Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants.
BACKGROUND
Several genome-wide association studies have recently linked a group of single nucleotide polymorphisms in the 9p21 region with cardiovascular disease. The molecular mechanisms of this link are not fully understood. We investigated five different expression microarray datasets in order to determine if the genotype had effect on expression of any gene transcript in aorta, mammary artery, carotid plaque and lymphoblastoid cells.


RESULTS
After multiple testing correction, no genes were found to have relation to the rs2891168 risk genotype, either on a genome-wide scale or on a regional (8 MB) scale. The neighbouring ANRIL gene was found to have eight novel transcript variants not previously known from literature and these varied by tissue type. We therefore performed a detailed probe-level analysis and found small stretches of significant relation to genotype but no consistent associations. In all investigated tissues we found an inverse correlation between ANRIL and the MTAP gene and a positive correlation between ANRIL and CDKN2A and CDKN2B.


CONCLUSIONS
Investigation of relation of the risk genotype to gene expression is complicated by the transcript complexity of the locus. With our investigation of a range of relevant tissue we wish to underscore the need for careful attention to the complexity of the alternative splicing issues in the region and its implications to the design of future gene expression studies.
Folkersen
Lasse
L
Department of Medicine, Karolinska Institute, Stockholm, Sweden. lasse.folkersen@ki.se
Kyriakou
Theodosios
T
Goel
Anuj
A
Peden
John
J
Mälarstig
Anders
A
Paulsson-Berne
Gabrielle
G
Hamsten
Anders
A
Hugh Watkins
Franco-Cereceda
Anders
A
Gabrielsen
Anders
A
Eriksson
Per
P
D017398:Alternative Splicing; D001011:Aorta / Q000378:metabolism; D002899:Chromosomes, Human, Pair 9; D003324:Coronary Artery Disease / Q000175:diagnosis / Q000235:genetics*; D050762:Cyclin-Dependent Kinase Inhibitor p15 / Q000096:biosynthesis; D019941:Cyclin-Dependent Kinase Inhibitor p16 / Q000096:biosynthesis; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D008214:Lymphocytes / Q000378:metabolism; D008869:Microtubule-Associated Proteins / Q000096:biosynthesis; D020411:Oligonucleotide Array Sequence Analysis; D012306:Risk
C493966:CDKN2B protein, human; D050762:Cyclin-Dependent Kinase Inhibitor p15; D019941:Cyclin-Dependent Kinase Inhibitor p16; D008869:Microtubule-Associated Proteins