Extensive sequencing of seven human genomes to characterize benchmark reference materials

By Justin M. Zook, D. Catoe, Jennifer McDaniel, Lindsay K. Vang, Noah Spies, Arend Sidow, Z. Weng, Yuling Liu, Christopher E. Mason, Noah Alexander and 43 more. Scientific Data, 2015

739 citations recorded by the source corpus.

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. Design Type(s) reference design • replicate design • protocol optimization design • individual genetic characteristics comparison design Measurement Type(s) whole genome sequencing Technology Type(s) DNA sequencing Factor Type(s) ethnic group Sample Characteristic(s) Homo sapiens • EBV-LCL cell Design Type(s) reference design • replicate design • protocol optimization design • individual genetic characteristics comparison design Measurement Type(s) whole genome sequencing Technology Type(s) DNA sequencing Factor Type(s) ethnic group Sample Characteristic(s) Homo sapiens • EBV-LCL cell Machine-accessible metadata file describing the reported data (ISA-Tab format)

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Citations in the corpus

Structural variant calling: the long and the short of it (2019, background): “Current efforts such as Genome in the Bottle [30] and the FDA-led initiative SEQC2 (https://www.access-data.fda.gov/scripts/fdatrack/view/track_project.cfm?program=nctr&id=NCTR-DBB-PM-SEQC2-Phase-II) aim at better characterizing false positives and false negatives in SV calling.”
Accurate detection of complex structural variations using single molecule sequencing (2017, unknown): “With the accuracy established, we next used genuine sequencing of an Arabidopsis thaliana trio (Col-0, CVI and the Col-0 x CVI F1 progeny) 38 and Ashkenazi human trio data set from Genome-in-a-Bottle (GiaB) 39 to assess the recall and Mendelian consistency (Table 1 and Supplementary Notes 4 & 5).”
Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing (2019, methodology): “The real datasets of HG00514, including Illumina HiSeq and Pac-Bio RS data [36], and HG002 PacBio RS dataset from the Genome in a Bottle (GIAB) Consortium [79] were downloaded from DDBJ.”
KMC 3: counting and manipulating k‐mer statistics (2017, unknown): “/dsk -file fv.fastq -kmer-size 28 -max-memory 12000 -verbose”
A draft human pangenome reference (2022, methodology): “These assemblies include 29 samples with long and linked read sequencing data generated entirely by the HPRC, and 19 samples sequenced by other efforts (Porubsky et al., 2021; Shafin et al., 2020; J. M. Zook et al., 2016), denoted HPRC+.”
SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data (2017, methodology): “A ∼ 30 × human genome dataset published by GIAB [43] was extracted as testing data (see Additional file 4).”
SvABA: genome-wide detection of structural variants and indels by local assembly (2018, methodology): “To evaluate the genotyping accuracy of SvABA, we jointly called variants on awhole-genome sequencing trio from anAshkenazi Jewish family (Zook et al. 2016).”
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes (2020, result): “These four samples were added for the purposes of comparison with other studies that are using them 23 .”
Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis (2017, methodology): “The accuracy was assessed on NA12878 using the NIST high-con ﬁ dence (HC) calls 51 as the gold standard (Fig.”