Cytogenetics

Front 1

What are three ways to identify a chromosome using light microscopy?

Back 1

1.) size
2.) banding pattern
3.) position of the centromere

Front 2

What can improve banding resolution?

Back 2

A stretched out chromosome will make bands more apparent compared to a highly-condensed one.

Front 3

Name the parts of a chromosome and where they’re located.

Back 3

Telomere – located at the ends of the chromosome, characterized by TTAG repeats

Short arm – a.k.a. “p arm” for “petit”

Long arm – a.k.a. “q arm” b/c it’s the next letter in the alphabet

Centromere – what separates the two arms of the chromosome, where kinetochores attach during mitosis, meiosis.

Front 4

What is the term for a chromosome that is divided evenly in half by the centromere?

What is the term for a chromosome that is not divided evenly in half, but still has a short arm.

What is the term for a chromosome with virtually no short arm?

Back 4

Metacentric
Sub-metacentric
Acrocentric

Front 5

List the acrocentric chromosomes.

Back 5

13, 14, 15, 21, 22

Front 6

What are the two regions of the acrocentric short arm? What genetic material is contained in the short arm of the acrocentric chromosome?

Back 6

“Stalk” at the base and “Satellite” at the tip

Like heterochromatic blocks, the acrocentric short arm is very repetitive. The length varies from individual to individual.

It contains mainly DNA information for making ribosomal RNA.

Front 7

On the molecular level, how can telomeres be characterized?

Back 7

Located at the end of chromosomes, has TTAG repeats.

Front 8

What are heterochromatic blocks and where in particular are they found?

Back 8

Formally known as “junk DNA” → now more accurately referred to as “inactive DNA.”

Heterochromatin is defined by its property of remaining in the condensed state. So it stains darkly even in the nondividing (interphase) cells. Similar to the acrocentric short arm, the heterochromatic blocks consist of highly repetitive regions that vary considerably in length from one individual to another.

Large heterochromatic regions can be found on chromosomes 1, 9, 16, Y

**ALSO – don’t forget that the centromere is heterochromatic.

Front 9

What two regions of the chromosome can be deleted without enormous problems?

Back 9

The short arms of the acrocentric chromosome and the heterochromatic blocks are largely expendable, as they are very repetitive, often inactive, and the same genetic information may be found elsewhere.

Front 10

Describe the international standard for chromosome nomenclature and band designation.

Back 10

Numbering starts from the centromere and goes up and down the p and q arms. For example, the first band from the centromere on the short arm would be p.11. Subbands are included as well (for example p.11.1, p.11.2).

Front 11

What is the term for the drawn representation of a banded chromosome?

Back 11

Ideogram

Front 12

What is the most commonly used banding method in the U.S.? What does its name stand for?

Back 12

G-banding – “Giemsa banding”
Also known as “GTG banding,” which stands for “G bands produced with Trypsin using Giemsa”

Front 13

Which type of banding is used specifically to stain constitutive heterochromatin around the centromeres and heterochromatic blocks? What does the name stand for?

Back 13

C-banding
a.k.a. “CBG banding” C bands produced with Barium hydroxide using Giemsa

Front 14

Give a quick overview of the 4 main types of banding. Which method was the first one ever developed?

Back 14

G-banding → most commonly used method
Q-banding → requires fluoroscope microscopy, dim and bright patterns
C-banding → used to stain centromeres / heterochromatin
R-banding → gives opposite stain from G-band, used in Europe (esp. France)

Q-banding was the first developed.

Front 15

What is Q-banding? What stain is used? What is the banding pattern like?

Back 15

This type of stain requires fluoroscope microscopy and requires staining with the fluorochrom QUINACRINE mustard. The result is dim and bright banding patterns. The dim bands are referred to as “Q bands” and the bright bands correspond with dark G bands.

**Note: this was the first method ever developed, but fluoroscopy is expensive so other methods were eventually created.

Front 16

What banding technique produces a staining pattern that is the inverse of G banding (i.e. G light regions are dark, G dark regions are light)?

Back 16

R-banding

**Note: This technique is only really routinely used in France, but can be helpful to view areas that are difficult to discern.

Front 17

You see a cocktail of chromosomes from different individuals and line them up together. You see 5 different Y chromosomes that are 5 different sizes. What do you know about these chromosomes?

Back 17

Chromosomes 1, 9, 16, and Y contain large heterochromatic blocks. It is ONLY the heterochromatic regions that vary in these Y chromosomes. The euchromatic material will be identical.

Front 18

You see a bunch of dark spots on a C-banding image. What are they?

Back 18

You are seeing either the heterochromatic blocks on chromosomes 1, 9, 16 or Y – or you’re seeing the centromeres.

Front 19

In order to study chromosomes using banding techniques, what state must they be in and what must you do to accomplish this?

Back 19

Cells are in interphase (non-condensed state) the majority of the time, but chromosomes can only be viewed when they are in their condensed state. So you have to catch the active division of the cell and arrest it during METAPHASE.

Front 20

The four steps in banding techniques:

1.) Push a cell to active cell division using ________.
2.) _______ will produce metaphase arrest.
3.) Hypotonic solution can be used to __________.
4.) Differential staining (most commonly _________).

Back 20

*Mitogens (PHA)
*Spindle poisins (colchicine)
*Rupture the nucleus (swell the cell and get all the chromosomes spread out)
*Giemsa

Front 21

What is PHA?

Back 21

phytohemagglutinin (kidney bean extract) – used to activate cell division.

Front 22

What is the difference between genetic imbalance and chromosomal imbalance?

Back 22

A genetic imbalance involves an incorrect amount of genetic material, and may disturb normal growth pattern. The effects of a genetic imbalance may be seen at any stage, from fetal to adult life.

A chromosomal imbalance will involve 100s or 1000s of genes and have much more catastrophic effects. A chromosomal imbalance will usually be lethal at some point in the zygotic through fetal stages. If it is viable, it will probably be seen immediately in the newborn stage (for example, Down’s syndrome). If it IS NOT seen in the newborn stage, but presents in the adolescent to adult stages of life, it will probably be related to a SEX CHROMOSOMAL abnormality.

Front 23

Of the aneuploidies, ______ is typically more devastating than _______.

Back 23

Monosomy
Trisomy

Front 24

What is aneuploidy?

Back 24

The gain or loss of a full chromosome leading to an abnormal chromosome number (i.e. not a complete set).

Front 25

A chromosome complement with any chromosome number other than 46 is said to be _________. An exact multiple of the haploid chromosome number (n) is called _______, and any other chromosome number is _______.

Back 25

Heteroploid
Euploid
Aneuploid

Front 26

Describe mosaicism. What can cause it?

Back 26

Generally, the chromosomal complement is the same for all cells of the body, and therefore a chromosomal abnormality will be present in all cells. Sometimes, however, two or more chromosomal complements are present in a single individual. This is known as mosaicim. → (***For example, a 46/47 +21 mosaic. Only a certain % of all the cells in the body are trisomy while the rest are normal.***)

A common cause would be non-disjunction of an early postzygotic mitotic division. Because of this, levels of mosaicism often vary by tissue type as tissue types are assigned very early in development.→ (***For example, high levels of trisomy in the cartilage, very low levels or no levels in the blood.***)

Front 27

What is “complex mosaicism”?

Back 27

This is the type of mosaicism that involves 3 or more different cell lines with different chromosomal complements. (Ex: 20% cells have 45 chromosomes, 40% cells have 46 chromosomes, 40% of cells have 47 chromosomes.)

Front 28

What is trisomy? What is triploidy? What is monosomy? What is partial aneuploidy?
What is multiple aneuploidy?

Back 28

Trisomy – extra chromosome (47)

Triploidy – complete extra set

Monosomy – missing chromosome (45)

Partial aneuploidy – loss or gain of only part of a chromosome

Multiple aneuploidy – more than one aneuploidy. For example 2 extra chromosomes. Or one extra AND one missing chromosome.

Front 29

What is the most common trisomy seen in miscarriage (POC) studies? What are the second most common trisomies seen?

Back 29

Trisomy 16 – never seen in a liveborn

Next most common: Trisomy 21 & 22 (tied for 2nd place)

Front 30

What is “ploidy.” What is the common cause of triploidy? What is the common cause of tetraploidy?

Back 30

Ploidy involves the addition or loss of COMPLETE SETS of chromosomes.

Triploidy would involve the addition of an entire chromosomal complement. It is usually caused by POLYSPERMY (when egg is fertilized by more than one sperm).

Tetraploidy, on the other hand, would result from failure of the FIRST ZYGOTIC MITOTIC DIVISION. (**Note: failure in subsequent zygotic mitotic divisions can also happen, and would result in mosaicism where only some cells in certain tissues of the body are tetraploidy)

**Both are lethal and result in spontaneous abortion.

Front 31

What is the usual cause of aneuploidy? What type of monosomies can be seen in live birth?

Back 31

Failure of a single chromosome (or bivalent) to complete division.

No autosomal monosomies will be seen in live birth. Most abort before conception is even recognized. You may see monosomies in mosaicism, though. The only complete monosomies that is survivable is single X (Turner’s syndrome).

Front 32

What are the aneuploidies in Down syndrome? Edward Syndrome? Patau Syndrome? Turner Syndrome?

Back 32

Down: trisomy 21
Edward: trisomy 18
Patau: trisomy 13
Turner: monosomy X

Front 33

Why are proportions of trisomy seen higher in chorionic villi sampling compared to amniocentesis?

Back 33

CVS can be done at an earlier stage in pregnancy. By the time amniocentesis is an option, spontaneous abortion of many of these aneuploidies has already happened.

Front 34

What are the “typical” phenotypes of the 4 survivable chromosomal abnormalities (i.e. down, Edward, patau, turner)

Back 34

*Mental retardation
*Characteristic facial features (“dismorphic feature”)
*Growth delay
*Internal organ malformation – esp. cardiac

Front 35

What is MCA/MR

Back 35

Indication for chromosome analysis: Multiple Congenital Abnormalities, Mental Retardation

Front 36

95% of Down Syndrome is caused by _________. 95% of trisomies are due to the ____(maternal or paternal)______ line. 75% of errors occur during ________.

Back 36

Nondisjunction
Maternal (nondisjunction)
Meiosis I

Remember: MATERNAL MEIOSIS I NONDISJUNCTION

Front 37

What are the characteristic physical traits seen in Down Syndrome?

Back 37

• Hypotonia (“floppiness”)
• Flat occiput
• Low set ears with characteristic pinnae (folded ears, absent earlobes)
• Protuding/Large tongue
• Abnormal dermatoglypics (“Simian line” → single palm crease)
• Clinodactyly (curved pinky finger)
• Wide space between 1st and 2nd toes
• Brushfield spots (gray and white spots on periphery of iris)
• Epicanthal folds (eyes)

Front 38

What are the medical problems associated with Down Syndrome?

Back 38

• Mental retardation (100%)
• Congenital heart defect (40%)
• Leukemia (15-20%)
• Respiratory & GI problems → less common

Front 39

What are the physical and medical features associated with Edward Syndrome?

Back 39

Physical:
• Prominent occiput, Micrognathia (abnormally small jaw) & Microcephaly (small head circumference)
• Low set/malformed ears
• Clenched fists
• Rocker-bottom feet & Short, dorsiflexed big toe

Medical:
• Congenital heart defect (90%), esp VSD
• Growth deficiency
• Congenital lung, diaphragm, kidney abnormalities
• Hernias, cryptorchidism (failure of testicle descent)
• Scoliosis, Apnea, seizures

*This is the most common defect in stillborn births with multiple congenital abnormalities. Only 10% are alive after the first year.

Front 40

What are the physical and medical features associated with Patau Syndrome?

Back 40

Physical:
• Distinctive craniofacial and CNS malformation
• Microcephaly (small head circumference) / sloping forehead
• Holoproencephaly (failure of forebrain to develop)
• Eye problems
• Cleft lip/palate
• Low set ears
• Polydactyly
• Rockerbottom feet
• Aplasia cutis congenital (no skin, esp. on scalp)

Medical:
• Cryptorchidism/Bicornate uterus
• Cardiac defects
• Polycystic kidney

*Similar to Edward’s → 95% spontaneously aborted, low survival rate

Front 41

In instances of Patau syndrome, 75% arise due to __________. 20% are due to _________. 5% are due to ___________ (i.e. postzygotic mitotic nondisjunction).

Back 41

meiotic nondisjunction
translocations
mosaicism

Front 42

What are four commonly-seen sex chromosome abnormalities?

Back 42

1.) Turner syndrome (monosomy X)
2.) Kleinfelter syndrome (XXY)
3.) Triple X
4.) XXY

Front 43

It is estimated that ____% of Turner syndrome embryos are spontaneously aborted. Those that survive are most likely _________. 80% of all Turner cases are due to the loss of the ___(maternal or paternal)_____ X chromosome.

Back 43

99%
mosaic
paternal

Front 44

What are the phenotypic traits of Turner syndrome? How would you treat a child born with Turner syndrome? How are IQ and lifespan affected?

Back 44

*Short stature (always)

And to a varying degree …
*Infertility (due to ovarian dysgenesis)
*Broad chest
*Webbed neck
*Triangular face/posteriorly rotated ears
*Shield chest
*Lymphedema at birth
*Coarction of aorta
*Kidney defects

Early dx is key because treatment with growth hormones and estrogen is very effective. REMEMBER: IQ and Life span are NOT affected!!! (Though learning disability for spatial perception sometimes occur.)

Front 45

What is the genotype of Kleinfelter Syndrome? What are some phenotypic features?

Back 45

47, XXY

Overall the phenotype is a slightly feminized physique:

• Small testes that fail to produce normal levels of testosterone
• Gynecomastia (40%)
• Sterility
• Taller and thinner than average
• Osteoporosis
• Slight IQ reduction (though XXXY or XXXXY would lead to severe retardation)
• Poor beard growth / female pubic hair pattern

Front 46

What is the effect of an extra X chromosome in females (Triple X)?

Back 46

Very little effect. Individuals are fertile and do not transmit the extra chromosome. There is a slight reduction in IQ, comparable to the reduction seen in Kleinfelter males.

Incidence is 1/1000, just like incidence of Kleinfelter syndrome

Front 47

What is the effect of an extra Y chromosome in Males (XYY)?

Back 47

May be nothing. XYY Males are tall, but normally proportioned. Also a small IQ reduction, like in Kleinfelters and XXX. Also 1/1000 incidence.

*Some question about the “supermale” theories → is the proportion of XYY males higher in prison than in the general population? If so, probably not due to higher levels of aggression (“male behaviors”), but rather the lower IQ and impulse control.