{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T07:31:05Z","timestamp":1775979065737,"version":"3.50.1"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,1,10]],"date-time":"2020-01-10T00:00:00Z","timestamp":1578614400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Fondazione Cassa di Risparmio Trento e Rovereto"},{"DOI":"10.13039\/100000054","name":"National Cancer Institute SPORE","doi-asserted-by":"crossref","award":["P50-CA211024"],"award-info":[{"award-number":["P50-CA211024"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000289","name":"Cancer Research UK","doi-asserted-by":"publisher","award":["A13239"],"award-info":[{"award-number":["A13239"]}],"id":[{"id":"10.13039\/501100000289","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000771","name":"Prostate Cancer UK","doi-asserted-by":"publisher","award":["PG12-49"],"award-info":[{"award-number":["PG12-49"]}],"id":[{"id":"10.13039\/501100000771","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The use of liquid biopsies for cancer patients enables the non-invasive tracking of\u00a0treatment response and tumor dynamics through single or serial blood drawn tests. Next-generation sequencing assays allow for the simultaneous interrogation of extended sets of somatic single-nucleotide variants (SNVs) in circulating cell-free DNA (cfDNA), a mixture of DNA molecules originating both from normal and tumor tissue cells. However, low circulating tumor DNA (ctDNA) fractions together with sequencing background noise and potential tumor heterogeneity challenge the ability to confidently call SNVs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present a computational methodology, called Adaptive Base Error Model in Ultra-deep Sequencing data (ABEMUS), which combines platform-specific genetic knowledge and empirical signal to readily detect and quantify somatic SNVs in cfDNA. We tested the capability of our method to analyze data generated using different platforms with distinct sequencing error properties and we compared ABEMUS performances with other popular SNV callers on both synthetic and real cancer patients sequencing data. Results show that ABEMUS performs better in most of the tested conditions proving its reliability in calling low variant allele frequencies somatic SNVs in low ctDNA levels plasma samples.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>ABEMUS is cross-platform and can be installed as R package. The source code is maintained on Github at http:\/\/github.com\/cibiobcg\/abemus, and it is also available at CRAN official R repository.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa016","type":"journal-article","created":{"date-parts":[[2020,1,8]],"date-time":"2020-01-08T04:28:25Z","timestamp":1578457705000},"page":"2665-2674","source":"Crossref","is-referenced-by-count":13,"title":["ABEMUS: platform-specific and data-informed detection of somatic SNVs in cfDNA"],"prefix":"10.1093","volume":"36","author":[{"given":"Nicola","family":"Casiraghi","sequence":"first","affiliation":[{"name":"Department of Cellular , Computational and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francesco","family":"Orlando","sequence":"additional","affiliation":[{"name":"Department of Cellular , Computational and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yari","family":"Ciani","sequence":"additional","affiliation":[{"name":"Department of Cellular , Computational and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jenny","family":"Xiang","sequence":"additional","affiliation":[{"name":"Caryl and Israel Englander Institute for Precision Medicine , New York Presbyterian Hospital-Weill Cornell Medicine"},{"name":"Genomics and Epigenomics Core Facility"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrea","family":"Sboner","sequence":"additional","affiliation":[{"name":"Caryl and Israel Englander Institute for Precision Medicine , New York Presbyterian Hospital-Weill Cornell Medicine"},{"name":"Institute for Computational Biomedicine , Weill Cornell Medicine, New York, NY 10021, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olivier","family":"Elemento","sequence":"additional","affiliation":[{"name":"Caryl and Israel Englander Institute for Precision Medicine , New York Presbyterian Hospital-Weill Cornell Medicine"},{"name":"Institute for Computational Biomedicine , Weill Cornell Medicine, New York, NY 10021, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gerhardt","family":"Attard","sequence":"additional","affiliation":[{"name":"UCL Cancer Institute , University College London, London WC1E 6BT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Himisha","family":"Beltran","sequence":"additional","affiliation":[{"name":"Caryl and Israel Englander Institute for Precision Medicine , New York Presbyterian Hospital-Weill Cornell Medicine"},{"name":"Department of Medical Oncology , Dana Farber Cancer Institute, Boston, MA 02215, USA"},{"name":"Department of Medicine , Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY 10021, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8266-8631","authenticated-orcid":false,"given":"Francesca","family":"Demichelis","sequence":"additional","affiliation":[{"name":"Department of Cellular , Computational and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy"},{"name":"Caryl and Israel Englander Institute for Precision Medicine , New York Presbyterian Hospital-Weill Cornell Medicine"},{"name":"Institute for Computational Biomedicine , Weill Cornell Medicine, New York, NY 10021, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessandro","family":"Romanel","sequence":"additional","affiliation":[{"name":"Department of Cellular , Computational and Integrative Biology (CIBIO), University of Trento, Trento 38123, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,1,10]]},"reference":[{"key":"2023013110301274400_btaa016-B1","doi-asserted-by":"crossref","first-page":"11428","DOI":"10.1073\/pnas.1902651116","volume":"116","author":"Abida","year":"2019","journal-title":"Proc. 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