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GiM 2 > GiM 2 + Critical numbers > Flashcards

GiM 2 + Critical numbers Flashcards

1
Q

What kind of variable is Height?

A

Numeric continuous

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2
Q

What kind of variable is Sex?

A

Categorical nominal

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3
Q

What kind of variable is number of children?

A

Numeric discrete

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4
Q

What kind of variable is severity of symptoms eg. Absent, mild, severe

A

Categorical ordinal

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5
Q

What kind of variable is types of degree?

A

Categorical nominal

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6
Q

What graph is an appropriate way to visually display the frequency distribution of continuous variables?

A

Histograms

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7
Q

What is the statistical value below which half of the distribution lies

A

Median

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8
Q

What can standard deviation be loosely described as?

A

a measure of the average distance of all of the data values from the mean.
- A useful measure of spread when there is a large amount of data

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9
Q

What are the lower and upper quartile?

A

Lower quartile = the median of the lower half of the data

Upper quartile = the median of the upper half of the data

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10
Q

What method can you use if a gene is too big for PCR?

A

Southern blotting

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11
Q

Why is fragile X mutation in FMR1 unsuitable for PCR and what should you use instead?

A

fragile X mutation in FMR1 gene is repetitive tract of (CGG)n sequence

GC-rich regions are difficult to PCR!

use Southern blotting

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12
Q

Which variants in apo-lipoprotein E (APOE) confer increase in susceptibility to Alzheimer’s or a protective effect?

A
  • E4 haplotype confers increase in susceptibility

* E2 haplotype confers a protective effect

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13
Q

When is the non-disjunction of chromosomes most likely to occur?

A

Meiosis I (80-90%)

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14
Q

What risk to gametogenesis increases with maternal age?

A

Aneuploidy

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15
Q

What are the trisomies of Down’s, Edwards and Patau’s?

A

21, 18, 13

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16
Q

What is Turner’s syndrome?

A

45 X

Phenotypically female
Short stature, no puberty, infertility

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17
Q

What is Klinefelter’s syndrome?

A

47 XXY

Phenotypically male - mostly undiagnosed
May be infertily, hypogonadism, gynaecomastia
Adults may have long legs and arms

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18
Q

What are the three origins of triploidy?

A

Digyny - 2N (egg) + N (sperm)

Diplospermy - N (egg) + 2N (sperm)

Dispermy - 1 egg + 2 sperm

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19
Q

What does the maternal genome focus on in comparison to the paternal genome?

A

Maternal genome for foetus

Paternal genome for placenta

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20
Q

How does a molar pregnancy occur?

A

Haploid sperm fertilises an empty egg

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21
Q

What can mitotic non-disjunction cause in the early embryo?

A

Mosaicism

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22
Q

What are the two types of chromosomal translocations?

A

Reciprocal - break & exchange
5-10% phenotype risk and reproductive risk

Robertsonian- whole arm fusion, only on acrocentrics (13, 14, 15, 21, 22)
no phenotype risk but reproductive risk

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23
Q

What are the two types of chromosomal inversions?

A

2 breaks, rotation, then rejoining

Pericentric - beaks on either side of the centromere

Paracentric - inversion on one arm (one side of the centromere)

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24
Q

In what direction is DNA and RNA synthesised?

A

5’ - 3’

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25
Q

What is pseudogene?

A

Is from the same gene family as a functional gene but is mutated and no longer functional?

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26
Q

How are gene families created?

A

Duplication and Divergence

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27
Q

What are processed genes?

A

Intronless copies of other genes

mRNA undergoes Reverse transcription and reintegration

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28
Q

What is Alphoid DNA

A

A type of satellite DNA found at centromeres
171-bp repeat unit
Repeat unit sequence shows chromosome-specific sequence variation

29
Q

What is chromosome-specific alphoid DNA useful for?

A

identifying individual human chromosomes using probe hybridisation

30
Q

What may be missed by PCR-based screening methods if heterozygous?

A

Large insertions or deletions
eg. Duchenne muscular dystrophy (deletions)
Charcot-Marie-Tooth disease (duplication)

31
Q

Which nucleotide sequences signal the beginning and end of an intron?

A

GT = end of exon, beginning of intron

AG = end of intron, beginning of exon

32
Q

What are one third of point mutations caused by?

A

Hypermutability of CpG dinucleotides

  • Methylation
  • Deamination CG -> TG
  • Mismatched repair
33
Q

What trinucleotide repeat expansion is seen in Huntington’s disease and spinocerebellar ataxias?

A

Polyglutamine repeats (CAG)

34
Q

What trinucleotide repeat expansion is causative in Fragile X syndrome?

A

CGG repeat expansion
befor Fragile X mental retardation 1 (FMR1) gene on the X chromosome

Normal: n = 5 - 50
Unstable pre-mutation: n = 50 - 200
Full mutation: n > 200

35
Q

What syndrome is caused by a 22q11.2 deletion?

A

Di George syndrome
1 in 5,000

  • Congenital heart defects
  • Learning difficulties
36
Q

Describe Achondroplasia

A

Short stature
Rhizomelic limb shortening
Foramen magnum compression/ hydrocephalus

1 in 20,000
Autosomal dominant- often new mutation 80%
Risk increases with paternal age

37
Q

Describe Beckwith-Wiedemann syndrome

A 
1 in 10,000
Large tongue
Ear pits/ creases
Exomphalos
Hemihypertrophy
Neonatal hypoglycaemia
Increased risk of Wilms tumour (nephroblastoma)
38
Q

Describe Kabuki syndrome

A 
1 in 30,000
Persistent fetal finger pads (96%)
Learning difficulties
Congenital heart disease (50%)
Poor growth
Hearing impairment
Cleft palate
Premature breast development
39
Q

What are Blaschko’s lines and what may cause them?

A

Mosaicism

Hypo- &/ or hyper-pigmented patches

40
Q

What is Peutz-Jeghers syndrome?

A

Otherwise known as hereditary intestinal polyposis syndrome

41
Q

What is Treacher-Collins syndrome?

A 
1 in 50,000
Autosomal dominant
Very variable
Cleft palate
Hearing impairment
Downwards slanting eyes and absent cheekbones
42
Q

What is Waardenburg syndrome?

A 
1 in 250,000
Sensorineural hearing impairment
Iris heterochromia
Premature greying
White forelock
Areas of skin hypopigmentation
43
Q

What is William’s syndrome?

A

7q11 deletion

1 in 20,000
Elf like appearance
Learning difficulties
‘Cocktail party’ speech
Congenital heart disease
Hypercalcaemia
44
Q

What are three examples of whole genome testing?

A

G-banding
Next generation sequencing
Microarrays

45
Q

What are three examples of targeted genetic testing?

A

Fluorescent in situ hybridisation (FISH)
Multiplex ligation dependent probe amplification (MLPA)
QF-PCR and qPCR

46
Q

What are some applications of FISH

A 
Copy number imbalance
Aneuploidy
Confirmation/ clarification of G-banding
Confirmation of array CGH
Identifying specific abnormalities in cancer
47
Q

What are the advantages of array CGH?

A

Early diagnosis -1st line test, ”
High resolution = increased diagnostic hit rate
Greater accuracy of location/size of imbalances
Information on relevant genes

48
Q

What are the disadvantages of array CGH?

A
  • Dosage changes only – not balanced rearrangements or mutations
  • Low level mosaics not detected
  • Non-pathogenic & uncertain pathogenic changes detected
  • Needs good quality DNA
49
Q

What test is used for prenatal aneuploidy detection?

A

Quantitative fluorescent PCR (QF-PCR)
If abnormal then G-banding

DNA extraction from amniotic fluid or chorionc villi
PCR amplification – primers from chromosomes 13, 18, 21, X and Y
aneuploidy =>2 markers with abnormal dosage

50
Q

What is a Philadelphia chromosome and what is it seen in?

A

t(9;22) )(q34.1;q11.2).

Found in CML (also in some AML and ALL)

51
Q

How does a Philadelphia chromosome occur?

A

Reciprocal translocation between chromosomes 9 & 22,
Juxtaposition of BCR gene and ABL1 gene
Creates a fusion gene BCR-ABL1
Codes for a hybrid protein - a tyrosine kinase signalling protein that is “always on”
= uncontrolled cell division

52
Q

What are the clinical features of Angelman syndrome?

A

Facial dysmorphism:

  • Prognathism, wide mouth, drooling
  • Smiling/laughing appearance

Mental handicap:

  • Microcephaly
  • Absent speech

Seizure disorder
Ataxic, jerky movements
‘‘Happy Puppet children’’

53
Q

What are the clinical features of Prader-Willi syndrome?

A 
Infantile hypotonia: Feeding problems, Gross motor delay
Mental handicap
Male hypogenitalism/cryptorchidism
Small hands and feet
Hyperphagia - Obesity
Stereotypic behaviour
54
Q

What deletion is found in Angelman syndrome and Prader-Willi syndrome?

A

del 15(q11-q13)

Always de novo

55
Q

Loss of the paternal 15q11-13 contribution due to deletion or uniparental disomy (UPD)
will cause what?

A

Prader-Willi syndrome

56
Q

Loss of the maternal 15q11-13 contribution due to deletion or uniparental disomy (UPD)
will cause what?

A

Angelman syndrome

57
Q

What is the genomic imprinting of 11p15.5 in a normal child?

A

Maternal = No methylation

Paternal = methylated

Normal dosage of Insulin-like growth factor 2
– major fetal growth promoter

58
Q

What does hypomethylation of the paternal 11p15.5 cause?

A

Hypomethylation = decrease in Insulin-like growth factor 2

Russell-Silver syndrome

59
Q

What are the clinical features of Russell-Silver syndrome?

A

Growth retardation

  • Fetal (IUGR)
  • Persistent postnatal growth failure

Triangular face
- Brain size more preserved
Asymmetry
Sporadic occurrence

60
Q

What does hypermethylation of the maternal 11p15.5 cause?

A

Hypermethylation = increase in Insulin-like growth factor 2

Beckwith-Wiedemann syndrome

61
Q

Gene polymorphs in Thiopurine methyltransferase (TPMT) can cause what?

A

Reduces TPMT protein activity - TPMT inactivates certain drugs

Increases toxicity of: Azathioprine, 6-mercaptopurine, 6-thioguanine

62
Q

G>A mutation in mitochondrial gene MT-RNR1 which encodes for rRNA can increase the risk of what?

A

Mutation changes the structure of the rRNA to resemble E-coli rRNA

Aminoglycosides more likely to bind to patients rRNA
→ Accounts for 30% of tendency to aminoglycoside ototoxicity

63
Q

Genetic variation in CYP2C9 explains 50% of the variability of which drugs activity?

A

Warfarin

64
Q

What is protein is over expressed in 20% of breast cancers?

A

Human epidermal growth factor receptor 2 (HER2)

65
Q

What is Herceptin?

A

Trastuzumab

a monoclonal antibody to the HER2 receptor

66
Q

What are BRAF inhibitors used to treat?

A

Melanoma

50% of melanomas have a somatic mutation in the BRAF gene

67
Q

Huntington’s disease is caused by what?

A

an expansion of CAG repeats ≥ 40

in HTT gene at 4q16.3

68
Q

What effect does an increase in CAG repeats have on the Huntingtin protein?

A

Increased number of Glutamine amino acids
= polyglutamine (polyQ) expansion

Changes structure and causes protein to form aggregates

GiM 2 (1 decks)

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