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 21

When is FISH used?

Answer 21

Specific chromosome regions

Eg. Myeloma
Lymphoma
Breast & Gastric Cancer

Question 22

Monogenic diabetes

Answer 22

Presents like type 1 diabetes at older age

Question 23

Examples of clinically critical samples

Answer 23

neonates
advanced cancer
dead

Question 24

separate test requests

Answer 24

separate referrals

Question 25

When is cell culture used?

Answer 25

Haematological malignancy

Question 26

Chromosomes are only condensed and visible in ____phase.

Answer 26

meta

Question 28

In general, ________ cultures produce higher quality cells.

Answer 28

longer

Question 29

Karyotyping uses _ bands.

Answer 29

G

Question 30

MLPA steps

Answer 30

DNA denaturation and probes hybridization

Ligation reaction

PCR amplification

Electrophoresis

Data analysis

Question 33

QF PCR identifies alleles by…

Answer 33

size.

Question 34

Low level peaks in Sanger sequencing

Answer 34

Mosaicism

Question 35

Errors in Sanger sequencing

Answer 35

Unclean traces or artifacts

Question 36

How does NGS work?

Answer 36

Different colours for different bases

Question 37

What is a pseudogene

Answer 37

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

Question 38

How do arrays work?

Answer 38

Template and patient DNA dyed and bound together to compare

• Deletion - loss of homozygosity

Question 39

What information does interphase FISH provide?

Answer 39

Presence and absence of genes

Question 40

What information does metaphase FISH provide?

Answer 40

Specific gene regions

Question 41

Hemizygous variant

Answer 41

X linked recessive variant in a male

Question 42

Which translocations can NIPT be used on?

Answer 42

Robertsonian translocations, not complete

Question 44

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

Answer 44

13 and 15

Question 45

Most common Robertsonian translocation (75%)

Answer 45

13-14

Question 46

Chromosomes in haematological malignancies

Answer 46

Stubby