ArticlePLoS genetics2006
Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.
Article in PLoS genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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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.
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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
22 citing papers in PubMed.
- Insights from the Biorepository and Integrative Genomics pediatric resource.Nature communications · 2025Article
- The Biorepository and Integrative Genomics resource for inclusive genomics: insights from a diverse pediatric and admixed cohort.medRxiv : the preprint server for health sciences · 2025Article
- How far from the SNP may the causative genes be?Nucleic acids research · 2016Article
- Collaborative science in the next-generation sequencing era: a viewpoint on how to combine exome sequencing data across sites to identify novel disease susceptibility genes.Briefings in bioinformatics · 2016Article
- Applying genome-wide gene-based expression quantitative trait locus mapping to study population ancestry and pharmacogenetics.BMC genomics · 2014Article
- A genome wide association study of pulmonary tuberculosis susceptibility in Indonesians.BMC medical genetics · 2012Article
- You've gotta be lucky: Coverage and the elusive gene-gene interaction.Annals of human genetics · 2011Article
- Label-free microarray imaging for direct detection of DNA hybridization and single-nucleotide mismatches.Biosensors & bioelectronics · 2010Article
- (Too) great expectations: the challenges in replicating asthma disease genes.American journal of respiratory and critical care medicine · 2009Article
- From the Cover: Whole-genome association study identifies STK39 as a hypertension susceptibility gene.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Association studies for untyped markers with TUNA.Bioinformatics (Oxford, England) · 2008Article
- Article
- A Bayesian approach to copy-number-polymorphism analysis in nuclear pedigrees.American journal of human genetics · 2007Article
- Effects of environment, genetics and data analysis pitfalls in an esophageal cancer genome-wide association study.PloS one · 2007Article
- Genome-wide association with diabetes-related traits in the Framingham Heart Study.BMC medical genetics · 2007Article
- Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study.BMC medical genetics · 2007Article
- Genome-wide association with bone mass and geometry in the Framingham Heart Study.BMC medical genetics · 2007Article
- Article
- A new approach for using genome scans to detect recent positive selection in the human genome.PLoS biology · 2007Article
- Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation.BMC genomics · 2007Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Improvements in technology have made it possible to conduct genome-wide association mapping at costs within reach of academic investigators, and experiments are currently being conducted with a variety of high-throughput platforms. To provide an appropriate context for interpreting results of such studies, we summarize here results of an investigation of one of the first of these technologies to be publicly available, the Affymetrix GeneChip Human Mapping 100K set of single nucleotide polymorphisms (SNPs). In a systematic analysis of the pattern and distribution of SNPs in the Mapping 100K set, we find that SNPs in this set are undersampled from coding regions (both nonsynonymous and synonymous) and oversampled from regions outside genes, relative to SNPs in the overall HapMap database. In addition, we utilize a novel multilocus linkage disequilibrium (LD) coefficient based on information content (analogous to the information content scores commonly used for linkage mapping) that is equivalent to the familiar measure r2 in the special case of two loci. Using this approach, we are able to summarize for any subset of markers, such as the Affymetrix Mapping 100K set, the information available for association mapping in that subset, relative to the information available in the full set of markers included in the HapMap, and highlight circumstances in which this multilocus measure of LD provides substantial additional insight about the haplotype structure in a region over pairwise measures of LD.
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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.