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

Genome biology (2014-11-20)
Lewis Z Hong, Shuzhen Hong, Han Teng Wong, Pauline P K Aw, Yan Cheng, Andreas Wilm, Paola F de Sessions, Seng Gee Lim, Niranjan Nagarajan, Martin L Hibberd, Stephen R Quake, William F Burkholder
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.

MATERIALS
Product Number
Brand
Product Description

USP
Levothyroxine, United States Pharmacopeia (USP) Reference Standard
Sigma-Aldrich
L-Thyroxine sodium salt pentahydrate, ≥98% (HPLC), powder
Sigma-Aldrich
L-Thyroxine sodium salt pentahydrate, γ-irradiated, powder, BioXtra, suitable for cell culture