ArticleNature methods2008
Identification of genetic variants using bar-coded multiplexed sequencing.
Article in Nature methods, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 158 papers, 1 of them a synthesis that pooled it.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
158 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes.BMC biology · 2009Pooled it
- Analysis of genetic linkage of HIV from couples enrolled in the HIV Prevention Trials Network 052 trial.The Journal of infectious diseases · 2011Trial
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- An ultra-dense linkage map identified quantitative trait loci corresponding to fruit quality- and size-related traits in red goji berry.Frontiers in plant science · 2024Article
- BaM-seq and TBaM-seq, highly multiplexed and targeted RNA-seq protocols for rapid, low-cost library generation from bacterial samples.NAR genomics and bioinformatics · 2023Article
- Population admixtures in medaka inferred by multiple arbitrary amplicon sequencing.Scientific reports · 2022Article
- Genotyping-by-sequencing and genomic selection applications in hexaploid triticale.G3 (Bethesda, Md.) · 2022Article
- Genotyping by Sequencing Advancements in Barley.Frontiers in plant science · 2022Review
- Analysis of allelic variants of RhMLO genes in rose and functional studies on susceptibility to powdery mildew related to clade V homologs.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Integrative Study of Genotypic and Phenotypic Diversity in the Eurasian Orchid GenusFrontiers in plant science · 2021Article
- Skim sequencing: an advanced NGS technology for crop improvement.Journal of genetics · 2021Review
- Network-based approaches for understanding gene regulation and function in plants.The Plant journal : for cell and molecular biology · 2020Review
- Effects of Heat stress and molecular mitigation approaches in orphan legume, Chickpea.Molecular biology reports · 2020Review
- Genetic Diversity and Phylogenetic Relationships of Annual and PerennialG3 (Bethesda, Md.) · 2019Article
- High-Resolution Copy Number Patterns From Clinically Relevant FFPE Material.Scientific reports · 2019Article
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- Analysis of the Chromosomal Localization of Yeast SMC Complexes by Chromatin Immunoprecipitation.Methods in molecular biology (Clifton, N.J.) · 2019Article
98 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
Abstract
We developed a generalized framework for multiplexed resequencing of targeted human genome regions on the Illumina Genome Analyzer using degenerate indexed DNA bar codes ligated to fragmented DNA before sequencing. Using this method, we simultaneously sequenced the DNA of multiple HapMap individuals at several Encyclopedia of DNA Elements (ENCODE) regions. We then evaluated the use of Bayes factors for discovering and genotyping polymorphisms. For polymorphisms that were either previously identified within the Single Nucleotide Polymorphism database (dbSNP) or visually evident upon re-inspection of archived ENCODE traces, we observed a false positive rate of 11.3% using strict thresholds for predicting variants and 69.6% for lax thresholds. Conversely, false negative rates were 10.8-90.8%, with false negatives at stricter cut-offs occurring at lower coverage (<10 aligned reads). These results suggest that >90% of genetic variants are discoverable using multiplexed sequencing provided sufficient coverage at the polymorphic base.
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Registered trials
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.