A New Workflow for Whole-Genome Sequencing of Single Human Cells

Binder V, Bartenhagen C, Okpanyi V, Gombert M, Moehlendick B, Behrens B, Klein H-U, Rieder H, Krell P, Dugas M, Stoecklein NH, et al. (2014)
Human mutation.

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Abstract
: Unbiased amplification of the whole-genome amplification (WGA) of single cells is crucial to study cancer evolution and genetic heterogeneity, but is challenging due to the high complexity of the human genome. Here, we present a new workflow combining an efficient adapter-linker PCR-based WGA method with second-generation sequencing. This approach allows comparison of single cells at base pair resolution. Amplification recovered up to 74% of the human genome. Copy-number variants and loss of heterozygosity detected in single cell genomes showed concordance of up to 99% to pooled genomic DNA. Allele frequencies of mutations could be determined accurately due to an allele dropout rate of only 2%, clearly demonstrating the low bias of our PCR-based WGA approach. Sequencing with paired-end reads allowed genome-wide analysis of structural variants. By direct comparison to other WGA methods, we further endorse its suitability to analyze genetic heterogeneity.
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Binder V, Bartenhagen C, Okpanyi V, et al. A New Workflow for Whole-Genome Sequencing of Single Human Cells. Human mutation. 2014.
Binder, V., Bartenhagen, C., Okpanyi, V., Gombert, M., Moehlendick, B., Behrens, B., Klein, H. - U., et al. (2014). A New Workflow for Whole-Genome Sequencing of Single Human Cells. Human mutation.
Binder, V., Bartenhagen, C., Okpanyi, V., Gombert, M., Moehlendick, B., Behrens, B., Klein, H. - U., Rieder, H., Krell, P., Dugas, M., et al. (2014). A New Workflow for Whole-Genome Sequencing of Single Human Cells. Human mutation.
Binder, V., et al., 2014. A New Workflow for Whole-Genome Sequencing of Single Human Cells. Human mutation.
V. Binder, et al., “A New Workflow for Whole-Genome Sequencing of Single Human Cells”, Human mutation, 2014.
Binder, V., Bartenhagen, C., Okpanyi, V., Gombert, M., Moehlendick, B., Behrens, B., Klein, H.-U., Rieder, H., Krell, P., Dugas, M., Stoecklein, N.H., Borkhardt, A.: A New Workflow for Whole-Genome Sequencing of Single Human Cells. Human mutation. (2014).
Binder, Vera, Bartenhagen, Christoph, Okpanyi, Vera, Gombert, Michael, Moehlendick, Birte, Behrens, Bianca, Klein, Hans-Ulrich, Rieder, Harald, Krell, Pina, Dugas, Martin, Stoecklein, Nikolas Hendrik, and Borkhardt, Arndt. “A New Workflow for Whole-Genome Sequencing of Single Human Cells”. Human mutation (2014).
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The Performance of Whole Genome Amplification Methods and Next-Generation Sequencing for Pre-Implantation Genetic Diagnosis of Chromosomal Abnormalities.
Li N, Wang L, Wang H, Ma M, Wang X, Li Y, Zhang W, Zhang J, Cram DS, Yao Y., J Genet Genomics 42(4), 2015
PMID: 25953353

40 References

Data provided by Europe PubMed Central.

Integrative genomics viewer.
Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP., Nat. Biotechnol. 29(1), 2011
PMID: 21221095
Whole genome amplification and de novo assembly of single bacterial cells.
Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW., PLoS ONE 4(9), 2009
PMID: 19724646
Spectral karyotyping refines cytogenetic diagnostics of constitutional chromosomal abnormalities.
Schrock E, Veldman T, Padilla-Nash H, Ning Y, Spurbeck J, Jalal S, Shaffer LG, Papenhausen P, Kozma C, Phelan MC, Kjeldsen E, Schonberg SA, O'Brien P, Biesecker L, du Manoir S, Ried T., Hum. Genet. 101(3), 1997
PMID: 9439652
A geometric approach for classification and comparison of structural variants.
Sindi S, Helman E, Bashir A, Raphael BJ., Bioinformatics 25(12), 2009
PMID: 19477992
Immune escape and survival mechanisms in circulating tumor cells of colorectal cancer.
Steinert G, Scholch S, Niemietz T, Iwata N, Garcia SA, Behrens B, Voigt A, Kloor M, Benner A, Bork U, Rahbari NN, Buchler MW, Stoecklein NH, Weitz J, Koch M., Cancer Res. 74(6), 2014
PMID: 24599131
SCOMP is superior to degenerated oligonucleotide primed-polymerase chain reaction for global amplification of minute amounts of DNA from microdissected archival tissue samples.
Stoecklein NH, Erbersdobler A, Schmidt-Kittler O, Diebold J, Schardt JA, Izbicki JR, Klein CA., Am. J. Pathol. 161(1), 2002
PMID: 12107088
Direct genetic analysis of single disseminated cancer cells for prediction of outcome and therapy selection in esophageal cancer.
Stoecklein NH, Hosch SB, Bezler M, Stern F, Hartmann CH, Vay C, Siegmund A, Scheunemann P, Schurr P, Knoefel WT, Verde PE, Reichelt U, Erbersdobler A, Grau R, Ullrich A, Izbicki JR, Klein CA., Cancer Cell 13(5), 2008
PMID: 18455127
Regression shrinkage and selection via the lasso
Tibshirani, J Roy Statist Soc Ser B 58(), 1996
Occurrence of TEL-AML1 fusion resulting from (12;21) translocation in human early B-lineage leukemia cell lines.
Uphoff CC, MacLeod RA, Denkmann SA, Golub TR, Borkhardt A, Janssen JW, Drexler HG., Leukemia 11(3), 1997
PMID: 9067587
Single-cell paired-end genome sequencing reveals structural variation per cell cycle.
Voet T, Kumar P, Van Loo P, Cooke SL, Marshall J, Lin ML, Zamani Esteki M, Van der Aa N, Mateiu L, McBride DJ, Bignell GR, McLaren S, Teague J, Butler A, Raine K, Stebbings LA, Quail MA, D'Hooghe T, Moreau Y, Futreal PA, Stratton MR, Vermeesch JR, Campbell PJ., Nucleic Acids Res. 41(12), 2013
PMID: 23630320
One bacterial cell, one complete genome.
Woyke T, Tighe D, Mavromatis K, Clum A, Copeland A, Schackwitz W, Lapidus A, Wu D, McCutcheon JP, McDonald BR, Moran NA, Bristow J, Cheng JF., PLoS ONE 5(4), 2010
PMID: 20428247
Assembling the marine metagenome, one cell at a time.
Woyke T, Xie G, Copeland A, Gonzalez JM, Han C, Kiss H, Saw JH, Senin P, Yang C, Chatterji S, Cheng JF, Eisen JA, Sieracki ME, Stepanauskas R., PLoS ONE 4(4), 2009
PMID: 19390573
Genome-wide detection of single-nucleotide and copy-number variations of a single human cell.
Zong C, Lu S, Chapman AR, Xie XS., Science 338(6114), 2012
PMID: 23258894

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