Advanced Forensic Biology

Owner	Master Forensic Science
Coordinator	dr. ir. Titia Sijen
Part of	Master Forensic Science, year 2

Course manual 2020/2021

Course content

Trace evidence is the domain of the forensic scientist. She or he deals with the recognition, the collection, the selection, identification, individualization and interpretation of the physical and biological evidence. In the forensic context: the perpetrator of a violent crime may leave biological traces at the scene of the crime and conversely take traces away. In case of a rape the rapist usually leaves his semen behind and may take away a hair or a smear of blood from the victim. Molecular biology has become one of the most dominant technologies applied nowadays in the forensic field.

The course Advanced Forensic Biology is designed to provide students with fundamental information on state of the art molecular biology technologies. Special attention will be paid to research topics that fall within the scope of forensic biology. The course concentrates on the nature and significance of biological evidence and the underlying (molecular) biological principles of scientific methods employed for forensic analysis and interpretation.

 

The course Advanced Forensic Biology consists of four modules:

I. Advanced methods in forensic case work
II. Forensic data analysis, genomics and proteomics
III. Forensic Epigenetics
IV. Research Proposal

Ad IV Research proposal:

The compiling of a research proposal by the students is an integral part of the course Advanced Forensic Biology. Your research proposals must outline a relevant research topic in the field of Forensic Biology and must contain a formulated research question, an overview of the existing literature related to the topic and the necessary research methods to answer the specific research question. The aim is to present a proposal with an original research idea and to show that you have developed a thought-out strategy that enables the researcher to address relevant research questions. At the end of the course it is expected that you hand over a written research proposal, present your proposal to lecturers and students and present a poster of your proposal at the CLHC symposium. During the CLHC symposium the best poster presentation will be awarded at the end of the symposium.

Study materials

Literature

• Module I

  PDF files from the PowerPoint presentations will be posted on Canvas.  Files for the hands-on lecture will be posted on Canvas. Details will be announced during lectures. The book from John Butler: Advanced topics in Forensic DNA Typing: methodology (Academic Press, February 2011) is optional for this module.

• Module II

  Students will be provided with a reader and a number of relevant scientific papers. Details will be announced during the lectures and posted on Canvas.

• Module III

  To be announced on Canvas.

Objectives

• 1. Understand the forensic potential of modern forensic DNA, RNA, protein and epigenetic technologies for applications beyond human identification.
• 2. Critically weigh the forensic relevance and added value of an application in a case scenario. Applications refer to inference of physical characteristics, biogeographical origin, age and cell type and the role of prevalence, transfer, persistence and recovery of cell material in activity-level forensic questions.
• 3. Understand how research data are analyzed correctly with assistance of bioinformatic tools.
• 4. Conceptualize a strategy to develop a novel forensic application. Substantiate the proposed research with scientific literature.
• 5. Clearly explain the proposed research in writing and verbal presentations. Use solid argumentation in discussions.

Teaching methods

• Lecture
• Presentation/symposium
• Writing a research proposal
• Self-study
• Laptop seminar

Lectures, tutorials, exercises, computer practical, group presentations of studied literature and research proposals.

Learning activities

Attendance

This programme does not have requirements concerning attendance (OER part B).

Additional requirements for this course:

It is presupposed that all students will be present during the lectures. Students must inform the lecturers if there is an urgent reason for absence during one of the lectures.

The attendance during workshops and group presentations is mandatory. Absence will result in the loss of credit for that particular part of the course.

Attendance in week 4 during the presentations of the research proposals and the Poster Presentations is mandatory. Absence will result in the loss of credit for the course.

Assessment

Item and weight	Details
Final grade
20% Presentation science behind research proposal Module III	Must be ≥ 5.5, Mandatory
60% Research Proposal	Must be ≥ 5.5, Mandatory
1% Hand in final poster	Must be ≥ pass
10% research proposal poster presentation plus video
40% research proposal report
10% research proposal verbal presentation
20% Tentamen	Must be ≥ 5.5, Mandatory
Individual exam Topic 1
Individual exam Topic 2
Individual exam Topic 3
Individual exam Topic 4
Indvidual exam resit

Module I: Advanced methods in forensic case work (lecturer dr. Titia Sijen)

Learning Outcomes

At the end of Module 1 of this course the student will be able to:

1. Understand the role, objective, and meaning of biological evidence in the criminal justice system;
2. Understand the forensic possibilities for haploid markers and inferring informative characteristics
3. Understand the forensic relevance of body fluid and organ typing
4. Understand how mRNA profiling assays are established and applied in forensic cases
5. Understand the effect and impact of DNA transfer issues in forensic context
6. Discuss experimental design regarding DNA transfer studies.

 

1. Advanced DNA analysis; On haploid markers and inferring informative characteristics

When no match is obtained in the comparison of the DNA profile of an evidentiary trace and the references profiles in the case or DNA database, the forensic scientist has several options at hand to obtain investigative leads. These include familial searching, forensic genealogy, Y-chromosome marker analysis, mitochondrial DNA analysis and the prediction of biogeographic ancestry, age and appearance.

The scientific background will be explained and various online tools will be shown that assist analysis. Students will formulate their views through interactive discussion.

The purpose of this interactive lecture is that students become aware of the wide range of possibilities that go beyond STR profiling and also understand the complexity of inference and prediction assays.

 

2. Body fluid and organ typing through mRNA profiling

Identification of the tissue or body fluid origin of the suspect's or victim's DNA is often an important issue in forensic casework. Therefore, it is important for the fact finders that biological stains are being identified definitively and accurately. Currently, the serological approaches for stain identification involve enzymatic or immunologic tests. While these tests have improved in selectivity and sensitivity over the years, several problems still exist such as the lack of specificity and sensitivity for particular tissues and body fluids. In addition, not for all body fluids are tests available.

While the DNA of all tissues from an individual is essentially identical, the mRNA spectrum made by the different cells in each tissue is very different. Each tissue or cell type makes a unique constellation of mRNAs, some specific for only that tissue or cell type. Some body fluids, such as blood, contain cells as part of their function while other fluids, such as menstrual secretion, contain cells that have been shed from their tissue of origin. Therefore, analysis of the “RNA profile” in a sample can uniquely identify the fluid or tissue of origin. Since forensic evidentiary stains can be mixed or minute, interpretation guidelines for RNA results in casework have been developed and the why and how will be discussed. Case examples are presented.

The purpose of this interactive lecture is that students can analyze and interpret RNA profiling results in casework context.

 

3. DNA transfer in forensic genetics
   Understanding the variables impacting DNA transfer, persistence, prevalence and recovery (DNA-TPPR) has become increasingly relevant in investigations of criminal activities to provide opinion on how the DNA of a person of interest became present within the sample collected. Appropriately trained forensic practitioners are best placed to provide opinion and guidance on the interpretation of profiles at the activity level. In this lecture we will explore our current state of knowledge regarding DNA-TPPR. It will be explored how relevant information from ground truth experiments can be obtained to feed TPPR understanding. Case examples will demonstrate how this information can be used in casework. Through

The purpose of this interactive lecture is that students translate their insights regarding TPPR to an experimental design on an activity-level question.

 

4. Assessment Module 1

The forensic relevance and other aspects of a previous research proposal will be critically assessed in an individual assignment that is assessed by grading.

Module II: Forensic Bioinformatics (lecturers dr. Peter Henneman, dr. Gertjan Kramer and dr. Marc Galland)

Learning Outcomes

At the end of Module 2 of this course the student will be able to:

1. describe the fundamentals of sequencing and microarray technologies.
2. describe the experimental pipeline for microarray and sequencing based RNA expression analysis and
3. describe principal components analysis, and is able to interpret its
4. describe the analysis of case-control association
5. describe why multiple testing correction is applied to microarray data.
6. explain the following concepts: single nucleotide polymorphism, allele frequency distribution, linkage disequilibrium, population stratification, and haplotype
7. describe the difference between a genotype-phenotype association, and a predictive test.
8. design an experiment, or a set of experiments, that can serve as a basis for a research proposal that is relevant for

Content

In this module several concepts, methods, and state of art potentialities of –omics technologies and bioinformatics applications in forensic (molecular) science will be introduced. The applicability bioinformatics will be demonstrated using examples which are important in the context of Module A.

The focus is on:

• Analysis of genotype-phenotype relationships.
• Analysis of tissue specific (micro)RNA
• Analysis of proteome.

Information on genotype-phenotype relationships is required to infer phenotypic characteristics (hair colour, eye colour, geographical origin etc) from an unknown DNA sample. The analysis of tissue specific RNA expression (transcriptome) is presented and discussed in the context of RNA-based cell typing, which is further discussed in module II and module III.

Skills obtained

• To acquire a basic understanding of molecular, statistical and conceptual principles related to genome wide association studies and transcriptome
• To critically read and draw conclusions from scientific literature on genome wide association studies and transcriptome
• To get acquainted with high dimensional microarray and sequencing and proteomics data.
  
  
  

Module III: Forensic Epigenetics (lecturer dr. Pernette Verschure, dr. Peter Henneman)

Learning Outcomes

At the end of Module 3 of this course the student will be able to:

1. describe chromatin-based epigenetic regulation in cellular
2. explain (epi)genetic network behaviour
3. reconstruct epigenetic regulation in research data
4. assess epigenetic related (forensic) research
5. present and defend epigenetic related (forensic) research interpretation
6. use epigenetic knowledge to devise applications / methods in order to solve problems in the forensic field

Content

The focus of this module is on understanding epigenetics: the heritable inheritance of genetic states without change in DNA sequence. In forensics epigenetics has become an area under intensive scientific investigation and the course will focus on recent advances in understanding the principles.

There are several research topics where epigenetics can aid forensic science. While the DNA profile identifies an individual, the epigenetic information can add informative layers to that evidence*. Here are some examples**:

• Determining tissue or bodily fluid origin of crime scene
• Age identification from DNA methylation markers
• Discriminating between identical
• DNA methylation signatures that relate to time of death or cause of

*The National Academy of Sciences 2009, Strengthening Forensic Science in the United States: A Path Forward.
**  http://epiexperts.com/blog/can-epigenetics-improve-forensic-science-matters-of-life-liberty-death/

Skills obtained

• To critically read and analyze and draw conclusions of scientific literature in the field of
• To present through presentations knowledge from lectures and
• To be able to critically assess science and scientific results

Presentation literature studies on the science behind the research proposal with student feedback panel

The literature study presentation must deal with the science behind your research proposal. For this purpose students must select one or maximum two scientific core papers on their topic. The scientific papers are not necessarily from forensic journals.

Intended learning outcomes: assisting students in the evaluation of scientific literature and to develop skills in the presentation of scientific data in oral formats.



Module IV: Research Proposal writing and presentation (lecturers: dr. Titia Sijen, dr. Pernette Verschure, prof. Ate Kloosterman, Dr. Peter Henneman)

Learning Outcomes

At the end of Module 4 of this course the student will be able to:

1. translate a scientific problem into relevant forensic research questions, suitable for research development and for use in forensic DNA identification;
2. interpret scientific literature on research methods on the application of epigenetics and bioinformatics correctly, and to communicate the science to professionals within the Criminal Justice System.
3. formulate hypotheses and designing a research plan to test the formulated research questions, according to existing methodological and scientific standards;
4. develop effective presentation skills (use aids such as a PowerPoint presentation and a poster to support the key messages)

Content

This module provides coverage of some elements of research proposal writing, a skill that is required throughout one's scientific career. Students will be provided with a general overview of the conceptualization and writing of a research proposal.

A review of the relevant scientific literature review is incorporated into this section. Students will be guided to develop the skills of critical thinking.

The intention is to make certain that students are able to undertake the initiative to investigate the scientific literature in one of the areas from the Advanced Forensic Biology course and to provide a detailed description of the topic they want to investigate. In their research proposal students must convince the scientific community that they have identified a research question that is relevant for the forensic community and to justify the effort of doing the research. In their proposal students must provide a theoretical background and a feasible methodical way to solve the research questions within a realistic framework of financial resources.


The calculation of the final grade

All components will be graded on a scale from 1 to 10, with a maximum of one decimal after the point. These grades are used to calculate the final grade. In order to pass the course, all components and the final grade have to be sufficient, i.e. at least a five and a half. When a student has not fulfilled this requirement, the examiner will register the mark ‘did not fulfil all requirements’ (NAV) whether or not the averaged grade is sufficient.

The components will be weighted as follows:

1. Exam (30%)
2. Science behind the research proposal (group work, 20%)
3. Research proposal (50%): verbal presentation (10%), report (30%), poster presentation (group work, 10%)

The final grade will be announced at the latest on Friday November 13th, 2020 (= 15 working days after the final course activity). Between Friday November 13th to Friday December 11th, 2020 (= 35 working days after the final course activity) a post-course discussion or inspection moment can be planned.

Table of specification

		Exit qualifications
Learning outcome	Components (see above)	1	2	3	4	5	6	7	8	9	10
1	1, 2, 3			x
2	1			x	x	x		x
3	2, 3		x			x
4	2,3					x		x	x
5	2, 3							x	x	x

Table 1: Table of specification: the relation between the Learning Outcomes (LO) of the course, the assessment components of the course and the Exit Qualifications (EQ) of the Master’s Forensic Science (described in the Introduction in the Course Catalogue)

 

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

Timetable

The schedule for this course is published on DataNose.

Additional information

Students must have passed the exam of the course of Forensic statistics and DNA evidence. The Bayesian paradigm is assumed known.

 

Last year's course evaluation

In order to provide students some insight how we use the feedback of student evaluations to enhance the quality of education, we decided to include the table below in all course guides.

Advanced Forensic Biology (6 EC)	N 12
Strengths Overall the course was evaluated positively. Particularly the computer practicals by Martijs and the poster were evaluated positively.	Notes for improvement The students experienced the partial exam as frustrating. There was not much time to study for the exam, and the instructions about the exam were unclear. It had been said that if the students paid attention at the lecture, they wouldn’t need to study for the exam. However, the exam turned out to be very difficult, even though students had internet access and could bring their own notes. It was expected to write a complete research proposal but there were not enough examples how to do so. It occurred that a supervisor was not present during a feedback moment, which was not very satisfying.
Response lecturer/programme coordinator: Next year the instructions for the partial exam will be adjusted. It should be clear it is a tough exercise and that it is a good idea to go over your notes, even though it is an open-book-exam. The feedback about examples of the research proposal and to supply these earlier is curious. There were examples available and provided at the moments the students needed them (first abstract, later on complete proposals). In addition, proposal examples were discussed during one of the lecture hours. It was not clear to all teachers that they were scheduled in DataNose for several feedback moments. If they are listed as one of the teachers present they should be there as students will expect them to be there. For next year the schedule for feedback moments and how to plan these (groups could also make an appointment with their own supervisor separate from other groups) will be reviewed.

Contact information

Coordinator

• dr. ir. Titia Sijen