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Challenges and standards in integrating surveys of structural variation.

ABSTRACT: There has been an explosion of data describing newly recognized structural variants in the human genome. In the flurry of reporting, there has been no standard approach to collecting the data, assessing its quality or describing identified features. This risks becoming a rampant problem, in particular with respect to surveys of copy number variation and their application to disease studies. Here, we consider the challenges in characterizing and documenting genomic structural variants. From this, we derive recommendations for standards to be adopted, with the aim of ensuring the accurate presentation of this form of genetic variation to facilitate ongoing research.

SUBMITTER: Scherer SW

PROVIDER: S-EPMC2698291 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature

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Challenges and standards in integrating surveys of structural variation.

Scherer Stephen W SW Lee Charles C Birney Ewan E Altshuler David M DM Eichler Evan E EE Carter Nigel P NP Hurles Matthew E ME Feuk Lars L

Nature genetics 20070701 7 Suppl

There has been an explosion of data describing newly recognized structural variants in the human genome. In the flurry of reporting, there has been no standard approach to collecting the data, assessing its quality or describing identified features. This risks becoming a rampant problem, in particular with respect to surveys of copy number variation and their application to disease studies. Here, we consider the challenges in characterizing and documenting genomic structural variants. From this, ...[more]

PMID: 17597783

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Project description:Decades of environmental DNA (eDNA) method application, spanning a wide variety of taxa and habitats, has advanced our understanding of eDNA and underlined its value as a tool for conservation practitioners. The general consensus is that eDNA methods are more accurate and cost-effective than traditional survey methods. However, they are formally approved for just a few species globally (e.g., Bighead Carp, Silver Carp, Great Crested Newt). We conducted a meta-analysis of studies that directly compare eDNA with traditional surveys to evaluate the assertion that eDNA methods are consistently "better."Environmental DNA publications for multiple species or single macro-organism detection were identified using the Web of Science, by searching "eDNA" and "environmental DNA" across papers published between 1970 and 2020. The methods used, focal taxa, habitats surveyed, and quantitative and categorical results were collated and analyzed to determine whether and under what circumstances eDNA outperforms traditional surveys.Results show that eDNA methods are cheaper, more sensitive, and detect more species than traditional methods. This is, however, taxa-dependent, with amphibians having the highest potential for detection by eDNA survey. Perhaps most strikingly, of the 535 papers reviewed just 49 quantified the probability of detection for both eDNA and traditional survey methods and studies were three times more likely to give qualitative statements of performance. Synthesis and applications: The results of this meta-analysis demonstrate that where there is a direct comparison, eDNA surveys of macro-organisms are more accurate and efficient than traditional surveys. This conclusion, however, is based on just a fraction of available eDNA papers as most do not offer this granularity. We recommend that conclusions are substantiated with comparable and quantitative data. Where a direct comparison has not been made, we caution against the use of qualitative statements about relative performance. This consistency and rigor will simplify how the eDNA research community tracks methods-based advances and will also provide greater clarity for conservation practitioners. To this end suggest reporting standards for eDNA studies.

Dataset Information

Challenges and standards in integrating surveys of structural variation.

Publications

Challenges and standards in integrating surveys of structural variation.

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