Single-cell somatic copy number variants in brain using different amplification methods and reference genomes

dc.citation.articleNumber1288en_US
dc.citation.journalTitleCommunications Biologyen_US
dc.citation.volumeNumber7en_US
dc.contributor.authorKalef-Ezra, Esteren_US
dc.contributor.authorTuran, Zeliha Gozdeen_US
dc.contributor.authorPerez-Rodriguez, Diegoen_US
dc.contributor.authorBomann, Idaen_US
dc.contributor.authorBehera, Sairamen_US
dc.contributor.authorMorley, Caoimheen_US
dc.contributor.authorScholz, Sonja W.en_US
dc.contributor.authorJaunmuktane, Zaneen_US
dc.contributor.authorDemeulemeester, Jonasen_US
dc.contributor.authorSedlazeck, Fritz J.en_US
dc.contributor.authorProukakis, Christosen_US
dc.date.accessioned2024-11-04T16:25:13Zen_US
dc.date.available2024-11-04T16:25:13Zen_US
dc.date.issued2024en_US
dc.description.abstractThe presence of somatic mutations, including copy number variants (CNVs), in the brain is well recognized. Comprehensive study requires single-cell whole genome amplification, with several methods available, prior to sequencing. Here we compare PicoPLEX with two recent adaptations of multiple displacement amplification (MDA): primary template-directed amplification (PTA) and droplet MDA, across 93 human brain cortical nuclei. We demonstrate different properties for each, with PTA providing the broadest amplification, PicoPLEX the most even, and distinct chimeric profiles. Furthermore, we perform CNV calling on two brains with multiple system atrophy and one control brain using different reference genomes. We find that 20.6% of brain cells have at least one Mb-scale CNV, with some supported by bulk sequencing or single-cells from other brain regions. Our study highlights the importance of selecting whole genome amplification method and reference genome for CNV calling, while supporting the existence of somatic CNVs in healthy and diseased human brain.en_US
dc.identifier.citationKalef-Ezra, E., Turan, Z. G., Perez-Rodriguez, D., Bomann, I., Behera, S., Morley, C., Scholz, S. W., Jaunmuktane, Z., Demeulemeester, J., Sedlazeck, F. J., & Proukakis, C. (2024). Single-cell somatic copy number variants in brain using different amplification methods and reference genomes. Communications Biology, 7(1), 1–10. https://doi.org/10.1038/s42003-024-06940-wen_US
dc.identifier.digitals42003-024-06940-wen_US
dc.identifier.doihttps://doi.org/10.1038/s42003-024-06940-wen_US
dc.identifier.urihttps://hdl.handle.net/1911/118003en_US
dc.language.isoengen_US
dc.publisherSpringer Natureen_US
dc.rightsExcept where otherwise noted, this work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives (CC BY-NC-ND) license. Permission to reuse, publish, or reproduce the work beyond the terms of the license or beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.en_US
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/4.0/en_US
dc.titleSingle-cell somatic copy number variants in brain using different amplification methods and reference genomesen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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