ArticlePloS one2013
Comparison of sequencing platforms for single nucleotide variant calls in a human sample.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 1 of them a synthesis that pooled it.
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Who cites it
40 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analyses of studies of the human microbiota.Genome research · 2013Pooled it
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- Pet-Human Gut Microbiome Host Classifier Using Data from Different Studies.Microorganisms · 2020Article
- Benchmarking of computational error-correction methods for next-generation sequencing data.Genome biology · 2020Article
- Adapting SureSelect enrichment protocol to the Ion Torrent S5 platform in molecular diagnostics of craniosynostosis.Scientific reports · 2020Article
- A comparison between SOLiD 5500XLand Ion Torrent PGM-derived miRNA expression profiles in two breast cell lines.Genetics and molecular biology · 2020Article
- SM-RCNV: a statistical method to detect recurrent copy number variations in sequenced samples.Genes & genomics · 2019Article
- Valection: design optimization for validation and verification studies.BMC bioinformatics · 2018Article
- MSeq-CNV: accurate detection of Copy Number Variation from Sequencing of Multiple samples.Scientific reports · 2018Article
- Genome of Leptospira borgpetersenii strain 4E, a highly virulent isolate obtained from Mus musculus in southern Brazil.Memorias do Instituto Oswaldo Cruz · 2018Article
- Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants.Plant methods · 2018Article
- Analytical "bake-off" of whole genome sequencing quality for the Genome Russia project using a small cohort for autoimmune hepatitis.PloS one · 2018Article
- Somatic Mutations in TSC1 and TSC2 Cause Focal Cortical Dysplasia.American journal of human genetics · 2017Article
- Whole genome sequencing of Guzerá cattle reveals genetic variants in candidate genes for production, disease resistance, and heat tolerance.Mammalian genome : official journal of the International Mammalian Genome Society · 2017Article
- ReliableGenome: annotation of genomic regions with high/low variant calling concordance.Bioinformatics (Oxford, England) · 2017Article
- Clinical Versus Research Sequencing.Cold Spring Harbor perspectives in medicine · 2016Review
- Improving alignment accuracy on homopolymer regions for semiconductor-based sequencing technologies.BMC genomics · 2016Article
- Human genetic variation database, a reference database of genetic variations in the Japanese population.Journal of human genetics · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencings platforms coupled with advanced bioinformatic tools enable re-sequencing of the human genome at high-speed and large cost savings. We compare sequencing platforms from Roche/454(GS FLX), Illumina/HiSeq (HiSeq 2000), and Life Technologies/SOLiD (SOLiD 3 ECC) for their ability to identify single nucleotide substitutions in whole genome sequences from the same human sample. We report on significant GC-related bias observed in the data sequenced on Illumina and SOLiD platforms. The differences in the variant calls were investigated with regards to coverage, and sequencing error. Some of the variants called by only one or two of the platforms were experimentally tested using mass spectrometry; a method that is independent of DNA sequencing. We establish several causes why variants remained unreported, specific to each platform. We report the indel called using the three sequencing technologies and from the obtained results we conclude that sequencing human genomes with more than a single platform and multiple libraries is beneficial when high level of accuracy is required.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.