Shared SstI RFLPs by HLA-Aw19, A23/24 and A3/11 crossreacting groups

Three novel restriction fragment length polymorphisms (RFLPs) have been identified using a pan-HLA class I probe and the endonuclease SstI. This study, in conjunction with previously reported SstI RFLPs, now allows the identification of the HLA-crossreacting antigens Aw19 (A29/30/31/32/w33), A23/24 and A3/11 by specific hybridization patterns with a single enzyme/probe combination. Three of the corresponding polymorphic SstI restriction sites map within the HLA-A gene and generate two allelic RFLPs (5.06, 5.92 kb) and one single RFLP (5.92 kb) that show an absolute correlation with HLA-A23/24 and A29/32 crossreacting antigens, respectively. However, other SstI RFLPs (7.97, 9.4, 9.6, 9.8 and 13.34 kb), also linked to HLA-A crossreacting antigens, map outside the HLA-A gene and probably correspond to non-HLA-A,B,C class I genes in strong linkage disequilibrium with the HLA-A gene. These data show that HLA-A crossreacting antigens share more SstI RFLPs than neighboring non-HLA-A,B,C class I genes or pseudogenes; also, this has raised the possibility that some crossreacting HLA-A alloantisera might additionally recognize shared antigenic determinants in non-HLA-A,B,C proteins since the HLA-Aw19 crossreactivity cannot be fully explained by analyzing the HLA-A amino acid sequence.     

Extragenic factor IX gene RFLP is useful for detecting carriers of Japanese hemophilia B

Seventy-eight X chromosomes from 25 normal Japanese subjects and 22 family members with hemophilia B (coagulation factor IX deficiency) were examined with an extragenic factor IX DNA probe, pX58dIIIc at DXS99 locus. In contrast to the previously described nonpolymorphic RFLPs in the factor IX gene, DXS99 locus RFLP produced by SacI digestion was detected among those Japanese subjects with allelic frequencies of 0.48 and 0.52. The estimated heterozygosity rate of this extragenic RFLP among Japanese females was about 50%. The study of hemophilia B family members showed that DXS99 locus RFLP was informative in 9 out of 13 families tested (69.2%). No recombination events between the factor IX gene locus (F9) and DXS99 locus have been noted among nine families analyzed. DXS99 SacI RFLP is a useful gene indicator of carrier-ship of hemophilia B.     

Assignment of an erbB-like DNA sequence to linkage group VI in fishes of the genus Xiphophorus (Poeciliidae)

The inheritance of 23 protein polymorphisms was compared with the inheritance of a DNA restriction fragment length polymorphism (RFLP) of a strongly cross-hybridizing erbB-related sequence, epidermal growth factor receptor-like-1 (EGFRL1), in Xiphophorus clemenciae X X. milleri-derived backcross hybrids. Two polymorphic bands were noted in this cross with a v-erbB probe after PstI digestion: a 10-kilobase (kb) band in X. clemenciae and a 9-kb band in X. milleri. Joint segregation analysis of the RFLPs and protein polymorphisms indicate that this erbB-related sequence can be assigned to Xiphophorus linkage group VI, which also comprises genes coding for glutamine synthetase (GLNS), nucleoside phosphorylase-2 (NP2), and transferin (TF). We have designated this RFLP as alleles at a locus called EGFRL1 because of very strong cross-hybridization with the v-erbB probe, known to be homologous to the mammalian EGFR gene. This mapping assignment is the first autosomal linkage of an oncogene sequence reported in fish, which provide a large number of genetically controlled experimental tumor models.     

正常汉族人群醛固酮合酶基因-344C/T多态性的研究

目的 :探讨中国汉族人群醛固酮合酶 (CYP11B2 )基因 -3 44C/T多态性分布特点。方法 :应用PCR RELP技术对 189名中国汉族人的CYP11B2基因 -3 44C/T多态性进行分析。结果 :中国汉族人群CYP11B2基因 -3 44C/T多态性以TT和CT为主要基因型 ,C等位基因较少见 ,其频率为 0 .2 3 ,明显低于文献报道的欧洲白种人 (P均<0 .0 1) ,亦较日本人为低 (P <0 .0 5 )。结论 :CYP11B2基因 -3 44C/T多态性频率分布在不同的人种中存在差异。     

Restriction fragment length polymorphisms within proximal 15q and their use in molecular cytogenetics and the Prader-Willi syndrome

Restriction fragment length polymorphisms (RFLPs) are described in detail for 6 DNA probes (D15S9-13, D15S18) that localize to the proximal long arm of human chromosome 15 (15q11-15q13: this report and Tantravahi et al., Am. J. Med. Genet. 33:78-87. Multiple RFLPs are detected by the probe that identifies locus D15S13, and these RFLPs are shown by genomic mapping to result from a nearby insertion or deletion of 1.8 kilobases (kb) of DNA. This set of RFLPs detected by proximal 15q probes can be used for studies on the Prader-Willi syndrome (PWS) and on mentally retarded individuals with a supernumerary inv dup(15) chromosome. Five of the polymorphic loci (D15S9-13) map to the region implicated in the cause of the PWS (15q11.2-15q12). Each of 4 families tested with these probes, as well as an additional "PWS-like" patient, was informative by RFLP analysis. The two PWS deletions studied, which occurred de novo, were inherited from the chromosome 15 provided by the father. By contrast, the 2 inv dup(15) chromosomes analyzed were of maternal origin. The use of RFLPs can also simplify the molecular determination of copy number in chromosomal aneuploidy, as exemplified by analysis of individuals with the PWS and a deletion, patients with an inv dup(15), and one patient with a more complex rearrangement involving chromosome 15. Our studies demonstrate the application of DNA probes for both molecular cytogenetic studies on this chromosome region and the development of diagnostic molecular markers to aid early clinical diagnosis of the PWS.     

Population differences in DNA sequence variation and linkage disequilibrium at the PON1 gene

Polymorphisms of the promoter region (?108C/T) and the coding region (192Q/R) of the paraoxonase 1 gene (PON1) showed differences in association with cardiovascular disease risk in various populations. To characterize the genetic variation underlying these important polymorphisms, we examined DNA sequence variation both in a 1.3‐kb promoter region 16.5 kb from codon 192, and in a 1.7‐kb region centered on the 192Q/R polymorphic site of the coding region of PON1, in 30 Africans, 30 Europeans and 64 Japanese. We found 10 polymorphic sites and 11 haplotypes in the 1.3‐kb promoter region and 10 biallelic polymorphic sites and 10 haplotypes in the 1.7‐kb region. From the PON1 sequences of chimpanzees and an orangutan, the ancestral type of codon 192 was found to be R. The number of pairs of polymorphic sites between the promoter and 1.7‐kb regions that were in significant linkage disequilibrium was much higher in a Japanese population than in African and European populations. In addition, the pairs of polymorphic sites in linkage disequilibrium differed among the three populations. These results suggest that some of the population differences in association with risk for coronary heart disease can be explained by population differences in haplotype frequency of PON1 haplotypes.     

Molecular-genetic study of Duchenne and Becker muscular dystrophies: deletion analyses of 45 Japanese patients and segregation analyses in their families with RFLPs based on the data from normal Japanese females

This study consisted of 1) molecular deletion analyses in patients with Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) using the entire cDNA for the DMD gene as hybridization probes, 2) RFLP analyses in a large number of Japanese normal women using 11 DMD-linked cloned DNAs as probes, and 3) segregation analyses with these RFLP data in 17 DMD families in which prenatal or carrier diagnosis was required. The deletion study showed that 18 (43%) of 42 male DMD patients had a deletion within the DMD gene, while no detectable deletion was found in 3 BMD patients. These deletions were preferentially observed at the 5' end of the DMD gene, while no deletion was found in the 3' portion of the gene. Of a total of 15 RFLPs detected with the 11 probes, one was a new RFLP (probe/enzyme: P20/MspI). In 6 RFLPs, the allele frequencies in the Japanese were statistically different from those in the Caucasian. Based on the RFLP data combined with the result of the deletion study, an estimated diagnostic rate for prenatal diagnosis and/or carrier detection in the Japanese DMD families was 63%. The real diagnostic rate obtained from the prenatal and carrier diagnoses, which were practically performed in 17 families, corresponded to the estimation. A protocol useful for the diagnosis in Japanese DMD families is presented.     

Restriction fragment length polymorphisms in Septoria tritici occur at a high frequency

Summary A set of probes that detect restriction fragment length polymorphisms (RFLPs) in nuclear DNA has been developed for genetic studies of the phytopathogenic fungus Septoria tritici. Two plasmid libraries containing 0.5–1.3 or 1.3–2.4 kb fragments of S. tritici nuclear DNA were constructed. Seventeen random clones from each library were used as probes to screen for RFLP variation among a geographically-diverse group of six S. tritici isolates. Among the 196 probe-enzyme combinations tested, 145 detected RFLPs among the six isolates. The restriction enzymes EcoRV and PstI detected RFLPs most efficiently. Three probes detected deletions. A ribosomal DNA probe from yeast did not detect a significant amount of variation. These probes will be useful for studying genetic variation, population genetics, and genome organization of S. tritici.     

Mutant genes of cytochrome P-450IID6, glutathione S-transferase class Mu,and arylamine N-acetyltransferase in lung cancer patients

Summary Epidemiological studies suggested a protective effect of certain phenotypes of polymorphic foreign-compound-metabolizing enzymes in some types of cancer. Poor metabolizers (PM) of debrisoquine 4-hydroxylase (cytochrome P-450IID6, CYP2D6) were found to be underrepresented among patients with lung cancer. Recent advances in molecular genetic characterization of CYP2D6, glutathione S-transferase (GST) class Mu, and arylamine N-acetyltransferase enabled genotypical determination of mutant alleles in lung cancer patients. Restriction fragment length polymorphism (RFLP) with a cDNA gene probe of CYP2D6 was analyzed in 79 lung cancer patients who were phenotyped with debrisoquine. Mutant alleles were detected by allele-specific polymerase chain reaction (PCR). In the same individuals, genotype of GST class Mu was analyzed by PCR and correlated with ex vivo activity of glutathione conjugation towards trans-stilbene oxide. RFLP patterns allowed discrimination between the slow and fast genotype of N-acetyltransferase as well as the heterozygotes. Three phenotypical PMs of debrisoquine (3.8%) were confirmed by PCR and RFLP. No PM could be unambiguously recognized only by RFLP patterns. The PMs were characterized by PCR and RFLP as carriers of the 29B/29B (n=1), 29A/29B (n=1), and 29A/44 (n = 1) mutant alleles. Higher debrisoquine hydroxylase activities were found in the homozygous EMs, who possess two active genes, as compared to heterozygous EMs, who have only one active gene. The patients with phenotypically impaired GST Mu activity were confirmed as such by PCR. A complete correspondence between phenotyping of N-acetyltransferase (with caffeine) and genotyping was found. The new genetic techniques proved to be powerful tools for molecular-epidemiological studies aimed at establishing host factors of cancer susceptibility.Abbreviations AFMU 5-acetylamino-6-formylamino-3methyluracil - by base pair - cDNA complementary DNA - CYP2D6a cytochrome P-450IID6 (debrisoquine hydroxylase) - CYP2D6a gene locus coding for CYP2D6 - EM extensive metabolizer - GST glutathione S-transferase - MR metabolic ratio - NAT arylamine N-acetyltransferase - NATa gene locus coding for NAT - PCR polymerase chain reaction - PM poor metabolizer - RFLP restriction fragment length polymorphism - wt wild type - 1X 1-methylxanthine     

T-cell antigen receptor alpha chain polymorphisms in insulin-dependent diabetes

Insulin-dependent diabetes is a chronic autoimmune disease probably mediated by T cells. We examined the alpha chain of the T-cell antigen receptor in two models of this illness (man and BB rat) to determine any association with autoimmune diabetes. We conducted a population study in man, using a human alpha chain probe, pGA-5, and restriction enzyme Bgl 11. Two allelic forms and three RFLP patterns, 2.8 and 3.0 kb homozygous and 2.8/3.0 heterozygous, were detected. There was no difference in the frequency of these RFLPs among the 50 Type I diabetic patients and 48 controls tested. BB rats develop a spontaneous T-cell mediated autoimmune diabetes. The diabetes has been linked in several breeding studies to an undetermined autosomal recessive gene causing T-cell lymphopenia. We were able to differentiate the T-cell antigen receptor alpha chain of the diabetic BB and control BBN rats using the restriction enzyme EcoR1 and a murine alpha chain probe, TT11. The BB rat had a haplotype characterized by the presence of 4.7 and 5.8 kb bands, and the absence of 1.4, 2.2, 2.6, 3.6, 3.9, 4.1, and 6.1 kb bands. In a breeding study with BB and BBN rats, diabetic animals of the F2 generation demonstrated no linkage with the BBs' alpha chain, nor was lymphopenia linked to the alpha chain of the BB rat. These results suggest that autoimmune diabetes is not linked to the T-cell antigen receptor alpha chain in the BB rat, nor is it associated with alpha chain constant region polymorphisms in Type I diabetes in man.     

Molecular mechanisms associated with increased fetal hemoglobin G gamma-type in part-aboriginal family with beta thalassemia

A part-Aboriginal family with beta thalassemia and raised hemoglobin F (HbF) was studied at the molecular level to determine if there were identifiable gene changes associated with increased production of HbF. Two beta thalassemia heterozygotes aged eight years and 18 months had raised HbF levels of 2.9% and 22% respectively. HbF was predominantly G gamma in composition. Five family members were typed for restriction fragment length polymorphisms (RFLPs) using nine restriction enzymes and five DNA probes specific for the beta globin cluster on chromosome 11. RFLPs were combined to construct haplotypes for the beta thalassemia and the high HbF defects. A beta globin subhaplotype comprising only 5' RFLP markers (-(+)-(+) +) co-segregated with the high HbF determinant. This has previously been associated with increased G gamma expression in beta thalassemia and sickle cell anemia. An additional Xmnl RFLP 5' to the G gamma gene, which has been described in individuals with elevated G gamma expression, was also demonstrated in those family members with increased G gamma levels. In this study both the 5' beta globin subhaplotype (-(+)-(+) +) and the Xmnl/gamma RFLP are present in the one family but the relative contributions of each cannot be determined.     

DNA-RFLP analysis and genotyping of HLA-DR alleles in the south of Spain.

42 healthy individuals previously HLA-DR typed by serology, were HLA class II typed using RFLPs. The pattern of hybridization revealed allele specific DNA fragments for some DR specificities. Three fragments highly associated with HLA-DR antigens: a 7 kb RFLP with DR1; a 10 kb RFLP with DR-3/DR-5 and a 13 kb band with DR4/DR7.     

DNA analysis of Duchenne and Becker muscular dystrophy using pERT87 genomic probes and dystrophin cDNA probes

DNA analysis was performed on 19 unrelated Duchenne muscular dystrophy (DMD) families and one Becker muscular dystrophy (BMD) family in Japan to determine their carrier status. The intragenic genomic probe pERT87 with its subclones 87-1, 87-8, and 87-15 were used together with five cDNA probes from the 5 end of the dystrophin gene. The tests with both a high polymorphism information content (P.I.C.) and a high observed P.I.C. were most effective,i.e., pERT87-1/XmnI, pERT87-15/XmnI, pERT87-8/TaqI, and pERT87-8/BstXI. These test combinations were useful in the Japanese population but pERT87-15/TaqI was not, although it was effective in Caucasians. Two additional test combinations of pERT87-1/MspI and pERT87-15/BamHI, were highly useful in detecting restriction fragment length polymorphisms (RFLPs) when other tests were not informative. Carrier status could be determined in 18 out of 20 clients who were at risk for DMD/BMD carrier status from 20 families, similar to the rate of detection in Caucasians. The total detection rate of deletions was 74% with the five cDNA probes. Deletions were concentrated on two hot spots where 92% of all deletions were detected by only two probes, 1-2a and 8. Deletions were detected in two males with DMD who had none of the eight RFLPs tested. Our results emphasize the usefulness of DNA analysis with pERT87 genomic probes and cDNA probes. In addition, an optimum strategy for carrier detection in Japanese DMD/BMD families was proposed.     

First trimester prenatal diagnosis of haemophilia a using factor VIII gene probe

Accurate first-trimester prenatal diagnosis was achieved in a Japanese haemophilia A family by the use of a restriction fragment length polymorphism (RFLP) located within the F.VIII gene. Since the pregnant woman's heterozygosity forBclI polymorphism in F.VIII/intron 18 (F8A) probe was informative, chorionic villus sampling (CVS) was performed at 9 weeks of gestation. Restriction analysis showed that the fetus was heterozygous for theBclI site and had received a normal paternal X chromosome (0.9 kb) and a normal maternal X (1.2 kb). Therefore, we concluded that the fetus was a non-carrier female. Pregnancy went to term and woman gave birth to an apparently healthy female. At one week after birth a coagulation study confirmed that the newborn infant is not a carrier. The first-trimester prenatal diagnosis of haemophilia A is possible by CVS due to a RFLP in the F.VIII gene.     

Polymorphisms in the human CYP1A1 gene as susceptibility factors for lung cancer: exon-7 mutation (4889 A to G), and a T to C mutation in the 3′-flanking region

Genetic differences in the metabolism of carcinogens may codetermine individual predisposition to cancer. Cytochrome P-4501A1 (CYP1A1) metabolically activates precarcinogens in cigarette smoke, such as benzo(a)pyrene, which is also an inducer of CYP1A1. Two point mutations have been reported, m1 in the 3-flanking region (6235T to C), and m2 within exon 7 (4889A to G), the latter leading to an isoleucine to valine exchange. In the Japanese population ml and m2 are correlated with lung cancer, suggesting an increased susceptibility to cigarette smoking related lung cancer. We studied 142 lung cancer and 171 reference patients in an ethnically homogeneous German group for m1 and m2 mutations by restriction fragment length polymorphism and allele-specific polymerase chain reaction, respectively. No statistically significant difference was found in the distribution of m1 alleles between lung cancer and controls; the frequency was 8.5% and 7.3% of the alleles, respectively (odds ratio = 1.17). A trend to an overrepresentation of ml alleles was observed among 52 squamous cell carcinoma patients (odds ratio = 1.65). In contrast, the frequency of m2 alleles in lung cancer patients was twofold higher (6.7%) than in the reference group (3.2%; odds ratio = 2.16; 95% confidence limits 0.96–5.11, P = 0.033); the odds ratio of m2 alleles in squamous cell carcinoma was 2.51 (95% confidence limits 0.85–7.05, P = 0.05). There was a close genetic linkage of m2 to m1 (10 of 11 reference patients), but a significantly higher number of cancer patients showed no linkage compared to the controls (odds ratio = 8.89, 95% confidence limits 0.83–433, P = 0.04). Thus no association was found between presence of ml alleles and lung cancer, but, in contrast, m2 alleles proved as a hereditary risk factor, especially if not linked with m1 alleles.Abbreviations Ah aryl hydrocarbon - CYP1A1 cytochrome P4501A1 - CYP1A1 CYP1A1 gene - PCR polymerase chain reaction - PY pack years - RFLP restriction fragment length polymorphism Correspondence to: N. Drakoulis     

Genomic diversity of oral Candida krusei isolates as revealed by DNA fingerprinting and electrophoretic karyotyping

Candida krusei is receiving increasing attention as an important human pathogen, especially in compromised patients, who frequently manifest with multiepisodes of candidosis. As there is scant information on the genetic diversity of this pathogen the present study was undertaken to establish its genetic profiles using three different typing methods: PFGE (pulsed-field gel electrophoresis), RFLP (restriction fragment length polymorphism), RAPD (randomly amplified polymorphic DNA). When 11 oral isolates of C. krusei were molecular typed by PFGE, 3 to 5 chromosomes with sizes ranging from 1000 kb to 3000 kb per isolate were revealed. All isolates produced a single bright band at approximately 1,100 kb and two to three bands between 2,500 kb and 3,000 kb, demonstrating 5 different karyotypes. RFLP with HinfI yielded 9 different genotypes, while DNA fingerprinting by RAPD with 3 primers (RSD6 (5'GCGATCCCCA3'), RSD7 (5'AGTGAATTCG CGGTGA-GATGCC3') and RSD12 (5'GCATATCAATAAGC GCAGGAAAAG 3')), resulted in 8, 3 and 11 different genotypes, respectively. This study provides evidence hitherto unavailable on the genetic polymorphism of C. krusei isolates colonizing the oral niche under different clinical conditions. Such genotypic polymorphism should help strain delineation in epidemiologic surveillance of either nosocomial or community outbreaks of C. krusei infections.     

Human insulin-related DNA sequences map to chromosomes 2 and 11

The insulin-related hormone family consists of four known peptides: insulin, the insulin-like growth factors I and II, and relaxin. To investigate the hypothesis that the family contains additional members, we have isolated a series of human genomic clones using the insulin gene as a hybridization probe. Two of these single copy DNA sequences, hIr 1 and hIr 2, have been localized to chromosome 2 and 11p11q13, respectively, by Southern blot analysis of mouse-human somatic cell hybrids, a result consistent with other evidence supporting the dispersal of the insulin gene family throughout the genome. Although a biological function for these DNA sequences has not yet been established, hIr1 and hIr2 are potentially useful as molecular probes for mapping, by analysis of restriction fragment length polymorphisms (RFLP), genetic disorders linked to chromosomes 2 or 11.     

Fluorescencein situ hybridization analysis of chromosomal localization of three human cytochrome P450 2C genes (CYP2C8, 2C9, and 2C10) at 10q24.1

Summary Chromosomal localization of three human cytochrome P450 genes belonging to the CYP2C subfamily (CYP2C8, 2C9, and 2C10) was identified by fluorescencein situ hybridization (FISH). An original MP-8 clone was used as a DNA probe for the assignment of the CYP2C10 gene, while two cDNA probes, a 1.37 kb fragment of CYP2C8 and a 1.19 kb fragment (MP-20 and MP-4 clones, respectively) by polymerase chain reaction using a single human liver cDNA library. The results showed that three human CYP2C8, 2C9, and 2C10 cDNAs were located at the same subchromosomal region, 10q24.1.The coding sequences of the genes termed CYP2C9 and CYP2C10 differ in only two amino acids, 358 and 417 (Gedet al., 1988; Srivastavaet al., 1991). The CYP2C10 sequence corresponds to the first cDNA we isolated from this family (Umbenhaueret al., 1987). We reported that the two cDNAs now termed 2C9 (MP-4) and 2C10 (MP-8) differed considerably in their 3 non-coding sequences, and oligonucleotide probes were used to identify both groups of sequences in the mRNA of a single liver sample (Gedet al., 1988). It is conceivable that the existence of the two cDNA clones (within an expression library generated from a single individual) is an artifact of the library construction, or that the sequences recognized by the probes are parts of other genes. Nevertheless, P450 2C9 and P450 2C10 are treated here as the products of individual genes. When proteins purified from the liver are considered here, they are designated P450 2C9/10 because no amino acid sequence analysis was done in the regions where differences occur (Gedet al., 1988; Srivastavaet al., 1991).     

Prenatal diagnosis of haemophilia B by the use of polymerase chain reaction and direct sequencing

Summary A second prenatal diagnosis of severe haemophilia B was carried out in a family with no prior history of the disease. The first prenatal diagnosis was based on linkage analysis and showed the male fetus not to be affected because he had inherited the same X-chromosome as his healthy brother. Carrier status in the female at risk could not be assessed by restriction fragment length polymorphisms (RFLPs). She was found to have inherited the same marker constellation as her affected brother. However, due to the fact that a pedigree with no prior history of haemophilia B has been examined diagnosis was impossible. In addition factor IX coagulant and antigen values gave no definitive clue to a haemophilia B carriership. The problems with RFLP analysis in this pedigree were circumvented by polymerase chain reaction (PCR) based direct sequencing of the factor IX gene. A previously unknown mutation could be detected in patient haemophilia B (Kleve) and the carrier status in the female at risk could be confirmed. The second prenatal diagnosis showed that the male fetus had inherited the mutation and will therefore be afflicted with haemophilia B.Abbreviations bp basepairs - FIX:Ag factor IX antigen - FIX:C factor IX activity - kb kilobasepairs - PCR polymerase chain reaction - RFLP restriction fragment length polymorphism