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                            Library & Multimedia
 TRcaller: A novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads
NCJ Number
              308049
Journal

*Frontiers in Genetics* Volume: 14 Dated: 2023
Author(s)
          Xuewen Wang;
                        Meng Huang;
                        Bruce Budowle;
                        Jianye Ge
Date Published

2023
Annotation
              This study describes a novel algorithm for tandem repeat variant genotyping in massively parallel sequencing reads.
Abstract
              This study describes a novel algorithm to retrieve tandem repeat (TR) regions from sequence alignment and a software program TRcaller that has been developed and integrated into a web portal to call TR alleles from both short- and long-read sequences, both whole genome and targeted sequences generated from multiple sequencing platforms. All TR alleles are genotyped as haplotypes and the robust alleles will be reported, even multiple alleles in a DNA mixture. TRcaller could provide substantially higher accuracy (>99% in 289 human individuals) in detecting TR alleles with magnitudes faster (e.g., ∼2s for 300x human sequence data) than the mainstream software tools. The web portal preselected 119 TR loci from forensics, genealogy, and disease related TR loci. TRcaller is validated to be scalable in various applications, such as DNA forensics and disease diagnosis, which can be expanded into other fields like breeding programs. Calling tandem repeat (TR) variants from DNA sequences is of both theoretical and practical significance. Some bioinformatics tools have been developed for detecting or genotyping TRs. However, little study has been done to genotyping TR alleles from long-read sequencing data, and the accuracy of genotyping TR alleles from next-generation sequencing data still needs to be improved. (Published Abstract Provided)
      
  
          Additional Details
Grant Number(s)
        15PNIJ-21-GG-04159-RESS


  
  
        
  Agencies
        NIJ-Sponsored


  
  
        
  Publication Type
        Research (Applied/Empirical)


  
  
        
  Award
        Enhanced mixture interpretation with long-read DNA sequencing
    
  
  
Date Published: January 1, 2023
    
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