Linkage disequilibrium at the SCA2 locus

Spinocerebellar ataxia type 2 (SCA2) is caused by the expansion of an unstable CAG repeat encoding a polyglutamine tract. Repeats with 32 to 200 CAGs are associated with the disease, whereas normal chromosomes contain 13 to 33 repeats. We tested 220 families of different geographical origins for the SCA2 mutation. Thirty three were positive (15%). Twenty three families with at least two affected subjects were tested for linkage disequilibium (LD) between the SCA2 mutation and three microsatellite markers, two of which (D12S1332-D12S1333) closely flanked the mutation; the other (D12S1672) was intragenic. Many different haplotypes were observed, indicating the occurrence of several ancestral mutations. However, the same haplotype, not observed in controls, was detected in the German, the Serbian, and some of the French families, suggesting a founder effect or recurrent mutations on an at risk haplotype.     

Molecular studies in Finnish patients with familial juvenile nephronophthisis exclude a founder effect and support a common mutation causing mechanism.

Familial juvenile nephronophthisis (NPH) is an autosomal recessive tubulointerstitial kidney disease associated with formation of medullary and corticomedullary cysts. It progresses to end stage renal failure and its biochemical defect is unknown. An NPH locus has been assigned to a 2 cM interval on chromosome 2q13 by linkage studies. Homozygous deletions of approximately 250 kb have been detected in 80% of familial cases and 65% of sporadic cases and a common mutation mechanism has been suggested. We examined 14 Finnish families for the presence or absence of a deletion. After detecting a deletion in 12 patients belonging to nine families, we studied a possible founder effect by haplotype analysis using markers D2S340, D2S1889, and D2S1893. No common ancestral disease associated haplotype was found suggesting no founder effect. Results of pairwise linkage analyses were suggestive of linkage in the nine families with a deletion (lod scores of 1.39-3.89 at a recombination fraction of 0). Negative lod scores were obtained in the five families without a deletion suggesting that the disease locus in these families lies elsewhere. The end stage renal disease occurred at a more advanced age in patients without a deletion compared to patients with a deletion, indicating a phenotypic difference between these two groups.     

The USH2A c.2299delG mutation: dating its common origin in a Southern European population

Usher syndrome type II is the most common form of Usher syndrome. USH2A is the main responsible gene of the three known to be disease causing. It encodes two isoforms of the protein usherin. This protein is part of an interactome that has an essential role in the development and function of inner ear hair cells and photoreceptors. The gene contains 72 exons spanning over a region of 800 kb. Although numerous mutations have been described, the c.2299delG mutation is the most prevalent in several populations. Its ancestral origin was previously suggested after the identification of a common core haplotype restricted to 250 kb in the 5′ region that encodes the short usherin isoform. By extending the haplotype analysis over the 800 kb region of the USH2A gene with a total of 14 intragenic single nucleotide polymorphisms, we have been able to define 10 different c.2299delG haplotypes, showing high variability but preserving the previously described core haplotype. An exhaustive c.2299delG/control haplotype study suggests that the major source of variability in the USH2A gene is recombination. Furthermore, we have evidenced twice the amount of recombination hotspots located in the 500 kb region that covers the 3′ end of the gene, explaining the higher variability observed in this region when compared with the 250 kb of the 5′ region. Our data confirm the common ancestral origin of the c.2299delG mutation.     

Familial hypomagnesemia maps to chromosome 9q, not to the X chromosome: genetic linkage mapping and analysis of a balanced translocation breakpoint

Familial hypomagnesemia with secondary hypocalcemia (HSH) (MIM 307600) was studied in three inbred Bedouin kindreds from Israel. The three kindreds, one extended and two nuclear families, contained 13 affected individuals, 11 males and two females. Assuming that the individuals affected with hypomagnesemia shared a chromosomal region inherited from a common ancestor, we used a DNA pooling strategy in a genome-wide search for loci which show homozygosity for shared alleles in affected individuals. DNA samples from affected individuals within a single kindred were pooled and used as the template for PCR amplification of short tandem repeat polymorphic markers (STRPs). Pooled DNA from unaffected siblings and parents were used as controls. A shift towards homozygosity was observed in the affected DNA pool compared with the control pools with D9S301 (GATA7D12). Genotyping of individual DNA samples with D9S301 and several flanking markers confirmed linkage to chromosome 9 with maximum LOD scores of 3.4 (theta = 0.05), 3.7 (theta = 0) and 2.3 (theta = 0) for the three families. We have identified a 14 cM interval on chromosome 9 (9q12-9q22.2), flanked by proximal marker D9S1874 and distal marker D9S1807, within which all affected individuals from the three kindreds are homozygous for a shared haplotype. The disease segregates with a common affected haplotype in the three families, suggesting that hypomagnesemia is caused by a common ancestral mutation in these families. Although HSH has been previously reported to be X linked, these linkage data demonstrate that the disorder is an autosomal recessive disease in these kindreds. Mapping of a chromosomal breakpoint in a somatic cell line established from a patient with HSH and a balanced X;9 translocation placed the chromosomal breakpoint in a 500 kb region flanked by D9S1844 and D9S273. Identification of the gene responsible for hypomagnesemia will provide insight into the regulation of this essential cation.      

染色体单体型分析及突变检测在Wilson病临床诊断中的应用

目的建立染色体单体型分析法与突变检测相结合的Ｗｉｌｓｏｎ病（Ｗｉｌｓｏｎ＇ｓｄｉｓｅａｓｅ,ＷＤ）的基因诊断方法。方法以８个汉族ＷＤ家系为对象,用Ｄ１３Ｓ３１６、Ｄ１３Ｓ１３３和Ｄ１３Ｓ３１４３个［ＣＡ］ｎ重复遗传标记构建染色体单体型,进行ＷＤ家系内的诊断研究;对先证者的致病突变已明确的５个家系,同时用ＰＣＲ－ＳＳＣＰ检测法检测突变以完善诊断。结果找到了１例无症状期ＷＤ患者,５例杂合子。结论通过分析Ｄ１３Ｓ３１６、Ｄ１３Ｓ１３３、Ｄ１３Ｓ３１４构成的染色体单体型,基本可为先证者同胞兄妹明确诊断;对致病突变已确定的家系,突变检测能为诊断提供直接而肯定的依据。两种方法的联合使用可为诊断提供更多的依据     

Spinocerebellar ataxia 1 (SCA1) in the Japanese in Hokkaido may derive from a single common ancestry.

Spinocerebellar ataxia 1 (SCA1) is caused by expansion of an unstable CAG triplet repeat located on the short arm of chromosome 6. Precise mapping has shown a positional relationship to closely linked markers in the order of D6S109-D6S274-D6S288-SCA1-AM10GA-D6S89+ ++-EDN1 from centromere to telomere. The haplotype which cosegregated with the disease was determined in 12 Japanese pedigrees with SCA1. Although the alleles of the SCA1 haplotype varied from pedigree to pedigree, depending on the distance from the SCA1 locus, the affected and presymptomatic subjects carried the same alleles at D6S288 and D6S274. All the families with SCA1 had migrated from either Miyagi or Yamagata Prefectures, neighbouring areas in the Tohoku District, the northern part of Honshu which is the main island of Japan. It seems highly likely that SCA1 in the Japanese, at least those residing in Hokkaido, derives from a single common ancestry.     

Dutch myotonic dystrophy type 2 patients and a North-African DM2 family carry the common European founder haplotype

Myotonic dystrophy type 2 (DM2) is a progressive multisystem disease with muscle weakness and myotonia as main characteristics. The disease is caused by a repeat expansion in the zinc-finger protein 9 (ZNF9) gene on chromosome 3q21. Several reports show that patients from European ancestry share an identical haplotype surrounding the ZNF9 gene. In this study, we investigated whether the Dutch DM2 population carries the same founder haplotype. In all, 40 Dutch DM2 patients from 16 families were genotyped for eight short tandem repeat markers surrounding the ZNF9 gene. In addition, the single-nucleotide polymorphism (SNP) rs1871922 located in the first intron of DM2 was genotyped. Results were compared with previously published haplotypes from unrelated Caucasian patients. The repeat lengths identified in this study were in agreement with existing literature. In 36 patients of our population, we identified three common haplotypes. One patient showed overlap with the common haplotype for only one marker closest to the ZNF9 gene. The haplotype from a family originating from Morocco showed overlap with that of the patients of European descent for a region of 222 kb. All patients carried at least one C allele of SNP rs1871922 indicating that all patients carry the European founder haplotype. We conclude that DM2 patients from the Netherlands, including a North-African family, harbor a common haplotype surrounding the ZNF9 gene. This data show that the Dutch patients carry the common founder haplotype and strongly suggest that DM2 mutations in Europe and North Africa originate from a single ancestral founder.     

一个表皮松解性掌跖角化病维吾尔家系致病基因研究

目的 对一个维吾尔族表皮松解性掌跖角化病(epidermolytic palmoplantar keratoderma,EPPK)家系角蛋白9基因(keratin 9 gene,KRT9)进行测序,以检测其是否为该病的致病基因.方法 提取新疆地区一个维吾尔族EPPK家系外周血基因组DNA,针对已知候选基因KRT9和KRT1,分别对其所在染色体位置17q12-q21和12q13选取遗传标记进行连锁分析研究,确定连锁区域后,对区域内KRT9基因所有外显子进行测序分析.结果 分别得到48个家庭成员遗传标记的基因型和单倍型,经Linkage软件计算分析,发现标记D17S1787在=0时Lod值达到8.65,并最终将该病候选区域定位于遗传标记17/TG/36620115-D17S846之间约1 Mb范围内.排除该病与位于染色体12q13上的遗传标记DI2S96(θ=0时Lod=-∞)连锁.未发现KRT9基因存在致病性突变.结论 提示该表皮松解性掌跖角化病家系的致病基因位于染色体17q21.2上(chr17:36620083-37146934)约1 Mb区域内,且突变位点不位于KRT9基因编码区.     

Haplotype analysis of two recurrent genomic rearrangements in the BRCA1 gene suggests they are founder mutations for the Greek population

Pertesi M, Konstantopoulou I, Yannoukakos D. Haplotype analysis of two recurrent genomic rearrangements in the BRCA1 gene suggests they are founder mutations for the Greek population. The deletions of 4.4 and 3.2 kb identified in exons 24 and 20, respectively, are two of the four most common mutations in the BRCA1 gene in Greek breast cancer patients. They have been reported previously six and three times, respectively, in unrelated Greek families. A total of 11 more families have been identified in the present study. In order to characterize these recurrent mutations as founder mutations, it is necessary to identify the disease‐associated haplotype and prove that it is shared by all the mutation carriers, suggesting that it occurred only once in a common ancestor. Haplotype analysis was performed on 24 mutation carriers and 66 healthy individuals using 10 short tandem repeat markers located within and flanking the BRCA1 gene locus, spanning a 5.9 Mb interval. Results indicate that most of the carriers of the exon 24 deletion share a common core haplotype ‘4‐7‐6‐6‐1‐3’ between markers D17S951 and D17S1299, for a stretch of 2.9 Mb, while the common haplotype for the exon 20 deletion is ‘6‐7‐4‐2‐6‐7‐1‐3’ between markers D17S579 and D17S1299, for a stretch of 3.9 Mb. Both genomic rearrangements in BRCA1 gene are Greek founder mutations, as carriers share the same, for each mutation, disease‐associated haplotype, suggesting the presence of a distinct common ancestor for both mutations.     

Molecular analysis of Wilson disease in Taiwan: identification of one novel mutation and evidence of haplotype-mutation association

Wilson disease (WND) is caused by a deficiency of the copper-transporting enzyme, P-type ATPase (ATP7B). Twelve different mutations have previously been identified in Taiwan Chinese with Wilson disease. We, herein, report another 4 missense mutations, 1 of which is novel. We did haplotype analysis of Taiwanese WND chromosomes, using three well characterized short tandem repeat markers (haplotype was assigned in the order of D13S314-D13S301-D13S316). Association correlation was found between the mutations and their respective haplotypes. Haplotype-deduced pedigree analysis was shown to be helpful in the mutation analysis of WND chromosomes and in the molecular assessment of both pre-symptomatic WND patients and carriers. Given the complexity and heterogeneity of the mutation spectrum of ATP7B, we suggest that haplotype analysis should be performed before full-scale mutation analysis. Received: April 21, 2000 / Accepted: June 2, 2000     

Ancient origin of the CAG expansion causing Huntington disease in a Spanish population

Huntington disease (HD) is an autosomal dominant neurodegenerative disorder characterized clinically by progressive motor impairment, cognitive decline, and emotional deterioration. The disease is caused by the abnormal expansion of a CAG trinucleotide repeat in the first exon of the huntingtin gene in chromosome 4p16.3. HD is spread worldwide and it is generally accepted that few mutational events account for the origin of the pathogenic CAG expansion in most populations. We have investigated the genetic history of HD mutation in 83 family probands from the Land of Valencia, in Eastern Spain. An analysis of the HD/CCG repeat in informative families suggested that at least two main chromosomes were associated in the Valencian population, one associated with allele 7 (77 mutant chromosomes) and one associated with allele 10 (two mutant chromosomes). Haplotype A-7-A (H1) was observed in 47 out of 48 phase-known mutant chromosomes, obtained by segregation analysis, through the haplotype analysis of rs1313770-HD/CCG-rs82334, as it also was in 120 out of 166 chromosomes constructed by means of the PHASE program. The genetic history and geographical distribution of the main haplotype H1 were both studied by constructing extended haplotypes with flanking short tandem repeats (STRs) D4S106 and D4S3034. We found that we were able to determine the age of the CAG expansion associated with the haplotype H1 as being between 4,700 and 10,000 years ago. Furthermore, we observed a nonhomogenous distribution in the different regions associated with the different extended haplotypes of the ancestral haplotype H1, suggesting that local founder effects have occurred.     

Genetic heterogeneity of dominantly inherited olivopontocerebellar atrophy (OPCA) in the Japanese: Linkage study of two pedigrees and evidence for the disease locus on chromosome 12q (SCA2)

Summary We did a linkage study of 2 multigenerational pedigrees with dominant olivopontocerebellar atrophy (OPCA) other than SCA1, with chromosome 12q microsatellites. Multipoint linkage analysis led to the conclusion that the disease locus locates within the 6.2 cM interval between IGF1 and D12S84/D12S105. This result coincides with that of Cuban ataxia pedigrees designated as SCA2. Our study provides genetic evidence that dominant OPCA in the Japanese consists of at least two genetically different disorders: SCA1 and SCA2.     

Haplotype analysis of the 4p16.3 region in Portuguese families with Huntington's disease

Huntington's disease (HD) is a neurodegenerative disorder characterized by involuntary choreic movements, cognitive impairment, and behavioral changes, caused by the expansion of an unstable CAG repeat in HTT. We characterized the genetic diversity of the HD mutation by performing an extensive haplotype analysis of ～1Mb region flanking HTT in over 300 HD families of Portuguese origin. We observed that haplotype A, marked by HTT delta2642, was enriched in HD chromosomes and carried the two largest expansions reported in the Portuguese population. However, the most frequent HD haplotype B carried one of the largest (+12 CAGs) expansions, which resulted in an allele class change to full penetrance. Despite having a normal CAG distribution skewed to the higher end of the range, these two core haplotypes had similar expanded CAG repeat sizes compared to the other major core haplotypes (C and D) and there was no statistical difference in transmitted repeat instability across haplotypes. We observed a diversity of HTT region haplotypes in both normal and expanded chromosomes, representative of more than one ancestral chromosome underlying HD in Portugal, where multiple independent events on distinct chromosome 4 haplotypes have given rise to expansion into the pathogenic range. © 2015 Wiley Periodicals, Inc.     

Association of ulcerative colitis with the inflammatory bowel disease susceptibility locus IBD2 in non-Jewish Caucasians and evidence of genetic heterogeneity among racial and ethnic populations with Crohn disease

Genomewide scanning has been used to identify chromosomal regions encoding susceptibility loci to inflammatory bowel disease (IBD). The greatest evidence for linkage to IBD has been reported for a region of chromosome 12q14 surrounding the microsatellite marker D12S83, with a logarithm of odds score of 5.47 and a positive transmission disequilibrium test, and which was subsequently named IBD2. We wished to confirm this locus by genotyping the highly polymorphic microsatellites D12S1022, D12S1056, and D12S83, spanning a continuous region on chromosome 12 of 342 kb, in a cohort of nonrelated individuals with ulcerative colitis (89 patients), Crohn disease (121 patients), and population-based control subjects (100 patients). In non-Jewish Caucasians, one D12S1022 allele, one D12S1056 genotype, and three D12S83 alleles were found to have statistically significant differences in distribution between the two disease groups and the control population. These data support a significant association of IBD with the IBD2 locus in close vicinity to the three markers studied. The replication of genetic risk loci in a case control association study may indicate susceptibility genes in this region and may facilitate identification of candidate genes for IBD. Subgroup analysis revealed a notable difference in genotype distribution among Jewish Caucasian and African American patients affected with Crohn disease when compared with similarly affected non-Jewish Caucasians. Using Fisher exact test, statistically significant distribution differences were observed for D12S1022 and D12S83. These data indicate that there may be significant genetic heterogeneity between different ethnic and racial IBD populations or may simply reflect differences in marker allele frequencies among populations.     

NRL S50T mutation and the importance of 'founder effects' in inherited retinal dystrophies

The aim of this work was to identify NRL mutations in a panel of 200 autosomal dominant retinitis pigmentosa (adRP) families. All samples were subjected to heteroduplex analysis of the three exons of the NRL gene, and HphI restriction digest analysis of exon 2 (to identify the S50T mutation). Families found to have the S50T mutation, and six additional larger pedigrees (which had previously been excluded from the other nine adRP loci) underwent linkage analysis using polymorphic markers located in the region of 14q11. HphI restriction analysis followed by direct sequencing of the amplified NRL exon 2 product demonstrated the presence of the NRL S50T sequence change in three adRP families. Comparison of marker haplotypes in affected individuals from these families with those of affected members of the original 14q11 linked family revealed a common disease haplotype for markers within the adRP locus. Recombination events observed in these families define an adRP critical interval of 14.9 cM between D13S72 and D14S1041. Linkage analysis enabled all six of the larger adRP pedigrees to be excluded from the 14q11 locus. The NRL S50T mutation represents another example of a 'founder effect' in a dominantly inherited retinal dystrophy. Identification of such 'founder effects' may greatly simplify diagnostic genetic screening and lead to better prognostic counselling. The exclusion of several adRP families from all ten adRP loci indicates that at least one further adRP locus remains to be found.     

Characterization of a susceptibility locus for SLE, SLEB5, on chromosome 4p14-13

Systemic lupus erythematosus is a systemic autoimmune disorder of unknown aetiology but is most likely caused by an interaction between several genetic factors and the environment. In a previously published genome scan we presented linkage to a marker on chromosome 4p13 in Icelandic families. Fine mapping of the region has been performed using 10 multicase families from Iceland and the maximum two-point LOD score was given by marker D4S2974 (Z = 3.57, alpha = 1). Multipoint analyses of the markers in the region suggest a putative disease gene to be located between markers D4S405 and D4S2381. The maximum multipoint LOD score (Z = 3.76) was given for marker D4S2974 in combination with the novel repeat GT4C2. A family-specific haplotype was segregating with the disease in each of eight families although a founder haplotype could not be identified. Analysis of recombination events in the patients delimited the susceptibility locus to approximately 3 cM. The susceptibility locus identified probably contains a mutation that has been enriched in the Icelandic population but is less common in other populations. We also show that this region is not identical to a susceptibility locus for SLE located on 4p16 where we detect no linkage.     

三个短串联重复序列位点的等位基因遗传变异研究

目的 探讨短串联重复序列（short tandem repeats,STRs）遗传变异的方式及机理。方法 用银染方法对3个STR位点（FGA、D12S391、D11S554)共19个发生突变的家系父、母、子的DNA样本进行SRT基因分型，将需测序的等位基因条带从凝胶上切下，再进行PCR扩增，产物经纯化作为测序模板，采用循环测序法测序。结果 19个家系中有18个家系子代新产生的等位基因变异表现为一个重复单位的增加或减少（表现为一个重复单位增加的有8个家系，减少的有7个家系，不确定的有3个家系），只有1个家系表现为2个重复单位的减少，子代新产生的等位基因来自父亲的有13个家系，来自母亲的有3个家系，不能确定的有3个家系，来自父与母的比较约为4：1。3个STR位点等位基因突变都出现在长的、连续的四核苷酸重复区（FGA的“CTTT”区、D12S391的“AGAT”区、D11S554的“AAAG”区）。结论 FGA、D12S391和D11S5543个STR位点的等位基因突变主要表现为一个重复单位的增加或减少占95％，其次是两个重复单位的变化，没有碱基的插入或缺失，突变主要来自父亲，在这3个STR位点中的长的、连续的四核苷酸重复区可能是等位基因突变的敏感点。     

French myotonic dystrophy families show expansion of a CTG repeat in complete linkage disequilibrium with an intragenic 1 kb insertion.

The molecular basis of myotonic dystrophy (DM) has been characterised. All DM mutations characterised to date appear as an unstable elongation of a fragment containing a tandem repeat of a CTG motif, which can be visualised in both EcoRI and BamHI digests. It has been shown that the fragment is polymorphic in the normal population. Another 1 kb insertion/deletion polymorphism located near the unstable CTG repeat region has been identified. The 1 kb insertion allele is present in all DM patients. These different polymorphic systems can be distinguished using cDNA25 and BamHI, because this enzyme cuts between the site of the 1 kb insertion and the CTG repeat. We thus haplotyped DM patients from 72 French families and clearly showed that all chromosomes (100%) with the DM mutation carried the 1 kb insertion as well. In addition to this association, we detected significant linkage disequilibrium between the DM locus and D19S63 for which allelic frequencies were different from other European populations. Our results in the French DM population are thus in agreement with the hypothesis that the CTG expansion occurred on one or a few ancestral chromosomes carrying the large 1 kb insertion allele.     

家族性高甘油三酯血症家系的候选基因位点连锁分析

目的 对一个家族性高甘油三酯血症(familial hypertriglyceridemia,FHTG)家系进行遗传连锁定位及基因突变分析.方法 32名家系成员,其中12例为高甘油三酯血症(hypertriglyceridemia)患者.应用短串联重复(short tandem repeat,STR)片段微卫星标记物对其中的22名成员进行了16个与脂代谢有关的候选基因和(或)位点的遗传连锁分析和单倍型分析,并对其中的两个候选基因APOA2和USF1直接测序以筛查突变.结果 APOA5、LIPI、RP1、APOC2、ABC1,LMF1、APOA1-APOC3-APOA4、LPL,APOB、CETP、LCAT,LDLR,APOE等候选基因位点与该家系表型不连锁,Lod值均小于-1.0(θ=0).遗传连锁分析提示位于1q23.3-24.2染色体区域,疾病表型在D1S104至D1S196之间(遗传间距为5.87 cM)存在连锁,其中D1S194两点间最大Lod值为2.44(θ=0).对APOA2和USF1基因的序列分析未发现致病突变.结论 排除了上述候选基因为本家系的致病基因;提示在1q23.3-1q24.2染色体区域可能存在一个新的与FHTG相关的基因.     

Association of ulcerative colitis with the inflammatory bowel disease susceptibility locus IBD2 in non‐Jewish Caucasians and evidence of genetic heterogeneity among racial and ethnic populations with Crohn disease

Genomewide scanning has been used to identify chromosomal regions encoding susceptibility loci to inflammatory bowel disease (IBD). The greatest evidence for linkage to IBD has been reported for a region of chromosome 12q14 surrounding the microsatellite marker D12S83, with a logarithm of odds score of 5.47 and a positive transmission disequilibrium test, and which was subsequently named IBD2. We wished to confirm this locus by genotyping the highly polymorphic microsatellites D12S1022, D12S1056, and D12S83, spanning a continuous region on chromosome 12 of 342 kb, in a cohort of nonrelated individuals with ulcerative colitis (89 patients), Crohn disease (121 patients), and population‐based control subjects (100 patients). In non‐Jewish Caucasians, one D12S1022 allele, one D12S1056 genotype, and three D12S83 alleles were found to have statistically significant differences in distribution between the two disease groups and the control population. These data support a significant association of IBD with the IBD2 locus in close vicinity to the three markers studied. The replication of genetic risk loci in a case control association study may indicate susceptibility genes in this region and may facilitate identification of candidate genes for IBD. Subgroup analysis revealed a notable difference in genotype distribution among Jewish Caucasian and African American patients affected with Crohn disease when compared with similarly affected non‐Jewish Caucasians. Using Fisher exact test, statistically significant distribution differences were observed for D12S1022 and D12S83. These data indicate that there may be significant genetic heterogeneity between different ethnic and racial IBD populations or may simply reflect differences in marker allele frequencies among populations. © 2002 Wiley‐Liss, Inc.