{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,5]],"date-time":"2026-11-05T14:52:57Z","timestamp":1793890377894,"version":"4.8.0"},"reference-count":40,"publisher":"MDPI AG","issue":"22","license":[{"start":{"date-parts":[[2025,11,14]],"date-time":"2025-11-14T00:00:00Z","timestamp":1763078400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"BYU CURA"},{"name":"Simmons Center for Cancer Research"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Whole-genome sequencing (WGS) is integral to precision oncology, yet most cancer biospecimens used for WGS are formalin-fixed paraffin-embedded (FFPE) due to their widespread availability in clinical practice. However, FFPE processing can degrade DNA quality. This study compares WGS outcomes from matched cryopreserved (CP) and FFPE tumor samples, hypothesizing that CP tissues yield superior sequencing quality and variant detection. Fifty matched pairs of CP and FFPE tumor samples spanning multiple cancer types were obtained from a biobank. DNA was extracted, and WGS was performed. We assessed sequencing quality metrics and variant analysis between the two preservation methods. Presequencing metrics favored CP tissue, with a significantly higher gDNA concentration, DIN, and DNA fragment size. The WGS results showed that the CP samples had a higher mean read depth and larger insert size. Although the mapping percentages were similar, FFPE exhibited higher tumor mutation burden (13.7 vs. 6.4 mutations\/Mb) and lower concordance with CP in variant calls (43.5% overlap). CP samples detected more structural variants and enabled the improved identification of oncogenic driver mutations. Cryopreserved tissues consistently outperform FFPE in terms of DNA quality and WGS metrics, enabling the more accurate detection of clinically relevant mutations. These findings support prioritizing CP sample preservation for genomic profiling in cancer care.<\/jats:p>","DOI":"10.3390\/ijms262211038","type":"journal-article","created":{"date-parts":[[2025,11,14]],"date-time":"2025-11-14T14:37:52Z","timestamp":1763131072000},"page":"11038","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Cryopreserved Tissue Biospecimens Offer Superior Quality for Whole-Genome Sequencing of Various Cancers Compared to Paired Formalin-Fixed Paraffin-Embedded Tissues"],"prefix":"10.3390","volume":"26","author":[{"given":"Ken","family":"Dixon","sequence":"first","affiliation":[{"name":"Specicare Inc., Gainesville, GA 30501, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0315-2080","authenticated-orcid":false,"given":"Jeong-Hoon","family":"Lee","sequence":"additional","affiliation":[{"name":"Inocras Inc., San Diego, CA 92121, USA"},{"name":"Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1674-7929","authenticated-orcid":false,"given":"Ryan","family":"Miller","sequence":"additional","affiliation":[{"name":"Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Booker","sequence":"additional","affiliation":[{"name":"Specicare Inc., Gainesville, GA 30501, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"DeLaney","family":"Anderson","sequence":"additional","affiliation":[{"name":"Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2283-3586","authenticated-orcid":false,"given":"Jeffrey","family":"Okojie","sequence":"additional","affiliation":[{"name":"Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Kirkham","sequence":"additional","affiliation":[{"name":"Specicare Inc., Gainesville, GA 30501, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eun Kyoung","family":"Lee","sequence":"additional","affiliation":[{"name":"Inocras Inc., San Diego, CA 92121, USA"},{"name":"Department of Ophthalmology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunyang","family":"Bao","sequence":"additional","affiliation":[{"name":"Inocras Inc., San Diego, CA 92121, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Islam Oguz","family":"Tuncay","sequence":"additional","affiliation":[{"name":"Inocras Inc., San Diego, CA 92121, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jung-Ah","family":"Kim","sequence":"additional","affiliation":[{"name":"Inocras Inc., San Diego, CA 92121, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sangmoon","family":"Lee","sequence":"additional","affiliation":[{"name":"Inocras Inc., San Diego, CA 92121, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6059-9009","authenticated-orcid":false,"given":"Jared","family":"Barrott","sequence":"additional","affiliation":[{"name":"Specicare Inc., Gainesville, GA 30501, USA"},{"name":"Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA"},{"name":"Simmons Center for Cancer Research, Brigham Young University, Provo, UT 84602, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,14]]},"reference":[{"key":"ref_1","first-page":"229","article-title":"Global cancer statistics 2022: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries","volume":"74","author":"Bray","year":"2024","journal-title":"CA Cancer J. 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