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Cytogenetics & Molecular Genetics Flashcards

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1
Q

Define karyotype

A

A picture, or organized graphic representation of the chromosomes in a single cell. Normal human karyotypes show 23 pairs of chromosomes, numbered from larger to smaller. The 23rd pair is the sex chromosomes (XX = female; XY = male) for a total of 46.

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2
Q

Define genome

A

All of the DNA of a given organism.

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3
Q

Define acrocentric

Give examples of which chromosomes are acrocentric

A

A chromosome that has its centromere close to one end

Chromosomes 13,14, 15, 21, 22, and Y

Results in a long q arm and a short p arm

Capable of participating in Robertsonian translocations

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4
Q

What is a ring chromosome? How can this happen?

A

A visible ring shaped chromosome structure on karyotype

A ring chromosome can happen in two ways. One is demonstrated in the picture; the end of the p and q arm breaks off and then stick to each other. The blue parts of each are lost thus resulting in loss of information. Second, the ends of the p and q arm stick together (fusion), usually without loss of material. However the ring can cause problems when the cell divides and can cause problems for the individual.

It is also possible to have a ring and be apparently healthy with no delays in development. As with all chromosome abnormalities it depends on what is actually found, the size of the ring, how much material was lost, which chromosomes are involved etc.

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5
Q

What is a balanced translocation? Should these individuals have health problems?

A

Translocation=structural abnormality in which two chromosomes swap non-homologous segments

Balanced translocation=no loss or gain of genetic material

Usually does not pose consequences to the carrier. Risk is to pass on an unbalanced translocation, which can be a source of miscarriages of a fetus with an unbalanced translocation or result in a child with an unbalanced translocation and have special health care needs

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6
Q

del

A

=deletion (part of a missing chromosome)

What a deletion causes depends on how big a piece is missing and what genes are missing in the section (i.e. where the deletion is

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7
Q

dup

A

=duplication (part of an extra chromosome)

A duplication is sometimes referred to as a ‘partial trisomy’. b/c they have three copies of the duplicated genes instead of two.

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8
Q

t

A

=translocation (chromosomes break off and swap physical locations)

balanced=just change in position but no loss or gain of genetic material

unbalanced=change in position WITH loss of some genetic material and gain of other genetic material

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9
Q

46,XY,dup(7)(q11.2q22)

A

Male with a duplication of chromosome 7 on the long arm (q) between bands 11.2 to 22

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10
Q

46,XX,del(1)(q24q31)

A

Female with a deletion of chromosome 1 on the long arm (q) between bands q24 to q31.

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11
Q

Centromere

A

nonstaining primary constriction of a chromosome which is concerned with chromosome movement during cell division and divides the chromosome into two arms.

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12
Q

inv

A

=inversion= a structural abnormality in which part of a chromosome is in the wrong orientation compared to the rest

Can be pericentric (involving the centromere) or paracentric (not involving the centromere

When a parent has an inversion there is an increased risk for offspring with an incorrect amount of genetic material–depends on which chromosome, how big the inversion is, and type of inversion

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13
Q

Autosome

A

any chromosome that is not the X or Y sex chromosome

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14
Q

Chromatid

A

In a dividing cell, a chromosome consists of two identical sister chromatids joined at the centromere. After cell division, and until the DNA is next replicated, a chromosome consists of a single chromatid.

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15
Q

Chromatin

A

A general term for the DNA-protein complex that makes up chromosomes

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16
Q

Euchromatin

A

chromatin with a relatively open structure in which genes can be active, the opposite of heterochromatin

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17
Q

G-banding

A

A standard procedure in which chromosomes are treated so that they stain in a characteristic pattern of dark and pale bands

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18
Q

Heterochromatin

A

Chromatin that is highly condensed and genetically inactive. This is found mainly at the centromeres

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19
Q

Homologous chromosomes

A

The two #1 or #2 chromosomes in a person.

Note that unlike sister chromatids, homologous chromosomes are NOT copies of one another any they may differ in ways that are small (minor sequence variations) or large (ie secondary to translocation)

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20
Q

Metacentric

A

A chromosome that has its centromere in the middle

Chromosomes 3 and 20

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21
Q

Robertsonian translocation

A

A special type of translocation in which two acrocentric chromosomes are joined close to their centromeres

Inappropriate recombination of 2 non-homologous chromosomes produces the fusion chromosome made up of the two q arms and the two p arms are lost. The fusion chromosome will function as a normal single chromosome in mitosis

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22
Q

Chromosomes for clinical genetic analysis (karyotype, CGH array, etc) are always prepared from ________ cells.

A

Dividing cells -> therefore DNA has already been replicated and under the microscope two sister chromatids joined at the centromere can be visualized

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23
Q

Pericentric inversion

A

Break in the chromosome includes the centromere. Involves a break in the q arm and the p arm and then the segment of chromosome is inverted or oriented the wrong way relative to the rest of the chromosome

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24
Q

True or false: some inversions are normal variants

A

true

Inv(9) and Inv(2).

These inversions are not related to an increased risk of birth defects and/or developmental difficulties.

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25
Q

Paracentric inversion

A

Inversion that does not include the centromere.

The chromosome breaks are in the same arm of the chromosome

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26
Q

Telomere

A

=special structures at each end of a chromosome

  • Contain long arrays of tandemly repeated DNA sequences
  • Lose 10-20 bps with each cell division
  • If whole telomere is lost -> unstable chromosome -> cell death
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27
Q

Which 2 types of cells contain telomerase? What is the function of this enzyme?

A

=germ line cells and cancer cells

-this enzyme adds back bps that were lost from telomere ends with cell division -> makes cells immortal

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28
Q

When does DNA replication occur during the cell cycle?

A

=S phase

-by end, copy of the DNA is made and each chromosome contains 2 sister chromatids

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29
Q

What are the 2 purposes of meiosis?

A

Meiosis generates gametes

  1. Number of chromosomes reduced to 23 so when combined with egg or sperm the zygot will have 46 chromosomes
  2. Pair into homologous chromosomes and undergo recombination (swapping of regions of chromosome) -> ensures a unique combination of parental genes in each gamete
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30
Q

What is the product of meiosis I? Meiosis II?

A

Meiosis 1:
-Generates 2 daughter cells with 23 chromosomes each, each still with 2 sister chromatids
Meiosis 2:
-Generates 4 daughter cells with 23 chromosomes, each with a single sister chromatid

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31
Q

What are the possibilities to create a triploidy zygote?

A

= 69 XXX, 69 XYY, 69 XXY or 69 YYY

  1. 2 sperm (each 23 chromosomes) fertilizing a single egg (23 chromosomes)
  2. Failure of meiosis generates a diploid (46 chromosomes) egg or sperm that then is fertilized with a normal haploid (23 chromosomes) egg or sperm

Triploidy is a common error of human conception but basically never survives to term.

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32
Q

Aneuploidy

A

=cells with 1 extra or 1 missing chromosome

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33
Q

What are the 2 major types of chromosome abnormalities?

A
  1. Numerical abnormalities
    - errors of ploidy
    - aneuploidy
  2. Structural abnormalities
    - reciprocal translocations
    - Robertsonian translocations
    - Deletions
    - Duplications
    - Inversions
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34
Q

Name 2 types of chromosomal deletions. What structure can be generated from a deletion?

A
  1. Interstitial
    = somewhere in the middle of the chromosome
  2. terminal
    =the end of the chromosome
    b/c absent telomeres would make the chromosome unstable, new ones must somehow be acquired

-A ring chromosome can be generation from a terminal deletion

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35
Q

Give 4 examples where a balanced translocation can lead to problems (other than risk of offspring with unbalanced translocation).

A
  1. One or more breakpoints slice through a gene and prevent it from working properly
  2. Breakpoint disrupts a control element for a gene that prevents the gene from working properly
  3. Faulty DNA recombination or faulty DNA repair joins together segments from different chromosomes and makes a novel gene out of the parts of 2 genes that were located on the breakpoints -> chimeric gene
  4. translocation between X chromosome and an autosome leads to problems in a female due to X inactivation.
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36
Q

True or false; Turner syndrome is due to non-disjunction in meiosis and the incidence of this condition increases with age

A
  • False
  • It is due to a lag in anaphase and one X chromosome moves too slowly and ends up outside the nucleus and thus is not included in one of the offspring gametes
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37
Q

Mosaicism is due to a _________ event.

A

post-zygotic event–since it occurs after formation of the egg or sperm the recurrence risk for a second affected offspring is low

in the child with mosaic feature, if the mosaicism extends to the germline, then it is possible for him or her to pass on the abnormality

People can be mosaic for either a chromosome abnormality or a single gene disorder and the mosaic cells may be confined only to certain tissues (thus not detected in the blood)

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38
Q

What is the difference between heterochromatin and euchromatin?

A

Heterochromatin=tightly packed nucleosomes (protein complexes of DNA + histones). Genes on heterochromatin are not expressed.

Euchromatin=more open and variable structure of nucleosomes. Genes in euchromatic regions of the chromosome may or may not be expressed.

Euchromatin and heterochromatin have different patterns of DNA methylation with corresponds to their activity level. Heterochromatin is methylated and inactive.

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39
Q

List 11 mechanisms of single gene mutations

A
  1. deletions of whole gene
  2. duplications of whole gene
  3. disruption of gene by a chromosomal rearrangement
  4. deletions or duplications of one or more exons of a gene
  5. mutations in the promoter or other cis-acting regulatory sequence
  6. mutations that affect splicing by altering an existing splice site
  7. mutations that affect splicing by activating a cryptic splice site
  8. mutations that alter the triplet reading frame (frameshifts)
  9. mutations that introduce a premature stop codon (nonsense)
  10. mutations that replace one amino acid in the protein with another (missense)
  11. mutations that alter one codon for an amino acid into another codon for the same amino acid (synonymous substitution)
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40
Q

List the classification of mutations based on functional outcomes

A
  1. null or amorphic (no product made or no function)
  2. hypomorphic (too little product or too little function)
  3. hypermorphic (too much product or excessive function)
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41
Q

Define what is meant by a gene that is “dosage sensitive”

A

if 50% decrease or increase in copy number (ie having 1 or 3 copies of the gene that is normally present in 2 copies) causes a phenotypic change

42
Q

What are the 2 outcomes of a chromosomal rearrangement that disrupts a gene? Give a clinical example of a condition where this is exhibited.

A
  1. No production of the normal full-length transcript
    - partial mRNAs are unlikely to be stable or encode protein product
    - ex: Hemophilia A (inversions are a common mutation in the F8 gene)
  2. Creation of a novel chimeric gene
    - via bringing together the exons of 2 different genes
    - ex: cancer
43
Q

What is the difference between cis and trans acting mutations?

A

cis= causative mutations affect the expression of an immediately adjacent gene

trans=causative mutations affect the expression of distant genes, often on different chromosomes

44
Q

What are some considerations with regulatory mutations (ie changes in the promoter or other regulatory sequence)

A
  • often difficult to identify and characterize
  • affect gene expression (wrong quantity or expression in wrong tissue)
  • one example of a mutation is a sequence change in the promoter that affects a binding site for a transcription factor
45
Q

How might a mutation at an existing splice site create a problem?

A

splice site=mark the beginnings and end of introns

  • It is difficult to predict the functional outcome of these mutations. Possibilities include:
  • exon could be skipped
  • incorporate sequence of intron in mature mRNA
  • affect the function of splice enhancers or suppressors
  • prevent generation of functional mRNA transcript
  • or change balance between the different isoforms of a gene
46
Q

How does a frameshift mutation work?

A

=insertion or deletion of any number of nucleotides that is NOT a multiple of 3

  • changes the entire reading of the downstream DNA
  • potential to generate a novel polypeptide but usually no peptide generated b/c of introduction of premature stop codon or protein does not fold properly and gets degraded
47
Q

True or false: when one or more complete exons of a gene are deleted or duplicated, the effect will partly depend on whether or not this produces a frameshift

A

=true

48
Q

True or false: mRNAs containing nonsense mutations always result in the generation of a truncated protein.

A

=false

  • can produce truncated protein but often cells have sensitive mechanisms that detect and then degrade mRNAs with premature stop codons
  • thus, effect of a nonsense mutation is the same as complete deletion of a gene
49
Q

Define dominant negative mutation

A

Mutations are referred to as dominant negative if the mutant product prevents normal product from functioning

50
Q

What is the most important question to ask for any mutation?

A

=how does the mutation affect the function of a gene:
1. Loss of function (partial or total)
=failure to do its normal job
-can be result of nonsense or frameshift mutations
2. Gain of function
=new harmful function or functioning of the normal product when it should not
-Require mutant allele to produce an abnormal protein
-result of mis-sense or regulatory mutations

51
Q

Define gain of function mutation

A

=new harmful function or functioning of the normal product when it should not (ex constitutively active receptor)

  • Require mutant allele to produce an abnormal protein
  • result of mis-sense or regulatory mutations
  • less common than loss of function
52
Q

True or false: genes are dominant or recessive

A

False–they are neither
-Traits (the expressed phenotype) of the genes are referred to as dominant (present in a heterozygote) or recessive (not present in a heterozygote)

53
Q

List ___ points to consider when interpreting a missense mutation

A
  1. Has the change been previously reported as a cause of the disease
  2. Is the change found in unaffected people?
  3. If the patient is from a large family with several affected members, is the change found in all affected people?
  4. Does the amino acid replaced have a vital role in the function or structure of the protein?
    - If the AA is highly evolutionary conserved across species, this is evidence for a vital role
54
Q

Give 2 examples where somatic mutations can cause problems.

A
  1. Somatic mutation occurs very early in embryogenesis and the mutant cell gives rise to a substantial number of cells and result in morphologic or other developmental effects
  2. If the mutation in a somatic cell causes it to start multiplying out of control -> cancer
55
Q

What are the 2 major mechanisms by which mutations originate?

A
  1. Errors in replication

2. DNA damage or errors in DNA repairgy

56
Q

Define derivative chromosome

A

=Abnormal chromosome consisting of segments from two or more chromosomes joined together as the result of a translocation, insertion , or other rearrangement.

57
Q

What is the cause of triploidy? Recurrence risk?

A

Triploidy (69 XXX, 69 XXY or 69 XYY) is a lethal chromosome disorder

Due to dispermy (fertilization with 2 sperm -> results in 2 sets of paternally derived chromosomes).
Associated with multiple malformations, hydatitiform placenta

Recurrence is unlikely

58
Q

What are G bands?

A

=dark staining regions on the chromosome on a karyotype

  • AT rich
  • each band contains as many as 50 or more genes
59
Q

Karyotype are generated on cells in which part of the cell cycle?

A

=in metaphase of the mitosis part of the cell cycle (in dividing cells)
-cells are maximally condense at this point

60
Q

What is meiosis?

A

=process by which a diploid cell generates haploid gametes

-consists of 1 round of DNA replication followed by 2 rounds of chromosome segregation and cell division

61
Q

True or false: which each chromatid generated in meiosis contains segments of the chromosome from each member of the original parental pair

A

=true

62
Q

True or false: there is an S phase between the divisions in meiosis I and meiosis II.

A

=false

63
Q

What are the pseudo-autosomal regions of the X and Y chromosome?

A

=short identical segments at the ends of the short and long arms of the X and Y chromosomes
-these segments undergo pairing and meiotic crossing over during meiosis I

64
Q

What is the main cause of numerical chromosome anomalies in humans?

A

=meiotic non-disjunction events

65
Q

What is the basis of mosaicism?

A

=post-zygotic non-disjunction events

66
Q

What is the start codon?

A

AUG

codes for methionine

67
Q

Name 3 stop codons

A

UGA
UAA
UAG

Stop codons signal the termination of translation process by binding release factors, which cause the ribosomal subunits to disassociate, releasing the amino acid chain

68
Q

Which bands on a G-banded karyoptype are gene rich and high in GC content:

light bands (G negative bands) or dark bands (G positive bands)?

A

=Light bands (G negative)

  • higher GC content
  • rich in transcribed sequences
  • rich in SINE and Alu repeats
  • contain housekeeping genes
  • early replicating
69
Q

What is contained at the centromere?

A

=alpha satellite DNA (171 bp tandem repeat sequence)

-there is sequence diversity of the alpha satellites that allows chromosome specific FISH probes for most chromosomes (except acrocentric chromosomes)

. Transcripts of alpha satellite play an important role in kinetochore formation and the establishment of pericentromeric heterochromatin and are indispensable for the proper cell division.

70
Q

Where does most chromosome specific (unique) DNA begin?

A

=most begin ~200-300 kb from the end of the chromosome.

71
Q

What are the characteristics of telomeres?

A
  1. Located at the end of the chromosomes
  2. Made up of a simple DNA sequence repeat
    - This is the substrate for telomerase (the enzyme that helps with telomere shortening)
  3. Impt for meiosis
    - synapsis of homologous chromosomes begins at the telomeres
  4. high gene density (high GC content, G-negative bands)
  5. shorten with age
  6. high rates of recombination, esp in males
72
Q

What is interphase? What are the 3 components?

A

Interphase=the resting state in the cell cycle (ie not undergoing mitosis)

3 parts:
1. G1 phase 
(interval between mitosis and replication)
2. S phase
DNA replication occurs; synthesis of RNA and proteins
3. G2 phase
interval between S phase and mitosis
DNA repair occurs
73
Q

What is the DNA content in a cell during G1 phase (hint #n, #c)

A

=2n, 2c

74
Q

During which part of Meiosis does the reduction division (from 46 -> 23 chromosomes) occur?

A

=meiosis I

-homologous chromosomes separate, each still with 2 sister chromatids

75
Q

When does recombination occur during meiosis?

A

=proprphase I or meiosis I

-crossing over events typically occur between sister chromatids of two homologous chromosomes

76
Q

Males vs females:

1) when does meiosis start?
2) when is it completed?

A

Males:

  • meiosis starts at puberty
  • completed every 2 months

Females:

  • Starts early in embryonic life
  • Complete only of fertilization of the ovum
77
Q

Males vs females:

1) what are the products of 1 complete meiosis cycle?

A

Males: 4 spermatids

Females: 1 ovum and 2 or 3 polar bodies (depending on whether the 2nd polar body divides again)

78
Q

What is the most common parent of origin for the extra chromosome in a trisomy?

A

=usually maternal in origin as a result of an M1 error (non-disjunction of homologous chromosomes)

79
Q

True or false: 45, X is mainly due to maternal non-disjunction.

A

=false–mainly due to paternal non-disjunction event

80
Q

True or false: meiotic non-disjunction events resulting in aneuploidy are associated with aberrant recombination events (too many or too few, too close to centromere or too distal)

A

=true

81
Q

What is the frequency of chromosomal abnormalities in spontaneous 1st trimester miscarriages?

A

=50%

82
Q

What is the frequency of chromosomal abnormalities in stillbirth or perinatal deaths?

A

=5%

83
Q

What is the frequency of chromosomal abnormalities in individuals with congenital anomalies with intellectual disability?

A

=23%

84
Q

What is the frequency of chromosomal abnormalities in individuals with congenital heart disease?

A

=13%

85
Q

What percent of couples with multiple spontaneous abortions will carry a balanced rearrangement?

A

=5%

86
Q

True or false: a couple who has a triploidy fetus (69, XXY) has an increased recurrence risk for future pregnancies.

A

=false!

87
Q

What is the most common cause of triploidy?

A

=dispermy (2/3 of cases)

88
Q

What percent of Down Syndrome is due to Trisomy 21 (ie a free trisomy)?

A

=95%,

the remaining 5% are the result of translocations or mosaicism

89
Q

True or false: the presence of a trisomy identified on microarray tells you the mechanism of the trisomy.

A

=false
-no information about mechanism, therefore karyotype needed to inform recurrence risk (ie if T21 due to robertsonian translocation)

90
Q

You are looking at a karyotype with the following translocation: t(2;8)(q33;q24.1). What does der(2) and der(8) mean?

A

=der(2)= the derivative (or resulting) chromosome from the translocation that has the #2 chromosome centromere

91
Q

In meiosis, the pairing of reciprocal translocations is called a _______, for a Robertsonian translocation it is a ___________.

A

reciprocal translocation= quadrivalent

Robertsonian translocation=trivalent

92
Q

True or false: the empirical risk for a trisomy for balanced reciprocal translocation or robertsonian translocation is greater than the theoretical risk.

A

False–reduced risk
Risk with balanced reciprocal translocation: 10-15%
Risk with robertsonian translocation for T21 varies based on whether male or female carrier of transloation:
male: 0-2%
female: 10-15%

93
Q

What is a marker chromosome?

A

=structurally abnormal chromosome unable to be identified in origin from karyotype
-use FISH or array to identify what material is on the marker chromosome -> then it is a derivative chromosome

94
Q

All of the following recurrent deletion/duplication disorders are due to unequal recombination in regions flanked by segmental duplications EXCEPT:

  1. Prader-Willi/Angelman syndrome
  2. Digeorge syndrome
  3. Cat eye syndrome
  4. Cri du chat syndrome
  5. Williams syndrome
A

=Cri du chat (idiopathic, variable breakpoints), also observed with 1p36 microdeletion

95
Q

True or false: X-inactivation is always non-random

A

False

  1. Structurally abnormal X chromosome
    - > structurally abnormal X is almost always inactivated
  2. X;autosome translocation
    - > if balance translocation, structurally normal X is almost always inactivated (b/c want to maintain expression of the autosome)
96
Q

Name 3 limitations of chromosomal microarray

A
  1. Cannot detect balanced abnormalities
  2. Cannot detect low lying mosaicism
  3. Does not provide information regarding location or mechanism of the copy number abnormality
97
Q

True or false: A chromosomal microarray shows Trisomy 21. You don’t need to obtain a karyotype.

A

False! Still need karyotype because you don’t know the mechanism of the T21 (have not excluded a robertsonian translocation).

98
Q

State the significance of each allele range for the CAG repeats in the HD gene for Huntington’s disease.

26 CAG repeats or less
27-25 CAG repeats
36-39 CAG repeats
40 or more CAG repeats

A

26 CAG repeats or less= normal allele

27-25 CAG repeats= intermediate
-not at risk for disease but b/c of instability could have a child with # of repeats in the disease range

36-39 CAG repeats=disease causing with reduced penetrance

40 or more CAG repeats= fully penetrant disease causing

99
Q

Where is the CAG repeat located within the HD gene?

a. near the promoter
b. intron
c. exon
d. 3’ UTR

A

c= located in the exon

100
Q

State the significance of each allele range for the CGG repeats in the FMR1 gene for Fragile X syndrome.

5-44 repeats
45-58 repeats
59-200 repeats
>200 repeats

A

5-44 repeats= normal FMR1 allele

45-58 repeats= intermediate/gray zone allele
◦Do not cause fragile X syndrome. However, about 14% of intermediate alleles are unstable and may expand into the premutation range when transmitted by the mother (but offspring not at risk for Fragile X because it doesn’t expand that much)

59-200 repeats= permutation carrier
increased risk for FXTAS and POI
Women permutation carriers have risk of Fragile X affected offspring (due to instability and repeat expansion)

> 200 repeats=disease causing

101
Q

Mutations in the ________ gene are associated with a rare inherited form of Parkinson’s disease.

A

=alpha synuclein

102
Q

True or false: epigenetic changes are permanent, heritable changes to the DNA.

A

False!

  1. Not permanent
  2. Not heritable

Genetics (16 decks)

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