Chromosomal Abnormalities

Front 1

When there is a translocation of genetic material, what are the possibilities for gamete formation? How many are balanced?

Back 1

There are multiple options for gametes, only two of which are balanced. The 4 options for the gamete are to receive:

Both normal chromosomes → balanced
Both abnormal chromosomes → balanced
One abnormal and one normal chromosome (x 2) → unbalanced

Front 2

What is Reciprocal Translocation and what are its consequences?

Back 2

Results from breakage of NONHOMOLOGOUS chromosomes and reciprocal exchange of the broken-off segments.

This is a mutual exchange with no loss of genetic material, thus there are usually no clinical implications. NO PHENOTYPE.

BUT they are associated with a high risk of UNBALANCED GAMETES and abnormal progeny (more commonly found in couples with multiple miscarriages).

Front 3

What is an inversion and what are the 2 types?

Back 3

Inversions occur when a single chromosome undergoes two breaks and is reconstitute with the segments between breaks inverted. (In other words → the thing breaks and gets glued back together turned around.)

Paracentric – (“para” = same) → does not include the centromere, both breaks occur in one arm.

Pericentric – Does include the centromere → there is a break in each arm.

Front 4

When might a reciprocal translocation result in a clinical implication?

Back 4

Very rare → if the breakpoint occurs within a critical gene, which disrupts that gene. Phenotype would be similar to a single gene defect.

OR → there may be microdeletions at the breakpoint sites.

Front 5

What will be the result of an unbalanced derivative of a translocation?

Back 5

A gamete with partial monosomy AND partial trisomy

Front 6

Describes what happens during meiosis to the chromosomes of a carrier of a balanced reciprocal translocation. What are the options for segregation? Which one is the most rare?

Back 6

A QUADRIVALENT (cross-shape) is formed in order to line up the homologous parts. At anaphase, chromosomes usually segregate in one of three ways (for a total of four options):

1.) Alternate ( x 2) (balanced) → homologous centromers go to separate daughter cells. Daughter cells end up with either either 2 normal (no translocation) or 2 abnormals (exactly like the parent).
2.) Adjacent-1 (unbalanced)→ homologous centromeres go to separate daughter cells. Daughter cells end up with 1 normal, 1 abnormal.
3.) Adjacent-2 (unbalanced)→ homolgous centromeres go to the same daughter cell, this is the MOST RARE in prenatal testing (doesn’t usually make it to gestation.

**Note: you can also get nondisjunction events, but these are theoretical imbalances → you’ll never see it clinically because it won’t result in fertilization/implantation.

Front 7

Describes what happens during meiosis to the chromosomes of a carrier of an inversion.

Back 7

In order for the homologous parts to line up, INVERSION LOOPS are formed. Recombination is usually suppressed in inversion loops, but IF RECOMBINATION OCCURS while the chromosomes are in this state that can lead to an UNBALANCED GAMETE (partial monosomy AND partial trisomy in the regions distal to the break points)

Front 8

What type of inversion (paracentric/pericentric) is “preferable” (leads to fewer children with unbalanced karyotype)? Why?

Back 8

If recombination occurs in the inversion loop during meiosis, the result will be partial monosomy AND partial trisomy in the regions DISTAL to the break points.

When recombination occurs with the paracentric inversion loops, the result will either be 1.) normal 2.) balanced 3.) or unbalanced ACENTRIC or DICENTRIC (no centrosome or 2 centrosomes). The acentric or dicentric are the two unbalanced options, and are NEVER VIABLE.

Meanwhile, the pericentric unbalanced options will lead to partial trisomy and partial monosomy. The centromeres are present and normal in all 4 cases (balanced and unbalanced), so these unbalanced gametes MAY BE VIABLE.

Therefore, the “BETTER OPTION” is to have a PARACENTRIC INVERION, since the unbalanced possibilities for that one will not make it to gestation, so your offspring will either be normal or exactly like you – whereas the unbalanced possibilities for pericentric might result in a live birth and the attendant problems.

Front 9

What is a Robertsonian Translocation? What is the phenotypic effect?

Back 9

A translocation between ACROCENTRIC chromosomes (i.e. chromosomes 13, 14, 15, 21, 22). The break is always at the centromere, and the long arms of the chromosomes fuse into one. Results in the LOSS OF THE SHORT ARMS for both chromosomes, and a BALANCED 45 KARYOTYPE.

There are 5 (x 2) short arms in all with repetitive genetic information, so the loss of 2 short arms is not deleterious. The other 7 can make up for it. So NO CLINICAL SEQUELA (despite the 45 karyotype).

Front 10

The most common type of Robertsonian translocation involves _____ and ______. These translocations account for 5% of all ________ cases.

Back 10

13
14
Down Syndrome (Trisomy 21)

Front 11

Like reciprocal translocation, though there is no phenotype associated with Robertsonian translocation, it can lead to unbalanced gamete formation. What is one key difference between recriprocal translocation and Robertsonian translocation in terms of its derivatives?

Back 11

Instead of partial monosomy AND partial trisomy (as seen in reciprocal translocation), an unbalanced Robertsonian derivative will be partial monosomy OR partial trisomy.

Front 12

Even though inversions have no phenotype, what keeps them from propagating in the population to a huge extent?

Back 12

The inversion interferes with reproduction (the chromosomes literally tie themselves into knots trying to pair up during meiosis). Plus, when recombination occurs, the resultant gametes that do form are not viable about 50% of the time (i.e. the unbalanced gametes).

Front 13

What are the four options for breaks in the chromosome?

Back 13

1.) 2 breaks on same arm that rejoin: paracentric inversion
2.) 2 breaks on same arm that get lost: interstitial deletion (or intrachromasomal deletion)
3.) 2 breaks on different arms that rejoin: pericentric inversion
4.) 2 breaks on different arms that get lost: ring chromosome (b/c telomeres are lost, chromosomes don’t like the exposed ends).

Front 14

Deletion in 5p results in _____ syndrome. Deletion in 4p results in ______ syndrome. In the latter (4p), 87% are the result of ______ interstitial deletion of _______ origin. What do the remaining 13% result from?

Back 14

Cri-du-chat
Wolf Hirshhorn
De novo
Paternal

Other 13%: Unbalanced derivation of reciprocal translocation

Front 15

What are isochromosomes?

Back 15

You either have two of the same long arms or two of the same short arms on a single chromosome (duplicated in a mirror-image fashion). The opposite arm is then missing.

So you get …

Single copy of the genetic material of one arm (partial monosomy) and three copies of the genetic material of the other arm (partial trisomy).

If you have two normal homologues in addition to the isochromosome, then you’d have full tetrasomy for the arm involved in the isochromosome.

Front 16

What are “cryptic rearrangements”

Back 16

These are the chromosomal rearrangements that cannot be seen via visual inspection (light microscopy and banding) → These submicroscopic variations may account for the wide clinical variability of different chromosomal abnormalities. As technology advances to detect these smaller rearrangements, we’re finding a greater proportion of chromosomal abnormalities then previously thought (especially in developmentally disabled populations).

Front 17

Why would you want to examine parental blood when a prenatal chromosomal abnormality is detected? What counseling needs to be offered to a parent found to have a balanced abnormality?

Back 17

If the parent has the same abnormality, you can predict a more favorable prognosis. A de novo or familial unbalanced rearrangement, on the other hand, is most often associated with an adverse outcome. If it’s balanced, though, it is 94% favorable outcome.

Someone with a balanced abnormality (often discovered during prenatal evaluation) needs to be advised about problems that will probably occur with subsequent pregnancies.

Front 18

What are SMCs? SMCs containing euchromatin are more likely to be associated with _________ phenotypes. SMCs containing heterochromatin are more likely to be associated with ________ phenotypes. Why is counseling parents about SMCs difficult? What is one technique that can determine the origin of an SMC?

Back 18

Marker chromosomes is the general term for small, unidentified chromosomes seen in chromosome preparations → they may be the arms that break and get “lost,” though often they are supernumerary (partial trisomy) marker chromosomes (SMCs). 1/5 of SMCs are inherited in a familial fashion.

Abnormal
Normal

SMCs are hard to identify, and their clinical significance can range from none to 100% risk of abnormality. The assessment of risk is based on size, morphology, and origin → but as stated, this is very difficult to determine.

FISH using whole chromosome paints is a good way to determine the origin of an unknown SMC (or marker chromosome in general).

Front 19

What does FISH stand for? How does it work? What are the 4 steps involved in this technique?

Back 19

Fluorescence In Situ Hybridization

First example of “Molecular Cytogenetics” (Molecular bio meets cytogenetics)

It’s a physical DNA mapping technique that uses a DNA PROBE that’s made up of known nucleotides and labeled with a fluorescent marker (fluorochrome or hapten). The DNA hybridizes with the chromosomes on a slide and can be visualized with a fluorescence microscope.

1.) denature DNA to separate strands (heat)
2.) apply probe
3.) probe recognizes Target DNA sequences
4.) DNA reaneals with probe attached, can be viewed w/ fluoroscopes

Front 20

What are the targets for these probes?

Beta satellites
Alpha satellites
Classical satellites
Telomeric sequences

Back 20

Beta → Acrocentric short arms
Alpha → Centromeric sequences
Classical → Just below centromere
Telomeric → End of chromosomes (TTAGGG)

Front 21

List some examples of microdeletion syndromes.

Back 21

DiGeorge
Prader-Willi
Angelman
Miller-Dieker
Williams

Front 22

Which two syndromes result from the same microdeletion? How are they different? What genetic phenomenon is this an example of?

Back 22

Prader-Willi Syndrome and Angelman Syndrome both result from a deletion in 15q. The differences in these two syndromes arise based on whether the deletion is inherited from the mother or father.

This is an example of IMPRINTING (different phenotype depending on parental origin)

Front 23

This area has the highest concentration of genes of any chromosomal region, and therefore submicrosopic deletions or duplications in this area would have the most significant impact.

Back 23

Telomeres

Front 24

Why are telomeres important? Is there more or less genetic recombination at telomeres? Is the rate of recombination higher in males or females?

Back 24

They play a critical role in chromosome pairing at meiosis.

There is INCREASED genetic recombination at telomeres.

Recombination rate is higher in males usually.

Front 25

Prenatal diagnosis aneuploidy screening by FISH looks at _________ derived from _________ or ___________.

Preimplantation Genetic Diagnosis aneuploidy screening by FISH looks at __________.

Back 25

Interphase nuclei
Chorianic villi
Amniocytes
Interphase blastomere nuclei

Front 26

What chromosomes are usually looked at by Rapid Prenatal Interphase FISH?

Back 26

Trisomies 13, 18, 21 an Monosomy X are the most common aneuploidies related to maternal age or fetal abnormality.

Front 27

What are the main advantages of using FISH over routine chromosome analysis? What are the disadvantages?

Back 27

Advantages: Quicker. Routine takes 7-10 days, FISH takes 1-2 days. The cells can be in interphase or metaphase in FISH analysis, whereas Routine analysis requires the cells to be in metaphase.

Disadvantages: Reduced sensitivity. Also, cytogenetic abnormalities other than the most common ones (13, 18, 21, X) will not be detected → because you’re not looking for it!

Front 28

What are some common indications for Prenatal Interphase FISH?

Back 28

• Advanced Maternal Age
• Abnormal maternal serum screening indicating increased risk for trisomy 18 or 21
• Abnormal maternal serum alpha fetal protein, which would indicate an increased risk for neural tube defects (which might be caused by trisomy 13 or 18).
• Prenatal ultrasound abnormalities (esp. heart or kidney).

Front 29

What is PGD? How is it done?

Back 29

“Preimplantation Genetic Diagnosis” → the earliest form of prenatal diagnosis.

Oocytes or Embryos are obtained in vitro and biopsied. They are analyzed via FISH or PCR.

What’s taken:
Polar bodies for oocytes
Blastomeres for embryos (at the 6-10 cell stage / day 3 / “cleavage stage.”) 1-2 cells are taken for analysis.

Embryos found to be free of the disease under consideration are subsequently used for transfer.

Front 30

What types of abnormalities will be missed using PGD?

Back 30

Mosaics
Balanced Translocations

Front 31

What is SKY?

Back 31

Spectral KarYotyping

This is a multiple painting technique in which each chromosome gets its own color. Helps you to see minute translocations and inversions that you normally wouldn’t see. (If you see splatters of a 2nd color on a chromosome, you know it doesn’t belong there.)

(Like a rainbow in the SKY)

Front 32

What is CGH?

Back 32

Comparative Genomic Hybridization

This is a type of procedure that gives you GAINS and LOSES in a SINGLE STEP!

Uses a marker probe AND a control probe.

(Key: SINGLE STEP)

Front 33

With DNA Chip technology (a.k.a. _________), you’re using _______ as your target instead of _______, which was the target in older techniques.

Back 33

Microarray
Known DNA sequences
Chromosomes

Front 34

What are 2 microarray platforms? And 2 microarray designs? What are the key advantages and disadvantages of microarrays?

Back 34

PLATFORMS:
* 1.) BAC (Bacterial artificial chromosome) → used to detect LARGER gains and losses (>100kb)
* 2.) Oligonucleotide → used to detect much SMALLER gains and losses (1-100 kb)

DESIGNS:
* 1.) Targeted → interrogate specific genomic regions of known clinical significance (ex: microdeletion syndromes), esp. telomeric/pericentromeric regions.
* 2.) Whole Genome/Tiled → Array spreads across the entire genome at various intervals. May reveal clinically-insignificant gains and losses.

Key disadvantage: lower specificity and sensitivity.
Key advantage: A MUCH bigger scope – greater scale of interrogation. (Hundreds of thousands simultaneously!!). Plus, there is a more accurate location, so we can now look up to see exactly what genes are located in the hot spots on the microarray.

Front 35

What is a SNP? What is SOMA?

Back 35

Sincle Nucleotide Polymorphism → used in Oligonucleotide Microarray Analysis (SOMA)

SNP is a DNA sequence variation occurring when a single nucleotide in the genome differs between members of a species (or between paired chromosomes in an individual). There are ½ million SNPs in the genome, with a mean spacing of 5.8 kb, so this type of array offers a very comprehensive scan. Hundreds of thousands of probes are used to interrogate each SNP – SIMULTANEOUSLY!! Deletions and duplications can be precisely defined using the SNP positions on the genome browser.

Front 36

What are the 5 diagnostic categories in SOMA?

Back 36

The five categories are listed from most macroscopic to most miniscule (from what G-banding formally did, to most specialized → what molecular cytogenetics now can do).

1.) Normal
2.) Aneuploidy → (ex: Trisomy 21)
3.) Partial Aneuploidy → (ex: Small (2-5Mb) unbalanced translocations, Intrachromosomal deletions/duplications, Marker Chromosomes) … here you’re reached the limits of G-banding resolution.
4.) Known Microdeletions/Microduplications and Subtelomeric imbalances → (ex: Prader-Willi, Di-George, Cryptic unbalanced translocations, Cryptic subtelomeric deletions/duplications)
5.) Partial Aneuploidies far below the resolution of G-banding → (newly discovered microdeletions/microduplications of clinical significance, all the way down to SPECIFIC GENES that cause clinical symptoms)