chromosome analysis

Question 1

what is allele specific PCR used for? (ARMS)

How does it work

Answer 1

specific known point mutations

Create specific primers (need to know what you are looking for if you are going to create these)

Question 2

techniques used for detection of sub-microscopic duplications and deletions

Answer 2

MLPA and aCGH

Question 3

how are aneuplodies tested for rapidly in a pre-natal setting?

Answer 3

You are trying to detect the presence of an abnormal number of chromosomes where it is not a multiple of 23.
QF-PCR (quantitative PCR): markers for chromosomes 12, 18 and 21 are used and then using the number of peaks created by the PCR amplification you can detect the presence of additional chromosomes.

Question 4

What is FISH used for?

Answer 4

Analysis of particular parts of a chromosome e.g. a deletion

Question 5

Two things you will filter a VCF file (from massively parallel sequencing) for

Answer 5

those that are not common variants (not polymorphisms)

those that are predicted to be damaging to the protein

Question 6

how does MLPA work

Answer 6

looks for a deletion or duplication of between 500 and 2000 nucleotides.
PCR-based technique.

Question 7

How does Array comparative genomic hybridisation (aCGH) work?

Answer 7

looks for a deletion or duplication across all of the chromosome all at once - a big change. The DNA of the patient is compared against a reference.
Useful when the location of an alteration is not already known but pehnotype suggests a deletion may be present but standard karyotyping has not revealed anything.