RESEARCH ARTICLE Bipolar Disorder in the Bulgarian Gypsies: Genetic Heterogeneity in a Young Founder Population Radka Kaneva, 1 Vihra Milanova, 2 Dora Angelicheva, 3 Stuart MacGregor, 4 Christian Kostov, 2 Rositza Vladimirova, 2 Spiridon Aleksiev, 2 Mina Angelova, 1 Vessela Stoyanova, 2 Angeline Loh, 3 Joachim Hallmayer, 5 Luba Kalaydjieva, 3 and Assen Jablensky 6 * 1 Molecular Medicine Centre and National Genetic Laboratory, Medical University of Sofia, Sofia, Bulgaria 2 Department of Psychiatry, Medical University of Sofia and First Psychiatric Clinic, Alexandrovska University Hospital, Sofia, Bulgaria 3 Centre for Medical Research and Western Australian Institute for Medical Research, The University of Western Australia, Perth, Australia 4 Genetic Epidemiology, Queensland Institute of Medical Research, Royal Brisbane Hospital, Brisbane, Australia 5 Department of Psychiatry and Behavior Sciences, Stanford, California 6 School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Perth, Australia Received 9 December 2007; Accepted 27 March 2008 We report the results of follow-up analyses of 12 genomic regions showing evidence of linkage in a genome-wide scan (GWS) of Gypsy families with bipolar affective disorder (BPAD). The Gypsies are a young founder population compris- ing multiple genetically differentiated sub-isolates with strong founder effect and limited genetic diversity. The BPAD families belong to a single sub-isolate and are connected by numerous inter-marriages, resulting in a super-pedigree with 181 mem- bers. We aimed to re-assess the positive GWS findings and search for evidence of a founder susceptibility allele after the addition of newly recruited subjects, some changes in diagnos- tic assignment, and the use of denser genetic maps. Linkage analysis was conducted with SimWalk2, accommodating the full complexity of pedigree structure and using a conservative narrow phenotype definition (BPAD only). Six regions were rejected, while 1p36, 13q31, 17p11, 17q21, 6q24, and 4q31 produced nominally significant results in both the individual families and the super-pedigree. Haplotypes were recon- structed and joint tests for linkage and association were done for the most promising regions. No common ancestral haplo- type was identified by sequencing a strong positional and functional candidate gene (GRM1) and additional STR geno- typing in the top GWS region, 6q24. The best supported region was a 12 cM interval on 4q31, also implicated in previous studies, where we obtained significant results in the super- pedigree using both SimWalk2 (P ¼ 0.004) and joint Pseudo- marker analysis of linkage and linkage disequilibrium (P ¼ 0.000056). The size of the region and the characteristics of the Gypsy population make it suitable for LD mapping. Ó 2008 Wiley-Liss, Inc. Key words: bipolar disorder; linkage; genetic isolate; haplotypes; linkage disequilibrium INTRODUCTION Bipolar affective disorder, BPAD, (lifetime risk 1%; heritability >80%) is a severe mood disorder, characterized by early onset, This article contains supplementary material, which may be viewed at the American Journal of Medical Genetics website at http://www.interscience. wiley.com/jpages/1552-4841/suppmat/index.html. Radka Kaneva, Vihra Milanova, Luba Kalaydjieva, and Assen Jablensky contributed equally to this work. Grant sponsor: National Health and Medical Research Council of Australia; Grant number: 353648; Grant sponsor: National Science Fund, Ministry of Education and Science, Bulgaria; Grant number: G2/2003. Christian Kostov’s present address is Pfalzklinikum, Klinik fuer Psychiatrie und Psychotherapie, Rockenhausen, Germany. *Correspondence to: Prof. Assen Jablensky, School of Psychiatry & Clinical Neurosciences, University of Western Australia, MRF Building, 50 Murray Street, Mail Bag Delivery Point M571, Perth, WA 6000, Australia. E-mail: assen@cyllene.uwa.edu.au Published online 28 April 2008 in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/ajmg.b.30775 How to Cite this Article: Kaneva R, Milanova V, Angelicheva D, MacGregor S, Kostov C, Vladimirova R, Aleksiev S, Angelova M, Stoyanova V, Loh A, Hallmayer J, Kalaydjieva L, Jablensky A. 2009. Bipolar Disorder in the Bulgarian Gypsies: Genetic Heterogeneity in a Young Founder Population. Am J Med Genet Part B 150B:191–201. Ó 2008 Wiley-Liss, Inc. 191 Neuropsychiatric Genetics