分≤0.5的变异则归类为“中性（Neutral）”[47]。表格的“效应（Effect）”列报告了核苷酸变异对蛋白质的影响。表格最后三列分别报告了基因组聚合数据库（Genome Aggregation Database, GnomAD）频率、基于Sorting Intolerant From Tolerant（SIFT，错义突变功能预测工具）的蛋白质预测效应，以及保守性评分基因组进化速率分析（Genomic Evolutionary Rate Profiling, GERP）。
表格中同时报告了SIFT的转换秩评分（rankscore）：首先将SIFT原始得分转换为SIFTnew = (1 - SIFTori)，随后将该转换后的得分在dbNSFP数据库的所有SIFTnew得分中进行排序，秩评分为该排序位次与dbNSFP数据库中SIFTnew得分总数量的比值。若存在多个评分，仅保留最大（即损伤程度最高）的秩评分。秩评分的取值范围为0.02654~0.87932。
基因组进化速率分析（GERP）是一种通过比对35种哺乳动物的同源基因组序列，量化直系同源序列间的替换缺失情况所计算得到的保守性评分，其取值范围为−12.3~6.17，其中6.17代表最高保守性[48]。
缩写说明：VC：变异检出器（Variant Caller）；−：无可用数据；GERP：基因组进化速率分析（Genomic Evolutionary Rate Profiling）；SIFT：错义突变功能预测工具（Sorting Intolerant From Tolerant）；GnomAD：基因组聚合数据库（Genome Aggregation Database）。