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Genome Biology

, 15:517

Genomics of infectious diseases special issue


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.

AbbreviationsBAsE-SeqBarcode-directed Assembly for Extra-long Sequences

bpbase pair

BWABurrows-Wheeler Aligner

HBVhepatitis B virus

MAFminor allele frequency

ORFopen reading frame

PCRpolymerase chain reaction

SNPsingle nucleotide polymorphism

SNVsingle nucleotide variant

Electronic supplementary materialThe online version of this article doi:10.1186-s13059-014-0517-9 contains supplementary material, which is available to authorized users.

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Autor: Lewis Z Hong - Shuzhen Hong - Han Teng Wong - Pauline PK Aw - Yan Cheng - Andreas Wilm - Paola F de Sessions - Seng Ge


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