Midterm Solutions Fall 2018

PwnHero BME501/CPS501 Bioinformatics Solutions Midterm, Oct. 25, 2018 Family Name:_____________ First Name: _____________ Student Number: ____________ Answer all questions on the question pages, right below the question. No aids of any kind, including no calculators. You can express values as fractions if necessary. 1. Database (12 points) (a) In a certain genome wide association study (GWAS) the researchers found a dozen SNPs that were associated with the disease in question. What are the next steps that could be taken to look for genes associated with the disease? (5 points) (i) Use the human genome browser to see what genes are close to or line up with each SNP. (ii) If the SNP lines up with gene G, then does it line up with intron or exon ? It is more likely to be important if it lines up with exon, and if so, what kind of mutation does it cause (silent, nonsense, missence). (iii) Look at the Multiz track to see how well conserved is the SNP region -- the more conserved, the more fundamentally important. (iv) Look at OMIM track or go to OMIM and see if the SNP is already associated with the disease in question. (v) Look at the tissue expression track to see if the gene is over or under expressed for the organ related to the disease. (vi) Look at the disease track to see if the SNP region has genes associated with the disease. (b) You would like to find the sequence of the mRNA for the human gene for dystrophin. You go to NCBI Nucleotide and search for 'dystrophin', and you get 74,818 hits. (i) Write a query that you think would narrow the results down, hopefully to the single reference sequence that you want. (ii) What do you expect as the first two letters of the accession? (2 points) (i) dystrophin [title] AND homo sapiens AND mRNA [title] AND refseq (ii) NM (c) Cystic Fibrosis: One in twenty-five people of a certain population are carriers. (i) Without knowing anything about the genes of the parents, what is the likelihood that their child will have Cystic Fibrosis? (Explain your calculation). (ii) A clinic gives you the sequence of your CFTR gene, which is 257,188 bp. You are a bit overwhelmed by the length of the sequence, because you know the protein is only about 1500 amino acids long. Why is the DNA sequence so long, and what can you do with it to check if you are a carrier for CF. (5 points) 1 PwnHero.com