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Long-read whole-gen...
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Hård, JoannaDepartment of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; ETH AI Center, ETH Zurich, Zurich, Switzerland
(author)
Long-read whole-genome analysis of human single cells
- Article/chapterEnglish2023
Publisher, publication year, extent ...
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Springer Nature,2023
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printrdacarrier
Numbers
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LIBRIS-ID:oai:DiVA.org:kth-336707
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https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-336707URI
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https://doi.org/10.1038/s41467-023-40898-3DOI
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https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-515623URI
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http://kipublications.ki.se/Default.aspx?queryparsed=id:237620373URI
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http://kipublications.ki.se/Default.aspx?queryparsed=id:155256003URI
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Language:English
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Summary in:English
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
Notes
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QC 20240402
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Long-read sequencing has dramatically increased our understanding of human genome variation. Here, we demonstrate that long-read technology can give new insights into the genomic architecture of individual cells. Clonally expanded CD8+ T-cells from a human donor were subjected to droplet-based multiple displacement amplification (dMDA) to generate long molecules with reduced bias. PacBio sequencing generated up to 40% genome coverage per single-cell, enabling detection of single nucleotide variants (SNVs), structural variants (SVs), and tandem repeats, also in regions inaccessible by short reads. 28 somatic SNVs were detected, including one case of mitochondrial heteroplasmy. 5473 high-confidence SVs/cell were discovered, a sixteen-fold increase compared to Illumina-based results from clonally related cells. Single-cell de novo assembly generated a genome size of up to 598 Mb and 1762 (12.8%) complete gene models. In summary, our work shows the promise of long-read sequencing toward characterization of the full spectrum of genetic variation in single cells.
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Mold, Jeff E.Karolinska Institutet
(author)
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Eisfeldt, JesperDepartment of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
(author)
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Tellgren-Roth, Christian,1971-Uppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)chrte903
(author)
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Häggqvist, SusanaUppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)susha415
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Bunikis, IgnasUppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för immunologi, genetik och patologi(Swepub:uu)ignbu776
(author)
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Contreras-Lopez, OrlandoKTH,Genteknologi,Science for Life Laboratory, SciLifeLab(Swepub:kth)u172njsb
(author)
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Chin, Chen ShanGeneDX LLC, Stamford, CT, 06902, USA
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Nordlund, JessicaUppsala universitet,Science for Life Laboratory, SciLifeLab,Molekylär precisionsmedicin(Swepub:uu)jesno775
(author)
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Rubin, Carl-JohanUppsala universitet,Institutionen för medicinsk biokemi och mikrobiologi(Swepub:uu)carub021
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Feuk, LarsUppsala universitet,Science for Life Laboratory, SciLifeLab,Genomik och neurobiologi(Swepub:uu)larsfeuk
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Michaëlsson, JakobKarolinska Institutet
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Ameur, AdamUppsala universitet,Institutionen för immunologi, genetik och patologi,Science for Life Laboratory, SciLifeLab(Swepub:uu)adame789
(author)
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Karolinska InstitutetDepartment of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; ETH AI Center, ETH Zurich, Zurich, Switzerland
(creator_code:org_t)
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In:Nature Communications: Springer Nature14:12041-1723
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Hård, Joanna
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Mold, Jeff E.
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Eisfeldt, Jesper
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Tellgren-Roth, C ...
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Häggqvist, Susan ...
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Bunikis, Ignas
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Contreras-Lopez, ...
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Chin, Chen Shan
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Nordlund, Jessic ...
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Feuk, Lars
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Ameur, Adam
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