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                            Library & Multimedia
 Single nucleotide polymorphism typing with massively parallel sequencing for human identification
NCJ Number
              256095
Journal

*International Journal of Legal Medicine* Volume: 127 Issue: 6 Dated: 2013 Pages: 1079-1086
Author(s)
          J. King;
                        S. B. Seo;
                        D. Warshauer;
                        D. Davis;
                        J. Ge;
                        B. Budowle
Date Published

2013
Length
              8 pages
Annotation
              In this study, the Ion AmpliSeqTM HID single nucleotide polymorphism (SNP) panel, a primer pool of 103 autosomal SNPs and 33 Y-SNPs, was evaluated using the Ion 314TM Chip on the Ion PGMTM Sequencer with four DNA samples.
Abstract
              The study focused on the sequencing of DNA at three different initial target quantities, related interpretation issues, and concordance of results with another sequencing platform, i.e., Genome Analyzer IIx. With 10 ng of template DNA, all genotypes at the 136 SNPs were detected. With 1 ng of DNA, all SNPs were detected and one SNP locus in one sample showed extreme heterozygote imbalance on allele coverage. With 100 pg of DNA, an average of 1.6 SNP loci were not detected, and an average of 4.3 SNPs showed heterozygote imbalance. The average sequence coverage was 945–600× at autosomal SNPs and 465–209× at Y-SNPs for 10 ng–100 pg of DNA. The average heterozygote allele coverage ratio was 89.6–61.8 percent for 10 ng–100 pg of DNA. At 10 ng of DNA, all genotypes of the 95 SNPs shared between the two different sequencing platforms were concordant except for one SNP, rs1029047. The error was due to the misalignment of a flanking homopolymer. Overall, the data support that genotyping a large battery of SNPs is feasible with massively parallel sequencing. With barcode systems, better allele balance, and specifically designed alignment software, a more comprehensive rapid genotyping and more cost-effective results may be obtained from multiple samples in one analysis than are possible with current typing and capillary electrophoresis systems. (publisher abstract modified)
      
  
          Additional Details
Grant Number(s)
        2012-DN-BX-K033


  
  
        
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        Development of Reference Sample DNA Profiling for Databases Using Next Generation Sequencing Technologies
    
  
  
Date Published: January 1, 2013
    
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      PatentsRelated Topics
        
                DNA typing
        Assault and battery
        Single nucleotide polymorphism (SNP)
        Forensic medicine
        University of Texas



  
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