{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:45Z","timestamp":1772138025837,"version":"3.50.1"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T00:00:00Z","timestamp":1731974400000},"content-version":"vor","delay-in-days":57,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["KO2155\/7-1 and 7-2"],"award-info":[{"award-number":["KO2155\/7-1 and 7-2"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["BR 1782\/5-2"],"award-info":[{"award-number":["BR 1782\/5-2"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["GE2811\/4-1 and 4-2"],"award-info":[{"award-number":["GE2811\/4-1 and 4-2"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["KO 2155\/6-1"],"award-info":[{"award-number":["KO 2155\/6-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"German Ministry of Education and Science"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Motivation: By accounting for variants within measured transcripts, it is possible to evaluate the status of somatic variants using single-cell RNA-sequencing (scRNA-seq) and to characterize their clonality. However, the sparsity (very few reads per transcript) or bias in protocols (favoring 3\u2019 ends of the transcripts) makes the chance of capturing somatic variants very unlikely. This can be overcome by targeted sequencing or the use of mitochondrial variants as natural barcodes for clone identification. Currently, available computational tools focus on genotyping, but do not provide functionality for combined analysis of somatic and mitochondrial variants and functional analysis such as characterization of gene expression changes in detected clones. Results: Here, we propose SIGURD (SIngle cell level Genotyping Using scRna Data) (SIGURD), which is an R-based pipeline for the clonal analysis of scRNA-seq data. This allows the quantification of clones by leveraging both somatic and mitochondrial variants. SIGURD also allows for functional analysis after clonal detection: association of clones with cell populations, detection of differentially expressed genes across clones, and association of somatic and mitochondrial variants. Here, we demonstrate the power of SIGURD by analyzing single-cell data of colony-forming cells derived from patients with myeloproliferative neoplasms.<\/jats:p>","DOI":"10.1093\/bib\/bbae604","type":"journal-article","created":{"date-parts":[[2024,11,5]],"date-time":"2024-11-05T07:24:18Z","timestamp":1730791458000},"source":"Crossref","is-referenced-by-count":2,"title":["SIngle cell level Genotyping Using scRna Data (SIGURD)"],"prefix":"10.1093","volume":"25","author":[{"given":"Martin","family":"Grasshoff","sequence":"first","affiliation":[{"name":"Institute for Computational Genomics, RWTH Aachen University , Pauwelsstr. 30, 52074 Aachen, NRW ,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Milena","family":"Kalmer","sequence":"additional","affiliation":[{"name":"Department of Hematology , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,","place":["Germany"]},{"name":"RWTH Aachen University , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,","place":["Germany"]},{"name":"Center for Integrated Oncology Aachen Bonn Cologne D\u00fcsseldorf (CIO ABCD) , D\u00fcsseldorf ,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicolas","family":"Chatain","sequence":"additional","affiliation":[{"name":"Department of Hematology , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,","place":["Germany"]},{"name":"RWTH Aachen University , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,","place":["Germany"]},{"name":"Center for Integrated Oncology Aachen Bonn Cologne D\u00fcsseldorf (CIO ABCD) , D\u00fcsseldorf ,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kim","family":"Kricheldorf","sequence":"additional","affiliation":[{"name":"Department of Hematology , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,","place":["Germany"]},{"name":"RWTH Aachen University , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,","place":["Germany"]},{"name":"Center for Integrated Oncology Aachen Bonn Cologne D\u00fcsseldorf (CIO ABCD) , D\u00fcsseldorf ,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Angela","family":"Maurer","sequence":"additional","affiliation":[{"name":"Department of Hematology , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,","place":["Germany"]},{"name":"RWTH Aachen University , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,","place":["Germany"]},{"name":"Center for Integrated Oncology Aachen Bonn Cologne D\u00fcsseldorf (CIO ABCD) , D\u00fcsseldorf ,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ralf","family":"Weiskirchen","sequence":"additional","affiliation":[{"name":"Institute of Molecular Pathobiochemistry , Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), , Pauwelstr 30, 52074 Aachen, NRW ,","place":["Germany"]},{"name":"RWTH Aachen University , Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), , Pauwelstr 30, 52074 Aachen, NRW ,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steffen","family":"Koschmieder","sequence":"additional","affiliation":[{"name":"Department of Hematology , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,","place":["Germany"]},{"name":"RWTH Aachen University , Oncology, Hemostaseology and Stem Cell Transplantation, , Pauwelstr 30, 52074 Aachen, NRW ,","place":["Germany"]},{"name":"Center for Integrated Oncology Aachen Bonn Cologne D\u00fcsseldorf (CIO ABCD) , D\u00fcsseldorf ,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ivan G","family":"Costa","sequence":"additional","affiliation":[{"name":"Institute for Computational Genomics, RWTH Aachen University , Pauwelsstr. 30, 52074 Aachen, NRW ,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,11,19]]},"reference":[{"key":"2024111907575891500_ref1","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1016\/j.exphem.2018.09.004","article-title":"The human cell atlas bone marrow single-cell interactive web portal","volume":"68","author":"Hay","year":"2018","journal-title":"Exp Hematol"},{"key":"2024111907575891500_ref2","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1038\/s41586-020-2157-4","article-title":"Construction of a human cell landscape at single-cell 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