WEEK 10 COMPLEX DISEASES III Flashcards
Which components comprise multifactorial diseases?
- Polygenic and environmental components
Are PRS (polygenic Risk scores) going to be implemented in modern healthcare?
- Yes likely
Do PRS (Polygenic Risk scores) have the potenital to impact clinical practice (and related fields) and the management of complex diseases to the same extent as WGS in the diagnosis of rare diseases?
- YES
Will PRS redirect resources from treatment to prevention in complex diseases from “diagnose and treat” to “predict and prevent”?
- YES
In terms of pharmacogenomics (PGx), what % of people on average is a drug effective in?
- On average effective in 50% of people
What are three uses for genotype data in terms of pharmacogenomics?-
- select the right drug (specificity)
- choose appropriate dosage (efficacy)
- Avoid adverse events (safety)
What is the scale of NGS compared to genotyping?
- Exome (WES–> whole coding part) or whole genome (everything) for NGS compared to small scale (dozens to hundreds of SNPs), medium scale (thousands of markers) to large scale 500K-5 million
What are 4 reasons for genetic testing?
- Medical, health related
- Legal
- Ancestry/family tree
- Any other reason–> curiosity?
Does genetic testing mean that your DNA is tested and if not, what are some examples?
- NO! You can look for genetic answers elsewhere!!
- E.g. RNA (indirect DNA sequence information)
- Protein/metabolites (absence of gene products, byproducts)
- Ultrasound (prenatal nuchal translucency)
How can an ultrasound give an indicating of Trisomy 21 (Down Syndrome)?
- Used to measure the thickness of the fluid buildup at the back of the developing baby’s neck–>if area is THICKER than normal, early sign of down syndrome OR trisomy 18
Why is prenatal diagnosis performed? (8 reasons)
- If there is family history of disorder
- If pervious child has had a chromosomal abnormality
- Either parent has had a chromosomal abnormality
- Parents have been tested and are carriers
- Increasing maternal age
- Risk of a neural tube disorder
- Abnormal results from ultrasound
- Routine screening test
What are the non-invasive prenatal techniques that are performed?
- Ultrasound (ultrasonography)
- Maternal serum tests, MSAFP and NIPTS
What are the two invasive techniques that are performed for pre natal tests?
- AMniocentesis
- Chorionic villus sampling
What is a comparison b/w next generation sequencing and genotyping?
- NCS is like reading a whole book and genotyping is like looking at a few words
What are the main differences between NGS and Genotyping?
NGS: - Complete information - All (new) variants - Expensive - Slower - Already in healthcare - Diagnosis - Direct to consumer Genotyping: - (very) partial information - Known (common) variants - Cheap - Rapid - Research (maybe healthcare soon) - Risk, disease prevention (predict risk of disease) - Direct to consumer
What is the rough process in NGS?
- DNA fragmentation–> library preparation (primers, adapters) –> sequencing (by synthesis, ligation etc.)
What are the applications of NGS (WES and WGS)? (3 things)
- Genome sequencing
- Metagenomics/microbiota studies
- Expression profiling RNA-seq (diagnostic)
How is NGS used for mutations/SNV (Single Nucleotide Variant) detection?
- Whole Exome Sequencing (WES)
- Whole Genome Sequencing (WGS)
- Targeted sequencing –> gene panel (i.e. cancer), single gene
What particular odyssey has been resolved from NGS and what is it?
- The diagnostic odyssey
- The time taken between a patient first developing symptoms of their condition and receiving a correct medical diagnosis–> rare disease patient’s diagnostic odyssey lasts on average 4 years
What type of disease is NGS good for?
- Rare diseases
Where is NGS going in the future?
- Towards WGS implementation in healthcare –>current focus on RARE diseases
- Partial successes in CANCER healthcare –> HER2+ve breast cancer
Is NGS good for cancer?-
- Not really (not yet)
What are the limitations of NGS? (5 things)
- Tissue highly heterogenous (mix of wt cells and often different types of tumour cells)
- WGS coverage is INADEQUATE
- Therapies targeting single mutations usually fail die to resistance (new mutations)
- Driver vs. passenger mutations
- Variants of uncertain significance (i.e. How do we decide if it is pathogenic or not?)
What is involved in WES as part of NGS?
- > 60 000 variants (different from the reference genome)
- Mostly coding variants (WES)
- Mostly synonymous variants
- Several hundreds of MISSENSE variants
What is involved in SNV as part of NGS?
- Predicting whether a variant is misfunctional using bioinformatic tools (predicting functional consequences of individual SNPs/SNVs)
- Many variants are often reclassified to pathogenic many years after original test
What types of crimes require a person to provide a DNA sample?
-All felony and some misdemeanour convictions
What is a misdemeanor conviction?
- Graffiti
- Disorderly conduct
What deos genotyping require knowledge on?
- This requires knowledge of the type and sequence context of the SNP/mutation
- Everything is on arrays now
Has the possibilityfor genotyping several thousands of SNPs at once revolutionised the filed of complex disease genetics?
- YES!!
What is a Manhattan plot?
- Where each dot is a SNP reported based on its p value for association
In terms of the Manhattan plot, what is the threshold for GWAS significance?
- 5E-8
What do you do to get the polygenic risk scores?
- Multiply the allele by the odds ratios
Is there a better predictive power using 6 millions of SNPs?
- YES
What can polygenic score identify?
- Subset of the population with risk of heart attack equivalent to a monogenic mutation
How can you translate GWAS findings to personalized medicine? (3 step)
- Predict
- Screen
- Prevent
Is pharmacogenomics important in personalised medicine?
-YES e.g Several known drug interactions –> response, dosage, specificity, efficacy, adverse reactions
What does DTC testing mean?
- Direct to consumer testing genetic test you can provide at home without a healthcare provider or prescription. Collect DNA sample and send it to company –> they analyse it and produce report based on genetics
What are the different types of tests based on? (4 things)
- Ancestry
- Kinship
- Lifestyle /health factors
- Disease risk
What are the two key factors in DTC genetic testing?
- Quality control–> Test quality is largely unregulated in DTC compared to traditional medical testing which has quality and control systems in place
- Data interpretation regulation–> Information interpreters typically not accredited compared to licensed people for traditional medical testing
