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Characterization of the standard and recommended CODIS markers.

ABSTRACT: As U.S. courts grapple with constitutional challenges to DNA identification applications, judges are resting legal decisions on the fingerprint analogy, questioning whether the information from a DNA profile could, in light of scientific advances, reveal biomedically relevant information. While CODIS loci were selected largely because they lack phenotypic associations, how this criterion was assessed is unclear. To clarify their phenotypic relevance, we describe the standard and recommended CODIS markers within the context of what is known currently about the genome. We characterize the genomic regions and phenotypic associations of the 24 standard and suggested CODIS markers. None of the markers are within exons, although 12 are intragenic. No CODIS genotypes are associated with known phenotypes. This study provides clarification of the genomic significance of the key identification markers and supports--independent of the forensic scientific community--that the CODIS profiles provide identification but not sensitive or biomedically relevant information.

SUBMITTER: Katsanis SH

PROVIDER: S-EPMC8591976 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature

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Characterization of the standard and recommended CODIS markers.

Katsanis Sara H SH Wagner Jennifer K JK

Journal of forensic sciences 20120824

As U.S. courts grapple with constitutional challenges to DNA identification applications, judges are resting legal decisions on the fingerprint analogy, questioning whether the information from a DNA profile could, in light of scientific advances, reveal biomedically relevant information. While CODIS loci were selected largely because they lack phenotypic associations, how this criterion was assessed is unclear. To clarify their phenotypic relevance, we describe the standard and recommended CODI ...[more]

PMID: 22925064

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Project description:BackgroundEach year, 10%-20% of patients with tuberculosis (TB) in low- and middle-income countries present with previously treated TB and are empirically started on a World Health Organization (WHO)-recommended standardized retreatment regimen. The effectiveness of this retreatment regimen has not been systematically evaluated.Methods and findingsFrom July 2003 to January 2007, we enrolled smear-positive, pulmonary TB patients into a prospective cohort to study treatment outcomes and mortality during and after treatment with the standardized retreatment regimen. Median time of follow-up was 21 months (interquartile range 12-33 months). A total of 29/148 (20%) HIV-uninfected and 37/140 (26%) HIV-infected patients had an unsuccessful treatment outcome. In a multiple logistic regression analysis to adjust for confounding, factors associated with an unsuccessful treatment outcome were poor adherence (adjusted odds ratio [aOR] associated with missing half or more of scheduled doses 2.39; 95% confidence interval (CI) 1.10-5.22), HIV infection (2.16; 1.01-4.61), age (aOR for 10-year increase 1.59; 1.13-2.25), and duration of TB symptoms (aOR for 1-month increase 1.12; 1.04-1.20). All patients with multidrug-resistant TB had an unsuccessful treatment outcome. HIV-infected individuals were more likely to die than HIV-uninfected individuals (p<0.0001). Multidrug-resistant TB at enrollment was the only common risk factor for death during follow-up for both HIV-infected (adjusted hazard ratio [aHR] 17.9; 6.0-53.4) and HIV-uninfected (14.7; 4.1-52.2) individuals. Other risk factors for death during follow-up among HIV-infected patients were CD4<50 cells/ml and no antiretroviral treatment (aHR 7.4, compared to patients with CD4≥200; 3.0-18.8) and Karnofsky score <70 (2.1; 1.1-4.1); and among HIV-uninfected patients were poor adherence (missing half or more of doses) (3.5; 1.1-10.6) and duration of TB symptoms (aHR for a 1-month increase 1.9; 1.0-3.5).ConclusionsThe recommended regimen for retreatment TB in Uganda yields an unacceptable proportion of unsuccessful outcomes. There is a need to evaluate new treatment strategies in these patients.

Project description:BackgroundRecently, the Combined DNA Index System (CODIS) Core Loci Working Group established by the US Federal Bureau of Investigation (FBI) reviewed and recommended changes to the CODIS core loci. The Working Group identified 20 short tandem repeat (STR) loci (composed of the original CODIS core set loci (minus TPOX), four European recommended loci, PentaE, and DYS391) plus the Amelogenin marker as the new core set. Before selecting and finalizing the core loci, some evaluations are needed to provide guidance for the best options of core selection.MethodThe performance of current and newly proposed CODIS core loci sets were evaluated with simplified analyses for adventitious hit rates in reasonably large datasets under single-source profile comparisons, mixture comparisons and kinship searches, and for international data sharing. Informativeness (for example, match probability, average kinship index (AKI)) and mutation rates of each locus were some of the criteria to consider for loci selection. However, the primary factor was performance with challenged forensic samples.ResultsThe current battery of loci provided in already validated commercial kits meet the needs for single-source profile comparisons and international data sharing, even with relatively large databases. However, the 13 CODIS core loci are not sufficiently powerful for kinship analyses and searching potential contributors of mixtures in larger databases; 19 or more autosomal STR loci perform better. Y-chromosome STR (Y-STR) loci are very useful to trace paternal lineage, deconvolve female and male mixtures, and resolve inconsistencies with Amelogenin typing. The DYS391 locus is of little theoretical or practical use. Combining five or six Y-chromosome STR loci with existing autosomal STR loci can produce better performance than the same number of autosomal loci for kinship analysis and still yield a sufficiently low match probability for single-source profile comparisons.ConclusionA more comprehensive study should be performed to provide the necessary information to decision makers and stakeholders about the construction of a new set of core loci for CODIS. Finally, selection of loci should be driven by the concept that the needs of casework should be supported by the processes of CODIS (or for that matter any forensic DNA database).

Dataset Information

Characterization of the standard and recommended CODIS markers.

Publications

Characterization of the standard and recommended CODIS markers.

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