Oxford-Nanopore eBook - 11

Impact
This study demonstrated the capacity of Cas9 enrichment and long-read
nanopore sequencing to thoroughly characterise cancer driver genes. Providing
both sequence and modification data in a single experiment, this rapid, low-cost
method can help further our understanding of complex diseases.

Results
Several hundred-fold enrichment of target loci enabled identification
of known large structural variants, SNPs, and differential methylation
patterns in genes with prognostic implications in breast cancer.

10

165x

150 kb

KRT19

GSTP1

cancer-associated
loci enriched in
multiplex

median coverage per
locus from one
MinION™ Flow Cell

deletion detected
in GM12878

gene
hypomethylation
in two breast
cancer cell lines

gene promoter
hypermethylation
in ER(+) breast
cancer cell line

HOW?

Kit

Oxford Nanopore Ligation Sequencing Kit

Available here: store.nanoporetech.com/ligation-sequencing-kit.html

Ten cancer-associated loci were
enriched in DNA from 3 human breast
cell lines and the well-studied
GM12878 cell line, then sequenced in
multiplex. Structural variants and
SNPs were identified, and CpG
methylation evaluated.

Device

GridION™ with MinION and Flongle Flow Cells

Tools

Custom analysis pipeline, including:
- Minimap2 or NGMLR (alignment)
- Nanopolish (CpG methylation calling)
- Sniffles (structural variant calling)
- Nanopolish or samtools (de novo variant calling)
- HapCUT2 (haplotype assembly)

Find out more about analysis pipelines available here:
community.nanoporetech.com/knowledge/bioinformatics

Find out more at: nanoporetech.com/applications/targeted-sequencing
Publication

Presentation

T. Gilpatrick et al. Targeted Nanopore Sequencing with Cas9 for studies
of methylation, structural variants, and mutations. BioRxiv (2019). DOI:
https://doi.org/10.1101/604173

Timothy Gilpatrick - Targeted nanopore sequencing with Cas9 for studies
of methylation, structural variants and mutations. Available at: https://
nanoporetech.com/resource-centre/targeted-nanopore-sequencing-cas9studies-methylation-structural-variants-and-0 [Accessed 25 June 2019]

Oxford Nanopore Technologies, the Wheel icon and MinION are registered
trademarks of Oxford Nanopore Technologies in various countries.
© 2019 Oxford Nanopore Technologies.

Twitter: @nanopore
www.nanoporetech.com

Oxford Nanopore Technologies products are currently for research use only.
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http://store.nanoporetech.com/ligation-sequencing-kit.html http://community.nanoporetech.com/knowledge/bioinformatics http://www.nanoporetech.com/applications/targeted-sequencing http://www.nanoporetech.com/resource-centre/targeted-nanopore-sequencing-cas9-studies-methylation-structural-variants-and-0 http://www.nanoporetech.com/resource-centre/targeted-nanopore-sequencing-cas9-studies-methylation-structural-variants-and-0 https://www.doi.org/10.1101/604173 http://www.nanoporetech.com/resource-centre/targeted-nanopore-sequencing-cas9-studies-methylation-structural-variants-and-0 http://www.nanoporetech.com

Oxford-Nanopore eBook

Table of Contents for the Digital Edition of Oxford-Nanopore eBook

Contents
Oxford-Nanopore eBook - 1
Oxford-Nanopore eBook - 2
Oxford-Nanopore eBook - Contents
Oxford-Nanopore eBook - 4
Oxford-Nanopore eBook - 5
Oxford-Nanopore eBook - 6
Oxford-Nanopore eBook - 7
Oxford-Nanopore eBook - 8
Oxford-Nanopore eBook - 9
Oxford-Nanopore eBook - 10
Oxford-Nanopore eBook - 11
Oxford-Nanopore eBook - 12
Oxford-Nanopore eBook - 13
Oxford-Nanopore eBook - 14
Oxford-Nanopore eBook - 15
Oxford-Nanopore eBook - 16
Oxford-Nanopore eBook - 17
Oxford-Nanopore eBook - 18
Oxford-Nanopore eBook - 19
Oxford-Nanopore eBook - 20
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