Mendelian Genetics Flashcards
Define the law of segregation
- Mendels first law
- Pairs of elements pen\alleles separated during gamete formation and combine at random during fertilisation.
Define the law of independence
- Mendels second law
- For 2 given alleles, the inheritance of one does not influence the inheritance of the other
Define the law of dominance
- For every pair of alleles, one is more likely to be expressed than the other
Characterise Autosomal recessive inheritance
- Affected individual has two faulty genes
- Manifests in homozygous state
- Parent of an affected child are obligate
carriers of the condition - Males and females are equally affected
- Affected individuals are not always present in each generation
Explain Pseudo-dominance
- When an autosomal recessive condition appears to be inherited in a autosomal dominant manner in a family .In two or more generations of a family
Explain common explanations for Pseudo-dominance
- High carrier frequency in the population
- Birth of an affected child to an affected
individual and a genetically related partner
or a partner from a population group with a
high carrier frequency of the condition
An example of pseudo-dominance in real life.
Oculocutaneous albinism
1. In SA we often see Black families having
affected individuals in several generations
2. OCA2gene on chromosome 15q21.3
3. Individuals of sub-Saharan African heritage have a common 2.7kb deletion
4. Carrier Frequency: 1 in 30
Locus heterogeneity
A single disorder caused by mutations in
genes at different chromosomal loci
What are double heterozygotes
- An individual may have 2 mutations at 2 loci but they will not be affected
- They are carriers of two recessive mutations
- Need to have 2 mutations in the same gene to have the condition.
Explain Compound heterozygosity
- The presence of two different mutant alleles at a particular gene locus, one on each chromosome of a pair
- Most individuals with recessive disease are
compound
Explain the founder effect
- A genetic condition may become common
within a population because all individuals are descended from a small number of ancestors, with one or more ancestor having had, or were carriers of the conditions.
Heterozygote advantage
- Resistance to certain diseases causes an
increase in frequency of carriers - Possession of 1 mutant allele is advantageous
under certain circumstances - Examples: sickle cell
Describe autosomal dominance
- Affected individual has one faulty and one
normal gene (manifests in the heterozygous
state) - With every pregnancy, an affected parent has
half (50%) chance of having an affect a child - Affected individuals tend to be present in
each generation
What is variable expression
Variation in phenotype (disease expression) among individuals with the same genotype. This can be dramatic among individuals in a family and variability is difficult to predict because mechanism is poorly understood.
Define incomplete penetrance
Penetrance is the proportion of individuals carrying a particular genetic variant that also express an associated trait.
Examples:
□HD = 100% penetrant
□HBOC = 80% penetrant
□Celiac disease = 10% penetrant
Explain when we will consider someone to have germline mosaicism.
▣Suspect if there are two or more affected siblings with
unaffected parents
▣May have no somatic effect
▣Not rare in dominant conditions
▣Influences recurrence risks and makes it har
Why does the cell undergo X-inactive
▣Two X chromosomes are Potentially toxic double dose of X-linked
genes
▣To correct this imbalance, individuals who are XX have evolved a unique mechanism of dosage compensation
Steps in X-inactivation
▣Each cell counts its number of X chromosomes
▣Random choice of one X to remain active (Xa)
▣Silencing the future inactive X (Xi)
□Involving the recruitment of many specialised factors, e.g. histone variants and chromatin
modifiers
▣The inactivated X chromosome then condenses into a compact structure called a Barr body, and it is stably maintained in a silent state
How does one X remain active?
▣Hypothesis: binding of an autosomally encoded ‘blocking factor’ complex to XIC
which prevents X chromosome from being inactivated.
▣Thought to be a limiting blocking factor & so once bound there is none available to provide ‘protection’ against inactivation for other X chromosome/s
Why do some females with sex chromosome aneuploidies have an
abnormal phenotype?
▣Not all of the X chromosome is inactivated
□Some genes on inactive X remain active (15-20%)
□Genes in pseudoautosomal region remain active (tip of
short arm)
Describe X-linked recessive inheritance
▣Males are affected (faulty gene on X
chromosome) and no back-up copy
▣Females are carriers or affected
Describe X-linked dominant inheritance
▣A single dose of mutant allele will affect
phenotype of female
▣Condition may be milder in females
▣Males are usually more severely affected
▣Condition can be lethal in males
Symptoms/ presentation Oculocutaneous albinism
• Lack of pigmentation
– Sun sensitivity
–1. Risk of skin cancers
• squamous and basal cell cancer
• Visual problems
– 2Melanin required for development of normal vision
• Misrouted optic tracts
• Foveal hypoplasia
– 3.Resultant nystagmus, strabismus, decreased visual acuity
• Intelligence: normal range
Correlation of albinism and skin cancer
- Lack of melanin in the skin - susceptible to skin cancer
- Most children with albinism as young as 10 in sub-Saharan Africa have some form of early-stage skin cancer
- Only 2% live beyond age 40y
- Many are not aware of the danger from the sun and how to protect themselves
- Access to sunscreen is limited or non-existent
The 4 most common types of albinism
OCA1- autosomal recessive -Locus TYR
OCA2(classic)-autosomal recessive -Locus OCA2
OCA3- autosomal recessive -Locus OCA2
OCA4- autosomal recessive - LOCUS TYRP1
Characterise OCA type 1
- Skin is white
- Hair is white
- Eyes light blue
- 50% of OCA in European
patients - very rare in black Africans
Characterise classic OCA type 2
- Slightly milder phenotype than OCA1
—Eyes are usually pigmented
(blue-gray or light brown)
—Straw-coloured hair, pigment
accumulates over time
—May develop patchy
pigmentation
– (freckles / ephelides) - Prevalence in black SA:
• 1 in 3 900
– 1 in 40 individuals are carriers
Characterise A sub-type of OCA2:
Brown OCA (BOCA)
- Light cream/brown skin colour
- Ability to tan
- Freckles
- Hair colour – light brown to ginger (hair is darker than the skin colour)
- Hazel or brown eye colour
- Eye involvement – may or may not be present
Characterise OCA3 / Rufous OCA
- Reddish-bronze skin colour
- Ginger coloured hair (lighter in colour than the skin)
- Eyes are blue or brown
- Visual anomalies mild
- Prevalence in southern Africa:
estimated 1 in 8500
Genetic testing for OCA (albiNism)
Diagnostic strategy:
–NGS for all of the 18 genes known to be involved in albinism
–Array-CGH to look for gross genomic rearrangements (dup/del)
•E.g.: Diagnostic Service for pigment disorders in Bordeaux, France
•N=640 patients over last 15 years
What are The 3 types of non-Mendelian disorder.
- Mitochondrial disorders
- Multi factorial disorders
- Epigenetic disorders
Define Mendelian inheritance
One gene/ factor controls one trait or phenotype.
Define polygenic inheritance
Two or more genes influence the expression of one trait or phenotype
Familial tendencies in multifactorial inheritance
- Do exist but less than single gene disorders
- No set pattern of inheritance
- Recurrence risk depends on the degree of relation to Proband
What are some principles of multifactorial inheritance
- Number of genes involved changes depending on the trait.
- Genes may differ among individuals (trait or disease)
- Environmental may modify gene expression.
- Gene expression can change over time
In polygenetic disorder Gene effects may be
- Additive
- Protective
- Synergistic
- Complex
In polygenetic disorder environmental effects may be
- Trigger
- Exacerbate
- Accelerate
- Protect
What does multifactorial inheritance look like on a pedigree ?
- Family members share a greater proportion of genetic information and environmental exposure.
- Therefore they will experience similar gene-gene and gene-environmental interactions
- Therefore disease may present similarly in family members.
What is a continuous trait
Results in a range of phenotypes between two extremes. The change in phenotype can be gradual.
What is a discontinuous trait
Result in a limited number of phenotypes with no intermediates but instead distinct groups.
What is genetic liability
- Collectively describes all of the genetic and environmental factors that contribute to the development of multifactorial disease.
- Can’t measure the liability of a single individual
- Can measure the liability of a group of people and its estimated based on the number of affected individuals within that group.
If someone develops a multifactorial disorder later in life, what does this mean.
Generally, the later in life a multifactorial disorder develops, the more dependent on environmental factors it is
What is heritability
A statistic that estimates the degree of variation in a phenotypic trait in a population that is due to genetic variation between individuals in that population.
If heritability = 0.0
Total variation is totally due to environmental contribution
If heritability = 1.0
Total variation is totally due to genetic contribution
What is concordance
If both twins share a trait or if a trait is absent in both twins then the there is concordance
What is discordance
If one twin expresses a trait and the other does not then there is discordance
Heritability does not indicate what proportion of a trait is determined by genes and what proportion is determined by the environment
- A heritability of 0.7 does not mean that thee trait is 70% caused by genetic factors and 30% caused by environmental factors.
- It means that 70% of the variability in the trait in a population is due to genetic differences among individuals within that population.
Why would we want to identify genes associated to multifactorial traits.
- Provides the ability to better predict who will develop disease
- Prospect of novel therapeutics and management
- Disease prevention
- Genomic medicine
Methods of identifying genetic variation in a population.
- Twin studies
- Adoption studies
- Sib-pair analysis
- Case control studies
- Association studies
What is the principle of GWAS
GWAS compare genetic markers across the genome to identify markers associated to a trait or disease. They typically involve a comparison between two large samples - one with a particular disease or trait (case group) and one without (control group)
Benefit of GWAS (6)
- Identified risk loci for a vast number of diseases and traits.
- Has led to the discovery of novel biological mechanism underlying disease
- Identify high risk individuals can improve disease detection/prevention/treatment
- Drug development
- Identify various used to determine drug selection and dosage, prevent adverse reactions
- Provide insight into ethnic variation of complex traits
Limitation of GWAS (7)
- GWAS loci typically have small effect sizes
- Need a large sample size to reach statistical significance
- GWAS can only explain a small portion of the estimates heritability of complex traits.
- Many associations map to non-coding regions of the genome- how do you interpret that ?
- Hypotheses about the underlying mechanism are typically required
- Cannot identify all genetic determinants of complex traits.
- Population stratification and cryptic relatedness
Function of mitochondria
- Well known role energy generation.
- Free radical generation and removal.
- Apoptosis
- Calcium homeostasis
- Steroid metabolism
The matrix of mitochondria contains how many copies of mtDNA.
2-10 DNA
How many genes are encoded by mitochondrial DNA.
- 37 genes
22 tRNA genes
2 for ribosomal RNA
13 for protein subunit
Clinical features of mitochondrial disease
- Given the critical functions of mitochondria dysfunction of the cause multisystem disease,that usually progresses over time.
- May affect any organ but especially those with high energy need. Eg brain,nerves, muscles and heart.
Primary causes of mitochondrial dysfunction
- Genetic basis in genes that related specifically to mitochondrial function..
- Due to pathogenic variants (mutations) in either gDNA or mtDNA.
- Occurs in 1 in 4500 people
Secondary causes of mitochondrial dysfunction
Secondary to other effects e.g toxins, medications
Difference between human gDNA and mtDNA copies per cell.
GDNA- 2 (in diploid cells)
MtDNA- numerous 10 copies per mitochondrion
Difference between human gDNA and mtDNA DNA replication.
GDNA- AT CELL DIVISION
Mt-DNA- ongoing
Difference between human gDNA and mtDNA recombination.
GDNA- yes
Mt-DNA- no
Difference between human gDNA and mtDNA mutation rate.
GDNA- very low
MtDNA- HIGHER
What does genetic variation in mitochondria mean for detecting ancestry.
- An mtDNA change may randomly occur once in 100 people.
- Variant will be passed from mother and child .
- Thus mtDNA differences slowly accumulate over the generations
- The number of mtDNA differences between 2 people indicates how long ago they share a female ancestor.
What are Mitochondrial haplotypes ?
Specific regions of mitochondrial DNA that cluster with other mitochondrial sequences to show the phylogenetic origins of maternal lineages.
Out of Africa hypothesis.
The subsequent out of africa hypothesis state that Homo sapiens first evolved in Africa, and these spread across the globe.
How mitochondrial holotypes prove the out of africa hypothesis.
- The greatest DNA diversity in mitochondrial genomes is in AFRICA
- The relationships between mitochondrial haplogroups suggest how they were transmitted around the globe.
- Mitochondrial eve was African
Correlation between gDNA vs mtDNA and age.
- Frequency of DEVELOPING gDNA DISEASES in from infancy to adulthood decreases.
- Frequency of DEVELOPING mfDNA DISEASES in from infancy to adulthood increases.
Features of mitochondrial inheritance in a pedigree.
- Both males and females affected.
- Transmitted by females, but not by males
Homoplasmy
If all mitochondrial copies in a person have the same DNA findings.
If a woman is homoplasmic for a pathogenic variant how will this affect her children?
- Then all her children will inherit that variant.
- If the condition has completely penetrance then all her offspring will be clinically affected.
Heteroplasmy
If a genetic variant arises in an individual, it typically affects only some of the many mitochondrial DNA copies.
Explain threshold effect during mitochondrial inheritance.
- Many mtDNA pathogenic variants only cause clinical manifestations when present in a given tissue at a sufficient Heteroplasmy level.
- In addition, a particular variant may cause different clinical features at different level of heteroplasmy.
Heteroplasmy level can vary greatly between different:
- Children of an affected woman
- Tissues of an affected person
Give an example of a mitochondrial variant and disorder.
The m.3243A>G variant is a pathogenic variant in mtDNA that was originally associated with a condition called MELAS syndrome.
What happens due to the m.3243A>G variant
- Occurs if a guanine instead of adenine is present at mtDNA base position 3243.
- Causes dysfunction of the MT-TL1 gene.
What are the features of MELAS
ME: Mitochondrial Encephalopathy (dementia)
LA: Lactic Acidosis (due to OXPHOS dysfunction)
S: stroke-like episode
What is the cause of large deletions or duplications of mtDNA
Deletion may arise sporadically, but the presence of multiple different deletions suggested e.g dysfunction of the POLG exonuclease
What is the cause depletion of the total amount mtDNA.
Depletion may occur secondary to medication toxicity e.g AZT, but may be due to dysfunction of gDNA genes involved in mtDNA synthesis and maintenance eg. POLG, MPV17.
Investigating Mitochondrial disease: approach
- Screening: biochemical investigations such as plasma lactate and pyruvate levels are relevant, but imperfect.
- Muscle biopsy histology and immunohistochemisty used to be mainstays of diagnosis.
Investigating mitochondrial disease: genomics
- Vey broad, and include both mtDNA and gDNA
- Be able to detect low level heteroplasmy
- Broad NGS methods lend themselves to this, but may need to be supplemented by specific quantitative methods.
Investigating mitochondrial disease: samples
- GDNA variants disorder can usually be successfully diagnosed by testing easily accessible tests. Eg. Blood or saliva
- MtDNA variants even if heteroplasmic may be detectable testing of blood or early morning urine if the genomic method is sensitive enough.
- However, heteroplasmy may require that symptomatic tissue be tested eg. Muscle biopsy.
How do mutations occur?
- Exogenous causes:
-chemical
-radiation
-pollution - Endogenous
-spontaneous
-replication and recombination errors
-repairs errors
What places in the genome are more mutated.
- Certain genes are seen to have higher mutation rate maybe due to size.
- Mitochondrial genes mutated at a much higher rate vs nuclear genes because of DNA repair mechanisms.
- Mutation hotspots such as repetitive DNA
What is a static variant
Do not change when passed to offspring
Example: point mutations
Deletion and insertion
Splice site mutations
What are dynamic variants
Have teh potential to change when passsed to offspring.
Example: triplet repeats
Haploinsufficiency
- For certain genes, loss of function of one allele doe produce a phenotype.
- 50% (half) the amount of protein product is not enough .
- Dominant inheritance is observed
Example of a disease caused by a deletion mutation.
Cystic fibrosis
C.1521_1523del,pPhe508del
Consequences of silent mutation
Usually no effect
Consequences of missense mutation
- Chemistry of amino acid
- Size amino acid
- Location of amino acid
Consequences of nonsense mutations
- No protein due to nonsense mediated decay
- Truncated protein
Consequences of splice site mutation
- Intron retention
- Exon skipping
Examples of multifactorial inheritance
- Talipes -club foot
- Cleft lip/palate
- Neural tube defect
4,. Psychiatric disorders
Characterise clubfoot
- Clubfoot is a birth defect where one or both feet are rotated inward and downward.
- Up to 50% o cases are bilateral
- Incidence of 2/1000 live births
- Male: Female 2:1
Causes of clubfoot
- Neurological/ Neuromuscular
- Chromosome condition
- Neural tube defect
- Environmental (oligohydramnios, twin pregnancy)
(77% of cases are isolated)
Clinical approach to finding out if club foot is genetic related or environmental (isolation)
- Ask for family history
- Check prenatal and medical history
- Is is unilateral or bilateral
- Check for other clinical features / abnormalities
- Check spine, brain and fetal movement
If the clubfoot is isolated, counsel on multifactorial inheritance.
- Reccurance risk -2-5% (empirical risk )
- Detectable on ultrasound scan
- Corrected with surgery/poinsettia casting
Causes of cleft lip/palate
- Neurological (holoprosencephaly)
- Chromosome condition
- Syndromic (Ad,AR,XL)
- Teratogenic
- Environmental
(Isolated 80%)
Clinical approach to finding out if cleft lip/palate is genetic related (isolated) or environmental
- Ask for family history
- Prenatal and medical history
- Clinical examination
Genes that increase susceptibility to CL/P
- Genome wide association studies have identified many loci and genes that confer susceptibility
- PVRL1,TBS22,IRF6
- IRF6 plays a substantial role with an attributable risk of 12%
Environmental factors that increase susceptibility to CL/P. (8)
- Smoking
- Maternal diabetes
- Obesity
- Anticonvulsant agents
- Alcohol
- Folic acid antagonist
- Corticosteroids
- Isotretinoin
Causes of neural tube defects
- Teratogenic
- Chromosomal
- Maternal obesity
- Maternal diabetes
- Folic acid deficiency
how do we manage the Recurrence risk 2-5%, for neural tube defects.
- Folate prevention
- 400 micrograms FA daily, one month pre-conception
- 5mg if previous child with NTD
- Fortified food
- Prevent >50% of NTDs
Genetic counselling for multifactorial conditions (6)
- Usually not about genetic testing
- Interpret family history
- Give empiric risk ranges when unsure
- Discuss appropriate risk factors
- Discuss appropriate management
- Discuss appropriate prevention
How do parents of affected (recessive diseases) child present. And what are some Exceptions
Clinically normally
Are obligate carriers
One normal, one faulty gene
Exceptions:
Rare
Non-paternity
Uniparental disomy
New mutations
Proposed mechanism that causes triple nucleotide repeats.
Due to repetitive nature of the DNA sequence ‘loop out’ structure may form during DNA replication while maintaining complementary base pairing between the parent strand and daughter strand being synthesised.
Explain what a threshold is in triplet nucleotide disease
Above a certain number, threshold value, the repeat becomes unstable and can expand.
Coding triplet repeat diseases
- Coding repeats are (CAG) repeats that code for repeat stretches of the amino acid glutamine (Q)
- These diseases are commonly referred to as polyglutamine disease
- Gain- of-function mutation , mutant protein has a Toxic effect.
Non-coding triplet repeat disorders.
- The non-coding triplet repeat diseases typically have large and variable repeat expansions that result in multiple tissue dysfunction or degeneration.
- CGG, GCC, GAA, CTG OR CAG
- Usually loss-of function mutation
Diseases with triple repeats in non coding regions.
- Fragile X syndrome (CGG)
- Fragile XE syndrome (GCC)
- Friedreich ataxia (GAA)
- Myotonic dystrophy (CTG)
- Spinocerebellar ataxia type 8 (CTG)
- Spinocerebellar ataxia type 12 (CAG)
Disease with (CAG) repeats in coding regions
- Spinobulbar muscular atrophy
2 huntingtons disease - Dentatorubral-pallidoluysian atrophy
- Spinocerebellar ataxia types 1,2,3,6,7 and 17
Why are repeats that are not a multiple of three not viable.
Trinucleotide repeat expansions usually in or near coding regions. If repeat were not multiple of three would cause Frameshift mutations - much more severe consequences of the protein.
What is anticipation
Increasing repeat size is correlated with decreasing age of onset or increasing disease severity in successive generations
Explain parent of origin effect
- Anticipation is often influenced by the gender of the transmitting parent:
- The likelihood an expansion will occur is based on the size of the permutation and wether the triplet repeat is inherited from the mother or thee father
Characterise Huntington’s disease
- HD gene is on chr 4p
- Huntingtin gene
- CAG repeats are in an exon-represented in the protein
- Autosomal dominant
- Death of nerve tissue in brain
Explain parent of origin effect using Huntington’s disease
- Parent of origin effect; more severe HD / juvenile HD is usually always inherited from the male parent
- Early—onset Huntington disease have revealed a significant increase in sperm trinucleotide repeat (CAG0 lengths compared with the repeat lengths of the father.
Predictive testing in Huntington disease , age of onset.
- The mean age of onset is 35 to 44 years- median survival time is 15 to 18 years after the onset of symptoms.
- Predictive molecular testing is available
What is fragile X syndrome
Observe a secondary constriction on the long arm of the X chr in several mentally retarded men, the fragile region (Xq27.3)
Characterise the autosomal dominant form of muscular dystrophy.
- Most common form of muscular dystrophy in adults
- Multi-systemic disorder affect skeletal and smooth muscle, eye, Heart, endocrine system and CNS.
Myotonic dystrophy genetics
- Myotonin protein kinase gene (DMPK) on Chr 19q13.3
- Trinucleotide repeat disorder (CTG repeat in 3’ untranslated region)
- Maternal origin of congenital form
Genetics of myotonic dystrophy 2 (DM2)
- ZNF9 gene
- CCTG repeat
- Similar clinical phenotype (classical)
- Rare
Techniques to detect myotonic dystrophy
- PCR: detect normal alleles (and repeats to -100)
- Triplet primed PCR (long range)
2.1 replace PCR/southern blot
2.2 size normal alleles
2.3 detect expansion
Define mosaicism
Mosaicism refers to the presence of two or more genetically different cell lines in one individual who has developed From a single fertilised egg.
What causes mosaicism
Mosaicism is caused when a mitotic mutation arise early in development. The resulting individual will be a mixture of cells, some with the mutation and some without the mutation.
What is trisomic mosaic and explain its mechanism.
- The most common form of mosaicism found through prenatal diagnosis involves trisomies.
- Mechanism: nondisjunction event during an early cell division in a normal embryo leads to a fraction of the cells with a trisomy.
- OR a trisomic embryo undergoes nondisjunction and some of the cells in the embryo revert to the normal chromosomal arrangement.
Explain what germline mosaicism
- Mutation confined to a portion of germ cells (ova and sperm)
- Mutations can be transmitted to offspring
Explain what somatic mosaicism
- Normal and abnormal cell lines within the cells of the body (may or may not include the (germline)
- Mutation cannot be transmitted to offspring unless present in the germline.
Germ-line mosaicism is typically seen in?
autosomal dominant or X-linked disorders.
Diagnosing mosaicism
- Cytogenetic analysis on blood can detect mosaicism- a percentage of cells will show the abnormal karyotype while the rest of the cells will show a normal karyotype.
- Sometimes more difficult -may need to look at different tissue.
What is a chimera
An organism carrying cell populations derived from two or more different zygotes of the same or different species.
What are the three haemoglobinopathies and what is its more of inheritance.
- Beta-thalassemia
- Sickle cell anaemia
- Alpha-thalassemia
Autosomal recessive inheritance
What does the geographical distribution of haemoglobinopathies tell you about.
- Distribution of haemoglobinopathies reflects endemic malaria areas.
- Heterozygotes have selective advantage against malaria.
Mutation that causes sickle cell anaemia.
- A-T at codon 6 of Beta-globin gene
- Glutamic acid (neg charge) to valine (uncharged )
- Causes abnormal haemoglobin folding
Characterise heterozygotes for sickle cell anaemia
- Asymptomatic
- Detectable on haemoglobin electrophoresis
Characterise homozygous for sickle cell anaemia
- Variable severity
- Present on first year of life
- Cells sickle with low oxygen tension
- Sludge in capillaries and block
Targeted gene therapy for thalassaemia
- Globin genes expression only in haemopoietic system.
- Stem-cell transplantation well developed from haemopoietic system
- But requires high level of gene expression and balanced expression
What is the principle of therapy for sickle cell anaemia.
- Increase HbF by activating gamma-globin gene.
- By turning on Gamma genes which are expressed in foetuses but turned off in adults.
- PROBLEM: potential risk to turn on many genes. Can we turn them off.
What are current sickle cell anaemia therapy
- DNA demethylation agents = hypomethylate the Y-globin genes
- Deacetylase inhibitors= increase Y-globin expression via histone acetylation
