Genomic Browsers

Question 1

What is OncoPrint? (cBioPortal)

Answer 1

A visualization of genomic DNA for a cohort of patients. Each column represents a patient and each row shows genetic information for a given gene.

Question 2

How does cBioPortal present its information?

Answer 2

By study

Question 3

Why would some mutations tend not to appear together in a tumour? e.g unlikely to see both EGFR and KRAS mutations

Answer 3

Indicates either functional redundancy of the mutation (no advantage of mutating both genes) or synthetic lethality (having both mutations would be lethal to the cells)

Question 4

How do mutations in tumour suppressor genes differ to those in proto-oncogenes?

Answer 4

Proto-oncogene mutations occur in hotspots whilst tumour suppressor mutations occur along the length of the protein

Question 5

What gene is mutated most in ER-positive breast cancer

Answer 5

PIK3CA

Question 6

What gene is mutated most in HER-positive breast cancer?

Answer 6

PIK3CA

Question 7

What mutation is most common on the BRAF gene?

Answer 7

V600E

Question 8

Which chromosome does the EGFR gene lie on in the human genome?

Answer 8

Chr 7.

Question 9

What does the accession number represent when it begins with NM

Answer 9

mRNA

Question 10

What tissue type shows the highest expression of EGFR?

Answer 10

The placenta

Question 11

What is blastn?

Answer 11

Used to compare a chosen query nucleotide sequence against the nucleotide database at NCBI

Question 12

what is blastp?

Answer 12

Compares a translation of a protein sequence against the NCBI protein database

Question 13

What is tblastn

Answer 13

Compares a query protein sequence against the NCBI nucleotide database

Question 14

What is tblastx

Answer 14

Compares a translation of a nucleotide query against a translation of the NCBI nucleotide database

Question 15

The coding sequence (CDS) region for EGFR variant 1 mRNA (NM_005228.5) is 262 bp – 3894 bp. Why do you think the EGFR isoform a protein only matches against the mRNA sequence from 262 bp to 3891 bp?

Answer 15

The final three nucleotides in the CDS make up the stop codon that doesn’t encode for an amino acid so does not appear in the protein sequence.

Question 16

What two genome browsers provide annotation of the human genome (and other species)

Answer 16

UCSC and Ensembl

Question 17

What is the result of intron inclusion when designing primers?

Answer 17

Ensures the primers lie in different exons, which means that they will give a different sized product from mRNA (which lacks introns) compared to from genomic DNA (where introns are present). As a result, genomic DNA contamination will not produce a false positive result in an RT-PCR experiment.

Question 18

Is a high 3’ complimentary scoring of a primer mean it is more or less likely to form secondary structures that might inhibit the PCR reaction?

Answer 18

Higher 3’ complimentary score = more likely to form secondary structures

Question 19

What can be done using PROSITE and PHYRE

Answer 19

Prediction of potential functional domains and secondary structures that may be important for protein function. The software compares protein sequences to identify homology to known protein domains.