ArticleBMC genomics2012
A mechanistic basis for amplification differences between samples and between genome regions.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 39 citations in OpenAlex.
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- Next-generation sequencing of newborn screening genes: the accuracy of short-read mapping.NPJ genomic medicine · 2020Article
- Bioinformatics Strategies, Challenges, and Opportunities for Next Generation Sequencing-Based HLA Genotyping.Transfusion medicine and hemotherapy : offizielles Organ der Deutschen Gesellschaft fur Transfusionsmedizin und Immunhamatologie · 2019Review
- The kinetic requirements of extreme qPCR.Biomolecular detection and quantification · 2019Article
- Sample tracking in microbiome community profiling assays using synthetic 16S rRNA gene spike-in controls.Scientific reports · 2018Article
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- Computational identification of putative lincRNAs in mouse embryonic stem cell.Scientific reports · 2016Article
- Post-zygotic Point Mutations Are an Underrecognized Source of De Novo Genomic Variation.American journal of human genetics · 2015Article
- Exome Sequencing: Current and Future Perspectives.G3 (Bethesda, Md.) · 2015Article
- Obesity, starch digestion and amylase: association between copy number variants at human salivary (AMY1) and pancreatic (AMY2) amylase genes.Human molecular genetics · 2015Article
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- Molecular Detection of 10 of the Most Unwanted Alien Forest Pathogens in Canada Using Real-Time PCR.PloS one · 2015Article
- The Use of Non-Variant Sites to Improve the Clinical Assessment of Whole-Genome Sequence Data.PloS one · 2015Article
- Multi-template polymerase chain reaction.Biomolecular detection and quantification · 2014Review
- Variant detection sensitivity and biases in whole genome and exome sequencing.BMC bioinformatics · 2014Article
- Sequencing depth and coverage: key considerations in genomic analyses.Nature reviews. Genetics · 2014Review
- A 129-kb deletion on chromosome 12 confers substantial protection against rheumatoid arthritis, implicating the gene SLC2A3.Human mutation · 2014Article
Corrections and comments
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Authors and funding
11 authors at 6 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFor many analytical methods the efficiency of DNA amplification varies across the genome and between samples. The most affected genome regions tend to correlate with high C + G content, however this relationship is complex and does not explain why the direction and magnitude of effects varies considerably between samples.
resultsHere, we provide evidence that sequence elements that are particularly high in C + G content can remain annealed even when aggressive melting conditions are applied. In turn, this behavior creates broader 'Thermodynamically Ultra-Fastened' (TUF) regions characterized by incomplete denaturation of the two DNA strands, so reducing amplification efficiency throughout these domains.
conclusionsThis model provides a mechanistic explanation for why some genome regions are particularly difficult to amplify and assay in many procedures, and importantly it also explains inter-sample variability of this behavior. That is, DNA samples of varying quality will carry more or fewer nicks and breaks, and hence their intact TUF regions will have different lengths and so be differentially affected by this amplification suppression mechanism - with 'higher' quality DNAs being the most vulnerable. A major practical consequence of this is that inter-region and inter-sample variability can be largely overcome by employing routine fragmentation methods (e.g. sonication or restriction enzyme digestion) prior to sample amplification.
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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.