We present a genome-wide association study of ileal Crohn's disease (CD) and two independent replication studies that identify five novel regions of association to CD. Specifically, in addition to the previously established CARD15 and IL23R associations, we report strong associations with independent replication to variation in the genomic regions encoding the PHOX2B, NCF4 and ATG16L1 genes, as well as a predicted gene on 16q24.1 (FAM92B) and an intergenic region on 10q21.1. We further demonstrate that the ATG16L1 gene is expressed in intestinal epithelial cell lines and that functional knock down of this gene abrogates autophagy of Salmonella typhimurium. Together these findings suggest that autophagy and host cell responses to intra-cellular microbes are involved in the pathogenesis of CD.Crohn's disease (CD) and ulcerative colitis (UC) represent the two common forms of idiopathic inflammatory bowel disease (IBD), each with a prevalence of roughly 100-150 per 100,000 individuals of European ancestry 1 . CD most commonly involves the ileum and colon but can affect any region of the gut. UC always involves the rectum, and inflammation may extend as far as the cecum in a contiguous pattern 2 . Strong familial aggregation, twin studies and established genetic associations attest to the important role of genetics in IBD pathogenesis [3][4][5] . There is also very strong evidence that the enteric microflora plays a central role in the initiation and maintenance of disease. Therefore, like most complex trait diseases, IBD results from a combination of genetic and non-genetic risk factors, where each individual factor may be expected to have a relatively modest effect on diseaserisk.While a combination of genome-wide linkage, candidate gene and targeted association mapping studies have been successful in the identification of CD-associated genetic variants in CARD15 and the IBD5 haplotype, these explain only a small fraction of the heritability of CD [6][7][8] . We therefore embarked upon a genome-wide association (GWA) study of CD in order to find additional genetic risk factors. Phenotypes for both CD and UC vary considerably among individuals, primarily with regard to sites of inflammation, disease behavior, severity and extraintestinal manifestations. Furthermore, CD site and behavior are likely under genetic control based on clustering within affected sibling pairs 9 , as well as specific observations that CARD15 mutations are a greater risk factor for ileal CD and stricturing behavior 10 . Therefore we have exclusively focused on patients with CD involving the ileal region of the small intestine (with or without other sites of involvement) in an attempt to minimize clinical and genetic heterogeneity. Based on an interim analysis approximately halfway through this study, we identified, confirmed and published the discovery of genetic variants in the IL23R gene that significantly influence risk to developing CD and UC 11 . Specifically at that point, 567 nonJewish ileal CD cases had been scanned and analyz...

Normal development of the cerebral cortex requires long-range migration of cortical neurons from proliferative regions deep in the brain. Lissencephaly ("smooth brain," from "lissos," meaning smooth, and "encephalos," meaning brain) is a severe developmental disorder in which neuronal migration is impaired, leading to a thickened cerebral cortex whose normally folded contour is simplified and smooth. Two identified lissencephaly genes do not account for all known cases, and additional lissencephaly syndromes have been described. An autosomal recessive form of lissencephaly (LCH) associated with severe abnormalities of the cerebellum, hippocampus and brainstem maps to chromosome 7q22, and is associated with two independent mutations in the human gene encoding reelin (RELN). The mutations disrupt splicing of RELN cDNA, resulting in low or undetectable amounts of reelin protein. LCH parallels the reeler mouse mutant (Reln(rl)), in which Reln mutations cause cerebellar hypoplasia, abnormal cerebral cortical neuronal migration and abnormal axonal connectivity. RELN encodes a large (388 kD) secreted protein that acts on migrating cortical neurons by binding to the very low density lipoprotein receptor (VLDLR), the apolipoprotein E receptor 2 (ApoER2; refs 9-11 ), alpha3beta1 integrin and protocadherins. Although reelin was previously thought to function exclusively in brain, some humans with RELN mutations show abnormal neuromuscular connectivity and congenital lymphoedema, suggesting previously unsuspected functions for reelin in and outside of the brain.

Exome sequencing is emerging as a popular approach to study the effect of rare coding variants on complex phenotypes. The promise of exome sequencing is grounded in theoretical population genetics and in empirical successes of candidate gene sequencing studies. Many projects aimed at common diseases are underway, and their results are eagerly anticipated. In this Perspective, using exome sequencing data from 438 individuals, we discuss several aspects of exome sequencing studies that we view as particularly important. We review processing and quality control of raw sequence data, evaluate the statistical properties of exome sequencing studies, discuss rare variant burden tests to detect association to phenotypes, and demonstrate the importance of accounting for population stratification in the analysis of rare variants. We conclude that enthusiasm for exome sequencing studies of complex traits should be combined with the caution that thousands of samples may be required to reach sufficient statistical power.

Disruption of human neural precursor proliferation can give rise to a small brain (microcephaly), and failure of neurons to migrate properly can lead to an abnormal arrest of cerebral cortical neurons in proliferative zones near the lateral ventricles (periventricular heterotopia). Here we show that an autosomal recessive condition characterized by microcephaly and periventricular heterotopia 1 maps to chromosome 20 and is caused by mutations in the gene ADP-ribosylation factor guanine nucleotide-exchange factor-2 (ARFGEF2). By northernblot analysis, we found that mouse Arfgef2 mRNA levels are highest during embryonic periods of ongoing neuronal proliferation and migration, and by in situ hybridization, we found that the mRNA is widely distributed throughout the embryonic central nervous system (CNS). ARFGEF2 encodes the large (>200 kDa) brefeldin A (BFA)-inhibited GEF2 protein (BIG2), which is required for vesicle and membrane trafficking from the trans-Golgi network (TGN). Inhibition of BIG2 by BFA, or by a dominant negative ARFGEF2 cDNA, decreases cell proliferation in vitro, suggesting a cell-autonomous regulation of neural expansion. Inhibition of BIG2 also disturbed the intracellular localization of such molecules as E-cadherin and β-catenin by preventing their transport from the Golgi apparatus to the cell surface. Our findings show that vesicle trafficking is an important regulator of proliferation and migration during human cerebral cortical development.Autosomal recessive periventricular heterotopia with microcephaly (ARPHM) is a severe malformation of the cerebral cortex, characterized by severe developmental delay and recurrent infections 1 . No anomalies extrinsic to the CNS, such as dysmorphic features or grossly abnormal endocrine or other conditions, have been observed in individuals with ARPHM. Magnetic resonance imaging of the brains of affected individuals shows notable periventricular heterotopia, resulting from the failure of neurons to migrate normally from the lateral ventricular proliferative zone, where they are formed, to the cerebral cortex ( Fig. 1a-d). Abnormal magnetic resonance image signals in subcortical white matter and elsewhere also suggest a delay in the normal myelination by glial cells.An initial genome-wide screen at 10-cM intervals of two Turkish families with ARPHM identified shared homozygosity at a single locus on chromosome 20q11.21-13.2, which we refined by further marker analysis (Fig. 1e,f). Because the two families had indistinguishable clinical and radiographic features, we assumed that they had an allelic disorder and summed their linkage results. The ARPHM region (66.16-77.75 cM on chromosome 20) that was identical by descent in each of the two families yielded a summed multipoint lod score of 4.41 (Fig. 1g). Two-point analyses gave combined maximal lod scores of 3.28 (pedigree 1 = 1.53 and pedigree 2 = 1.75) at marker D20S109 (Fig. 1h).We sequenced several candidate genes in the minimal linked region and found a different deleterious mutation in ARFGEF2 (encod...