{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:46:37Z","timestamp":1792788397360,"version":"4.5.0"},"reference-count":29,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T00:00:00Z","timestamp":1776384000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T00:00:00Z","timestamp":1779926400000},"content-version":"vor","delay-in-days":41,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Harvard Undergraduate Research Fellowship"},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["F31CA264958"],"award-info":[{"award-number":["F31CA264958"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["R01CA269805"],"award-info":[{"award-number":["R01CA269805"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["R01HG012573"],"award-info":[{"award-number":["R01HG012573"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Genome Biol"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>The sequencing-by-synthesis technology by Illumina, Inc. enables efficient and scalable readouts of mutations from genomic data. To enhance sequencing speed and efficiency, Illumina has shifted from the four-color base calling chemistry of the HiSeq series to a two-color fluorescent dye chemistry in the NovaSeq series. Benchmarking sequencing artifacts due to biases in the newer chemistry is important to evaluate the quality of identified mutations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We re-analyze a series of whole-genome sequencing experiments in which the same samples were sequenced on the NovaSeq 6000 (two-color) and HiSeq X10 (four-color) platforms by independent groups. In several samples, we observe a higher frequency of T-to-G and A-to-C putative substitutions (\u201cT\u2009&gt;\u2009G\u201d) at the read level for NovaSeq 6000 versus HiSeq X10. As the per-base error rate is still low, the artifactual substitutions have a negligible effect in identifying germline or high variant allele frequency (VAF) somatic mutations. However, such errors can confound the detection of low-VAF somatic variants in high-depth sequencing samples, particularly in studies of mosaic mutations in normal tissues, where variants have low read support and are called without a matched normal. The artifactual T\u2009&gt;\u2009G variant calls disproportionately occur at NT[TG] trinucleotides, and we leverage this observation to bioinformatically reduce the T\u2009&gt;\u2009G excess in somatic mutation callsets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>We identified a recurrent artifact specific to the Illumina two-color chemistry platform on the NovaSeq 6000 with the potential to contaminate low-VAF somatic mutation calls. Thus, an unexpected enrichment of T\u2009&gt;\u2009G mutations in mosaicism studies warrants caution.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13059-026-04081-3","type":"journal-article","created":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T10:15:03Z","timestamp":1776420903000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["A recurrent sequencing artifact on Illumina sequencers with two-color fluorescent dye chemistry and its impact on somatic variant detection"],"prefix":"10.1186","volume":"27","author":[{"given":"Beverly J.","family":"Fu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vinayak V.","family":"Viswanadham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dominika","family":"Maziec","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hu","family":"Jin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter J.","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,4,17]]},"reference":[{"key":"4081_CR1","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1038\/nature07517","volume":"456","author":"DR Bentley","year":"2008","unstructured":"Bentley DR, et al. 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