ArticleGenome research1999
Using quality measures to facilitate allele calling in high-throughput genotyping.
Article in Genome research, 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- PeakSeeker: a program for interpreting genotypes of mononucleotide repeats.BMC research notes · 2009Article
- A drastic reduction in the life span of cystatin C L68Q carriers due to life-style changes during the last two centuries.PLoS genetics · 2008Article
- A genome-wide scan for type 1 diabetes susceptibility genes in nuclear families with multiple affected siblings in Finland.BMC genetics · 2007Article
- Genomewide scan for linkage reveals evidence of several susceptibility loci for alopecia areata.American journal of human genetics · 2007Article
- Evaluation of DNA pooling for the estimation of microsatellite allele frequencies: a case study using striped bass (Morone saxatilis).Genetics · 2006Article
- A genome wide linkage disequilibrium screen in Parkinson's disease.Journal of neurology · 2005Article
- A genome wide search for alcoholism susceptibility genes.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2004Article
- Novel algorithm for automated genotyping of microsatellites.Nucleic acids research · 2004Article
- Localization of a gene for migraine without aura to chromosome 4q21.American journal of human genetics · 2003Article
- A novel method for automatic genotyping of microsatellite markers based on parametric pattern recognition.Human genetics · 2003Article
- Localization of a susceptibility gene for type 2 diabetes to chromosome 5q34-q35.2.American journal of human genetics · 2003Article
- Genomewide scan for hand osteoarthritis: a novel mutation in matrilin-3.American journal of human genetics · 2003Article
- Anxiety with panic disorder linked to chromosome 9q in Iceland.American journal of human genetics · 2003Article
- A major susceptibility gene for asthma maps to chromosome 14q24.American journal of human genetics · 2002Article
- Localization of a susceptibility gene for common forms of stroke to 5q12.American journal of human genetics · 2002Article
- Localization of a gene for peripheral arterial occlusive disease to chromosome 1p31.American journal of human genetics · 2002Article
- Toward high-throughput genotyping: dynamic and automatic software for manipulating large-scale genotype data using fluorescently labeled dinucleotide markers.Genome research · 2001Article
- Estimating Scandinavian and Gaelic ancestry in the male settlers of Iceland.American journal of human genetics · 2000Article
- Identification and analysis of error types in high-throughput genotyping.American journal of human genetics · 2000Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Currently, the main limitation in high-throughput microsatellite genotyping is the required manual editing of allele calls. Even though programs for automated allele calling have been available for several years, they have limited capability because accurate data could only be assured by manual inspection of the electropherograms for confirmation. Here we describe the development of a parametric approach to allele call quality control that eliminates much of the time required for manual editing of the data. This approach was implemented in an editing tool, Decode-GT, that works downstream of the allele calling program, TrueAllele (TA). Decode-GT reads the output data from TA, displays the underlying electropherograms for the genotypes, and sorts the allele calls into three categories: good, bad, and ambiguous. It discards the bad calls, accepts the good calls, and suggests that the user inspect the ambiguous calls, thereby reducing dependence on manual editing. For the categorization we use the following parameters: (1) the quality value for each allele call from TrueAllele; (2) the peak height of the alleles; and (3) the size of the peak shift needed to move peaks into the nearest bin. Here we report how we optimized the parameters such that the size of the ambiguous category was minimized, and both the number of miscalled genotypes in the good category and the useable genotypes in the bad category were negligible. This approach reduces the manual editing time and results in <1% miscalls.
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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.