Genetics Flashcards
Causes of disease x 3
Genetic - Down syndrome, Huntington, Cystic Fibrosis etc
Multifactorial - Cleft lip, diabetes, Heart disease (due to a mix of genetic and environmental factors)
Environmental - Diet, Drugs, infection
Definitions: Genotype Phenotype Allele Polymorphism Homozygous Heterozygous Hemizygous
Genotype - genetic makeup of an individual
Phenotype - appearance/physical characteristics (mix of environment and genes)
Allele - Alternative form of a gene
Polymorphism - DNA sequence variation
Homozygous - both alleles the same
Heterozygous - alleles at the locus are different
Hemizygous - only 1 allele present at the locus
Classification of genetic diseases:
Chromosomal:
- change in the structure or number of chromosomes
Mendelian:
- disorder due to alteration in one gene - AD, AR, SD, SR
Non Mendelian:
- imprinting/epigenetics
- Mitochondria mutations
- Mosaicism
Mitochondria DNA
Ring of DNA used to produce proteins for the mitochondria
Mitochondria are mostly from your mum as many more fir in the egg cell - hence condition will be passed on via women
De novo mutation
A mutation that happens in the sperm or egg cell and can be passed on to offspring
Translocation chromosome variation
Chromosome breaks and a portion reattaches to another chromosome.
Reciprocal = no genetic material lost - not effect parent but may effect offspring
Robertsonian = long arms of 2 chromosomes fuse to form 1, short arm is lost and hence there is a loss of genetic material
Inversion chromosome variation
c/some breaks and a section joins reversed.
Paracentric doesn’t include the centromere
Pericentric does
Deletion chromosome variation
Deletion of a single base to a large piece of chromosome during DNA replication.
Interstital = in middle of the chromosome
Terminal = on the end
Duplication chromosome variation
Production of one or more copies of a gene, part or whole chromosomes.
Tandem = same way Inverted = added on in reverse
Ring chromosome
When the ends of a c/some becomes deleted the ends may join to form a ring.
Fragile site
Part of the chromosome that may break when exposed to partial replication stress.
Autosomal recessive inheritance
Only shown in heterozygous state
Male and female affected in equal proportions
Uncommon in pedigree with few individuals affected
To work out the risk factor of a baby having a genetic disease…
Chance carrier x chance carrier x risk of child affected if both carriers
Definitions: Autosome Allelic heterogeneity Consanguinity Autozygosity Penetrance Expressivity Anticipation
- Any chromosome other than the sex chromosomes
- Situation where different mutations result in the same genetic condition
- Reproductive union between 2 relatives
- Homozygosity by descent - inheritance of same allele through two branches of the family
- % of individuals with a specific genotype showing the expected phenotype
- Refers to the range of phenotypes expressed by a specific genotype
- Where by genetic disorder affects successive generations earlier and more serve - usually due to expansion of triplet repeat
Autosomal Dominant inheritance
Male and female affected in equal proportions
In multiple generations and more common than recessive
Somatic mosaicism
Genetic fault in some tissues of the body
E.g. cancer that develops only in some certain tissues.
Gonadal mutation
Genetic fault present in gonadal tissue
As it is present in germ cells it develops into all cells and hence can be passed on.
X linked inheritance
Usually only males affected
Not passed from males to males as X chromosome is responsible.
Lyonization
Generally only 1 of 2 chromosomes active in each female cell as only one lot of product is needed. Which cell is activated can be switched .
Mitochondria DNA
Mostly inherited from mother
Homoplasmy = a eukaryotic cell whose mitochondrial DNA copies are identical
Heteroplasmy = multiple copies of mtDNA in each cell, with only a proportion being affected by a mutation. Level of severity can vary.
Most Mt diseases are caused by DNA in the nucleus (85%)
Variant
Nucleotide sequence of the gene varies of that from from the normal population
Incidental/secondary findings
Additional findings concerning a patient that may or may not have potential health implications. They are discovered during the genetic test, but are beyond the aims of the original investigation.
E.g - non paternal discovery, risk of early onset of…
Important to have full conscientious before the investigation takes place
Sequencing DNA - Sanger
Uses PCR to amplify regions of interest followed by sequencing of products. Useful for a single gene test.
Time consuming and expensive, but very accurate
NGS - next generation sequencing
Massively parallel sequencing
Low cost per gene
Very fast
But less accurate and a huge about of raw data
Interpretation
Genes vary from Normal — variant of unknown significance — pathogenic variant
If the variant is unknown we can compare it to a healthy control population, check it against the healthy family members.
If a.a change is significant e.g charge polarity etc then we can predict the variation will be pathogenic.
Wild type variant
The normal variant
RNA sequencing
Can be used to analyse transcriptome and hence detect if a variant produces a non functioning protein and hence the severity of its impact.
Ideogram:
Diagram showing expected chromosome banding after G staining
How to produce a karyotype?
Take your sample e.g blood
Add PHA to culture medium to increase cell division
Incubate at 37C for 48 hours
Add colcemid - inhibit metaphase and this is when c/some are most clear
Add a hypotonic solution to make the chromosomes swell
Spread cells on to a slide
G stain the chromosomes to get banding
Karyotype
Arranges chromosomes in pairs 1 — 22
Longest to shortest with X and Y at the end
Numerical chromosome abnormalities:
Trisomy - gain of a whole chromosome (47, XX, +21)
Monosomy - loss of a whole chromosome
Polyploidy - gain of a whole set of chromsomes
Structural abnormalities
Translocation
Inversion
Duplication
Deletion
How do numerical chromosome abnormalities occur?
Non-disjunction can lead to gametes witch are monosomic or trisomic for a certain chromosome.
Common numerical chromosome conditions:
Down syndrome (+21) - facial features, LD, heart and digestive problems
Edwards syndrome (+18) - small head unable to walk - only 10% survive first year
Note many numerical chromosome babies do no survive to birth
Deletion on 15q leads to…
Prayer will I or Angelman
How does F.I.S.H work?
DNA is labelled with fluorescent probes which are hybridised to the chromosome. They attach to the target gene or section and hence if fluorescent then it shows the presence of that DNA fragments.
E.g when used for +21 each cell will have 3 fluorescent chromosomes showing presence of Down Syndrome
Also used to locate broken part of chromosome origin
Microarrays benefits?
Genetic testing technique that allows higher resolution and hence the detection of small deletions up to 1 Mb. Much higher than microscopy.
Cytogenetics?
The study of inheritance in relation to the structure and function of chromosomes.
Constitutional vs acquired abnormalities…
Constitutional = occur at gametogenesis, affects all cells of the body, heritable.
Acquired = changes occur during life, restricted to malignant tissue, not heritable
How do c/some abnormalities cause cancer?
They can cause cancer via:
Fusion - breakpoints occur within the two genes involved, fusion creates a hybrid which gives rise to a chimaeric protein.
Deregulation = juxtaposition of a gene to a regulating gene altered regulation can lead to an increased level of transcription.
Different types of variants:
Deletion - removal of nucleotide if not a multiple of three then it will result in a frame shift
Splice site variant - affects the accurate removal of intron/exons
Non-sense variant - substitution producing a stop codon, leading to a truncated protein
Mis-sense variant - single base substitution may not result in anew a.a due to the degenerate nature of the code.
Expansion of tri-nucleotide repeat - There are sections of the genetic code where everyone has a certain number/ range of repeats but once a threshold is reached then the repeat becomes pathogenic.
Examples of diseases with an expansion of a tri-nucleotide repeat:
Huntington’s disease - CAG
Fragile X - CGG
Heterogeneity meaning?
The state of being heterozygous
Diagnostic genetic test:
Patient has signs suggesting a disease, a genetic test will be used to confirm diagnosis.
Predictive testing…
Testing health at risk family members for a familial variant
Carrier testing
For x linked and autosomal recessive disorders carrier testing can be used to see if you are a carrier
Pre-natal test
Genetic test using placenta or amniotic fluid sample. Only done when there is a chance of a sever pathogenic variant as 1-2% chance of miscarriage.
PGD - Pre implantation gents diagnosis
Make an embryo
Extract DNA - test for the genetic variant
Implant healthy embryos into the uterus
Normal variant
Pathogenic variant
Benign variant
Allele of undetermined significance
Normal = age tic info which is present in 95% of the population
Pathogenic = variant that causes the disease
Benign = variant found in less than 5% of the population - rare - doesn’t cause pathogenic effects
Allele of undetermined significance = not enough information to determine if the variant is benign of pathogenic.
What is multifactorial inheritance?
Diseases due to an combination of genetic and environmental factors.
They are the most common types of diseases.
Risk greatest for 1st degree relatives then falls rapidly.
How do you identify that a condition has a genetic component?
Family studies
Twin studies
Adoption studies
How do family studies work when looking for multifactorial inheritance?
Compare the incidence of a disease amongst the family of an affected individual with the general population.
In the family the condition risk will be dramatically higher - genetic
And will vary depending on the degree of the genetic relationship
The risk will vary depending on the number of the family affected.
How do twin studies work when looking at multifactorial inheritance?
Compare genetically identical monozygotic twins with genetically non identical twins.
The concordance rate is the % of twin pairs studied that both have the condition. If genetic component you would expect the concordance rate to be higher in monozygotic than dizygotic twins.
Further showed genetic if still high risk even when monozygotic twins reared apart.
Adoption studies:
Adopted children with a parent with a multifactorial condition still have a high risk of developing the disease.
But the condition rate will still be higher in family’s where child has not be adopted also showing environmental factors play a role.
Heritability
The portion of the causes for a disease that is due to genetic factors rather than the environment.
Expressed as a % or between 1 and 0
Calculated from concordance rate in MZ
The liability model:
What does it show?
What is liability?
The factors that influence the development of a multifactorial condition, genetic and environmental can be considered as a single entity known a liability.
The liabilities for an individual form a continuous normal distribution curve
The curve for relatives is shifted to the tight.
A threshold exists above which a normal phenotype exists.
Past threshold is known as the population incidence.
How to know that part of the condition Is environmental?
Take a sample of patients and scope the whole genome for differences between their genes. Look for a SNP etc that is more common in the disease population.
I presume not everyone with the gene will have the condition and hence there must be an environmental factor to the condition.
Environmental factors that can affect multifactorial inheritance?
Drugs, alcohol, maternal infections — prenatal
Obesity — Type 2 diabetes
Pill, obesity, breast feeding — breast cancer
Smoking — lung cancer
Drugs — schizophrenia
What is eugenics?
The study of how to arrange reproduction in a population to increase occurrence of heritable characteristics regarded as desirable.
Positive eugenics = characteristics you want to increase
Negative eugenics = stop breeding
Genetic counselling =
The process by which patients or relatives at a risk of a genetic disorder that may be hereditable are advised on the consequences, probability of transmitting and the ways it may be prevented.
What is directive vs non directive genetic counselling?
Direct = family may not fully understand consequences, may expect to be told what to do, you may feel you have a duty to reduce disease frequency.
Non-direct = family may have extensive personal experience, decisions are personal to them, your aim is to help the individual.
Non-directive, non judgemental counselling is what you aim to do
What is a screening test?
Process of identifying people with an increased chance of a condition. Note someone who is screened positive may not have or develop the condition.
What is a diagnostic test?
Confirms whether the condition is present or not. May have screened positive before.
When does the foetus have full moral status?
After 24 weeks.
What is an invasive prenatal test?
Diagnostic test for prenatal conditions
2 types include, chronic villus sampling and amniocentesis.
CVS - at 10 weeks
Needles and/or probes are inserted into the uterus and the fluid collected is tested.
05-1% of a miscarriage.
amniocentesis = from 14 weeks
What is NIPT?
Non-invasive pre-natal testing
Circulating in the mother blood stream is foetal DNA from the placenta. Therefore you can take the mothers blood and analyse the foetal DNA with in.
Therefore you can check or prenatal conditions such as extra chromosome 21 material.
Positives and benefits of NIPT?
Less invasive prenatal tests and hence less miscarriages.
If the risk is 1/150 results in 91% confirmed diagnosis
Issues:
False positive may lead to termination of a “healthy” foetus
There may be an increased number of terminations
May lead to eugenics (social pressures of family and society)
What is PGD?
Pre-implantation genetic diagnosis
Eggs fertilised in vitro, embryos develop.
A few cells are then tested for genetic conditions and if non are found embryo can be planted into mother.
How Is PGD regulated?
It is regulated by human fertilisation and embryology authority
Also have to be licensed for IVF and PGD
Risk of serious condition > 10%
Female partner under 40 years
No living unaffected child
= expensive 12,000 and up to 3 cycles for the couple
Altering the germ line, example and ethical issues…
The germ line cells result in sperm and eggs cells. Alter the germ line and it will be passed on.
E.g mitochondria replacement therapy
The Mitochondria contains 37 genes.
Take the mothers egg and fathers sperm, just before they fuse transfer them to a new eggs cell with working mitochondria — forms a reconstructed zygote.
Nuclear DNA still intact, but are you sure the mitochondria genes are only involved in the mitochondria???
Why should altering the germ line not take place?
Genetic enhancement
Eugenics
Safety for future generations
