DNA Mixture Interpretation: Basic (full day)

Presenters:  Michael Coble, Steven Myers
Date and Time:  Monday August 29th, 9 AM – 6 PM
Course Level:  Basic

DNA mixtures can be complex and confounding for the analyst to interpret. In a survey from the Promega Corporation published in late 2015, when analysts were asked to share their greatest challenges in casework, 40% said “mixture interpretation” – the highest vote getter among the top 6 answers. Over the past decade, many laboratories around the world have moved from binary to probabilistic methods of interpretation. Certainly, probabilistic methods of interpretation can make better use of the data compared to threshold-based binary methods, but there is still a need to critically evaluate the outputs of a probabilistic approach.

In this workshop, we will focus on basic concepts of mixture interpretation to understand how stutter ratios, peak height ratios, number of contributors, and mixture proportions (to name a few) are applied to the deconvolution of DNA mixtures. We will use practical examples to demonstrate these concepts, including some exercises with manual calculations.

With the “explosion” of software available to assist in the interpretation of mixtures, it is critically important now (more than ever) to develop a solid foundation to understand the intuitive results of a probabilistic interpretation. Examples will illustrate the application of these basic concepts to improve comprehension and troubleshooting of probabilistic interpretation of mixtures.

Michael Coble | View Bio

Steven Myers | View Bio

DNA Mixture Interpretation: Advanced (full day)

Presenters: Peter Gill, Corina Benschop, Oyvind Bleka
Date and Time: Monday August 29th, 9 AM – 6 PM
Course Level: Advanced

This is an advanced course intended for case-work scientists who alreadyhave some basic experience of mixture analysis and interpretation. Theworkshop will explain the theory relating to the analysis of complex DNAprofiles where the material may be degraded, and consists of mixtures oftwo or more individuals. The likelihood ratio theory will be explained, alongwith basic principles that underpin the models. Different software solutions will be demonstrated: EuroForMix, DNAStatistX, CaseSolver and DNAxs.

The aim of the workshop is to provide sufficient information and support sothat users will be able to run software. To facilitate, we will provideinstructions to enable users to download software onto their computersbeforehand. The workshop will include hands-on exercises using the latestversions of EuroForMix and DNAStatistX using provided exercises and usingparticipants’ own data. Further information is available from the following websites:

Peter Gill | View Bio

Corina Benschop | View Bio

Y Chromosome: YHRD, typing and interpretation (full day)

Presenters: Sascha Willuweit, Lutz Roewer
Date and Time: Tuesday August 30th, 9 AM – 6 PM

Forensic genetic laboratories perform a large amount of STR analyses of theY chromosome, in particular to analyze the male part of complex DNAmixtures. However, the statistical interpretation of evidence retrieved fromY-STR haplotypes is challenging. Due to the uni-parental inheritance mode,Y-STR loci are connected to each other and thus haplotypes show patterns ofrelationship on the familial and population level. This precludes thetreatment of Y-STR loci as independently inherited variables and theapplication of the product rule. Instead, the haplotype frequency needs to beestimated based on collections of individual samples from the relevantpopulation. Such data collections are provided in form of annotateddatabases, for example the Y Chromosome Haplotype Reference Database(YHRD). In forensic casework the probability of a Y-STR match is evaluated either using count or model-based estimators of the profile frequency. The workshop will provide practical exercises and worked examples to get acquainted with the different methods and interpreting tools.

Questions that will be addressed in this workshop:
  • I found a puzzling Y-STR profile. Any help out there?
  • I got a Y-STR match. How can I get a match probability?
  • I am used to counting methods with lineage markers. What about Discrete Laplace?
  • I got a mixture. How does the program Mixture analysis work?
  • I am doing a complicated paternity case. Could I apply the program Kinship analysis?
  • I’ve been asked to identify a victim. How can I infer biogeographical ancestry using Y markers?
  • I don’t care much on populations. What is so special with reference populations used in Y casework ?
  • I have to write a report on a Y-STR match. I need help with the wording.
  • I want to write a research paper. How can I analyze my populations – how does AMOVA work?

Sascha Willuweit | View Bio

Lutz Roewer | View Bio

Testimony in US Courts (full day)

Presenters:  Charlotte Word, Raymond Valerio, Lewis Buzzell
Date and Time: Tuesday August 30th, 9 AM – 6 PM

DNA test results have played a significant role in many criminal and civil court cases in the United States since they were first introduced into courts in the mid-to-late 1980s. In some cases, the DNA test results provide the key evidence for exoneration or conviction; thus, it is imperative that accurate and reliable DNA testing results be presented to the decision-makers involved in the cases in a useful and meaningful way without prejudice or bias. Good communication between well-trained and informed DNA analysts, attorneys, judges and law enforcement personnel both in and outside of the courtroom is essential to achieving this. However, the adversarial environment of the judicial system and limitations in resources in many jurisdictions may significantly impact this ideal scenario in individual cases. The focus of this workshop will be on improving effective communications and interactions between the relevant parties in a legal case prior to and during expert witness testimony. This workshop will be presented by a veteran prosecutor who is the Director of Forensic Sciences in the Queens County District Attorney’s Office, a criminal defense attorney with forty-four years of litigation experience, and an expert with extensive experience testifying in various types of court proceedings.

Attendees of this workshop will gain an understanding of the:

  • Role of each of the key participants in the courtroom with a particular focus on the responsibilities of expert witnesses in their interactions with the other individuals in the judicial system;
  • Lessons learned over the past 30+ years regarding DNA in the courtroom;
  • Ways to provide effective, accurate and neutral expert witness testimony, including discussing errors and the limitations of DNA testing and the results, while facing legal and scientific challenges, often within an adversarial situation;
  • Need to testify within the limits of individual expertise;
  • Expert as an advocate for science and scientific methods and not for either party involved;
  • Multijurisdictional criminal justice system in the United States;

Interactive discussions during the workshop will focus on:

  • Mechanisms of effective communication and testimony without bias;
  • Correcting examples of inaccurate testimony;
  • Addressing issues and questions from the audience;
  • Contrasting the US courts to the courts and experiences in other countries;
  • Recommendations for improvement.

Current and future expert witnesses in DNA testing or other disciplines, laboratory directors, supervisors, trainers and quality assurance managers, as well as law enforcement personnel, attorneys and judges are encouraged to attend this workshop.

Charlotte Word | View Bio

Raymond Valerio | View Bio

Lewis Buzzell | View Bio

MPS Bioinformatics 101: Exploring Massively Parallel Sequencing Data Analysis using the STRait Razor Suite and FDS Tools

Presenters: Jonathan King, Jerry Hoogenboom
Date and Time: Tuesday August 30th, 9 AM – 6 PM
Course Level: This workshop is intended as an introduction for novice users; however, some advanced topics will be discussed.

This workshop will focus on employing the STRait Razor Suite and FDSTools software for analysis of Massively Parallel Sequencing (MPS) data. Attendees will be instructed on the usage of primary (STRait Razor v3 and FDSTools2.0)and secondary analysis (STRait Razor Online) tools to analyze data from commercially available kits. Additionally, guidance will be given for modifying the default settings, developing configuration files for both primary and secondary analysis of laboratory-developed tests (e.g., in-house PCR multiplex assays), and considerations for further processing the output. The strengths of and rationale behind the different methods will be explored by examining the results. This way, attendees will gain a deeper insight into the powers and challenges (and solutions!) that arise from the application of MPS to forensic samples.

Attendees should be familiar with general constructs of DNA markers and formats of standard sequencing data storage file types (e.g., BED, FASTQ, SAM/BAM, etc.). While no formal familiarity with any programming languages(e.g., R, Python, etc.) is required, modification of open-source materials may require some basic understanding of computer programming.

Jonathan King

Jonathan King | View Bio

Jerry Hoogenboom | View Bio

KINSHIP ANALYSIS (FULL DAY)

Presenters: Daniel Kling, Andreas Tillmar
Date and Time: Monday August 29th, 9 AM – 6 PM

Inference of relationships – From basic to advanced kinship statistics

The workshop will cover the basics of relationship inference using genetic markers as well as reach into more advanced topics such as linked markers and genetic genealogy. The workshop is divided into three parts, where the first part will cover basic principles of inheritance and how likelihoods for pedigrees can be calculated based on genetic data. In the second part we will introduce software that can be used for such likelihood calculations. This part will also contain guided examples and exercises. In the last part we will focus on advanced topics such as statistical inference for expanded marker panels and the possibilities to solve distant relationship cases. This part will include alternative biostatistical approaches, genetic genealogy and concepts like linkage and linkage disequilibrium.

Daniel Kling | View Bio

Andreas Tillmar | View Bio

Forensic STR Genomics: Sequence variation and nomenclature resources (HALF DAY)

Presenters: Katherine Gettings, Tunde Huszar
Date and Time: Monday August 29th, 9 AM – 1 PM

Description: This workshop will introduce attendees to autosomal, X and Y STR sequencing, with a target audience of students and practitioners having minimal sequencing experience or background knowledge. The workshop will be divided into three modules: 1) Anatomy of an STR Locus, 2) STR Sequencing and Analysis Methods, and 3) STR Sequencing Nomenclature Resources.

In the first module, we will use example loci to explore the concepts of sequence representation through bracketing (e.g. [GATA]8, considering historical precedent and evolving, modern guidance) and short designator systems. Then we will venture out into the flanking regions to find examples of SNPs and Indels, exemplifying their role in concordance between both length- and sequence-based assays. We will also explore minimum and kit-specific sequencing ranges and issues of CE backward compatibility.

In the second module, we will consider historical STR sequencing challenges and the benefits of modern sequencing platforms. We will learn about commercial STR sequencing assays and bioinformatic tools designed specifically for the forensic community. We will explore interpretation issues specific to STR sequencing, and additional quality control measures which may be useful.

In the third module, we will discuss the proliferation of STR population sequence data, and present resources for recommended STR sequence formatting and allele frequency data. These will include the STRSeq BioProject managed by NIST and hosted by NCBI, the STRidER allele frequency database, efforts to develop tools to convert STR sequence strings to various formats, and resources supporting the characterization of non-traditional STR loci.

Finally, we will end by discussing and contextualizing upcoming talks on STR sequencing in the main session, so that attendees will have a firm foundation for the coming days.

Katherine Gettings | View Bio

Tunde Huszar | View Bio

PHENOTYPING (HALF DAY)

Presenters: Susan Walsh
Date and Time: Monday August 29th, 2 PM – 6 PM

Hands on practical workshop that will provide an overview of all current systems that may be used to generate physical appearance predictions from DNA. These include but are not limited to the use of VISAGE tools, HIrisPlex-S and Snipper Suite. We will explore how to generate the genotypic data needed as input for these tools, both CE and MPS data derived, in addition to interpretation, comparisons of systems and example workflows. Participants will receive mock case examples and data and we will work through predictions from input to interpretation and reporting of results. Participants are expected to bring personal laptop computers to get the best experience from this workshop. Further details on what programs will be needed will be provided before the workshop begins.

Susan Walsh | View Bio

NGS Workflows for Forensic Genetics (HALF DAY)

Presenters: Peter Vallone
Date and Time: Monday August 29th, 9 AM – 1 PM

This workshop aims to review and explore the details of various NGS/MPS sequencing methods. Common sequencing methods, kits, and platforms that may be applied to forensic genetic analyses will be discussed. The laboratory workflow steps involved in sequencing library preparation and their specific purposes will be presented. These include: targeted PCR, incorporation of sequencing adapters and unique indices, quantification/normalization of final products prior to sequencing. Examples of the process will be illustrated through forensically-relevant workflows for the sequencing of STRs, SNPs and the mitochondrial genome. Brief examinations of the resulting sequence data will be demonstrated by the instructor using open source and/or commercial software tools. This workshop is intended for attendees with some basic familiarity with sequencing methods and interested in the basic and practical aspects of carrying out sequencing experiments in support of adopting these methods of genetic analysis in their laboratory. Questions related to the scope of the workshop can be directed to the instructor. [peter.vallone@nist.gov]

Peter M. Vallone | View Bio

MTDNA INTERPRETATION (HALF DAY)

Presenters: Walther Parson
Date and Time: Monday August 29th, 2 PM – 6 PM

The forensic field has witnessed major developments in mitochondrial DNA (mtDNA) analysis in the past three years, particularly in association with Massively Parallel Next Generation Sequencing (MPS) techniques.

This workshop showcasts the highlights and discusses various issues with the interpretation of MPS-based mtDNA sequences, including validation studies, the interpretation of sequence raw data with particular focus on NUMTs, heteroplasmy, artefacts and mixtures, database searches with EMPOP.

The workshop provides a brief introduction to the mtDNA molecule and field and is thus suitable for beginners and experts. Participants are invited to send challenging samples/cases beforehand to be included in the discussion.

Walther Parson

Walther Parson | View Bio

SCIENTIFIC PUBLICATION: READING, WRITING AND REVIEWING (HALF DAY)

Presenters: John Butler
Date and Time: Monday August 29th, 9 AM – 1 PM

Science benefits from effective communication of ideas. Research results are shared with others through publications and presentations. Scientific publication involves efforts in reading, writing and reviewing the literature.Editors of peer-reviewed journals rely on input from scientific colleagues to judge the merits of submitted manuscripts. Knowledgeable reviewers providing timely feedback are important for a successful peer-review process. This workshop will share insights based upon editorial experience with Forensic Science International: Genetics as well as extensive writing practice in preparing five textbooks and over 170 research articles and invited book chapters. Reviewing manuscripts is a chance to provide an important service and to influence the scientific community for good. In addition to discussing approaches to reading, writing and reviewing relevant literature, some recent articles covering forensic genetics will be considered and examined.

John M. Butler | View Bio

CONTACT TRACES AND DNA TRANSFER (HALF DAY)

Presenters: Roland van Oorschot, Bianca Szkuta and Georgina Meakinr
Date and Time: Tuesday August 30th, 9 AM – 1 PM

This workshop will provide a general update on our understanding of factors impacting the transfer, persistence, prevalence and recovery of DNA (DNA-TPPR). Then through a series of exercises explore the identification of potentially relevant factors impacting DNA-TPPR, the identification and use of relevant data to determine probabilities of profile types given particular actions and circumstances, and limitations of the available data. We will also consider areas requiring further research to improve our understanding of DNA-TPPR and availability of relevant probability data, and explore the types of experiments required to address these. This workshop will not be focused on activity level reporting.

Rolan van Oorschot | View Bio

EVALUATIVE REPORTING FOR CONTACT TRACES (HALF DAY)

Presenters: Lydie Samie-Foucart and Tacha Hicks
Date and Time: Tuesday August 30th, 2 PM – 6 PM
Course Level: Intermediate

Target audience: DNA reporting officers with experience in writing statements given sub-source level propositions. Participants are expected to have theoretical and practical background in probabilistic reasoning.

The aim of this workshop is to provide a framework allowing to assess and report DNA results when the issue regards not so much the source of the DNA, but the activities from which it resulted. It will be based on the guidelines produced by the DNA commission of the International Society for Forensic Genetics. Using real cases, participants will explore how to take into consideration transfer, persistence and background level of DNA in a transparent, logical and balanced way. The workshop will consist of presentations showing the essential building blocks for interpretation. Through those presentations and exercise(s), participants will develop ways to assign likelihood ratios in such cases and during debriefing will be introduced to Bayesian Networks. During the workshop, difficulties encountered will be explored and practical solutions to these challenges presented: (e.g., how to manage cases when experimental data are limited).

Lydie Samie

Lydie Samie | View Bio

Tacha Hicks

Tacha Hicks | View Bio

Introduction to Key Concepts in Probability and Statistics for Forensic Science (HALF DAY)

Presenters: Hari Iyer, Steven Lund
Date and Time: Tuesday August 30th, 9 AM – 1 PM

Target audience:  Forensic scientists and practitioners with minimal prior training in probability and statistics who have an interest in statistical tools and probabilistic approaches to interpreting and communicating evidence. Participants are expected to have background in high school level algebra.

The aim of this workshop is to develop concepts of probability and statistics from the ground up.

Module-1:
We begin with counts and proportions and then discuss the relationship between relative frequencies and the notion of quantifying uncertainty using probability. Rules of probability and Bayes theorem will be derived by simple counting arguments without any advanced mathematics.

Module-2:
Likelihood ratios (LRs) will be introduced using simple examples designed to elicit an intuitive understanding. The LR framework and its logical basis will be discussed, along with difficulties associated with the actual assignment of a LR value in any given casework situation. The role played by statistical models in facilitating LR assessments will be elaborated.

Module-3:
We will further introduce the concept of Receiver Operator Characteristic (ROC) curves as a way to understand the ability of a LR system to discriminate between a pair of mutually exclusive and exhaustive propositions H1 and H2. In addition, we will discuss the notion of a well-calibrated LR system versus an ill-calibrated LR system.

Module-4:
Finally, time permitting, we will discuss the notion of a ‘factor space’ and its relevance in the process of examining the performance of an LR system.

It is our intention to encourage audience participation throughout the workshop.

Hariharan (Hari) K. Iyer | View Bio

Steven Lund | View Bio

Validation – Experimental Design and Analysis using STR-validator

Presenters: Oskar Hansson
Date and Time: Tuesday August 30th, 2 PM – 6 PM
Course Level: This workshop is suitable for DNA analysts/technicians, QA/QC managers, consultants, and other interested individuals. A minimal background in forensic human identification testing would be beneficial. Programming or statistical background is helpful but not required.

Validation of new STR typing kits are often time consuming which can delay implementation of new technology. STR-validator is a free open-source software tool designed to help forensic genetic laboratories evaluate the data. Lectures and demonstrations will exemplify experimental design and efficient evaluation. Examples will highlight quality control of the data and result. The goal is to introduce STR-validator as an efficient tool to analyze validation data in accordance to ENFSI recommendations and SWGDAM guidelines.

Learning Outcomes

  • Understanding the STR-validator framework and its possibilities.
  • Experimental design and analysis according to ENFSI recommendations and SWGDAM guidelines.
  • Documentation and interpretation of the validation result.
  • Demonstration of automated analysis and report generation using R markdown.

Prepare for the workshop [PRELIMINARY]

  1. Download and install the statistical software R (usually installed together with a graphical user interface RGui or RStudio).
  2. Open RGui or RStudio and install the package strvalidator version 2.3.0 or higher by typing install.packages(“strvalidator”, dependencies=TRUE) in the R console, or using the installation menu.
  3. Download the zip file with exercises and unpack to a folder of your choice.
  4. It is recommended that you follow the instructions in the installation guide to create an icon for STR-validator in your folder.

Links: STR-validator website

Related publications

Coauthor of the book  Forensic Practitioner’s Guide to the Interpretation of Complex DNA Profiles – 1st Edition (elsevier.com).

Fun fact

In 1999, age 20, I attended an apnea (free diving) course in Båstad (Sweden) hosted by Jean-Jacques Mayol, son of  Jacques Mayol – Wikipediawho’s life inspired the famous film The Big Blue – Wikipedia .  Jean-Jacques Mayol is still teaching a combination of Apnea and Yoga, but now located in Italy at his late father’s home  Teammayol.

Oskar

Oskar Hansson | View Bio

BIOGEOGRAPHICAL ANCESTRY (HALF DAY)

Presenters: Torben Tvedebrink
Date and Time: Tuesday August 30th, 9 AM – 1 PM

In recent years, biogeographical ancestry markers have gained attention in the forensic genetics community with their ability to associate geographical and ethnic origins to DNA samples. Ancestry Informative SNP (AISNP) markers and panels have been selected and designed in order to provide investigational leads and for predicting the geographical origin of the investigated individuals in crime and identification cases. There exists several methods for modelling AISNPs, including principal components analysis (PCA), model based clustering (e.g. implemented in the software STRUCTURE and ADMIXTURE) and classification methods. However, a common assumption of these approaches is that a true population exists in the reference material. Using a statistical based outlier detection approach (implemented in Genogeographer: http://genogeographer.org, [1, 2]) this assumption is not needed. The workshop will discuss the strengths and weaknesses of the listed methodologies, introduce the participants to the ideas behind genogeographer.org, and show how to use this tool in relation to casework.

Genogeographer references:[1] T. Tvedebrink et al. (2018) Weight of the evidence of genetic investigations of ancestry informative markers. Theoretical Population Biology 120: 1–10[2] T. Tvedebrink et al. (2017) GenoGeographer – A tool for genogeographic inference. Forensic Science International: Genetics Supplement Series 6: e463-e465

Torben Tvedebrink

Torben Tvedebrink | View Bio

Special Sessions

The O.J. Simpson Trial:  A Retrospective

It has been over 25 years since O.J. Simpson was acquitted of the murder of his ex-wife Nicole Brown Simpson and her friend Ronald Goldman, yet this case remains one of the most notorious criminal trials in American history…

Panelists:

Robin Cotton, PhD; expert witness (DNA) in People v. O.J. Simpson
Bruce Weir, PhD; expert witness (statistics) in People v. O.J. Simpson
Rockne Harmon; prosecutor in People v. O.J. Simpson
Barry Scheck; defense attorney in People v. O.J. Simpson

Learn More