{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T08:25:37Z","timestamp":1768551937268,"version":"3.49.0"},"reference-count":7,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2023,8,31]],"date-time":"2023-08-31T00:00:00Z","timestamp":1693440000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,8,31]],"date-time":"2023-08-31T00:00:00Z","timestamp":1693440000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100008316","name":"Baden-W\u00fcrttemberg Stiftung","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008316","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Deutsches Krebsforschungszentrum (DKFZ)"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Here we present scSNPdemux, a sample demultiplexing pipeline for single-cell RNA sequencing data using natural genetic variations in humans. The pipeline requires alignment files from Cell Ranger (10\u00d7\u2009Genomics), a population SNP database and genotyped single nucleotide polymorphisms (SNPs) per sample. The tool works on sparse genotyping data in VCF format for sample identification.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The pipeline was tested on both single-cell and single-nuclei based RNA sequencing datasets and showed superior demultiplexing performance over the lipid-based CellPlex and Multi-seq sample multiplexing technique which incurs additional single cell library preparation steps. Specifically, our pipeline demonstrated superior sensitivity and specificity in cell-identity assignment over CellPlex, especially on immune cell types with low RNA content.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>We designed a streamlined pipeline for single-cell sample demultiplexing, aiming to overcome common problems in multiplexing samples using single cell libraries which might affect data quality and can be costly.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-023-05440-8","type":"journal-article","created":{"date-parts":[[2023,8,31]],"date-time":"2023-08-31T11:02:08Z","timestamp":1693479728000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["scSNPdemux: a sensitive demultiplexing pipeline using single nucleotide polymorphisms for improved pooled single-cell RNA sequencing analysis"],"prefix":"10.1186","volume":"24","author":[{"given":"John K. L.","family":"Wong","sequence":"first","affiliation":[]},{"given":"Lena","family":"Jassowicz","sequence":"additional","affiliation":[]},{"given":"Christel","family":"Herold-Mende","sequence":"additional","affiliation":[]},{"given":"Martina","family":"Seiffert","sequence":"additional","affiliation":[]},{"given":"Jan-Philipp","family":"Mallm","sequence":"additional","affiliation":[]},{"given":"Peter","family":"Lichter","sequence":"additional","affiliation":[]},{"given":"Marc","family":"Zapatka","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,8,31]]},"reference":[{"issue":"7","key":"5440_CR1","doi-asserted-by":"publisher","first-page":"619","DOI":"10.1038\/s41592-019-0433-8","volume":"16","author":"CS McGinnis","year":"2019","unstructured":"McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, Hu JL, Murrow LM, Weissman JS, Werb Z, et al. MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices. Nat Methods. 2019;16(7):619\u201326.","journal-title":"Nat Methods"},{"issue":"23","key":"5440_CR2","doi-asserted-by":"publisher","first-page":"4569","DOI":"10.1093\/bioinformatics\/btab358","volume":"37","author":"XJ Huang","year":"2021","unstructured":"Huang XJ, Huang YH. Cellsnp-lite: an efficient tool for genotyping single cells. Bioinformatics. 2021;37(23):4569\u201371.","journal-title":"Bioinformatics"},{"issue":"1","key":"5440_CR3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-019-1865-2","volume":"20","author":"YH Huang","year":"2019","unstructured":"Huang YH, McCarthy DJ, Stegle O. Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference. Genome Biol. 2019;20(1):1\u201312.","journal-title":"Genome Biol"},{"issue":"9","key":"5440_CR4","doi-asserted-by":"publisher","first-page":"giab062","DOI":"10.1093\/gigascience\/giab062","volume":"10","author":"LM Weber","year":"2021","unstructured":"Weber LM, Hippen AA, Hickey PF, Berrett KC, Gertz J, Doherty JA, Greene CS, Hicks SC. Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design. Gigascience. 2021;10(9):giab062.","journal-title":"Gigascience"},{"issue":"2","key":"5440_CR5","doi-asserted-by":"publisher","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","volume":"10","author":"P Danecek","year":"2021","unstructured":"Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021;10(2):giab008.","journal-title":"Gigascience"},{"issue":"6190","key":"5440_CR6","doi-asserted-by":"publisher","first-page":"1396","DOI":"10.1126\/science.1254257","volume":"344","author":"AP Patel","year":"2014","unstructured":"Patel AP, Tirosh I, Trombetta JJ, Shalek AK, Gillespie SM, Wakimoto H, Cahill DP, Nahed BV, Curry WT, Martuza RL, et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science. 2014;344(6190):1396\u2013401.","journal-title":"Science"},{"issue":"13","key":"5440_CR7","doi-asserted-by":"publisher","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","volume":"184","author":"YH Hao","year":"2021","unstructured":"Hao YH, Hao S, Andersen-Nissen E, Mauck WM, Zheng SW, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M, et al. Integrated analysis of multimodal single-cell data. Cell. 2021;184(13):3573\u201387.","journal-title":"Cell"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-023-05440-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-023-05440-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-023-05440-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,20]],"date-time":"2023-11-20T20:04:18Z","timestamp":1700510658000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-023-05440-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,8,31]]},"references-count":7,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["5440"],"URL":"https:\/\/doi.org\/10.1186\/s12859-023-05440-8","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,8,31]]},"assertion":[{"value":"11 January 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 August 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 August 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The study of breast cancer samples was approved by the ethics committee of the Medical Faculty, University of Heidelberg (Heidelberg, Germany; reference number: 005\/2003) and written informed consent was obtained from all patients in accordance with the Declaration of Helsinki and its later amendments.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"326"}}