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Detecting and annotating genetic variations using the HugeSeq pipeline

Nature Biotechnology volume 30, pages 226–229 (2012)Cite this article

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Deciphering genome sequences is important for the mapping of genetic diseases and prediction of their risks. Advances in high-throughput DNA sequencing technologies using short read lengths have enabled rapid sequencing of entire human genomes and unlocked the potential for comprehensive identification of their underlying genetic variations. Various computational algorithms for identifying and characterizing variants have been developed; however, most of these computational methods are neither integrated nor interoperable, making it difficult for biologists to extract all the genetic information from billions of sequences generated by these sequencing technologies. Here, we present HugeSeq, an integrated computational pipeline to fully automate the process of variant detection from alignment of these genomic sequences to detection and annotation of all types of genetic variations (single nucleotide polymorphisms (SNPs), short insertions or deletions (indels) and larger structural variations (SVs)).

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Figure 1: A MapReduce approach for detecting genetic variants from high-throughput genome sequencing.
Figure 2: Accuracy and sensitivity of variant detection.

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Acknowledgements

We acknowledge support from the US National Institutes of Health. We also thank K. Ye, K. Chen and A. Abyzov for helpful discussions.

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Author notes

  1. Hugo Y K Lam

    Present address: Present address: Personalis, Inc., Palo Alto, California, USA.,

Authors and Affiliations

  1. Department of Genetics, Stanford University, Stanford, California, USA

    Hugo Y K Lam, Cuiping Pan, Michael J Clark, Phil Lacroute, Rui Chen, Rajini Haraksingh, Maeve O'Huallachain, Jeffrey M Kidd, Carlos D Bustamante & Michael Snyder

  2. Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA

    Mark B Gerstein

  3. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA

    Mark B Gerstein

  4. Department of Computer Science, Yale University, New Haven, Connecticut, USA

    Mark B Gerstein

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  1. Hugo Y K Lam
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Corresponding author

Correspondence to Michael Snyder.

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Competing interests

M.S. is a scientific advisory board member for Genapsys, Inc.; a scientific advisory board member and cofounder of Personalis, Inc.; and a scientific advisory board member for DNA Nexus.

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Supplementary Methods, Supplementary Tables 1, 2 and Supplementary Figs. 1–3 (PDF 1481 kb)

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Lam, H., Pan, C., Clark, M. et al. Detecting and annotating genetic variations using the HugeSeq pipeline. Nat Biotechnol 30, 226–229 (2012). https://doi.org/10.1038/nbt.2134

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