Seminar Assignment HT 2011

Seminar assignment Handed out at course start Group work / individual assessment Research based aspects, requires independent work Obtain appropriate information - lectures, discussions, web, articles..… Time scheduled to prepare answer Presentation of assignment in seminar format: Groups 3 + 4Thursday 17 th November Groups 5 + 6Friday 18 th November Groups 1 + 2Thursday 24 th November Grading = pass / fail

Examination In groups Verbal examination - round table discussion Examiners = Rachel Fisher Ferdinand van ‘t Hooft Every student must be prepared to answer every part of the question Take no papers with you in to the exam

Seminar assignment - Why? Training for the exam Attain “core” knowledge Apply knowledge from previous courses Sort out misunderstandings

Common genetic variants associated with plasma lipoprotein levels chromosome LDL-C HDL-C TG

Imagine that you have joined a research group which aims to discover novel mechanisms underlying cardiovascular disease. This group has previously measured cholesterol in plasma and performed a genome-wide SNP (single nucleotide polymorphism) analysis in DNA samples from 5,000 subjects from the Sami population in Northern Sweden. i) Explain how the research group would have used these data to obtain information about novel mechanisms underlying cardiovascular disease. In your answer you must explain a)how a genome-wide association study (GWAS) for plasma cholesterol concentration is performed b)how the GWAS results are used to identify genetic loci of interest c)why the study of the Sami population could lead to the discovery of a new genetic locus for plasma cholesterol concentration d)why this strategy enables the identification of “novel” mechanisms for cardiovascular disease

The GWAS led the research group to become interested in a specific SNP near “gene X”. You have been recruited to perform further research into the gene X locus. The first thing that you are to do is to genotype for this SNP in a new cohort of 5,000 Sami subjects in whom plasma cholesterol concentrations are available. ii) Explain the scientific rationale for doing this new genotyping.

You obtain the genotyping results from this new cohort for the SNP near gene X. You immediately calculate the allele frequencies and genotype frequencies to check that they are similar to those in the initial cohort. iii) Explain the difference between allele frequency and genotype frequency.

Your new data confirm the initial observation that the rare allele of this SNP is associated with increased cholesterol concentrations. The next step in your research plan is to perform a fine-mapping analysis. iv) Explain a)what a fine-mapping analysis is b)how you perform a fine-mapping analysis c)what the scientific rationale is for this analysis

The fine-mapping analysis identifies a SNP in the promoter of gene X. You suspect that the SNP might have an impact on the rate of transcription of gene X. You therefore decide to investigate the mRNA expression of gene X in a set of liver biopsies from 100 Sami subjects. You discover that there is a strong relationship between hepatic gene X mRNA levels and circulating cholesterol concentrations.

v) a)How do you interpret these data? Include in your answer a statement as to the expected relationship between hepatic gene X expression and cardiovascular disease. b)Why do you analyse liver samples and not samples from other tissues?

You decide to genotype for the promoter SNP in gene X in the 100 donors of the liver biopsies. vi) Based on the information that you now posses draw a figure (graph) to illustrate how you would predict the hepatic gene expression of gene X would look if you divided your subjects up according to gene X genotype (your graph should only show mean mRNA levels according to genotype). Explain why you have drawn the graph the way you have.

The fine-mapping data and the expression studies indicate that the SNP in the promoter of gene X is the functional SNP involved in the regulation of the plasma cholesterol concentration. vii) Explain what experimental approach you would choose to functionally analyse a promoter SNP with respect to transcriptional regulation of genes.

Gives extensive information – don’t get weighed down by the details!

Focus on the right things! We want you to know How gene X was identified Why gene X could be of importance for cardiovascular disease How to proceed after the initial identification of gene X How to functionally characterise gene X and a SNP in its promoter We do NOT want Suggestions as to what gene X (or the SNP) actually is Detailed methodological protocols

Focus on the right things! We want you to understand how to go from the results from an initial genome wide association study to the detailed investigations of a gene of interest and a functional SNP This knowledge should be applicable to genetic studies of any multi-factorial disease

Questions? Talk to one another! If the assignment is unclear, contact us ( )