ArticleHuman mutation2013
Rapid multiplexed genotyping of simple tandem repeats using capture and high-throughput sequencing.
Article in Human mutation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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.
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
18 citing papers in PubMed, 29 citations in OpenAlex.
- PolyG-DS: An ultrasensitive polyguanine tract-profiling method to detect clonal expansions and trace cell lineage.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Short Tandem Repeats as a High-Resolution Marker for Capturing Recent Orangutan Population Evolution.Frontiers in bioinformatics · 2021Article
- Primary immunodeficiency diseases in a tuberculosis endemic region: challenges and opportunities.Genes and immunity · 2019Review
- Mapping the landscape of tandem repeat variability by targeted long read single molecule sequencing in familial X-linked intellectual disability.BMC medical genomics · 2018Article
- HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay.Genome research · 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
- A microsatellite repeat in PCA3 long non-coding RNA is associated with prostate cancer risk and aggressiveness.Scientific reports · 2017Article
- High-depth, high-accuracy microsatellite genotyping enables precision lung cancer risk classification.Oncogene · 2017Article
- CRISPR-Cas9-targeted fragmentation and selective sequencing enable massively parallel microsatellite analysis.Nature communications · 2017Article
- Systematic Profiling of Short Tandem Repeats in the Cattle Genome.Genome biology and evolution · 2017Article
- Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome.Scientific reports · 2016Article
- Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans.Nucleic acids research · 2016Article
- Abundant contribution of short tandem repeats to gene expression variation in humans.Nature genetics · 2016Article
- Tandem repeat variation in human and great ape populations and its impact on gene expression divergence.Genome research · 2015Article
- MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals.Genome research · 2015Article
- The overdue promise of short tandem repeat variation for heritability.Trends in genetics : TIG · 2014Review
- Large-scale analysis of tandem repeat variability in the human genome.Nucleic acids research · 2014Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Although simple tandem repeats (STRs) comprise ~2% of the human genome and represent an important source of polymorphism, this class of variation remains understudied. We have developed a cost-effective strategy for performing targeted enrichment of STR regions that utilizes capture probes targeting the flanking sequences of STR loci, enabling specific capture of DNA fragments containing STRs for subsequent high-throughput sequencing. Utilizing a capture design targeting 6,243 STR loci <94 bp and multiplexing eight individuals in a single Illumina HiSeq2000 sequencing lane we were able to call genotypes in at least one individual for 67.5% of the targeted STRs. We observed a strong relationship between (G+C) content and genotyping rate. STRs with moderate (G+C) content were recovered with >90% success rate, whereas only 12% of STRs with ≥ 80% (G+C) were genotyped in our assay. Analysis of a parent-offspring trio, complete hydatidiform mole samples, repeat analyses of the same individual, and Sanger sequencing-based validation indicated genotyping error rates between 7.6% and 12.4%. The majority of such errors were a single repeat unit at mono- or dinucleotide repeats. Altogether, our STR capture assay represents a cost-effective method that enables multiplexed genotyping of thousands of STR loci suitable for large-scale population studies.
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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.