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Main Topics > 1. Cytogenetics > Flashcards

1. Cytogenetics Flashcards

1
Q

History of cytogenetics: Tell me what is the order of discovery

A

Y, hypotonic, 46chr, tri21, phil in CML, banding methods, FISH, aCGH, copy number in normal pop, copy number from genome

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2
Q

In a clinial settings when do we order chromosomes? (5 points)

A
  • Rule out (T21, T13, T18, XXY)
  • Ambigouse genetila
  • Short stature (Turner synd, 45 X)
  • Cancer diagnosis or prognesis
  • Balanced rearengments (recurrent preg loss, inv/ins/trans, Rings
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3
Q

What are the limitations of karyotyping?

A

Resolution >5-10 Mbp gain/loss
breakpoints imprecise
requires dividing cells: tech difficult, T cells only, biased ell population

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4
Q

How frequent do we see different chr abnormality?
Spont abortion %? and what are the two most common chr abnormality in spon abortion?
still birth and prenatal birth
Live births % which includes: congenital anomaly and ID, Congenital hert disease, ID

A

Spont abortion 60%, Tri 16 (30%) and 45,X (20%)
still birth and prenatal birth 6%
Live births 0.6% which includes: congenital anomaly and ID 23%, Congenital hert disease 13%, ID 12%

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5
Q

What are the reasons for prenatal lethal abnormalities (no live births)?
In Tri21 what % are live births?

A

Triploid / Tetraploid & Tri16 -100% no live births
45,X and other Tri- >99% no live births - (all 45,X are mosaic)

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6
Q

What are the reasons for numerical chr abnormality?

A

Whole set- Errors in fertilization: Triploidy (dispermy or diploid gamete), Tetraploidy (Failiure of first division after fertilization)
single chr- Error in meiosis or mitosis: nondisjunction in meiosis (Trisomy or monosomy), nondisjunction in mitosis (mosaicism)

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7
Q
  1. What are the possible gametes from Meiosis I nondisjunction and parental origins?
  2. What are the possible gametes from Meiosis II nondisjunction and parental origins?
  3. How do we find the origin of nondijunction?
A

1/2 Tisomy, !/2 monosomy- both paternal and maternal
1/2 normal, 1 trisomy (one parent only with or without xover), 1 monosomy
DNA markers near centromier MII (proximal), near telomere MI (distal)

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8
Q

If a child is born with a partial deletion and partial duplication involving the same chromosome.
Which parental chromosomal abnormalities is most likely to lead to this occurrence?

A

pericentric inversion

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9
Q

What is optimal pairing during meiosis?

A

one chiasma per chromosome arm, or two per chromosome

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10
Q

Overall recombination rate is higher in males or females?
Near telomeres, recombination rate is higher in……
Recombination is suppressed near………., and increases greatly near ……… in both males and females (but more so in males)

A

Overall, recombination rates in human females are significantly higher (~50%) than males, except near telomeres, where male recombination rates are higher than female. Human recombination is about twice as high as that in mouse, perhaps due to our biarmed chromosomes compared to all telocentric chromosomes in mice (remember the obligatory 1 crossover per chromosome arm for stable pairing and segregation). Recombination is suppressed near centromeres, and increases greatly near telomeres in both males and females (but more so in males)

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11
Q

If a phenotypically normal individual is a carrier for a Robertsonian translocation between chromosomes 14 and 21, after adjacent segregation during meiosis I, which of the following possibilities is the most likely karyotypic outcome for this woman’s liveborn offspring?

What are the reproductive risk robertsonian carriers? Tri 13 and tri 21

A

Offspring with 1 copy of chromosome 14, 2 copies of chromosome 21 and a Robertsonian chromosome 14;21

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12
Q

What are the parental origin % of the following aneuploidies?
+21, +18, +16
XXX, XXY, X

A
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13
Q
  • Each metaphase chr is composed of 2 ……
  • Each…..bp of DNA is wrapped around one histone octamer (eight protein) which contains two of each 4 different unit called…,…,….,….,
  • Each histone octamer form a …… which is about …..nm
  • ….(H?) brings nucleosomes together to form a …… which contain…..(how many) nucleosomes per turn
  • Each solenoid is about…..nm
  • Solenoids further twisted into thicker loop domains which are attached to a non-histone protein scaffold at intervals of approx…….kb
A
  • sister chromatids
  • histones
  • H2A,H2B,H3,H4
  • nucleosome (beads on string), 10nm
  • H1, solenoid, 6
  • 30nm
  • 100 kb
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14
Q

What are the main types of repetitive DNA?
What is the other name for clustered?
What are the different types of dispersed rep DNA?
ALu is found in ….rich regions and Line is found in…..rich regions

A

Clustered and dispersed
satellite DNA (alpha)- Tandem arrays of a 171bp unit around centromere
Alu and Line
GC, AT

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15
Q

What are the 4 main stages of cell cycle?

A

Cell growth
DNA replication
Chromosome segregation
Cytoplasmic division

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16
Q

What are the stages of intrephase and which one is the longeset?

A
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17
Q

Cell cycle regulation includes many check points, where are the check points in the cell cycle?

A
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18
Q

In the spindle structure what are:
Centrosome
Kinetochore

A
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19
Q

What are n and c represent in the cell cyle?

A

*
n-number of sets of chromosomes (the ploidy state):
n tracks the total amount of information in the cell
c–total DNA content as measured by the number of chromatids in the cell
c tracks the total mass of DNA in the cell

n > number>ploidy c > content > chromatids

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20
Q

During mitosis what are the chr number (n) and contents (c) through out different stages?
G1
S
M
Cytokinesis

A
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21
Q

Mitosis is … round of DNA synthesis with…..round of cell division (how many)
Meiosis is … round of DNA synthesis with…..round of cell division (how many)

A

1 , 1
1 , 2 (meiosis I and II)

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22
Q

Meiotic products are non identical, what are the processes that lead to this?

A

Independent assortment: of maternal and paternal homologs = 2to the power of 23 possibilities.

Recombination: pairing and crossing over of homologous parental chromosomes

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23
Q

What stage does recombination happen in meiosis?

A

Prophase I

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24
Q

What are the different stages of meiosis prophase I

A

Let Ziggy Please Double Dip (LZPDD)

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25
Q

What are the number and content of chr at the:
Begining of meiosis I?
End of meiosis I?
End of meiosis II?

A

2n, 4c
1n, 2c
1n,1c

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26
Q

What are the main events in LZPDD of meiosis prophase I?
Leptotene:
Zygotene:
Pachytene:
Diplotene:
Diakinesis:

A

Leptotene: chr condense, align
Zygotene: Synapsis (formation of Synaptonemal complex (SC), Bivalents (paired homologs)
Pachytene: Bivalent chromosome, tetrad chromatids, and crossing over observed
Diplotene: Paired homologs start to repel (SC breaks down), but held together at chiasmata (sites of crossover)
Diakinesis: Chromosomes maximally condensed

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27
Q

When does sperrmatogenesis begin and when does it end?
When does oogenesis begin when does it arrest, complete and when does it end?

A

spermatogenesis begin at puberty and continues through adult life
oogenesis begin at fetal development, arrests in Diplotene(Prophase I) called dictyotene, completed at fertilization and ends at menoupause.

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28
Q

In oogenesis, when does MI completed and when does MII completed?

A

MI completed at ovulation and MII initiated (and paused at Metaphase)
MII completed at fertilization

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29
Q

…… oocytes present at birth, but only~…. will mature through ovulation (how many)

A

several million oocytes present at birth, but only~400 will mature through ovulation

30
Q

In spermatogenesis, recombination of X and Y occure in …..

A

pseudoautosomal regions
(PAR1 and PAR2) only

31
Q

Is this correct?
Spermatids differentiate into sperm without further division

A

yes

32
Q

What are different types of CNVs?
What are the underlying mechanism for each?
Give one example of each

A
33
Q

Name the classic microdeletion syndromes and underlying mechanisms?

A
34
Q

What are the genomic disorders due to recurrent microdel and their receprocal duplication?

A
35
Q

Recurrent microdeletions and their reciprocal microduplications are the result of which
molecular mechanism?

A

Non-allelic homologous recombination (NAHR)

36
Q

What are the mechanisms for Triploidy?

A
  1. Dispermy (66%): Two sperms fertilize one ovum
  2. Failure of one of the meiotic divisions, resulting in a diploid egg or sperm (34%):
    - In spermatogenesis (24%)
    - In oogenesis (10%)
37
Q

What are the different types of Triploidy?

A
38
Q

What are different types of Molar pregnencies?

A
39
Q

Balanced translocation chromosomes during meiosis form a…….. in the……..stage of the cell cycle

A

quadrivalent
pachytene

40
Q

In balanced translocation what are the most viable gametes?

A

Alternative and adjacent-1

41
Q

It is possible to predict segregation outcome in balanced translocation:

  • if translocated segments small:……..most likely
  • if centricsegments small:…….most likely
  • If one of the whole chromosomes of the quadrivalent is small in content (eg 13,18,21), ……. disjunction is the most likely
  • If the translocated and centric segments both are large:………
A
  • adjacent-1
  • adjacent-2
  • 3:1
  • no unbalanced segregation, all viable
42
Q

What is the most likely gamete in t(11;22)(q23;q11.2) and what is the zygote?

A
43
Q

What are possible gametes after insertion?

A

Normal, balanced, deletion, duplication

44
Q

What are the possible gamete of a parent with pericentric inversion?

A

Partial trisomy for one segments and partial monosomy for the other

45
Q

What are the possible gamete of a parent with paracentric inversion?

A

Theoritically not viable, offspring is either dicentric or acentric, hterefore if offspring survives it must be normal

46
Q

What are the two common inversions in the population? what type are they?

A

inv(9)(p12q13)
inv(2)(p11.2q13)
Pericentric

47
Q

How do we recognize ring chr abnormality on the microarray?

A

p and q telomere deletions on the same chromosome would point to the likelihood of 46,(r)

48
Q

What are the charactristics of genral ring syndrome?

A

Growth delay, mild to moderate cognetive impairment, minor dysmorphism and intact fertility

49
Q

What features are often seen in ring syndrome?

A

Café-au-lait spots

50
Q

Name the most common ring chromosome syndrome? which chr is involved?

A

Phelan McDermid syndrome, chr 22

51
Q

Very small rings/ supernumerary chromosomes are mitotically unstable, and this is likely the basis of the frequently observed………

A

mosaicism

52
Q

What type of chromosomes are major source of marker chromosomes? which chr is the most common?

A

80% are from acrocentrics: 13,14,15,21,22
15 is most common (40%)

53
Q

if a ring chr determined its origin should be identified:
If from X: what test do you do and why?
if from Y: what do you do and why?

A

X- FISH for XIST
Lack of XIST in a ring cause more severe phenotype (developmental disability)

Y- PCR or FISH for Y chr
due to risk of gonadoblastoma

54
Q

What is the most common cause of hypogonadism and infertility in male?

A

47,XXY (Klinefelter syndrome)

55
Q

With age we can see** loss of X chromosomes in females** (usually the inactive X) :
Found in ……… not in bone marrow
Mechanism 1: premature centromere division of X and loss is anaphase lag
Mechanism 2: Telomere shortening

With age we can see loss of Y chromosome in males:
Found more often in…….. than in blood

A

blood
bone marrow

56
Q

X;Autosome translocation
More severe in ……..than in ……
In females: if balanced inactivation of ………, if unbalanced inactivation of structurally …….. (del/dup/unb trns)

A

normal X
abnormal X

57
Q

In males …….. on chr 17 is primary testis inducing gene, SRY gene on Y chr initiates the process but other genes also get activated- disruption of the process that SRY starts leads to XY female.

A

SOX9

58
Q

What is the most common congenital adrenal hypoplasia (CAH)

A

21-hydroxylase deficiency

59
Q

In IVF five embryos are biopsied. The embryo with which of the following PGT-A karyotypes might be chosen for the transfer?
A. 47,XX, +15 / 46,XX
B. 47,XX, +16
C. 47, XX, + 18 / 46,XX
D. 47,XY, +2 / 46,XY
E. 47,XY,+22 / 46, XY

A

D
mosaicism in the early blastocyst is common, The smaller the chromosome, the greater the likelihood a conception could result in a liveborn with mosaicism with long-term complications .Similarly, for those chromosomes in which imprinting is a factor in development, the trisomic rescue to a disomic state increases the chance of uniparental disomy.

60
Q

Which of the following chromosome studies would most likely be detected in a phenotypically normal woman with infertility?
A. 46,XY
B. 45,X
C. 46,XX/45,X
D. 47,XXY
E. 47,XYY

A

C

61
Q

If both X are active, we can get severe…….

A

mental retadation

62
Q

What were the order of cytogenetic techniques as they discovered?

A

Y chromosome identified in humans >Hypotonic treatment of cells > Correct chromosome number is 46 > Chromosome banding techniques> Fragile sites and fragile X syndrome

63
Q

A balanced parental insertion can result is an offspring with:

balanced karyotype (…….)
unbalanced karyotype (……)

A

balanced karyotype (normal karyotype and balanced insertion)
unbalanced karyotype (interstitial deletion or duplication)

64
Q

What % mosaicism is picked by:
* G band
* FISH
* CMA

A

more than 20%
more than 5%
more than 20%

65
Q

In slide making what are the two major factors affecting chromosome spreading?

A
  • Ambient temperature 24-27 C
  • Humidity 50-60% humidity
66
Q

How do we age the slides?

A
  • room temperature: airtight container for 3 days/6 wks before G-banding
  • high temperature: Overnight at 60C, 2 hrs at 75C, 20 min at 90C
  • by chemicals: 15% H2O2 for 2-7 min, rinse and dry thoroughly
67
Q

What is good aging of slides result in?

A

better contrast and crispness

68
Q

If evaporate too slow and you see overspreading of chromosomes, increase…… in fixative

A

methanol

69
Q

What is the concentration of trypsin?
What should be the pH?
Temp of trypsin?

A
  • 0.01-0.02% diluted in Hanks, without Ca2+ and Mg3+ ions. These ions inactivate its enzymatic action.
  • Best is pH=7.0-7.2. Becomes inactive at 6.8. Too effectively at pH=8.5, too strong and cause fuzzy, distorted or uneven banding.
  • Optimum is 37C
70
Q

What is a Giasma mix of?

A

methylene blue and eosin stains

71
Q

What % of Giesma is prepared?

A

4% Giemsa stain prepared in a PO4 buffer

72
Q

In CVS sampling, which cells require culture and which cells do not require culture?

A

Mesodermal core: culture
Cytotrophoblas: direct (lower chance of MCC)

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