Midterm 2 - Notes 5 (Part 2)

Question 1

What 3 signals help to regulate the cell cycle?

Answer 1

1. GPCR
2. Protein phosphatase
3. Nucleotide exchange factor

Question 2

What 2 ways can transport proteins?

Answer 2

1. Peptide/drug transporter

2. Cadherin family protein

Question 3

What does the 2nd case study describe?

Answer 3

Whole genome cancer approach

- mutation evolution in a lobular breast tumour profiled at single nucleotide resolution

Question 4

What type of tools did they use on metastatic tumours? (3)

Answer 4

1. Whole genome sequencing
2. Transcriptome sequencing
3. Illumia sequencing

Question 5

What was the control sample in the 2nd case study?

Answer 5

Blood sample from same patient

- provides reference genome

Question 6

Why were the lengths made longer?

Answer 6

To make it easier to detect differences

Question 7

What could the tumour transcriptome not do?

Answer 7

Give coverage

Question 8

What were the mutations likely caused by?

Answer 8

Somatic tumours

Question 9

How can you tell if its a somatic mutation or not?

Answer 9

See if it was present in the reference genome

Question 10

What indicates the expression level of a gene?

Answer 10

The number of genes that are counted

Question 11

How can you tell if there is over/under expression in a gene?

Answer 11

Compare it to the reference genome

Question 12

What can changes of expression be caused from?

Answer 12

Epigenetic change

Question 13

What did they use in the experimental design?

Answer 13

Used whole genome sequencing to look for differences and re-arrangements
- didnt use whole genome sequencing on the control

Question 14

What did they use for the control instead of whole genome sequencing?

Answer 14

Used a pipeline to identify candidate differences in protein coding genes and then went back to the target to use PCR and Sanger sequencing to see what the differences were

Question 15

What did they develop to detect alterations?

Answer 15

Algorithms

Question 16

What were the alterations tested? (4)

Answer 16

1. Insertions/deletions
2. Inversions
3. Gene fusions
4. Copy number alterations
   - used FISH for this one

Question 17

What was the easiest thing to detect?

Answer 17

SNVs

Question 18

What did they remove from the SNVs? (2)

Answer 18

1. Pseudogenes

2. HLA sequences

Question 19

When they re-sequenced, what did they use?

Answer 19

Sanger

Question 20

What were they surprised they found in the 2nd case study?

Answer 20

Finding 5 transcriptomes in the sequencing data

Question 21

Were somatic mutations identified?

Answer 21

Yes

Question 22

What did they want to identify?

Answer 22

If the mutation actually was present in a few cells in the primary tumour and if so how many in the cell had these mutations
- 5 of them (most common)

Question 23

What happens if you amplify these genes?

Answer 23

99% of them dont have the mutations, the PCR products will have the WT base and only 1% will have the mutated base at this position

Question 24

What did they use for sequencing? And what did they use to confirm the sequencing?

Answer 24

Used Illiuma to sequence and Sanger to confirm

Question 25

What is an example of an RNA enzyme?

Answer 25

ADAR

Question 26

Where is ADAR expressed?

Answer 26

It is highly expressed in tumour samples

Question 27

What does ADAR mediate?

Answer 27

A –> G edits in target RNA

Question 28

What is highly regulated?

Answer 28

RNA editing

Question 29

What did they discover?

Answer 29

That performing NGS on tumours is feasible