13000_2020_1052_MOESM2_ESM.xlsx (31.35 kB)
Download file

Additional file 2 of Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

Download (31.35 kB)
posted on 2020-12-21, 09:06 authored by Irene Vanni, Milena Casula, Lorenza Pastorino, Antonella Manca, Bruna Dalmasso, Virginia Andreotti, Marina Pisano, Maria Colombino, Ulrich Pfeffer, Enrica Teresa Tanda, Carla Rozzo, Panagiotis Paliogiannis, Antonio Cossu, Paola Ghiorzo, Giuseppe Palmieri
Additional file 2. List of exonic genetic variants called by PGM™ 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 PGM 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 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


Ministero della Salute Associazione Italiana per la Ricerca sul Cancro