DNA was extracted from blood using the QIAcube system with QIAmp DNA kit (Qiagen, Hilden, Germany), and 10 ng were used for sequencing by NGS technology. The customized designed SNP panel was composed of n =139 SNPs (Supplementary Table S1 ), present in n =89 amplicons (size range 125–375 bp). This panel permitted to identify 417 genetic variants in total (Supplementary Table S1 ). The analysed SNPs were selected based on an extensive review of articles on the association between psoriasis and SNPs or response to biologics [7 (link),9 (link),12 (link),18 (link),22 (link),23 (link),24 (link)].
NGS was performed using the Ion GeneStudio™ S5 Plus platform (Thermo Fisher Scientific, Massachusetts, USA). Libraries were amplified by the Ion AmpliSeq™ Library kit Plus (Thermo Fisher Scientific) and quantified using the Qubit 4 Fluorometer and 2100 Bioanalyzer with dsDNA HS assay and High Sensitivity DNA kit (Thermo Fisher Scientific), respectively. Sequencing data were processed with the Ion Torrent Suite software v.5.10.
Positive calls were selected with a read depth >30X and allelic frequency higher than 0.3 (range 0–1.0). Reads were aligned to human genome sequence (build GRCh37/human genome 19). Variants were collected using Variant Caller plugin and systematically evaluated, filtered, and annotated using tailored R scripts. Variants’ annotations were finally verified using ANNOVAR.
NGS was performed using the Ion GeneStudio™ S5 Plus platform (Thermo Fisher Scientific, Massachusetts, USA). Libraries were amplified by the Ion AmpliSeq™ Library kit Plus (Thermo Fisher Scientific) and quantified using the Qubit 4 Fluorometer and 2100 Bioanalyzer with dsDNA HS assay and High Sensitivity DNA kit (Thermo Fisher Scientific), respectively. Sequencing data were processed with the Ion Torrent Suite software v.5.10.
Positive calls were selected with a read depth >30X and allelic frequency higher than 0.3 (range 0–1.0). Reads were aligned to human genome sequence (build GRCh37/human genome 19). Variants were collected using Variant Caller plugin and systematically evaluated, filtered, and annotated using tailored R scripts. Variants’ annotations were finally verified using ANNOVAR.
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