ArticlePloS one2012
Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism.
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 17 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed, 43 citations in OpenAlex.
- Genomics-based assessment of the geographic origin of spongy moths (Lymantria dispar) intercepted during vessel inspections, using SpongySeq, an amplicon sequencing panel.BMC genomics · 2026Article
- Article
- A new genomic resource to enable standardized surveys of SNPs across the native range of brook trout (Salvelinus fontinalis).Molecular ecology resources · 2025Article
- A Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species.Molecular ecology resources · 2025Article
- A Review on Microbiological Source Attribution Methods of Human Salmonellosis: From Subtyping to Whole-Genome Sequencing.Foodborne pathogens and disease · 2024Review
- Mining whole genome sequence data to efficiently attribute individuals to source populations.Scientific reports · 2020Article
- Single nucleotide polymorphisms reveal a genetic cline across the north-east Atlantic and enable powerful population assignment in the European lobster.Evolutionary applications · 2019Article
- Range-wide population genomics of the Mexican fruit fly: Toward development of pathway analysis tools.Evolutionary applications · 2019Article
- Misassembly of long reads undermines de novo-assembled ethnicity-specific genomes: validation in a Chinese Han population.Human genetics · 2019Article
- Temporal stability and assignment power of adaptively divergent genomic regions between herring (Ecology and evolution · 2019Article
- High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool.Scientific reports · 2018Article
- A panel of 130 autosomal single-nucleotide polymorphisms for ancestry assignment in five Asian populations and in Caucasians.Forensic science, medicine, and pathology · 2017Article
- Identification of Multiple QTL Hotspots in Sockeye Salmon (Oncorhynchus nerka) Using Genotyping-by-Sequencing and a Dense Linkage Map.The Journal of heredity · 2016Article
- Article
- Linkage Mapping Reveals Strong Chiasma Interference in Sockeye Salmon: Implications for Interpreting Genomic Data.G3 (Bethesda, Md.) · 2015Article
- Reduced SNP panels for genetic identification and introgression analysis in the dark honey bee (Apis mellifera mellifera).PloS one · 2015Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single nucleotide polymorphisms (SNPs) are valuable tools for ecological and evolutionary studies. In non-model species, the use of SNPs has been limited by the number of markers available. However, new technologies and decreasing technology costs have facilitated the discovery of a constantly increasing number of SNPs. With hundreds or thousands of SNPs potentially available, there is interest in comparing and developing methods for evaluating SNPs to create panels of high-throughput assays that are customized for performance, research questions, and resources. Here we use five different methods to rank 43 new SNPs and 71 previously published SNPs for sockeye salmon: F(ST), informativeness (I(n)), average contribution to principal components (LC), and the locus-ranking programs BELS and WHICHLOCI. We then tested the performance of these different ranking methods by creating 48- and 96-SNP panels of the top-ranked loci for each method and used empirical and simulated data to obtain the probability of assigning individuals to the correct population using each panel. All 96-SNP panels performed similarly and better than the 48-SNP panels except for the 96-SNP BELS panel. Among the 48-SNP panels, panels created from F(ST), I(n), and LC ranks performed better than panels formed using the top-ranked loci from the programs BELS and WHICHLOCI. The application of ranking methods to optimize panel performance will become more important as more high-throughput assays become available.
Indexed as
Identifiers
What OpenQuestion holds
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.