Genetics 11 - Genetic Diversity and Complex Genetic Diseases Flashcards
learning outcomes
monozygotic twins
single zygote that underwent mitosis post fertilisation
sources of genetic diversity
differing patterns of random X inactivation
somatic mutation/recombination (e.g. cells of the immune system)
different degrees of heteroplasmy (mtDNA)
copy number variants (CNVs)
CNVs
cause of…
relevance of variation it causes
very highly variable regions in human genome
cause of structural variation
comprised of variable number of repears (>90% identical) of a particular unit of sequence
contribute to human genetic variation (5-10% of genome)
play an important role in evolution
represent functional (disease causing) mutations as well as genomic polymorphisms of uncertain relevance (CNPs)
genes associated with disease are least affected by CNVs whereas paralogous genes are most affected (2+ genes descended from same ancestral gene but original gene was duplicated and received some type of mutation that gave rise to new function which is closely related to ancestral gene - usually changes in species - form of evolution)
paralogous genes
2+ genes descended from same ancestral gene but original gene was duplicated and received some type of mutation that gave rise to new fucntion which is closely related to ancestral gene - usually changes in species - form of evolution
categories of CNV
smaller CNVs (<10kb)
copy number polymorphisms (CNPs)
common in the general population (freq < 1%)
often encode proteins involved in drug metabolism and immunity
associated with susceptibility to complex inflammatory/immune disease e.g. psoriasis and Chron’s
larger CNVs
size
type of mutations
prevalence
associated with
10kb - 5Mb
microdeletions/microduplications
rare in general population
associated with susceptibility to neurocognitive diseases
autism, schizophrenia, behavioural, language, sleep, intellectual, complex types
William Syndrome
micro del 7q11.23
Smith-Magenis syndrome
micro del 17p11.2
Potocki-Lupski syndrome
micro dup 17p11.2
duplication vs deletion
Microdeletions are usually more severe than duplication syndromes
detection of larger CNVs (microdeletions) - SNP array
copy # - will tell us if there is something missing/extra
genotype - heterozygosity, along middle line - no dots on the middle line ⇒ LOH - may indicate deletion
immunoglobulin structure
how is it formed
2 heavy chains - (γ,α,μ,ε,δ - G, A, M, E, D)
2 light chains - either 2λ or 2κ
each chain (heavy and light) has both:
constant region (C)
variable region (V)
building an Ig requires 2 of 3 families of genes on 3 different chromosomes - Irreversible recombination of germline genes during prenatal development
Ig gene organisation
V = variable
J - junction
C = constant
D = diversity with heavy chain, as well as V, J and C
For either light or heavy only use 1 type of exon
Spliced at random to make different type of globulin
κ gene family
regions present
C REGION
1 C (constant) region
V REGION
250 V regions (2 exons - L codes for a leader region and V for most of variable region
several J exons
J exons are located between V and C regions
λ gene family
C REGION
4 C region genes, 1 for each subtype of λ chain
V REGION
30 V regions
J (joining) regions, in between Cs
the L, V, J and C exons are separated by introns
arrangement of κ and λ light chain genes in germ line of undifferentiated cells
4 steps in making a κ light chain
- somatic DNA recombination
- transcription of pre-mRNA
- RNA splicing
- translation into protein
5.
- somatic DNA recombination
occurs in B cell precursors (somatic DNA recombination)
V and J are joined together to encode the variable domain of the Ig light chain
any 1 V and any 1 J can join (intervening introns and exons excised)
- transcription of pre-mRNA and 3. RNA splicing
- translation into protein
translation into protein
light chain protein transport to ER, carried out by leader sequence
removal of leader sequence (L)
a light chain rearrangement of the exons
making a heavy chain - what is needed
when is heavy chain made
germ line
9 C genes
> 1 for each class M (μ), D (δ), G 1-4 (γ1-γ4), E (ε), A 1-2 (α1-α2)
H gene for hinge region
V gene (L and V)
J gene
D genes (D for diversity)
heavy chain gene family
heavy chain DNA rearrangement
making a heavy chain - alternative ways of processing of the same pre-mRNA
- LVDJ spliced to be contiguous with Cmu
- LVDJ spliced to be contiguous with Cdelta
expression of IgM heavy chain or IgD heavy chain
heavy chain transcription and translation
Goes to ER and leader sequence is cleaved off
how is DNA rearrangement co-ordinated
recombination signal sequences
non-coding DNA sequences that are found directly adjacent to the points at which recombination takes place (VDJ)
function as signals for the recombination process that rearranges the gene segments
located 3’ side of each V segment, 5’ side of each J segment and both sides of D segments
recombination of signal sequences (RSS)
nonmer
heptamer
1 (12 bp) or 2 (23 bp) turn signals
Rag-1 and Rag-2 - Cleave out introns and exons in between
how does rearrangement occur
kappa, lambda and heavy chains
ONLY between a 1 and 2 turn signal - 12/23 rule
κ light chains
a 1 turn signal downstream (3’) of V
a 2 turn signal upstream (5’) of J
so κ V and J can join, but V won’t join to another V
λ light chains
a 2 turn signal downstream (3’) of V
a 1 turn signal upstream (5’) of J
so λ V and J can join, but V won’t join to another V
heavy chains - 2-1-1-2
a 2 turn signal downstream (3’) of the V gene
1 turn signals on each side of the D exon
a 2 turn signal upstream (5’) of the J exon
only 2 to 1 and 1 to 2 recombination is permitted
V cannot recombine directly to J
recombination - removal of itrons
catalysed by Rag-1 and Rag-2 (also involved with TCRs)
mutations in the genes for these proteins results in severe combined immunodeficiency disease (SCID) as the recombination mechanisms are also involved in generation of TCRs
terminal transferase - diversity
randomly inserts nucleotides at the junction between D and J
further diversity in this hypervariable region - junctional diversity
result = 107 - 108 idiotypes of Ig
order of Ig gene expression
Heavy chain expressed first
Recombination - in frame - go on to form heavy chain - pre b cell (either maternal or paternal)
B cell is diploid - only 1 allele expressed so whatever allele makes a heavy chain first is going to be expressed
how is the mature B cell formed
somatic hypermutation
enzyme involved
mutation rate
a process of affinity maturation of the V segments which occurs in the subset of B cells that can bind to a specific foreign antigen post-stimulation
involves activation-induced deaminase (AID)
mutation rate increase to 103 per bp per generation
some Igs have high affinity binding and B cells with these Igs are selected and proliferate extensively
result = population of mature plasma cells secreting highly specific Ig
Ig gene expression - irreversible somatic genetic change
excision of introns and somatic hypermutation constitutes irreversible somatic genetic change
considerable element of random recombination and mutation
Fred and George - almost certainly end up with a different repertoire of their 1010 - 1011 idiotypes of Ig
similarly different TCR idiotypes and olfactory receptors
things to remember
learning outcomes
Copy Number Variants
for most of maternal chr 1 the sequence in both monozygotic twins are identical
for CNV loci the number of copies at a given locus on maternal chr 1 may differ between the 2 twins
in a twin with a duplication of the CNV on mat chr 1 the 2nd/duplicate copy (paralogous sequence) may differ slightly from the original copy
importance of CNVs in MZ twins
if twin A develops complex disease and twin B does not - regions of the genome with CNV can be investigated further
changes in CNV may identify whether a missing gene, or multiple copies of a gene, are implicated in disease onset
pathogenic CNVs are particularly enriched for genes involved in development
link to dosage sensitivity and neurodevelopmental disorders
haploinsufficiency
bi-allelic expression is usual - from both maternal and paternal
some genes normal physiological function requires full gene dose - 2 functional alleles
individual with only 1 functional allele is haploinsufficient
may be because of:
heterozygous with 1 functional and 1 non-functional (null) allele
OR hemizyogus (del) - allele deleted on 1 chr
e.g. CNV microdeletion syndrome - Smith-Magennis syndrome (SMS) - haploinsufficiency of RAI1. microdel 17p11.2
genetic determination triangle
inheritance of genes vs characters
genes - mendelian
characters (phenotype) - never entirely Mendelian
environmental influence
genetic interactions
chance (stochastic) events
* Penetrance and Expressivity
multifactorial traits/disorders
traits/disorders showing familial clustering, but no recognised Mendelian inheritance pattern
determined by the additive effects of many genes at different loci (polygenic), combined with effects of environmental factors
e.g. height, T2DM, hypertension, CV disease, schizophrenia, Alzheimer’s disease
mendelian vs complex traits
polygenic theory
a useful framework for considering the inheritance patterns of traits/disorders that rely on the interaction of a large number of genetic factors, each of which make a small contribution to overall phenotype
2 main concepts of polygenic theory
HERITABILITY
estimates how much of differences between populations are down to their genes
THRESHOLDS
explains how dichotomous characters can be polygenic
heritability
proportion of total phenotypic variance that is attributable to genetic variance in a population
how much of differences between people in a group are down to genetic differences between them, and how much is down to differences in their environments
nature (genes) vs nurture (environment)
heritability is not about individuals - relates to populations
heritability compares
what does a heritability of 0.5 mean
compares incidence in relatives of affected individual vs incidence in general population
heritability of 0.5 does not mean that a trait is 50% caused by genetic factors - it means that 50% of variability in the trait in a population is due to genetic differences among people
e.g. heritability of religion is 0
intelligence is somewhere between 0 and 1
Phenylketonuria (PKU)
gene
symptoms
caused by mutations in the PAH gene - phenylalanine hydroxylase
mutations prevent conversion of the AA phenylalanine to other compounds
builds up toxic levels, affecting nerve cells - brain damage
what is the heritability (proportion of total phenotypic variance that is attributable to genetic variance in a population) of PKU in Ireland
as we screen for PKU now, heritability of PKU is close to 0 - diet adjusted
concordance
co twin also affected
higher rate with monozygotic twins
discordance
co twin unaffected
higher rate in fraternal (dizygotic) twins - share 50% of genes - siblings
family studies - evidence for genetic involvement in complex diseases
weaker evidence as family environment is shared and so could be responsible for the effect
adoption studies - evidence for genetic involvement in complex diseases
stronger evidence than family studies as separates the effects of genes and family environment
adopted twin studies - evidence for genetic involvement in complex diseases
rare, but very strong evidence as genetics are matched and family environment is different
threshold theory
what does it explain
explains how dichotomous characters can be polygenic
susceptibility to a disease is a continuous character that depends on combined effect of many genes
if your susceptibility exceeds a threshold you will manifest the disease - all or nothing
relatives will therefore be more likely to also manifest the disease, than the general population
explains why complex diseases tend to run in families
Julie
Already have 2 children with cleft palate - threshold is low - a lot of susceptibility genes
multifactorial inheritance
recurrence risk rules
polygenic threshold characters run in families
parents with several affected children have more high risk alleles than parents with one affected
RECURRENCE RISK RULES
the more seriously affected, the higher the risk for siblings
the more affected children you have, the higher risk of recurrence
the closer the relative to the index case, the higher the risk of recurrence
gender biased polygenic inheritance
e.g.
symptoms
hypertonic pyloric stenosis
projectile vomiting and failure to thrive
5x more common in males
must be higher threshold for girls than boys
offspring of affected males vs offspring of affected females - who is more likely to manifest hypertrophic pyloric stenosis
offspring of affected females
As females have higher threshold, she must have a lot of susceptibility genes for this disorder so more likely to pass on gene
the Carter effect
higher recurrence risk if the index case is of the less commonly affected sex
e.g. HPS - Male - lower threshold
Most likely to have it - a male child of an affected female
how do we finds genes involved in complex disorders
linkage analyses - microsatellites
association
candidate gene testing - gene you think might be involved - haplotyping
genome-wide association studies (GWAS)
linkage analysis
relationship between loci not alleles
specifically genetic phenomenon
linkage analysis looks at physical chunks of the genome of related individuals with the phenotype and associates them with given traits
PRINCIPLE
if we find a common genetic marker (e.g. microsatellite, SNP) we assume that the gene that causes the disease is somewhere in the same area
genetic association - phenomenon
goal
method
purely statistical phenomenon and not specifically genetic
GOAL = identify 1 or more allels within a population that co-occur with a particular phenotypic trait more often than would be expected by chance
METHOD = gather some people with a disease (cases) and some people without a disease (controls) in a population and look to see what alleles are present more in cases than controls
association is not causation - may be on same haplotype, or by chance present in higher frequency in subgroup with the disease - Gene involved - but molecular investigation must prove it
linkage analysis vs association
candidate gene testing
targets can be informed by:
knowledge of the disease apthology (functional cloning) - quicker, but need prior knowledge to make an educated guess
linkage and association testing (positional cloning)
GWAS
scans all genes in genome
no prior knowledge needed
high resolution SNP chips used
WGS also used
cases of diabetes
DM
HYPERGLYCAEMIA
> 7mmol/L fasting
> 11 mmol/L non fasting
TYPE 1 = sudden onset in youth related to autoimmune pancreatitis
TYPE 2 = gradual onset in middle/later years associated with obesity and inactivity (diabetes epidemic)
MODY
mature onset diabetes of the young
autosomal dominant pattern of inheritance
not associated with obesity or sedentary lifestyle
7 different single gene defects identified
mitochondrial T2D
severe single gene defects
some associated with deafness
T2DM - evidence for genetic factors
ethnic differences
family and twin studies - 2.4x risk for families
15-25% of first degree relatives develop impaired glucose tolerance or T2D
> 30 genes with susceptibility alleles (linkage/GWAS studies)
things to remember
