Lab genetics

Question 1

FISH

Answer 1

Identifies specific changes using fluorescent markers that hybridise to chromosomes

Question 2

Karyotyping

Answer 2

Uses banding patterns to identify chromosomes and structural changes

Question 3

Array

Answer 3

Uses tag markers across the genome to show whole-genome copy change

Question 4

QF-PCR

Answer 4

Uses common variance in repeat lengths to determine copy number

Question 5

Fragment analysis

Answer 5

Amplifying and comparing obtained length to expected length

Question 6

TaqMan

Answer 6

Uses paired, labelled probes for a single variant to determine zygosity

(2 probes released that can each bind to specific allele and release gas - used to figure out which allele)

Question 7

ARMS

Answer 7

Uses paired probe mixes to determine presence / absence of specific variants

Question 8

MLPA

Answer 8

Copy number determination dependant on probe ligation and amplification

Question 9

Sanger

Answer 9

Uses chain termination to provide sequence for small regions (usually <1kbp)

Question 10

What are the 2 types of NGS?

Answer 10

Targeted panel

Clinical exome

Question 11

How is MSI detected?

Answer 11

PCR

Question 12

What is MSI sensitive to?

Answer 12

Immunotherapy

Question 13

How does ARMS work?

Answer 13

One primer only extends if variant present

Other primer only extends if variant absent

Question 14

When is TaqMan used?

Answer 14

small number of effect alleles

e.g. pharmacogenomics, haemochromatosis, OPMD

Question 15

When is PCR used?

Answer 15

Aneuploidy

Question 16

How does Sanger work?

Answer 16

Fluorescent nucleotides in base specific colours

Question 16

NIPT

Answer 16

Differentiates foetal and maternal cfDNA based on length and creates a foetal:maternal ratio

Question 17

Euchromatin

Answer 17

Gene rich, stains lightly

Question 18

Heterochromatin

Answer 18

Gene poor, stains darkly

Question 19

What is the only method of detecting changes to chromosome structure?

Answer 19

Karyotyping

Question 20

When is FISH used?

Answer 20

Specific chromosome regions

Eg. Myeloma
Lymphoma
Breast & Gastric Cancer

Question 21

Monogenic diabetes

Answer 21

Presents like type 1 diabetes at older age

Question 22

Examples of clinically critical samples

Answer 22

neonates
advanced cancer
dead

Question 23

separate test requests

Answer 23

separate referrals

Question 24

When is cell culture used?

Answer 24

Haematological malignancy

Question 25

Chromosomes are only condensed and visible in ____phase.

Answer 25

meta

Question 26

In general, ________ cultures produce higher quality cells.

Answer 26

longer

Question 27

Karyotyping uses _ bands.

Answer 27

G

Question 28

MLPA steps

Answer 28

DNA denaturation and probes hybridization

Ligation reaction

PCR amplification

Electrophoresis

Data analysis

Question 29

QF PCR identifies alleles by…

Answer 29

size.

Question 30

Low level peaks in Sanger sequencing

Answer 30

Mosaicism

Question 31

Errors in Sanger sequencing

Answer 31

Unclean traces or artifacts

Question 32

How does NGS work?

Answer 32

Different colours for different bases

Question 33

What is a pseudogene

Answer 33

A severely mutated gene that can end up in another gene and cause disease

Question 34

How do arrays work?

Answer 34

Template and patient DNA dyed and bound together to compare

• Deletion - loss of homozygosity

Question 35

What information does interphase FISH provide?

Answer 35

Presence and absence of genes

Question 36

What information does metaphase FISH provide?

Answer 36

Specific gene regions

Question 37

Hemizygous variant

Answer 37

X linked recessive variant in a male

Question 38

Which translocations can NIPT be used on?

Answer 38

Robertsonian translocations, not complete

Question 39

Which 2 chromosomes can lose their p arms and become linked by the q arms with no consequence?

Answer 39

13 and 15

Question 40

Most common Robertsonian translocation (75%)

Answer 40

13-14

Question 41

Chromosomes in haematological malignancies

Answer 41

Stubby