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PubMed1999

Analysis of simulated data: evidence for genetic and environmental effects.

We approached the simulation as though it were an international study with similar but not identical information being collected from different populations. In keeping with this we analyzed one replicate from each population. Initially we examined the risk of disease in relatives of cases to determine whether the disease appeared to be "more genetic" in one population than in the others and we examined the evidence for environmental risk factors in each population. Nonparametric linkage analysis and transmission/disequilibrium testing (TDT) were used to search for loci linked to the disease in each population. Using these methods we identified several candidate regions for a susceptibility gene which on examination of the answers are explicable in terms of the underlying model.

Environment↗

PubMed1999

Meta-analysis by combining p-values: simulated linkage studies.

Meta-analysis has been little explored to make an overall assessment of linkage from different studies. In practice, it is likely that published linkage studies will only report p-values. We compared the performance of the widely used Fisher method for combining p-values with that of pooling raw data. More loci were consistently found by pooling raw data. In the absence of further information, combining p-values can provide an overall, but limited, assessment of different linkage studies. However, meta-analysis would be better viewed as a preliminary step toward the goal of analyzing the pooled raw data.

Genetic Linkage↗

PubMed2002

Determining sequence length or content in zero, one, and two dimensions.

High-throughput assays are essential for the practical application of mutation detection in medicine and research. Moreover, such assays should produce informative data of high quality that have a low-error rate and a low cost. Unfortunately, this is not currently the case. Instead, we typically witness legions of people reviewing imperfect data at astronomical expense yielding uncertain results. To address this problem, for the past decade we have been developing methods that exploit the inherent quantitative nature of DNA experiments. By generating high-quality data, careful DNA-signal quantification permits robust analysis for determining true alleles and certainty measures. We will explore several assays and methods. In a one-dimensional readout, short tandem repeat (STR) data display interesting artifacts. Even with high-quality data, PCR artifacts such as stutter and relative amplification can confound correct or automated scoring. However, by appropriate mathematical analysis, these artifacts can be essentially removed from the data. The result is fully automated data scoring, quality assessment, and new types of DNA analysis. These approaches enable the accurate analysis of pooled DNA samples, for both genetic and forensic applications. On a two-dimensional surface (comprised of zero-dimensional spots) one can perform assays of extremely high-throughput at low cost. The question is how to determine DNA sequence length or content from nonelectrophoretic intensity data. Here again, mathematical analysis of highly quantitative data provides a solution. We will discuss new lab assays that can produce data containing such information; mathematical transformation then determines DNA length or content.

Artifacts↗

PubMed2003

A multiplex methylation PCR assay for identification of uniparental disomy of chromosome 7.

Uniparental disomy of chromosome 7 (UPD7) is associated with abnormal phenotypic effects because of inappropriate expression of imprinted genes on chromosome 7. Based on the differential methylation of the promoter region of the imprinted PEG1/MEST locus at 7q32, we designed a multiplex methylation PCR (mPCR) assay to rapidly distinguish UPD7 from biparental inheritance of chromosome 7. Primers were designed to produce different sized PCR amplicons based on the parent of origin-specific methylation at this locus; electrophoresis of PCR amplicons showed a 189-bp product from the methylated maternal allele and a 109-bp product from the unmethylated paternal allele. This mPCR assay correctly predicted the chromosome 7 imprinting status in normal control and UPD7 samples. Previous assays for UPD7 required genotyping of the proband and parents, or separate maternal- and paternal-specific mPCR reactions. The advantage of this assay is that parental samples are not required and that amplification of both alleles in the same reaction is simpler and provides an internal control. This multiplex mPCR assay will be useful in screening for UPD7 in patients with Silver-Russell syndrome (SRS; also Russell-Sliver syndrome, RSS), primordial growth retardation, and in patients with supernumerary marker chromosomes or chromosome rearrangements of chromosome 7 origin.

Alleles↗

PubMed2006

Comprehensive mutation analysis of GLDC, AMT, and GCSH in nonketotic hyperglycinemia.

Nonketotic hyperglycinemia (NKH) is an inborn error of metabolism characterized by accumulation of glycine in body fluids and various neurological symptoms. NKH is caused by deficiency of the glycine cleavage multi-enzyme system with three specific components encoded by GLDC, AMT, and GCSH. We undertook the first comprehensive screening for GLDC, AMT, and GCSH mutations in 69 families (56, six, and seven families with neonatal, infantile, and late-onset type NKH, respectively). GLDC or AMT mutations were identified in 75% of neonatal and 83% of infantile families, but not in late-onset type NKH. No GCSH mutation was identified in this study. GLDC mutations were identified in 36 families, and AMT mutations were detected in 11 families. In 16 of the 36 families with GLDC mutations, mutations were identified in only one allele despite sequencing of the entire coding regions. The GLDC gene consists of 25 exons. Seven of the 32 GLDC missense mutations were clustered in exon 19, which encodes the cofactor-binding site Lys754. A large deletion involving exon 1 of the GLDC gene was found in Caucasian, Oriental, and black families. Multiple origins of the exon 1 deletion were suggested by haplotype analysis with four GLDC polymorphisms. This study provides a comprehensive picture of the genetic background of NKH as it is known to date.

Adolescent↗

PubMed2006

Denaturing temperature selection may underestimate keratin mutation detection by DHPLC.

Keratins 8 and 18 (KRT8 and KRT18 genes; K8 and K18 proteins) variants are risk factors for developing end-stage liver disease and may be associated with inflammatory bowel disease and chronic pancreatitis. The frequency of K8/K18 variants in American, British, German, and Italian populations differs. For example, one study showed no amino acid-altering K8/K18 mutations in 256 German patients with liver disorders, while another found 58 out of 467 American liver disease patients with K8/K18 mutations. Both studies used the WaveSystem, which utilizes DHPLC. We hypothesized that experimental conditions contribute to the discrepancy, and we tested this hypothesis using previously described K8/K18 variants and a novel KRT18 c.1057C>G variant (K18 p.R353G) to optimize the DHPLC conditions in 10 examined exons under a range of denaturing temperatures. Six of 16 tested variants in three of the 10 exons, including the frequent KRT8 c.184G>T (K8 p.G62C), KRT8 c.187A>G (K8 p.I63V), and KRT8 c.1022G>A (K8 p.R341H), could not be reliably detected when using temperatures suggested by the prediction software, but all these variants were readily detectable at 2 degrees C higher denaturing temperatures. Using optimized temperatures, we then tested available genomic DNA from 151 out of the 256 German liver disease patients for the presence of K8 variants in exons 1 and 6, where most of the American cohort K8 variants occur. We identified 12 exonic and two intronic K8 variants: one KRT8 c.184G>T (K8 p.G62C), two KRT8 c.187A>G (K8 p.I63V), seven KRT8 c.1022G>A (K8 p.R341H), one KRT8 c.1128G>A (K8 p.E376E), two intronic KRT8 c.1202+46 A>T, and one hitherto undescribed KRT8 c.1138G>A (K8 p.V380I). Therefore, although DHPLC offers a robust and high throughput means for mutation analysis, assessment of denaturing temperature ranges, and possible inclusion of control mutants should be considered.

Chromatography, High Pressure Liquid↗

PubMed2006

Determination of the mutation spectrum of the EXT1/EXT2 genes in British Caucasian patients with multiple osteochondromas, and exclusion of six candidate genes in EXT negative cases.

We describe here the spectrum and distribution of mutations in the EXT1 and EXT2 genes in the largest reported British Caucasian multiple osteochondromas (MO) population. Furthermore, we report for the first time the screening of the EXT1 and EXT2 promoters, 5'UTRs, and 3'UTRs, and exclude six potential MO candidate genes in individuals without a detectable mutation within the coding region of EXT1 and EXT2. The coding exons of EXT1 and EXT2 were screened in 72 unrelated probands affected with MO. Forty-six different mutations were identified in 56 probands, of which 29 were novel. Mutation in the EXT1 and EXT2 genes each accounted for 50% of the mutations identified. Of the 72 probands, 42 were of British Caucasian descent, which when added to the 41 British Caucasian families previously reported from our total cohort, gave a total of 83 families. This cohort's proportional frequency for EXT1/EXT2 mutation was 53%/47%. We also validated the technique of high-resolution melting analysis in a blind study using 27 unique EXT1 or EXT2 mutations. This technique was found to be sensitive with a detection rate of 100% regarding heterozygote detection for EXT mutation scanning. Furthermore, this technique has a very high throughput and is very cost-effective.

Chromatography, High Pressure Liquid↗

PubMed1994

Distinct functions of capsid protein in assembly and movement of tobacco etch potyvirus in plants.

Tobacco etch potyvirus engineered to express the reporter protein beta-glucuronidase (TEV-GUS) was used for direct observation and quantitation of virus translocation in plants. Four TEV-GUS mutants were generated containing capsid proteins (CPs) with single amino acid substitutions (R154D and D198R), a double substitution (DR), or a deletion of part of the N-terminal domain (delta N). Each modified virus replicated as well as the parental virus in protoplasts, but was defective in cell-to-cell movement through inoculated leaves. The R154D, D198R and DR mutants were restricted essentially to single, initially infected cells. The delta N variant exhibited slow cell-to-cell movement in inoculated leaves, but was unable to move systemically due to a lack of entry into or replication in vascular-associated cells. Both cell-to-cell and systemic movement defects of each mutant were rescued in transgenic plants expressing wild-type TEV CP. Cell-to-cell movement, but not systemic movement, of the DR mutant was rescued partially in transgenic plants expressing TEV CP lacking the C-terminal domain, and in plants expressing CP from the heterologous potyvirus, potato virus Y. Despite comparable levels of accumulation of parental virus and each mutant in symptomatic tissue of TEV CP-expressing transgenic plants, virions were detected only in parental virus- and delta N mutant-infected plants, as revealed using three independent assays. These data suggest that the potyvirus CP possesses distinct, separable activities required for virion assembly, cell-to-cell movement and long-distance transport.

Amino Acid Sequence↗

PubMed2026

Simultaneous detection of glyphosate and glufosinate target-site resistance in Eleusine indica via multiplex TaqMan qPCR.

BACKGROUND: Continuous use of glyphosate followed by glufosinate-ammonium has selected for multiple resistance to both herbicides in Eleusine indica worldwide. Managing such resistant weeds requires fast, accurate molecular detection assay. To address this critical need, we developed a robust multiplex TaqMan quantitative (q)PCR assay that simultaneously detects five well-characterized target-site resistance markers in E. indica: EPSPS copy number variation; T102I in EPSPS; P106A and P106S in EPSPS; and S59G in GS1-1. RESULTS: The multiplex qPCR assay showed analytical specificity when tested on genomic DNA from nine reference accessions: three susceptible, three glyphosate-resistant (with EPSPS CNV) and three multiple-resistant. Subsequent analysis of 56 field-collected samples demonstrated 98.2% concordance (55 of 56) with Sanger sequencing across all five resistance-associated markers: EPSPS CNV, T102I, P106A, P106S and GS1-1 S59G, confirming the reliability and practical value of the multiplex qPCR assay. Only samples 7-8 showed discordance at EPSPS position 102, where Sanger chromatograms showed overlapping peaks at this position, which is likely to be a result of heterozygous mutation distribution among amplified EPSPS gene copies. This case further underscores the advantages of the multiplex qPCR assay over Sanger sequencing in detection sensitivity and accuracy. Moreover, a strong correlation (R2 = 0.8935) in gene copy number estimation between the two methods across all samples further supports the reliability of the qPCR assay. CONCLUSIONS: In summary, this study delivers a simple, robust and high-throughput diagnostic tool for the rapid, simultaneous identification of dual herbicide target-site resistance in goosegrass, offering superior sensitivity, quantitative resolution and throughput compared with Sanger sequencing. © 2026 Society of Chemical Industry.

Herbicides↗

PubMed2001

Isolation and characterization of acetoacetyl-CoA thiolase gene essential for n-decane assimilation in yeast Yarrowia lipolytica.

Yarrowia lipolytica is a yeast which can utilize n-alkane as a sole carbon source. We isolated a Y. lipolytica peroxisomal acetoacetyl-CoA thiolase gene, PAT1, by complementation of a mutant that cannot utilize n-decane as a sole carbon source. We found that the putative PAT1 product had conserved features of peroxisomal acetoacetyl-CoA thiolase. We showed that the PAT1 disruptant was not able to grow on n-decane, and that n-decane-inducible acetoacetyl-CoA thiolase activity largely depended on PAT1. The original mutant carried a mutation involving the replacement of Gly382 with Glu. This mutation inactivated the ability of PAT1 to complement the defective n-decane utilization of the disruptant. These results indicate that PAT1 encodes peroxisomal acetoacetyl-CoA thiolase and is essential for n-decane utilization in Y. lipolytica.

Acetyl-CoA C-Acetyltransferase↗

PubMed2002

Asb4, Ata3, and Dcn are novel imprinted genes identified by high-throughput screening using RIKEN cDNA microarray.

Genes differentially expressed between parthenogenetic and androgenetic embryos are candidates for the identification of imprinted genes, which are expressed specifically from the maternal or paternal allele. To search for genes differentially expressed between parthenogenetic and androgenetic embryos, we used the RIKEN full-length enriched mouse cDNA microarray. The 25 candidates obtained included 8 known imprinted genes (such as IgfII, Snrpn, and Neuronatin) and 3 new ones--Asb4 (ankyrin repeat and SOCS box-containing protein 4), Ata3 (amino acid transport system A3), and Decorin--which were confirmed by using normal diploid embryos from the reciprocal F1 crosses of B6 and JF1 mice. The 25 candidates also included genes that showed no imprinting-associated expression in normal diploid embryos. We describe a feasible high-throughput method of screening for novel imprinted genes by using the RIKEN cDNA microarray.

Amino Acid Transport System A↗

PubMed1998

CAG/CTG and CGG/GCC repeats in human brain reference cDNAs: outcome in searching for new dynamic mutations.

CAG and CGG expansion is associated with 10 inherited neurological diseases and is thought to be involved in other human genetic diseases. To identify new candidate genes, we have undertaken a large-scale screening project for CAG/CTG ([CAG]n) and CGG/GCC ([CGG]n) repeats in human brain reference cDNAs. Here, we present the final classification for 597 cDNAs selected by CAG and CGG hybridization from two libraries (100,128 clones) and the updated characterization of [CAG]n- and [CGG]n-positive cDNAs (repeat polymorphism and cDNA localization). We have selected 124 CAG and 83 CGG hybridization-positive clones representing new genes, from which 49 CAG and 7 CGG repeats could be identified. New [CAG]n and [CGG]n with more than seven to nine units were rare (1/2000), and perfect [CAG]n 9 were more likely polymorphic. Overall, highly polymorphic to monomorphic new [CAG]n > 9 and [CGG]n > 7 were characterized. The comparison of our data with other [CAG]n and [CGG]n resources suggests that the screening of reference cDNAs leads to unique sources of new [CAG]n and [CGG]n and will enhance the study of enlarged triplet repeats in human genetic diseases.

Brain↗

PubMed2000

A sequence-ready BAC clone contig of human chromosome 10p15 spanning the loss of heterozygosity region in glioma.

Deletion of chromosome 10 is one of the most common chromosomal alterations in glioma. At 10p15, the telomeric region of the short arm of chromosome 10, loss of heterozygosity (LOH) has been frequently observed by microsatellite analysis, suggesting the presence of a tumor suppressor gene. We examined LOH in 34 gliomas on chromosome 10, and frequent LOH on 10p was detected on 10p15, in agreement with deletion mapping studies on chromosome 10. We then constructed a bacterial artificial chromosome (BAC) clone contig covering the critical region, which spanned the interval between D10S249 and D10S533 on 10p15. The map contained 68 BAC clones connected by 74 sequenced tag sites (STSs) and covered approximately 2.7 Mb, with one gap. A total of 74 STSs, including 6 microsatellite markers, 29 expressed sequenced tags (ESTs), and 39 BAC end STSs, were physically arranged. Twenty-eight ESTs were mapped in the interval between D10S249 and D10S559 (approximately 1200 kb), and another EST was mapped in the interval between D10S559 and D10S533 (approximately 1300 kb). This sequence-ready BAC clone contig map will be a basic resource for high-quality sequencing and positional cloning of the putative tumor suppressor gene at 10p15 in glioma.

Base Sequence↗

PubMed1993

A mutation of cauliflower mosaic virus gene I interferes with virus movement but not virus replication.

A 300-bp deletion was made in gene I of a multimeric copy of cauliflower mosaic virus (CaMV). The deleted and wild-type constructs were mobilized into Agrobacterium tumefaciens and used for the inoculation of plants and leaf discs of the host plant, turnip, by "agroinfection." Infection induced by the wild-type construct gave characteristic viral symptoms on the inoculated and systemically infected leaves of whole plants whereas no infection was detected using the deletion mutant. The possibility that the deletion in gene I affected a cis-related function (e.g., encapsidation) was tested by complementation of mutant gene I with wild-type CaMV. Double infection experiments showed that replication and spread of both viruses occurred without detectable recombination of the mutant. In contrast to the situation in plants, agroinfection (Grimsley et al., 1986, Proc. Natl. Acad. Sci. USA 83, 3282-3286) of leaf discs, detected as the accumulation of encapsidated forms of virion DNA, was recorded for both the wild-type and the deleted constructs. The reduced level of virus accumulation from the mutant was consistent with virus replication occurring only in cells involved in the primary interaction with Agrobacterium, and accordingly progeny viral DNA was only detected in cells around the edge of the tissue disc. These data provide definitive evidence that CaMV gene I encodes a movement protein and show that this function can act in trans in a virus infection.

Brassica↗

PubMed1993

Complementation and recombination between mutants of complementary sense genes of DNA A of Abutilon mosaic virus.

Mutations have been inserted into the complementary sense ORFs of DNA A of Abutilon mosaic virus (AbMV). Mutation in both ORF AC1 and ORF AC2/3 resulted in clones incapable of infecting Nicotiana benthamiana following agroinoculation. Mutation in ORF AC1 but not in ORF AC2/3 prevented DNA replication in leaf discs. Thus ORF AC1 is essential for AbMV DNA replication whereas ORF AC2/3 is probably involved in some aspect of the spread of the virus through the plant. Coagroinoculation of both mutants and wild-type DNA B resulted in complementation and recombination. Complementation precedes recombination and once recombination is established mutant DNA can no longer be detected. Plants in which complementation alone is occurring are symptomless and contain relatively low amounts of virus double-stranded DNA whereas following recombination a wild-type infection is established.

Blotting, Southern↗

PubMed1996

Homologous and heterologous complementation of HBV and WHV capsid and polymerase functions in RNA encapsidation.

Successful encapsidation of hepadnaviral pregenomic RNA requires the orchestrated interaction of the viral capsid and polymerase proteins with each other and with the RNA packaging substrate. The early steps of this process involve binding of the polymerase to the encapsidation signal, epsilon, and are already understood in some detail. However, the underlying macromolecular interactions resulting in the subsequent encapsidation of this polymerase-epsilon complex by capsid proteins are less clearly defined. To approach this issue we have examined the ability of two different hepadnaviruses to encapsidate each other's pregenomic RNA. H. Okamoto et al. ((1990) J. Gen. Virol. 71, 959-963) have previously demonstrated that WHV polymerase could encapsidate an HBV pregenome, but the origin of the capsid proteins (i.e., HBV- or WHV-derived) required for this reaction was not clear; some evidence suggested that heterologous capsid and polymerase proteins might not be capable of interaction. To clarify this, we analyzed encapsidated RNA isolated from cytoplasmic cores produced following transient transfection of HepG2 cells with different combinations of plasmids encoding HBV or WHV core and polymerase genes. We found that (i) the essential encapsidation signal of WHV is comprised of a short region including epsilon, as in HBV; (ii) HBV and WHV polymerases are each competent to recognize both HBV and WHV packaging signals; therefore the encapsidation signals are functionally interchangeable; and (iii) HBV capsids encapsidate a WHV polymerase-epsilon complex, and vice versa, although the efficiency of heterologous packaging is slightly lower than that of homologous encapsidation. Our results underscore the close relationship of these two mammalian hepadnaviruses.

Animals↗

PubMed1998

Cell-to-cell movement of turnip crinkle virus is controlled by two small open reading frames that function in trans.

Previous studies on turnip crinkle virus (TCV) have suggested that the two small, centrally located ORFs, conserved in all Carmoviruses, are both required for cell-to-cell movement (Hacker et al., 1992). We now demonstrate that the cell-to-cell movement of TCV is mediated by in trans complementation of the two proteins. First, both of the putative movement proteins (MPs p8 and p9) were shown to be translated in vitro from transcripts representing the 1.7-kb subgenomic RNA. Western blot analysis, using antisera prepared against GST fusion proteins of both genes, was then used to show that the p8 but not the p9 protein accumulated to detectable levels in particulate fractions of infected cells. Cell-to-cell movement of various MP mutants in Arabidopsis was evaluated by in situ hybridization of inoculated leaves. Changes in either of the two MP genes resulted in failure of the mutants to move cell-to-cell. Coat protein was found to be unnecessary for cell-to-cell movement. Complementation of cell-to-cell movement by co-inoculating p8-defective mutants with a p9-defective mutant resulted in delayed systemic infection. In contrast, efficient cell-to-cell movement was achieved when the MP mutants were inoculated into transgenic plants expressing the corresponding functional gene(s). These experiments provide further evidence that both MP genes encoded by Carmoviruses must function in trans in the same cell in order to mediate cell-to-cell movement.

Arabidopsis↗

PubMed1999

In vivo detection, RNA-binding properties and characterization of the RNA-binding domain of the p7 putative movement protein from carnation mottle carmovirus (CarMV).

Biochemical and structural characterization studies on the p7 putative movement protein from a Spanish isolate of carnation mottle carmovirus (CarMV) have been conducted. The CarMV p7 gene was fused to a sequence coding for a six-histidine tag and expressed in bacteria, allowing the purification of CarMV p7 and the production of a specific antiserum. This antiserum led to the immunological identification of CarMV p7 in infected leaf tissue from the experimental host Chenopodium quinoa. Putative nucleic acid-binding properties of the CarMV p7 have been explored and demonstrated with both electrophoretic mobility shift and RNA-protein blot in vitro assays using digoxigenin-labeled riboprobes. CarMV p7 did not show preferential binding to any of the different regions of the CarMV genomic RNA tested, suggesting that RNA binding was sequence nonspecific. Quantitative analyses of the data allowed calculation of the apparent dissociation constant of the p7-RNA complex (Kd approximately 0.7 microM) and supported a cooperative type of binding. A small 19-amino-acid synthetic peptide whose sequence corresponds to the putative RNA-binding domain of CarMV p7, at the basic central part of the protein, was synthesized, and it was demonstrated that it binds viral RNA probes. Peptide RNA binding was as stable as p7 binding, although data indicated it was not cooperative, thus suggesting that this cooperative binding requires another motif or motifs within the p7 amino acid sequence. The peptide could be induced to fold into an alpha-helix structure in which amino acids that are conserved among carmovirus p7-like proteins are distributed on one side. This alpha-helix motif could define a new and previously uncharacterized RNA-binding domain for plant virus movement proteins.

Amino Acid Sequence↗