Molecular Genetics Flashcards
What are the phases of the cell cycle?
G1 phase
S phase
G2 phase
M phase
What is the G1 phase?
Growth phase
What is the S phase?
Synthetic phase
What is the G2 phase?
Growth phase 2
What is the M phase?
Mitosis phase
What happens to cells in the G0 phase?
Stimulated by growth factor, resulting in activation of transcription factors that lead to the initiation of DNA synthesis, followed by mitosis and cell division.
What happens in G1 phase?
Chromosones are prepared for replication.
What happens in synthetic phase?
46 chromosomes are duplicated into chromatids
When are chromosomes prepared for replication?
G1 phase
Which cells pause/freeze cycle temporarily and stay in G0?
Liver cells
Which cells stay in G0 indefinitely?
Neurons
What is the phase before a cell undergoes mitosis?
Interphase
What happens in interphase?
Replication of cellular genetic material and organelles to prepare for next division
What is the longest phase in the cell cycle?
INterphase
Which steps in the cell cycle constitute the interphase?
G0
G1
G2
S
Stages of mitosis?
Prophase
Metaphase
Anaphase
Telophase
What happens during prophase?
Condensation of chromatin to discrete chromosomes, breakdown of nuclear envelope and formation of spindles at opposite cellular poles
What happens during metaphase?
Alignment of chromosomes at metaphase plate
What is the metaphase plate?
Plane that is equidistant from two spindle poles
What is equatorial alignment
When chromosomes align at metaphase plate
What happens during anaphase?
Separation of paired chromosomes (sister chromatids) followed by migration to opposite ends of cells.
This separation preserves chromosomal numbers in daughter cells.
What happens during telophase?
Chromosomes are packed into distinct new nuclei in emerging daughter cells.
Cytokinesis (division of cytoplasm) also starts.
What can meiosis be divided into?
Meiosis I
Meiosis II
What is produced at the end of the meiotic process?
Four daughter cells
What do four daughter cells contain at the end of meioitc phase?
Each contains one half of the number of chromosomes as the parent cell
What is formed at the end of the mitotic phase?
Two daughter cells
What do the daughter cells contain at the end of mitotic process?
Each daughter cell has same number of chromosomes as parent.
What happens in Meiosis I?
Occurrence of synapsis in prolonged prophase phase and non-separation of sister chromatids during anaphase 1
What happens in Meiosis 2?
Same as normal mitosis
Structure of chromosome
Intranuclear structure
Contains one linear molecule of DNA
Why are human cells called diploids?
Contain 46 chromosomes, 23 from each parent
What type of chromosomes do human cells contain?
22 pairs of autosomes
2 sex chromosomes
What happens during gametogenesis to the chromosome?
Number of chromosomes is halved with meiosis that after conception the number of chromosomes remains the 2 same and not doubled.
What type of cells are gametes?
Haploid cells
Which is the largest chromosome?
Chromosome 1
What is a centromere?
Constriction in the chromosome which divides chromosome into short and long arm; p and q
What type of chromosome is a metacentric chromosome?
Metacentric; p and q are equal length
What is a acrocentric/submetacentric chromosome?
Centromere is at one end, so arms are of unequal length.
What is telocentric?
When centromere is at tail end of chromosome.
What is a holocentric chromosome?
Entire length of chromosome acts as centromere.
When types of chromosomes are not seen in humans?
Telocentric
Holocentric
What is an aneuploid cell?
When a cell possesses chromosomal numbers different from normal diploid status.
What type of chromosome results in sponataneous abortion?
Triploidy and tetraploidy
What failure results in triploidy/tetraploidy?
Non-disjunction - failure of chromosome/chromatid to separate in meiosis, with one gamete receiving two copies of that chromosome and the other no copies.
What is triosmic?
Extra chromosome - three copies of chromosome instead of two
What is monosomic?
One instead of two copies of chromosome.
Which children with Trisomy survive birth?
Trisomy 13, 18, 21
What results in a mosaic individual?
Non-disjunction occurring during mitosis immediately after two gametes have fused, leading to formation of two cell lineages, each with different chromosomal make-up.
What is a mosaic individual?
Exhibit milder malformations
What is Trisomy 21?
Downs
Rate of Downs?
1:700
Prominent findings in Downs?
Reduced maternal levels of alpha-fetoprotein
Increased beta-hCG
Increased nuchal fold thickness in fetal USS
Signs of Downs in children
Mental retardation Flat facial profile Prominent epicanthal folds Simian palmar crease Duodenal atresia Hypothyroidism Septum prim-type ASD due t endocardial cushion defects
Which diseases are more common in adults with Downs?
Alzheimers
Leukaemia
What is 95% of Downs attributed to?
Meiotic nondisjunction of homologous chromosomes, which is associated with advanced maternal age
What are 4% of Downs due to?
Robertsonian Translocation
What are 1% of Downs due to?
Downs mosaicism
Features of mosaic Downs?
Milder but similar features of Downs
What characterises Edwards syndrome?
Severe mental retardation Rocker bottom feet Low-set eats Micrognathia (small jaw) Congenital heart disease Clenched hands Prominent occiput
What causes Edwards Syndrome?
Trisomy 18
Frequency of occurrence of Edwards syndrome?
1:8000
When does death often occur in Edwards syndrome?
Within 1 year of birth
Which gender is Edwards syndrome more common in?
Three times more common in girls
Which syndrome is Trisomy 13?
Patau’s
Characteristics of Trisomy 13?
Severe mental retardation Microphthalmia Microcephaly Cleft lip/plate Coloboma eye Abnormal forebrain structures Polydactyly Congenital heart disease
Rate of occurrence of Patau’s?
1:6000
What is Trisomy X?
Metafemale
Features of Turners?
Low hairlind Broad chest Short stature Retrognathism Webbed neck
Cause of Turners in 80%?
Origin of aneuploidy is from paternal X chromosome, so Turners is of maternal origine
Occurene of Turners?
1:2000 live-born female infants
IQ profile of Turners?
Lower than general population by mean of 10 points (nearly one SD) due to reduced performance IQ
Verbal IQ preserved
When might females with Turners have higher verbal skills?
With 45X karyotype where X chromosome is paternally derived rather than maternal.
Where is genetic information stored?
DNA
What are DNA and RNA?
Nucleic acids
What are DNA and RNA composed of?
Nucleotides
What are nucleotides?
Phosphorylated versions of nucleosides.
What are nucleosides composed of?
Nitrogenous base
Pentose sugar
What is each strand of DNA made of?
Deoxyribose-phosphate backbone
Series of purine (adenine and guanine) and pyrimidine (thymine and cytosine) bases of nucleic acid
What types of nucleic acid are there in DNA?
Purine
Pyrimidine
What are the purine nucleic acids in DNA?
Adenine
Guanine
What are the pyrimidine nucleic acids in DNA?
Thymine
Cytosine
How is DNA measured?
Numbers of base-pairs.
What is each nucleotide in DNA joined to?
Sugar-phosphate unit
How are the two strands of DNA held together?
Hydrogen bonds between the bases
What types of nucleotide pairs are possible in DNA?
TA
AT
GC
CG
Difference between DNA and RNA?
RNA is single stranded in humans
DNA is double stranded
Define gene
Sub-portion of DNA
What does a gene contain?
Codes for a polypeptide sequence
What is a codon?
Three adjacent nucleotides
What does a codon do?
Codes for a specific amino acid
Initiates or terminates hpolypeptide chain synthesis
How many amino acids are there?
20
10 essential
What is an essential amino acid?
One that is not found in food and therefore must be synthesized
How many possible codons can make up the genetic code?
64
What is an exon?
Polypeptide coding sequences in DNA
What is an intron?
Non-coding dequence in DNA
Types of sequences in introns?
Satellite
Mini-satellite
Micro-satellite
When are introns removed?
Introns are removed from mRNA before it leaves the nucleus and starts protein synthesis.
What is replication?
Production of new DNA copies from template copies of DNA
What is the name of synthesis of RNA from nuclear DNA?
Transcription
Where does transcription take place?
Nucleus of cell
What is heterogenous nuclear RNA?
Transcripted RNA which contains junk sequences (introns) that do not code for polypeptides,
How does hnRNA transform into messenger RNA?
hnRNA undergoes splicing aided by nucleosomes in nucleus to remove introns
Where are transfer RNAs synthesized?
Synthesized from DNA in nucleus
What is translation?
Production of proteins from RNA
Where does translation take place?
On ribosomes where specific mRNA are involved, within the cytoplasm
What aids translation in cytoplasm?
Ribosomes
Where are ribosomes?
Attached to rough endoplasmic reticulum
What happens to tRNAs as they enter the cytoplasm?
Attached to specific aa according to codon sequence.
What is aa activation?
When specific aa are attached to tRNAs in the cytoplasm according to codon sequences
What catalyzes the aa activation?
Specific aa activating enzyme - aminoacyl-tRNA synthetase in presence of Mg2+
Separate enzyme for each aa
Where does the energy come from in making peptide bonds in protein translation?
Energy stored in activated aa is used
What do tRNAs with their aa bind to?
Sequentially bind to various sites along mRNA in zipper like fashion
What are the steps of translation?
Initiation
Elongation
Termination
Structure of ribosomes
Peptidyl P site where methionine-containing tRNA binds
Aminoacyl A site where each new incoming tRNAs with activated aa can bind
What happens in elongation in translation?
Aa are added in string like fashion to produce proteins
What happens in termination?
Chain termination is signaled by one of three codons; UAA, UGA, UAG
Which codons signal termination in translation?
UAA
UGA
UAG
What is modification?
Post-translational changes in a protein molecule before it becomes functionally active.
Purpose of post-translational modifications?
To transport synthesized proteins to appropriate cellular sites.
Where do modifications take place?
Endoplasmic reticulum
Golgi bodies
What does the golgi complex do?
Acts as temporary protein repository that gives off vesicles and vacuoles for further processing and transport.
What type of processes occur from vesicles sent from Golgi complex?
Covalent modifications
Protein folding
Tagging with signal peptides to dispatch to appropriate cellular destination
Which process is essential to tag wrongly folded/aberrant proteins for destruction?
Post-translational chemical modifications
Where does protein destruction occur?
Lysosome
What is transcriptomics?
Study of mRNA using microchip arrays
What do microsatellite tandem repeats give rise to?
Trinucleotide sequences
What do trinucleotide sequences result in?
Trinucleotide repeat disorders - non-Mendelian disorder
What do minisatellite introns lead to?
Telomeric repeats - needed for integrity of chromosome
Hypervariable repeat - used in DNA fingerprinting
What is a satellite?
Large series of simple repeats
What is a microsatellite?
Single, di or tri nucleotide repeats
What can introns be divided into?
Tandem repeats
Interspersed
What are tandem repeats divided into?
Satellite
Mini-satellite
Micro-satellite
What can interspersed introns be divided into?
Long interspersed and short interspersed nuclear elements
Define a mutation
Sudden, permanent and heritable change in DNA sequence
How does a mutation lead to disease?
Mutation in DNA will be transcripted to mRNA and then get translated into proteins leading to disease expression.
What is a point mutation?
Single-base alteration in DNA
What can lead to point mutations?
Substitution - one base replaced by another
Transition - if purine is replaced by another purine/pyrimidine with pyrimidine
Transversion - purine replaced by pyrimidine and vice versa
What is a frame shift mutation?
Deletion or insertion of bases is not in multiple of three codons, thereby leading to a shift in triplet reading frame.
What happens in frame mutation?
Changes in multiples of 3 bases, therefore no disturbance in actual reading frame
Types of effects of mutations on protein product
Silent
Mis-sense
Nonsense
What is a silent mutation?
No change in protein product
What is a mis-sense mutation
New mutant codon specifies a different aa with variable effects in final protein.
Give e.g. of mis-sense mutation
Haemophilia
Sickle cell anaemia
What happens in non-sense mutation?
New codon is either: UUA UGA UAG which signal stop to aa sequence, therefore nonfunctional protein
Which codons occur in non-sense mutation?
UUA
UGA
UAG
Why do point substitutions not shift reading frame?
Often occur in non-coding region, thereby go unnoticed
What is translocation?
Refers to exchange of chunks of genetic material from one chromosome to another
What are most translocations described as?
Reciprocal - one segment is exchanged for another segment among chromosomes
What is the Robertsonian translocation?
Non-reciprocal (unequal exchange) resulting in single fused chromosome from 2 acrocentric chromosomes.
What happens following a Robertsonian translocation?
Small p arms are discarded and metacentric fusion chromosome results.
Result of Robertsonian translocation?
From 2 chromosomes a single chromosome is formed with no significant loss of genetic material
What is unbalanced translocation?
Translocation in gametes.
What happens in unbalanced translocation?
Only one of two gametes can have whole translocated metacentric fusion chromosome, which results in monosomy for one gamete if fertilized and trisomy for the gamete dused with chromosome.
Location of transmission in DiGeorge?
22q11.2
Type of transmission of DiGeorge?
Autosomal dominant
Risk of DiGeorge to offspring?
50%
Risk of deletion of DiGeorge in parents?
5-10%
Risk of schizophrenia if offspring has deletion for DiGeorge?
25%
Features of DiGeorge?
Mild-moderate LD Facial deformities (cleft palate) Absent/malformed parathyroids leading to hypocalcaemia Broad nasal bridge Articulatory speech and swallow problems
MH problems in DiGeorge?
> 25% have psychosis
Location of transmission in Williams syndrome?
7q11 microdeletion
Features of Williams syndrome?
Hypercalcaemia at birth Supra valvular aortic stenosis Moderate LD Disinhibited disposition Speech appears superficially fluent Hyperacusis
Mode of transmission in Angelman syndrome?
Deletion of 15q11-13 maternally inherited
Features of Angelman syndrome?
Developmental delay Low IQ Jerky movements - especially hand flapping Frequent smiling Seizures
Transmission of Prader-Willi?
Deletion of 15q11-13 paternally inheritred
Features of Prader-Willi?
Obesity Short stature Small limbs Decreased IQ Hyperphagia and skin pricking
Transmission of Cri-du-chat?
Deletion of chromosome 5p
Which locus is responsible for phenotype in Cri-du-chat?
5pm15.2
Features of Cri-du-chat?
Feeding problems due to difficulty swallowing and sucking
Cat-like cry
Poorly developed facial features
First law of Mendelian inheritance?
Law of uniformity;
if two organisms that differ in one trait are crossed, resulting hybrid will be uniform in that trait (either or)
What is the second law of Mendelian inheritance?
Principle of segregation;
for any particular trait, the pair of alleles of each parent separate and only one allele passes from each parent to the offspring, based on chance.
What is the third law of Mendelian inheritance?
Principle of independent assortment;
different pairs of alleles are passed to offspring independent of each other, so new combinations of genes are possible.
What happens in autosomal dominant disorders?
Each cell contains two copies of all autosomes.
AD occurs when one of these copies has a mutation and the protein produced by normal form of gene cannot compensate - mutant allele is dominant.
What is a heterozygous individual?
One who has two different alleles of the same gene and will manifest the disease.
Recurrence risk if both parents are heterozygous?
75%
What is incomplete penetrance in AD?
If patient has dominant disorder but it does not manifest clinically.
What does incomplete penetrance increase risk of?
Having an unaffected child
What is variable expression in AD?
Differences in severity of disease expressed.
What types of diseases are due to spontaneous mutations?
Achondroplasia
Tuberous sclerosis
What is phenocopy?
When aberrant production of AD disorder w/o FH may be due to phenotypically indistinguishable disorder w/o genotype
E.g. of phenocopy
Antipsychotic medication causes patients to manifest same symptoms as those genetically determined by Parkinsons
Genotypically determined Pendred syndrome being mimicked by endemic cretinism
Which type of disorders are only manifest when an individual is homozygous for the disease allele?
Autosomal recessive
What does it mean to be homozygous for a disease allele?
Both chromosomes carry mutated gene
What does it mean to be heterozygous for the disease allele?
Unaffected but carriers of disease allele
What is skipping in genetics?
No FH but defective gene is passed through generations
When can offspring of a homozygous individual have the disease?
If both parents are carriers
If carriers of a diseased allele (heterozygous) have offspring, likelihood of offspring being homozygous?
1 in 4
If carriers of a diseased allele (heterozygous) have offspring, likelihood of offspring being heterozygous?
1 in 2
What increases risk of AR disorders?
Consanguinity
Who do males inherit an X chromosome from?
Mother
Who do males inherit Y chromosome from?
Father
Who do females inherit X chromosome from?
Each parent
What is X inactivation?
The fact that the Y chromosome contributes less genetic material to a mans genetic make up and therefore there must be a mechanism to simulate this deficiency in females to preserve natural equality
What is visualised thwen an X chromosome is inactivated?
Barr body in the nuclei of interphase cells
Does an inactivated X chromosome get transcripted?
No
Which females have two Barr bodies?
Trisomy X
How does X inactivation occur?
DNA methylation
What are X0linked recessive disorders?
Where a recessive disease-causing mutation occurs in the X chromosome of a man (as men only have one X)
Who is at risk of X-linked recessive disorders?
Men
What is unfavourable Lyonisation?
When during random X inactivation, most X chromosomes carrying normal alleles are inactivated
When can unfavourable Lyonisation lead to?
Females manifesting disease phenotypes - manifesting heterozygotes
Mode of transmission of Tuberous sclerosis
9q34/16p13
What type of inheritance is Tuberous sclerosis?
AD
Risk of Tuberous sclerosis?
1 in 30000
Features of Tuberous sclerosis
Adenona sebaceum Normal to severe MR (heart) Ash leaf macules Brain hamartomas Heart and kidney cysts
Mode of transmission of Treacher Collins
5q31
Type of inheritance of Treacher-Collins
AD
Risk of Treacher-Collins
1 in 40000
Features of Treacher Collins
Maxilla-mandibular hypoplasia
Malformed pinna
Down slanting palpebra
Mild to moderate MR
Location of transmission of Apert syndromee
5q31
Type of inheritance of Apert syndrome?
AD
Features of Apert syndrome?
Variable MR Cranio synostosis Shallow orbits Trapezoid mouth Mitten hands and feet
Type of transmission of Noonan syndrome
Chr 12
Inheritance of Noonan syndrome?
AD
Risk of Noonan syndrome?
1 in 1500
Features of Noonan syndrome?
Mild MR Short stature Nuchal oedema/webbed neck Pulmonary stenosis Cryptorchidism
Mode of transmission of Hurler syndrome
4p16
Inheritance of Hurler syndrome
ER
Risk of Hurler syndrome
1 in 100000
Features of Hurler syndrome
Deteriorating IQ after 2 years of age
Coarse facies
Clouded cornea
Joint stiffness
Mode of transmission of Lesch-Nyhan syndrome
Xq 26-27
Type of inheritance of Lesch-Nyhan syndrome
X linked recessive
Underlying cause of Lesch-Nyhan syndrome
Deficiency of enzyme hypoxanthine-guanine phosphoribosyltransferase
Features of Lesch-Nyhan syndrome
Poor muscle control
Moderate mental retardation - year 1
Self-mutilating behaviour - lip and finger biting
Hyperuricaemia and Hyperuricosuria (gout and kidney problems)
Which type of transmission is not seen in X linked inheritance?
Male to male
What happens if a male with an X-linked disorder mates with a homozygous female?
All daughters will be heterozygous carriers
All sons will be homozygous normal
What happens if a female who carries an X-linked inheritance mates with a normal male?
Half of sons will be affected
Half of daughters will be carriers
Give e.g. of X-linked inheritance
Haemophilia A/B
Duchenne Muscular Dystrophy
Androgen insensitivity syndrome
When is male to male transmission not seen?
X-linked recessive and dominant disorders
Why do females have twice as much chance to inherit X-linked disease-causing mutation?
Females have higher gene frequency for X chromosomes
E.g. of X-linked dominant disorder
Vitamin D resistant rickets
Retts syndrome
What is needed for a male and female to inherit an X-linked dominant disorder?
Heterozygous female for mutant gene
Males who have one copy of mutant gene on their X chromosome
What happens if a male with an X-linked dominant disorder mates with a homozygous normal female?
None of sons will be affected
All of daughters will be affected
What will happen if a female who is heterozygous for an X-linked dominant disorder mates a normal male?
50% of sons affected
50% of daughters affected
What type of inheritance is non-Mendelian?
Mitochondrial Mosaicism Trinucleotide expansions Genomic imprinting Polygenic and multifactorial disorders
Where is mitochondrial DNA inherited from?
Ovum
Where does the mitochondria of an embryo come from?
Mother
How many introns are in the mitochondrial chromosome?
None
Significance of mitochrondrial chromosome having no introns?
High chance of a mutation having an effect
What are most mitochondrial diseases?
Myopathies
Neuropathies
What do mitochondrial DNA abnormalities result in?
MELAS: Mitochondrial myopathy Encephelopathy Lactic acidosis Recurrent stroke syndrome Leber hereditary optic neuropathy
Commonest cause of blindness in young men?
Lebers hereditary optic neuropathy
Features of Leber’s hereditary optic neuropathy?
Bilateral loss of central vision
Cardiac arrhythmias
How is Leber’s hereditary optic neuropathy inherited?
Purely maternal
What does mitochondrial DNA code?
13 proteins involved in respiratory chain and
22 tRNAs and
2 ribosomal RNAs
How is Kearus-Sayre syndrome inherited?
Maternal (mitochondrial)
Features of Kearus-Sayre syndrome?
Ophthalmoplegia Heart block Cerebellar Ataxia Deafness Mental deficiency
What are trinucleotide repeat disorders?
Set of genetic disorders caused by trinucleotide repeats (codons) in certain genes exceeding normal number of repeats.
Mutation results in an unstable site.
What is anticipation?
Pattern of inheritance in which individuals in an earlier generation develop a disease at an earlier age and with greater severity than those of previous generations.
What causes anticipation?
Gradual expansion of trinucleotide repeat polymorphisms - instability is called dynamic mutation
Examples of Trinucleotide repeat disordesr
Fragile X
Friedreich Ataxia
Huntingtons
Myotonic dystrophy
Where is the mutation in Fragile X?
cGG
Where is the mutation in Friedreich?
gAA
Where is the mutation in Huntington?
CAg
Where is the mutation in myotonic dystrophy?
cTG
Frequency of Fragile X
1 in 4000
Which two conditions result in most cases of mental retardation in males?
Downs
Fragile X
Which gene results in Fragile X?
Expansion of CGG proximal to FMR1 gene
What is the relation between Fragile X and low IQ?
Being born with one FMR1 allele with 200 or more repeats results in lower I in men and 60% of women
Mild signs in women shown with Fragile X heteozygous females?
Early menopause
Mild LD
Features of Fragile X (male)
Enlarged testes Prominent ear lobes Protracting jaw High pitched voice Mental retardation
What are premutation carriers in Fragile X?
Those who carry increased number of CGG repeats in FMR1 locus but do not have clinical phenotype
What are premutant carriers of Fragile X at risk of?
Developing intention tremor and ataxia after middle taxia
What are women who are premutation carriers for Fragile X at risk of?
Premature ovarian failure
Mild cognitive/behavioural abnormalities
Fragile sites in Fragile X syndrome
FRAXA: first exon of FMR1
FRAXE - Xq28 - linked to mental retardation
FRAXF - sensitive to folate.
In which x-linked diseases are anticipation rates higher in maternal rather than paternal inheritance?
Myotonic dystrophy
Fragile X
Why do some x-linked disorders result in higher anticipation rates if maternal inheritance?
Because further trinucleotide expansion occurs during oogenesis.
Genetics of Huntingtons
AD
Full penetrance
Prevalnce of Huntingtons?
5 per 100000
What is the gene that causes Huntingtons?
Expanded and unstable CAG trinucleotide repeat on short arm of chromosome 4-4p16.3 resulting in translation of extended flutamine sequence in huntingtin - protein product of gene.
Onset of Huntingtons?
30-50 years of ago
Which genetics leads to childhood onset of Huntingtons?
> 70 repeats of CAG expansion
Is paternal or maternal inheritance related to anticipation of Huntingtons?
Paternal
What is characteristic of Huntingtons?
Characteristic protein deposits form nuclear inclusions in neurons in HD patients
What is the underlying cause of Myotonic dystrophy?
CTG repeats are expanded.
What causes anticipation of Myotonic dystrophy?
Trinucleotide instability is higher if inherited expansion comes from mother, as oogenesis, due to long dormancy, results in higher instability.
Which genetic cause leads to Prader-Willi syndrome if paternally inherited?
Deletion of part of long arm of chromosome 15 - 15q11-q13
The maternal chromosome of this is expressed in hypothalamus leading to neuronal damage in its absence.
What causes genomic imprinting?
DNA methylation
What is genomic imprinting?
Where the disease phenotype expressed depends on whether allele is maternally or paternally intherited.
What is maternal uniparental disomy?
When both copies are inherited from mother when embryo is formed
What is quasi-continuous in genetics?
Patients affected with the genes are affected along a continuum.
What is the liability/threshold model?
In disorders in which there is an underlying liability to develop disorder which is continuously distributed in the population, those who pass a certain thresfold manifest the condition.
What is polygenic inheritance?
Where multiple genes are involved but environmental factors are not.
What is polymorphism?
Variations in genetic make-up at a particular locus noted in the healthy population - at least in 1% of population.
E.g. of polymorphism
ABO blood grou[
What is a restriction fragment length polymorphism?
Variations that change sites at which restriction enzymes can act as DNA molecule, rendering differences in final cleaved DNA when enzymes are applied in vitro.
What are single nucleotide polymorphisms?
If polymorphism is to due to change in single nucleotide in a sequence.
How can single based polymorphisms be assayed?
DNA sequencing
DNA chips
What are length polymorphinsm?
Variations due to changes in length of genetic sequence
What are variable number of tandem repeats?
Polymorphism due to varying number of repeats in specific region of chromosome.
How are variable number of tandem repeats classified?
Short tandem repeat polymorphism
Microsatellite (2-6 bases)
Minisatelle (20-bases)
Why are microsatellite tandem repeat polymorphisms used as genetic markers in disease mapping?
They can be detected using PCR
How are polymorphisms mantained in the general population?
Founder effect
Genetic drift
Natural selection
Where do most polymorphisms occur in a gene?
Introns
What are seretonin transporter polymorphisms?
Noted in promoter regions - non-coding part od DNA (5HTTLPR).
What % of Europeans carry the long allele of 5HTTLPR?
55%
Features of those with short allele of 5HTTLPR?
Low expression of serotonin transporter
What is short variant of 5HTTLPR speculated to be linked to?
Higher incidence of affective disorders, neuroticism, anxiety and PTSD
What are the three types of blotting techniques?
Southern
Western
Northern
When is southern blotting used?
For detecting specific sequence of DNA
When is western blotting used?
Detection of specific protein after electrophoresis.
When is northern blotting used?
Detection method for specific RNA after electrophoresis.
What does PCR do?
Amplifies minute amounts of DNA, allowing further analysis
Which part of the DNA is amplified in PCR?
The DNA between two short single-stranded DNA fragments called oligonucleotide primers which are complementary to the sequences at each end of the DNA of interest.
What happens in step 1 of PCR?
Double stranded genomic DNA is denatured by heart into single-stranded DNA.
Reaction is then cooled to favour DNA annealing and primers bind to their target DNA.
What happens in step 2 of PCR?
DNA polymerase is used to extend primers in opposite directions using the target DNA as a template.
After one cycle there are 2 copies of the dsDNA.
After 2 cycles there are 4 copies etc.
What happens in step 3 of PCR?
Cycling is set to produce necessary number of amplifications
What is fluorescent in situ hybridisation used for?
To detect and localize specific DNA sequences in chromosome.
How does fluoroscent in situ hybridisation work?
Uses fluorescent probes that bind to only those parts of chromosome with which probes have high degree of sequence similarity.
What is a plasmid?
Bacterial DNA
Extra chromosomal
Independently replicating
What happens in DNA cloning?
Particular DNA fragment of interest is isolated and inserted using DNA ligase enzyme into genome of self-replicating plasmid, then called a vector i.e. used for DNA replication.
This allows replication of vectors and clone.
What is concordance?
When both twins have same disease expression.
What is discordance?
When one twin harbours a disease while the other does not.
What would you expect in twin studies if a trat has no genetic basis?
Equivalent concordance rates in MZ and DZ twins.
How is the relative influence of genetic factors in defining the variance in a trait expressed?
Heritability
What is narrow-sense heritability?
Proportion of total phenotypic variance attributable to additive genetic variance
What is broad-sense heritability?
When heritability is used to describe the proportion of variation explained by total genetic variance - additive and non-additive.
What are non-additive genetic influences?
Phenomena such as epistasis (gene-gene interaction) and dominance effects where presence of one gene mitigates the effect of the other
What does high heritability mean?
Most of the variation observed in population is caused by variation in genotypes
In which type of heritability is a phenotype a good predictor of genotype?
High heritability
What does heritability of 80% mean for the individual?
That 80% of variability in in whether an individual becomes affected is inherited.
Heritability estimate of schizophrenia
80
Heritability estimate of bipolar
> 80
Heritability estimate of major depression
40
Heritability estimate of generalized anxiety
30
Heritability estimated of panic disorder
40
Heritability estimate of phoba
35
Heritability estimate of EtOH dependence
60
What is the Hardy Weinberg equilibrium based on?
The principle that in the absence of mutation, non-random mating, selection and genetic drift, the genetic constitution of the population remains the same between generations.
What does the Hardy Weinberg equilibrium determine?
The frequency of an abnormal gene or genotype in the population.
Describe the components of the Hardy Weinberg equilibrium
p = frequency of normal gene
q = frequency of abnormal gene
p squared = frequency of normal homozygote
q squared = frequency of affected abnormal homozygote
2pq = carrier frequency
p+q = 1
What is genetic drift?
Gene frequency change caused by limitations in population size.
What is gene flow?
Exchange of genes between populations.
What is epistasis?
Gene-gene interaction, particularly between different alleles
What is locus heterogeneity?
When same disease phenotype can be caused by mutations in different loci.
Which mutations can cause Alzheimers?
Mutations in chromosomes 1, 14 or 21
What is allelic heterogeneity?
Same disease phenotype resulting form different types of mutations at same loci.
What is pleiotropy?
When single disease-causing mutation affects multiple organ systems.
Four types of genetic studies
Basic genetic epidemiology
Advanced genetic epidemiology
Gene finding
Molecular genetics
What is basic genetic epidemiology useful for?
To quantify degree of familial aggregation and heritability estimates
What is advanced genetic epidemiology useful for?
To explore mechanism of action of genetic risk factors
When is gene finding useful for?
Determine genomic location and identity of offending genes
What is molecular genetics useful for?
Trace biological pathways from DNA to disorder
What is gene mapping?
Any strategy that permits finding the chromosomal location of one or more genes
When are MZ twins cleaved?
Embryo is cleaved during early dvelopment
How are DZ twins formed?
Result of fertilization of two different ova by two different sperm cells.
How much of genes do DZ twins share?
50%
What is the pairwise concordance rate?
Number of twin pairs who both have the disorder divided by the total number of pairs
What is probandwise concordance rate?
umber of affected twins divided by total number of co-twins
When is a probandwise concordance rate possible?
If a twin register is mantained
Why is probandwise concordance rate more useful?
Allows comparison of general population risk with rate in co-twins of probands
What is chorionicity?
How many amnions and chorions are present for both foetuses
What are the two types of family studies?
Family history
Family study
What is the family history study?
History taken from the probands themselves.
What is the family study?
All available relatives are interviewed.
What is complete case ascertainment?
Identification of all affected individuals in given population.
What is multiple incomplete ascertainments?
Consecutive referrals are identified - chance that more than one proband may come from same family.
Why is age correction important in family studies?
As some individuals may not have reached the age of risk for the disorder
Relative risk of schizophrenia
10
Relative risk of bipolar
7-11
What is the basic method of adoption study?
Compare rates of disorder in biological relatives and adoptive relatives
What is the parent as proband adoption study?
Group 1: adopted away children of ill parents
Compared group: adopted away children of well parents
What is the adoptee as proband study?
Group 1: biological relatives if ill and well adoptees
Compared group: adoptive relatives of ill and well adoptees
What is the cross-fostering adoption study?
Group 1: children with ill biological parents but raised by well adoptive parents
Compared group: children with well biological parents but raised by ill adoptive parents
Problems of adoption studies
Possibility of higher rates of some MH problems amongst adopted children as adoption itself leads to difficult social circumstances.
Adoptive parents more likely to resemble biological parents as social agencies match families.
What is synapsis/crossover?
In prophase I of meiosis, homologous chromosomes lin eup and sometimes exchange portions of their DNA
What happens when synpasis occurs?
Resulting chromosome may contain new combination of alleles at both loci - called recombination
Which loci are more likely to experience recombination of alleles?
Loci located further apart
Which alleles of loci are likely to be inherited together?
Those that are close together - this is called linked
How can alleles be linked?
Alleles on same chromosome are more likely to be inherited
How can the distance between two loci be inferred?
Estimating the frequency with which cross-overs occur among them
What is recombination frequency?
Looking at recombination in families
What does recombination frequency measure?
Genetic distance between any pair of linked loci
How are genetic distances expressed?
In centimorgans
What is one centimorgan equal to?
1% recombination frequency between 2 loci
1 million base pairs of DNA (1 MB)
Do crossovers occur more commonly at telomeres or centromeres?
More common at telomeres
Less common at centromeres
What is the log of odds used for?
To estimate the likelihood that two loci are truly linked with a specific recombination frequency
What is the calculation of log of odds?
Log10(probability that recombination frequency is observed value)(probability that recombination frequency is 50% i.e. chance)
Why is logarithm used in log of odds?
Allows scores from different individual families studied to be added together later for overall score.
What does LOD >3 suggest?
Statistical evidence of linkage
What does LOD of 2 or less suggest?
Two loci not linked
When are 2 loci said to be linkage disequilibrium?
If specific combinations of alleles at loci are seen together on chromosomes more often than expected bychance.
Which loci are more likely to show linkage disequilibrium?
Closely linked loci
What are the two approaches to linkage studies?
Candidate gene approach
positional cloning approach
What is the candidate gene approach?
Protein is suspected to be involved then gene is traced from this pathogenetic knowledge
What is positional cloning approach?
Genes are identified through their positions in genome rather than functions.
Which linkage study approach is supported by the human genome project?
Position cloning approach
What is a prerequisite for successful linkage analysis?
Availability of large number of highly polymorphic markers dispersed throughout genome
What is the Sib pair analysis?
Several hundred DNA markers roughly evenly spaced along 23 pairs of human chromosomes are taken and genotyping is carried out in a series of concordant sibling pairs.
Reasoning underlying sib pair analysis
Probability that siblings share 0, 1 or 2 alleles at any marker locus is 0.25, 0.5 and 0.25 respectively.
If marker locus is close to a locus conferring susceptibility to disease, this will be detectable as increased allele sharing at the marker.
Drawback of sib pair analysis
Susceptibility loci of very small effect (relative risk <2) may require large numbers of sib pairs to be detected.
What type of analysis is a whole genome scan?
Linkage analysis
What happens in a whole genome scan?
Markers are placed at regular intervels covering whole genomic typed.
What is an association study?
Sample of cases affected by disorder compared with controls.
Frequency of alleles at marker locus is compared in two groups.
What is the name of loci chosen for association studies?
Candidate genes - must predispose to illness
How can false positives occur in association studies?
If 2 groups are not carefully matched for ethnic background.
What is the transmission disequilibrium test?
Association study in which control group is parents or relatives of affected individual - alleles not transmitted to affected child compose control group
What approach was used in genome wide association studies?
Several thousands of single nucleotide polymorphisms are assayed in thousands of individuals.
What type of question are twin and adoption studies used for?
What is the relative contribution of genetic and environmental factors i.e. heritability
What is the appropriate method to investigate mode of transmission?
Segregation analysis
What is linkage analysis used for?
Finding culprit genes
What is association analysis used for
Which actual genes are responsible.
Whatis transgenesis?
Transfer of gene from one species to another
What are transgenic studies?
Insertion of modified mouse gene into mouse genome to study gene function.
Who coined the term epigenetics
Waddington
What causes epigenetics?
DNA methylation
Histone modification
What is an endophenotype?
Unseen but measurable phenomenon present in distal genotype to disease pathway.
Criteria of endophenotype according to Gottesman
Associated with candidate gene or region
Present with high relative risk in relatives
Parameter associated with disease
Independently expressed in clinical state (trait marker)
Heritable
Present in relatives more than population
Link between schizophrenia & bipolar and risk re genetics
Rapid, non-linear decrease of risk when moving from genetically identical individual to an individual who shares half of genes.
What is the non-contingent gene-disorder association?
Relationship is not influenced by other factors like environment or presence of other genes i.e. not polygenic or multifactorial.
What is the common disease-rare variant model?
Rarely occurring mutations cause diseases, and various different mutations can also explain disease.
But each mutation is sufficient but not necessary to cause disease.
What is the common disease-common variant model?
Diseases are a result of co-action of multiple variants (polymorphisms) each of which has a small effect on illness susceptibility. When an individual inherits several, they have a sizeable influence.
MZ concordance for schizophrenia
41-65%
DZ concordance for schizophrenia
0-28%
What is higher familial risk to schizophrenia linked to?
Earlier age of onset
Who is morbid risk of schizophrenia greater among?
Relatives of those probands who had onset before 21 years of age
Risk of child having a mood disorder whose parent has a mood disorder
10-25%
Risk of child having mood disorder if both parents have one
20-50% (double that of one parent)
MZ concordance for bipolar
40-70%
Genes suspected in schizophrenia
NRG1 - neuregulin DTN - dysbindin G72 DAAO - D aa oxidase RGS4 - regulator of G protein signalling 4 COMT DISC1 - disrupted in schizophrenia
Locu of neuregulin
8p12-p21
Locus of dysbindin
6p22
Locus of G72
13q34
Locus of DAAO for schizophrenia
12q24
Locus of RGS4
1q21-22
Locus of COMT
22q11
Locus of DISC1
1q42
Genes suspected in bipolar
BDNF - brain derived neurotrophic factor
DAO G72/G30 - D aa oxidade
COMT
Locus of DAO F72/G30 for bipolar
13q33
Locus of BDNF
11p13
Which chromosome is in both schizophrenia and bipolar?
Chr 21q
Which chromosome is associated with rapid cycling in bipolar?
Low activity allele in COMT
Which gene is associated with SAD?
seretonin transporter gene (hSERT) and 5HT2A gene
Risk of unipolar disorder in first degree relatives?
5-30£
RR of unipolar depression in first degree relatives?
1.14
MZ twin concordance for unipolar depression?
40%
DZ twin concordance for unipolar depression
11%
Heritability of unipolar depression
31-42%
What increases risk of unipola depression in first degree relatives?
Early onset
Recurrent episodes
What does schizoaffective disorder increase risk of in first degree relatives?
Any psych disorder
Which genes are seen more in mood disorders than schizophrenia
DAO and BDNF
Which genes are shared in schizophrenia and schizoaffective
DISC1
NRG
Which gene is seen in unipolar depression
CREB1 (chr2)
