Chromosomal Nomenclature & Structure Clinical Cytogenetics at a Glance

Question 1

What is cytogenetics?

Answer 1

A subspeciality of genetics which studies the chromosome number and structure at the chromosome level

Question 2

How many genes are in a chromosome band? About how many bases is this?

Answer 2

80 genes -> about 6 Megabases

Question 3

At what phase in the cell cycle are chromosomes analyzed?

Answer 3

Metaphase, since they are most condensed

Question 4

What are the three types of chromosomes?

Answer 4

1. Metacentric - centromere near middle
2. Submetacentric - centromeres are closer to one end
3. Acrocentric - really short p arms which end in satellites of repetitive DNA

Question 5

Which are the important acrocentric chromosomes?

Answer 5

13, 14, 15, 21, 22 -> important in translocations

Question 6

Once treated with trypsin to denature proteins and stained with Giemsa, how do the chromosomes appear?

Answer 6

Dark bands - gene poor AT rich regions

Light bands - gene rich GC rich regions

Question 7

What are normal male and normal female karyotypes?

Answer 7

46,XY = male
46,XX = female

Question 8

What is a germline vs somatic mutation?

Answer 8

Germline = constitutional, occurs before fertilization or in zygote. The mutation will be present in all tissues and inherited

Somatic = acquired = cancer

Question 9

What is aneuploidy vs polyploidy?

Answer 9

Aneuploidy - gain or loss of one or more whole chromosomes

Polyploidy - gain or loss of entire sets

Question 10

What is the karyotype of Down’s syndrome female?

Answer 10

47,XX,+21

Question 11

What is the most common cause for aneuploidy? How do they differ?

Answer 11

Nondisjunction in meiosis I or II.

Meiosis I: all gametes will be off

Meiosis II: only 2/4 gametes will be off

Question 12

What is the most common cause of polyploidy?

Answer 12

Two sperms fertilizing one oocyte

Question 13

What is the leading risk factor for aneuploidy?

Answer 13

Maternal age - higher nondisjunction chance. This is the single leading cause of productive failure in humans

(half of all 1st semester miscarriages are chromosomal abnormalities)

Question 14

What are three balanced karyotype chromosomal abberations?

Answer 14

1. Translocation - reciprocal / robinsonian
2. Inversion
3. Insertion

Question 15

What are three unbalanced karyotype chromosomal abberations?

Answer 15

1. Translocations - when two chromosomes involved are not inherited together
2. Deletion
3. Duplication

Question 16

When can a balanced abberation cause abnormal phenotype?

Answer 16

If the translocation disrupts a critical gene

Question 17

What is a reciprocal translocation?

Answer 17

Exchange of chromosomal material between non-homologous chromosomes

Question 18

What is a reproductive risk of people with reciprocal translocations?

Answer 18

Partial trisomy or monosomy depending on the gametes. For instance, if chromosome 4 carries some genes from chromosome 20 and this is passed down, you will have a partial trisomy 20 in the offspring, or a partial monosomy 4 if chromosome 20 is not inherited with it

Question 19

What is a Robertsonian translocation?

Answer 19

Translocation between acrocentric chromosomes - two acrocentric chromosomes fuse at centromere with loss of short arm

Question 20

What is the karyotype for a normal woman with a balanced Robersonian translocation of chromosomes 13 and 14?

Answer 20

45,XX,der(13;14)

Question 21

What are the two types of inversions?

Answer 21

Paracentric - two breaks in one arm

Pericentric - breaks in both arms, involving the centromere

Both reverse the orientation of the genes

Question 22

How many chromosomal breaks is needed for an insertion (balanced)?

Answer 22

At least 3: 2 to make DNA leave one chromosome, 1 to insert it into the other.

Question 23

What are some advantages of standard karyotype / routine chromosome analysis?

Answer 23

Can view the entire genome on the microscope level

Detects all types of gross chromosomal abnormalities >5 Mb in size

Question 24

What are some disadvantages of routine chromosome analysis?

Answer 24

Cannot detect changes less than 5 Mb
Low detection rate
Needs actively growing cells, with turnaround of 3 to 21 days (cells must be blocked at metaphase with colchicine to stop spindle formation, cells swelled in hypotonic solution)

Question 25

What does FISH stand for? What type of disorders does it generally detect?

Answer 25

Fluorescence in situ hybridization Detects microdeletion and microduplication syndromes

Question 26

How does FISH work?

Answer 26

Use probes of cDNA to target a specific gene. Heat the DNA to denature the DNA strands, let them hybridize and try to visualize the fluorescent tag

Question 27

What are the advantages of FISH?

Answer 27

``` Do not need to have dividing cells, can be done during any phase High resolution (>100Kb) Rapid turnaround ```

Question 28

What are the disadvantages of FISH?

Answer 28

Not a global genome analysis -> need to know the target Limited amount of targets in your cell Does not tell you the size of the genes involvled

Question 29

When do you run a FISH?

Answer 29

When you have suspicion of a specific targeted disorder or are looking for a disorder in a patient. Especially used for prenatal detection of common trisomies or monosomies.

Question 30

What does Array-CGH stand for?

Answer 30

Array Based Comparative Genomic Hybridization?

Question 31

How does Array-CGH work?

Answer 31

Uses a reference genome to compare hybridization patterns. Can detect small and large deletions and duplications throughout all chromosomes with a high success rate

Question 32

What is Array-CGH used for (its benefits)?

Answer 32

Assessing common and cryptic (strange or uncommon) abberations throughout all chromosomes, standard of care for children of idopathic developmental delay or multiple congenital abnormalities (20% detection vs 3% for routine karyotype). Even has a faster turnaround time

Question 33

What are the limitations of Array-CGH?

Answer 33

Does not detect single gene mutations (unlike FISH, which can target specific genes) Does NOT detect BALANCED rearrangements (FISH or regular karotyping will do this) -> cannot physically see chromsomes Identifies copy number variants which may not be clinically significant -> causes anxiety

Question 34

How does a genomic deletion vs genomic duplication appear on Array-CGH?

Answer 34

Deletion: A dip in signal intensity on chromosome array graph (due to loss of patient fluorescence as compared to control DNA) Duplication: A jump in signal intensity on chromosome array graph (due to gain of patient fluorescence as compared to control DNA)