Compound haplotypes at Xp11.23 and human population growth in Eurasia

To investigate patterns of diversity and the evolutionary history of Eurasians, we have sequenced a 2.8 kb region at Xp11.23 in a sample of African and Eurasian chromosomes. This region is in a long intron of CLCN5 and is immediately flanked by a highly variable minisatellite, DXS255, and a human‐specific Ta0 LINE. Compared to Africans, Eurasians showed a marked reduction in sequence diversity. The main Euro‐Asiatic haplotype seems to be the ancestral haplotype for the whole sample. Coalescent simulations, including recombination and exponential growth, indicate a median length of strong linkage disequilibrium, up to ～9kb for this area. The K_a/K_s ratio between the coding sequence of human CLCN5 and its mouse orthologue is much less than 1. This implies that the region sequenced is unlikely to be under the strong influence of positive selective processes on CLCN5, mutations in which have been associated with disorders such as Dent's disease. In contrast, a scenario based on a population bottleneck and exponential growth seems a more likely explanation for the reduced diversity observed in Eurasians. Coalescent analysis and linked minisatellite diversity (which reaches a gene diversity value greater than 98% in Eurasians) suggest an estimated age of origin of the Euro‐Asiatic diversity compatible with a recent out‐of‐Africa model for colonization of Eurasia by modern Homo sapiens.     

X-linked mental retardation exhibiting linkage to DXS255 and PGKP1: a new MRX family (MRX14) with localization in the pericentromeric region

Gene localization was determined by linkage analysis in a large French family with X-linked mental retardation (MRX). Seven living affected males were clinically studied and the clinical picture was characterized by moderate to severe mental handicap with poor secondary speech acquisition. Seizures, slight microcephaly, simian crease, anteverted pinnae, and macroorchidism were observed in some patients only. Linkage analysis revealed no recombination between the MRX gene and two loci: DXS255 at Xp11.22 (Zmax = 3.31 at θ= 0.00) and PGKP1 at Xq11.2-q12 (Zmax = 3.08 at 9 = 0.00). One recombination was observed between the gene and the two loci DXS164 at Xp21.2 and DXS441 at Xq13.3, respectively. These results suggested gene localization in the pericentromeric region of the X chromosome, and the LOD scores justified assignment of the symbol MRX14 to this family.     

Linkage disequilibria between HLA-B and the rarer properdin factor B alleles, BfF1 and BfS1

Phenotypic association and highly significant linkage disequilibria have been demonstrated for HLA-B18 and Bf^F1 and HLA-Bw50 and Bf^S1 alleles among Caucasians from Australia and the United States (San Francisco Bay area). The HLA-B18, Bf^uF1 association appears to be associated with HLA-Aw30. It is possible that Bf^S1 as a mutation, after the evolutionary splitting of HLA-Bw21, on an HLA-Bw50 haplotype, and that Bf^F1 arose on an HLA-Aw30, B18 haplotype.     

Properdin deficiency in a large Swiss family: identification of a stop codon in the properdin gene, and association of meningococcal disease with lack of the IgG2 allotype marker G2m(n).

Properdin deficiency was demonstrated in three generations of a large Swiss family. The concentration of circulating properdin in affected males was < 0.1 mg/l, indicating properdin deficiency type I. Two of the nine properdin-deficient males in the family had survived meningitis caused by Neisseria meningitidis serogroup B without sequel. Two point mutations were identified when the properdin gene in one of the properdin-deficient individuals was investigated by direct solid-phase sequencing of overlapping polymerase chain reaction (PCR) products. The critical mutation was found at base 2061 in exon 4, where the change of cytosine to thymine had generated the stop codon TGA. The other mutation was positioned at base 827 in intron 3. The stop codon in exon 4 was also demonstrated by standard dideoxy sequencing in three additional family members. The question was asked if genetic factors such as partial C4 deficiency and IgG allotypes could have influenced susceptibility to meningococcal disease in the family. No relationship was found between C4 phenotypes and infection. Interestingly, the two properdin-deficient males with meningitis differed from the other properdin-deficient persons in that they lacked the G2m(n) allotype, a marker known to be associated with poor antibody responses to T-independent antigens. This implies that the consequences of properdin deficiency might partly be determined by independent factors influencing the immune response.     

Linkage analysis in a family with the Opitz GBBB syndrome refines the location of the gene in Xp22 to a 4 cM region.

The Opitz GBBB syndrome (OS) is characterized in part by widely spaced inner ocular canthi and hypospadias. Recently, linkage analysis showed that the gene for the X-linked form to be located in an 18 cM region spanning Xp22. We have now conducted linkage analysis in a family previously published as having the BBB syndrome and found tight linkage to DXS7104 (Z=3.3, τ=0.0). Our data narrows the candidate region to 4 cM and should facilitate the identification and characterization of one of the genes involved in midline development.     

Fulminant meningococcal septic shock in a boy with combined inherited properdin and protein C deficiency.

A 7-year-old patient with fulminant septic shock due to Neisseria meningitidis of the uncommon serogroup Y developed extensive gangrene of the limbs. Multiple amputations were necessary and a pulmonary embolism occurred within 2 days post-operatively. Complement and haemostatic system studies, done after recovery, showed a complete absence of properdin antigen and a low protein C antigen and activity level in plasma. Defective haemolytic activity in gel by the alternative pathway of complement activation could be restored with purified properdin, indicating a properdin deficiency type 1. Protein C antigen level as well as activity were in agreement with a protein C deficiency type I. The polymerase chain reaction (PCR) product of exon five of the protein C gene showed a substitution of 72Gly by Arg. Both deficiencies were traced among relatives of the patient. Serum of the father of the patient's mother was also properdin-deficient. Microsatellite haplotyping of the X-chromosome of the patient and his relatives showed that a distinct haplotype cosegregated with the properdin deficiency (Lodscore 2.25; four informative meioses). The protein C type I deficiency was present in the patient's mother and her mother and cosegregated with the mutation found. So far as is known, this is the first patient described with combined inherited properdin deficiency and protein C deficiency.     

Prevalence of hereditary properdin, C7 and C8 deficiencies in patients with meningococcal infections.

High incidence of hereditary complement (C) deficiencies was found among 101 patients who had a meningococcal disease. This study revealed 11 non-related patients with complete C deficiency: five deficient in C7, three in C8, two in properdin and one in C2. Additional C-deficient individuals, most of them with no history of severe bacterial infections, were detected in family studies. The C8-deficient patients were found to have a selective deficiency of the C8-beta subunit and a reduced expression of the alpha/gamma subunit. Only a few families with properdin deficiency have been described so far. However, it is likely that frequent analysis of the activity of the alternative C pathway in survivors of severe bacterial infections will disclose numerous properdin-deficient patients. All our C7-, C8- and properdin-deficient patients are Sephardic Jews whose families originated from Morocco, Yemen (C7 and C8 deficient) or Tunisia (properdin deficient). This and other findings indicate that the type of complement abnormality found in association with meningococcal infections varies with the ethnic origin of the patient.     

Linkage analysis in three families with nonspecific X-linked mental retardation

Nonspecific X-linked mental retardation (XLMR) is a common disorder. The number of genes involved in this condition is not known, but it is estimated to be more than 10. We present a clinical and linkage study on 3 families with XLMR. All families were analyzed using highly polymorphic markers covering the X chromosome; screening for the fragile X mutation was negative. The first family (MRX 36) consisted of 1 female and 4 male patients in 3 generations and 7 healthy individuals. Considering the female as an expressing heterozygous carrier, a maximum LOD score of 3.41 was reached in region Xp21.2–Xp22.1. Considering her phenotype to be unknown, a LOD_max of 1.97 was reached in the same region. The second family consisted of 5 affected and 6 healthy males with mild to borderline mental retardation. Linkage analysis using an X-linked recessive model with full penetrance and no phenocopies excluded linkage over almost the entire X chromosome. Using alternative models, including an affecteds-only analysis, a LOD_max of 1.49 was found in region Xq24–28. The third family, consisting of 4 male patients with moderate mental retardation in 1 generation yielded a LOD_max of 0.9 in region Xp22.13–11.3. However, even in this small pedigree, exclusion mapping was able to exclude very large parts of the X chromosome and in this way identify a likely candidate region. © 1996 Wiley-Liss, Inc.     

21-羟化酶缺乏症家系的基因突变研究

目的通过对3个21-羟化酶缺乏症家系的21-羟化酶基因(steroid21-hydroxylase gene,CYP21)直接测序研究,探讨家系中该基因突变类型。方法收集4例患者及其部分家系成员外周血,提取基因组DNA,PCR扩增CYP21基因后直接测序。结果CYP21基因序列分析共检测到6种突变类型。家系1中患者CYP21基因存在4种杂合突变:clusteE6、Q318X、A391T、P459H,其中前3种突变串联排列于同一条染色体上,P459H突变目前国内外尚未见报道,A391T为罕见突变;家系2中患者CYP21基因存在clusteE6、R483W两种杂合突变,其中R483W为罕见突变类型;家系3中患者第4外显子存在I172N纯合突变。结论在3个21-羟化酶缺乏症家系中共检测出6种突变类型,其中P459H为新发现的突变,A391T、R483W为罕见突变。虽然导致21-羟化酶缺乏症的突变主要是一些从假基因(CYP21P)转位到CYP21的序列,但随机突变也是21-羟化酶缺乏症的原因。     

A genetic epidemiologic investigation of breast cancer in families with bilateral breast cancer. II. Linkage analysis

We conducted genetic linkage analyses of breast cancer in 20 pedigrees, each having at least one case of bilateral breast cancer diagnosed before 50 years of age. We tested for linkage using inheritance models from previous segregation analyses, incorporating differences in risk based on menopausal status into the analyses. We tested for heterogeneity by predividing the data set based on the interval between diagnoses of the proband's two primaries (less than 1 year (synchronous) versus at least 2 years (asynchronous], and on the histological types of breast cancer in the pedigrees. Very tight linkage could be excluded between breast cancer and ABO, GC, GPT, MNS, and PGM1 for some of the different linkage analyses. A maximum lod score of +1.01 (at theta = 0.001) between ACP1 and a breast cancer susceptibility locus was seen in the asynchronous all-cases subsample.     

Neurofibromatosis type I (NFI) in Israeli families: Linkage analysis as a diagnostic tool

Linkage analysis of 18 neurofibromatosis type I (NFI) families was performed using intragenic and flanking polymorphic markers. The aims of the analysis were prenatal diagnosis of at-risk fetuses, and of asymptomatic individuals who were relatives of NFI patients. Prenatal diagnosis was performed in 9 pregnancies of 7 families; 5 fetuses were diagnosed as affected. In 6 families with an affected spouse, the request was to identify informative polymorphisms to be used in future pregnancies. Presymptomatic diagnosis was performed in 4 families. One individual, a brother of an NFI patient, was found to have Lisch nodules as the only NFI symptom. Linkage analysis indicated that if this person is a carrier of the NFI gene, he must be a product of intragenic crossover. In 2 individuals with a new NFI mutation, the origin of the NFI-bearing chromosomes was paternal. The same observation was noted by others. A summary of published cases shows that some 90% of the NFI-bearing chromosomes of patients with new mutations were of paternal origin. We therefore suggest that for the purpose of prenatal diagnosis in carriers of NFI new (and unidentified) mutations, the paternal chromosome will be considered as the NFI-bearing chromosome. © 1994 Wiley-Liss, Inc.     

Genetic heterogeneity in familial hypobetalipoproteinemia: Linkage and non-linkage to the apoB gene in caucasian families

Familial hypobetalipoproteinemia (FHBL) is an autosomal dominant disorder of lipid metabolism characterized by extremely low plasma levels of apolipoprotein B (apoB), and total-, and low-density lipoprotein (LDL) cholesterol. Various truncated forms of apoB have been found to cosegregate with the FHBL phenotype in more than 30 kindreds. By contrast, no truncated forms of apoB protein were detected with sensitive immunoblotting in the plasmas of any of the 6 kindreds reported here. Individuals with apoB levels in the 5th centile for their age and sex were considered as affected with FHBL. Linkage analysis was performed using 3 microsatellite markers flanking the apoB gene (D2S131, D2S149, and D2S144), a 3′ variable number of tandem repeats (VNTR) marker and one intragenic marker. Two-point linkage of FHBL was established to the 3′ VNTR marker with a combined maximum LOD score of 8.5 at θ = 0 for 5 of the 6 families. Maximum LOD scores for flanking microsatellite markers were 5.0, 2.4, 1.3, 1.2 and 2.1 for these kindreds (D, T, De, C and Z, respectively). A test of homogeneity differentiated the 6th family (F kindred) from the other five. LOD scores of −25.2 at the 3′ VNTR and −7.8 at the intragenic apoB/Xbal marker at θ = 0 excluded linkage to the apoB gene in the F kindred. These kindreds demonstrate the heterogeneity of FHBL and also offer the possibility to investigate as yet undescribed mutations of apoB, resulting in alterations of apoB metabolism. The F kindred may shed light on novel gene(s) contributing to the low apoB-phenotype. Am. J. Med. Genet. 76:79–86, 1998. © 1998 Wiley-Liss, Inc.     

Linkage analysis in von Willebrand disease

We studied a 3-generation kindred to determine whether the gene responsible for one form of von Willebrand disease (vWD) is linked to 1) the HLA locus, or 2) a polymorphic locus for a serum enzyme or red cell antigen. HLA haplotypes were determined in 12 affected family members, in 10 cases by direct analysis and in 2 cases by deduction. Seven of 12 affected individuals were A2, B7, as compared to 0 of 9 unaffected. However, the maximum lod score was only 0.41 at a recombination frequency of 0.2. Of the 17 serum red cell and plasma protein markers studied, 5 (Kell, ADA, AK1, BF, GC) did not segregate, and 12 (ABO, Rh, JK, Fy, P, PGM1, ACPI, ESD, GLOl, MN, HP, GPT) gave lod scores less than +1.0. We conclude that there is no strong evidence for linkage between the locus for vWD and any of the markers studied.     

Linkage analysis using heterozygote detection in phenylketonuria

This linkage investigation was undertaken utilizing an improved method for phenylketonuria (PKU) heterozygote detection. This method is based on studies of semi-fasting, noon-time, blood specimens obtained from 85 obligate heterozgotes and 45 controls who were neither pregnant nor on birth control medication. The best separation between heterozygotes and normals was achieved with a discriminant function involving the logarithms of the serum concentrations of phenylalanine, tyrosine and tryptophan. The theoretical overlap area between the distributions of heterozygotes and controls, based on the above function, was between the distributions of heterozygotes and controls, based on the above function, was 3.75%. In 19 obligate heterozygotes and 13 controls who were either pregnant or on birth control medication, the best separation was achieved with a discriminant function involving the logarithms of the serum concentrations of phenylalanine and tyrosine. The theoretical overlap area was 8.23%. These equations identified heterozygotes with sufficient accuracy to permit efficient genetic linkage analysis. We were unable to demonstrate genetic linkage between the PKU locus and 15 common blood, serum, and urinary markers. All but loose linkage (theta greater than 0.3) was excluded for Rh, ABO, Gc, Kidd, and AP. Moderate linkage exclusion (theta less than 0.2) was shown for PGM, Duffy, Hp, MNS, HL--A, and Kell. Close linkage (theta less than 0.1) was excluded for Amy2, 6PGD, P, and ADA. We were unable to find linkage heterogeneity between the Amish and non-Amish populations.     

Linkage analysis in Spanish families with nonspecific X‐linked mental retardation: Significant linkage at Xq13–q21

Mental retardation (MR) is a genetically heterogeneous, clinically variable condition. Many cases of MR are linked to the X chromosome. The aim of this study was to identify candidate loci for nonspecific MR in Spanish samples. We selected seven families with nonspecific MR and a pattern of inheritance compatible with an X‐linked disorder and a group of 26 sib pairs of mentally retarded individuals. We performed linkage analysis with a panel of 15 markers evenly distributed along the X chromosome. The study showed linkage to marker DXS8076, located in Xq21.1, by the lod score method (z = 2.11 at θ = 0.155) and the nonparametric extended relative pair analysis method (χ² = 5.32; P < 0.03). Genetic heterogeneity was found, with an estimated 75% of the families linked at recombination fraction θ = 0.10 to the DXS8076 locus (χ² = 9.51; P < 0.009). Xq13–q21 is one of the critical regions for X‐linked MR previously reported, and our study supports the idea that this region may contain a locus for MR in Spanish patients. © 2001 Wiley‐Liss, Inc.     

Ornithine carbamoyltransferase deficiency: molecular characterization of 29 families

Ornithine carbamoyltransferase deficiency is the most common inherited defect of the urea cycle. We examined 28 male and 9 female patients from 29 families and identified 25 distinct mutations in OTC, 14 of which were novel. Three novel missense mutations (p.Ala102Pro, p.Pro158Ser, p.Lys210Glu) and a novel deletion of the Leu43 are not directly involved either in the enzyme active site or in the intersubunit interactions; however, the mutations include conserved residues involved in intramolecular interaction network essential for the function of the enzyme. Three novel large deletions – a 444 kb deletion affecting RPGR, OTC and TSPAN7, a 10 kb‐deletion encompassing OTC exons 5 and 6 and a 24.5 kb‐deletion encompassing OTC exons 9 and 10 – have probably been initiated by double strand breaks at recombination‐promoting motifs with subsequent non‐homologous end joining repair. Finally, we present a manifesting heterozygote carrying a hypomorphic mutation p.Arg129His in combination with unfavorably skewed X‐inactivation in three peripheral tissues.     

Complement component C7 deficiency in two Spanish families

Different genetic mutations have been described in complement component C7 deficiency, a molecular defect clinically associated with an increased susceptibility to neisserial recurrent infections. In this work we report the genetic basis of C7 deficiency in two different Spanish families (family 1 and family 2). In family 1, of Gypsy ethnical background, exon-specific polymerase chain reaction and sequencing revealed a not previously described single base deletion of nucleotide 1309 (exon 10) in the patient, as well as in her father, leading to a stop codon that causes the premature truncation of the C7 protein (K416 X 419). Additionally, the patient and her mother displayed a missense mutation at position 1135 (exon 9) located in the first nucleotide of the codon GGG (CGG), resulting in a change of amino acid (G357R). This mutation was firstly described in individuals of Moroccan Sephardic Jewish ancestry and has been also reported among Spaniards. In family 2, another novel mutation was found in homozygosity in two siblings; a two base-pair deletion of nucleotides 1922 and 1923 in exon 14 leading to the generation of a downstream stop codon causing the truncation of the C7 protein product (S620 X 630). Our results provide more evidence for the heterogeneous molecular basis of C7 deficiency as well as for the subsequent susceptibility to meningococcal disease, since different families carry different molecular defects. On the other hand, certain C7 defects appear to be prevalent in individuals from certain populations or living in defined geographical areas.