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Overview

Topics

Introduction

OSIRIS is a public domain quality assurance software package that facilitates the assessment of multiplex short tandem repeat (STR) DNA profiles based on laboratory-specific protocols. OSIRIS evaluates the raw electrophoresis data contained in .fsa or .hid files using an independently derived mathematically-based sizing algorithm. OSIRIS currently supports ABI capillary analysis and RAPID DNA analysis platforms and numerous commercially available marker kits including all CODIS-compliant kits as well as those favored by biomedical laboratories.

OSIRIS was initiated in response to recommendations of a multidisciplinary advisory group (the Kinship and DNA Analysis Panel, KADAP) empanelled by the U.S. Department of Justice. KADAP was assembled to assist the New York City Office of the Medical Examiner (OCME) and New York State Police (NYSPD) DNA laboratories in the unprecedented challenges of the World Trade Center victim identifications focusing on ways to enhance the number and quality of identifications that could be made. Developed in collaboration with state, local and federal forensic laboratories and NIST, the National Center for Biotechnology Information (NCBI) created OSIRIS using C++ and object oriented design to facilitate the development of add-on applications by those using the program.

Use cases

Clinical testing

STR analysis is used in clinical and research laboratories to monitor stem cell and bone marrow transplants, microsattelite instability testing, and triplet expansion diseases. - The Molecular Hematology Laboratory at the NIH Clinical Center uses OSIRIS to monitor stem cell transplant engraftment and to guide treatment. Using OSIRIS the laboratory provides sensitive, rapid-turnaround testing of various cell types that allows clinicians to modify treatment to support stem cell grafts and prevent transplant failure. OSIRIS saves the laboratory over 3 hours per week of analysis time of their high volume of chimerism tests. Trinucleotide Repeat expansion testing is used by clinical and research laboratories to diagnose trinuclotide repeat disorders (TRDs) such as Huntington's disease, Fragile X syndrome, Myotonic dystrophy, and Spinocerebellar ataxia. - Microsattelite Instability (MSI) testing is used by clinical laboratories to identify MMR-gene associated tumors such as in Lynch Syndrome.

Forensic testing

Identification

STR analysis is used for kinship anlysis, paternity testing, biosample identification, and cell line authentication.

Training

OSIRIS is used by universities and other organizations to train DNA analysts in STR profiling. Benefits include explicit artifact identification, portability, Windows and Macintosh versions and easy data exchange.

How OSIRIS works

OSIRIS searches for peaks by iteratively fitting expected parametric data signatures to the observed data, usually achieving matches with correlations in excess of 0.999. Parametric peak locations are determined with sub-second accuracy and transformed to base pair coordinates. Traditional sizing methods for DNA fragments usually rely on either the local or global Southern methods to interpolate the internal lane standard (ILS) into base pair estimates. OSIRIS departs from this approach, using instead the correspondence between a sample's ILS and an associated allelic ladder to map the time scale of the ladder into that of the sample. This integration of the ladder with the sample permits a straightforward and accurate comparison of sample peaks with ladder locus peaks. Typically, OSIRIS-analyzed sample peaks align within 0.1 base pair of the position within a locus. Thus, in addition to providing reliable and accurate peak analysis, OSIRIS offers two new peak quality measures: fit level and sizing residual.

Based on a laboratory's own protocols, these two measures can enhance quality metrics currently available to assess STR DNA profiles. OSIRIS can be customized to accommodate laboratory-specific signatures including settings sensitive to typical background noise and can include any customized naming conventions or additional internal laboratory controls.

 

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