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Biomedical subjects

H A Erlich

Publications and source records attributed to H A Erlich.

At least 127 records · Page 7Linked to original sources
PubMed1992

Two new HLA DRB1 alleles found in African Americans: implications for balancing selection at positions 57 and 86.

Two new DRB1 alleles have been identified (DRB1*0303 and DRB1*0805) in African Americans that differ from known DRB1 alleles only by a glycine to valine exchange at position 86. The novel DRB1*0303 allele, found in one individual, has the same DQA1*0401-DQB1*04 haplotype as DRB1*0302, suggesting that it may be a recent diversification of *0302. The novel DRB1*0805 allele, identified in 4 individuals, was found on two haplotypes, sharing a DQA1*0501-DQB1*0301 haplotype with DRB1*0804, and a DQA1*0102-DQB1*0602 haplotype found with DRB1*0801 in some African populations. DRB1*0805 differs from *0804 only at position 57 and differs from *0801 only at position 86. Assuming that DRB1*0801 and DRB1*0802 are ancestral, based on their distribution in various human populations, DRB1*0805 may have been generated twice by two independent mutations or gene conversion events at each of these positions. Alternatively, DRB1*0805 may have arisen from a single gene conversion event (or mutation) and recombined to generate multiple DR-DQ haplotypes. These findings increase the number of DRB1 allelic pairs that differ only at position 86 to 9, suggesting strong balancing selection at this position. A number of DRB1 alleles for DR8 and DR4 also differ only at position 57, a site previously postulated to be strongly influenced by balancing selection in DQB1 alleles by phylogenetic analysis.

Africa↗
PubMed1992

Genetic analysis using the polymerase chain reaction.

The ability of PCR to amplify a specific DNA segment from a complex template in an automated reaction has made molecular analysis more accessible both to basic research and diagnostic laboratories. Modifications of the basic PCR method using generic primers now allow DNA amplification even in the absence of specific nucleotide sequence information. Although PCR has proved extremely valuable for detecting the presence or absence of a given sequence (e.g. diagnosis of infectious disease pathogens like HIV), it is uniquely suited to analyze genetic variation in the amplified DNA. The capacity to analyze DNA variation from limited samples like hair or cheek scrapings has made genetic diagnosis and population genetics studies much simpler and the amplification of specific sequences from individual cells (e.g. sperm) has opened new approaches to genetic mapping.

Biological Evolution↗
PubMed1992

HLA-DQa allelic frequencies detected with PCR in a variety of human populations.

Polymerase chain reaction (PCR) amplification and oligonucleotide probe hybridization may be used to detect DNA polymorphisms rapidly in large samples. In this study, 475 individuals from thirteen human populations were allelotyped at the human leukocyte antigen (HLA) DQa (DQA1) locus. A 242 or 239 bp fragment was amplified from each individual's DNA. Each of six alleles was detected by hybridization to allele specific oligonucleotide probes (ASOs). Allelic frequencies varied between populations, but the measure of gene frequency variation among populations, the FST value, was relatively low. Most populations had genotypic frequencies in agreement with Hardy-Weinberg equilibrium expectations. Principal component analysis was performed on the populations, and results are presented in graphic form. The heterozygosity at this locus is high in all populations; the average (74%) is close to the theoretical maximum (83%) for a 6 allele system. It is likely that this system is affected by stabilizing selection, which makes it less than optimal for the study of random evolutionary divergence between populations.

Alleles↗
PubMed1992

Amplification and characterization of the retinoblastoma gene VNTR by PCR.

VNTR regions are informative genetic markers for linkage mapping and individual identification. Using PCR, we have developed a procedure for the enzymatic amplification of the VNTR located in the 16th intron of the human retinoblastoma (RB1) gene. We have also prepared a nonisotopically labeled oligonucleotide probe which facilitates detection of the amplification products. In examining 250 individuals from four different populations, we have detected 11 alleles ranging from 650 to 1,800 bp in size. The core repeat is approximately 50 bp in length. On the basis of the observed allele frequencies for Caucasian, African-American, and Hispanic populations from the United States and for the Mexican Hispanic population, the heterozygosities have been calculated to be 62%, 75%, 61%, and 50%, respectively. The observed genotype frequencies do not deviate from the values expected under Hardy-Weinberg equilibrium. The effect of varying primer sequences, annealing temperature, and cycle number on the amplification are also discussed. Amplification of this marker may also prove useful for detecting the heterozygosity loss that is associated with tumor formation in retinoblastoma.

Alleles↗
PubMed1991

Recent advances in the polymerase chain reaction.

The polymerase chain reaction (PCR) has dramatically altered how molecular studies are conducted as well as what questions can be asked. In addition to simplifying molecular tasks typically carried out with the use of recombinant DNA technology, PCR has allowed a spectrum of advances ranging from the identification of novel genes and pathogens to the quantitation of characterized nucleotide sequences. PCR can provide insights into the intricacies of single cells as well as the evolution of species. Some recent developments in instrumentation, methodology, and applications of the PCR are presented in this review.

Binding Sites↗
PubMed1991

Genetic diversity at class II DRB loci of the primate MHC.

The evolution of polymorphism at loci encoding the beta-chains of the MHC class II DR Ag was studied in primates by DNA amplification (polymerase chain reaction). Phylogenetic analysis of 63 DRB sequences from the polymorphic second exon (first domain) of nonhuman primates and 53 human sequences indicates the presence of five DRB loci in primates, derived from a DRB1-like ancestral locus over 20 million yr ago. Many of the allelic types at the DRB1 locus predate the divergence of hominoids (5 million yr ago) and some (DR4, DR3, 5, 6) predate the divergence of Old world monkeys and hominoids (20 million yr ago). The DRB3 locus appears to have arisen before the divergence of hominoids on an ancestral DRB1 lineage. The DRB2 and DRB5 loci were generated more than 20 million yr ago and the DRB4 locus more than 5 million yr ago. The DRB2 locus, a pseudogene in humans, is polymorphic in the nonhuman primates.

Amino Acid Sequence↗
PubMed1991

Allelic diversity is generated by intraexon sequence exchange at the DRB1 locus of primates.

The loci encoding the class II cell surface antigens HLA-DR, -DQ, and -DP exhibit a remarkable degree of allelic polymorphism. Most of the class II allelic diversity is localized to the second exon, which encodes a beta-pleated sheet followed by an alpha-helical domain. Here, phylogenetic analysis of 39 human DRB1 alleles and 21 DRB1 alleles obtained by polymerase chain reaction (PCR) amplification from a set of closely related primates reveals that sequences encoding the beta-pleated sheet and those encoding the alpha-helix of the second domain have different evolutionary histories. The polymorphisms in the beta-pleated sheet have been conserved between species and appear to reflect the ancestral relationships among haplotypes, whereas polymorphic segments encoding the alpha-helical domain appear to have been inserted by interallelic sequence exchange into the framework of different ancestral DRB1 sequences. Allelic polymorphism at the DRB1 locus may thus have been generated in part by combining different variants of the two structural domains.

Alleles↗
PubMed1991

Bladder cancer. Human leukocyte antigen II, interleukin-6, and interleukin-6 receptor expression determined by the polymerase chain reaction.

The prediction of tumour biology rarely rests upon a single characteristic of the malignancy. The analysis of a single gene can complement standard histologic evaluation. The investigation of new parameters as well as the routine clinical analysis of gene expression is often limited because of the small amount of tissue available. This is particularly true of de novo human bladder cancers because they are generally small or handled in such a way as to hinder the analysis of multiple different parameters. Analysis of expressed mRNA by the polymerase chain reaction (RNA/PCR) is a method that allows the development of a profile of bladder cancer gene expression. The authors report the use of the RNA/PCR method to examine in bladder cancer the expression of the human leukocyte antigen (HLA) class II gene family (HLA-DR, DQ, and DP) as well as interleukin-6 (IL-6) and the interleukin-6 receptor (IL-6R). All de novo transitional cell carcinomas, one squamous carcinoma, and two transitional cell carcinoma cell lines expressed the majority of HLA class II genes. All samples expressed IL-6R RNA whereas production of IL-6 message was limited to one of the cell lines and to the high-grade bladder cancers. These results were combined with stage, grade, and DNA content to develop a profile of the cancers examined. Although an improved predictive index based on gene expression analysis by RNA/PCR has not been realized, a broader survey of human tumors for expression of these genes and others is likely to refine the classification of bladder cancer.

Base Sequence↗
PubMed1991

Sequencing of HLA-D in responders and nonresponders to short ragweed allergen, Amb a V.

We investigated the molecular basis for the striking association between HLA-DR2,Dw2 and human immune responsiveness to the Ambrosia artemisiifolia (short ragweed) pollen allergen Amb a V by sequencing the second exons of the DRB and DQB1 genes of 17 selected ragweed-allergic Caucasoid subjects. We also studied the DQA1 allelic polymorphic regions (APRs) in these patients by dot-blotting using sequence-specific oligonucleotides (SSOs). The deduced amino acid sequences of the respective class II beta and alpha polypeptides were compared, with particular emphasis on residues in the APRs that are implicated in antigen binding. No evidence for "new" HLA-DRB or DQB sequences unique to Amb a V responders were found on sequencing seven Dw2+ subjects. This suggests that the presence of a particular Dw2-associated class II molecule usually provides a necessary, but not always sufficient condition for responsiveness to Amb a V. The HLA phenotypes of three subjects suggest that they possess novel recombinant haplotypes containing either DRB1*1501 and DRB5*0101 (DR2.2-associated) or DQB1*0602 (DQ1.2-associated) sequences. In these subjects, responsiveness to Amb a V was associated with the DR2.2 but not the DQ1.2 sequences, suggesting that DR alpha beta I or DR alpha beta V class II molecules are involved in antigen presentation. We investigated whether there may be shared HLA-D-encoded responder sequences present in all responders, including some exceptional DR2- Amb a V responders. The 13 subjects producing antibody (Ab) responses to Amb a V [either from natural exposure and/or after ragweed immunotherapy (Rx)] possessed DRB1*1501, 1601, 1602, 0103, 0402, 0404, 0801, or 1101 sequences, which share the majority of their aa residues in the APRs 2-4. Some of these shared residues might be important for the binding of a common Amb a V agretope prior to presentation of the class II Amb a V complex to the T-cell receptor (Tcr). An alternative postulate is that the recognition of two different Amb a V agretopes may be determined by the beta 1 polypeptides of molecules having the DR2 and DQw3 specificities.

Alleles↗
PubMed1991

Rapid typing of HLA-DQB1 DNA polymorphism using nonradioactive oligonucleotide probes and amplified DNA.

The allelic sequence diversity at the HLA-DQB1 locus has been analyzed by polymerase chain reaction (PCR) amplification and sequencing. Fifteen amino acid sequence-defined alleles (one previously unreported) and several silent nucleotide polymorphisms which subdivide these alleles have been identified. Here, we describe the specific amplification of the DQB1 second exon by several different PCR primer pairs and a simple and rapid typing procedure using a panel of 16 horseradish peroxidase (HRP)-labeled oligonucleotide probes capable of distinguishing these DQB1 alleles.

Alleles↗