Pivotal Role of High Sensitivity Variant Calls and Confirmation Methods for Next-Generation Sequencing Findings: A Case Report

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dc.contributor.authorGorenjak, Marioen_US
dc.contributor.authorJezernik, Gregoren_US
dc.contributor.authorRepnik, Katjaen_US
dc.contributor.authorVarda, Natasa Marcunen_US
dc.contributor.authorPotocnik, Urosen_US
dc.date.accessioned2019-12-06T09:18:03Z
dc.date.available2019-12-06T09:18:03Z
dc.date.issued2018-04
dc.description.abstractAims: The aim of this case report is to demonstrate the importance of prioritization of sensitivity over specificity, coupled with additional confirmation by using standard methods. Next-generation sequencing has revolutionized genetic research as it has allowed sequencing of human genomes within days. Generated raw sequencing data are manipulated using bioinformatic approaches for variant detection. Variant discovery should be performed on appropriately pre-processed data with the aforementioned prioritization of sensitivity over specificity. Presentation of the Case: Here, we report a case of a low quality variant call, emitted due to prioritization of sensitivity over specificity. This call was found to be a causative variant for the patient’s phenotype. DNA extracted from peripheral venous blood of a young female with encephalopathy was sequenced on a MiSeq apparatus. The obtained and analyzed call set emitted a low quality heterozygous insertion with a high probability of a false negative call. Annotation revealed a known pathogenic insertion rs758946412 with a frameshift consequence flagged with “Early infantile epileptic encephalopathy type 9” in ClinVar. The emitted insertion was validated and confirmed by using SANGER sequencing and RFLP. Conclusion: In the presented case, the variant could have easily been missed without the prioritization of sensitivity over specificity. Furthermore, the presented case also demonstrates the importance of additional methods for confirmation of NGS calls that do not meet the thresholds.en_US
dc.identifier.affiliationsCentre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska 8, 2000 Maribor, Slovenia.en_US
dc.identifier.affiliationsCentre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska 8, 2000 Maribor, Slovenia.en_US
dc.identifier.affiliationsCentre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska 8, 2000 Maribor, Slovenia and Laboratory of Biochemistry, Molecular Biology and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia.en_US
dc.identifier.affiliationsDivision of Paediatrics, University Medical Centre Maribor, Ljubljanska Ulica 5, 2000 Maribor, Slovenia.en_US
dc.identifier.affiliationsCentre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska 8, 2000 Maribor, Slovenia and Laboratory of Biochemistry, Molecular Biology and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia.en_US
dc.identifier.citationGorenjak Mario, Jezernik Gregor, Repnik Katja, Varda Natasa Marcun, Potocnik Uros. Pivotal Role of High Sensitivity Variant Calls and Confirmation Methods for Next-Generation Sequencing Findings: A Case Report. Annual Research & Review in Biology. 2018 Apr; 25(4): 1-5en_US
dc.identifier.issn2347-565X
dc.identifier.placeIndiaen_US
dc.identifier.urihttps://imsear.searo.who.int/handle/123456789/187823
dc.languageenen_US
dc.publisherScience Domain Internationalen_US
dc.relation.issuenumber4en_US
dc.relation.volume25en_US
dc.source.urihttps://doi.org/10.9734/ARRB/2018/40312en_US
dc.subjectNext-generation sequencingen_US
dc.subjectDNA sequencingen_US
dc.subjectbioinformaticsen_US
dc.subjectvariant-callingen_US
dc.titlePivotal Role of High Sensitivity Variant Calls and Confirmation Methods for Next-Generation Sequencing Findings: A Case Reporten_US
dc.typeJournal Articleen_US
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