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PubMed1990

Gene mapping in the idiopathic generalized epilepsies: juvenile myoclonic epilepsy, childhood absence epilepsy, epilepsy with grand mal seizures, and early childhood myoclonic epilepsy.

Idiopathic generalized epilepsies, i.e., juvenile myoclonic epilepsy (JME), childhood absence epilepsy, and epilepsy with grand mal [generalized tonic-clonic seizures (GTCS)], are the most common genetic epilepsies. Linkage studies using Bf, HLA serologic, and DNA markers by three independent investigators, one from Los Angeles and two from Berlin, have localized the JME locus to the short arm of chromosome 6 (6p). Because members of the same JME family have the same JME phenotype of childhood absence epilepsy, epilepsy with grand mal (GTCS) seizures, or early childhood myoclonic epilepsy (ECME), our observations give evidence for a single-locus etiology in 6p for JME and for at least some of the childhood absence seizures, epilepsy with grand mal (GTCS) seizures, and ECME. Studies should now address whether locus heterogeneity exists within childhood absence epilepsy, epilepsy with grand mal (GTCS) seizures, or ECME. Markers linked to JME (Bf, HLA serologic, and DNA markers in the DQ region) can be used to resolve etiologic heterogeneity. Using such markers, both linked and unlinked forms of phenotypes that are clinically indistinguishable may be detected and provide evidence for etiologic heterogeneity. Studies should also concentrate on narrowing the JME locus to 2 to 3 cm by screening families with recombinant events using RFLPs, candidate genes, and new expressed sequences on chromosome 6.

Adolescent↗

PubMed2000

Loss of heterozygosity analysis on chromosome 5p defines 5p13-12 as the critical region involved in tumor progression of bladder carcinomas.

We have previously observed loss of heterozygosity (LOH) at a single locus (del-27) on human chromosome 5p13-12 to correlate with bladder tumor progression. In this study, we examined 33 bladder tumors for their pattern of allelic loss on chromosome 5p using 7 microsatellite markers. In 14 of 15 bladder tumors with LOH at locus del-27, allelic loss was confined to chromosomal region 5p13-12. This region included the microsatellite marker D5S2025 that showed LOH in 5 of 11 (45%) informative cases with LOH at del-27. This suggests that D5S2025 and del-27 are located within a single critical region of LOH on 5p13-12 harboring a tumor suppressor gene involved in bladder tumor progression. Recurrent LOH at other loci was observed at microsatellite markers located at 5p15. However, these losses appeared to be independent of LOH at 5p13-12 and occurred predominantly in poorly differentiated (G3) and advanced (T3-T4) tumors.

Alleles↗

PubMed1989

A homozygous S genotype of Brassica oleracea expresses two S-like genes.

The sporophytic self-incompatibility system of Brassica species is controlled by a single locus, S. Recognition of self between pollen and stigma is probably mediated by S locus-specific glycoproteins (SLSGs). We describe the isolation, from an S29 homozygote of Brassica oleracea, of two different cDNA clones for transcripts which are equally abundant in stigmas competent for self-incompatibility and each of which is homologous to previously reported SLSG sequences. Extensive DNA sequence divergence between the two clones precludes their cross-hybridisation and each acts as a gene-specific probe. All S genotypes appear to have a single copy of each gene but there are significantly different levels of polymorphism associated with each. The clear structural homology between the two indicates a gene duplication involving the S locus and, perhaps, related to the evolution of self-incompatibility.

Amino Acid Sequence↗

PubMed1988

Molecular organization of the chicken ets locus.

Chicken DNA segments homologous to the ets region from the transforming gene of avian erythroblastosis virus, E26, were molecularly cloned and shown to be almost identical to v-ets by sequence analysis. The transforming gene acids from two cell-derived sequences, myb and ets. Whereas the mammalian ets genes are present on two chromosomes, the chicken ets sequence is present as a single locus with v-ets homologous sequences found in nine regions over about 60 kb of genomic DNA. The major sequence difference between the v-ets and c-ets is found at the 3' end, resulting in different carboxy termini of p135 and the chicken proto-ets product. The chicken locus is primarily expressed in normal thymus cells as a 7.5-kb mRNA. The first two viral homologous regions are not found in this c-ets transcript or any other minor species, suggesting that they may not be true exons. Thus, the v-ets region of E26 demonstrates that two major structural differences may have occurred during the transduction of proto-ets sequences by the virus: (1) Truncation of sequences present at the 5' and 3' ends of the gene; and (2) Acquisition of noncoding proto-ets sequences into the virus. Either or both of these differences may be, in part, responsible for the oncogenic potential of this retrovirus.

Alpharetrovirus↗

PubMed2007

Genetic association between the PRKCH gene encoding protein kinase Ceta isozyme and rheumatoid arthritis in the Japanese population.

OBJECTIVE: Analyses of families with rheumatoid arthritis (RA) have suggested the presence of a putative susceptibility locus on chromosome 14q21-23. This large population-based genetic association study was undertaken to examine this region. METHODS: A 2-stage case-control association study of 950 unrelated Japanese patients with RA and 950 healthy controls was performed using >400 gene-based common single-nucleotide polymorphisms (SNPs). RESULTS: Multiple SNPs in the PRKCH gene encoding the eta isozyme of protein kinase C (PKCeta) showed significant single-locus disease associations, the most significant being SNP c.427+8134C>T (odds ratio 0.72, 95% confidence interval 0.62-0.83, P = 5.9 x 10(-5)). Each RA-associated SNP was consistently mapped to 3 distinct regions of strong linkage disequilibrium (i.e., linkage disequilibrium or haplotype blocks) in the PRKCH gene locus, suggesting that multiple causal variants influence disease susceptibility. Significant SNPs included a novel common missense polymorphism of the PRKCH gene, V374I (rs2230500), which lies within the ATP-binding site that is highly conserved among PKC superfamily members. In circulating lymphocytes, PRKCH messenger RNA was expressed at higher levels in resting T cells (CD4(+) or CD8(+)) than in B cells (CD19(+)) or monocytes (CD14(+)) and was significantly down-regulated through immune responses. CONCLUSION: Our results provide evidence of the involvement of PRKCH as a susceptibility gene for RA in the Japanese population. Dysregulation of PKCeta signal transduction pathway(s) may confer increased risk of RA through aberrant T cell-mediated autoimmune responses.

Adult↗

PubMed2003

Allele substitution at a flower colour locus produces a pollinator shift in monkeyflowers.

The role of major mutations in adaptive evolution has been debated for more than a century. The classical view is that adaptive mutations are nearly infinite in number with infinitesimally small phenotypic effect, but recent theory suggests otherwise. To provide empirical estimates of the magnitude of adaptive mutations in wild plants, we conducted field studies to determine the adaptive value of alternative alleles at a single locus, YELLOW UPPER (YUP). YUP controls the presence or absence of yellow carotenoid pigments in the petals of pink-flowered Mimulus lewisii, which is pollinated by bumblebees, and its red-flowered sister species M. cardinalis, which is pollinated by hummingbirds. We bred near-isogenic lines (NILs) in which the YUP allele from each species was substituted into the other. M. cardinalis NILs with the M. lewisii YUP allele had dark pink flowers and received 74-fold more bee visits than the wild type, whereas M. lewisii NILs with the M. cardinalis yup allele had yellow-orange flowers and received 68-fold more hummingbird visits than the wild type. These results indicate that an adaptive shift in pollinator preference may be initiated by a single major mutation.

Adaptation, Physiological↗

PubMed1991

X-linked thrombocytopenia and Wiskott-Aldrich syndrome: similar regional assignment but distinct X-inactivation pattern in carriers.

While inherited X-linked (XL) isolated thrombocytopenia is a mild condition, the Wiskott-Aldrich syndrome (WAS) associates severe thrombocytopenia with an immunodeficiency component and has a poor prognosis. Whether these conditions correspond to separate genetic entities or to different mutations of the same gene(s) remains unresolved. The Wiskott-Aldrich syndrome locus has been assigned to Xp 11.2 by means of RFLP studies. The X-inactivation pattern in female carriers has been found to follow a skewed pattern in the hematopoietic cells, thus allowing carrier detection. We studied a family with four members affected by XL thrombocytopenia and report the results of genetic segregation analysis, together with the X-inactivation pattern of hematopoietic cells from an obligate female carrier. Although the affected locus mapped to the same region as that of WAS, lymphocytes presented a skewed pattern of X-inactivation, whereas polymorphonuclear lymphocytes (PMN) did not. These results provide further evidence that the Wiskott-Aldrich syndrome and XL thrombocytopenia are different expressions of mutations within a single locus and that the severity of the disease corresponds to distinct hematopoietic cell selections in obligate carriers.

Adult↗

PubMed2001

Genomic and spectral analyses of long to middle wavelength-sensitive visual pigments of common marmoset (Callithrix jacchus).

The genetic basis of red-green color vision of common marmoset (Callithrix jacchus) is not fully understood. Here, we have cloned and characterized the three alleles at a locus that encode the long to middle wavelength-sensitive (LWS/MWS) visual pigments of this species. Using in situ hybridization, we localized this locus to the telomeric region of the long arm of X chromosome. The three visual pigments achieve the wavelengths of maximal absorption at 561, 553, and 539 nm and fully explain the red-green color vision of the common marmoset. The 'tri-allelic single-locus X-chromosome' model operates under the unique phenomenon, known as blood chimerism.

Animals↗

PubMed2001

Genetic mapping and functional analysis of the tomato Bs4 locus governing recognition of the Xanthomonas campestris pv. vesicatoria AvrBs4 protein.

Xanthomonas campestris pv. vesicatoria is the causal agent of bacterial spot disease on pepper (Capsicum spp.) and tomato (Lycopersicon spp.). Analysis of 17 different Lycopersicon accessions with avrBs4-expressing X. campestris pv. vesicatoria strains identified 15 resistant and two susceptible tomato genotypes. Genetic analysis revealed that AvrBs4 recognition in tomato is governed by a single locus, designated Bs4 (bacterial spot resistance locus no. 4). Amplified fragment length polymorphism and bulked DNA templates from resistant and susceptible plants were used to define a 2.6-cM interval containing the Bs4 locus. A standard tomato mapping population was employed to localize Bs4-linked markers on the short arm of chromosome 5. Investigation of X. campestris pv. vesicatoria hrp mutant strains revealed that AvrBs4 secretion and avirulence activity are hrp dependent. Agrobacterium-based delivery of the avrBs4 gene into tomato triggered a plant response that phenotypically resembled the hypersensitive response induced by avrBs4-expressing X. campestris pv. vesicatoria strains, suggesting symplastic perception of the avirulence protein. Mutations in the avrBs4 C-terminal nuclear localization signals (NLSs) showed that NLSs are dispensable for Bs4-mediated recognition. Our data suggest that tomato Bs4 and pepper Bs3 employ different recognition modes for detection of the highly homologous X. campestris pv. vesicatoria avirulence proteins AvrBs4 and AvrBs3.

Bacterial Proteins↗

PubMed2006

Towards multilocus sequence typing of the Leishmania donovani complex: resolving genotypes and haplotypes for five polymorphic metabolic enzymes (ASAT, GPI, NH1, NH2, PGD).

Multilocus enzyme electrophoresis is the gold standard for identification of Leishmania species and strains. Drawbacks include: only amino acid polymorphisms affecting electrophoretic mobility are detected; distinct allozymes can have coincident mobilities; few characters are available; and parasites must be cultured in bulk. So far, thousands of Leishmania strains have been phenotyped by multilocus enzyme electrophoresis. Here, we sequence enzyme-coding genes to provide a PCR-based higher resolution equivalent of multilocus enzyme electrophoresis, particularly for Leishmania infantum. Of 15 enzymes used for multilocus enzyme electrophoresis (MON typing) we have sequenced aspartate aminotransferase, glucose-6-phosphate isomerase, nucleoside hydrolase 1, nucleoside hydrolase 2 and 6-phosphogluconate dehydrogenase. Heterozygous alleles were common, with multiple heterozygous sites within a single locus for several of the genes. Haplotypes were resolved by allele-specific PCR and allele-specific sequencing. Heterozygous haplotypes conformed to the haplotypes of putative parents. One strain appeared to be hybrid across two genetic groups of the Leishmania donovani complex. In most cases, a single amino acid polymorphism was responsible for change in enzyme mobility. Some indistinguishable phenotypes were produced by distinct genotypes. Silent genetic polymorphisms provided enhanced discrimination over multilocus enzyme electrophoresis, for example, by subdividing the zymodeme MON-1. The PCR-based genotyping that we describe could be applied directly to clinical samples or to small volume cultures and in a multilocus sequence typing format. Furthermore, it can be used to detect recombination indirectly and for population genetics studies.

Alleles↗

PubMed1992

A multilocus extension of the affected-pedigree-member method of linkage analysis.

The affected-pedigree-member (APM) method of linkage analysis is designed to detect departures from independent segregation of disease and marker phenotypes. The underlying statistic of the APM method operates on the identity-by-state relations implied by the marker phenotypes of the affected within a pedigree. Here we generalize the APM statistic to multiple linked markers. This generalization relies on recursive computation of two-locus kinship coefficients by an algorithm of Thompson. The distributional properties of the extended APM statistic are investigated theoretically and by simulation in the context of one real and one artificial data set. In both examples, the multilocus statistic tends to reject, more strongly than the single-locus statistics do, the null hypothesis of independent segregation between the disease locus and the marker loci.

Genetic Linkage↗

PubMed1981

The regulation of nitrate assimilation in Neurospora crassa: the isolation and genetic analysis of nmr-1 mutants.

Four mutants of Neurospora crassa have been isolated which have altered regulation of nitrate reductase. They each carry a mutation which results in derepressed synthesis of nitrate reductase even in the presence of glutamine. They map to a single locus which has been designated nmr-1 and which is located between am and gln on linkage group VR. The mutations appear to affect only nitrate assimilation. The nit-2, nit-3 and nit-4/5 mutations are epistatic to nmr-1 since the double mutants have the single nit mutant phenotype. For nitrate reductase synthesis, the nmr-1 mutation is epistatic to am such that the double mutant is derepressed even in the presence of glutamate or glutamine. In all other respects however, the double mutant exhibits the am phenotype. We suggest therefore that the nmr-1 mutations do not directly affect the regulation of nitrate reductase at the level of transcription but instead act post-transcriptionally.

Alleles↗

PubMed2002

An osmosensing histidine kinase mediates dicarboximide fungicide resistance in Botryotinia fuckeliana (Botrytis cinerea).

A two-component histidine protein kinase gene, homologous to os-1 from Neurospora crassa, was cloned and sequenced from a single ascospore isolate of Botryotinia fuckeliana. A series of nine spontaneous mutants resistant to dicarboximide fungicides was selected from this strain and characterized with respect to fungicide resistance and osmotic sensitivity. Genetic crosses of the mutants with an authentic Daf1 strain showed that the phenotypes mapped to this locus. Single point mutations (seven transitions, one transversion, and one short deletion) were detected in the alleles of the nine mutants sequenced. The mutational changes were shown to cosegregate with the dicarboximide resistance and osmotic sensitivity phenotypes in progeny obtained from crossing selected resistant strains with a sensitive strain. All mutations detected are predicted to result in amino acid changes in the coiled-coil region of the putative Daf1 histidine kinase, and it is proposed that dicarboximide fungicides target this domain.

Amino Acid Sequence↗

PubMed2002

HRPT2, encoding parafibromin, is mutated in hyperparathyroidism-jaw tumor syndrome.

We report here the identification of a gene associated with the hyperparathyroidism-jaw tumor (HPT-JT) syndrome. A single locus associated with HPT-JT (HRPT2) was previously mapped to chromosomal region 1q25-q32. We refined this region to a critical interval of 12 cM by genotyping in 26 affected kindreds. Using a positional candidate approach, we identified thirteen different heterozygous, germline, inactivating mutations in a single gene in fourteen families with HPT-JT. The proposed role of HRPT2 as a tumor suppressor was supported by mutation screening in 48 parathyroid adenomas with cystic features, which identified three somatic inactivating mutations, all located in exon 1. None of these mutations were detected in normal controls, and all were predicted to cause deficient or impaired protein function. HRPT2 is a ubiquitously expressed, evolutionarily conserved gene encoding a predicted protein of 531 amino acids, for which we propose the name parafibromin. Our findings suggest that HRPT2 is a tumor-suppressor gene, the inactivation of which is directly involved in predisposition to HPT-JT and in development of some sporadic parathyroid tumors.

Adenoma↗

PubMed2003

Two-locus heterogeneity cannot be distinguished from two-locus epistasis on the basis of affected-sib-pair data.

The observation of multiple linkage signals in the course of conducting genome screens for complex disorders raises the question of whether distinct genes represent independent causes of disease (heterogeneity) or whether they interact to produce the phenotype of interest (epistasis); and there has been a corresponding interest in statistical methods for detecting and/or exploiting the distinction between these two possibilities. At the same time, researchers are increasingly relying on affected-sib-pair (ASP) data. Here, we demonstrate an apparently unrecognized fact about two-locus (2L) models and ASP data, namely, 2L heterogeneity and 2L epistasis cannot, in general, be distinguished from one another on the basis of ASP marker data, as a matter of mathematical principle and therefore regardless of sample size. By the same token, correlations across ASPs in single-locus LOD scores or other measures also cannot be used to distinguish 2L heterogeneity from 2L epistasis. This raises questions about the measurement of gene-gene interactions in terms of patterns of correlation in marker data. Portions of our results carry over to larger pedigree structures as well, as long as only affected individuals are included in analyses; the extent to which our overall findings apply to general pedigrees (including unaffected individuals) remains to be investigated.

Alleles↗

PubMed1999

Physical mapping of the autoimmune disease susceptibility locus, Bphs: co-localization with a cluster of genes from the TNF receptor superfamily on mouse chromosome 6.

An important approach to understanding complex diseases is to reduce them into well-characterized subphenotypes that are under monogenic control. One such example is Bordetella pertussis toxin-induced histamine sensitization in mice, a subphenotype of experimental allergic encephalomyelitis and experimental allergic orchitis. This subphenotype is controlled by a single locus, Bphs, previously mapped to a 33 cM region on mouse Chromosome (Chr) 6. We achieved considerable reduction of this candidate region and constructed a YAC contig across the refined interval. Our results demonstrate that Bphs is located between D6Mit151 and a newly developed marker, EC108RR, a region containing a small cluster of genes belonging to the TNF receptor superfamily. Sequence and quantitative analysis of the candidate gene, tumor necrosis factor receptor 1 (Tnfr1, p55), indicates that it is unlikely to be Bphs. However, the location of Bphs, together with physiologic effects it shares with Tnfr1 activation, suggest that Bphs may prove to be another member of the TNF receptor superfamily.

Animals↗

PubMed1983

Genetic variation at a pig serum protein locus, Po-2 and its assignment to the Phi, Hal, S, H, Pgd linkage group.

Two-dimensional agarose gel (pH 5.4)-polyacrylamide gel (pH 9.0) electrophoresis of pig serum samples revealed a new serum protein (postalbumin-2, PO-2) polymorphism. Family data supported the hypothesis that the three PO-2 phenotypes observed were controlled by two codominant, autosomal alleles (Po-2F and Po-2s) at a single locus. The frequency of Po-2F in Swedish Landrace and in Swedish Yorkshire breeds was estimated at 0.74 and 0.65, respectively. Evidence was presented for close genetic linkage between Po-2 and the red cell phosphohexose isomerase locus (Phi). A recombination frequency of 3.2% was obtained from double backcross material. Data obtained in a Danish Landrace material showing linkage between the Po-2 locus and the H blood group locus, the Pgd locus and Hal (locus for halothane sensitivity) are also given. A total of seven recombinants were observed. They show that Po-2 is a new locus in a previously established linkage group. The likely sequence of the loci is: Phi, Hal, S, H, Po-2, Pgd.

Animals↗

PubMed2001

NZM2328: a new mouse model of systemic lupus erythematosus with unique genetic susceptibility loci.

Among NZB/W-derived New Zealand mixed (NZM) strains, only NZM/Aeg2410 (NZM2410) has been well characterized. In contrast to NZM2410, NZM2328 mice develop autoantibodies and acute and severe chronic glomerulonephritis (GN) with female predominance similarly to NZB/WF1 and humans with systemic lupus erythematosus (SLE). Chronic GN with glomerular sclerosis and tubular atrophy but not acute GN was correlated with severe proteinuria. In a backcross analysis of (NZM2328 X C57L/J) F1 X NZM2328, four SLE susceptibility genomic intervals were identified. One of them (Cgnz1) is on the telomeric end of chromosome 1 and close to Sle1. It was significantly linked to chronic GN. A locus (Agnz1) distinct from Cgnz1 on this interval was suggestively linked to acute GN. Two genetic intervals on chromosome 17 were also suggestively linked to acute GN, one of which is the H-2-Tnf complex, while the other (Agnz2) is on the distal end of the chromosome. A single locus (Adaz1) identified in the midregion of chromosome 4 in NZM2328 mice was suggestively linked to plasma levels of IgG anti-dsDNA autoantibodies. These results differ significantly from those in the backcross analysis of (NZM2410 X C57BL/6)F1 X NZM2410 by other investigators. They support the concept that different sets of genes are involved in acute and chronic GN. The genomic differences between the NZM strains and between C57L/J and C57BL/6 account for the differences between our analysis and that on NZM 2410. These results provide evidence for the importance of background genes on the expression of SLE, with implications for genetic studies of human SLE.

Animals↗