Contiguity-Preserving Transposition Sequencing (CPT-Seq) for Genome-Wide Haplotyping, Assembly, and Single-Cell ATAC-Seq View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2017

AUTHORS

Lena Christiansen , Sasan Amini , Fan Zhang , Mostafa Ronaghi , Kevin L. Gunderson , Frank J. Steemers

ABSTRACT

Most genomes to date have been sequenced without taking into account the diploid nature of the genome. However, the distribution of variants on each individual chromosome can (1) significantly impact gene regulation and protein function, (2) have important implications for analyses of population history and medical genetics, and (3) be of great value for accurate interpretation of medically relevant genetic variation. Here, we describe a comprehensive and detailed protocol for an ultra fast (<3 h library preparation), cost-effective, and scalable haplotyping method, named Contiguity Preserving Transposition sequencing or CPT-seq (Amini et al., Nat Genet 46(12):1343-1349, 2014). CPT-seq accurately phases >95 % of the whole human genome in Mb-scale phasing blocks. Additionally, the same workflow can be used to aid de novo assembly (Adey et al., Genome Res 24(12):2041-2049, 2014), detect structural variants, and perform single cell ATAC-seq analysis (Cusanovich et al., Science 348(6237):910-914, 2015). More... »

PAGES

207-221

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-1-4939-6750-6_12

DOI

http://dx.doi.org/10.1007/978-1-4939-6750-6_12

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1074247286

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/28138849


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