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Genetics > Chromosomal Nomenclature & Structure Clinical Cytogenetics at a Glance > Flashcards

Chromosomal Nomenclature & Structure Clinical Cytogenetics at a Glance Flashcards

1
Q

What is cytogenetics?

A

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

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2
Q

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

A

80 genes -> about 6 Megabases

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3
Q

At what phase in the cell cycle are chromosomes analyzed?

A

Metaphase, since they are most condensed

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4
Q

What are the three types of chromosomes?

A
  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
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5
Q

Which are the important acrocentric chromosomes?

A

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

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6
Q

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

A

Dark bands - gene poor AT rich regions

Light bands - gene rich GC rich regions

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7
Q

What are normal male and normal female karyotypes?

A 
46,XY = male
46,XX = female
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8
Q

What is a germline vs somatic mutation?

A

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

Somatic = acquired = cancer

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9
Q

What is aneuploidy vs polyploidy?

A

Aneuploidy - gain or loss of one or more whole chromosomes

Polyploidy - gain or loss of entire sets

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10
Q

What is the karyotype of Down’s syndrome female?

A

47,XX,+21

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11
Q

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

A

Nondisjunction in meiosis I or II.

Meiosis I: all gametes will be off

Meiosis II: only 2/4 gametes will be off

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12
Q

What is the most common cause of polyploidy?

A

Two sperms fertilizing one oocyte

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13
Q

What is the leading risk factor for aneuploidy?

A

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)

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14
Q

What are three balanced karyotype chromosomal abberations?

A
  1. Translocation - reciprocal / robinsonian
  2. Inversion
  3. Insertion
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15
Q

What are three unbalanced karyotype chromosomal abberations?

A
  1. Translocations - when two chromosomes involved are not inherited together
  2. Deletion
  3. Duplication
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16
Q

When can a balanced abberation cause abnormal phenotype?

A

If the translocation disrupts a critical gene

17
Q

What is a reciprocal translocation?

A

Exchange of chromosomal material between non-homologous chromosomes

18
Q

What is a reproductive risk of people with reciprocal translocations?

A

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

19
Q

What is a Robertsonian translocation?

A

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

20
Q

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

A

45,XX,der(13;14)

21
Q

What are the two types of inversions?

A

Paracentric - two breaks in one arm

Pericentric - breaks in both arms, involving the centromere

Both reverse the orientation of the genes

22
Q

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

A

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

23
Q

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

A

Can view the entire genome on the microscope level

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

24
Q

What are some disadvantages of routine chromosome analysis?

A

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)

25
Q

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

A

Fluorescence in situ hybridization

Detects microdeletion and microduplication syndromes

26
Q

How does FISH work?

A

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

27
Q

What are the advantages of FISH?

A 
Do not need to have dividing cells, can be done during any phase
High resolution (>100Kb)
Rapid turnaround
28
Q

What are the disadvantages of FISH?

A

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

29
Q

When do you run a FISH?

A

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.

30
Q

What does Array-CGH stand for?

A

Array Based Comparative Genomic Hybridization?

31
Q

How does Array-CGH work?

A

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

32
Q

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

A

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

33
Q

What are the limitations of Array-CGH?

A

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

34
Q

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

A

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)

Genetics (20 decks)

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