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Peter J Oefner

Publications and source records attributed to Peter J Oefner.

At least 37 records · Page 2Linked to original sources
PubMed2003

Mutation scanning by ion-pair reversed-phase high-performance liquid chromatography-electrospray ionization mass spectrometry (ICEMS).

Partially denaturing high-performance liquid chromatography has emerged as the most sensitive physical mutation scanning method. However, there are a few reports of mutations missed or only detectable at unique temperatures. The combined use of ion-pair reversed-phase high-performance liquid chromatography under completely denaturing conditions and electrospray ionization quadrupole ion trap mass spectrometry (ICEMS) obviates the need for selecting appropriate temperatures for resolving heteroduplices and allows the discrimination of different alleles even when they co-elute due to distinct mass differences between nucleobases. This was demonstrated for the detection of four mutations (259G>A, 286A>G, 300T>G, and 331+1G>A) in exon 5 and intron 5 of BRCA1, respectively. Current mass resolution of quadrupole ion trap mass spectrometers limits the identification of single A>T or T>A transversions with a mass difference of 9 Da to fragments <80 base pairs (bp). The presence of all other mutations can be detected in fragments up to approximately 105 bp. The approach may prove particularly useful in the mutational scanning of AT- or GC-rich sequences that are recalcitrant to most other methods.

Chromatography, High Pressure Liquid↗
PubMed2003

Genotyping African haplotypes in ATM using a co-spotted single-base extension assay.

Human genetic analysis, including population genetic studies, increasingly calls for cost-effective, high-throughput methods for the rapid screening of single nucleotide polymorphisms (SNPs) across many individuals. The modified single-base extension assay described here (arrayed SBE) is a highly accurate and robust method for SNP genotyping that can deliver genotypes at 3.5 cents each, following PCR. Specifically, amino-modified probe/target pairs were prehybridized, then co-spotted in a microarray format prior to enzymatic addition of allele-specific nucleotides. Probe/target identity was determined solely by its physical location on the array rather than by hybridization to a complementary target, resulting in a call rate of 99-100%. These innovations result in an inexpensive, accurate assay with exceptional signal-to-noise ratios, depending on the glass surface employed. Comparison of glass slides from three different manufacturers indicated that aldehyde-based Zyomyx slides provided superior performance for this assay. Arrayed SBE was applied to study the geographic distribution of three African-specific haplotypes in the human ATM gene. Four selectively neutral markers, which define the haplotypes H5, H6, and H7, were screened in a total of 415 individuals. Region-specific haplotype frequencies were consistent with patterns of human migration across and outside of Africa, suggesting a possible haplotype origin in East Africa. Arrayed SBE was a robust tool for this analysis that could be applied to any situation requiring the genotyping of a few SNPs in many individuals.

Africa, Eastern↗
PubMed2003

First-generation SNP/InDel markers tagging loci for pathogen resistance in the potato genome.

A panel of 17 tetraploid and 11 diploid potato genotypes was screened by comparative sequence analysis of polymerase chain reaction (PCR) products for single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels), in regions of the potato genome where genes for qualitative and/or quantitative resistance to different pathogens have been localized. Most SNP and InDel markers were derived from bacterial artificial chromosome (BAC) insertions that contain sequences similar to the family of plant genes for pathogen resistance having nucleotide-binding-site and leucine-rich-repeat domains (NBS-LRR-type genes). Forty-four such NBS-LRR-type genes containing BAC-insertions were mapped to 14 loci, which tag most known resistance quantitative trait loci (QTL) in potato. Resistance QTL not linked to known resistance-gene-like (RGL) sequences were tagged with other markers. In total, 78 genomic DNA fragments with an overall length of 31 kb were comparatively sequenced in the panel of 28 genotypes. 1498 SNPs and 127 InDels were identified, which corresponded, on average, to one SNP every 21 base pairs and one InDel every 243 base pairs. The nucleotide diversity of the tetraploid genotypes (pi = 0.72 x 10(-3)) was lower when compared with diploid genotypes (pi = 2.31 x 10(-3)). RGL sequences showed higher nucleotide diversity when compared with other sequences, suggesting evolution by divergent selection. Information on sequences, sequence similarities, SNPs and InDels is provided in a database that can be queried via the Internet.

Journal Article↗
PubMed2003

Analysis of FAS (CD95) gene mutations in higher-grade transformation of follicle center lymphoma.

The FAS antigen (CD95/APO-1) is suggested to be a tumor suppressor gene since mice and patients with congenital FAS mutations are prone to B cell lymphomas and somatic FAS mutations are described in hematological and solid tumors. Indeed, mutations of the FAS antigen have been found in 13% of multiple myelomas, 6% of follicle center lymphomas (FCL) and 21% of diffuse large B-cell lymphomas (DLBCL). To assess the possible role of FAS mutations in higher-grade transformation of FCL, biopsy specimens from 16 FCL patients were analyzed by denaturing high performance liquid chromatography and direct sequencing. Overall, 17 biopsy specimens obtained at the time of FCL diagnosis (2 biopsy specimens from one patient), 4 sequential biopsies obtained at the time of FCL relapse and 14 sequential biopsies from the time of morphologic transformation to DLBCL were evaluated. Ten polymorphisms were detected, only 4 of which have been reported previously. Nine of the polymorphisms occurred in non-translated regions, while one silent mutation was located in exon 7. Neither loss of heterozygosity nor occurrence of new mutations was observed upon higher-grade transformation of FCL to DLBCL.

Biopsy↗
PubMed2002

Polymerase chain reaction fidelity and denaturing high-performance liquid chromatography.

Incorporation of non-complementary nucleotides during polymerase chain reaction can result in ambiguous denaturing high-performance liquid chromatography profiles that reduce both sensitivity and specificity of mutation analysis. The use of proofreading DNA polymerases increases the fidelity of polymerase chain reaction and, consequently, reduces background noise in the chromatograms. This is demonstrated for several BRCA1 and BRCA2 mutations hat had yielded previously chromatograms of poor quality using non-proofreading enzyme for amplification. Interestingly, despite the reduced level of background heteroduplices, the ability of denaturing high-performance liquid chromatography to detect mutant alleles at a frequency <10% in pools of chromosomes did not improve significantly.

Base Sequence↗
PubMed2002

Sequence variation and the biological function of genes: methodological and biological considerations.

Single nucleotide polymorphisms (SNPs) are expected to facilitate the chromosomal mapping and eventual cloning of genetic determinants of complex quantitative phenotypes. To date, more than 2.5 million non-redundant human SNPs have been reported in the public domain, of which approximately 100000 have been validated by either independent investigators or by independent methods. Equally impressive is the myriad of methods developed for allelic discrimination. Nevertheless, reports of successful applications of SNPs to genome-wide linkage analysis of both mono- and polygenic traits are rare and limited to a few model organisms, that provide affordable platforms to test both novel methodological and biological concepts at a whole-genome scale under conditions that can be reasonably controlled. Progress in the analysis of SNPs needs to be complemented by methods that allow the systematic elucidation of both primary and secondary phenotypes of genes. Importantly, observations made in one species may very well be of immediate applicability to other species including human. This is particularly true for conserved biological processes such as mitochondrial respiration and DNA repair.

Arabidopsis↗
PubMed2002

A decade of high-resolution liquid chromatography of nucleic acids on styrene-divinylbenzene copolymers.

The introduction of alkylated, nonporous poly-(styrene-divinylbenzene) microparticles in 1992 enabled the subsequent development of denaturing HPLC that has emerged as the most sensitive screening method for mutations to date. Denaturing HPLC has provided unprecedented insight into human origins and prehistoric migrations, accelerated the cloning of genes involved in mono- and polygenic traits, and facilitated the mutational analysis of more than a hundred candidate genes of human disease. A significant step toward increased sample-throughput and information content was accomplished by the recent introduction of monolithic poly(styrene-divinylbenzene) capillary columns. They have enabled the construction of capillary arrays amenable to multiplex analysis of fluorescent dye-labeled nucleic acids by laser-induced fluorescence detection. Hyphenation of denaturing HPLC with electrospray ionization mass spectrometry, on the other hand, has allowed the direct elucidation of the chemical nature of DNA variation and determination of phase of multiple alleles on a chromosome.

Chromatography, High Pressure Liquid↗
PubMed2002

Capillary array high-performance liquid chromatography of nucleic acids and proteins.

An array of monolithic poly(styrene/divinylbenzene) capillaries with individual column thermostats was constructed to demonstrate its utility for the separation of nucleic acids, proteins, and tryptic digests in combination with UV absorbance detection. Because of polymerization-related variation in surface area of monolithic columns, the concentration of acetonitrile required for elution of DNA fragments in denaturing HPLC may vary sufficiently to affect the degree of denaturation. Modulation of column temperature offers a convenient way to harmonize elution profiles among columns. Individual regulation of column temperature also provides the means to determine rapidly in a single parallel run the optimum temperature for resolution of biomolecules. Given the high reproducibility of separations among columns and the ease with which poly(styrene/divinylbenzene)-based stationary phases can be modified to accommodate different modes of chromatography, such arrays will find broad applicability in proteogenomics.

Chromatography, High Pressure Liquid↗
PubMed2002

Systematic screen for human disease genes in yeast.

High similarity between yeast and human mitochondria allows functional genomic study of Saccharomyces cerevisiae to be used to identify human genes involved in disease. So far, 102 heritable disorders have been attributed to defects in a quarter of the known nuclear-encoded mitochondrial proteins in humans. Many mitochondrial diseases remain unexplained, however, in part because only 40-60% of the presumed 700-1,000 proteins involved in mitochondrial function and biogenesis have been identified. Here we apply a systematic functional screen using the pre-existing whole-genome pool of yeast deletion mutants to identify mitochondrial proteins. Three million measurements of strain fitness identified 466 genes whose deletions impaired mitochondrial respiration, of which 265 were new. Our approach gave higher selection than other systematic approaches, including fivefold greater selection than gene expression analysis. To apply these advantages to human disorders involving mitochondria, human orthologs were identified and linked to heritable diseases using genomic map positions.

Biological Transport↗
PubMed2002

Neutrality condition and response law for nonlinear reaction-diffusion equations, with application to population genetics.

We study a general class of nonlinear macroscopic evolution equations with "transport" and "reaction" terms which describe the dynamics of a species of moving individuals (atoms, molecules, quasiparticles, organisms, etc.). We consider that two types of individuals exist, "not marked" and "marked," respectively. We assume that the concentrations of both types of individuals are measurable and that they obey a neutrality condition, that is, the kinetic and transport properties of the "not marked" and "marked" individuals are identical. We suggest a response experiment, which consists in varying the fraction of "marked" individuals with the preservation of total fluxes, and show that the response of the system can be represented by a linear superposition law even though the underlying dynamics of the system is in general highly nonlinear. The linear response law is valid even for large perturbations and is not the result of a linearization procedure but rather a necessary consequence of the neutrality condition. First, we apply the response theorem to chemical kinetics, where the "marked species" is a molecule labeled with a radioactive isotope and there is no kinetic isotope effect. The susceptibility function of the response law can be related to the reaction mechanism of the process. Secondly we study the geographical distribution of the nonrecurrent, nonreversible neutral mutations of the nonrecombining portion of the Y chromosome from human populations and show that the fraction of mutants at a given point in space and time obeys a linear response law of the type introduced in this paper. The theory may be used for evaluating the geographic position and the moment in time where and when a mutation originated.

Biochemical Phenomena↗
PubMed2002

Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.

The natural history of follicular lymphoma (FL) is frequently characterized by transformation to a more aggressive diffuse large B cell lymphoma (DLBCL). We compared the gene-expression profiles between transformed DLBCL and their antecedent FL. No genes were observed to increase or decrease their expression in all of the cases of histological transformation. However, two different gene-expression profiles associated with the transformation process were defined, one in which c-myc and genes regulated by c-myc showed increased expression and one in which these same genes showed decreased expression. Further, there was a striking difference in gene-expression profiles between transformed DLBCL and de novo DLBCL, because the gene-expression profile of transformed DLBCL was more similar to their antecedent FL than to de novo DLBCL. This study demonstrates that transformation from FL to DLBCL can occur by alternative pathways and that transformed DLBCL and de novo DLBCL have very different gene-expression profiles that may underlie the different clinical behaviors of these two types of morphologically similar lymphomas.

Base Sequence↗
PubMed2002

Dissecting the architecture of a quantitative trait locus in yeast.

Most phenotypic diversity in natural populations is characterized by differences in degree rather than in kind. Identification of the actual genes underlying these quantitative traits has proved difficult. As a result, little is known about their genetic architecture. The failures are thought to be due to the different contributions of many underlying genes to the phenotype and the ability of different combinations of genes and environmental factors to produce similar phenotypes. This study combined genome-wide mapping and a new genetic technique named reciprocal-hemizygosity analysis to achieve the complete dissection of a quantitative trait locus (QTL) in Saccharomyces cerevisiae. A QTL architecture was uncovered that was more complex than expected. Functional linkages both in cis and in trans were found between three tightly linked quantitative trait genes that are neither necessary nor sufficient in isolation. This arrangement of alleles explains heterosis (hybrid vigour), the increased fitness of the heterozygote compared with homozygotes. It also demonstrates a deficiency in current approaches to QTL dissection with implications extending to traits in other organisms, including human genetic diseases.

Alleles↗
PubMed2002

A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes.

The variation of 77 biallelic sites located in the nonrecombining portion of the Y chromosome was examined in 608 male subjects from 22 African populations. This survey revealed a total of 37 binary haplotypes, which were combined with microsatellite polymorphism data to evaluate internal diversities and to estimate coalescence ages of the binary haplotypes. The majority of binary haplotypes showed a nonuniform distribution across the continent. Analysis of molecular variance detected a high level of interpopulation diversity (PhiST=0.342), which appears to be partially related to the geography (PhiCT=0.230). In sub-Saharan Africa, the recent spread of a set of haplotypes partially erased pre-existing diversity, but a high level of population (PhiST=0.332) and geographic (PhiCT=0.179) structuring persists. Correspondence analysis shows that three main clusters of populations can be identified: northern, eastern, and sub-Saharan Africans. Among the latter, the Khoisan, the Pygmies, and the northern Cameroonians are clearly distinct from a tight cluster formed by the Niger-Congo-speaking populations from western, central western, and southern Africa. Phylogeographic analyses suggest that a large component of the present Khoisan gene pool is eastern African in origin and that Asia was the source of a back migration to sub-Saharan Africa. Haplogroup IX Y chromosomes appear to have been involved in such a migration, the traces of which can now be observed mostly in northern Cameroon.

Africa↗
PubMed2002

The extent of linkage disequilibrium in Arabidopsis thaliana.

Linkage disequilibrium (LD), the nonrandom occurrence of alleles in haplotypes, has long been of interest to population geneticists. Recently, the rapidly increasing availability of genomic polymorphism data has fueled interest in LD as a tool for fine-scale mapping, in particular for human disease loci. The chromosomal extent of LD is crucial in this context, because it determines how dense a map must be for associations to be detected and, conversely, limits how finely loci may be mapped. Arabidopsis thaliana is expected to harbor unusually extensive LD because of its high degree of selfing. Several polymorphism studies have found very strong LD within individual loci, but also evidence of some recombination. Here we investigate the pattern of LD on a genomic scale and show that in global samples, LD decays within approximately 1 cM, or 250 kb. We also show that LD in local populations may be much stronger than that of global populations, presumably as a result of founder events. The combination of a relatively high level of polymorphism and extensive haplotype structure bodes well for developing a genome-wide LD map in A. thaliana.

Arabidopsis↗
PubMed2002

Population genetic implications from DNA polymorphism in random human genomic sequences.

Denaturing high performance liquid chromatography (DHPLC) in combination with dye-terminator sequencing was used to survey 516 random genomic sequence tagged sites (STSs) for biallelic polymorphisms in 24 representatives of the major ethnic groups residing in the United States. Of the 301 polymorphic STSs (58.3%), 172 contained a single simple sequence polymorphism (SSP), while 78, 35, and 16 contained 2, 3, and 4-6 SSPs, respectively. Of the 541 SSPs identified, 342 (63%), 152 (28%), and 47 (9%) were transitions, transversions, and insertions or deletions, respectively. Only 21% of the STSs contained SSPs with a minor-allele frequency >20%. The nucleotide diversity estimate for random genomic sequences theta = 8.23 x 10(-4) was on average 50% higher than that for intragenic non-coding regions of the human genome ( theta = 5.52 x 10(-4). The discrepancy in Tajima's D statistic between 22 autosomal genes (D=-1.304+/-0.622, mean+/-SD) and random STSs (D=-0.27) suggests that, in the absence of significant mutation rate heterogeneity, the more negative values for genes are a consequence of directional selection rather than population growth.

Base Sequence↗
PubMed2002

Multiplex analysis of single-nucleotide extension products on a 16-capillary, denaturing, high-performance liquid chromatography array.

We constructed a high-performance liquid chromatography array consisting of 16 monolithic poly(styrene/divinylbenzene) capillaries for the parallel multiplex analysis of fluorescent dye-labeled single-nucleotide extension products. Because of the high chemical and physical robustness of the column bed that is covalently linked to the inner surface of the fused silica capillary, the array can be reused thousands of times without replenishment. The choice of fluorophore exerts a significant effect on resolution of the extension products. FAM, HEX, and TAMRA allowed complete resolution of all four possible allelic extension products not only from the extension primer but also from each other. The quantitative accuracy of the method enables the genetic typing of bi- and triallelic single-nucleotide polymorphisms in polyploid genomes and pooled samples.

Chromatography, High Pressure Liquid↗