ArticleBMC genetics2005
Estimating haplotype frequencies in pooled DNA samples when there is genotyping error.
Article in BMC genetics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 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
6 citing papers in PubMed.
- Associations between polymorphisms in the myostatin gene with calving difficulty and carcass merit in cattle.Journal of animal science · 2023Article
- Impact of genotyping errors on the type I error rate and the power of haplotype-based association methods.BMC genetics · 2009Article
- Genotyping error detection in samples of unrelated individuals without replicate genotyping.Human heredity · 2009Article
- Estimating the single nucleotide polymorphism genotype misclassification from routine double measurements in a large epidemiologic sample.American journal of epidemiology · 2008Article
- A survey on haplotyping algorithms for tightly linked markers.Journal of bioinformatics and computational biology · 2008Article
- A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.Malaria journal · 2006Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
backgroundMaximum likelihood estimates of haplotype frequencies can be obtained from pooled DNA using the expectation maximization (EM) algorithm. Through simulation, we investigate the effect of genotyping error on the accuracy of haplotype frequency estimates obtained using this algorithm. We explore model parameters including allele frequency, inter-marker linkage disequilibrium (LD), genotyping error rate, and pool size.
resultsPool sizes of 2, 5, and 10 individuals achieved comparable levels of accuracy in the estimation procedure. Common marker allele frequencies and no inter-marker LD result in less accurate estimates. This pattern is observed regardless of the amount of genotyping error simulated.
conclusionGenotyping error slightly decreases the accuracy of haplotype frequency estimates. However, the EM algorithm performs well even in the presence of genotyping error. Overall, pools of 2, 5, and 10 individuals yield similar accuracy of the haplotype frequency estimates, while reducing costs due to genotyping.
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.