ArticlePloS one2012
Massively parallel haplotyping on microscopic beads for the high-throughput phase analysis of single molecules.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Exploring FGFR3 Mutations in the Male Germline: Implications for Clonal Germline Expansions and Paternal Age-Related Dysplasias.Genome biology and evolution · 2024Article
- Exploring the Micro-Mosaic Landscape ofGenes · 2024Article
- Discovery of an unusually high number of de novo mutations in sperm of older men using duplex sequencing.Genome research · 2022Article
- Increased yields of duplex sequencing data by a series of quality control tools.NAR genomics and bioinformatics · 2021Article
- Optimized methodology for product recovery following emulsion PCR: applications for amplification of aptamer libraries and other complex templates.Journal of biological methods · 2020Article
- Challenging the proposed causes of the PCR plateau phase.Biomolecular detection and quantification · 2019Article
- Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- Pitfalls of haplotype phasing from amplicon-based long-read sequencing.Scientific reports · 2016Article
- Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data.BMC genomics · 2015Article
- Crossovers are associated with mutation and biased gene conversion at recombination hotspots.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Aquaporin 5 expression in mouse mammary gland cells is not driven by promoter methylation.BioMed research international · 2015Article
- Establishment of a reborn MMV-microarray technology: realization of microbiome analysis and other hitherto inaccessible technologies.BMC biotechnology · 2014Article
- Killer-cell Immunoglobulin-like Receptor gene linkage and copy number variation analysis by droplet digital PCR.Genome medicine · 2014Article
- New evidence for positive selection helps explain the paternal age effect observed in achondroplasia.Human molecular genetics · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
In spite of the many advances in haplotyping methods, it is still very difficult to characterize rare haplotypes in tissues and different environmental samples or to accurately assess the haplotype diversity in large mixtures. This would require a haplotyping method capable of analyzing the phase of single molecules with an unprecedented throughput. Here we describe such a haplotyping method capable of analyzing in parallel hundreds of thousands single molecules in one experiment. In this method, multiple PCR reactions amplify different polymorphic regions of a single DNA molecule on a magnetic bead compartmentalized in an emulsion drop. The allelic states of the amplified polymorphisms are identified with fluorescently labeled probes that are then decoded from images taken of the arrayed beads by a microscope. This method can evaluate the phase of up to 3 polymorphisms separated by up to 5 kilobases in hundreds of thousands single molecules. We tested the sensitivity of the method by measuring the number of mutant haplotypes synthesized by four different commercially available enzymes: Phusion, Platinum Taq, Titanium Taq, and Phire. The digital nature of the method makes it highly sensitive to detecting haplotype ratios of less than 1:10,000. We also accurately quantified chimera formation during the exponential phase of PCR by different DNA polymerases.
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