Title: LRRK2 G2019S in Families with Parkinson Disease Who Originated from Europe and the Middle East: Evidence of Two Distinct Founding Events Beginning Two Millennia Ago
Abstract: The leucine-rich repeat kinase 2 (LRRK2) G2019S mutation is the most common genetic determinant of Parkinson disease (PD) identified to date. It accounts for 1%–7% of PD in patients of European origin and 20%–40% in Ashkenazi Jews and North African Arabs with PD. Previous studies concluded that patients from these populations all shared a common Middle Eastern founder who lived in the 13th century. We tested this hypothesis by genotyping 25 microsatellite and single-nucleotide–polymorphism markers in 22 families with G2019S and observed two distinct haplotypes. Haplotype 1 was present in 19 families of Ashkenazi Jewish and European ancestry, whereas haplotype 2 occurred in three European American families. Using a maximum-likelihood method, we estimated that the families with haplotype 1 shared a common ancestor 2,250 (95% confidence interval 1,650–3,120) years ago, whereas those with haplotype 2 appeared to share a more recent founder. Our data suggest two separate founding events for G2019S in these populations, beginning at a time that coincides with the Jewish Diasporas. The leucine-rich repeat kinase 2 (LRRK2) G2019S mutation is the most common genetic determinant of Parkinson disease (PD) identified to date. It accounts for 1%–7% of PD in patients of European origin and 20%–40% in Ashkenazi Jews and North African Arabs with PD. Previous studies concluded that patients from these populations all shared a common Middle Eastern founder who lived in the 13th century. We tested this hypothesis by genotyping 25 microsatellite and single-nucleotide–polymorphism markers in 22 families with G2019S and observed two distinct haplotypes. Haplotype 1 was present in 19 families of Ashkenazi Jewish and European ancestry, whereas haplotype 2 occurred in three European American families. Using a maximum-likelihood method, we estimated that the families with haplotype 1 shared a common ancestor 2,250 (95% confidence interval 1,650–3,120) years ago, whereas those with haplotype 2 appeared to share a more recent founder. Our data suggest two separate founding events for G2019S in these populations, beginning at a time that coincides with the Jewish Diasporas. 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A single LRRK2 mutation (G2019S) accounts for 0.7%–1.6% of sporadic and 2.8%–6.6% of familial PD cases of European origin.11Goldwurm S Di Fonzo A Simons EJ Rohe CF Zini M Canesi M Tesei S et al.The G6055A (G2019S) mutation in LRRK2 is frequent in both early and late onset Parkinson's disease and originates from a common ancestor.J Med Genet. 2005; 42: e65Crossref PubMed Scopus (146) Google Scholar, 12Kay DM Zabetian CP Factor SA Nutt JG Samii A Griffith A Bird TD Kramer P Higgins DS Payami H Parkinson's disease and LRRK2: frequency of a common mutation in U.S. movement disorder clinics.Mov Disord. 2006; 21: 519-523Crossref PubMed Scopus (75) Google Scholar, 13Gilks WP Abou-Sleiman PM Gandhi S Jain S Singleton A Lees AJ Shaw K Bhatia KP Bonifati V Quinn NP Lynch J Healy DG Holton JL Revesz T Wood NW A common LRRK2 mutation in idiopathic Parkinson's disease.Lancet. 2005; 365: 415-416Abstract Full Text Full Text PDF PubMed Scopus (587) Google Scholar, 14Nichols WC Pankratz N Hernandez D Paisan-Ruiz C Jain S Halter CA Michaels VE Reed T Rudolph A Shults CW Singleton A Foroud T Genetic screening for a single common LRRK2 mutation in familial Parkinson's disease.Lancet. 2005; 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76: 672-680Abstract Full Text Full Text PDF PubMed Scopus (416) Google Scholar, 17Lesage S Durr A Tazir M Lohmann E Leutenegger AL Janin S Pollak P Brice A LRRK2 G2019S as a cause of Parkinson's disease in North African Arabs.N Engl J Med. 2006; 354: 422-423Crossref PubMed Scopus (426) Google Scholar, 18Ozelius LJ Senthil G Saunders-Pullman R Ohmann E Deligtisch A Tagliati M Hunt AL Klein C Henick B Hailpern SM Lipton RB Soto-Valencia J Risch N Bressman SB LRRK2 G2019S as a cause of Parkinson's disease in Ashkenazi Jews.N Engl J Med. 2006; 354: 424-425Crossref PubMed Scopus (531) Google Scholar Data from five studies of 90 unrelated G2019S-bearing subjects of European or Middle Eastern–North African (MENA) origin revealed that all shared the same haplotype, consistent with a common founder.11Goldwurm S Di Fonzo A Simons EJ Rohe CF Zini M Canesi M Tesei S et al.The G6055A (G2019S) mutation in LRRK2 is frequent in both early and late onset Parkinson's disease and originates from a common ancestor.J Med Genet. 2005; 42: e65Crossref PubMed Scopus (146) Google Scholar, 16Kachergus J Mata IF Hulihan M Taylor JP Lincoln S Aasly J Gibson JM Ross OA Lynch T Wiley J Payami H Nutt J Maraganore DM Czyzewski K Styczynska M Wszolek ZK Farrer MJ Toft M Identification of a novel LRRK2 mutation linked to autosomal dominant parkinsonism: evidence of a common founder across European populations.Am J Hum Genet. 2005; 76: 672-680Abstract Full Text Full Text PDF PubMed Scopus (416) Google Scholar, 17Lesage S Durr A Tazir M Lohmann E Leutenegger AL Janin S Pollak P Brice A LRRK2 G2019S as a cause of Parkinson's disease in North African Arabs.N Engl J Med. 2006; 354: 422-423Crossref PubMed Scopus (426) Google Scholar, 18Ozelius LJ Senthil G Saunders-Pullman R Ohmann E Deligtisch A Tagliati M Hunt AL Klein C Henick B Hailpern SM Lipton RB Soto-Valencia J Risch N Bressman SB LRRK2 G2019S as a cause of Parkinson's disease in Ashkenazi Jews.N Engl J Med. 2006; 354: 424-425Crossref PubMed Scopus (531) Google Scholar, 19Lesage S Leutenegger A-L Ibanez P Janin S Lohmann E Dürr A Brice A French Parkinson's Disease Genetics Study Group LRRK2 haplotype analyses in European and North African families with Parkinson disease: a common founder for the G2019S mutation dating from the 13th century.Am J Hum Genet. 2005; 77: 330-332Abstract Full Text Full Text PDF PubMed Scopus (113) Google Scholar The high prevalence of the mutation in Ashkenazi Jews and North African Arabs has led to the hypothesis that the mutation originated in the Middle East.18Ozelius LJ Senthil G Saunders-Pullman R Ohmann E Deligtisch A Tagliati M Hunt AL Klein C Henick B Hailpern SM Lipton RB Soto-Valencia J Risch N Bressman SB LRRK2 G2019S as a cause of Parkinson's disease in Ashkenazi Jews.N Engl J Med. 2006; 354: 424-425Crossref PubMed Scopus (531) Google Scholar Lesage and colleagues19Lesage S Leutenegger A-L Ibanez P Janin S Lohmann E Dürr A Brice A French Parkinson's Disease Genetics Study Group LRRK2 haplotype analyses in European and North African families with Parkinson disease: a common founder for the G2019S mutation dating from the 13th century.Am J Hum Genet. 2005; 77: 330-332Abstract Full Text Full Text PDF PubMed Scopus (113) Google Scholar used a likelihood-based haplotype approach20Genin E Tullio-Pelet A Begeot F Lyonnet S Abel L Estimating the age of rare disease mutations: the example of triple-A syndrome.J Med Genet. 2004; 41: 445-449Crossref PubMed Scopus (99) Google Scholar in the study of six families of North African or European origin carrying G2019S and estimated that these individuals shared a common founder ∼725 years ago.19Lesage S Leutenegger A-L Ibanez P Janin S Lohmann E Dürr A Brice A French Parkinson's Disease Genetics Study Group LRRK2 haplotype analyses in European and North African families with Parkinson disease: a common founder for the G2019S mutation dating from the 13th century.Am J Hum Genet. 2005; 77: 330-332Abstract Full Text Full Text PDF PubMed Scopus (113) Google Scholar Given the fact that G2019S is widely distributed across Europe and occurs at high frequency among Ashkenazi Jews and North African Arabs, this relatively recent estimated date is difficult to reconcile with established patterns of human migration.21Colombo R Age estimate of the N370S mutation causing Gaucher disease in Ashkenazi Jews and European populations: a reappraisal of haplotype data.Am J Hum Genet. 2000; 66: 692-697Abstract Full Text Full Text PDF PubMed Scopus (28) Google Scholar, 22Niell BL Long JC Rennert G Gruber SB Genetic anthropology of the colorectal cancer-susceptibility allele APC I1307K: evidence of genetic drift within the Ashkenazim.Am J Hum Genet. 2003; 73: 1250-1260Abstract Full Text Full Text PDF PubMed Scopus (49) Google Scholar Therefore, we collected genotype data on a larger sample of subjects, to examine the hypotheses that (1) patients with PD who are of European and MENA origin share a single ancestral haplotype and (2) the most recent common ancestor lived in the 13th century. The study population was derived from 1,611 unrelated patients with PD and 1,647 control individuals enrolled at seven movement-disorder clinics in three U.S. cities (Albany, NY; Portland, OR; and Seattle). All patients met standardized diagnostic criteria for PD, as determined by a movement-disorder specialist.23Gibb WR Lees AJ The relevance of the Lewy body to the pathogenesis of idiopathic Parkinson's disease.J Neurol Neurosurg Psychiatry. 1988; 51: 745-752Crossref PubMed Scopus (2594) Google Scholar Controls had no history of parkinsonism, and most were spouses of patients with PD. The institutional review boards at each participating site approved the study, and all subjects gave informed consent. Among these subjects, we identified 21 patients (1 homozygous, 20 heterozygous) and 1 control individual with G2019S (19 of these subjects have been reported elsewhere).12Kay DM Zabetian CP Factor SA Nutt JG Samii A Griffith A Bird TD Kramer P Higgins DS Payami H Parkinson's disease and LRRK2: frequency of a common mutation in U.S. movement disorder clinics.Mov Disord. 2006; 21: 519-523Crossref PubMed Scopus (75) Google Scholar, 24Zabetian CP Morino H Ujike H Yamamoto M Oda M Maruyama H Izumi Y Kaji R Griffith A Leis BC Roberts JW Yearout D Samii A Kawakami H Identification and haplotype analysis of LRRK2 G2019S in Japanese patients with Parkinson disease.Neurology. 2006; (electronically published May 25, 2006) (accessed August 11, 2006)(http://www.neurology.org/cgi/content/abstract/01.wnl.0000227732.37801.d4v1)Google Scholar For the present study, we included these 22 subjects, 23 of their family members (6 affected and 17 unaffected), and 30 unrelated G2019S-negative European American controls. Of the G2019S-positive families, 13 were of (non-Jewish) European origin, 3 defined themselves as Ashkenazi Jews, and 6 were of unspecified Jewish ancestry. However, the probands from those six families all indicated that their ancestors emigrated from central/eastern Europe or Russia and were thus likely descendants of the Ashkenazim. We systematically selected markers, to determine whether our subjects carrying G2019S shared a common haplotype, using data from an ongoing study in which we are screening the entire LRRK2 coding region and flanking intronic sequence for new mutations. Complete sequence data on all 51 exons were available for one subject homozygous and for three subjects heterozygous for G2019S. We compared these four individuals at 90 polymorphic sites and found five (rs28903073, rs2404834, rs10784522, rs10878405, and ss52051244) at which one subject (IPD584) differed from one or more of the others (IPD289, IPD452, and/or PD82801) at both alleles. We genotyped these five SNPs, 18 markers included in previous studies,11Goldwurm S Di Fonzo A Simons EJ Rohe CF Zini M Canesi M Tesei S et al.The G6055A (G2019S) mutation in LRRK2 is frequent in both early and late onset Parkinson's disease and originates from a common ancestor.J Med Genet. 2005; 42: e65Crossref PubMed Scopus (146) Google Scholar, 16Kachergus J Mata IF Hulihan M Taylor JP Lincoln S Aasly J Gibson JM Ross OA Lynch T Wiley J Payami H Nutt J Maraganore DM Czyzewski K Styczynska M Wszolek ZK Farrer MJ Toft M Identification of a novel LRRK2 mutation linked to autosomal dominant parkinsonism: evidence of a common founder across European populations.Am J Hum Genet. 2005; 76: 672-680Abstract Full Text Full Text PDF PubMed Scopus (416) Google Scholar, 17Lesage S Durr A Tazir M Lohmann E Leutenegger AL Janin S Pollak P Brice A LRRK2 G2019S as a cause of Parkinson's disease in North African Arabs.N Engl J Med. 2006; 354: 422-423Crossref PubMed Scopus (426) Google Scholar, 19Lesage S Leutenegger A-L Ibanez P Janin S Lohmann E Dürr A Brice A French Parkinson's Disease Genetics Study Group LRRK2 haplotype analyses in European and North African families with Parkinson disease: a common founder for the G2019S mutation dating from the 13th century.Am J Hum Genet. 2005; 77: 330-332Abstract Full Text Full Text PDF PubMed Scopus (113) Google Scholar,24Zabetian CP Morino H Ujike H Yamamoto M Oda M Maruyama H Izumi Y Kaji R Griffith A Leis BC Roberts JW Yearout D Samii A Kawakami H Identification and haplotype analysis of LRRK2 G2019S in Japanese patients with Parkinson disease.Neurology. 2006; (electronically published May 25, 2006) (accessed August 11, 2006)(http://www.neurology.org/cgi/content/abstract/01.wnl.0000227732.37801.d4v1)Google Scholar and two additional microsatellites (D12S331 and D12S1592) in all 75 subjects in our study population. The markers (12 SNPs and 13 microsatellites) spanned 9 Mb across the PARK8 region. SNP genotyping was performed by sequencing with the Applied Biosystems BigDye Terminator v3.1 Cycle Sequencing Kit. Microsatellites were amplified by PCR with use of fluorescently labeled F primers, were run on an ABI PRISM 3130 Genetic Analyzer, and were analyzed using GeneMapper 4.0 software (Applied Biosystems). We estimated the age of the most recent common founder using the program Estiage.20Genin E Tullio-Pelet A Begeot F Lyonnet S Abel L Estimating the age of rare disease mutations: the example of triple-A syndrome.J Med Genet. 2004; 41: 445-449Crossref PubMed Scopus (99) Google Scholar This maximum-likelihood method uses information on the recombination fractions between the mutation and each marker, the frequencies of the shared allele at each marker, and the position of the first marker in each direction that is no longer shared, to calculate the number of generations (with 95% CI) elapsed since the most recent common ancestor introduced the mutation into the population. We defined a marker as shared among families if a single (best-call) allele was included in all disease haplotypes or in at least half and at significantly greater frequency (Fisher's exact test α=.05) than in 60 inferred control haplotypes (collapsing all other alleles into a single bin). Genetic-map positions for each marker were derived from the linkage-mapping server MAP-O-MAT, and physical positions were taken from the National Center for Biotechnology Information (NCBI) human genome assembly Build 35.25Kong X Matise TC MAP-O-MAT: internet-based linkage mapping.Bioinformatics. 2005; 21: 557-559Crossref PubMed Scopus (26) Google Scholar Because many of the markers used in the present study were tightly linked, genetic distances between them could not be accurately estimated from available genetic maps. Instead, we used the genetic length and physical distance between the extreme markers (D12S2080 and D12S1301) to calculate an average of 0.30 cM per Mb across the entire analyzed region and then computed recombination fractions using the Kosambi mapping function. In instances where marker phase could not be unambiguously resolved by pedigree data, we used PHASE v2.1.126Stephens M Scheet P Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation.Am J Hum Genet. 2005; 76: 449-462Abstract Full Text Full Text PDF PubMed Scopus (1066) Google Scholar (Matthew Stephens' Web site) to infer haplotypes. Since the use of inferred haplotypes can introduce additional uncertainty into age estimates, we first divided PHASE calls for each allele at a given marker into three categories by probability: best (P>.5), plausible (.05<P<.5), and unlikely (P<.05). We then performed four separate runs, in Estiage, to estimate the age of the most recent founder by using haplotypes from only the families in which phase could be unambiguously resolved across shared markers or with the most likely (best call only), longest plausible, or shortest plausible haplotypes inferred by PHASE (Matthew Stephens' Web site) in all families. Two clearly distinct disease haplotypes (referred to hereafter as "haplotype 1" and "haplotype 2") became evident on inspection of the data (fig. 1). Haplotype 1 included a core region of 17 consecutive markers spanning 243 kb (D12S2514 to D12S2519) that was shared by 19 families, with the exception of one marker, D12S2515. Our group and others have argued that D12S2515 is unstable and that the allelic differences previously observed among disease haplotypes at this marker were likely due to recurrent mutation rather than recombination.11Goldwurm S Di Fonzo A Simons EJ Rohe CF Zini M Canesi M Tesei S et al.The G6055A (G2019S) mutation in LRRK2 is frequent in both early and late onset Parkinson's disease and originates from a common ancestor.J Med Genet. 2005; 42: e65Crossref PubMed Scopus (146) Google Scholar, 24Zabetian CP Morino H Ujike H Yamamoto M Oda M Maruyama H Izumi Y Kaji R Griffith A Leis BC Roberts JW Yearout D Samii A Kawakami H Identification and haplotype analysis of LRRK2 G2019S in Japanese patients with Parkinson disease.Neurology. 2006; (electronically published May 25, 2006) (accessed August 11, 2006)(http://www.neurology.org/cgi/content/abstract/01.wnl.0000227732.37801.d4v1)Google Scholar Data from the current study further support this idea; all 19 families with haplotype 1 shared alleles at three markers upstream from D12S2515, including the A allele of rs28903073, which was observed elsewhere in only 1 of 906 European American control chromosomes (fig. 1).24Zabetian CP Morino H Ujike H Yamamoto M Oda M Maruyama H Izumi Y Kaji R Griffith A Leis BC Roberts JW Yearout D Samii A Kawakami H Identification and haplotype analysis of LRRK2 G2019S in Japanese patients with Parkinson disease.Neurology. 2006; (electronically published May 25, 2006) (accessed August 11, 2006)(http://www.neurology.org/cgi/content/abstract/01.wnl.0000227732.37801.d4v1)Google Scholar This suggests that the A allele is identical by descent for haplotype 1 carriers and that any discordant alleles at intervening markers (between rs28903073 and G2019S) in these individuals arose via new mutations. Thus, D12S2515 was excluded from the data set used to reconstruct haplotypes and was not used in subsequent common founder-age estimates. Haplotype 2 was present in three families of European descent (fig. 1) and could be differentiated from the core region of haplotype 1 by five intragenic SNPs and one extragenic microsatellite (D12S2519). These included the two closest flanking markers, which were located 5 kb upstream (rs2404834) and 6 kb downstream (rs10784522) from G2019S. Haplotype 2 extended a minimum of 6 Mb across the PARK8 region, from the 5′-most marker assayed (D12S2080) to D12S1592. Haplotypes 1 and 2 appear to be rare in populations of European ancestry, since the frequency of haplotype 1 can be no greater than that of the A allele at rs28903073 (0.1%),24Zabetian CP Morino H Ujike H Yamamoto M Oda M Maruyama H Izumi Y Kaji R Griffith A Leis BC Roberts JW Yearout D Samii A Kawakami H Identification and haplotype analysis of LRRK2 G2019S in Japanese patients with Parkinson disease.Neurology. 2006; (electronically published May 25, 2006) (accessed August 11, 2006)(http://www.neurology.org/cgi/content/abstract/01.wnl.0000227732.37801.d4v1)Google Scholar and haplotype 2 was not observed in our sample of 60 control chromosomes. Taken together, these data strongly suggest that the disease chromosomes in our study population originated from two separate founders. We then estimated the age of the most recent common founder among the 19 families with haplotype 1, designating D12S2194 and D12S1048 as the boundaries of the shared haplotype as determined by the aforementioned criteria (table 1). Our first approach, which was the one most comparable to that used by Lesage and colleagues,19Lesage S Leutenegger A-L Ibanez P Janin S Lohmann E Dürr A Brice A French Parkinson's Disease Genetics Study Group LRRK2 haplotype analyses in European and North African families with Parkinson disease: a common founder for the G2019S mutation dating from the 13th century.Am J Hum Genet. 2005; 77: 330-332Abstract Full Text Full Text PDF PubMed Scopus (113) Google Scholar restricted the analysis to families with phase-known data within the shared region. This reduced the data set to five families (IPD289, IPD452, PD82801, PN184, and PN196) representing six disease chromosomes and produced an age estimate of 65 (95% CI 36–121) generations. After incorporating the remaining 14 families for which phase was inferred, the best-call and longest haplotypes were identical and yielded an estimate of 75 (95% CI 55–104) generations, whereas the shortest haplotypes estimate was 84 (95% CI 61–117) generations. With use of the most widely published intergenerational interval, 25 years,27Fenner JN Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies.Am J Phys Anthropol. 2005; 128: 415-423Crossref PubMed Scopus (305) Google Scholar our best-call data indicate that these families shared a common ancestor 1,875 (95% CI 1,375–2,600) years ago. However, several recent studies have concluded that 30 years is a better approximation of generation time for the period of human history in question.27Fenner JN Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies.Am J Phys Anthropol. 2005; 128: 415-423Crossref PubMed Scopus (305) Google Scholar, 28Tremblay M Vézina H New estimates of intergenerational time intervals for the calculation of age and origins of mutations.Am J Hum Genet. 2000; 66: 651-658Abstract Full Text Full Text PDF PubMed Scopus (139) Google Scholar, 29Sigurðardóttir S Helgason A Gulcher JR Stefansson K Donnelly P The mutation rate in the human mtDNA control region.Am J Hum Genet. 2000; 66: 1599-1609Abstract Full Text Full Text PDF PubMed Scopus (159) Google Scholar A 30-year interval with best-call haplotypes increases the age of the founding event to 2,250 (95% CI 1,650–3,120) years ago. We did not perform age estimates for the three families with haplotype 2, because the sample size was small and we were not able to define the 5′ limit of the shared region. However, since the genetic length of the shared region is inversely proportional to the age of the founding event, these three families likely shared a common ancestor more recently than did the haplotype 1 families.Table 1Data Used in Estimating the Age of the G2019S Haplotype 1 Common FounderData Used for FamilyMarkerIPD289(p)aThe proband of family IPD289 was homozygous for G2019S; thus, haplotypes from the paternal (p) and maternal (m) lineages are provided separately.IPD289(m)aThe proband of family IPD289 was homozygous for G2019S; thus, ha