Chromosomal Nomenclature & Structure Clinical Cytogenetics at a Glance Flashcards
What is cytogenetics?
A subspeciality of genetics which studies the chromosome number and structure at the chromosome level
How many genes are in a chromosome band? About how many bases is this?
80 genes -> about 6 Megabases
At what phase in the cell cycle are chromosomes analyzed?
Metaphase, since they are most condensed
What are the three types of chromosomes?
- Metacentric - centromere near middle
- Submetacentric - centromeres are closer to one end
- Acrocentric - really short p arms which end in satellites of repetitive DNA
Which are the important acrocentric chromosomes?
13, 14, 15, 21, 22 -> important in translocations
Once treated with trypsin to denature proteins and stained with Giemsa, how do the chromosomes appear?
Dark bands - gene poor AT rich regions
Light bands - gene rich GC rich regions
What are normal male and normal female karyotypes?
46,XY = male 46,XX = female
What is a germline vs somatic mutation?
Germline = constitutional, occurs before fertilization or in zygote. The mutation will be present in all tissues and inherited
Somatic = acquired = cancer
What is aneuploidy vs polyploidy?
Aneuploidy - gain or loss of one or more whole chromosomes
Polyploidy - gain or loss of entire sets
What is the karyotype of Down’s syndrome female?
47,XX,+21
What is the most common cause for aneuploidy? How do they differ?
Nondisjunction in meiosis I or II.
Meiosis I: all gametes will be off
Meiosis II: only 2/4 gametes will be off
What is the most common cause of polyploidy?
Two sperms fertilizing one oocyte
What is the leading risk factor for aneuploidy?
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)
What are three balanced karyotype chromosomal abberations?
- Translocation - reciprocal / robinsonian
- Inversion
- Insertion
What are three unbalanced karyotype chromosomal abberations?
- Translocations - when two chromosomes involved are not inherited together
- Deletion
- Duplication
When can a balanced abberation cause abnormal phenotype?
If the translocation disrupts a critical gene
What is a reciprocal translocation?
Exchange of chromosomal material between non-homologous chromosomes
What is a reproductive risk of people with reciprocal translocations?
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
What is a Robertsonian translocation?
Translocation between acrocentric chromosomes - two acrocentric chromosomes fuse at centromere with loss of short arm
What is the karyotype for a normal woman with a balanced Robersonian translocation of chromosomes 13 and 14?
45,XX,der(13;14)
What are the two types of inversions?
Paracentric - two breaks in one arm
Pericentric - breaks in both arms, involving the centromere
Both reverse the orientation of the genes
How many chromosomal breaks is needed for an insertion (balanced)?
At least 3: 2 to make DNA leave one chromosome, 1 to insert it into the other.
What are some advantages of standard karyotype / routine chromosome analysis?
Can view the entire genome on the microscope level
Detects all types of gross chromosomal abnormalities >5 Mb in size
What are some disadvantages of routine chromosome analysis?
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)
What does FISH stand for? What type of disorders does it generally detect?
Fluorescence in situ hybridization
Detects microdeletion and microduplication syndromes
How does FISH work?
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
What are the advantages of FISH?
Do not need to have dividing cells, can be done during any phase High resolution (>100Kb) Rapid turnaround
What are the disadvantages of FISH?
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
When do you run a FISH?
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.
What does Array-CGH stand for?
Array Based Comparative Genomic Hybridization?
How does Array-CGH work?
Uses a reference genome to compare hybridization patterns. Can detect small and large deletions and duplications throughout all chromosomes with a high success rate
What is Array-CGH used for (its benefits)?
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
What are the limitations of Array-CGH?
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
How does a genomic deletion vs genomic duplication appear on Array-CGH?
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)
