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Genomics > Chromosome Abnormalities and Genomic Rearrangements > Flashcards

Chromosome Abnormalities and Genomic Rearrangements Flashcards

1
Q

Definition of aneuploidy

A

Wrong no of chromosomes

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2
Q

Definition of cytogenetics

A

Study of chromosomes (no, structure, deletions, duplications, instability)

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3
Q

Definition of non disjunction

A

Failure of sister chromatids/homologous chromosomes to separate during cell division

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4
Q

Definition of disomic

A

1+ chromosome doubled without having the whole genome doubled

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5
Q

Definition of nullsomic

A

1+ chromosome missing in isolation

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6
Q

Definition of anaphase lag

A

Chromosome/chromatid does not properly migrate during anaphase and daughter cells lose some genetic info

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7
Q

Definition of germ cell

A

Embryonic cell with the potential of developing into a gamete

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8
Q

Definition of trisomy rescue

A

1 copy of 3 chromosome copies lost => normal diploid chromosome

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9
Q

What is cytogenetics

What 5 factors are studied in particular

A

Study of chromosomes

  • no
  • structure
  • deletions
  • duplication
  • instability
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10
Q

What are the 3 main types of chromosome abnormalities

A

Chromosome rearrangements
Whole chromosome aneuploidy
Copy number imbalance

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11
Q

What are the techniques used to investigate chromosomes

  • 3 traditional cytogenetic techniques
  • 3 molecular cytogenetic techniques
A 
Traditional cytogenetics
-G banding
-FISH
-Breakage
Cell culture needed to collect metaphase cells
Molecular cytogenetics
-QF-PCR
-MLPA
-Array CGH
Tests done on DNA
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12
Q

What is whole chromosome aneuploidy
What does it cause
What 3 chromosomes are less affected and why

A

Arises from non disjunction at mitosis/meiosis

Large genomic imbalance => loss of pregnancy unless affected chromosome is gene poor (13, 18, 21)

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13
Q

What are the 2 outcomes of non disjunction in meiosis

A

2 disomic daughter cells

2 nullsomic daughter cells

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14
Q

Describe the effects of whole chromosome aneuploidy on the zygote

Disomic + Normal?
Nullsomic + Normal?
Disomic + Nullsomic?

A

Disomic + Normal => Trisomic conceptus

Nullsomic + Normal => Monosomic conceptus

Disomic + Nullsomic => Uniparental disomy

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15
Q

Describe mosaicism

What can happen when a 47 +21 undergoes mosaicism and why

A

Presence of 2+ cell populations with different genotypes in individual who has developed from a single fertilised egg

47 +21 => 47 +21 and 46

Can be due to

  • non disjunction
  • anaphase lag
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16
Q

What are the 3 locations of mosaicism and their properties

A

Somatic

  • results in abnormal phenotypes
  • phenotype can be ameliorated by a normal cell line

Gonadal

  • during formation of germ cells
  • normally only found after 2 pregancies with same ‘de novo abnormality’

CPM (confined placental mosaicism)

  • confined to extraembryonic tissue, not always detected
  • normal outcome/can compromise placental function/uniparental disomy after trisomy rescue
17
Q

What are the 4 types of chromosome rearrangements

A

Robertsonian translocation
Reciprocal translocation
Inversion
Intrachromosomal insertions

18
Q

What are Robertsonian translocations

  • What are the most common Robertsonian translocations
  • What are the consequenes of balanced carriers
  • What is the prevalence
A

Results from fusion of 2 acrocentric chromosomes (13, 14, 15, 21, 22)

Most common (13,14) and (14,21)

Balanced carriers phenotypically normal with reproductive risks

  • recurrent miscarriages
  • Patau or Downs
  • male infertility
19
Q

What are the 2 types of Robertsonian translocation in meiosis

A

Alternate segregation

  • Both acrocentric chromosomes go to 1 daughter cell
  • Robertsonian allele isolated in other daughter cell

Adjacent segregation

  • Each acrocentric chromosome goes to each daughter cell
  • Robertsonian allele passed on with 1 chromosome
20
Q

What are reciprocal translocations

  • what are the consequences of balanced carriers
  • what are the most common reciprocal translocations
  • what is the prevalence
A

Can be between any segments of any non homologous

Almost always unique to the family

Balanced carriers phenotypically normal with reproductive risks but dependent on size of translocated segments

  • infertility
  • miscarriage
  • child with congenital anomalies

Only 1 recurrent RT : 46XX t(11,22)(q23.3, q11.2)

Prevalence of 1 in 500

21
Q

What are the 3 types of reciprocal translocation in meiosis

  • types of carrier
  • amount of genetic material
A

Alternate segregation

  • Balanced carriers
  • correct amount of genetic material found in each daughter cell

Adjacent segregation

  • unbalanced carrier
  • each daughter cell has a reciprocal translocated chromosome
  • has duplicated section of a chromosome

3: 1 segregation
- unbalanced carrier
- 1 daughter cell has the correct no of 1 chromosome and missing 1 haploid chromosome
- other daughter cell has correct no of 1 chromosome and diploid chromosome

22
Q

What are the 2 types of chromosome inversions

A

Pericentric inversion
-inversion that involves centromere

Paracentric inversion
-inversion that doesnt involve centromere

23
Q

What is the function of G banding

A

Can see whether large sections are missing by comparing lengths of chromosomes

24
Q

Describe the process of FISH

What are the 3 uses

A

Denatured target DNA + denatured DNA probe with fluorescent marker => target DNA marked with fluorescent marker

  • subtelomere probes
  • mbanding
  • whole chromosome paints
25
Q

How would you interpret the ratios from QF-PCR

  • 2 different chromosomes
  • 2 homologous and 1 different chromosome (trisomy)
  • 3 different chromosomes (trisomy)
  • 2 homologous chromosomes
A

2 different chromosomes
-1:1 => disomy

2 homologous and 1 different chromosome (trisomy)
-2:1 => trisomy

3 different chromosomes (trisomy)
-1:1:1 => trisomy

2 homologous chromosomes
-1:1 OR 1:1:1 => a mystery

26
Q

Describe the potential outcomes of segmental copy number imbalance

A

Small segments of the genome are repeated

  • deletions of repeats
  • duplications/triplications
27
Q

What are microdeletion syndromes
How are they recognizable as syndromes
How does microdeletion arise

A

Submicroscopic chromosomal deletions that can’t be detected by G banding

Recognizable as syndromes due to low frequency of occurence

Unequal crossing over within low copy repeat due to genetic structure
=> 1 chromosome has a microduplication, other has a microdeletion

28
Q

Describe the method of array CGH

A

Array=many DNA probes attached to a glass slide that can bind to complementary sequences

Test DNA and reference DNA marked with different fluorescent markers

Oligonucleotide arrays often include 60000 probes

29
Q

How would you interpret the results of an array CGH

  • red
  • yellow
  • green
A

Red spot
-more test material than reference => duplication in patient genome

Yellow spot
-equal amounts of test and reference => same no of repeats

Green spots
-more reference material than test => deletion in patient genome

30
Q

What are the 4 uses of array CGH

A

Whole chromosome aneuploidy
Microdeletion/duplication syndromes
Subtelomere imbalance
Other regions of imbalance

31
Q

Describe the variation found between humans in CNV

A

We normally have many small CNV
Different CNV combinations => phenotypic variation between individuals
Many gene imbalances have unknown functions

32
Q

How would you ascertain the clinical consequences of a previously unreported imbalance

A

Inheritance

  • de novo => pathogenic
  • from affected parent => pathogenic
  • healthy parent => benign

No of genes
Specific gene content

33
Q

What are the issues with accidentally finding pathogenic imbalances

A

Raise anxiety in family
Extensive, expensive monitoring

Don’t miss an opportunity to make a difference in someones future

Genomics (17 decks)

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