65318 Forensic Genotyping Technologies
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Subject handbook information prior to 2024 is available in the Archives.
Credit points: 6 cp
Result type: Grade and marks
Requisite(s): 91132 Molecular Biology 1 AND 91137 DNA Profiling
Description
The forensic application of DNA analysis was first introduced in the mid-1980s and began with restriction fragment length polymorphism (RFLP) analysis that required micrograms of DNA template. Soon after, polymerase chain reaction (PCR) amplification of short tandem repeats (STRs) proved capable of producing a full DNA profile from just a few cells. During the last thirty years, forensic DNA analysis has helped to solve a tremendous number of forensic cases worldwide, providing crucial evidence with unprecedented levels of sensitivity, specificity and statistical significance.
In recent years, rapid technological advancements in DNA sequencing methods have enabled additional progress in the area of forensic DNA genotyping, adding even more powerful tools to the forensic arsenal for investigation and solving of crimes. This research-inspired subject focuses on various technical aspects of emerging forensic DNA technologies and their implementation into operational casework. Specifically, the following topics are covered: novel genetic and epigenetic markers of forensic relevance, such as single nucleotide polymorphisms (SNPs), microhaplotypes and methylated DNA; advanced genotyping technologies, such as massively parallel sequencing and genetics of complex traits; analysis and interpretation of complex bioinformatic data; and ethical and legal considerations related to implementation of the novel forensic tools. These topics are addressed in an interdisciplinary context and in relation to the relevance and the probative value of the generated results.
Subject learning objectives (SLOs)
Upon successful completion of this subject students should be able to:
| 1. | Describe the principles of recent DNA sequencing technologies and their applications in forensic DNA analysis |
|---|---|
| 2. | Apply the basic principles of forensic DNA profiling using massively parallel sequencing (MPS) platforms. |
| 3. | Document laboratory work that is typical of professional practice in forensic science investigations |
| 4. | Perform basic bioinformatic analysis of DNA sequencing data and demonstrate understanding of sequencing metrics. |
| 5. | Interpret DNA sequencing results using various software tools and generate an expert report. |
| 6. | Effectively communicate forensic investigative leads, such as the biogeographical ancestry and pigmentation of a DNA donor, generated from sequencing data |
Course intended learning outcomes (CILOs)
This subject also contributes specifically to the development of following course intended learning outcomes:
- Demonstrate a command of forensic science practice, including the detection, collection, and analysis of traces in order to exploit and integrate the results of analyses into investigative, evaluative and intelligence frameworks. (1.1)
- Apply investigative, critical thinking and problem-solving skills to forensic science problems and design experimental methods to test hypotheses and critically analyse and interpret data. (2.1)
- Practise safe, ethical, and professional conduct with consideration for the role of forensic science in addressing current and future challenges faced by law enforcement, the legal system, security, and the wider community. (3.1)
- Apply forensic science professional skills with a high degree of personal autonomy and reflection to demonstrate initiative and innovative thinking in solving complex forensic problems. (4.1)
- Demonstrate skills in communicating experimental conclusions, expert opinion, and the justification of professional decisions related to forensic science processes effectively to expert, scientific, and non-expert audiences. (5.1)
Contribution to the development of graduate attributes
This subject contributes to the personal, professional and intellectual development of students by encouraging the following graduate attributes:
1. Disciplinary knowledge
You will develop an understanding of the disciplinary, professional and technical knowledge of state-of-the-art methods of forensic DNA profiling, as required for potential employment in operational forensic science laboratories and postgraduate studies. This will be achieved through interactive learning of advanced topics in forensic genetics, molecular biology, DNA sequencing technologies, bioinformatics and other disciplines and their application in forensic DNA analysis. You will also contribute to automatic extraction of DNA, quantitation of the extracted DNA, clonal amplification of specific regions of the genome and subsequent sequencing, as well as bioinformatic data analysis and interpretation of the DNA results in a case context.
2. Research, inquiry and critical thinking
You will develop skills to analyse information critically and creatively, as evidenced in the compilation of a forensic case file and in the analysis of the DNA profile data that you will generate. You will gain an introductory understanding of the role of bioinformatics in the analysis of DNA results in a forensic context and be able to objectively assess the value of DNA evidence through participation in tutorials and workshops which will help you to analyse and evaluate the DNA profiles you have produced.
3. Professional, ethical and social responsibility
You will develop a capacity to autonomously and collaboratively acquire technical, practical and professional skills within the context of forensic genotyping technologies and apply these in ethical ways to meet the current and future needs of the legal system.
4. Reflection, innovation, creativity
You will develop a capacity for innovation and creativity through the development of reflective practices as a self-directed learner, motivated by a responsibility to serve the justice system. You will challenge your scientific curiosity and the attitudes, knowledge and skills necessary for a commitment to lifelong learning in science; the gathering, evaluating and use of information from sources such as databases, research and review articles, textbooks, catalogues and technical references; and the management of workload required for scientific based practice and professional work. The lectures will also provide you with the opportunity to develop an understanding of the professional requirements of a forensic scientist. The practical sessions and tutorials/workshops, and their associated assessment tasks, will give you the opportunity to develop these skills.
5. Communication
You will learn to communicate effectively and professionally to law enforcement professionals using appropriate media. You will gain experience in compiling an accurate and reliable case file, and in providing succinct answers to forensic questions posed by legal actors. This will contribute to the development of excellence in written scientific communication; an appreciation of the importance of communicating science to the general community and of matching communication style, written and oral, to the target audience. A digital intelligence report will be a capstone assessment designed to communicate complex ideas.
Teaching and learning strategies
Lectures
Lecture material will be available on Canvas before online delivery in order to minimise time spent writing and maximise time spent actively participating. Lecture material will not be repeated nor will content be explained to non-attending students. There will be multiple opportunities for exchange between teaching staff and students. Preparation for lectures will include readings and activities available on Canvas. You should complete the preparation beforehand as it will give you the knowledge to further understand the subject content and be an active learner in the online classroom.
Laboratory practicals
The practical sessions will be conducted in a laboratory environment for the first part of the semester. The practical component is integrated with the lecture material and is designed to simulate laboratory procedures, which are routinely applied in forensic biology laboratories. The practicals will also incorporate a number of cutting-edge technologies to be implemented in the forensic workflow in the near future. Students will extract, quantify, amplify and sequence DNA samples and eventually produce forensically useful phenotyes for investigative leads. Laboratory work will be documented in a case file. Preparation for practical sessions will include readings and activities available on Canvas. You should complete the preparation beforehand as it will give you the knowledge to further understand the subject content and be an active learner in the laboratory.
Tutorials/workshops
In the second part of the semester, practical work will be replaced by tutorials/workshops. These will be used to review and further develop concepts introduced in the lectures and the practical sessions. The content of the tutorials will be dependent on the outcomes of the practicals. Bioinformatic data and DNA profiles generated in the practical classes will be used to analyse DNA sequencing performance and generate valuble metrics for subsequent incorporation into final reports. The DNA sequencing data will be further analysed using various bioinformatic tools to generate investigative leads in the form of human pigmentation traits and bio-geographical ancestry predictions. Discussion is strongly encouraged, and there will be opportunities for feedback from teachers and peers to clarify both the theory and practice of forensic genotyping technologies. Preparation for tutorials/workshops will include readings and activities available on Canvas. You should complete the preparation beforehand as it will give you the knowledge to further understand the subject content and be an active learner.
Canvas
Canvas will be used for all communication, subject announcements and posting of subject information and documents, therefore you must ensure that you check Canvas regularly. Canvas is linked to your UTS student email. If you use another email account, please make sure you activate a forwarding service from your student email.
All written communication should be through the Forensic Genotyping Technologies subject site on Canvas. Please post any messages in the relevant fora within the Discussion Board. Messages of a personal nature can be emailed to the subject coordinator from within Canvas.
Assessment tasks
It really pays to get started with assessment tasks as early as possible. A little each day or week will soon add up. Always read the task description carefully. Underlining key words and ‘unpacking’ the task can help you understand the main elements and different sections to the task. Then you can move on to planning your response and brainstorming initial ideas. Always remember to address the assessment criteria.
Do not procrastinate: there’s no time like the present to get started. If you are lacking direction or motivation, do some background reading on the subject/task to get you started and build your confidence and motivation. Do not leave assignments to the last minute; there’s no need to do so, and it will save you lots of anxiety and stress if you do not. It is also likely you will make make less mistakes and have a more thorough response if you start early.
Content (topics)
1. DNA sequencing technologies
- Contemporary forensic DNA markers and technologies
- First generation sequencing
- Second generaton sequencing
- Ion Torrent sequencing
- Solexa (Illumina) sequencing
- Third generation sequencing
- Nanopore sequencing
- Pacific Biosciences (PacBio) single molecule real time (SMRT) sequencing
- Sequencing steps
- Target enrichment
- Library preparation
- Template preparation
- Sequencing
2. Other genotyping technologies
- Single base extension (SBE) assays
- Molecular probes
- High resolution melt (HRM) analysis
- High density genotyping (microarrays)
3. Bioinformatics
- Sequence alignment
- Coverage analysis
- Variant calling
4. Forensic genetics for investigation/intelligence
- Externally visible traits
- Pigmentation
- Craniofacial morphology
- Fingerprints
- Biogeographical ancestry (BGA)
5. Forensic epigenetics for investigation/intelligence
- Age estimation
- Biological tissue source
6. Forensic genetics and society
- Forensic investigative genetic genealogy (FIGG)
- Legislation, privacy and ethics
Assessment
Assessment task 1: Case file
| Intent: | This assessment task contributes to the development of the following graduate attributes: 1. Disciplinary knowledge 2. Research, inquiry and critical thinking 3. Professional, ethical and social responsibility 4. Reflection, innovation, creativity 5. Communication |
|---|---|
| Objective(s): | This assessment task addresses subject learning objective(s): 2, 3, 4 and 5 This assessment task contributes to the development of course intended learning outcome(s): 1.1, 2.1, 3.1, 4.1 and 5.1 |
| Type: | Laboratory/practical |
| Groupwork: | Individual |
| Weight: | 30% |
| Length: | Case files should be sufficient to allow another forensic biologist to repeat the procedure exactly. However, they should also be concise. |
| Criteria: | You will be assessed against specific criteria, available on Canvas. The total mark for the assessment task will be adjusted to contribute 30 % to your final assessment. |
Assessment task 2: Quizzes
| Intent: | This assessment task contributes to the development of the following graduate attributes: 1. Disciplinary knowledge 2. Research, inquiry and critical thinking 4. Reflection, innovation, creativity 5. Communication |
|---|---|
| Objective(s): | This assessment task addresses subject learning objective(s): 4, 5 and 6 This assessment task contributes to the development of course intended learning outcome(s): 1.1, 2.1, 4.1 and 5.1 |
| Type: | Quiz/test |
| Groupwork: | Individual |
| Weight: | 40% |
| Length: | You will have a two hour window to complete each quiz. The beginning time (and the day) can suit your individual circumstances, as long as it is within a week of the release of the quiz. You only have one attempt at each quiz question. |
| Criteria: | You will be assessed on your understanding and interpretation of key concepts and problem solving. The total mark for the assessment task (four quizzes) will be adjusted to contribute 40 % to your final assessment. |
Assessment task 3: Digital intelligence report
| Intent: | This assessment task contributes to the development of the following graduate attributes: 1. Disciplinary knowledge 2. Research, inquiry and critical thinking 4. Reflection, innovation, creativity 5. Communication |
|---|---|
| Objective(s): | This assessment task addresses subject learning objective(s): 1, 2 and 6 This assessment task contributes to the development of course intended learning outcome(s): 1.1, 2.1, 4.1 and 5.1 |
| Type: | Presentation |
| Groupwork: | Group, group assessed |
| Weight: | 30% |
| Length: | 5 minute video |
| Criteria: | You will be assessed according to the following criteria: Professional skills
Enquiry and innovation
Disciplinary knowledge
Communication skills
For each criterion, you will receive a mark from 0 to 5. The highest possible mark for the assessment is therefore 5 × 6 = 30. You will be marked by your peers and academic staff. The average mark from your peers will be combined with the average mark from the academic staff in the ratio 1:1. |
Minimum requirements
In order to pass this subject you must obtain an overall mark of 50% or more.
Required texts
The UTS Coursework Assessments Policy and Procedures documents are required reading for students. These documents provide general guidelines for assessment and information about responsibilities. They can be found at:
http://www.gsu.uts.edu.au/policies/coursework-assessments.html
Recommended texts
There are a number of recommended texts freely available online from the UTS Library. They can be found in the Reading List in Canvas. Access requires student ID and password. Some are also available as hard copies at the City Campus Library (indicated in the Reading List).
References
Molecular biology education
https://www.thermofisher.com/au/en/home/brands/invitrogen/molecular-biology-technologies/mol-bio-school.html
Thermo Fisher Scientific
Making sense of forensic genetics
https://www.euroforgen.eu/dissemination-activities/making-sense-of-forensic-genetics/
European Forensic Genetics (EuroForGen) Network of Excellence.
Forensic genetics explained
https://www.euroforgen.eu/dissemination-activities/forensic-genetics-explained/
European Forensic Genetics (EuroForGen) Network of Excellence.
Frudakis (2008) Molecular photofitting: Predicting ancestry and phenotype using DNA. Elsevier Academic Press, Oxford.
McCord et al (2019) Forensic DNA analysis. Analytical Chemistry, 91:673-688.
Jordan & Mills (2021) Past, present and future of DNA typing for analyzing human and non-human forensic samples. Frontiers in Ecology & Evolution (9). DOI:10.3389/fevo.2021.646130
Pope & Puch-Solis (2021) Interpretation of DNA data within the context of UK forensic science — investigation. Emerging Topics in Life Sciences, DOI: 10.1042/ETLS20210165
These references, as well as readings for individual weeks, can be found in the Reading List in Canvas.