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Semester 4 > MCBHD (Molecular & Cellular Basis of Heath + Disease) > Flashcards

MCBHD (Molecular & Cellular Basis of Heath + Disease) Flashcards

1
Q

CFTR - things that could go wrong

A
  • Cystic fibrosis transmembrane conductance regulator, one of the mutations in there (delta f) are the ones that could cause a mutation. There are also common variants within this that may change an amino acid but are still harmless.
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2
Q

what is an allele?

A

unique position (locus) in genome, single base to entire gene.

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3
Q

what is a mutation?

A
  • Changing of the structure of a gene, resulting in a variant form which may be transmitted to subsequent generations, caused by the alteration of single base units in DNA
  • Or the deletion, insertion, or rearrangement of larger sections of genes or chromosomes
  • So mutation = variation, may or may not be damaging
  • Introduces genetic variation, beneficial increases survival chances, neutral if no effect, harmful if decreases chance of survival.
  • Relates to biological/genetic fitness
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4
Q

what is a Common variant?

A
  • See lots of these types of variant in genome, and frequency of different alleles is high - population frequency is high. Ie proportion of chromosomes that carry each allele in the population.
  • Polymorphism: minor allele frequency >1%, rare polymorphism: MAF 1-5%, common polymorphism MAF >5%
  • All variants start off rare and then there are selection pressures that cause increases
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5
Q

Types of common genetic variant?

A
  • Single Nucleotide Polymorphisms (SNPs) ~17 million identified; ~3 million/genome
  • Microsatellites ~3% of the genome
  • Mini satellites (variable number of tandem repeats, VNTRS)
  • Copy Number Variants (CNVs) >2000 identified; ~100 per genome
  • Remember everyone has every variant, what may differ between individuals is the genotype
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6
Q

SNP: single nucleotide polymorphisms characteristics?

A
  • High freq: 1 every 300 nucelotides, about 17 millions SNPs identified in human genomes, generated by mismatch repair, during mitosis
  • Occur because of replication and “proof reading”
  • Polymerase has a proof reading ability - sometimes this does not work properly and you should usually have a mismatch repair system that pops the correct one, but this sometimes does not work.
  • Mis match repair system inserts the correct, complementary base. But this change can still produce a different product. Which is a single nucleotide polymorphism.
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7
Q

Single base substitution - what can happen?

A
  • Transition = purine to purine, or pyrimidine to pyrimidine
  • Transversion = purine to pyrimidine or pyrimidine to purine
  • Transitions more common than transversions
  • They all have an “rs” number - the unique flanking sequence are places where no one is identical.
  • 2 forms = frequency of alleles in population. One of them is the minor allele that occurs left often.
  • Lower frequency = more likely to be pathogenic than those at a higher frequency
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8
Q

Microsatellites

A
  • Do not affect a single base - there are regions that are highly specific.
  • Variable number of tandem repeats - varied sizes
  • Number of repeats varies between individuals
  • Total length of microsatellite sequence varies between individuals
  • “D” numbers = microsatellites. Naturally inherited like any other locus in the genome.
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9
Q

what is the Polymerase slippage model?

A
  • During replication, polymerase slippage and the subsequent reattachment may cause a bubble to form in the new strand, slippage is thought to happen in sections of DNA that have repeated patterns of bases, like CAG.
  • DNA repair mechanism then realign
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10
Q

Example of SNP causally associated with trait : MC1R

A
  • Helps control our pigmentation.
  • Melanocortin 1 receptor - binds alpha MSH –> eumelanin
  • Alpha MSH does not bind –> phaemelanin
  • Some SNPs tend towards lack of binding and therefore red hair, freckling, pale skin
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11
Q

Where microsatellites occur

A

98% non coding region = exonic
- Intronic or UTR
• May affect gene expression
- Intergenic

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12
Q

what is Copy number variation

A
  • Change in the copy number of a genomic region, due to duplication or deletion. About 12% genome = CNV.
  • 10kb up to 5000kb
  • Repeated / absent
  • Lost the C locus = therefore the copy number for the c locus is 1, copy number variant that shows variability between individuals. Could also get a duplication event when you have too many copies.
  • This can occur without causing disease sometimes.
  • Intergenic - but are quite large (more than 1kb) so typically affect 1+ genes (parts of genes)
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13
Q

what is Non allelic homologous recombination

A
  • Misaligning of the chromosomes, can align incorrectly and when there is crossing over there can be deletion on some areas of the chromosome and then duplication on other areas of the chromosome.
  • Therefore potential increase in the copy number
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14
Q

What are the types of variation (rare)

A
  • Mutn s: MAF
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15
Q

What are the types of variation (common)

A
  • See lots of each of these types throughout the genome
  • SNPs: MAF>1%; ~17 million identified; ~3 million/genome
  • Microsatellites ~3% of the genome
  • CNVs >2000 identified; ~100 per genome

Most common variants are neutral (in terms of seln ) Some common variants are pathogenic Some common variants are beneficial

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16
Q

what is Disease gene mapping?

A

Finding the gene that actually causes the disease when not working properly

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17
Q

give examples of Beneficial single base substitution.

A
  • IL23R gene = interleukin 23 receptor
  • G to A transition at nucleotide 1142
  • Freqy A = 2.3%
  • p.Arg381Gln, i.e. missense
  • Protects against Crohns disease
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18
Q

give examples of Pathogenic single base substitutions

A
  • Freqy of variant allele (A) varies widely between popn s; can be as high as 25% How is this possible?
  • Negative selection should keep allele freqy low!
  • Mutn occurred spread widely through mign (gene flow)
  • Maintained by heterozygote advantage (selection)
  • Freqy of disease allele high in popn s where malaria has been/is endemic
  • Heterozygotes protected from infection by Plasmodium falciparum
  • So:
    • Homozygotes AA may die from malaria
    • Homozygotes aa may die from SCD
    • Heterozygotes Aa protected from both malaria & SCD
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19
Q

SCD characteristics

A

• Auto rec, 2 copies of mutn needed to lead to disease
- 1 in 500 people are homozygous for mutn If A=healthy allele, a=mutn , then..
• Genotype of healthy individual = AA
• Genotype of carrier = Aa
• Genotype of SCD patient = aa
- Incidence ~ 1 in 500 What is the carrier freqy?
- If A=healthy allele, a=mutn , then..
- Genotype of SCD patient = aa = 1/500 = 0.002
- What do you need to get an aa?

Two gametes each with an a Two carriers conceiving a child together

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20
Q

what is the HWE Formula?

A
  • p + q = 1
  • p 2 + 2pq + q2 = 1

If we know, or can measure p and q, we can work out the frequency of the 3 possible genotypes in a population If we know, or can measure, the frequency of the 3 possible genotypes, we can work out the allele frequencies

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21
Q

what is Linkage disequilibrium?

A
  • Also known as allelic association
  • When alleles at 2(+) loci are found together more frequently than would be expected by chance
  • Relates to the study of populations

Combination of alleles = haplotype

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22
Q

what is Multifactorial disease?

A

Multifactorial Disease = Genetics + Environment

- Many genes are involved

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23
Q

What is the definition of a learning disability?

A
  • Significantly reduced ability to be able to understand new/complex information
    • To learn new skills (from mild to profound)
    • Reduced ability to cope independently
    • This starts before adulthood and has lasting effects on development
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24
Q

What are the causes of learning difficulties

A
  • Genetic causes mainly. Issues during pregnancy and birth:
    • Maternal infection
    • Teratogens (things that are taken during pregnancy that cause problems with fetal development)
    • Prematurity
    • Pre/peri/postnatal trauma
  • Incidents after birth
    • Serious illness, head injury, poor nutrition, toxin exposure
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25
Q

Give examples of cytogenetic abnormalities

A
  • Aneuploidy
  • Translocations (Robertsonian + Reciprocal)
  • Deletions and duplications
    • Trisomy 21 (Downs)
    • XO rather than X (Turners), in girls
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26
Q

What is an aneuploidy

A
  • Abnormality of chromosome number
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27
Q

describe Reciprocal translocations?

A
  • Involve any part of chromosome, exchange material between 2 chromosomes. Carrier is totally normal. This can result in offspring with unbalanced amount of the 2 chromosomes.
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28
Q

Describe the 22q11 microdeletion

A
  • This can be antenatally detected VSD, repaired at birth
  • Significant speech + language difficulties
  • Moderate learning difficulties
  • Cleft palate / nasal speech, congenital heart diesase, hypocalcaemia, mild to moderate learning difficulties, renal abnormalities
  • A.k.a -
    • Velocardiofacial, DiGeorge syndrome
    • 90% occurs De Novo
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29
Q

describe how you would do a microarray?

A

Ø Label the patient sample with fluorescent dye, colour X
Ø Label reference sample with fluorescent dye, colour Y
Ø Mix them together & apply to slide

Hybridisation

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30
Q

Describe tuberous sclerosis?

A
  • Due to sun exposure

Ø Adenoma sebaceum, Shagreen patch, Ungual Fibroma

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31
Q

Autosomal recessive - pedigree

Describe the effect of consanguity

A

The effect of consanguinity: there are 2 unaffected parents, that produce an affected child

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32
Q

Describe phenylketonuria

A
  • Rarely seen in grown children, would treat by avoiding food that contains phenylalanine
  • Development delay + behavioural and social issues
  • Seizures + hyperactivity
  • Growth retardation
  • Eczema
  • Microcephaly
  • Musty odor on breath, skin, urine
  • Fair skin + blue eyes
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33
Q

Describe fragile X syndrome

A

Ø 50% of all men with Learning disability
Ø High forehead, long ears + face, prominent jaw
Ø Macro-orchidism

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34
Q

Describe how we would test for single genes

A

Ø Sanger sequencing = still mainstay
Ø Next generation sequencing panels
Ø Whole exome and whole genome

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35
Q

explain Triplet repeat expansions

A
  • Hard for the machinery copying DNA to copy
  • It slips and adds more
  • Gene stops functioning over a certain threshold of repeats
  • Unstable / dynamic expansions, therefore can increase in size in next generation
  • Instability depends on the parent of origin
  • General correlation between the size of expansion and severity of the disorder.
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36
Q

Describe anticipation in myotonic dystrophy

A

Myotonic dystrophy:
Ø start to get facial weakness as you get to generations lower down
Ø Indent in the muscles when tapped
Ø Becomes neonatal in the next gen
Ø The number of repeats is increasing as you go down generations

This is seen in conditions like Huntingtons

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37
Q

What is imprinting?

A
  • Changes in epigenetic silencing.
  • The disease is present, even though there is no apparent cytogenetic/ molecular genetic abnormality

Certain parts of the genome are imprinted (methylated), importance of having both parents contribution

38
Q

Describe prader willi sydrome and how it arises

A

Ø Short stature, hypotonia, obesity, hypogonadism, learning disability
Ø Loss, of paternally expressed SNRPN + the adjacent genes
• 75% is due to deletion of paternal 15q11-13
• 25% due to Maternal Uniparental Disomy 15

2% abnormalities @ ICR

39
Q

Describe Angelman syndrome

A

Ø Epilepsy, severe learning disability, ataxia, happy effect, “happy puppet”
Ø Loss of maternally expressed UBE3A
• 70% maternal microdeletion of 15q11-13
• 5% paternal uniparental disomy
• 10% mutation in UBE3A
• 5% abnormalities of ICR

40
Q

Describe fetal alcohol syndrome

A

Ø Heavy alcohol exposure during pregnancy
Ø Loss of definition of upper lip

Severe learning difficulties

41
Q

What is fetal valproate syndrome?

A

Ø Valproate = anti seizure, taken in pregnancy to prevent seizures happening
• 5-15% risk, LD, behavioural difficulty, characteristic facial features

42
Q

Human genome is polymorphic - what does this mean?

A
  • Has many forms
  • There is allelic variation, copy number variant
  • Single nucleotide polymorphism, SNP
  • Microsatellites
  • Some polymorphisms = important, biologically or scientifically, as markers
43
Q

What are the principles of genetic linkage?

A

Ø Tendency for alleles @ neighbouring loci, to segregate together at meiosis. This is the phenomenon of genetic linkage
Ø Therefore, to be linked together, 2 loci must lie very close together
Ø Alleles that are at linked loci = haplotype

These mark chromosomal segments which can be tracked via pedigrees + populations

44
Q

What is the “phenomenon” of genetic linkage

A

There is the tendency for alleles at neighbouring loci, to segregate together at meiosis.

45
Q

Name for alleles at a linked loci?

A
  • Haplotype
46
Q

What is a haploytype?

A

These mark chromosomal segments which can be tracked via pedigrees + populations

47
Q

Describe linkage + linkage disequilibrium

A

Ø Lack of recombination = loci are close together

Ø Recombination = loci NOT close together

48
Q

What is linkage?

A

Ø Phenomenon of 2 loci, being close together

And therefore alleles on same chromosome being likely to be inherited together

49
Q

What is linkage disequilibrium

A

Ø When 2 alleles from different loci are co inherited more than would be expected by chance.

50
Q

describe Genetic markers, e.g. microsatellites

A
  • Microsatellites are di, tri, tetra nucleotide sequences with a variable number of repeats
  • Number of repeats is constant within an individual, and varies between individuals
  • Example: D16S466
51
Q

describe the Steps to detect microsatellites

A
  1. Isolate DNA from individuals to be studied
  2. Design primers specific to flanking sequence
  3. PCR amplification
  4. Gel electrophoresis
  5. Use fragment length to determine the # of repeats
52
Q

Microsatellite genotyping

A
  • PCR amplification of microsatellite region, genotype size of fragments on gel based system
  • Homozygotes = single band and heterozygotes = 2 bands

Do not care about the size of repeat for linkage

53
Q

explain what ADPKD is?

A
  • Autosomal dominant polycystic kidney disease
  • ~1 in 1000 people affected
  • Cysts may go unnoticed until early adulthood/family screening
  • Other problems: hypertension; brain aneurysms; polycystic liver Incurable ESRF: 40-50%
  • PKD1: chr 16p13.3 85% more severe ~1000 mutns
  • PKD2: chr 4q22.1 15% >300 mutn s
  • Genetic testing direct sequencing linkage analysis
54
Q

PKD1 or not? - how would you work this out?

A
  • Microsatellite analysis
    • Not sure if PKD1 or 2
    • MGPKD1 = microsatellites and they are linked to one another, and linked to the disease locus, to prove that they have PKD1 rather than PKD2 you can check to see if a particular haplottype is travelling with the disease locus,
    • Affected people get 1, 2 and disease causing allele
    This proves because of the cosegregation that this is where the disease causing mutation is. Proves which form of PKD it is, pre symptomatic diagnosis, done this genotyping and showing that they have that haplotype and go on to get the disease.
55
Q

ADPKD - genetic testing

A
  • Licensed for PGD
  • Pre-symptomatic testing family members Improve treatment - prove genetically who is who and check you are making the right selection.
  • Confirmation, PKD1/PKD2
  • Testing potential donors - do not wany donor to be a presymptomatic sufferer
  • We are analysing genetic markers to help find the disease gene.
  • If we look at just one marker, the chance it is linked is very small.

Need to look at hundreds of microsatellites: - along chromosomes - across the genome.

56
Q

How do we know if recombination has occurred

A

By observing inheritance of genetic markers and/or phenotypes!

57
Q

how would we do Measurement of linkage?

A
  • Linkage can be measured by means of a LOD score
  • LOD logarithm of the ODDS
  • LOD score >3 = evidence of linkage, approx equivalent to a 1 in 1000 chance - e.g. 3.5 would say that this is evidence that it is linked to marker.
  • LOD score of
58
Q

genetic markers variability - explain

A
  • NOT variable within an individual, and variable between individuals
59
Q

what happens if 2 genetic loci are close together

A
  • If 2 genetic loci are close together, they ARE likely to be linked
60
Q

Linkage vs linkage disequilibrium

A
  • Linkage refers to loci and families
  • A gene & a marker are linked because they are close together & within a family recombination is rarely seen
  • Within a family, a particular marker allele will segregate with disease
  • In another family, marker locus & disease gene locus still linked but diff marker alleles
61
Q

Pregnancy screening tests that can be done?

A
  • Hb Electrophoresis in all women (and their partners if from high risk ethnic background) + Ask about consanguinity.

Sickle cell disease, Beta-Thalassaemia
Routine booking- • Metabolic disorders- e.g. MCAD, G6PD
• Cystic Fibrosis, Huntington, Hypercholesterolemia
• consanguinity
• Any other genetic disorder in the family
- Ultrasound scans • Nuchal translucency/combined test at 11-13 weeks
• Detailed anomaly scan 20-23 weeks

62
Q

what does a 11/12 week scan look for in pregnancy?

A
  • Nuchal translucency (area behind the neck), now combined in some hospitals - looks at PAPA levels, beta HCG, maternal age - thickness is correlated with genetic disorders and problems during pregnancy.
  • Increased NT associated with: Downs, chromosomal abnormalities, congenital heart disease, other genetic syndromes

Increasing nuchal thickness = adverse outcome chances will increase

63
Q

what is NIPT (non invasive prenatal testing)

A
  • Test fetal DNA from the mother. Short frgments of cell free DNA from the mother and fetus circulate in the plasma
  • Single nucleotide polymorphisms used to distinguish maternal and fetal DNA - non invasive and simple blood test on mum. Literally just a blood test and this makes it lower risk.
    • Find things like fetal sexing, which is indicated for linked conditions eg duchenne. Available from about 9 weeks.
64
Q

what are the 16-20 week scan + ultrasound abnormalities?

A
  • Fetal sex determination, structural abnormalities are seen, congenital heart disease can be detected - baby is larger and this is much more detailed.
  • Isolated structural abnormalities, prognosis, management, associations
  • Multiple structural abnormalities - chromosomal, syndrome, teratogen
65
Q

Fetal chromosome analysis - karyotype [QF]

A
  • Gene dosing can tell you that you have more genetic material, comparatively
  • Picks up and quantifies between babies with trisomy and babies that do not have trisomy.
66
Q

Fetal chromosome analysis - karyotype [Array CGH]

A

Front line test to pick up things on the early scans of concern. Take patient sample, quantify. Compare and then do the same with the reference DNA

67
Q

Fetal single gene tests?

A
  • Looking for specific problems in the genes - where there is a known genetic condition in the family, eg the parent
  • Any couple with affected child and germline mosiacism is a risk
  • Autosomal recessive disorders
  • X linked disorder
    • Just because you test both parents does not make it de novo, could be germline mosaicism.
68
Q

Prenatal diagnosis - amniocentesis

A
  • More than 16 weeks, extraction of aminotic fluid. Biochemical diagnosis is possible, lower miscarriage risk (0.5-1%)

Taking amniotic fluid from around the baby and has a slightly lower miscarrige risk = most accurate reflection and least likely to get contamination from using this

69
Q

Prenatal diagnosis - Non invasive diagnosis

A
  • Harmony test looks for trisomies 13, 18, 21
70
Q

how would you do Prenatal diagnosis of a known disorder?

A
  • Depends how pregnant the person is. Relationship to affected person with genetic disease, mode of inheritance, previous child / pregnancy with sporadic genetic disorder is low risk - but not zero
71
Q

What are the genomic technologies for looking @ chromosomes?

A
  • Karyotype, FISH, QF-PCR, Array CGH
72
Q

What are the genomic technologies for looking @ DNA sequencing?

A
  • Single gene sequencing, gene panel sequencing, exome sequencing, whole genome sequencing, 100k genome project
73
Q

DNA characteristics?

A
  • Deoxyribonucleic acid, molecule that encodes the genetic instruction that is used in development and functioning of living organisms
  • Made up of 4 nucleotide bases, GCAT (guanine, cytosine, adenine, thymine)
74
Q

what are genes?

A

Section of genetic code. Can be translated into a protein

75
Q

what is DNA?

A
  • Molecule that contains human genetic code
76
Q

what are genes?

A
  • Instructions that tell the body how to grow, develop and function
  • Consists of sections of DNA. Cell translates these sections into proteins
  • About 20k genes in the human genome
  • There are 2 copies of most genes - one on each chromosome
77
Q

what is the human genome

A
  • Entire length of DNA that is contained in human cells
78
Q

explain Genetic variation in relation to the population

A
  • This is what makes us unique = there are polymorphisms, which is basis of evolution, and basis of disease. Caused by intrinsic errors in DNA replication and repair.

Caused by external factors

79
Q

What happens in cancer

A

Normal cells will divide and replicate their DNA before division

- DNA replication is complication and can lead to errors in the genes, ie a somatic mutation 
- Normal cells die when an error cannot be repaired 
- Cancer results when mutations accumulate, cell does not die and cell growth is uncontrolled

Combination of genetic, environmental and lifestyle factors

80
Q

When do mutations occur in cancer

A
  • Multifactorial / sporadic cancers
  • Somatic mutations - occurs after division of fertilised egg, only present in subset of cells, not inherited from a parent, occasionally passed to offspring.
  • Hereditary cancers
  • Germline mutations
    • Present in the fertilised egg, and in every cell in the body
    • Can be inherited from a parent, and passed to offspring.
81
Q

describe Sporadic cancers?

A
  • No increased risk of other cancers
  • Usually small increased risk to relatives
  • No genetic testing indicated
  • Normal clinical management for affected individuals
82
Q

describe Hereditary cancers?

A
  • High risks of recurrence/other associated cancers
  • High cancer risks in relatives
  • We can offer testing to at risk individuals
  • We can offer screening and preventative management to gene carriers

May alter treatment of affected individuals

83
Q

what are the Cancer susceptibility genes

A

Oncogenes, tumour suppressor genes, DNA repair genes

84
Q

What is Knudsons “2 hit hypothesis” in sporadic cancer

A
  • Mutations in tumour suppressor gene
  • Regulates cell growth
  • Both of mutations are somatic
85
Q

What is Knudsons “2 hit hypothesis” in hereditary cancer

A
  • One mutation is germline, one mutation is somatic
86
Q

what is Penetrance?

A
  • Not every person with germline mutation develops the disease, this is reduced penetrance
  • We can give risks of developing disease for given phenotype, based on family and population studies
  • There are unknown modifying factors
87
Q

Screening for BRCA carriers

A
  • Breast screening
    • MRI, mammograms
  • Ovarian screening
    • Unproven efficiency and not recommended.
  • Can do a risk reducing masectomy, which is most effective way of reducing risk
  • Can do risk reducing bilateral salpingo oophorectomy
  • Offered at age 40 or after a completed family - can give HRT under specialist guidance, only proven way to reduce ovarian cancer risk
88
Q

describe Hereditary non polyposis colorectal cancer syndrome (HNPCC)

A
  • Lynch syndrome
  • There are germline mutations in DNA mismatch repair genes
    • MLH1, MSH2, MSH6, PMS2
  • Hereditary predisposition to colorectal, ovarian, endometrial cancer

Plus gastric, pancreatic, hepatobiliary tract, urothelial and small intestine cancers

89
Q

explain how you would screen for HNPCC

A
  • Colonoscopies

- Discuss endometrial screening age 35+, and discuss option of risk reducing TAH/BSO from early 40s

90
Q

hereditary cancer syndromes: what is - Li-Fraumeni Syndrome (TP53 gene)

A

Adrenocortical, sarcomas, childhood, breast

Highly penetrant (70-90% chance of cancer)

Semester 4 (10 decks)

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