BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads.


Hong, LZ; Hong, S; Wong, HT; Aw, PP; Cheng, Y; Wilm, A; de Sessions, PF; Lim, SG; Nagarajan, N; Hibberd, ML; Quake, SR; Burkholder, WF; (2014) BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads. Genome Biol, 15 (11). p. 517. ISSN 1474-760X DOI: https://doi.org/10.1186/PREACCEPT-6768001251451949

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Abstract

We present a method for obtaining long haplotypes, of over 3 kb in length, using a short-read sequencer, Barcode-directed Assembly for Extra-long Sequences (BAsE-Seq). BAsE-Seq relies on transposing a template-specific barcode onto random segments of the template molecule and assembling the barcoded short reads into complete haplotypes. We applied BAsE-Seq on mixed clones of hepatitis B virus and accurately identified haplotypes occurring at frequencies greater than or equal to 0.4%, with >99.9% specificity. Applying BAsE-Seq to a clinical sample, we obtained over 9,000 viral haplotypes, which provided an unprecedented view of hepatitis B virus population structure during chronic infection. BAsE-Seq is readily applicable for monitoring quasispecies evolution in viral diseases.

Item Type: Article
Faculty and Department: Faculty of Infectious and Tropical Diseases > Dept of Pathogen Molecular Biology
Related URLs:
PubMed ID: 25406369
Web of Science ID: 346607300016
URI: http://researchonline.lshtm.ac.uk/id/eprint/2869497

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