{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T05:29:11Z","timestamp":1764912551397,"version":"3.46.0"},"reference-count":44,"publisher":"MDPI AG","issue":"23","license":[{"start":{"date-parts":[[2025,12,3]],"date-time":"2025-12-03T00:00:00Z","timestamp":1764720000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003196","name":"Italian Ministry of Health","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100003196","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The growing demand for precision diagnostics in cystic fibrosis and other genetic disorders, such as cancers, is driving the need for sequencing platforms that combine analytical robustness, scalability, and cost-efficiency. In this study, we performed a direct comparison between two leading Next-Generation Sequencing (NGS) platforms, MiSeq (Illumina, CA, USA) and DNBSEQ-G99RS (MGI Tech Co., Shenzhen, China), using a CE-IVD-certified CFTR panel (Devyser AB), selected for its complexity and variant spectrum, including SNVs, CNVs, and intronic polymorphisms. A total of 47 genomic DNA samples from routine clinical activity were analyzed on both platforms. Illumina sequencing covered all CFTR variants using standard workflows, while MGI data were generated from residual diagnostic DNA, with informed consent. Sequencing data were processed using Amplicon Suite v3.7.0 for variant calling, annotation, and ACMG classification. Quality control metrics and platform-specific parameters were also evaluated. Both platforms demonstrated complete concordance in variant detection, including SNVs, CNVs, and complex alleles (e.g., Poly-T\/TG). Illumina exhibited slightly superior basecalling quality and allelic frequency uniformity, while MGI achieved higher sequencing depth (mean ~2793\u00d7) and demultiplexing efficiency. No false positives, false negatives, or discordant HGVS annotations were observed. The use of full-gene CFTR sequencing enabled granular and technically rigorous cross-platform validation. These findings confirm the analytical equivalence of Illumina and MGI for diagnostic genotyping. Moreover, MGI\u2019s greater data output and flow cell capacity may offer tangible advantages in high-throughput settings, including somatic applications such as liquid biopsy and molecular oncology workflows.<\/jats:p>","DOI":"10.3390\/ijms262311701","type":"journal-article","created":{"date-parts":[[2025,12,3]],"date-time":"2025-12-03T08:44:28Z","timestamp":1764751468000},"page":"11701","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Methodological Assessment of High-Throughput Sequencing Platforms: Illumina vs. MGI in Clinical-Grade CFTR Genotyping"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4575-8897","authenticated-orcid":false,"given":"Marianna","family":"Beggio","sequence":"first","affiliation":[{"name":"UOSD Genetica e Citogenetica, Dipartimento di Direzione Medica del Presidio Ospedaliero di Mestre, AULSS3 Serenissima, 30172 Venezia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2551-6295","authenticated-orcid":false,"given":"Edoardo","family":"Peroni","sequence":"additional","affiliation":[{"name":"Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eliana","family":"Greco","sequence":"additional","affiliation":[{"name":"UOSD Genetica e Citogenetica, Dipartimento di Direzione Medica del Presidio Ospedaliero di Mestre, AULSS3 Serenissima, 30172 Venezia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-6430-8748","authenticated-orcid":false,"given":"Giulia","family":"Favretto","sequence":"additional","affiliation":[{"name":"UOSD Genetica e Citogenetica, Dipartimento di Direzione Medica del Presidio Ospedaliero di Mestre, AULSS3 Serenissima, 30172 Venezia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3895-6011","authenticated-orcid":false,"given":"Dario","family":"Degiorgio","sequence":"additional","affiliation":[{"name":"UOSD Genetica e Citogenetica, Dipartimento di Direzione Medica del Presidio Ospedaliero di Mestre, AULSS3 Serenissima, 30172 Venezia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5263-8386","authenticated-orcid":false,"given":"Antonio","family":"Rosato","sequence":"additional","affiliation":[{"name":"Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, 35128 Padova, Italy"},{"name":"Department of Surgery Oncology and Gastroenterology, University of Padova, 35122 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mos\u00e8","family":"Favarato","sequence":"additional","affiliation":[{"name":"UOSD Genetica e Citogenetica, Dipartimento di Direzione Medica del Presidio Ospedaliero di Mestre, AULSS3 Serenissima, 30172 Venezia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/gim.2013.125","article-title":"Population-based carrier screening for cystic fibrosis: A systematic review of 23 years of research","volume":"16","author":"Ioannou","year":"2014","journal-title":"Genet. 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