Clinical Cytogenic Diagnosis

Question 1

Centromere + 2 arms

Answer 1

Centromere- point at which chromosome is attached to spindle in cell division; separates 2 arms

p= short arm ("petit")
q= long arm

Question 2

Metacentric

Acrocentric

Sub-Metacentric

Answer 2

• Centromere in middle
• Centromere near one end
• Centromere off center

Question 3

Which chromosome are acrocentric?

Answer 3

13 14 15 21 22 Y

Question 4

How are bands numbered?

Answer 4

High band number = further away from centromere

Question 5

Euploid v Aneuploid

Answer 5

Euploid- having correct complement of chromosomes

Aneuploid- incomplete complement
-trisomy, monosomy, partial monosomy, triploid or tetraploidy

Question 6

3 Classes of Tandem Repeats

Answer 6

Microsatellite DNA (repeats of 1-10 bps) - at centromeres

Minisatellite DNA (repeats of 9-64 bps)- at telomeres

Satellite DNA (repeats of 5-171 bps)- dispersed

Question 7

CNVs

Answer 7

Copy Number Variants

• Having more or less copies of gene than a reference genome
• Having too many or too few genes –> disease
• Both inherited and de novo

Question 8

LINEs & SINEs

Answer 8

LINE- long interspersed nuclear elements
SINE- short interspersed nuclear elements

**transposable/mobile genetic elements

Question 9

Karyotyping - 4 Bands

Answer 9

Use metaphase nuclei and cultivate cells ex vivo to get enough

• G banding (giesma) - most common
• Q banding (quinacrine) - under flur light
• R banding (reverse) - show dark and light strands in reverse to G and Q; used if G and Q cannot be used
• C banding (centromere) - stains constitutive heterochromatin

Question 10

General Format for Writing Chromosomes

Answer 10

chromosomes, sex chromosomes, defect abbreviation (chromo # of defect) (detail position)

• if position involves location on p AND q of SAME chromosome then no semi-colon between
• if position involves location on p OR q of DIFF chromosome then semi-colon between

+/- indicates which chromosome is missing if monosomy or added if trisomy

• inversion if positions listed out of numerical order (ex- p23p13)
• mat/pat listed at end if you know whether maternal or paternal

Question 11

Karyotyping v Microarray

Answer 11

Karyotyping- cheaper but cannot detect smaller changes
(best for gross chromosomal issues- like trisomy)

Microarray- more expensive; identifies greater number of cytogenic alterations (microdeletions and insertions) BUT cannot detect balanced translocations b/c tells quantity not position

Question 12

When is cytogenic analysis indicated?

Answer 12

• Child w/ growth or dev problems, short stature, ambiguous genitalia, facial probs
• Fertility issues
• Stillbirth or neonatal death
• Pregnant women over 35 yp
• If family hx
• Cancer

Question 13

Comparative Genomic Hybridization

Answer 13

• compare patient’s genome w/ reference genome on microarray
• can detect differences as small as 100 bps
• limited b/c tells you quantity not position (no translocations or inversions)
• same interpretation as other microarray (stain ea and look at which color the dots are)

Question 14

SNP Array

Answer 14

• detect single nucleotide changes

- use microarray of single known SNP

Question 15

FISH

Answer 15

• Fluorescent In Situ Hybridization
• Denature target chromosome then use probe (can use 2+ probes)
• Must know sequence you are looking for - to make probe; so primarily used to CONFIRM disease
• Can detect translocations, deletions and inversions

Question 16

Chromosome Painting

Answer 16

• Use different colored probes (SKY uses 24 colors-1 for ea chromosome)
• Used to detect translocations (esp cancer)
• EXPENSIVE

Question 17

Quantitative PCR

Answer 17

-Method to investigate copy # in certain region (copies shown as peaks)