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  • Cybergenetics :: Forensic DNA inference
    Handout Download PowerPoint Download Paper Abstract DNA evidence is a powerful casework approach to solving crimes Biological specimens are collected from the scene of crime from which scientists generate STR laboratory data and then infer DNA genotypes from the STR data peaks By comparing these genotypes against the genotypes of possible suspects including DNA databases matches between genotypes can help identify the culprit However not all groups compare inferred genotypes against genotypes Many laboratories have forensic scientists use the STR data peaks directly in their match comparison Others use a likelihood ratio LR to compare alternative forensic hypotheses about the peak data but without first inferring the genotype A likelihood ratio inference from DNA evidence assesses two competing hypotheses relative to the data Typically the likelihood data is comprised of the original STR peaks obtained from biological specimens However it is also possible to divide the DNA inference problem into two separate stages first obtaining genotypes from the evidence as posterior probability distributions and subsequently determining the strength of match using a general likelihood ratio statistic To implement this two phase DNA inference approach we describe a likelihood ratio statistic for inferring match strength that can accommodate uncertain genotypes This

    Original URL path: http://www.cybgen.com/information/presentations/2008/ICFIS/Perlin_Kadane_Cotton_Forensic_DNA_inference/page.shtml (2016-02-12)
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  • Cybergenetics :: Exploring forensic scenarios with TrueAllele mixture automation
    for forensic scientists to work with computer tools that can help them solve crimes In particular a forensic scientist can control the computer to perform different what if scenarios to elicit the most useful genetic identification information from the data Cybergenetics TrueAllele 174 Casework system has two input streams for each case 1 the user s selection of which DNA samples and their laboratory processed STR data to consider and 2 the underlying DNA sequencer lane data Once the user has made their sample selection the DNA interpretation that infers DNA profiles for each contributor is performed by automated objective statistical computation If case suspects are available their profiles are automatically compared against the inferred crime scene profiles to assess match strength By controlling the first input stream the selection of forensically significant DNA samples and data a scientist can explore different case scenarios For example a When initial data are insufficiently informative e g low match strength the computer result can suggest the need for processing additional DNA samples b A scientist can interpret the DNA samples from one location at a crime scene separately interpret the samples from a second location as well as interpret all the samples at once c Informative DNA specimens can be further developed in the laboratory to generate more sample data that can be used in computer interpretation d Low quality STR data e g having low signals or spike artifacts can be regenerated using any or all of the data in subsequent computer analyses e A scientist can separately and jointly analyze serial crime hypotheses in order to determine the strength of a link between the crime scenes f Alternative assumptions can be made about the number of mixture contributors The TrueAllele user interface enables this what if scenario analysis by providing

    Original URL path: http://www.cybgen.com/information/presentations/2007/AAFS/Perlin_Exploring_forensic_scenarios_with_TrueAllele_mixture_automation/page.shtml (2016-02-12)
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  • Cybergenetics :: Scientific validation of mixture interpretation methods
    for a testable approach whose error rate has been determined and has been communicated by peer review dissemination These Daubert criteria are typically met by conducting scientific validation studies that establish the reliability of an approach by testing it and determining an error rate Forensic STR data have undergone extremely rigorous scientific validation in this country with validation studies of laboratory processes routinely introduced as courtroom evidence in order to establish admissibility Similarly the DNA science of interpreting and matching single source profiles is solidly grounded in the rigor of population genetics Since there is only one correct designation of a pristine single source profile concordance studies can compare the theoretically identical results of two different examiners However interpretation of mixed DNA samples need not produce unambiguous results Different laboratories follow different mixture interpretation guidelines Moreover different examiners within the same laboratory who are following the same guidelines often infer different STR profiles Therefore there is no concordance in current forensic practice on what constitutes a correct mixture solution Thus it is not possible to conduct a mixture interpretation concordance study in order to validate a mixture interpretation method But it is essential to have some way of testing the reliability of mixture interpretation methods so that inferred profiles from DNA mixtures can be scientifically validated and admitted as legal evidence We have developed a general approach to scientifically validating mixed DNA profiles Instead of conducting a concordance comparison which is not possible our approach determines the amount of information present in the DNA match between an inferred mixture profile and a reference profile By examining these numerical measures of match information one can assess the reliability of a mixture interpretation method We have tested our validation approach on mixed DNA samples from multiple crime laboratories each of whom uses

    Original URL path: http://www.cybgen.com/information/presentations/2006/ISHI/Perlin_Scientific_validation_of_mixture_interpretation_methods/page.shtml (2016-02-12)
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  • Cybergenetics :: Real-time DNA investigation
    DNA matching process is driven by police investigations as in the United Kingdom criminals can be identified within days and then rapidly apprehended Such a DNA led policing approach can reduce crime by removing active criminals from society before they can commit more crimes DNA laboratory automation has introduced robotic batch processing that can transform biological specimens into informative data in less than a day However the task of human data review interpretation matching and reporting often takes months To complete DNA investigations within 48 hours it would be useful to have a computer system that can perform these information processing tasks and deliver investigative leads within several hours Cybergenetics TrueAllele 174 System 3 is an automated computer based system that interprets DNA evidence into profiles matches these profiles against other profiles and delivers profile and match results to end users via Internet The system can be distributed across multiple locations with DNA interpretation match and reporting occurring simultaneously for different cases on different computers that share a coordinating database Doubling the number of interpretation computers halves the processing time Once a case s DNA peak information has been uploaded to the TrueAllele database all downstream processing can proceed automatically without human intervention We have been scientifically assessing TrueAllele System 3 in several real time DNA investigative applications Useful measures for comparing the computer against current manual systems include speed accuracy capacity information labor and cost For property crimes we have looked at the system s interpretation match and reporting of crime scene samples against an offender database As reported previously at the 2003 Promega Symposium the mixture analysis functionality can rapidly infer profiles from unknown suspect sexual assault data these DNA profiles are highly informative relative to human review and can be automatically matched against offender databases We have

    Original URL path: http://www.cybgen.com/information/presentations/2005/ISHI/Perlin_Real-time_DNA_investigation/page.shtml (2016-02-12)
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  • Cybergenetics :: Simple reporting of complex DNA evidence: Automated computer interpretation
    consider thousands of numerical variables the computer can present the results of its rigorous deliberations as ordinary probabilities that are understandable to juries This paper describes the collaborative study design data generation analytic interpretation and scientific results obtained in validating our expert system The validation study was designed collaboratively with crime labs in Florida Maryland and Virginia The mock rape kit approach analyzed a set of two contributor sperm fraction DNA mixtures 10 30 50 70 and 90 proportions at 1 0 0 5 0 25 and 0 125 ng dilutions along with their victim reference samples NIST prepared the mixed DNA stock solutions in known proportions for two individual pairs and sent these materials to the ten participating forensic laboratories Each lab followed detailed study protocols generated PCR data for 56 templates and sent their original sequencer data to Cybergenetics for automated computer interpretation In addition each lab also provided about 100 single source samples that were used for calibrating their PCR process and artifacts stutter preferential amplification peak variation etc All STR chemistries and DNA sequencers in current forensic use were represented Cybergenetics ran their sequencer independent TrueAllele 153 program on the original lab data to generate a database of quality checked quantitated peaks under five minutes of human time per gel The interpretation expert system was then applied to these data no human time The calibration produced graphs of stutter and pref amp for each marker The automated mixture analysis for each lab s 40 unknown suspect cases mixture and reference data but no suspect data yielded an estimate of the mixing proportion the genotype confidence set at each locus and quantitative bar graphs that permitted rapid visual comparison between the observed data and the best genotype model These computer results were reviewed by each laboratory The

    Original URL path: http://www.cybgen.com/information/presentations/2003/ISHI/Perlin_Simple_reporting_of_complex_DNA_evidence:_Automated_computer_interpretation/page.shtml (2016-02-12)
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  • Cybergenetics :: Expert systems for automated STR analysis
    Newsroom Press Releases Trials Contact Directions Information Visiting Support FAQ File Transfer Sending Data Downloads Back to Presentations Expert Systems for Automated STR Analysis M W Perlin Expert systems for automated STR analysis Scientific Working Group on DNA Analysis Methods

    Original URL path: http://www.cybgen.com/information/presentations/2003/SWGDAM/Perlin_Expert_systems_for_automated_STR_analysis/page.shtml (2016-02-12)
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  • Cybergenetics :: Automated STR data analysis: Validation studies
    With casework samples including mixtures much information is not extracted from the data despite considerable examiner effort We are rapidly developing novel computational mathematical and statistical methods that help overcome these limitations This report focuses on the collaborative validation of these methods Convicted offender DNA databases must be accurate To minimize error the original STR data are carefully reviewed by two or more people Moreover in a troubleshooting capacity this review helps to continuously maintain high quality lab data But there are not enough skilled personnel for this arduous repetitive task To alleviate this critical labor shortage we developed the TrueAllele 153 expert system The computer program automates virtually every human review function and provides consistent quality assessment and allele designation The TrueAllele validation starts with the original data from 30 000 CODIS samples System parameters are adapted to the instruments ABI 310 ABI 3700 Hitachi FMbio and panels ProfilerPlus Cofiler Powerplex 1 1 and 2 1 used to generate the data Computer processing is then done with automated scoring of the high quality data followed by limited human review The computed expert system results are compared against previously manually scored results We will report on the relative accuracy and efficiency of the automated approach In casework DNA mixtures are analyzed to assess candidate suspects When inferred profiles are matched against a convicted offender database useful leads are generated When matched against a known suspect the mixture data can help convict or exonerate However data uncer tainty leads to inherently complex and ambiguous analysis We have developed a new technol ogy Linear Mixture Analysis LMA which uses multilocus quantitative data to automatically eliminate this complexity LMA objectively resolves mixtures into candidate profiles and provides highly informative statistical measures The LMA validation involves both synthetic mixtures and actual casework profiles derived

    Original URL path: http://www.cybgen.com/information/presentations/2001/ISHI/Perlin_Coffman_Crouse_Konotop_Ban_Automated_STR_data_analysis:_Validation_studies/page.shtml (2016-02-12)
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  • Cybergenetics :: An expert system for scoring DNA database profiles
    exonerating the innocent However constructing such databases is quite laborious After generating STR profiles in the lab people expend even greater effort visually reviewing the data before it enters the database All artifacts must be detected and no error can be tolerated With millions of forensic samples to be analyzed this bottleneck has become a formidable task We have developed software analysis methods that can automate this data review and potentially eliminate 90 of the work Our fully automated TrueAllele 153 system inputs raw fluorescent DNA sequencer gel or capillary files processes the gel image separating colors tracking and sizing lanes and analyzes the STR experiments quantitating and sizing peaks comparing with ladder peaks calling alleles For each allele call TrueAllele assigns a quality score and applies artifact detection rules These quality checks enable a user to focus on just the 5 10 of suspect data thereby eliminating most of the review effort TrueAllele models every step of the STR data generation process By computing hundreds of variables for each genotype the system can compare the observed data against expected behav ior Large deviations between expected and observed enable the software to flag potentially problematic data for human review TrueAllele automatically extracts the information it needs from the raw data e g ABI 377 collection files After automated image processing the software provides a user quality assur ance review for assessing data runs lane tracking gel quality control lanes etc Automated data processing continues with peak quantitation allele designation and quality scoring In the allele based quality assurance review the user focuses on those designations which TrueAllele has flagged as having specific problems After reviewing and possibly editing this small subset of data TrueAllele then generates files for submission to the DNA database e g CODIS TrueAllele operates independently of

    Original URL path: http://www.cybgen.com/information/presentations/2000/ISHI/Perlin_An_expert_system_for_scoring_DNA_database_profiles/page.shtml (2016-02-12)
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