{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T13:02:18Z","timestamp":1791378138049,"version":"4.3.2"},"reference-count":54,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T00:00:00Z","timestamp":1785196800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"FRM Espoirs de la Recherche Postdoctoral Fellowship"},{"name":"Pasteur Roux-Cantarini Fellowship"},{"name":"ANR GENOMEHET"},{"name":"PTR Carnot Pasteur"},{"DOI":"10.13039\/501100003762","name":"Institut Pasteur","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003762","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Chromosome copy-number variation is a major contributor to genome plasticity and adaptation in Candida albicans, a leading fungal pathogen of humans. Aneuploidy, defined as deviations from the normal diploid chromosome set, rapidly alters gene dosage and is often observed during exposure to host-imposed and antifungal stress. Accurate detection and quantification of chromosomal copy-number changes are thus essential to dissect the mechanisms by which C. albicans adapts and evolves. Here, we describe the development, optimization, and validation of a 6-color, 16-plex droplet digital PCR assay for simultaneous quantification of all C. albicans chromosome arms in a single reaction. Each target is detected by a unique dual-color or single-color combination of probes, enabling high-order multiplexing through binary fluorescence encoding. Following optimization of probe concentrations, PCR cycling parameters, genomic DNA extraction, and pretreatment with restriction enzymes, the assay provides accurate, reproducible chromosome-level copy-number estimates that correlate closely with whole-genome sequencing results across euploid and aneuploid isolates. Compared to whole-genome sequencing, the assay is rapid, cost-effective, and scalable, requiring minimal DNA input and allowing high-throughput analysis of large collections of isolates. The 16-plex assay thus provides a platform for dissecting genome instability and adaptive evolution in C. albicans.<\/jats:p>","DOI":"10.1093\/g3journal\/jkag201","type":"journal-article","created":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T12:50:11Z","timestamp":1785243011000},"source":"Crossref","is-referenced-by-count":0,"title":["A multiplex droplet digital PCR assay for chromosome copy-number determination in\n                    <i>Candida albicans<\/i>"],"prefix":"10.1093","volume":"16","author":[{"given":"Eli Isael","family":"Maciel","sequence":"first","affiliation":[{"name":"Fungal Heterogeneity Group, Department of Mycology, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9 , Inserm U1359, Paris 75015 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sylvain","family":"Ursuegui","sequence":"additional","affiliation":[{"name":"Life Science Group, Bio-Rad Laboratories, Inc. (LSG PARIS) , Villejuif 94280 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sana","family":"Ahmed-Seghir","sequence":"additional","affiliation":[{"name":"Life Science Group, Bio-Rad Laboratories, Inc. (LSG PARIS) , Villejuif 94280 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Corinne","family":"Maufrais","sequence":"additional","affiliation":[{"name":"Fungal Heterogeneity Group, Department of Mycology, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9 , Inserm U1359, Paris 75015 ,","place":["France"]},{"name":"Institut Pasteur, Universit\u00e9 Paris Cit\u00e9 Bioinformatic Hub, , Paris 75015 ,","place":["France"]},{"name":"Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9 , Inserm U1359, Paris 75015 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"St\u00e9phanie","family":"Roy","sequence":"additional","affiliation":[{"name":"Life Science Group, Bio-Rad Laboratories, Inc. (LSG PARIS) , Villejuif 94280 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C\u00e9cile","family":"Gautier","sequence":"additional","affiliation":[{"name":"Fungal Heterogeneity Group, Department of Mycology, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9 , Inserm U1359, Paris 75015 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philipp","family":"Brandt","sequence":"additional","affiliation":[{"name":"Fungal Heterogeneity Group, Department of Mycology, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9 , Inserm U1359, Paris 75015 ,","place":["France"]},{"name":"Fungal Biology and Pathogenicity Unit, Department of Mycology, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9 , Inserm U1359, Paris 75015 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C\u00e9cile","family":"Jovelet","sequence":"additional","affiliation":[{"name":"Life Science Group, Bio-Rad Laboratories, Inc. (LSG PARIS) , Villejuif 94280 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laras","family":"Pitayu","sequence":"additional","affiliation":[{"name":"Life Science Group, Bio-Rad Laboratories, Inc. (LSG PARIS) , Villejuif 94280 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0390-7084","authenticated-orcid":false,"given":"Iuliana V","family":"Ene","sequence":"additional","affiliation":[{"name":"Fungal Heterogeneity Group, Department of Mycology, Institut Pasteur, Universit\u00e9 Paris Cit\u00e9 , Inserm U1359, Paris 75015 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,7,28]]},"reference":[{"key":"2026100708170172700_jkag201-B1","doi-asserted-by":"publisher","first-page":"984377","DOI":"10.3389\/ffunb.2022.984377","article-title":"Tetraploidy accelerates adaptation under drug selection in a fungal pathogen","volume":"3","author":"Avramovska","year":"2022","journal-title":"Front Fungal 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