{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T11:57:39Z","timestamp":1768478259979,"version":"3.49.0"},"posted":{"date-parts":[[2017,11,3]]},"group-title":"Genomics","reference-count":36,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2017,11,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Querying cancer genomes at single-cell resolution is expected to provide a powerful framework to understand in detail the dynamics of cancer evolution. However, given the high costs currently associated with single-cell sequencing, together with the inevitable technical noise arising from single-cell genome amplification, cost-effective strategies that maximize the quality of single-cell data are critically needed. Taking advantage of five published single-cell whole-genome and whole-exome cancer datasets, we studied the impact of sequencing depth and sampling effort towards single-cell variant detection, including structural and driver mutations, genotyping accuracy, clonal inference and phylogenetic reconstruction, using recent tools specifically designed for single-cell data.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Altogether, our results suggest that, for relatively large sample sizes (25 or more cells), sequencing single tumor cells at depths &gt;5x does not drastically improve somatic variant discovery, the characterization of clonal genotypes or the estimation of phylogenies from single tumor cells.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>We demonstrate that sequencing many individual tumor cells at a modest depth represents an effective alternative to explore the mutational landscape and clonal evolutionary patterns of cancer genomes, without the excessively high costs associated with high-coverage genome sequencing.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/213744","type":"posted-content","created":{"date-parts":[[2017,11,4]],"date-time":"2017-11-04T01:10:12Z","timestamp":1509757812000},"source":"Crossref","is-referenced-by-count":0,"title":["Sensitivity to sequencing depth in single-cell cancer genomics"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2103-1060","authenticated-orcid":false,"given":"Jo\u00e3o M.","family":"Alves","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1407-3406","authenticated-orcid":false,"given":"David","family":"Posada","sequence":"additional","affiliation":[]}],"member":"54368","reference":[{"key":"2019071802240057000_213744v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/sj.bjc.6605912"},{"key":"2019071802240057000_213744v1.2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0452-9"},{"key":"2019071802240057000_213744v1.3","doi-asserted-by":"publisher","DOI":"10.1101\/gr.159913.113"},{"key":"2019071802240057000_213744v1.4","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004462"},{"key":"2019071802240057000_213744v1.5","doi-asserted-by":"publisher","DOI":"10.1038\/nature13600"},{"key":"2019071802240057000_213744v1.6","doi-asserted-by":"publisher","DOI":"10.1038\/nature15260"},{"key":"2019071802240057000_213744v1.7","doi-asserted-by":"publisher","DOI":"10.1016\/j.gde.2013.12.004"},{"key":"2019071802240057000_213744v1.8","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2015.05.005"},{"key":"2019071802240057000_213744v1.9","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms7822"},{"key":"2019071802240057000_213744v1.10","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1320659110"},{"key":"2019071802240057000_213744v1.11","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.02.025"},{"key":"2019071802240057000_213744v1.12","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.02.028"},{"key":"2019071802240057000_213744v1.13","first-page":"1303","volume":"arXiv","year":"2013","journal-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM"},{"key":"2019071802240057000_213744v1.14","first-page":"11.10.1","article-title":"From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline","volume":"43","year":"2013","journal-title":"Curr Protoc Bioinformatics"},{"key":"2019071802240057000_213744v1.15","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw227"},{"key":"2019071802240057000_213744v1.16","doi-asserted-by":"publisher","DOI":"10.1101\/gr.107524.110"},{"key":"2019071802240057000_213744v1.17","unstructured":"Picard software. http:\/\/broadinstitute.github.io\/picard. 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