![]() ![]() This step involves finding differences between a sample of interest (usually in a disease state) and a control sample (in a reference, healthy state). The next step is the downstream analysis of the amplicon sequencing data. Thus, amplicon sequencing is well suited as a routine clinical genetic diagnostic tool. It produces enough coverage for the genomic regions of interest to detect single nucleotide polymorphisms (SNPs) and other variants. Targeted sequencing lowers sequencing costs, runtime and the time required for downstream analysis of the sequencing output. Amplicon sequencing is one type of targeted sequencing where, before sequencing, PCR amplification of relevant parts of targeted genomic regions occurs. By discovering disease-related genes, targeted NGS has become an important sequencing method in clinical diagnostics. Benchtop next-generation sequencing (NGS) machines (e.g., MiniSeq and MiSeq from Illumina, Personal Genome Machine (PGM) using Ion Torrent technology from Thermo Fisher Scientific) facilitate patient genetic characterization in a routine clinical setting. ![]() Individualized medical genetics assists in therapy decisions in a way that it helps practitioners to prescribe an appropriate therapy to the particular patient. VARIFI is a web-based tool available at .at. VARIFI requires little computational experience and no in-house compute power since the analyses are conducted on our server. VARIFI automatically extracts variant information from publicly available databases and incorporates methods for variant effect prediction. Furthermore, VARIFI applies variant filters for biases associated with the sequencing technologies (e.g., incorrectly identified homopolymer-associated indels with Ion Torrent). In contrast to existing pipelines, VARIFI combines different analysis methods and, based on their concordance, assigns a confidence score to each identified variant. We optimized parameters in VARIFI by analyzing more than 170 amplicon-sequenced cancer samples produced on the Personal Genome Machine (PGM). Here we present VARIFI, a pipeline for finding reliable genetic variants (single nucleotide polymorphisms (SNPs) and insertions and deletions (indels)). ![]() Still, distinguishing genetic variants between healthy and diseased individuals from sequencing errors remains a challenge. Fast and affordable benchtop sequencers are becoming more important in improving personalized medical treatment. ![]()
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