Genomics Flashcards
What is genomics?
the study of the whole genome
What are the limitations of NGS?
- uses short fragments (150bp) so hard to characterise large variants
- accuracy is lower than Sanger sequencing
What is used to filter for variants that is frequently observed?
gnomAD
What sort of variants are identified for NGS?
pathogenic, conserved, affect functional elements or linked to the condition
What is the problem with relying on pathogenic variants to identify a cause?
there is a large number of false positives in databases
What types of diseases is WGS currently used for?
- monogenic
- clear phenotype
- currently have disease
What is WGS not currently used for?
- complex diseases
- risk prediction
- unexplained conditions
What 3 areas is the 100,000 genome project covering?
- rare diseases
- cancer
- infection
Where are participants for the 100,000 genomes project recruited?
genomic medicine centres
What is a tier 1 variant?
- in gene panel
- clear loss of function
- known pathogenic variants
What is a tier 2 variant?
- in gene panel
- missense or other VUS
What is a tier 3 variant?
- not in the gene panel
What is DNA linkage?
Genes that are in close proximity on a chromosome are likely to be co-inherited
How can linkage be used to find disease causing variants?
- use linkage to identify regions associated with the disease
- identify the genes in this region
- Select candidate genes based on their biological function
- Sequence candidate genes of affected individuals for mutations
How is the genetic linkage assessed?
LOD score:
>3 indicates linkage
What can confound genetic linkage?
non-penetrance and phenocopies
Which bases are purines?
A and G
Which bases are pyrimidines?
T and C
What is a transition SNP?
when the substitution conserves base chemistry (purine -> purine)
What is a transversion SNP?
when the substitution changes base chemistry (pyrimidine -> purine)
What is an amorph?
when mutation causes complete LOF
what is a hypomorph?
when a mutation causes partial LOF
What is a hypermorph?
When a mutation causes an increase in normal function
What is an antimorph?
when a mutation acts in opposition to the normal gene
What is a neomorph?
when a mutation causes a gain of new function
What effects can a LOF mutation have?
- lack of protein being produced
- unstable or inappropriate targeting causing protein degradation
- alteration e.g. of shape required for function
Are LOF mutations normally dominant or recessive?
recessive
- can be rescued by a normal allele
When can a LOF mutation have dominant effects?
- haploinsufficency
- dominant negative effect
- somatic second hits
Are GOF mutations normally dominant or recessive?
dominant
What effects can a GOF mutation have?
- loss of regulation
- novel function
What is the law of segregation?
Each individual has 2 alleles for a trait, and passes 1 on to their offspring
What is the law of independent assortment?
Genes at different loci segregate independently
What is the consultand in a pedigree?
The person of interest
What is the inheritance of an autosomal dominant trait?
- doesn’t skip generations
- an affected parent gives 50% risk of disease
When can it be difficult to predict inheritance of a mendelian disease?
If it has variable expression or penetrance
What is penetrance?
the proportion of carriers that manifest with phenotypic signs
- can be age/sex specific
What is an example of a disease that has variable penetrance?
Cherubism
- 100% penetrance in males
- 50-70% penetrance in females
tetralogy of Fallot (also varaible expression)
What is germline mosaicism?
When a parent has no mutation in their somatic cells, but in all or a % of their germline cells
What are the features of an autosomal recessive trait?
- skips generations
- offspring have a 25% chance of being affected
- 50% chance of being a carrier
What is compound heterozygosity?
When there is 2 different allele mutations at the same locus
What are the features of an x-linked recessive trait?
- females usually asymptomatic
- female carriers: 50% of sons are affected
- affected males: all daughters are carriers
- no male to male transmission
What is X-inactivation?
when 1 X chromosome is randomly switched off in each cell (in females) for dosage compensation
What are the features of an x-linked dominant trait?
- affects both sexes (males more)
- affective mothers pass 50% risk to both
- affected males pass to 100% of daughters and 0% to sons
What genetic tests are used in practice?
Karyotyping
FISH
aCGH
Single gene testing
With is aCGH?
= comparative genomic hybridisation array
- can identify very small genomic imbalances
- e.g. for autism
Give an example where single gene testing is used?
Duchenne and Becker muscular dystrophy
- affects same gene
- duchenne prognosis is much worse
When is pedigree assessment not suitable for risk assessment of a mendelian disease?
when it has variable penetrance or expression
What can be used for disease risk assessment?
pedigrees and Hardy-Weinberg
How can the genetic and environmental contribution to disease be assessed?
twin studies
What can family studies be used for in complex diseases?
to see if there is an increased risk to first degree relatives
What type of risk assessment is used for medelian diseases?
absolute risk
What type of risk assessment is used for polygenic diseases?
relative risk
What is the additive effect inheritance model?
When a trait increases for each copy of the allele present
What is the dominant effect inheritance model?
When the trait is the same with 1 or 2 copies of the allele
What is GWAS used for?
searches the whole genome for causal variants of disease
What is the only pre-requisite for GWAS?
that the trait in question is heritable
What is the significant threshold for GWAS?
p = 5x10^-8
- needs to be high to prevent false positives
How are GWAS results illustrated?
manhattan plot
What concept is relied on for GWAS studies?
genetic linkage - can identify susceptible loci, where the variant is likely to be
What is the polygenic risk score?
predicts an individual’s risk of disease based on their genotype and GWAS estimated effect size
How is the polygenic risk score calculated?
- find SNPs above a set P-threshold
- sum of the risk alleles which are weighted according to their GWAS-derived effect size
- regression test for association
What is epigenetic modification?
modification of the expression of DNA without altering the underlying DNA structure
- heritable
What are the main histone modifications?
DNA methylation
histone modification
What processes is epigenetics important for?
- pluripotency
- differentiation
- imprinting
- x inactivation
- transposon control
What enzymes carry out dna methylation?
DNA methyltransferases
e.g Dnmt1
What enzyme is responsible for de novo methylation in the embryo?
Dnmt3
What methyltransferase is responsible for maintenance of methylation?
Dnmt1
What enzyme removes methyl groups from DNA?
TET proteins
Where does histone modification occur?
on N-terminal tails of histones
What can the histone code be used for?
predicting regulatory regions
What model is used for studying epigenetics?
genomic imprinting
What is genomic imprinting?
when one of the alleles for a gene is switched off
What is uniparental disomy?
when both chromosomes come from 1 parent
What is the difference between the mechanism of Prader Wili Syndrome and Angleman’s syndrome?
PWS is inherited from father
AS is inherited from mother
- both have deletion on chromosome 15
What are the features of prader wili syndrome?
- central obesity
- short stature
- always hungry
What are some features of angleman’s syndrome?
- happy disposition
- wide mouth
- inappropriate laughter
- stiff arms
- mental retardation
How are PWS and AS diagnosed?
methylation status
What is Beckwith-Wiedman syndrome?
- genomic imprinting disease
- de-regulation of imprinting centres IC1 and IC2 on chromosome 11
Features?
- predisposition to some cancers
- large tounge, body and organs
- small head
What imprinting disease has a higher incidence in children born via IVF?
beckwith-wiedeman syndrome
What is silver-russell syndrome?
7% of sporadic cases have maternal UPD7
- low weight/growth, 5th finger clinodactyly
What is albright’s hereditary osteodystrophy?
- imprinted GNAS locus on ch 20
- abnormal response to PTH
What is the mechanism transient neonatal diabetes mellitus
requires mutation of the ZFP27 gene and epigenetic mutations
What are some diseases with an autoimmune and auto-inflammatory component?
- psoriasis
- IBD
- SLE (lupus)
What are the 2 types of IBD?
ulcerative colitis
Crohn’s disease
How can genetics be used to improve inflammatory disease?
by using GWAS to identify susceptibility loci, may be able to develop specific drug targets
What types of somatic mutation can occur in cancer?
- inactivation of tumour supressor gene
- activation of oncogene
- creation of new fusion gene
- mutation in DNA repair genes
What is a tumour?
a clonal expansion of genetically abnormal cells
What is bevacizumab?
targeted therapy for glioblastoma
binds VEGF
What is Imatinib?
targeted therapy for CML
blocks tyrosine kinase activity
What are the key features of cancer susceptibility genes?
- often dominant
- incomplete penetrance
- usually young onset of cancer
- can results in multiple primary tumours
- can show recognisable pattern of cancer in families
What factors are considered in cancer risk assessment?
- age
- number of family members affefcted
- closeness of affected relatives
- patterns e.g. breast + ovarian
- ethincity e.g. for founder mutatios
What is Lynch syndrome?
a mismatch repair deficiency thats gives predispositions to several cancers
How is Lynch syndrome mangaed?
regular colonoscopy, options of historectomy etc, symptom awareness, low dose daily aspirin (improves immune resposne to tumour cells)
What is familial adenomatous polyposis (FAP):
autosomal dominant mutation in APC
- 100% penetrance
- high risk of colon cancer
