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PubMed2001

Analysis of the TSC2 gene in human medulloblastoma.

Medulloblastoma (MB) represents the most frequent malignant brain tumor of childhood. Recent studies have shown that deregulation of developmental control genes may play an important role in its pathogenesis. Tuberous sclerosis is associated with hamartomas and cortical tubers, consisting of both glial and neuronal cellular components. MBs can also show markers of these lineages, raising the question of the potential involvement of TSC genes in these malignant tumors. Here we investigated tuberous sclerosis 2 (TSC2), one of the two genes responsible for tuberous sclerosis, in sporadic MBs. We analyzed MBs for allelic losses at the TSC2 locus and for the frequency of a polymorphism first described in gangliogliomas. Sixty-eight MBs were examined for this polymorphism located in intron 4, 3 base pairs 5' to the first coding nucleotide of exon 5. The distribution of the alleles was significantly different in MBs as compared to 208 control samples, (P=0.0017, Chi-square test). In MBs the frequency of the rare allele (A2) was 0.184 (18.4%), whereas in the control group it occurred in a frequency of 8.7%. Microsatellite analysis of the TSC2 region in 50 tumors did not identify allelic losses. TSC2 mRNA transcript was detectable via reverse transcription-PCR in all tumors as well as in normal cerebellum. Northern blot analysis of an MB cell line homozygous for the rare allele of the polymorphism and two other cell lines homozygous for the frequent allele revealed normal splicing patterns and normal expression levels of the TSC2 transcript. These findings may indicate that the presence of the rare TSC2 allele is associated with a predisposition for the development of MBs.

Blotting, Northern↗
PubMed2006

Association between serotonin transporter gene and borderline personality disorder.

Borderline personality disorder (BPD) is characterized by a pervasive pattern of instability in regulation of emotion, interpersonal relationships, self-image, and impulse control beginning in early adulthood. BPD affects about 1-2% of the general population and has a high mortality rate as a result of suicide and impulsive behaviour. The serotonin transporter gene (5-HTT) is considered as a candidate gene for BPD as multiple lines of evidence have suggested that it plays an important role in suicide, impulsive behaviour, and emotional liability. To test for an association between 5-HTT and BPD, we genotyped three common polymorphisms: the serotonin transporter linked promoter region (5-HTTLPR); a variable number of tandem repeat (VNTR) in intron 2, and a single nucleotide variant (A/G) within the LPR region. Eighty-nine Caucasian patients with BPD and 269 Caucasian healthy controls were analyzed. The program UNPHASED was used to compare allele and haplotype frequencies between cases and controls. Significant differences in allele frequencies of the VNTR marker (p=0.012) and haplotype frequencies (p=0.002) between patients and controls were found. Compared with healthy controls, patients with BPD showed higher frequencies of the 10 repeat of the VNTR marker and the S-10 haplotype, and lower 12 repeat and L(A)-12 haplotype. Our results suggest that the serotonin transporter gene may play a role in the aetiology of borderline personality disorder.

Adult↗
PubMed1985

Evolutionary and structural relationships among the group-specific component, albumin and alpha-fetoprotein.

The group-specific component (Gc) is a plasma protein that binds vitamin D. Recent characterization of human Gc cDNA demonstrated homology with serum albumin and alpha-fetoprotein. This study compares the sequences of the three proteins and demonstrates a strong evolutionary relationship. Albumin, alpha-fetoprotein and Gc evolved from an ancestral gene containing an intragenic triplication. Comparison of the amino acid sequences and patterns of double disulfide bonds suggests that the Gc gene may have diverged from an ancestral gene earlier in evolution than the genes encoding albumin and alpha-fetoprotein. Analysis of the amino acid and nucleotide sequences of the three internal domains of Gc revealed 19-23% amino acid sequence identity and the localization of three homology blocks with 40-44% nucleotide sequence identity. The deduced amino sequence of Gc furnished data for comparing its molecular configuration based on the predicted secondary structure with those predicted for human albumin and alpha-fetoprotein. Utilization of Gc cDNA has also led to the identification of its genomic DNA and detection of a human DNA polymorphism.

Albumins↗
PubMed2000

Suggestions for the nomenclature of human alleles: relevance to ecogenetics, pharmacogenetics and molecular epidemiology.

The current number of 9422 symbols for human gene names (http://www.gene.ucl.ac.uk/nomenclature/) is expected to increase 7- to 15-fold over the next 2 years. In and around each gene, a tremendous degree of single-nucleotide polymorphism (SNP) heterogeneity is now realized to exist. This review is intended to be visionary, to point out some of the enormously complex nomenclature issues that we face, and to offer some reasonable solutions to these issues. For example, I believe that a 'gene' should be defined as that region from the furthest 5'-ward enhancer to at least 150 bases downstream of the last exon. Just as established rules are critically important for the systematic naming of all new genes, standardized nomenclature rules for the naming of allelic variants are also desperately needed. The evolving consensus for naming the alleles of all human genes (ideally based on evolutionarily diverging haplotype patterns) is described herein. Because of the anticipated explosion in finding new genes and allelic variants due to high-throughput resequencing and DNA-chip technologies, this excess of new knowledge will undoubtedly overwhelm their publication by scientific journals alone. I suggest that the best approach to this staggering 'information overload' is to place the data on appropriate web sites--with numerous links between sites, and frequent updates of all information--so that colleagues in all fields of medical and genetic research can remain knowledgeable. Examples of successful web sites to date include those for the cytochrome P450 (CYP) genes and human CYP alleles, UDP glycosyltransferase (UGT) genes and human alleles, human N-acetylaminotransferase (NAT2, NAT1) alleles, and aldehyde dehydrogenase (ALDH) genes and human alleles. Many more web sites will be necessary. For each site, the webmaster will need to be responsible, accurate, energetic, highly organized, and keen to keep the site current. I believe that interactive discussions on these sites should be encouraged, and advisory committees must be willing to check frequently to ensure that all new information is accurate. Lastly, for the field of molecular epidemiology, the importance of correlating an informative genotype with an unequivocal phenotype is emphasized, and the emerging realization that racial and ethnic groups are highly admixed is summarized and updated.

Alleles↗
PubMed2026

The emergence of putative epistatic mutations and iSNVs in SARS-CoV-2 XBB.1.16 variants linked with alteration in immunogenic determinants.

The SARS-CoV-2 XBB variants have been proposed to evolve towards immune evasion against vaccination or natural infection, which may contribute to higher transmissibility. The XBB.1.16 independently emerged due to accumulation of two important substitutions, E180V and T478R in the spike protein. Its pseudoviral infectivity and evasion of humoral immunity were similar to XBB.1 and XBB.1.5. In March 2023, XBB.1.16 had outcompeted other dominant XBB variants in India, which indicate a potential growth advantage. Here, intra-host single nucleotide variations (iSNV) and mutations were screened in SARS-CoV-2 genomes in closely related individuals at two time points: at symptoms onset, and during recovery. The prominence of putative epistatic iSNVs (E180V, G184V, G252V, D253G, and P521S/T) in XBB.1.16 variants were detected during the recovery phase. E180V exhibits mutational constellations with the G252V and P521T in a subset of samples, and this pattern was also detected in contemporary SARS-CoV-2 genomes. Higher order protein structural predictions suggested that the putative epistatic interactions among E180V, G184V, and G252V, D253G may be associated with S protein folding and structural stability. This study involving genomics and computational analyses highlights the potential role of these putative epistatic interactions in immune evasion, which may have contributed to dominance of XBB variants.

Humans↗
PubMed2006

Patterns of association between PPARgamma genetic variation and indices of adiposity and insulin action in African-Americans and whites: the CARDIA Study.

We performed a combination of single-variant- and haplotype-based analyses to investigate the association of peroxisome-proliferator-activated receptor gamma (PPARgamma) gene sequence variation with indices of adiposity, including body mass index (BMI) and waist girth, as well as insulin action, including fasting blood glucose and insulin levels. Nine polymorphisms, selected based on race-specific pairwise linkage disequilibrium relations and/or potential functional relevance, were assayed in 3,875 African-American and white young adults from the Coronary Artery Risk Development in Young Adults Study. These polymorphisms were C25819G (C-681G), C65746G (Pro12Ala), G67222A, A69208G, G81556T, T95872C, T115432G, C127599T, and C148157T (C1431T). They defined seven and six common haplotypes in African-Americans and whites, respectively. Patterns of associations of PPARgamma genetic variation with the metabolic traits differed between the two racial groups, with some exceptions. Haplotype CCGGCTCC was associated with a significant reduction in glucose levels in both racial groups (P<0.001 in each group), and the G69208 allele was associated with lower glucose levels in lean African-Americans and in whites (both P=0.02). Two haplotypes, relatively unique to whites, were associated with measures of adiposity and glucose levels. Two haplotypes, relatively unique to African-Americans, were associated with glucose levels. There were no significant effects of PPARgamma haplotypes on measures of body size in this racial group, but a novel polymorphism, G67222A, significantly modulated the relation between BMI and glucose levels (P interaction, 0.003). This study provides evidence that variants, other than Pro12Ala, influence variation in body size and indices of insulin action. It underscores the role of genetic and environmental contexts in shaping the patterns of associations of PPARgamma sequence variants with metabolic traits in human populations.

Adiposity↗
PubMed2005

Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers.

The human SNP database was used to detect selection on 238 hexamers previously identified as exonic splicing enhancers (ESEs). We compared the distribution of the 238 putative ESEs in biallelic and triallelic SNPs within five different functional categories of the SNP database: synonymous, nonsynonymous, introns, UTRs, and nongenic SNPs. Since true ESEs do not function outside of exons, SNPs that disrupt ESE motifs were expected to be more common in nonexonic portions of the genome. Our results supported this expectation: ESEs were least prevalent within synonymous SNPs and most common in nongenic SNPs. There were approximately 11% fewer ESEs within synonymous biallelic SNPs than expected under no selective constraint. We also compared the frequency of neutral SNPs, those where neither allele was an ESE, with deleterious SNPs, those where one or more alleles was an ESE, across the five different functional classes of SNPs. In comparison with the other functional classes of SNPs, synonymous SNPs contained an excess of neutral variants (+1.64% and +6.04% for biallelic and triallelic SNPs, respectively) and a dearth of deleterious variants (-13.11% and -52.39% for biallelic and triallelic SNPs, respectively). The observed patterns were consistent with purifying selection on the 238 hexamers to maintain their function as ESEs. However, in contrast to previous work, we did not find evidence for selection to maintain ESE function at nonsynonymous SNPs because selection at the protein level probably obscured any difference at the level of ESE function.

Alternative Splicing↗
PubMed2005

[Sequence variation of TYR exon 1 and origin of pigs].

To investigate the origin and genetic diversity of domestic pigs, the porcine TYR exon 1 in 36 individuals from 12 Chinese indigenous breeds, three European breeds, eight Chinese wild boars and two Vietnamese wild boars was sequenced. Sequence analysis revealed six synonymous mutations, and all the sequences could be sorted into 4 haplotypes. Combining with the published sequences, we constructed a reduced median network (RM network), in which TYR*2 was a haplotype dominated by European domestic pigs and wild boars, plus only three chromosomes from Asian pigs. Most Asian domestic pigs and wild boars shared haplotype TYR*1, demonstrating that TYR*1 was an Asian specific haplotype. Meanwhile, some European domestic pigs and wild boars carried the haplotype TYR*1. TYR*3 and TYR*4 were two haplotypes with low frequencies, containing mainly Chinese indigenous pigs and Asian wild boars, plus some European domestic pigs. Independent domestication of pigs from Asia and Europe was supported by the pattern of RM network. The European commercial breeds had been suffered from introgression from Chinese pigs, and a few Chinese indigenous breeds and Japanese wild boars were also suffered from introgression from European pigs as well.

Animals↗
PubMed2003

Electrophoretic analysis of genetic variability within Cryptosporidium parvum from imported and autochthonous cases of human cryptosporidiosis in the United Kingdom.

Cryptosporidium parvum oocyst DNA samples (n = 184) from humans with cryptosporidiosis contracted during foreign travel or during outbreaks in the United Kingdom were characterized genetically and categorized by single-strand conformation polymorphism (SSCP)-based analysis of the small-subunit gene (pSSU) (approximately 300 bp) and second internal transcribed spacer (pITS-2) (approximately 230 bp) of nuclear ribosomal DNA. The two recognized genotypes (types 1 and 2) of C. parvum could be readily differentiated by a distinct electrophoretic shift in the pSSU SSCP profile, associated with a nucleotide difference of approximately 1.3 to 1.7%. Of the 102 samples from cases contracted during foreign travel, 88 (86.3%) were identified as C. parvum type 1 and 14 (13.7%) were identified as type 2. For outbreak samples, unequivocal differentiation between type 1 (n = 20; one child nursery outbreak) and type 2 (n = 62; two waterborne outbreaks) was also achieved. Nucleotide variation in pITS-2 (both within and among samples representing each genotype) was substantially greater (10 to 13 different profiles for each genotype, relating to sequence differences of approximately 1 to 42%) than that in pSSU. SSCP analysis of pITS-2 for all samples revealed that some profiles had a broad geographical distribution whereas others were restricted to particular locations, suggesting a link between some subgenotypes and the geographical origin or source. Comparative denaturing polyacrylamide gel electrophoretic analysis revealed the same genotypic identification and a similar subgenotypic classification of samples as SSCP analysis. The findings of this study, particularly the detection of intragenotypic variation by SSCP, should have significant diagnostic implications for investigating transmission patterns and the monitoring of outbreaks.

Animals↗
PubMed2005

Evaluation of seroneutralization and molecular diagnostic methods for echovirus identification.

In this study we compared the identification results of 41 echovirus clinical isolates using RIVM pools (National Institute for Public Health and the Environment RIVM, Bilthoven, The Netherlands) and reverse transcription-polymerase chain reaction (PCR) assays. Primer pair UG52-UC53 amplified a 433-bp segment in the 5' untranslated region. Restriction enzyme HpaII was used for subgrouping of our isolates into 2 different genetic clusters. Amplification of 315 bp that is located in 5' end of VP1 gene as well as of a long genomic fragment (1452 bp) including the VP1 3' end, the entire coding sequence of 2A, 2B, and the 5' moiety of the 2C-coding region was achieved by the application of PCR protocols with primers 292-222 and EUG2a, 2b, 2c-EUC2, respectively. Phylogenetic trees were constructed for the 5' end as well as for the 3' end of VP1 gene using nucleotide sequences derived from sequencing of clinical isolates and homologous sequences of all echovirus serotypes. The phylogenetic grouping pattern of the clinical isolates revealed a correlation of serotype and genotype either in the 5' or in the 3' end of the VP1 gene that was investigated in the present study claiming that they can be either used for molecular typing of echoviruses.

5' Untranslated Regions↗
PubMed2001

Human populations show reduced DNA sequence variation at the factor IX locus.

Levels and patterns of human DNA sequence variation vary widely among loci. However, some of this variation may be due to the different populations used in different studies. So far, few studies of diverse human populations have compared different genetic loci for the same samples of populations and individuals. Here, we present new polymorphism data from intron 4 of the Factor IX gene (FIX) sequenced in diverse Old World populations. An explicit comparison is made with another X-linked gene, PDHA1, for which the sampling of individuals was very similar. Despite having a similar amount of divergence from chimpanzees, as do other nuclear genes, FIX has comparatively much less DNA sequence variation among humans. Nucleotide diversity at FIX is the lowest among the existing non-Y chromosome nuclear gene datasets and is less than 10% of the diversity found at PDHA1. Estimates of effective population size based on FIX are 8,558, about half of the value obtained for PDHA1, and the time to the most recent common ancestry among human FIX gene copies (282,000 years) is one of the most recent estimates reported for human genes. Analyses presented here suggest a history for the FIX region that includes recent positive directional selection, or background, selection. The general conclusion emerging is that very large variations can exist between the histories of similar genomic regions, even when sampling differences are minimized.

Amino Acid Sequence↗
PubMed1996

Three new DPB1 alleles identified in a Bantu-speaking population from central Cameroon.

HLA-DPB1 genotyping of 241 individuals from an African Bantu-speaking population in central Cameroon using sequence-specific oligonucleotide probes identified five individuals with novel probe hybridization patterns. DNA sequence analysis of the second exon of the DPB1 alleles from these five individuals identified three new alleles, *6001, *6101N, and *6201. DPB1*6001, found in two individuals, contains a single nucleotide change that results in a polar amino acid, asparagine, at residue 65; this position in the beta 1 domain is occupied by a nonpolar amino acid in all other reported DPB1 alleles. DPB1*6101N, found in one individual, contains a single base mutation that results in a premature termination codon at position 67. DPB1*6201, found in two individuals, is characterized by the apparent motif shuffling that has been hypothesized to be responsible for the majority of DPB1 sequence polymorphism. These new sequences shed additional light on the potential mechanisms by which allelic diversity is generated at the HLA-DPB1 locus.

Africa↗
PubMed2002

Simultaneous differentiation and typing of Entamoeba histolytica and Entamoeba dispar.

Sequences corresponding to some of the polymorphic loci previously reported from Entamoeba histolytica have been detected in Entamoeba dispar. Comparison of nucleotide sequences of two loci between E. dispar strain SAW760 and E. histolytica strain HM-1:IMSS revealed significant differences in both repeat and flanking regions. The tandem repeat units varied not only in sequence but also in number and arrangement between the two species at both the loci. Using the sequences obtained, primer pairs aimed at amplifying species-specific products were designed and tested on a variety of E. histolytica and E. dispar samples. Amplification results were in complete agreement with the original species classification in all cases, and the PCR products displayed discernible size and pattern variations among the isolates.

Animals↗
PubMed2003

Molecular characteristics of human immunodeficiency virus type 1 subtype C viruses from KwaZulu-Natal, South Africa: implications for vaccine and antiretroviral control strategies.

The KwaZulu-Natal region of South Africa is experiencing an explosive outbreak of human immunodeficiency virus type 1 (HIV-1) subtype C infections. Understanding the genetic diversity of C viruses and the biological consequences of this diversity is important for the design of effective control strategies. We analyzed the protease gene, the first 935 nucleotides of reverse transcriptase, and the C2V5 envelope region of a representative set of 72 treatment-naïve patients from KwaZulu-Natal and correlated the results with amino acid signature and resistance patterns. Phylogenetic analysis revealed multiple clusters or "lineages" of HIV-1 subtype C that segregated with other C viruses from southern Africa. The same pattern was observed for both black and Indian subgroups and for retrospective specimens collected prior to 1990, indicating that multiple sublineages of HIV-1 C have been present in KwaZulu-Natal since the early stages of the epidemic. With the exception of three nonnucleoside reverse transcriptase inhibitor mutations, no primary resistance mutations were identified. Numerous accessory polymorphisms were present in the protease, but none were located at drug-binding or active sites of the enzyme. One frequent polymorphism, I93L, was located near the protease/reverse transcriptase cleavage site. In the envelope, disruption of the glycosylation motif at the beginning of V3 was associated with the presence of an extra protein kinase C phosphorylation site at codon 11. Many polymorphisms were embedded within cytotoxic T lymphocyte or overlapping cytotoxic T-lymphocyte/T-helper epitopes, as defined for subtype B. This work forms a baseline for future studies aimed at understanding the impact of genetic diversity on vaccine efficacy and on natural susceptibility to antiretroviral drugs.

AIDS Vaccines↗
PubMed1988

Structure and transcription of the actin gene of Trypanosoma brucei.

In Trypanosoma brucei, the actin gene is present in a cluster of two, three, or four tandemly linked copies, depending on the strain. Each cluster seems to exist in two allelic versions, as suggested by the polymorphism of both gene number and restriction fragment length in the DNA from cloned trypanosomes. The amplification of the gene copy number probably occurs through unequal sister chromatid exchange. The chromosomes harboring the actin genes belong to the large size class. The coding sequence was 1,128 nucleotides long and showed 60 to 70% homology to other eucaryotic actin genes. Surprisingly, this homology seemed weaker with Trypanosoma congolense, Trypanosoma cruzi, Trypanosoma vivax, Trypanosoma mega, or Leishmania actin-specific sequences. The mRNA was around 1.6 kilobases long and was synthesized at the same level in bloodstream and procyclic forms of the parasite. Large RNA precursors, up to 7.7 kilobases, were found in a pattern identical in strains containing either two or three gene copies. Probing of the flanking regions of the gene with either steady-state or in vitro transcripts, as well as S1 nuclease protection and primer extension experiments, allowed mapping of the 3' splice site of the actin mRNA, 38 nucleotides upstream from the translation initiation codon. A variably sized poly(dT) tract was found about 30 base pairs ahead of the splice site. The largest detected actin mRNA precursor seemed to give rise to at least two additional stable mRNAs. The RNA polymerase transcribing the actin gene exhibited the same sensitivity to inhibition by alpha-amanitin as that transcribing both the spliced leader and the bulk of polyadenylated mRNAs.

Actins↗
PubMed2004

Loss of heterozygosity and its correlation with expression profiles in subclasses of invasive breast cancers.

Gene expression array profiles identify subclasses of breast cancers with different clinical outcomes and different molecular features. The present study attempted to correlate genomic alterations (loss of heterozygosity; LOH) with subclasses of breast cancers having distinct gene expression signatures. Hierarchical clustering of expression array data from 89 invasive breast cancers identified four major expression subclasses. Thirty-four of these cases representative of the four subclasses were microdissected and allelotyped using genome-wide single nucleotide polymorphism detection arrays (Affymetrix, Inc.). LOH was determined by comparing tumor and normal single nucleotide polymorphism allelotypes. A newly developed statistical tool was used to determine the chromosomal regions of frequent LOH. We found that breast cancers were highly heterogeneous, with the proportion of LOH ranging widely from 0.3% to >60% of heterozygous markers. The most common sites of LOH were on 17p, 17q, 16q, 11q, and 14q, sites reported in previous LOH studies. Signature LOH events were discovered in certain expression subclasses. Unique regions of LOH on 5q and 4p marked a subclass of breast cancers with "basal-like" expression profiles, distinct from other subclasses. LOH on 1p and 16q occurred preferentially in a subclass of estrogen receptor-positive breast cancers. Finding unique LOH patterns in different groups of breast cancer, in part defined by expression signatures, adds confidence to newer schemes of molecular classification. Furthermore, exclusive association between biological subclasses and restricted LOH events provides rationale to search for targeted genes.

Breast Neoplasms↗
PubMed2001

Identification of a novel HLA-DQB1*06 allele, DQB1*0618.

We report here the identification of a novel DQB1*06 allele, DQB1*0618, found in a bone marrow donor. The new allele was detected during routine DNA-based HLA typing by an ambiguous pattern of probe hybridization, obtained by polymerase chain reaction using sequence-specific oligonucleotides (PCR-SSO). Molecular cloning and sequencing confirmed that the new allele is identical to DQB1*0609 at exon 2 except for 3 nucleotide substitutions at positions 353, 356 and 367, also found in other alleles. These nucleotide changes may explain its anomalous reactivity.

Alleles↗
PubMed2002

Allele frequencies and molecular genotyping of the ABO blood group system in a Kuwaiti population.

The phenotypic distributions of observed numbers of ABO blood groups in a Kuwaiti sample population of 18,558 subjects are 4962 (26.7%) with A, 4,462 (24.1%) with B, 858 (4.6%) with AB, and 8,276 (44.6%) with 0. The calculated gene frequencies are 0.6678 for ABO*O, 0.1768 for ABO*A, and 0.1554 for ABO*B. Molecular genotyping of the ABO blood group system in a Kuwaiti sample population was determined using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. The positions of nucleotides 258 and 700 of cDNA from A transferase were amplified by PCR. The amplified DNA was subjected to RFLP analysis to distinguish A, B, and O alleles. Blood samples of known ABO phenotype from 101 healthy unrelated Kuwaiti individuals (A, 29; B, 23; AB, 14; O,35) were used. Two DNA fragments of the ABO locus were designed to be amplified by 2 pairs of primers. To identify the 258th nucleotide, a 199- or 200-bp DNA fragment was amplified by PCR and digested with KpnI. For the 700th nucleotide, a 128-bp DNA fragment was amplified by PCR and digested with AluI. By analyzing the electrophoresis patterns,ABO genotypes were conclusively determined by examining the DNA fragments. The ABO genotypes of the known 101 samples were as follows: AA, 4.30%; AO, 24.41%; BB, 4.16%; BO, 24.2%; AB, 8.46%; and 00, 34.65%. These results were confirmed statistically using the calculated frequencies of IA, IB, and IO alleles.

ABO Blood-Group System↗

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