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BINF90002 Final exam
创建日期：2024-04-13 16:02:51
所属分类：生物biology
标签： BINF90002
Final exam

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BINF90002 

 Final exam    

Academic Integrity Declaration  By commencing and/or submitting this assessment I agree that I have read and  understood the  University’s policy on academic integrity.  I also agree that:  1. Unless paragraph 2 applies, the work I submit will be original and solely my own  work (cheating);  2. I will not seek or receive any assistance from any other person (collusion) except  where the work is for a designated collaborative task, in which case the  individual contributions will be indicated; and,  3. I will not use any sources without proper acknowledgment or referencing  (plagiarism).  4. Where the work I submit is a computer program or code, I will ensure that:  a. any code I have copied is clearly noted by identifying the source of that code  at the start of the program or in a header file or, that comments inline identify  the start and end of the copied code; and  b. any modifications to code sourced from elsewhere will be commented upon  to show the nature of the modification.  This exam opens at 9.00 AM Australian Eastern Standard Time (AEST) on Thursday  02/07/2020 in Canvas (lms.unimelb.edu.au). The exam must be completed by 3.30  PM AEST on Thursday 02/07/2020. This exam has 30 minutes of reading time, and  120 minutes of writing time. You have a 6 hour window in which to complete and  submit the exam.    Number of pages: This paper has 7 pages, including this cover page  Authorised Materials: This is an open book exam. All material delivered during  the teaching period and student notes are permitted.    Instructions to Students:  The total number of marks for the examination is 100. It accounts for 50% of your  final result for the subject. You should attempt all questions.     Write your answers in a separate word document and upload your document as a  word or pdf document as your submission in the Assignment for the Semester 1  exam.      You may include scanned drawings to illustrate your answer(s) if you wish but they  must be appropriately embedded within the document that is your final submission.     Page 1 of 7   Section 1. Short-answer questions (50 marks total)  1. 5 possible variants have been summarised by a variant finding program. The locations  (marked in red vertical lines) of the variants and the affected codon are shown on the  diagram above. For each variant (1-5), use the VCF entry and codon table to comment  on the type of mutation that may have occurred, and the effect the variant may have on  the gene transcript or its protein product.    (5 marks) 2. In your work for the Pathology department in a major public cancer hospital, you have  been asked to design a new whole genome sequencing test that will be applied to  every cancer patient who visits the hospital.      a) How deep will you sequence the tumour and matched normal samples?   b) Would you check the data for sample swaps and, if so, how?   c) What types of mutations should the assay cover? For each mutation type, what signal in  the sequencing reads would you expect the caller to use?  d) What other downstream analyses might you include? (5 marks) Page 2 of 7   3. You have been tasked with developing two diagnostic tests to identify bacterial  pathogens.     Test_1 must be able to detect the bacterial pathogen species B. pathogenesis in patient  throat swab samples. The samples are expected to contain many bacterial species due  to host microbiome contamination. B. pathogenesis has a very limited accessory  genome compared to the other species which may be present in a sample. There is a  reasonable evolutionary distance in terms of SNPs between B. pathogenesis and other  bacteria.    Test_2 must be able to detect and differentiate between strains of a pathogenic species  B. nauseous. Different strains of B. nauseous have high levels of sequence homology,  but each strain has unique genetic regions compared to the other strains within a large  accessory genome.    For each of the two tests above state:    a) which of the following metagenomics sequencing approaches would be the most  appropriate; 16S amplicon, MLST, or WGS.    b) 

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