Searching for Type 2 Diabetes Genes on Chromosome 20 Marshall Alan Permutt, Jonathan Wasson, Latisha Love-Gregory, Jiyan Ma, Gary Skolnick, Brian Suarez, Jennifer Lin, and Benjamin Glaser Genome scans in families with type 2 diabetes identified a putative locus on chromosome 20q. For this study, linkage disequilibrium mapping was used in an effort to narrow a 7.3-Mb region in an Ashkenazi type 2 diabetic population. The region encompassed a 1–logarithm of odds (LOD) interval around the microsatellite marker D20S107, which gave a LOD score of >3 in linkage analysis of a combined Caucasian population. This 7.3-Mb region contained 25 known and 99 predicted genes. Predicted single nucleotide polymorphisms (SNPs) were chosen from public databases and vali- dated. Two SNPs were unique to the Ashkenazi. Here, 91 SNPs with a minor allele frequency of >10% were genotyped in pooled DNA from 150 case subjects and 150 control subjects of Ashkenazi Jewish descent. The SNP association study showed that SNP rs2664537 in the TIX1 gene had a significant P value of 0.035, but the finding did not replicate in an additional case pool. In addition, HNF4a and Mybl2 were screened for muta- tions and new polymorphisms. No mutations were iden- tified, and a new nonsynonymous SNP (R687C in exon 14 of Mybl2) was found. The limits to this type of association study are discussed. Diabetes 51 (Suppl. 3): S308 –S315, 2002 T ype 2 diabetes is a complex metabolic disorder characterized by abnormal hepatic glucose out- put, insulin resistance, and impaired insulin pro- duction (1). Multiple environmental and genetic factors contribute, and genome scans in families with multiple affected individuals from several racial/ethnic groups have been undertaken (Table 1). A number of potential loci have been identified, but in general, the evidence for linkage has not been strong, and the regions identified have been quite broad. A major question remain- ing is how to proceed with the search for complex disease genes, knowing that a single gene is neither necessary nor sufficient and that recombinant mapping in families will not suffice. The next phase of the search for diabetes susceptibility genes will likely require new strategies. A genome scan with microsatellite markers at an aver- age distance of 9.5 cM was completed in type 2 diabetic sibling pairs (n = 472) of Ashkenazi Jewish descent (2). The Ashkenazi population is relatively young and homo- geneous, having undergone several constrictions and ex- pansions resulting in reduced genetic heterogeneity in comparison to that of most Western Caucasian subjects. Studies of DNA polymorphisms have suggested that present-day Ashkenazi Jews descended from a small founder population, numbering perhaps as few as 10,000 individuals who existed in Eastern Europe at about 1500 AD (3). Today, there are about 10 million, representing a 1,000-fold expansion in roughly 20 generations. In the genome scan, five regions on four chromosomes exhibited nominal evidence for linkage (P  0.05) (2). A maximal signal of Z = 2.05 was observed on chromosome 20 near D20S195. Because four other groups had previously re- ported evidence for linkage in the same region of chromo- some 20q in Caucasians (see summary in Table 1), this region was further considered. Subsequent to the Ashkenazi type 2 diabetes genome scan, several investigators contributed linkage data for chromosome 20 to the International Type 2 Diabetes Link- age Analysis Consortium (http://www.sfbr.org/external/ diabetes), a collaborative effort organized principally by the National Institute of Diabetes and Digestive and Kid- ney Diseases to map genes for the disease. Common markers on chromosome 20 were genotyped, and results were combined for a total of 1,852 families. The initial results of this analysis suggested a peak of linkage at D20S107 with a logarithm of odds (LOD) of 3. We therefore decided to target this region in our search in Ashkenazi patients with type 2 diabetes. Gene mapping by linkage disequilibrium analysis in related families identifies broad conserved regions of chromosomal DNA. In contrast, “unrelated” affected indi- viduals share smaller conserved chromosomal regions because there are many more meioses, resulting in greater recombination around the region harboring the disease gene. Theoretically, polymorphic markers in linkage dis- equilibrium with the disease locus can be used to find associations of regions containing the gene mutation. Linkage disequilibrium mapping has been shown to be an important tool for fine-mapping of monogenic diseases (10 –12), and recently there has been success in identifying a gene involved in a complex disease—inflammatory bowel disease (13). However, there is little doubt that linkage disequilibrium mapping for most other complex diseases will be more difficult (14). The distance over which disequilibrium extends between markers and dis- ease loci is not well understood nor is the degree of genetic risk contributed by any particular locus, suggest- ing that genotyping closely spaced markers in many case and control subjects would be required. Single nucleotide From the Washington University School of Medicine, Division of Endocrinol- ogy, Diabetes and Metabolism, St. Louis, Missouri. Address correspondence and reprint requests to M.A. Permutt, 660 S. Euclid Ave., Campus Box 8127, Saint Louis, MO 63110. E-mail: apermutt@im.wustl. edu. Received for publication 20 March 2002 and accepted in revised form 15 May 2002. LOD, logarithm of odds; PPAR, peroxisome proliferator-activated receptor; SNP, single nucleotide polymorphism. The symposium and the publication of this article have been made possible by an unrestricted educational grant from Servier, Paris. S308 DIABETES, VOL. 51, SUPPLEMENT 3, DECEMBER 2002