Skip to main content
Publications of the Week

Directional DNA Sequencing for Single Cells Using Nanoliter Biochemistry

By January 24, 2022January 31st, 2022No Comments

This week, we profile a publication in Cell Reports Methods from Vincent Hanlon (pictured)
and colleagues from Dr. Peter Lansdorp’s laboratory at the BC Cancer Research Institute.

Read the Publication

Since its development almost a decade ago (1) the single cell Strand-seq DNA sequencing method has proven to be an invaluable tool for a variety of studies in genetics and DNA repair (2-11). Specifically, Strand-seq is used for chromosome-length haplotyping, discovery of structural genomic variants including inversions and, more generally, genome assembly. Although the data are in high demand, the preparation of single cell Strand-seq libraries is technically challenging (9). Variable results and limited informative reads have hampered the widespread application of the Strand-seq method despite its obvious theoretical appeal. In the most recent issue of Cell Reports Methods, Vincent Hanlon and colleagues from the Lansdorp laboratory at the BC Cancer Research Institute report a simplified “one pot” (OP) method to make Strand-seq libraries that overcomes many of the previous technical challenges. Specifically, they developed a nanoliter-volume protocol in which reagents are added cumulatively, DNA purification steps are avoided, and enzymes are inactivated with a thermolabile protease. OP-Strand-seq libraries capture 10%–25% of the genome from a single cell with reduced costs and increased throughput, opening up a wide variety of studies that are being pursued in collaboration with investigators in and outside Vancouver and Canada.

  1. Falconer, E., Hills, M., Naumann, U., Poon, S.S., Chavez, E.A., Sanders, A.D., Zhao, Y., Hirst, M. and Lansdorp, P.M. (2012) DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution. Nat Methods, 9, 1107-1112.
  2. Chaisson, M.J.P., Sanders, A.D., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E.J., Rodriguez, O.L., Guo, L., Collins, R.L. et al. (2019) Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nat Commun, 10, 1784.
  3. Claussin, C., Porubsky, D., Spierings, D.C., Halsema, N., Rentas, S., Guryev, V., Lansdorp, P.M. and Chang, M. (2017) Genome-wide mapping of sister chromatid exchange events in single yeast cells using Strand-seq. Elife, 6.
  4. Ebert, P., Audano, P.A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M.J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R. et al. (2021) Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science, 372.
  5. Porubsky, D., Ebert, P., Audano, P.A., Vollger, M.R., Harvey, W.T., Marijon, P., Ebler, J., Munson, K.M., Sorensen, M., Sulovari, A. et al. (2021) Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. Nat Biotechnol, 39, 302-308.
  6. Porubsky, D., Garg, S., Sanders, A.D., Korbel, J.O., Guryev, V., Lansdorp, P.M. and Marschall, T. (2017) Dense and accurate whole-chromosome haplotyping of individual genomes. Nat Commun, 8, 1293.
  7. Porubsky, D., Sanders, A.D., Taudt, A., Colome-Tatche, M., Lansdorp, P.M. and Guryev, V. (2020) breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data. Bioinformatics, 36, 1260-1261.
  8. Sanders, A.D., Meiers, S., Ghareghani, M., Porubsky, D., Jeong, H., van Vliet, M., Rausch, T., Richter-Pechanska, P., Kunz, J.B., Jenni, S. et al. (2020) Single-cell analysis of structural variations and complex rearrangements with tri-channel processing. Nat Biotechnol, 38, 343-354.
  9. Sanders, A.D., Falconer, E., Hills, M., Spierings, D.C.J. and Lansdorp, P.M. (2017) Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs. Nat Protoc, 12, 1151-1176.
  10. Hills, M., Falconer, E., O’Neill, K., Sanders, A.D., Howe, K., Guryev, V. and Lansdorp, P.M. (2021) Construction of Whole Genomes from Scaffolds Using Single Cell Strand-Seq Data. Int J Mol Sci, 22.
  11. van Wietmarschen, N., Merzouk, S., Halsema, N., Spierings, D.C.J., Guryev, V. and Lansdorp, P.M. (2018) BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes. Nat Commun, 9, 271.

Read the Publication