Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction.

Zagordi O; Geyrhofer L; Roth V; Beerenwinkel N

doi:10.1089/cmb.2009.0164

Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction.

Zagordi O ¹,

Geyrhofer L ,

Roth V ,

Beerenwinkel N

Affiliations

1. Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
Authors
Zagordi O¹
(1 author)

ORCIDs linked to this article

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology, 01 Mar 2010, 17(3):417-428
https://doi.org/10.1089/cmb.2009.0164 PMID: 20377454

Abstract

We present a computational method for analyzing deep sequencing data obtained from a genetically diverse sample. The set of reads obtained from a deep sequencing experiment represents a statistical sample of the underlying population. We develop a generative probabilistic model for assigning observed reads to unobserved haplotypes in the presence of sequencing errors. This clustering problem is solved in a Bayesian fashion using the Dirichlet process mixture to define a prior distribution on the unknown number of haplotypes in the mixture. We devise a Gibbs sampler for sampling from the joint posterior distribution of haplotype sequences, assignment of reads to haplotypes, and error rate of the sequencing process, to obtain estimates of the local haplotype structure of the population. The method is evaluated on simulated data and on experimental deep sequencing data obtained from HIV samples.

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Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction.

Affiliations

Authors

ORCIDs linked to this article

Abstract

Full text links

References

Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing.

The year of sequencing.

Viral population estimation using pyrosequencing.

DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations.

Title not supplied

The impact of next-generation sequencing technology on genetics.

Title not supplied

Antigenic diversity thresholds and the development of AIDS.

HIV treatment failure: testing for HIV resistance in clinical practice.

Bioinformatics challenges of new sequencing technology.

Citations & impact

Impact metrics

Citations of article over time

Alternative metrics

Smart citations by scite.ai
Explore citation contexts and check if this article has been supported or disputed.
https://scite.ai/reports/10.1089/cmb.2009.0164

Article citations

Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species.

Epidemiological data analysis of viral quasispecies in the next-generation sequencing era.

Evaluation of haplotype callers for next-generation sequencing of viruses.

Genomic characterization of hepatitis C virus transmitted founder variants with deep sequencing.

Viral quasispecies reconstruction via tensor factorization with successive read removal.

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