Beyond Linkage Analysis and Genome-Wide Association Study

Recent work has demonstrated that copy number variation constitutes a substantial proportion of genetic differences among human beings, and provides an important contributor to disease susceptibility.  Copy number variants (CNVs) are not randomly distributed throughout the genome but cluster in regions where sequence architecture contributes to genomic instability.  One class of sequences affecting genomic instability is segmental duplications (SDs), or low copy repeats (LCRs).  These sequence elements are large (>10 kb), highly related to one another (>90% identity), and found in modest numbers of copies compared to smaller repeats such as LINES and SINES.  LCRs can promote instability in part via errors in homologous recombination, creating duplications, deletions, inversions and translocations.  We have been interested in understanding the contribution of CNVs to autism spectrum disorder (ASD), particularly in LCR-rich intervals.  We report on two studies, one focused on small variants detected by a finely-tiled array that examined 5 LCR-rich genomic intervals at high resolution, and a second that examined larger CNVs (>50 Kb) found among approximately 130 SD-rich intervals. The first study employed an array designed to detect CNVs as small as 1000 bp both within and surrounding the LCR-rich segments.  We detected significant increases in the total length of duplicated sequences in children with autism compared to typically developing controls matched for age and sex.  Validation of the copy number burden using Illumina sequence read-representation will also be presented.  The second study included 274 autism cases and 245 typically developing individuals assembled through the CHARGE study, a population-based case control study.  We have determined the prevalence of a number of CNVs previously implicated in autism or other behavioral disorders in this ethnically diverse cohort, as well as identified a number of novel variants not previously described nor found in large sets of control subjects. These findings suggest that discovery of the many genetic contributors to autism spectrum disorder remains incomplete. At both a fine scale (CNVs as small as 1 Kb) and a large scale (CNVs >50 Kb) our data indicate ASD is associated with elevated copy number burden in LCR-rich regions. The CHARGE cohort includes detailed clinical and environmental data allowing us to examine the range of phenotypes associated with a given disease-contributing CNV, as well as explore gene x environment interactions.