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Genetics in Medicine > Cytogenetic basis of inheritance and techniques > Flashcards

Cytogenetic basis of inheritance and techniques Flashcards

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Biology 101 flashcards
1
Q

What is conventional cytogenetics?

A

-Metaphase chromosome analysis= G banding

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2
Q

What is molecular cytogenetics?

A
  • Cytogenetic analysis at all stages of cell cycle (DNA/in situ)
  • FISH, Microarray CGH, MLPA, Next generation sequencing, QF-PCR, qPCR
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3
Q

How do cytogenetic abnormalities produce an abnormal phenotype?

A
  • Dosage effect
  • Disruption of a gene
  • Effect due to the parental origin
  • Position effect
  • Unmasking of recessive disorder
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4
Q

Describe Trisomy 21

A
  • 1/700
  • 75% spont abort
  • Eyes: upwards slanting, brush field spots
  • Ears: abnormally shaped/low set
  • Tongue: protruding
  • brachycephalic, short neck
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5
Q

Describe Trisomy 21 in adults

A
  • Fertility: fem-normal males-infertile
  • Average life 55-68
  • Medical problems: alzheimer’s, hypothyroid, obesity, diabetes, hearing loss, seizures, inc risk of cancer
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6
Q

Describe Edwards Syndrome

A
  • Trisomy 18
  • 1/6000 livebirths 95% spont abort
  • Head: microcephaly, low set ears, micrognathia, cleft lip/palate
  • Hands&feet: clenched hands, overlapping fingers, rockerbottom feet
  • Low birth weight
  • Short sternum
  • Severe mental retardation
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7
Q

What organ malformations occur in trisomy 18?

A
  • Umbilical/inguinal hernia
  • Congenital heart disease (90%)
  • Congenital kidney abnormalities
  • Eye abnormalities (cataracts, micropthalmia)
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8
Q

Describe Patau Syndrome

A
  • Trisomy 13
  • 1/12000 livebirths (95% spont abort)
  • Small at birth
  • Mental retardation severe
  • Microcephaly/sloping forehead
  • Defects of brain-holoprosencephaly
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9
Q

Describe the trisomy 13 phenotype

A
  • Abnormal genitalia
  • Heart defects
  • Polydactyly & fingers flexed
  • Ears abnormal & low
  • Cleft lip/palate
  • Eyes-retina dysplasia
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10
Q

What are features of Turner’s syndrome?

A
  • Loss of ovarian function
  • No puberty
  • Infertility
  • Webbed neck
  • Swelling of hands/feet
  • Skeletal abnormalities (short)
  • IQ normal
  • Coarctation of aorta
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11
Q

Describe Klinefelter’s syndrome

A
  • Most undiagnosed
  • Identified through infertility/hypogonadism
  • Infertility
  • May lack secondary sexual characteristics
  • Testicular dysgenesis
  • 30-50% gynaecomastia
  • Normal growth in infants then accelerates
  • Adults long legs &arms
  • IQ normal
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12
Q

What types of duplications are there?

A
  • Direct gain= 2 copies of segment on another chromosome is exactly the same way
  • Indirect gain= 2 copies of segment of a chromosome one the same way the other inverted
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13
Q

What is a ring chromosome?

A

-Breakage occurs then ends of chromosome join to form circularisation

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14
Q

How is the whole genome tested and how is a targeted part of the genome tested?

A 
Whole= G-banding, microarray, next generation sequencing
Part= FISH, MLPA, qPCR/QF-PCR
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15
Q

What are the stages of G-banding?

A

1) Cell culture
2) Mitotic arrest
3) Hypotonic
4) Fixation
5) Trypsin & Leishman’s stain
6) Banding-AT & GC rich regions

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16
Q

What molecular cytogenetic techniques are there?

A

-FISH
-MLPA
-Array CGH
-Next generation sequencing
-qPCR
QF-PCR

17
Q

What is the process of FISH?

A

1) Labelling (fluorochrome)
2) Denaturation
3) Target and hybridisation
4) Visualisation 24hr by post-hybridisation washing
5) UV light

18
Q

What types of probes can be used?

A
  • Unique sequence
  • Centromeric
  • Paints
19
Q

What are the applications of FISH?

A
  • Copy number imbalance
  • Aneuploidy
  • Confirmation/clarification G-banding or array CGH
  • Identifying specific abnormalities in cancer
20
Q

What is copy number variation?

A

A DNA segment with a variable copy number (compared with a reference genome.-the number of copies of a particular gene varies for individuals)

21
Q

What are the consequences of a copy number?

A

-Disease susceptibility or resistance (autism or cancer)

22
Q

What happens in microarray CGH?

A
  • Genomic imbalances at high resolution so inc detection rates
  • Hybridise sample & control DNA to a microarray chip with 1000s of DNA spots
23
Q

What is required for microarray CGH?

A
  • 3ml blood in EDTA
  • Control DNA from same sex
  • 1-2ml lithium heparin blood for cell culture
24
Q

What patients are used for array CGH?

A
  • Dysmorphic infants
  • Moderate-severe learning & developmental disabilities
  • > 40 genomic disorders
25
Q

What are the advantages of array CGH?

A
  • Early diagnosis
  • Greater accuracy of location/size of imbalance
  • Information on relevant genes
  • High resolution
  • 1st line test reduces need for other tests
26
Q

What are disadvantages of array CGH?

A
  • Dosage changes only not balanced rearrangements/mutations
  • Low level mosaicism not detected
  • Non-pathogenic & uncertain pathogenic changes detected
  • Needs good quality DNA
27
Q

What is the process of next generation sequencing?

A

1) sequencing libraries generated by fragmenting genomic DNA & adaptor ligation (ligated DNA selected)
2) Cluster generation (attach DNA to flow cell & amplify)
3) Sequencing (extent strand)

28
Q

What is QF-PCR

A
  • PCR amplification of short tandem repeats using fluorescent primers
  • Product visualised & quantified as peak areas using automated DNA sequencer
29
Q

How is prenatal aneuploidy detected?

A
  • DNA extraction from amniotic fluid/ chorionic villi
  • PCR amplification (primers from chromosomes 13,18,21,X,Y)
  • Aneuploidy = >2 markers with abnormal dosage
30
Q

What does relative quantification compare?

A

Difference in concentration between patient sample & normal control assessed by 2 different primer sets. Expressed as a ratio relative to 1 deletion= 0.5 and duplication=1.5

31
Q

What are the applications of cytogenetics?

A
  • Diagnosis
  • Family studies
  • Assessing reproductive risks
  • Cancer management
32
Q

What is a Trivalent?

A

Forms a chain at anaphase- meiosis 1

33
Q

What types of prenatal diagnoses are available?

A
  • Amniocentesis
  • Chorionic villus biopsy
  • NIPT
34
Q

What is NIPT?

A
  • Non invasive prenatal testing
  • Maternal blood sample
  • Extract circulating free metal DNA
  • Assess aneuploidy of 13,18,21
  • Risk for aneuploidy-invasive test to confirm
  • Reduces no. of invasive tests
35
Q

What are indicators for prenatal diagnosis?

A
  • inc maternal age
  • Serum screen risk
  • Abnormal ultrasound scan
  • FH/previous chromosome abnormality

Genetics in Medicine (11 decks)

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