In a case-control study, a set of cases is identified and their genotyping information is compared to a set of suitable controls in order to find genetic variants associated with the trait under study.
Here, we take advantage of a large effort to sequence 2000 exomes (1000 cases and 1000 controls, for details, see Albrechtsen et al). in order to find new variants associated with type 2 diabetes in a Danish population sample.
This highlights the challenge of gene re-sequencing and the importance of projects like the 1000 genomes [ 182] in order to find noncommon variants with highly penetrant effects in autoimmune diseases.
In order to find novel variants of known miRNAs, we searched small RNAs with 1 or 2 mismatches to known miRNAs in our small RNA sequencing data libraries by use of homolog analysis, which leading to 119 novel variants belonging to known miRNA families (Additional file 2: Table S2).
The Metabochip array of nearly 200 000 SNP markers aims to follow up the most significant associated variants from the GWAS meta-analysis on type 2 diabetes, CAD and myocardial infarction, and quantitative traits related to these diseases, in order to find additional variants and refine previous associations through fine mapping [ 20].
In order to find very rare variants with a population frequency <1 %, it is necessary to perform exome or WGS.
Finally, a Finnish cohort of familial CRC was also sequenced in order to find rare truncating variants present in two or more cases.
Our group is therefore performing whole exome sequencing in patients with severe IgAN, in order to find out rare variants strongly associated with this complex disease.
In order to find novel transcript variants as many as possible, we did not request an accurate signature of exon junction and cleavage site.
In order to find out how different variants of this approach perform, tests with real data from 420 INT2 sessions between Jan .1st, 2006 and May 30th, 2010 have been performed.
