Genome-wide association studies have identified hundreds of genetic variants associated with complex human diseases and traits, and have provided valuable insights into their genetic architecture. Most variants identified so far confer relatively small increments in risk, and explain only a small proportion of familial clustering, leading many to question how the remaining, 'missing' heritability can be explained. Here we examine potential sources of missing heritability and propose research strategies, including and extending beyond current genome-wide association approaches, to illuminate the genetics of complex diseases and enhance its potential to enable effective disease prevention or treatment.Many common human diseases and traits are known to cluster in families and are believed to be influenced by several genetic and environmental factors, but until recently the identification of genetic variants contributing to these 'complex diseases' has been slow and arduous 1 . Genome-wide association studies (GWAS), in which several hundred thousand to more than a million single nucleotide polymorphisms (SNPs) are assayed in thousands of individuals, represent a powerful new tool for investigating the genetic architecture of complex diseases 1, 2. In the past few years, these studies have identified hundreds of genetic variants associated with such conditions and have provided valuable insights into the complexities of their genetic architecture3 , 4.The genome-wide association (GWA) method represents an important advance compared to 'candidate gene' studies, in which sample sizes are generally smaller and the variants assayed are limited to a selected few, often on the basis of imperfect understanding of biological pathways and often yielding associations that are difficult to replicate 5,6. GWAS are also an important step beyond family-based linkage studies, in which inheritance patterns are related to several hundreds to thousands of genomic markers. Despite many clear successes in singlegene 'Mendelian' disorders7 , 8, the limited success of linkage studies in complex diseases has been attributed to their low power and resolution for variants of modest effect 9-11 .The underlying rationale for GWAS is the 'common disease, common variant' hypothesis, positing that common diseases are attributable in part to allelic variants present in more than 1-5% of the population12 -14. They have been facilitated by the development of commercial 'SNP chips' or arrays that capture most, although not all, common variation in the genome. Although the allelic architecture of some conditions, notably age-related macular degeneration, for the most part reflects the contributions of several variants of large effect (defined loosely here as those increasing disease risk by twofold or more), most common variants individually or in combination confer relatively small increments in risk (1.1-1.5-fold) and explain only a small proportion of heritability-the portion of phenotypic variance in a population attributable to additive ...

The apolipoprotein E type 4 allele (APOE-epsilon 4) is genetically associated with the common late onset familial and sporadic forms of Alzheimer's disease (AD). Risk for AD increased from 20% to 90% and mean age at onset decreased from 84 to 68 years with increasing number of APOE-epsilon 4 alleles in 42 families with late onset AD. Thus APOE-epsilon 4 gene dose is a major risk factor for late onset AD and, in these families, homozygosity for APOE-epsilon 4 was virtually sufficient to cause AD by age 80.

Eleven susceptibility loci for late-onset Alzheimer’s disease (LOAD) were identified by previous studies; however, a large portion of the genetic risk for this disease remains unexplained. We conducted a large, two-stage meta-analysis of genome-wide association studies (GWAS) in individuals of European ancestry. In stage 1, we used genotyped and imputed data (7,055,881 SNPs) to perform meta-analysis on 4 previously published GWAS data sets consisting of 17,008 Alzheimer’s disease cases and 37,154 controls. In stage 2,11,632 SNPs were genotyped and tested for association in an independent set of 8,572 Alzheimer’s disease cases and 11,312 controls. In addition to the APOE locus (encoding apolipoprotein E), 19 loci reached genome-wide significance (P < 5 × 10−8) in the combined stage 1 and stage 2 analysis, of which 11 are newly associated with Alzheimer’s disease.