ArticleBioinformatics (Oxford, England)2014
Discretized Gaussian mixture for genotyping of microsatellite loci containing homopolymer runs.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 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
15 citing papers in PubMed, 20 citations in OpenAlex.
- A detailed analysis of second and third-generation sequencing approaches for accurate length determination of short tandem repeats and homopolymers.Nucleic acids research · 2025Article
- Molecular Surveillance of Malaria Using the PF AmpliSeq Custom Assay forBio-protocol · 2023Article
- Assessment of Microsatellite Instability from Next-Generation Sequencing Data.Advances in experimental medicine and biology · 2022Article
- Germline microsatellite genotypes differentiate children with medulloblastoma.Neuro-oncology · 2020Article
- Low temperature isothermal amplification of microsatellites drastically reduces stutter artifact formation and improves microsatellite instability detection in cancer.Nucleic acids research · 2019Article
- CAGm: a repository of germline microsatellite variations in the 1000 genomes project.Nucleic acids research · 2019Article
- Article
- Detecting Expansions of Tandem Repeats in Cohorts Sequenced with Short-Read Sequencing Data.American journal of human genetics · 2018Article
- Whole-exome sequencing reveals microsatellite DNA markers for response to dofetilide initiation in patients with persistent atrial fibrillation: A pilot study.Clinical cardiology · 2018Article
- Article
- Exceptionally long-range haplotypes in Plasmodium falciparum chromosome 6 maintained in an endemic African population.Malaria journal · 2016Article
- A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer.BMC medical genomics · 2016Article
- Novel variation at chr11p13 associated with cystic fibrosis lung disease severity.Human genome variation · 2016Article
- Pheno2Geno - High-throughput generation of genetic markers and maps from molecular phenotypes for crosses between inbred strains.BMC bioinformatics · 2015Article
- Exome-wide somatic microsatellite variation is altered in cells with DNA repair deficiencies.PloS one · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
motivationInferring lengths of inherited microsatellite alleles with single base pair resolution from short sequence reads is challenging due to several sources of noise caused by the repetitive nature of microsatellites and the technologies used to generate raw sequence data.
resultsWe have developed a program, GenoTan, using a discretized Gaussian mixture model combined with a rules-based approach to identify inherited variation of microsatellite loci from short sequence reads without paired-end information. It effectively distinguishes length variants from noise including insertion/deletion errors in homopolymer runs by addressing the bidirectional aspect of insertion and deletion errors in sequence reads. Here we first introduce a homopolymer decomposition method which estimates error bias toward insertion or deletion in homopolymer sequence runs. Combining these approaches, GenoTan was able to genotype 94.9% of microsatellite loci accurately from simulated data with 40x sequence coverage quickly while the other programs showed <90% correct calls for the same data and required 5∼30× more computational time than GenoTan. It also showed the highest true-positive rate for real data using mixed sequence data of two Drosophila inbred lines, which was a novel validation approach for genotyping. AVAILABILITY: GenoTan is open-source software available at http://genotan.sourceforge.net.
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.