ArticleGene2013
Population-scale analysis of human microsatellites reveals novel sources of exonic variation.
Article in Gene, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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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.
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.
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Who cites it
21 citing papers in PubMed, 29 citations in OpenAlex.
- Native functions of short tandem repeats.eLife · 2023Article
- Mapping the landscape of tandem repeat variability by targeted long read single molecule sequencing in familial X-linked intellectual disability.BMC medical genomics · 2018Article
- Fluorescence spectroscopic detection and measurement of single telomere molecules.Nucleic acids research · 2018Article
- Dysfunctional DNA repair pathway via defective FANCD2 gene engenders multifarious exomic and transcriptomic effects in Fanconi anemia.Molecular genetics & genomic medicine · 2018Article
- GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing.BMC bioinformatics · 2018Article
- Tandem repeats mediating genetic plasticity in health and disease.Nature reviews. Genetics · 2018Review
- Mismatch repair-based stratification for immune checkpoint blockade therapy.American journal of cancer research · 2018Review
- High-depth, high-accuracy microsatellite genotyping enables precision lung cancer risk classification.Oncogene · 2017Article
- Tandem repeat variation in human and great ape populations and its impact on gene expression divergence.Genome research · 2015Article
- 'Cut from the same cloth': Shared microsatellite variants among cancers link to ectodermal tissues-neural tube and crest cells.Oncotarget · 2015Article
- Population analysis of microsatellite genotypes reveals a signature associated with ovarian cancer.Oncotarget · 2015Article
- The landscape of human STR variation.Genome research · 2014Article
- Somatic intronic microsatellite loci differentiate glioblastoma from lower-grade gliomas.Oncotarget · 2014Article
- VNTRseek-a computational tool to detect tandem repeat variants in high-throughput sequencing data.Nucleic acids research · 2014Article
- Divergence of Drosophila melanogaster repeatomes in response to a sharp microclimate contrast in Evolution Canyon, Israel.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Nicotine and oxidative stress induced exomic variations are concordant and overrepresented in cancer-associated genes.Oncotarget · 2014Article
- Microsatellite genotyping reveals a signature in breast cancer exomes.Breast cancer research and treatment · 2014Article
- Article
- Large-scale analysis of tandem repeat variability in the human genome.Nucleic acids research · 2014Article
- 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 2 institutions in 1 country.
Funding
Abstract
Using our microsatellite specific genotyping method, we analyzed tandem repeats, which are known to be highly variable with some recognized as biomarkers causative of disease, in over 500 individuals who were exon sequenced in a 1000 Genomes Project pilot study. We were able to genotype over 97% of the microsatellite loci in the targeted regions. A total of 25,115 variations were observed, including repeat length and single nucleotide polymorphisms, corresponding to an average of 45.6 variations per individual and a density of 1.1 variations per kilobase. Standard variant detection did not report 94.2% of the exonic repeat length variations in part because the alignment techniques are not ideal for repetitive regions. Additionally some standard variation detection tools rely on a database of known variations, making them less likely to call repeat length variations as only a small percent of these loci (~6000) have been accurately characterized. A subset of the hundreds of non-synonymous variations we identified was experimentally validated, indicating an accuracy of 96.5% for our microsatellite-based genotyping method, with some novel variants identified in genes associated with cancer. We propose that microsatellite-based genotyping be used as a part of large scale sequencing studies to identify novel variants.
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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.