MCBHD (Molecular & Cellular Basis of Heath + Disease) Flashcards
CFTR - things that could go wrong
- 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.
what is an allele?
unique position (locus) in genome, single base to entire gene.
what is a mutation?
- 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
what is a Common variant?
- 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
Types of common genetic variant?
- 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
SNP: single nucleotide polymorphisms characteristics?
- 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.
Single base substitution - what can happen?
- 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
Microsatellites
- 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.
what is the Polymerase slippage model?
- 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
Example of SNP causally associated with trait : MC1R
- 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
Where microsatellites occur
98% non coding region = exonic
- Intronic or UTR
• May affect gene expression
- Intergenic
what is Copy number variation
- 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)
what is Non allelic homologous recombination
- 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
What are the types of variation (rare)
- Mutn s: MAF
What are the types of variation (common)
- 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
what is Disease gene mapping?
Finding the gene that actually causes the disease when not working properly
give examples of Beneficial single base substitution.
- 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
give examples of Pathogenic single base substitutions
- 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
SCD characteristics
• 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
what is the HWE Formula?
- 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
what is Linkage disequilibrium?
- 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
what is Multifactorial disease?
Multifactorial Disease = Genetics + Environment
- Many genes are involved
What is the definition of a learning disability?
- 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
What are the causes of learning difficulties
- 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
Give examples of cytogenetic abnormalities
- Aneuploidy
- Translocations (Robertsonian + Reciprocal)
- Deletions and duplications
• Trisomy 21 (Downs)
• XO rather than X (Turners), in girls
What is an aneuploidy
- Abnormality of chromosome number
describe Reciprocal translocations?
- 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.
Describe the 22q11 microdeletion
- 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
describe how you would do a microarray?
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
Describe tuberous sclerosis?
- Due to sun exposure
Ø Adenoma sebaceum, Shagreen patch, Ungual Fibroma
Autosomal recessive - pedigree
Describe the effect of consanguity
The effect of consanguinity: there are 2 unaffected parents, that produce an affected child
Describe phenylketonuria
- 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
Describe fragile X syndrome
Ø 50% of all men with Learning disability
Ø High forehead, long ears + face, prominent jaw
Ø Macro-orchidism
Describe how we would test for single genes
Ø Sanger sequencing = still mainstay
Ø Next generation sequencing panels
Ø Whole exome and whole genome
explain Triplet repeat expansions
- 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.
Describe anticipation in myotonic dystrophy
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