Cytogenetics

Question 1

define cytogenetics

Answer 1

study genetic material (chromo) of cells

Question 2

organisation of a karyogram

Answer 2

• length of chromosome: Lrg -> sml from 1 -> 22
• centromere position
• band pattern

Question 3

genereal formal of karyotype (written)

Answer 3

chromosomes, gender (XX / XY), abnormal derivative (on # chromo)variation(chromo/s affected)

Question 4

the 4 types of centromere positions

Answer 4

• metacentric: c.mere near middle: p = q
• sub-metacentric: closer to top end: p < q
• Acrocentric: c.mere at the top: p very small & have satellites (NOR region) on end
• Telocentric: centromere @ end = no p arm (*not present in human karyotype)

Question 5

Describe the steps of peripheral blood harvest

Answer 5

1. Blood cells CULTURED in growth media w/ phytohaemaglutanin (PHA) > stimulate lymphocytes to divide
2. add HYPOTONIC KCl > RBC lyse & WBC swell
3. ACETIC ACID > breakdown RBC & harden chromo
4. FIX w/ methanol:acetic acid > harden & preserve chromo

Question 6

things to consider when organising chromosomes in the karyogram

Answer 6

• size & shape
• centromere position
• banding pattern

Question 7

Describe what constitutional & acquired cytogenetic changes are

Answer 7

• Constitutional changes: present in early FETAL development

* acquired: changes occur DURING life

Question 8

2 cytogenetic changes (based on genetic info)

Answer 8

• Numerical: Aneuploid = # chromo varies (have extra or less)
• Structural: 1/+ structure of chrome altered

Question 9

Nemonclature of abnormal derivatives/variation

Answer 9

• t = translocation
• inv = inversions
• dup = duplications
• del = deletions
• ins = insertions
• r = rings
• mar = makers = extrastructurally abnormal chromo - not ID by cytogen.

Question 10

what are chromosome copy no. changes

Answer 10

• genome imbalance;
• Loss = deletion of chromo/gene
• Gain = duplication of chromo/gene

Question 11

Describe Fluorescence in situ hybridisation (FISH)

Answer 11

• cell on metaphase or interphase stage
• DNA probes bind to specific known sequ. on chromo
• probes fluoresc
• limited colours

Question 12

Types of probes

Answer 12

1. REPETITIVE sequ probes
   - CENTROMERIC or alpha stellite DNA probes
   - WHOLE chromosome paints
2. UNIQUE sequ. probes (locus specific inserts): not repeated & may code for a gene

Question 13

describe quantitiative Fluorescence PCR (QF-PCR)

Answer 13

• invasive sampling of amniotic fluid in preg women
• detect aenuploidies in fetal DNA
• multiplex PCR & gel capillary electro

Question 14

characteristics of genetic markers (4)

Answer 14

• Short repeated sequ. of DNA located throughout genome
• polymorphic: # of repeated unit varies b/w indiv.
• Diploid organisms = 2 copies of any genetic marker
• can be used for genetic fingerprint (genotyping)

Question 15

high resolution detection of copy no. changes: microarray & aCGH - compare them

Answer 15

• aCGH: hybridise normal reference DNA to patient DNA for comparison
• microarray: uses computer reference to compare & detect copy no. changes

Question 16

Categories in which cases of copy no. changes are divided into: (5) (microarray analysis)

Answer 16

1. Pathogenic: known syndromes
2. Likely pathogenic: strong evidence
3. Uncertain clinical significance (VOUS): incomplete penetrance
4. Unknown clinical significance: novel copy no. changes
5. Likely benign: found in “normal pop. w/ no visible phenotypic effect

Question 17

advantages of CGH & microarray

Answer 17

• SNP arrays available for genotyping & trio analysis for parental studies
• commercial arrays available
• multible loci tested
• whole genome & high resolution when <20kb

Question 18

disadvantages of CGH & microarray

Answer 18

• multiple loci (create uncertainty)
• Low-thrughput & labour-intensive
• $$$
• copy number neutral = not detect where located

Question 19

What is microarray & aCGH used for

Answer 19

genome wide screening of DNA for copy no. changes (not targeted to specific loci like FISH, MLPA, QF-PCR)

Question 20

how are genetic markers amplified?

Answer 20

fluorescently-tagged primers

Question 21

common gen. abnormal (deletions)

Answer 21

• Prader-willi
• Digeorge
• williams
• DMD
• Angel-man
• Charot-Marie