Extensive sequencing of seven human genomes to characterize benchmark reference materials

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Abstract

The Genome in a Bottle Consortium, hosted by the National Institute of Standards and Technology (NIST) is creating reference materials and data for human genome sequencing, as well as methods for genome comparison and benchmarking. Here, we describe a large, diverse set of sequencing data for seven human genomes; five are current or candidate NIST Reference Materials. The pilot genome, NA12878, has been released as NIST RM 8398. We also describe data from two Personal Genome Project trios, one of Ashkenazim Jewish ancestry and one of Chinese ancestry. The data come from 12 technologies: BioNano Genomics, Complete Genomics paired-end and LFR, Ion Proton exome, Oxford Nanopore, Pacific Biosciences, SOLiD, 10X Genomics GemCode WGS, and Illumina exome and WGS paired-end, mate-pair, and synthetic long reads. Cell lines, DNA, and data from these individuals are publicly available. Therefore, we expect these data to be useful for revealing novel information about the human genome and improving sequencing technologies, SNP, indel, and structural variant calling, and de novo assembly.

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SAMBLASTER: fast duplicate marking and structural variant read extraction

Gregory Faust, Ira Hall (2014)

Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the requirement to read, write, sort and compress large BAM files multiple times. Results: We present SAMBLASTER, a tool that reduces the number of times such costly operations are performed. SAMBLASTER is designed to mark duplicates in read-sorted SAM files as a piped post-pass on DNA aligner output before it is compressed to BAM. In addition, it can simultaneously output into separate files the discordant read-pairs and/or split-read mappings used for structural variant calling. As an alignment post-pass, its own runtime overhead is negligible, while dramatically reducing overall pipeline complexity and runtime. As a stand-alone duplicate marking tool, it performs significantly better than PICARD or SAMBAMBA in terms of both speed and memory usage, while achieving nearly identical results. Availability and implementation: SAMBLASTER is open-source C++ code and freely available for download from https://github.com/GregoryFaust/samblaster. Contact: imh4y@virginia.edu

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Highly efficient DNA synthesis by the phage phi 29 DNA polymerase. Symmetrical mode of DNA replication.

A Bernad, C Garmendia, Juan Lázaro … (1989)

The results presented in this paper indicate that the phi 29 DNA polymerase is the only enzyme required for efficient synthesis of full length phi 29 DNA with the phi 29 terminal protein, the initiation primer, as the only additional protein requirement. Analysis of phi 29 DNA polymerase activity in various in vitro DNA replication systems indicates that two main reasons are responsible for the efficiency of this minimal system: 1) the phi 29 DNA polymerase is highly processive in the absence of any accessory protein; 2) the polymerase itself is able to produce strand displacement coupled to the polymerization process. Using primed M13 DNA as template, the phi 29 DNA polymerase is able to synthesize DNA chains greater than 70 kilobase pairs. Furthermore, conditions that increase the stability of secondary structure in the template do not affect the processivity and strand displacement ability of the enzyme. Thus, the catalytic properties of the phi 29 DNA polymerase are appropriate for a phi 29 DNA replication mechanism involving two replication origins, strand displacement and continuous synthesis of both strands. The enzymology of phi 29 DNA replication would support a symmetrical model of DNA replication.

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Integrating sequencing datasets to form highly confident SNP and indel genotype calls for a whole human genome

Justin Zook, Jason Wang, David Mittelman … (2013)

Clinical adoption of human genome sequencing requires methods with known accuracy of genotype calls at millions or billions of positions across a genome. Previous work showing discordance amongst sequencing methods and algorithms has made clear the need for a highly accurate set of genotypes across a whole genome that could be used as a benchmark. We present methods to make highly confident SNP, indel, and homozygous reference genotype calls for NA12878, the pilot genome for the Genome in a Bottle Consortium. We minimize bias towards any method by integrating and arbitrating between 14 datasets from 5 sequencing technologies, 7 mappers, and 3 variant callers. Regions for which no confident genotype call could be made are identified as uncertain, and classified into different reasons for uncertainty. Our highly confident genotype calls are publicly available on the Genome Comparison and Analytic Testing (GCAT) website to enable real-time benchmarking of any method.

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Journal

Journal ID (nlm-ta): Sci Data

Journal ID (iso-abbrev): Sci Data

Title: Scientific Data

Publisher: Nature Publishing Group

ISSN (Electronic): 2052-4463

Publication date (Electronic): 07 June 2016

Publication date Collection: 2016

Volume: 3

Electronic Location Identifier: 160025

Affiliations

[1 ]National Institute of Standards and Technology , Gaithersburg, Maryland 20899, USA

[2 ]Stanford University , Stanford, California 94305, USA

[3 ]Department of Physiology and Biophysics, the Feil Family Brain and Mind Research Institute, and HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College, Cornell University , New York, New York 10065, USA

[4 ]Illumina Mission Bay , San Francisco, California 94158, USA

[5 ]BioNano Genomics , San Diego, California 92121, USA

[6 ]Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, USA

[7 ]Complete Genomics Inc. , Mountain View, California 94043, USA

[8 ]Thermo Fisher Scientific , South San Francisco, California 94080, USA

[9 ]Genome Sciences, University of Washington , Seattle, Washington 98105, USA

[10 ]National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , 45 Center Drive, Bethesda, Maryland 20892, USA

[11 ]PersonalGenomes.org , Boston, Massachusetts 02115, USA

[12 ]Harvard Medical School , Boston, Massachusetts 02115, USA

[13 ]10X Genomics , Pleasanton, California 94566, USA

[14 ]Department of Medical Genetics, Oslo University Hospital , Kirkeveien 166, Bygg 25, Oslo 0450, Norway

Author notes

[a ] J.Z. (email: jzook@ 123456nist.gov ).

[]

J.M.Z., M.L.S., and G.I.A.B. designed the overall study. J.M.Z., D.C., J.M., L.V., N.S., Z.W., Y.L., N.A., E.H., E.J., R.S., R.M.T., K.Z., Y.F., M.C., C.X., and M.L.S. wrote the manuscript. J.M.Z., D.C., J.M., L.V., and M.L.S. designed, sequenced, and analyzed the Illumina paired end W.G.S. J.M.Z., D.C., J.M., N.S., A.S., Z.W., and M.L.S. designed, sequenced, and analyzed the Illumina mate pair W.G.S. J.M.Z., D.C., J.M., N.S., A.S., Y.L., F.C., E.J., A.M., and M.L.S. designed, sequenced, and analyzed the Illumina synthetic long read W.G.S. C.E.M., N.A., and E.H. designed, sequenced, and analyzed the Oxford Nanopore W.G.S. K.P., W.S., T.L., M.S., Z.D., A.H., and H.C. designed, sequenced, and analyzed the BioNano mapping. R.M.T., C.C.C., and N.G. designed, sequenced, and analyzed the Complete Genomics W.G.S. K.Z., S.G., F.H., and Y.F. designed, sequenced, and analyzed the Ion Torrent exome sequencing. J.M.Z., J.M., G.D., E.S., R.S., A.B., M.C., and M.L.S. designed, sequenced, and analyzed the PacBio W.G.S. J.M.Z., A.W.Z., M.B., J.B., P.E., G.M.C., M.L.S., and G.I..A.B. designed the process for selecting the genomes from the P.G.P. P.M., S.K.-P., G.S..Y.Z., M.S.-L., H.S.O., and P.A.M. designed, sequenced, and analyzed the 10X Genomics data. Y.S. and K.B.R. designed, sequenced, and analyzed the Illumina W.E.S. data. J.M.Z., S.S., J.T., and C.X. designed and manage the GIAB FTP site and SRA submissions.

Article

Publisher Item ID: sdata201625

DOI: 10.1038/sdata.2016.25

PMC ID: 4896128

PubMed ID: 27271295

SO-VID: c09d37b1-f944-4d7e-a382-ecd6b6d2968f

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Extensive sequencing of seven human genomes to characterize benchmark reference materials

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Arabidopsis genomics

Most cited references 9

SAMBLASTER: fast duplicate marking and structural variant read extraction

Highly efficient DNA synthesis by the phage phi 29 DNA polymerase. Symmetrical mode of DNA replication.

Integrating sequencing datasets to form highly confident SNP and indel genotype calls for a whole human genome

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