Hereditary nonpolyposis colorectal cancer (HNPCC) is a dominantly inherited syndrome characterized by significantly increased risks for colon cancer as well as for cancers of the endometrium, stomach, small intestine, hepatobiliary system, kidney, ureter, and ovary.^1,2 Most studies have not reported increased risks for lung, breast, or prostate cancers in HNPCC kindreds. Many experts currently use the term HNPCC synonymously with a hereditary DNA mismatch repair (MMR) gene deficiency, and studies of cancer risks in the syndrome have generally focused on families with MMR deficiency. Based on fairly consistent cancer risks in studies of various designs, clinical screening guidelines have been proposed, focusing especially on screening for cancers of the colon and endometrium.^3-6 However, in the broader clinical realm and in some current medical literature, the term HNPCC continues to be based on pedigree criteria, typically the strict Amsterdam I criteria (AC-I),⁷ which have 3 elements: (1) there are at least 3 relatives with histologically verified colorectal cancer (1 a first-degree relative of the other 2), and familial adenomatous polyposis should be excluded; (2) at least 2 successive generations should be affected; and (3) 1 of the relatives’ colorectal cancers should be diagnosed before age 50 years.

While major inroads have been made in identifying the genetic causes of rare Mendelian disorders, little progress has been made in the discovery of common gene variations that predispose to complex diseases. The single gene variants that have been shown to associate reproducibly with complex diseases typically have small effect sizes or attributable risks. However, the joint actions of common gene variants within pathways may play a major role in predisposing to complex diseases (the paradigm of complex genetics). The goal of this study was to determine whether polymorphism in a candidate pathway (axon guidance) predisposed to a complex disease (Parkinson disease [PD]). We mined a whole-genome association dataset and identified single nucleotide polymorphisms (SNPs) that were within axon-guidance pathway genes. We then constructed models of axon-guidance pathway SNPs that predicted three outcomes: PD susceptibility (odds ratio = 90.8, p = 4.64 × 10⁻³⁸), survival free of PD (hazards ratio = 19.0, p = 5.43 × 10⁻⁴⁸), and PD age at onset (R² = 0.68, p = 1.68 × 10⁻⁵¹). By contrast, models constructed from thousands of random selections of genomic SNPs predicted the three PD outcomes poorly. Mining of a second whole-genome association dataset and mining of an expression profiling dataset also supported a role for many axon-guidance pathway genes in PD. These findings could have important implications regarding the pathogenesis of PD. This genomic pathway approach may also offer insights into other complex diseases such as Alzheimer disease, diabetes mellitus, nicotine and alcohol dependence, and several cancers. Complex diseases are common disorders that are believed to have many causes. Examples include Alzheimer disease, diabetes mellitus, nicotine and alcohol dependence, and several cancers. This study represents a paradigm shift from single gene to pathway studies of complex diseases. We present the example of Parkinson disease (PD) and a complex array of chemical signals that wires the brain during fetal development (the axon guidance pathway). We mined a dataset that studied hundreds of thousands of DNA variations (single nucleotide polymorphisms [SNPs]) in persons with and without PD and identified SNPs that were assigned to axon-guidance pathway genes. We then identified sets of SNPs that were highly predictive of PD susceptibility, survival free of PD, and age at onset of PD. The effect sizes and the statistical significance observed for the pathway were far greater than for any single gene. We validated our findings for the pathway using a second SNP dataset for PD and also a dataset for PD that studied RNA variations. There is prior evidence that the axon guidance pathway might play a role in other brain disorders (e.g., Alzheimer disease, Tourette syndrome, dyslexia, epilepsy, and schizophrenia). A genomic pathway approach may lead to important breakthroughs for many complex diseases.