Population genetic diversity in relation to microsatellite heterogeneity

Nine populations (Germans, Turks, Moroccans, Ovambos, Ugandans, Chinese, Japanese, Papuans, and Australian Aborigines) were investigated using six microsatellite systems (HumCD4, Hum F13B, HumFES/FPS, HumTH01, HumVWA, and D21S11), so-called STRs (short tandem repeats). Allele frequency data and sequencing results were used to compare the population genetic diversity among these populations. The genetic differences varied depending on the STR applied. According to the systems investigated, we defined three categories of STR microvariation: LOMs (low microvariation systems), INMs (intermediate microvariation systems), and HIMs (high microvariation systems). LOMs (STRs: CD4, FES, F13B, TH01) are characterised by a number of repeats between 5–15 and a stable repeat sequence. INMs and HIMs each showed an increasing number of repeats and additional sequence variation in the repeat motifs. The rate of new mutations was associated with the extent of microvariation. The reconstruction of phylogenetic trees led to a clustering in an early split of the African populations followed by further branching of the Asian/Melanesian and the Caucasian groups. Hum Mutat 11:135–144, 1998. © 1998 Wiley-Liss, Inc.     

Sub-Saharan African coding sequence variation and haplotype diversity at the NAT2 gene

A total of 530 chromosomes from 12 sub-Saharan African populations were sequenced at the human arylamine N-acetyltransferase NAT2 gene. We identified seven novel non-synonymous mutations observed at low frequencies (<11%) in our African multi-ethnic panel. By using algorithms based on evolutionary conservation, two mutations (c.70T>A [p.L24I] and c.578C>T [p.T193M]) for which the activity of their encoded protein has never been determined, were predicted to entail a potentially damaging effect on protein activity. In addition, approximately 5% of the overall NAT2 African haplotypes presented an unknown functional effect. More interestingly, NAT2 haplotype frequencies and acetylation status inference revealed that the hunter-gatherer Western Pygmies and !Kung San were mainly composed of fast and intermediate acetylators, in clear contrast with most agriculturalist populations. These observations highlight the need of a detailed genetic characterization of African populations at this locus to adapt medical treatment, such as the antitubercular isoniazid, to individual/population make-up in the most effective manner.     

中国北方汉族人群FUT5基因编码区序列特征

目的 揭示中国北方汉族人群岩藻糖基转移酶基因V(fucosyltransferase 5 gene,FUT5)编码区序列特征.方法 对160名健康中国北方汉族人群血液样品进行研究,DNA测序分析其中30例FUT5基因编码区序列;突变基因亚克隆后测序鉴定其单倍型;聚合酶链反应-限制性片段长度法分析130名C560T(rs778970)和C484A位点的遗传多态性.结果 DNA测序共鉴定出7个单核苷酸多态性(single nucleotide polymorphism,SNPs)及2个新突变点C484A(Leu162Met)和T684C;9种碱基替换共鉴定出7种单倍型;160名样本的rs778970位点遗传多态性分析结果显示等位基因频率C为0.3031,T为0.6969;而C484A未发现其具有多态性.结论 中国北方汉族人群FUT5基因编码区序列呈现出高度的变异性;rs778970位点等位基因分布具有较好多态性.     

High genetic diversity of the VP2 gene of a canine parvovirus strain detected in a domestic cat

This study reports the detection of co-infection by multiple CPV variants and the high genetic complexity of a CPV-2 strain detected in a domestic cat. The CPV variants selected by cloning the VP2 gene were sequenced, and genetic diversity and selection pressure were investigated. Comparison of the nucleotide sequences has evidenced 10 different viral populations, and, in the same animal, more CPV variants coexist. Our analysis excludes the possibility that the recombination events took place during infection and that negative selection acted on the VP2 gene. These findings confirm that CPV-2 shows high genetic heterogeneity resembling the quasispecies found in RNA viruses.     

SNP selection at the NAT2 locus for an accurate prediction of the acetylation phenotype.

PURPOSE: Genetic polymorphisms in the N-acetyltransferase 2 gene determine the individual acetylator status, which influences both the toxicity and efficacy profile of acetylated drugs. Determination of an individual's acetylation phenotype prior to initiation of therapy, through DNA-based tests, should permit to improve therapy response and reduce adverse events. However, due to extensive linkage disequilibrium between markers within NAT2, the genotyping of closely spaced markers yields highly redundant data: testing them all is expensive and often unnecessary. The objective of this study is to establish the optimal strategy to define, in the genetic context of a given ethnic group, the most informative set of single-nucleotide polymorphisms that best enables accurate prediction of acetylation phenotype. METHODS: Three classification methods have been investigated (classification trees, artificial neural networks and multifactor dimensionality reduction method) in order to find the optimal set of single-nucleotide polymorphisms enabling the most efficient classification of individuals in rapid and slow acetylators. RESULTS: Our results show that, in almost all population samples, only one or two single-nucleotide polymorphisms would be enough to obtain a good predictive capacity with no or only a modest reduction in power relative to direct assays of all common markers. In contrast, in Black African populations, where lower levels of linkage disequilibrium are observed at NAT2, a larger number of single-nucleotide polymorphisms are required to predict acetylation phenotype. CONCLUSION: The results of this study will be helpful for the design of time- and cost-effective pharmacogenetic tests (adapted to specific populations) that could be used as routine tools in clinical practice.     

Molecular genetic analysis of a diversity of Getah virus strains isolated from mosquitoes in the North-Eastern Asia

A molecular genetic study was performed of the Getah virus strains isolated in Russia (Eastern Siberia and Far East) and Mongolia. A phylogenetic analysis was made, by examining the nucleotide sequences of genome fragments that had been obtained by RT-PCR and that included the portions of the E1 and E2 surface glycoprotein genes and the 6K gene. A genetic diversity of Getah virus strains in North-Eastern Asia is discussed.     

NAT gene polymorphisms and susceptibility to Alzheimer's disease: identification of a novel NAT1 allelic variant

Background

Clefts of the lip, alveolus, and palate (CLPs) rank among the most frequent and significant congenital malformations. Leu10Pro and Arg25Pro polymorphisms in the precursor region and Thr263Ile polymorphism in the prodomain of the transforming growth factor β1 (TGF-β1) gene have proved to be crucial to predisposition of several disorders.

Methods

In this study, polymorphism analysis was performed by real-time polymerase chain reaction (LightCycler) and TGF-β1 levels determined by enzyme-linked immunosorbent assay.

Results

Only 2/60 Caucasian non-syndromic patients with CLP (3.3%) carried the Arg25Pro and another 2/60 patients (3.3%) the Thr263Ile genotypes, whereas, in a control group of 60 healthy Caucasian blood donors, these heterozygous genotypes were more frequent 16.7% having Arg25Pro (10/60; p < 0.035) and 10,0% having Thr263Ile (6/60), respectively. TGF-β1 levels in platelet-poor plasma of heterozygous Arg25Pro individuals were lower than those of homozygous members (Arg25Arg) in the latter group, but this discrepancy narrowly failed to be significant. Although polymorphisms in codon 10 and 25 were associated with each other, no difference was found between patients and controls concerning the Leu10Pro polymorphism.

Conclusions

The genetic differences in codons 25 and 263 suggest that TGF-β1 could play an important role in occurrence of CLP, however, functional experiments will be required to confirm the mechanisms of disturbed development.     

De novo mutation rates at the single-mutation resolution in a human HBB gene region associated with adaptation and genetic disease

Although it is known that the mutation rate varies across the genome, previous estimates were based on averaging across various numbers of positions. Here, we describe a method to measure the origination rates of target mutations at target base positions and apply it to a 6-bp region in the human hemoglobin subunit beta (HBB) gene and to the identical, paralogous hemoglobin subunit delta (HBD) region in sperm cells from both African and European donors. The HBB region of interest (ROI) includes the site of the hemoglobin S (HbS) mutation, which protects against malaria, is common in Africa, and has served as a classic example of adaptation by random mutation and natural selection. We found a significant correspondence between de novo mutation rates and past observations of alleles in carriers, showing that mutation rates vary substantially in a mutation-specific manner that contributes to the site frequency spectrum. We also found that the overall point mutation rate is significantly higher in Africans than in Europeans in the HBB region studied. Finally, the rate of the 20A→T mutation, called the “HbS mutation” when it appears in HBB, is significantly higher than expected from the genome-wide average for this mutation type. Nine instances were observed in the African HBB ROI, where it is of adaptive significance, representing at least three independent originations; no instances were observed elsewhere. Further studies will be needed to examine mutation rates at the single-mutation resolution across these and other loci and organisms and to uncover the molecular mechanisms responsible.

It is widely known that mutation rates vary across the genome at multiple scales (Hodgkinson and Eyre-Walker 2011; Rahbari et al. 2016; Carlson et al. 2018) and are affected by multiple factors, from the mutation type (Gojobori et al. 1982; Bulmer 1986), to the local genetic context (Gojobori et al. 1982; Bulmer 1986; Blake et al. 1992; Hwang and Green 2004; Rahbari et al. 2016; Carlson et al. 2018), to the general location in the genome (Wolfe et al. 1989; Matassi et al. 1999; Lercher et al. 2001; Ellegren et al. 2003). Although this knowledge is highly advanced now compared with what was known a mere decade ago (Campbell et al. 2012; Michaelson et al. 2012; Francioli et al. 2015; Rahbari et al. 2016; Carlson et al. 2018), it could be enhanced further. In particular, rate measurements to date all have been based on averages of various kinds, such as an average across the genome (Nachman and Crowell 2000; Rahbari et al. 2016), or across the instances of any particular motif (Hwang and Green 2004; Carlson et al. 2018), or in certain cases, across the entire stretch of a gene (Haldane 1949; Vogel and Motulsky 1997; Kondrashov 2003). In contrast, technological limitations have precluded measuring mutation rates at particular base positions and of particular mutations at such positions. However, such high-resolution knowledge of the mutation rate variation would bear on multiple open questions in genetics and evolution—from the relative importance of mutation rate variation to the site frequency spectrum (SFS) (Harpak et al. 2016; Lek et al. 2016; Mathieson and Reich 2017), to its importance for adaptive evolution and parallelism (Inoue et al. 2001; Crow et al. 2009; Dumas et al. 2012; Losos 2017; Kratochwil et al. 2019; Kratochwil and Meyer 2019; Lind 2019; Xie et al. 2019), to its contribution to recurrent genetic disease and cancer (Lupski 1998; McClellan and King 2010; Veltman and Brunner 2012; Shendure and Akey 2015).The most precise way of measuring mutation rates, free of biases attributable to past natural selection or random genetic drift events, is offered by de novo mutations—mutations that appeared for the first time in their carrier (Goldmann et al. 2016; Rahbari et al. 2016). These mutations are usually detected by studies comparing the genomes of children to those of their parents, also known as “trio studies” (Roach et al. 2010; Conrad et al. 2011). However, because each individual carries only a small number (e.g., several dozen in humans) of de novo mutations scattered across the genome, the chance of encountering any particular target mutation of interest is miniscule, rendering it impractical to measure rates of target mutations using such studies.To overcome this barrier, we have developed a method that enables identifying and counting, with high accuracy, ultrarare genetic variants of choice in extremely narrow regions of interest (ROIs) within large populations of cells, such as a single target mutant in 100 million genomes. Because this method has both an error rate lower than the human mutation rate and sufficient yield for the purpose, it enables measuring the frequencies of target mutations of choice in human sperm samples by counting their de novo instances at a single-digit resolution. For variants that are not expected to affect sperm fertility and viability (as in the case below), this frequency is the evolutionarily relevant mutation rate in males. Note that aside from this evolutionary application, ultra-accurate methods of mutation-detection are sought after for early detection of cancer, noninvasive prenatal testing, early identification of virus within host, and more (Salk et al. 2018).As a first target for this method, we chose two sites: a 6-bp region spanning three codons within the human hemoglobin subunit beta (HBB) gene that is of great importance for adaptation and hematologic disease, and the identical, paralogous region within the hemoglobin subunit delta (HBD) gene. The former region includes, among others, the site of the hemoglobin S (HbS) mutation. The most iconic balanced polymorphism mutation (Pauling et al. 1949; Allison 1954; Ingram 1957; Cavalli-Sforza and Feldman 2003; Feng et al. 2004; Hartl and Clark 2007), the HbS mutation is an A to T transversion (GAG→GTG, Glu→Val) in codon 6 of HBB causing sickle-cell anemia in homozygotes (Pauling et al. 1949) and providing substantial protection against severe malaria in heterozygotes (Allison 1954; Flint et al. 1998; Kwiatkowski 2005; Piel et al. 2010). Malaria, in turn, has been a leading cause of human morbidity and mortality, often causing more than a million deaths per year in the recent past, with Africa bearing the brunt of the disease burden (Carter and Mendis 2002), and thus has been possibly the strongest known agent of selection in humans in recent history (Kwiatkowski 2005). Besides the HbS mutation, many other mutations, both point mutations and indels, are also known at this site, many of which are involved in hematologic illness (Hardison et al. 2002; Hardison and Miller 2002). In contrast to HBB, mutations in HBD have a more limited effect and are not thought to confer resistance to malaria, because the HBD’s lower expression levels make it account for <3% of the circulating red blood cell hemoglobin in adults (Steinberg and Adams 1991). Although the population prevalence of the HBB mutations, whether beneficial or detrimental, is normally attributed to natural selection, so far it has not been possible to examine to what degree, if at all, mutational phenomena may also be relevant to their prevalence. To address this gap, we sought to characterize the rates of mutations, including the HbS mutation, in the HBB and HBD ROIs in sperm samples of both African and European donors.     

HLA class I allele and haplotype diversity in Ugandans supports the presence of a major east African genetic cluster

The objective of this study was to characterize the class I human leukocyte antigen (HLA) genetic composition of the Ugandan population to better define its relationship with other African groups. Samples from 175 individuals from Kampala (Uganda) were subjected to class I HLA-A, -B, and -C sequence-based typing. The high concordance between the major alleles and haplotypes found in the current and Kenyan populations and interpopulation genetic distance analysis strongly supported the presence of an East African cluster that contained the current Ugandan population along with Kenyan Luo and Nandi populations. The congruence of major alleles in different populations would permit consideration of East Africa as an integrated setting when designing and evaluating much needed malaria, tuberculosis, and AIDS vaccines.     

Limited genetic diversity of the Plasmodium falciparum aquaglyceroporin gene

In Plasmodium falciparum small solutes like water, ammonium, glycerol and others are transported by a parasite-encoded channel into the parasite. The gene encoding this channel is termed P. falciparum aquaglyceroporin (PfAQP) and is a single-copy gene and highly homologous to other aquaporins from other protozoa. Aquaporins are considered to be attractive targets for drug treatment and more so since the human and parasite aquaporins show considerable sequence differences. To investigate whether PfAQP may be suitable as a conserved target for potential aquaporin blocking agents we determined the DNA sequences of PfAQP from 65 parasite strains, either from in vitro cultured laboratory strains or from parasites obtained in an malaria-endemic region of Gabon. Only two non-synonymous mutations were found and functionally tested by a methylamine efflux assay. The efflux activity of all variants tested was similar. The lack of functionally variability suggests an invariable protein core, which may restrict parasite populations from evading therapeutic pressure if PfAQP inhibitors will be found.     

Additional evidence that genetic variation of MAO-A gene supports a gender subtype in obsessive-compulsive disorder

Studies have recently reported a sexually dimorphic association between obsessive-compulsive disorder (OCD) and a polymorphism related with variations in MAO-A activity. These observations suggest the possibility of gender differences in genetic susceptibility for OCD. We thus reexamined the MAO-A/EcoRV polymorphism in a sample of 122 OCD patients and 124 healthy subjects. An excess of allele 1 in OCD females with major depression disorder was confirmed as previously reported. This difference was more strongly associated with OCD females than males in the total sample. Finally, we analyzed a sample of 51 OCD trios. Haplotype-based haplotype relative risk (HHRR) analysis of the inheritance of the MAO-A variants revealed in the female probands that 14 out of 19 transmitted the allele 1, providing significant evidence for an allelic association between OCD and MAO-A gene. In conclusion, our findings may provide molecular evidence to identify a clinically meaningful gender subtype. However, an effort should be made to replicate the analysis in larger samples of informative parents using strategies such as transmission disequilibrium test to allow definite conclusions.     

An essential role of the antioxidant gene Bcl-2 in myocardial adaptation to ischemia: an insight with antisense Bcl-2 therapy

Reperfusion of ischemic myocardium results in apoptotic cell death, which can be blocked by adapting the heart to ischemic stress induced by cyclic episodes of brief periods of ischemia and reperfusion. In concert, the antiapoptotic gene bcl-2 is decreased by ischemia/reperfusion, but increased in the ischemically adapted myocardium. To examine if bcl-2 plays a crucial role in cardioprotection, adaptive cardioprotection was further examined in the hearts treated with antisense bcl-2 oligodeoxynucleotides (ODN). Isolated Langendorff-perfused rat hearts were divided into three groups: control (perfused with Krebs-Henseleit bicarbonate buffer for 210 min); 30-min ischemia followed by 2-h reperfusion; ischemic adaptation followed by 30-min ischemia and 2-h reperfusion. The last (adapted heart) group was subdivided into another two groups: one was transfected 48 h earlier with antisense bcl-2 ODN, whereas the other group was transfected with sense bcl-2 ODN. Cardioprotection was examined by determining cardiomyocyte death due to necrosis and apoptosis. Antisense gene therapy almost completely abolished bcl-2 protein expression in the hearts. Bcl-2 mRNA was down-regulated in the ischemic/reperfused heart, but up-regulated in the adapted myocardium. Adapted myocardium showed decreased infarct size and reduced number of apoptotic cardiomyocytes. Ischemia/reperfusion resulted in increased oxidative stress as evidenced by increased malonaldehyde formation. Adapted myocardium had a reduced amount of malonaldehyde. Antisense bcl-2 ODN completely abolished the cardioprotective effects of adaptation by eliminating the antideath signal of bcl-2. In concert, reduced oxidative stress in the adapted myocardium no longer persisted. The results suggest an antioxidant role of bcl-2 that appeared to be essential for the cardioprotection achieved by ischemic adaptation.     

Genetic diversity in the VP1 gene of foot-and-mouth disease virus serotype Asia 1

Summary.  Complete nucleotide sequence of the 1D (VP1-encoding) gene of 61 foot-and-mouth disease (FMD) serotype Asia 1 virus isolates recovered from different outbreaks in India between 1985 and 1999 including two vaccine strains currently used were determined. The sequences were compared with each other and those from other Asian countries. On the basis of phylogenetic analysis the viruses could be grouped into four genotypes (genotypes I–IV). All the 61 isolates from India belong to a single genotype (genotype-II) which is further subdivided into three lineages (B1, B2 and B3) under the same genotype. The viruses of the lineage B1 and B3 were found to be more prevalent before 1996 while the viruses of lineage B2 appeared to be new variants responsible for most of the recent outbreaks. Most of the isolates of lineage B1 lack one amino acid in the VP1 protein (position 44) whereas most of the isolates of lineage B2 and B3 contain it which indicates the possibility of these lineages having evolved independently. The rate of evolution of FMDV Asia 1 virus was also estimated and found to be 2.7 × 10⁻² synonymous substitutions per nucleotide per year. Received May 7, 2001 Accepted August 1, 2001     

Global haplotype diversity in the human insulin gene region

The insulin minisatellite (INS VNTR) has been intensively analyzed due to its associations with diseases including diabetes. We have previously used patterns of variant repeat distribution in the minisatellite to demonstrate that genetic diversity is unusually great in Africans compared to non-Africans. Here we analyzed variation at 56 single nucleotide polymorphisms (SNPs) flanking the minisatellite in individuals from six populations, and we show that over 40% of the total genetic variance near the minisatellite is due to differences between Africans and non-Africans, far higher than seen in most genomic regions and consistent with differential selection acting on the insulin gene region, most likely in the non-African ancestral population. Linkage disequilibrium was lower in African populations, with evidence of clustering of historical recombination events. Analysis of haplotypes from the relatively nonrecombining region around the minisatellite revealed a star-shaped phylogeny with lineages radiating from an ancestral African-specific haplotype. These haplotypes confirmed that minisatellite lineages defined by variant repeat distributions are monophyletic in origin. These analyses provide a framework for a cladistic approach to future disease association studies of the insulin region within both African and non-African populations, and they identify SNPs which can be rapidly analyzed as surrogate markers for minisatellite lineage.     

NAT2 gene polymorphisms in three indigenous groups in the Colombian Caribbean Coast region

Objective:

To study the NAT2 gene polymorphisms 481T, 590A and 857A in the Chimila, Wiwa and Wayuu indigenous groups of the Colombian Caribbean to determine the frequencies of the alleles NAT2*4, NAT2*5, NAT2*6, and NAT2*7 and to determine the types of acetylators present in these populations.

Methods:

A total of 202 subjects were studied: 47 Chimila, 55 Wiwa, and 100 Wayuu. The polymorphisms were identified using a real-time PCR method for allelic discrimination designed using Taqman of Applied Biosystems.

Results:

The following alleles were found at the highest frequency in the following groups: the NAT2*4 allele (wild type) in the Wayuu group (55.3%), the NAT2*5 allele in the Wiwa group (34.5%), and the NAT2*7 allele in the Chimila group (24.2%). A higher frequency of the rapid acetylator status was found in the Wayuu group (31.3%) and Chimila group (29.5%) compared with the Wiwa group (12.7%). The intermediate acetylator status distribution was very similar in all three groups, and the frequency of the slow acetylator status was higher in the Wiwa group (32.7%) compared with the Chimila and Wayuu groups (20.5% and 21.2%, respectively).

Conclusion:

The results demonstrated the allelic distribution and pharmacogenetic differences of the three groups studied and revealed the most frequent acetylator status and phenotype. Because of the high prevalence of slow acetylators, a greater incidence of tuberculosis (TB) drug-induced hepatotoxicity is predicted in these populations, with a higher frequency in the Wiwa group.     

High genetic diversity of HIV-1 strains in Chad,West Central Africa

The genetic diversity of HIV-1 strains in Chad was documented with a total of 107 samples from patients attending the general hospital in N'Djamena, the capital city of Chad. The genetic subtypes were identified in the V3-V5 env and p24 gag regions by sequence and phylogenetic tree analyses. Of the 107 strains, 78 had the same subtype/CRF designation between env and gag. Four subtypes and three CRFs were found to cocirculate: subtype A, 20.5%; subtype D, 18.7%; CRF02_AG, 13.1%; CRF11_cpx, 13.1%; subtype G, 3.7%; CRF01_AE, 2.8%; and subtype F1, 0.9%. The remaining 29 strains (27%) had discordant subtypes or CRF designations between env and gag; in 15 of these 29 strains, a CRF was involved in the recombination event, and 10 were subtype G in gag and subtype A in env, forming a separate subcluster within subtypes G and A. Subtype D strains represent almost 20% of the HIV-1 strains circulating in Chad and form a separate subcluster in gag and env. Nearly full-length genome sequencing for two such strains (99TCD-MN011 and 99TCD-MN012) revealed that they represent nonrecombinant subtype D variants. Compared with neighboring countries, the genetic subtype distribution of HIV-1 strains in Chad is unique for several reasons: lower prevalence of CRF02, high prevalence of CRF11 and subtype D, and absence of CRF06. These data clearly show that subtype distribution is very heterogeneous in Africa, probably the result of different founder effects.