{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T15:01:13Z","timestamp":1767193273625,"version":"build-2065373602"},"reference-count":30,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2021,9,24]],"date-time":"2021-09-24T00:00:00Z","timestamp":1632441600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Horizon 2020","award":["875160"],"award-info":[{"award-number":["875160"]}]},{"DOI":"10.13039\/501100010774","name":"Consejer\u00eda de Educaci\u00f3n e Investigaci\u00f3n","doi-asserted-by":"publisher","award":["PEJD-2018-PRE\/BMD-8640","IND2019\/BMD-17258"],"award-info":[{"award-number":["PEJD-2018-PRE\/BMD-8640","IND2019\/BMD-17258"]}],"id":[{"id":"10.13039\/501100010774","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","award":["PI16\/18018"],"award-info":[{"award-number":["PI16\/18018"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"<jats:p>Next-generation sequencing (NGS) has enabled a deeper knowledge of the molecular landscape in non-small cell lung cancer (NSCLC), identifying a growing number of targetable molecular alterations in key genes. However, NGS profiling of liquid biopsies risk for false positive and false negative calls and parameters assessing the quality of NGS calls remains lacking. In this study, we have evaluated the positive percent agreement (PPA) between NGS and digital PCR calls when assessing EGFR mutation status using 85 plasma samples from 82 EGFR-positive NSCLC patients. According to our data, variant allele fraction (VAF) was significantly lower in discordant calls and the median of the absolute values of all pairwise differences (MAPD) was significantly higher in discordant calls (p &lt; 0.001 in both cases). Based on these results, we propose a new parameter that integrates both variables, named R-score. Next, we sought to evaluate the PPA for EGFR mutation calls between two independent NGS platforms using a subset of 40 samples from the same cohort. Remarkably, there was a significant linear correlation between the PPA and the R-score (r = 0.97; p &lt; 0.001). Specifically, the PPA of samples with an R-score \u2264 \u22121.25 was 95.83%, whereas PPA falls to 81.63% in samples with R-score \u2264 0.25. In conclusion, R-score significantly correlates with PPA and can assist laboratory medicine specialists and data scientists to select reliable variants detected by NGS.<\/jats:p>","DOI":"10.3390\/biology10100954","type":"journal-article","created":{"date-parts":[[2021,9,24]],"date-time":"2021-09-24T20:15:32Z","timestamp":1632514532000},"page":"954","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["R-Score: A New Parameter to Assess the Quality of Variants\u2019 Calls Assessed by NGS Using Liquid Biopsies"],"prefix":"10.3390","volume":"10","author":[{"given":"Roberto","family":"Serna-Blasco","sequence":"first","affiliation":[{"name":"Liquid Biopsy Laboratory, University Hospital Puerta de Hierro, 28222 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Estela","family":"S\u00e1nchez-Herrero","sequence":"additional","affiliation":[{"name":"Liquid Biopsy Laboratory, University Hospital Puerta de Hierro, 28222 Madrid, Spain"},{"name":"Atrys Health, I+D Department, 08025 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mar\u00eda","family":"Berrocal Renedo","sequence":"additional","affiliation":[{"name":"Liquid Biopsy Laboratory, University Hospital Puerta de Hierro, 28222 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7749-174X","authenticated-orcid":false,"given":"Silvia","family":"Calabuig-Fari\u00f1as","sequence":"additional","affiliation":[{"name":"CIBERONC, Liquid Biopsy WM, 28029 Madrid, Spain"},{"name":"Mixed Unit TRIAL, Pr\u00edncipe Felipe Research Center & General University Hospital of Valencia Research Foundation, 46012 Valencia, Spain"},{"name":"Department of Pathology, Universitat de Val\u00e8ncia, 46010 Valencia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8866-9881","authenticated-orcid":false,"given":"Miguel \u00c1ngel","family":"Molina-Vila","sequence":"additional","affiliation":[{"name":"Laboratory of Oncology\/Pangaea Oncology, Quir\u00f3n-Dexeus University Hospital, 08028 Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6315-7919","authenticated-orcid":false,"given":"Mariano","family":"Provencio","sequence":"additional","affiliation":[{"name":"Medical Oncology, University Hospital Puerta de Hierro, 28222 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Atocha","family":"Romero","sequence":"additional","affiliation":[{"name":"Liquid Biopsy Laboratory, University Hospital Puerta de Hierro, 28222 Madrid, Spain"},{"name":"Medical Oncology, University Hospital Puerta de Hierro, 28222 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2021,9,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"60291","DOI":"10.18632\/oncotarget.20016","article-title":"Dynamic circulating tumor DNA quantificaton for the individualization of non-small-cell lung cancer patients treatment","volume":"8","author":"Provencio","year":"2017","journal-title":"Oncotarget"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"504","DOI":"10.6004\/jnccn.2017.0050","article-title":"Non-small cell lung cancer, version 5.2017: Clinical practice guidelines in oncology","volume":"15","author":"Ettinger","year":"2017","journal-title":"JNCCN J. 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