{"id":106922,"date":"2025-10-22T14:50:36","date_gmt":"2025-10-22T12:50:36","guid":{"rendered":"https:\/\/www.pcb.ub.edu\/cnag-researchers-evaluate-dna-extraction-protocols-to-improve-long-read-genomic-sequencing\/"},"modified":"2025-10-22T16:25:58","modified_gmt":"2025-10-22T14:25:58","slug":"cnag-researchers-evaluate-dna-extraction-protocols-to-improve-long-read-genomic-sequencing","status":"publish","type":"post","link":"https:\/\/www.pcb.ub.edu\/en\/cnag-researchers-evaluate-dna-extraction-protocols-to-improve-long-read-genomic-sequencing\/","title":{"rendered":"CNAG researchers evaluate DNA extraction protocols to improve long-read genomic sequencing"},"content":{"rendered":"<p><strong>Researchers from the National Centre for Genomic Analysis (<a href=\"https:\/\/www.pcb.ub.edu\/en\/empresa\/centre-nacional-danalisi-genomica-cnag\/\" target=\"_blank\" rel=\"noopener\">CNAG<\/a>), located at the Barcelona Science Park, have collaborated in a study led by the UK National Measurement Laboratory (<a href=\"https:\/\/www.uknml.com\/\" target=\"_blank\" rel=\"noopener\">NML<\/a>) with the aim of evaluating the main DNA extraction protocols currently in use (Fire Monkey, Nanobind, Puregene, and Genomic-tip) using a reference cell line with known chromosomal alterations.<\/strong><\/p>\n<p>Long-read sequencing technologies are transforming genomics by allowing researchers to detect structural variants (SVs), which are changes in the genome such as duplications, deletions, or rearrangements of DNA letters or sections that can significantly affect how genes function and the role in diseases. Producing reliable long-read data requires high molecular weight (HMW) DNA of excellent quality and quantity, similar to how building a precise map depends on using intact, high-quality materials. Although several DNA extraction methods exist, their comparative performance in routine laboratory workflows had not been thoroughly evaluated.<\/p>\n<p>Now, a new study led by the UK National Measurement Laboratory has addressed this question. At CNAG, the <a href=\"https:\/\/www.cnag.eu\/teams\/cnag-sequencing-unit\" target=\"_blank\" rel=\"noopener\">Sequencing Unit<\/a>, led by <strong>Marta Gut<\/strong> and J<strong>avier Guti\u00e9rrez Cuesta<\/strong>, and the <a href=\"https:\/\/www.cnag.eu\/teams\/bioinformatics-unit\" target=\"_blank\" rel=\"noopener\">Bioinformatics Unit<\/a>, including <strong>Ra\u00fal Tonda<\/strong>, <strong>Marc Dabad<\/strong>, <strong>Jordi Morata<\/strong>, and <strong>Maria Cristina Frias-L\u00f3pez<\/strong>, carried out sample processing, sequencing, and primary analyses. CNAG Director <strong>Ivo Gut<\/strong> and the <a href=\"https:\/\/www.cnag.eu\/teams\/genome-research-unit\/bioinformatics-development-statistical-genomics-team\" target=\"_blank\" rel=\"noopener\">Bioinformatics Development and Statistical Genomics<\/a> team, with <strong>Simon Heath<\/strong>, supported the evaluation of structural variant detection and data interpretation.<\/p>\n<p>The study found that all DNA extraction methods produced samples of sufficient purity for sequencing, although the total amount of DNA recovered varied between protocols. Among the methods tested, Fire Monkey extracts generated the longest average DNA fragments, which helps produce longer sequencing reads and improves genome assembly. Genomic-tip extracts yielded the highest amount of DNA, providing more material for multiple sequencing runs, while Nanobind produced the largest proportion of ultra-long DNA fragments exceeding 100 kb, which is especially valuable for detecting large structural changes in the genome.<\/p>\n<p>The team also applied a digital PCR-based assay to measure DNA integrity. This method allowed them to predict which samples would produce ultra-long sequencing reads, offering a more precise and quantitative assessment than traditional gel-based tests. When analysing structural variants, the researchers found that both the length of the sequencing reads and the overall coverage (how many times each DNA region is read) were key factors for accurate detection. Very large or complex variants still required careful manual checking to confirm their presence.<\/p>\n<p>These results demonstrate that the choice of DNA extraction method and the quality of the DNA have a direct impact on the success of long-read sequencing and the ability to identify important genetic variations. By understanding the strengths and limitations of each method, laboratories can optimize their workflows to generate high-quality genomic data.<\/p>\n<p><strong>\u00bb Article of reference: <\/strong>Devonshire, A.S., Morata, J., Jubin, C. et al. Interlaboratory evaluation of high molecular weight DNA extraction methods for long-read sequencing and structural variant analysis.BMC Genomics 26, 698 (2025).\u00a0<a href=\"https:\/\/doi.org\/10.1186\/s12864-025-11792-7\">https:\/\/doi.org\/10.1186\/s12864-025-11792-7\u00a0<\/a><\/p>\n<p><strong>\u00bb Link to the news: <\/strong><a href=\"https:\/\/www.cnag.eu\/news\/ensuring-quality-long-read-sequencing-through-benchmark-dna-extraction-0\" target=\"_blank\" rel=\"noopener\">CNAG website [+]<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Researchers from the National Centre for Genomic Analysis (CNAG), located at the Barcelona Science Park, have collaborated in a study led by the UK National Measurement Laboratory (NML) with the&#8230;<\/p>\n","protected":false},"author":14,"featured_media":106917,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":""},"categories":[36],"tags":[235],"class_list":["post-106922","post","type-post","status-publish","format-standard","has-post-thumbnail","category-science","tag-cnag-en"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.3 - 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