Midterm 2 - Notes 5 (Part 1)

Question 1

Cancer critical genes

Answer 1

Gene that contribute to cancer formation when mutated

Question 2

What do individual cancers have?

Answer 2

Individual mutations

Question 3

What does an alteration in a given gene that contribute to cancer depend on? (4)

Answer 3

1. Type of mutation
2. Cell type
3. Interaction with other mutated gene products
4. Differentiation status

Question 4

Identification of mutations in a given cancer is starting point for what 3 things?

Answer 4

1. Identification of the mutation in cancer
2. Understanding cancers on a molecular level
3. Targets for diagnosis and drug development or other treatments

Question 5

What is the benefit of identifying the mutation in cancer?

Answer 5

It can be cataloged to see what went wrong, how it started and identify how to prevent them
- its the holy grail

Question 6

Why is it better to used short sequences when comparing genomes?

Answer 6

It makes it easier

Question 7

What can you conclude if the reference genome is different than the normal genome and not from higher up?

Answer 7

That is it a somatic mutation and not inherited

Question 8

What was detected in the cancer genome sequencing experiment?

Answer 8

Types of alterations in both coding and non-coding regions

Question 9

What can you discover information about when you compare cancer with normal genomes of the same individual?

Answer 9

You can identify the somatic mutation information

Question 10

What does it mean if a sequence map contains no reads?

Answer 10

We can conclude there was a homo deletion in the tumour DNA

Question 11

What does it mean if a sequence map contains a few reads?

Answer 11

We can conclude there was a hetero deletion in the tumour DNA

• will get 1/2 the amount of reads
• more than one copy leads to genome duplication

Question 12

What can you conclude from jumping from chromosome 1 to chromosome 5?

Answer 12

That there was some sort of gene translocation that took place

Question 13

What was being dealt with in the first attempt of cancer genome sequencing?

Answer 13

Highly malignant leukemia

Question 14

What are 3 things they found in the case study involving cancer genome sequencing?

Answer 14

1. No large alterations
   - chromosomes look fairly normal
2. Typical symptoms
3. Used both tumour (test) and skin (control) samples for sequencing
   - used this to identify the inherited gene

Question 15

What kind of sequencing did they use in the caner genome sequencing experiment?

Answer 15

Illumina sequencing

Question 16

What happened in the tumour sequencing for the experiment? (2)

Answer 16

1. Used short reads

2. Did quality filtering

Question 17

What did quality filtering allow?

Answer 17

Detection of heterozygous mutations

Question 18

What happened in the skin (control) sequencing for the experiment? (2)

Answer 18

1. Expected them to be similar to the reference

2. Didn’t need as much and wanted to save money

Question 19

What was the 2nd experiment sequencing mapping and variant calling about?

Answer 19

It was a proof of concept experiment

- needed to prove that it did work

Question 20

What did they do in the sequencing mapping and variant calling experiment? (3)

Answer 20

1. Aligned sequences to human reference genome
   - 3.8 million single nucleotide differences
   - could be SNP or SNV
2. Compared it to 2 other individual human genomes
   - number of SNP variants to hg18
   - used sanger and illumina sequencing
3. Used SNP array to determine variants

Question 21

What human genome did they use as a reference in the sequencing mapping and variant calling experiment?

Answer 21

hg 18

- human genome 18

Question 22

SNP

Answer 22

Single nucleotide polymorphism

- inherited differences

Question 23

SNV

Answer 23

Single nucleotide tumour variants

- somatic differences (but sometimes can also be inherited)

Question 24

What was the final conclusion about the sequencing mapping and variant calling experiment?

Answer 24

Was that yes we can use it to determine whole genome sequencing

Question 25

What did a high quality data filter do?

Answer 25

Reduced the number of SNPs

- different though from human genome sequencing

Question 26

Passenger mutations

Answer 26

Are mutations that do not provide a growth advantage to cancer
- do not contribute to cancer formation

Question 27

What is the type of mutation that is dealt with the most in this experiment?

Answer 27

Passenger mutations

Question 28

What are the candidate mutations?

Answer 28

Candidates for being somatic mutations

- higher than expected

Question 29

What does it mean that the candidates for somatic mutations were higher then expected?

Answer 29

That the tumour accumulated 10s of thousands of somatic mutations on its way to becoming cancerous

Question 30

What did they expect in this experiment?

Answer 30

Most were passenger mutations

Question 31

What did they focus on?

Answer 31

Protein coding gene regions

Question 32

SNVs filtered out due to what 3 things?

Answer 32

1. Present in the germ line of other individuals
   - unlikely this caused it to be cancerous
2. In non-coding regions
   - introns
3. Synonymous

Question 33

Synonymous

Answer 33

Silent mutations where codon changes but still produced the same amino acid protein
- unlikely to change the protein function

Question 34

What 2 things did they use to validate SNVs?

Answer 34

1. Targeted PCR

2. Sanger sequencing

Question 35

What did they find a large majority of?

Answer 35

False positives

- which created a high error rate

Question 36

Was the proof of concept successful?

Answer 36

Yes