BIOTECH 7040 - Application of Next Generation Sequencing

North Terrace Campus - Semester 1 - 2022

Second and third next-generation sequencing technologies are transforming all aspects of our lives. Some examples include; diagnostics in the clinical medicine, population genomics to identify rare disease-causing alleles in humans, and real-time identification of disease-causing pathogens in field hospitals and mobile laboratories. Applications of these next-generation technologies to improve humanity are almost endless. This mostly practical course provides an understanding of the specific considerations for using and applying different sequencing technologies, for example Sanger, Oxford Nanopore Technology or Illumina sequencing. By undertaking a real-life scenario, you will design, implement and practically undertake your sequencing strategy to answer the question in your selected scenario

  • General Course Information
    Course Details
    Course Code BIOTECH 7040
    Course Application of Next Generation Sequencing
    Coordinating Unit School of Biological Sciences
    Term Semester 1
    Level Postgraduate Coursework
    Location/s North Terrace Campus
    Units 3
    Contact Up to 7 hours per week throughout the semester. Practicals to be scheduled and workshops will be included in this this contact time. Lecturer to advise students of timetable schedule.
    Available for Study Abroad and Exchange N
    Assumed Knowledge BIOTECH 7005
    Restrictions Master of Biotechnology (Biomedical); Graduate Diploma in Biotechnology (Biomedical)
    Course Description Second and third next-generation sequencing technologies are transforming all aspects of our lives. Some examples include; diagnostics in the clinical medicine, population genomics to identify rare disease-causing alleles in humans, and real-time identification of disease-causing pathogens in field hospitals and mobile laboratories. Applications of these next-generation technologies to improve humanity are almost endless.

    This mostly practical course provides an understanding of the specific considerations for using and applying different sequencing technologies, for example Sanger, Oxford Nanopore Technology or Illumina sequencing. By undertaking a real-life scenario, you will design, implement and practically undertake your sequencing strategy to answer the question in your selected scenario
    Course Staff

    Course Coordinator: Associate Professor Iain Searle

    Course Timetable

    The full timetable of all activities for this course can be accessed from Course Planner.

  • Learning Outcomes
    Course Learning Outcomes
    1. Analyze a biological question in order to develop a small programme of research.
    2. Explain the importance of reproducible research and devise appropriate approaches to ensure reproducible results.
    3. Use appropriate and effective data recording methods.
    4. Employ effective communication techniques within a teamwork environment.
    5. Effectively communicate experimental findings to a broad audience.
    University Graduate Attributes

    This course will provide students with an opportunity to develop the Graduate Attribute(s) specified below:

    University Graduate Attribute Course Learning Outcome(s)

    Attribute 1: Deep discipline knowledge and intellectual breadth

    Graduates have comprehensive knowledge and understanding of their subject area, the ability to engage with different traditions of thought, and the ability to apply their knowledge in practice including in multi-disciplinary or multi-professional contexts.

    1, 2, 3, 4

    Attribute 2: Creative and critical thinking, and problem solving

    Graduates are effective problems-solvers, able to apply critical, creative and evidence-based thinking to conceive innovative responses to future challenges.

    1, 2, 4

    Attribute 3: Teamwork and communication skills

    Graduates convey ideas and information effectively to a range of audiences for a variety of purposes and contribute in a positive and collaborative manner to achieving common goals.

    3, 4

    Attribute 4: Professionalism and leadership readiness

    Graduates engage in professional behaviour and have the potential to be entrepreneurial and take leadership roles in their chosen occupations or careers and communities.

    1, 5

    Attribute 5: Intercultural and ethical competency

    Graduates are responsible and effective global citizens whose personal values and practices are consistent with their roles as responsible members of society.

    2

    Attribute 8: Self-awareness and emotional intelligence

    Graduates are self-aware and reflective; they are flexible and resilient and have the capacity to accept and give constructive feedback; they act with integrity and take responsibility for their actions.

    2, 3, 4
  • Learning & Teaching Activities
    Learning & Teaching Modes
    Practicals are supported by workshops that build students student’s understanding of the details of undertaking wet laboraory eperiments and supporting bioinformatics. Practical tasks and associated report preparation will help develop students’ capacity to perform next generation sequencing anlaysis and communicate analytical results to others in an effective way.
    Workload

    The information below is provided as a guide to assist students in engaging appropriately with the course requirements.

    The information below is provided as a guide to assist students in engaging appropriately with the course requirements.

    A student enrolled in a 3 unit course, such as this, should expect to spend, on average 12 hours per week on the studies required. This includes both the formal contact time required to the course (e.g., workshops and practicals), as well as non-contact time (e.g., reading and revision).
    Learning Activities Summary
    The course covers (wet laboratory) practical aspects of conducting genomics research using contemporary sequencing methods such as Illumina, sequence analysis, recording results in e-notbooks and presenting analyses to clients and other researchers.

  • Assessment

    The University's policy on Assessment for Coursework Programs is based on the following four principles:

    1. Assessment must encourage and reinforce learning.
    2. Assessment must enable robust and fair judgements about student performance.
    3. Assessment practices must be fair and equitable to students and give them the opportunity to demonstrate what they have learned.
    4. Assessment must maintain academic standards.

    Assessment Summary

    Assessment Task Type of Assessment Percentage of Total Hurdle Outcomes being Assessed Approximate Timing
    Quiz Formative and Summative 5 No 1 Before week 6
    Problem selection Formative and Summative 20 No 1, 2 Before week 6
    Infographic Summative 10 No 4, 5 Before week 6
    E-lab notebook Summative 10 No 3 Before week 13
    Poster & video  Summative 25 No 2, 4, 5 Before week 13
    Report Summative 30 No 2, 4, 5 Before week 13
    Assessment Detail
    Quiz (5%)
    Students will complete a small quiz at the end of the first workshop.

    Problem based learning (20%)
    Students will work in small groups to select a scenario from the practical manual, determine the ethical and regulatory requirements to undertake the scenario and determine the feasibility of undertaking the scenario within the semester. A 500-word document outlining the choice of scenario will be submitted.

    Infographic (10%)
    Students will prepare a single A4 page infographic and an accompanying 800-word pitching document on the novel application of next generation sequencing to a current or future industry scenario. 

    E-lab notebook (10%)
    While undertaking the practical, students will record data and observations in an e-notebook during the semester.

    Poster presentation video (25%)
    Students will invidually to prepare a scientific poster and a video to explain their findings from the practical. At a poster presentation day, students will orally present their poster and be asked questions by fellow students and tutors.

    Scientific report (30%)
    Students will write a scientific report of about 3,000 words explaining the findings from the practical undertaken during the semester.


    Assessment feedback, usually within 2 weeks, will be given to students after each assessment task.
    Submission
    If an extension is not applied for, or not granted then a penalty for late submission will apply. A penalty of 10% of the value of the assignment for each calendar day that the assignment is late (i.e. weekends count as 2 days), up to a maximum of 50% of the available marks will be applied. This means that an assignment that is 5 days late or more without an approved extension can only receive a maximum of 50% of the marks available for that assignment.
    Course Grading

    Grades for your performance in this course will be awarded in accordance with the following scheme:

    M10 (Coursework Mark Scheme)
    Grade Mark Description
    FNS   Fail No Submission
    F 1-49 Fail
    P 50-64 Pass
    C 65-74 Credit
    D 75-84 Distinction
    HD 85-100 High Distinction
    CN   Continuing
    NFE   No Formal Examination
    RP   Result Pending

    Further details of the grades/results can be obtained from Examinations.

    Grade Descriptors are available which provide a general guide to the standard of work that is expected at each grade level. More information at Assessment for Coursework Programs.

    Final results for this course will be made available through Access Adelaide.

  • Student Feedback

    The University places a high priority on approaches to learning and teaching that enhance the student experience. Feedback is sought from students in a variety of ways including on-going engagement with staff, the use of online discussion boards and the use of Student Experience of Learning and Teaching (SELT) surveys as well as GOS surveys and Program reviews.

    SELTs are an important source of information to inform individual teaching practice, decisions about teaching duties, and course and program curriculum design. They enable the University to assess how effectively its learning environments and teaching practices facilitate student engagement and learning outcomes. Under the current SELT Policy (http://www.adelaide.edu.au/policies/101/) course SELTs are mandated and must be conducted at the conclusion of each term/semester/trimester for every course offering. Feedback on issues raised through course SELT surveys is made available to enrolled students through various resources (e.g. MyUni). In addition aggregated course SELT data is available.

  • Student Support
  • Policies & Guidelines
  • Fraud Awareness

    Students are reminded that in order to maintain the academic integrity of all programs and courses, the university has a zero-tolerance approach to students offering money or significant value goods or services to any staff member who is involved in their teaching or assessment. Students offering lecturers or tutors or professional staff anything more than a small token of appreciation is totally unacceptable, in any circumstances. Staff members are obliged to report all such incidents to their supervisor/manager, who will refer them for action under the university's student’s disciplinary procedures.

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