Methods of detecting genetic damage in cancer

Question 1

What are the categories of genetic changes in cancer?

Answer 1

Chimeric
deletion/loss of function of gene
Gain or amplification

Question 2

How is chimeric proteins formed and it’s implication in cancer. Give example

Answer 2

Through translocation, inversion, insertion a balanced chromosome rearrangement takes place two genes form a fusion usually it’s t.f, this changes it’s regulation and is always tunred on leading to an endless activation of cascade
CML

Question 3

What rae examples of gene increase in unbalanced chromosomes? How about balanced

Answer 3

Gain of a segemnt of chromosome
amplification DM, HSR
Gain of extra chromosome
Translocation

Question 4

What categorizes a gene amplification

Answer 4

ploidy

more than 4 fold increase n copy level

Question 5

What are examples of unbalanced loss of genes? Banlanced?

Answer 5

Chromosome or part of chromosome lost.

Gene lost, loss of heterozygosity

Question 6

Both alleles of RB has to be lost so it can be retinoblastoma

Answer 6

true

Question 7

Loss of one tumour repressor can induce tumourigenesis

Answer 7

true

Question 8

What are ways to detect genetic changes

Answer 8

cytogenetics
PCR and RT-QPCR
FISH and M-FISH
CGH
next generation sequencing

Question 9

Cytogenetic positives and negatives

Answer 9

It requires dividing cells 
Measures balanced and unbalanced chromosomes
Low resolution
Nalyzes the whole genome in the cell
interpetation can be complex
requires experienced analyst

Question 10

FISH pros and cons

Answer 10

A fluorescently labelled probe that binds to a gene of interest
Can be used on non dividing cells and on archive material
detects balanced and unbalanced
less training required
very directed
unexpected signals hard to interpet

Question 11

RT-QPCR

Answer 11

directed DNA abnormalities tested for
very sensitive, quick and cheap
very directed
cant detect rearrangement with variable partners

Question 12

M-FISH

Answer 12

Genome wide screen
balanced and unbalanced and complex karyotype detection
Needs dividing cells
low resolution
expensive
can be difficult to interpet and doesn’t provide break through info

Question 13

Describe CGH

Answer 13

DNA from sample is fragmented and then hybridized iwth normal DNA both differentially labelled with fluorescence and the ratio between them are compared to see if balanced or not 1:1 normal

Question 14

What are the pros and cons of CGH?

Answer 14

Genome wide
dividing cells are not required
low resolution
only detects unbalanced
expensive 
dilution effect of normal dna

Question 15

Describe Microarrays

Answer 15

same preparation as CGH but uses specifc probes against target sequences, can see which genes are being over or underexpressed

Question 16

What are the pros and cons of microarrays

Answer 16

only can detect abnormal rearrangements 
expensive 
can be contaminated with normal cells
can study sepcifc questions
many loci can be detected at the same time
high resoloutions

Question 17

SNP array

Answer 17

Tests for SNP and unique variation in the same array using the same techniques as CGH. Detects loss of heterozygosity of tumour suppressor genes

Question 18

NGS

Answer 18

tests for changes in bases which will detect large changes in the chromosome levels. Tests for specific targets variations then classifies it as binign, unknown, pathogenic

Question 19

What are the positives and negatives of whole genome sequencing?

Answer 19

Hard to classify all the small changes and associate them with pathogenesis
expensive
high throughput