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Delineation of the critical interval of Bardet-Biedl syndrome 1 (BBS1) to a small region of 11q13, through linkage and haplotype analysis of 91 pedigrees.

Bardet-Biedl syndrome (BBS) is a genetically heterogeneous recessive disease characterized primarily by atypical retinitis pigmentosa, obesity, polydactyly, hypogenitalism, and mental retardation. Despite the presence of at least five loci in the human genome, on chromosomes 2q, 3p, 11q, 15q and 16q, as many as 50% of the mutations appear to map to the BBS1 locus on 11q13. The recessive mode of inheritance and the genetic heterogeneity of the syndrome, as well as the inability to distinguish between different genetic loci by phenotypic analyses, have hindered efforts to delineate the 11q13 region as a first step toward cloning the mutated gene. To circumvent these difficulties, we collected a large number of BBS pedigrees of primarily North American and European origin and performed genetic analysis, using microsatellites from all known BBS genomic regions. Heterogeneity analysis established a 40.5% contribution of the 11q13 locus to BBS, and haplotype construction on 11q-linked pedigrees revealed several informative recombinants, defining the BBS1 critical interval between D11S4205 and D11S913, a genetic distance of 2.9 cM, equivalent to approximately 2.6 Mb. Loss of identity by descent in two consanguineous pedigrees was also observed in the region, potentially refining the region to 1.8 Mb between D11S1883 and D11S4944. The identification of multiple recombinants at the same position forms the basis for physical mapping efforts, coupled with mutation analysis of candidate genes, to identify the gene for BBS1.

Bardet-Biedl Syndrome↗

Haplotype analysis of ABCB1/MDR1 blocks in a Japanese population reveals genotype-dependent renal clearance of irinotecan.

We performed comprehensive haplotyping of ABCB1/MDR1 gene blocks using 49 genetic polymorphisms, including seven novel ones, obtained from 145 Japanese subjects. The ABCB1/MDR1 gene was divided into four blocks (Blocks -1, 1, 2, and 3) based on linkage disequilibrium analysis of polymorphisms. Using an expectation-maximization based program, 1, 2, 8, and 3 haplotype groups (3, 12, 32, and 18 haplotypes) were identified in Blocks -1, 1, 2, and 3, respectively. Within Block 2, haplotype groups *1, *2, *4, *6, and *8 reported by Kim and colleagues (Clin Pharmacol Ther 2001; 70:189-199) were found, and additional three groups (*9 to *11) were newly defined. We analyzed the association of haplotypes with the renal clearance of irinotecan and its metabolites in 49 Japanese cancer patients given irinotecan intravenously. There was a significant association of the *2 haplotype in Block 2, which includes 1236C>T, 2677G>T and 3435C>T, with a reduced renal clearance of those compounds. Moreover, tendencies of reduced and increased renal clearance were also observed with *1f in Block 2 and *1b in Block 3, respectively. These findings suggest that the P-glycoprotein encoded by ABCB1/MDR1 in the proximal tubules plays a substantial role in renal exclusion of drugs and, moreover, that block-haplotyping is valuable for pharmacogenetic studies.

ATP-Binding Cassette Transporters↗

Haplotype analysis at the ETM2 locus in a Singaporean sample with familial essential tremor.

An ancestral haplotype on chromosome 2p24.1 described in an American sample with familial essential tremor (ET) was analyzed in a different ethnic sample from Singapore. Six polymorphic loci (etm1240, etm1231, etm1234, APOB, etm1241, and etm1242) in a 274-kb interval within an ET gene candidate region (ETM2) were analyzed in Singaporean individuals with a family history of ET (n = 52) and compared to Singaporean controls older than age 65 (n = 49). The allele frequencies were significantly different between cases and controls for the loci etm1234 (p = 0.0001) and APOB (p = 0.0320). An extended haplotype formed by the loci etm1231, etm1234, and APOB occurred with a frequency of 31% in Singaporean cases and in 1.8% of elderly Singaporean controls (p = 0.0005). Haplotype studies in two different population samples suggest that a disease locus for ET lies near or within the 100-kb interval between the loci etm1231 and APOB.

Adolescent↗

Identification of three novel mutations in the USH1C gene and detection of thirty-one polymorphisms used for haplotype analysis.

Usher syndrome (USH) is a clinically and genetically heterogeneous autosomal recessive disorder in which sensorineural hearing loss is associated with retinitis pigmentosa. Usher syndrome type 1, the most severe form, is characterized by profound congenital deafness, vestibular dysfunction, and prepubertal onset of retinitis pigmentosa. Six different USH1 genes have so far been mapped, of which two have already been identified. MYO7A, encoding the unconventional myosin VIIA, underlies USH1B. Recently, the USH1C gene was shown to encode harmonin, a PDZ domain-containing protein. A previous screening of 18 unrelated USH1 patients, without a detected MYO7A mutation, for the three USH1C mutations described to date had demonstrated the presence of the 238-239insC mutation in the heterozygous state in four of them. A complete USH1C mutation screening in these four carriers of the 238-239insC mutation resulted in the detection of the second mutation in all the individuals, and the identification of three novel mutations, namely two splice site mutations (IVS1+1G>T and IVS5+1G>A) and a nonsense mutation (R31X). Thirty-one polymorphisms were detected in the USH1C gene. We observed that the E519D substitution is non-pathogenic, which is of particular interest for molecular diagnosis. Our analysis indicated that all the carriers of the 238-239insC mutation share a common haplotype. A different common haplotype was found in the two IVS1+1G>T carriers. Future studies of additional carriers and non-carriers should document the here proposed founder effect of these two mutations.

Abnormalities, Multiple↗

Haplotype analysis of killer cell immunoglobulin-like receptor genes in 77 Korean families.

Killer cell immunoglobulin-like receptor (KIR) genes constitute a multigene family whose genomic diversity is achieved through variation in gene content and allelic polymorphism within individual KIR genes. To date, 16 KIR genes and pseudogenes have been identified, and group A and group B haplotypes are characterized by a dominance of genes encoding inhibitory and activating receptors, respectively. In the present study, we have investigated the presence or absence of 16 KIR genes and pseudogenes and subtypes of four genes (3DP1, 3DP1 variant; 2DL1, 2DL1 variant; expressed and nonexpressed variant of 2DL5; full length and deleted form of 2DS4) in 352 members of 77 unrelated Korean families using a PCR-based sequence-specific priming method. KIR haplotypes were determined by segregation analysis. A total of 29 different KIR genotypes and 19 (two group A and 17 group B) haplotypes were identified in 154 parents. The distribution of genotypes, in terms of combination of haplotypes, was AA 55.2%, AB 36.4%, and BB 8.4%. Different from Caucasians, full-length 2DS4 (80.5%) was the predominant subtype of 2DS4 and group A (73.4%) outnumbered group B haplotypes (26.6%). The KIR gene frequencies and the predominance of A haplotypes in Koreans are similar to those in the Japanese.

Gene Frequency↗

Intrathecal humoral immune response in HAM/TSP in relation to HLA haplotype analysis.

INTRODUCTION: In HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP), we correlated human leukocyte antigen (HLA) haplotypes to the fine specificities of intrathecally synthesized IgG antibodies against HTLV-1. PATIENTS AND METHODS: HLA haplotypes of HAM/TSP patients were determined by the standard NIH microcytotoxicity test and family HLA studies. IgG antibodies against HTLV-1 synthetic peptides in paired CSF and serum were measured by enzyme immunoassay, and intrathecal synthesis of antibodies was evaluated. RESULTS: HAM/TSP patients with particular HLA haplotypes (A24Cw7B7DR1DQ5, A2Cw7B7DR1DQ5, A24Cw-B52DR15DQ6, A11Cw1B54DR4DQ4, and A24Cw1B54DR4DQ4) showed more frequently intrathecal synthesis of antibodies against HTLV-1 synthetic peptides, especially against HTLV-1 env gp21 synthetic peptides. CONCLUSION: In HAM/TSP, a retrovirus-induced human chronic inflammatory disease of the CNS, this is the first report to provide evidence that the intrathecal antiviral immune response is influenced by immunogenetic factors of the HLA complex.

Antibody Formation↗

Y-chromosomal STR haplotype analysis reveals surname-associated strata in the East-German population.

In human populations, the correct historical interpretation of a genetic structure is often hampered by an almost inherent inability to differentiate between ancient and more recent influences upon extant gene pools. One method to trace recent population movements is the analysis of surnames, which, at least in Central Europe, can be thought of as traits 'linked' to the Y chromosome. Illegitimacy, extramarital birth and changes of surnames may have substantially obscured this linkage. In order to assess the actual extent of correlation between surnames and Y-chromosomal haplotypes in Central Europe, we typed Y-chromosomal short tandem repeat markers in 419 German males from Halle. These individuals were subdivided into three groups according to the origin of their respective surname, namely German (G), Slavic (S) or 'Mixed' (M). The distribution of the haplotypes was compared by Analysis of Molecular Variance. While the M group was indistinguishable from group G (PhiST=-0.0008, P>0.5), a highly significant difference (PhiST=0.0277, P<0.001) was observed between the S group and the combined G+M group. This surprisingly strong differentiation is comparable to that of European populations of much larger geographic and linguistic difference. In view of the major migration from Slavic countries into Germany in the 19th century, it appears likely that the observed concurrence of Slavic surnames and Y chromosomes is of a recent rather than an early origin. Our results suggest that surnames may provide a simple means to stratify, and thereby to render more efficient, Y-chromosomal analyses of Central Europeans that target more ancient events.

Chromosomes, Human, Y↗

Haplotype analysis at the low density lipoprotein receptor locus: application to the study of familial hypercholesterolemia in Israel.

Familial hypercholesterolemia (FH) results from mutations in the low density lipoprotein (LDL) receptor gene. It has been shown that restriction fragment length polymorphisms (RFLPs) associated with this gene may be used for family and population studies. The present investigation is a population-based study of 19 Jewish families with hypercholesterolemia representing 9 different countries of origin. Ten RFLP sites were used to construct 24 different haplotypes from 112 chromosomes. These haplotypes vary in frequency from 0.9% to 28.6%. Five previously undescribed haplotypes, which comprise 8.1% of the sample, are reported here. The six most common haplotypes account for 70% of the sample. Segregation analysis reveals that, in Israel, distinct LDL receptor haplotypes are associated with hypercholesterolemia in 12 (63%) out of the 19 Jewish families. Five LDL receptor haplotypes co-segregate with hypercholesterolemia. Two of these haplotypes seem to be unique to specific population groups in Israel and may therefore represent founder mutations.

Apolipoproteins B↗

Haplotype analysis of the linkage group HLA-A:HAL-B:Bf and its bearing on the interpretation of the linkage disequilibrium.

The analysis of 650 HLA-A:HAL-B:Bf three-factor haplotypes revealed significant associations only between alleles of the very closely linked genes HLA-A and HLA-B, and Bf, respectively. Most striking is the highly significnat association of the rare Bf variant F1 with HLA-B18 and of S1 with HLA-B13, HLA-B14, and HLA-Bw21. Only random allele distributions were observed when considering the somewhat more distant genes HLA-A and Bf or the higher order interaction at all three genes. From these findings it seems likely that the linkage disequilibrium within the MHC is not due to selective forces, but rather due to a short evolutionary period.

Chromosomes, Human, 6-12 and X↗

The serotonin transporter gene: polymorphism and haplotype analysis in Russian suicide attempters.

The focus on gender-specific genes associated with female suicide is justified by the possible dimorphic nature of the serotonergic system and by the greater number of suicide attempts in females. We performed analysis of the promoter (5-HTTLPR) and intron 2 (STin2 VNTR) polymorphisms and haplotypes of the serotonin transporter gene in Russian suicide attempters, separately in men and women. Our findings indicate the contribution of the SLC6A4 gene to susceptibility for suicidal behavior in women, but not in men. The L/L genotype (p = 0.013, OR = 2.09) and L10 haplotype (p = 0.04, OR = 1.77) were associated with suicide in Russian women only. Further investigations of this gene in different phenotypic groups are necessary.

Adult↗

Haplotype analysis of genomic polymorphisms in and around the myotonic dystrophy locus in diverse populations of India.

The frequencies of haplotypes based upon the (CTG)n repeat and three other biallelic markers in and around the myotonic dystrophy (DM) locus were estimated in 13 ethnically, linguistically and geographically diverse sub-populations of India. The range of CTG repeats in caste populations was 5-31, while in tribal populations the range was shorter (5-23). Extensive variation in frequencies of large (CTG)n alleles (> or =18 repeats) was found in Indian populations. The implications of this finding on DM epidemiology are discussed. Haplotype diversity was found to be very high in most populations. The majority of the Indian DM patients carried a haplotype that is commonly found among DM patients globally; this is the most common haplotype in the class of large (> or =18 repeats) CTG alleles. However, one haplotype was found to be present in particularly high frequency in Indian populations; this haplotype was also found among Indian DM patients. This haplotype may be a characteristic of Indian and possibly of other East Asian populations.

Alleles↗

Haplotype analysis of classical and mild phenotype of phenylketonuria in the German Democratic Republic.

The restriction fragment length polymorphism (RFLP)-haplotypes have been analysed in 16 families from the northern part of the GDR at risk for classical and mild phenylketonuria (PKU). Ten different RFLP haplotypes associated with the normal and mutant phenylalanine hydroxylase (PAH) alleles were identified. Of the 32 mutant alleles analysed, 29 (90.6%) were associated with haplotypes 1, 2, 3 and 4; 53.1% of the mutant alleles were linked with haplotype 2. The distribution of RFLP haplotypes in 16 patients of clinical different PKU phenotypes (classical and mild) is reported.

Alleles↗

Association and haplotype analysis of the insulin-degrading enzyme (IDE) gene, a strong positional and biological candidate for type 2 diabetes susceptibility.

The gene for insulin-degrading enzyme (IDE) represents a strong positional and biological candidate for type 2 diabetes susceptibility. IDE maps to chromosome 10q23.3, a region linked to diabetes in several populations; the rat homolog has been directly implicated in diabetes susceptibility; and known functions of IDE support an important role in glucose homeostasis. We sought evidence for association between IDE variation and diabetes by mutation screening, defining local haplotype structure, and genotyping variants delineating common haplotypic diversity. An initial case-control analysis (628 diabetic probands from multiplex sibships and 604 control subjects) found no haplotypic associations, although one variant (IDE2, -179T-->C) showed modest association with diabetes (odds ratio [OR]1.25, P = 0.03). Linkage partitioning analyses failed to support this association, but provided borderline evidence for a different variant (IDE10, IVS20-405A-->G) (P = 0.06). Neither variant was associated with diabetes when replication was sought in 377 early onset diabetic subjects and 825 control subjects, though combined analysis of all typed cohorts indicated a nominally significant effect at IDE2 (OR 1.21 [1.04-1.40], P = 0.013). In the absence of convincing support for this association from linkage partitioning or analyses of continuous measures of glycemia, we conclude that analysis of over 2,400 samples provides no compelling evidence that variation in IDE contributes to diabetes susceptibility in humans.

Blood Glucose↗

Measured haplotype analysis of the aldosterone synthase gene and heart size.

Gene-association studies of heart size and the aldosterone synthase (CYP11B2) gene have produced inconsistent results, possibly because of limitations in the sample size and/or the number and location of the polymorphisms. An analysis of six polymorphisms spanning 6 kb of the CYP11B2 gene in Caucasian British families revealed a limited number of haplotypes because of strong linkage disequilibrium over this small region. The genotype and haplotype information was used in an association study involving 955 members of 229 families phenotyped for echocardiographic measures of heart size. In a mixed effects linear modelling analysis, the G5937C polymorphism was associated with cardiac wall thickness (P=0.02), and the intron conversion and A4550C polymorphisms were associated with left ventricular cavity size (P=0.02 and 0.002, respectively). Measured haplotype analyses confirmed the association of alleles at the intron conversion and G5937C polymorphisms with cardiac wall thickness (P=0.02), and alleles at the intron conversion polymorphism with left ventricular cavity size (P=0.04). The polymorphisms contributed to 2.0-3.4% of the variability in these traits. In summary, genetic polymorphisms at the CYP11B2 gene make a small contribution to quantitative variation in echocardiographic measures of heart size. These results point to the importance of analysing the full extent of genetic variation that captures the haplotype structure of a locus in gene association studies.

Cytochrome P-450 CYP11B2↗