# Presentation: 727282

## Second Multi-IC SymposiumWorking Group 2:Follow-Up StudiesThomas Lehner, NIMHLisa Brooks, NHGRIRochelle Long, NIGMSAlan Michelson, NHLBIJoni Rutter, NIDAPeggy Tucker, NCI 

## Follow-Up Studies in WGA Designs

- How to choose fine mapping or sequencing approaches?
- What is the likely impact of new sequencing technologies?
- What don’t we know about the genome but could have great impact on follow up studies?
- At what point do we initiate functional studies and how do we determine function?
- What types and numbers of biospecimens are necessary for the different approaches?

## How to choose fine mapping or sequencing approaches

- The utility of the HapMap for fine mapping studies.
- Can the use of custom-SNP arrays fully capture variation in a gene/region?
- Rare variants in complex disorders and strategies to include them in study design.
- What does deep sequencing mean?
- Why don’t we sequence everything?
- Even if we could would we want to?
- Analytical challenges

## New sequencing technologies

-                                             _ABI        454        Solexa_
- Read lengths now (bases)  650        250           40
- Read lengths in a year        650        400           50
- Paired ends                         yes        year         soon
- Accuracy			       high       probs       high
-                                                           homopol
- 							  indels
- Cost / Mb                             $880       $160        $5
- (Rough indication: costs are
- uncertain and will change!)
- 						(data from Elaine Mardis, Wash. U.)

## What is the likely impact of new sequencing technologies?

- What new questions can be addressed by high-capacity human resequencing?
- What is the economic and scientific impact of new sequencing technologies?
- How many samples are needed?
- Are deep sequencing technologies feasible for complex traits?  At what cost?

## Which is the causal variant?

**Which is the causal variant?**

- An association hit shows a genome region associated with a disease,    and generally many variants in LD.

## What don’t we know about the genome but could have great impact on follow up studies?

- What types of variation are we missing in GWAS studies?
- What is the phenotypic impact of these genomic variants?  How do they contribute to genetic heterogeneity?
- How is function determined in coding regions and in non-coding regions, including gene deserts?
- Should we only focus on SNPs in Exons?
- How important are synonymous codon changes?
- What about Introns and regulatory regions?
- What have CNVs taught us about the genome?
- Most of the genome codes for nothing – what if we get a hit there?

## At what point do we initiate functional studies and how do we determine function?

- What are functional studies?
- How do we understand and assay function?
- What is needed to establish causality?
- E.g. Association between a variant(s) and phenotype (e.g. drug response) is not sufficient
- Multiple lines of evidence must agree; integrated approaches are best.
- A multi-pronged approach is best (e.g. cells, mice, humans)
- Understanding mechanism often leads to paradigm shifts in thinking

## What strategies should be considered to have sufficient sample materials available for follow-up studies?

- Make sure study subjects are consented appropriately.
- In the beginning decide to store DNA, create cell lines or both. Can be cryo-preserverd almost indefinitely.
- The quantities of DNA required are very low.
- First choice is always DNA extracted from peripheral blood
- DNA extracted from saliva or cheek swab is an option as is whole genome amplification  but with caveats