Long-read whole-genome analysis of human single cells.

Hård J, Mold JE, Eisfeldt J, Tellgren-Roth C, Häggqvist S, Bunikis I, Contreras-Lopez O, Chin C, Nordlund J, Rubin C, Feuk L, Michaëlsson J, Ameur A

Nat Commun 14 (1) 5164 [2023-08-24; online 2023-08-24]

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.

Bioinformatics Support for Computational Resources [Service]

NGI Long read [Technology development]

NGI Single cell [Technology development]

NGI Stockholm (Genomics Applications) [Collaborative]

NGI Uppsala (Uppsala Genome Center) [Technology development]

National Genomics Infrastructure [Technology development]

PubMed 37620373

DOI 10.1038/s41467-023-40898-3

Crossref 10.1038/s41467-023-40898-3

pmc: PMC10449900
pii: 10.1038/s41467-023-40898-3

Publications 9.5.0