scholarly journals GST M1-T1 null Allele Frequency Patterns in Geographically Assorted Human Populations: A Phylogenetic Approach

PLoS ONE ◽  
2015 ◽  
Vol 10 (4) ◽  
pp. e0118660 ◽  
Author(s):  
Senthilkumar Pitchalu Kasthurinaidu ◽  
Thirumurugan Ramasamy ◽  
Jayachitra Ayyavoo ◽  
Dhvani Kirtikumar Dave ◽  
Divya Anantray Adroja
Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2906-2906
Author(s):  
Julie R. Boiko ◽  
Bita Sahaf ◽  
David B. Miklos

Abstract Allogeneic immune responses provide beneficial graft-versus-leukemia (GVL) and detrimental graft-versus-host disease (GVHD). To characterize allogeneic B cells and their antibodies in relation to GVHD and GVL, antigen specific assays are required to distinguish donor and recipient antibodies. Inherited polymorphisms in heavy chain constant regions of immunoglobulin can be recognized by allotype specific monoclonal antibodies. We hypothesize that B cell reconstitution differs after myeloablative and nonmyeloablative (NMA) HCT with clinical implications. To test this, we developed allotype ELISAs to quantify donor and recipient antibody responses for specific infectious and allogeneic antigens. Human sera were screened by ELISA coating monoclonal antibodies specific for human allotypes (IgG1m(f), m(z), m(a), IgG2m(n), and IgG3m(g1)) at titers providing shared dynamic ranges. Pre-transplant sera from 48 patients and their donors were serially diluted, and allotype-specific immunoglobulin was detected by alkaline phosphatase-conjugated polyclonal anti-human IgG. Allotype-null sera clearly segregated from wild-type sera with 10-fold absorbency differences. Each null phenotype was confirmed by total IgG and isotype-specific quantification. Overall, IgG1m(f) was null in 8 of 96 sera (null allele frequency 29%), and IgG2m(n) was null in 23 of 96 (null allele frequency 48%). Six patients were null for both, and overall 17 of 48 donor/recipient transplant pairs were informative for either allotype. Nulls for the remaining three allotypes were infrequently recognized limiting their clinical utility. Additionally, we measured monoclonal IgG1 purified from 5 multiple myeloma patients identifying three null alleles, one wild-type, and a single intermediate polymorphism. Labeled conjugation of the wild-type monoclonal IgG1 enables competitive inhibition analysis of null allotype improving null allotype sensitivity for engraftment less than 5%. Sera were collected monthly from all HCT patients informative for allotype antibody. Three NMA HCT patients who underwent total lymphoid irradiation and anti-thymoglobulin (TLI/ATG) conditioning have donors that are null for IgG2m(n) and are being prospectively assessed for recipient antibody loss. Their recipient allotype-specific IgG persists at pretransplant recipient levels in all three patients measured six months after NMA HCT, and the lead patient expresses 100% pretransplant recipient allotype antibody ten months after HCT. Conversely, a single NMA patient null for IgG2m(n) with a wild-type donor has no detectable IgG2m(n) donor antibodies four months after HCT despite having 100% donor peripheral B cell engraftment measured 30 days after NMA HCT. In contrast, an informative patient undergoing myeloablative HCT developed 25% IgG2m(n) donor specific antibodies 3 months post-transplant, and 50% at 7 months. Others have reported donor allotype specific antibody achieves full engraftment by 6 months after myeloablative HCT (Van Tol et al. Blood 1996). Our ongoing preliminary studies suggest NMA HCT patients experience delayed donor antibody onset and prolonged recipient antibodies as compared to patients undergoing myeloablative HCT. In order to confirm this, we are measuring antigen-specific donor allotype antibody reconstitution for infectious antigens (EBV and tetanus) and allogeneic H-Y antigens.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 349-349 ◽  
Author(s):  
Julie R. Boiko ◽  
Bita Sahaf ◽  
Antonia M.S. Mueller ◽  
George L. Chen ◽  
Dolly Tyan ◽  
...  

Abstract Allogeneic hematopoietic cell transplantation (HCT) is an effective treatment for hematologic malignancies through graft-versus-leukemia/lymphoma (GVL) responses and replacement of the patient’s immune system. Conditioning intensity may influence hematopoietic reconstitution, persistent recipient immunity, and donor alloimmune responses. High-dose conditioning (HDC) causes rapid conversion to full donor T- and B-cell chimerism, while patients who undergo reduced-intensity conditioning (RIC) progress through a dynamic mixed chimerism extending weeks to months. We hypothesize that long-lived recipient plasma cells persist, providing beneficial antimicrobial serologic immunity, while donor B cells target allo-antigens, contributing to both GVL and GVHD. Furthermore, recipient humoral immunity persists longer following RIC than HDC, leading to fewer infections and decreased transplant-related mortality. Inherited polymorphisms in IgG heavy chain constant regions can be recognized by allotype-specific monoclonal antibodies and thus distinguish donor and recipient antibodies. We developed a quantitative ELISA by coating mouse monoclonal antibodies specific for the G1m(f) and G2m(n) allotypes. Serial dilutions of 63 patients and their donors were incubated and detected by alkaline phosphatase-conjugated anti-human IgG polyclonal antibody. Twenty-eight HDC patients were conditioned with VP-16 and total body irradiation, while 35 RIC patients received total lymphoid irradiation and anti-thymocyte globulin (TLI-ATG). One hundred fifteen of the total 126 subjects (91%) expressed G1m(f) (null allele frequency: 0.29), and 100 of 126 (79%) expressed G2m(n) (null allele frequency: 0.45). Twenty-six of the 63 pairs (41%) were informative because either the donor or recipient was homozygous null for an allotype. Following both RIC and HDC when the recipient was allotype null, the donor allotype was first detected six months post-HCT and reached 50–80% of donor levels by 12 months (n=8 pairs). Eighteen donors were homozygous allotype null, and recipient-specific antibody was prospectively determined. By 12 months after HDC, recipient antibody levels fell to <10% of pre-HCT allotype levels (n=11 pairs). In contrast, RIC patients retained the allotype at >90% of pre-HCT levels through 12 months post-HCT (n=7 pairs), demonstrating a significant difference from HDC patients in one-year median recipient allotype levels (p=0.016). We confirmed RIC humoral immune persistence by DNA chimerism detection of CD38+CD138+ plasma cells from bone marrow aspirates collected 12 months post-HCT. Analysis revealed 30–58% donor levels of plasma cells, suggesting that RIC patients maintain long-lived plasma cells. Allotype-informative patients were measured by ELISA for total IgG and allotype-specific IgG against Epstein-Barr virus (EBV), varicella zoster virus (VZV), pneumococcus, and influenza. HDC patients displayed loss of recipient antimicrobial allotype between five and eight months in conjunction with loss of bulk allotype. RIC patients maintained >90% pre-HCT allotype levels through one year correlating to levels of total IgG against all four infectious agents when they were seropositive before HCT. In addition, new donorspecific responses to influenza, pneumococcus, and VZV were detected in both sets of patients within seven to 14 months. In the allotype-informative setting, H-Y antibody analysis confirmed that donor-derived allogeneic antibodies against UTY2 and DDX3Y developed after nine and 12 months, respectively, and persisted in both HDC and RIC male patients with female donors. In summary, RIC recipients benefit from a twofold effect: persistent recipient-derived antimicrobial humoral immunity and donor-derived allogeneic B-cell responses. Our studies may explain why RIC results in decreased infectious complications in the post-HCT setting.


2021 ◽  
Vol 12 ◽  
Author(s):  
Bruna Kulmann-Leal ◽  
Joel Henrique Ellwanger ◽  
José Artur Bogo Chies

The genetic background of Brazilians encompasses Amerindian, African, and European components as a result of the colonization of an already Amerindian inhabited region by Europeans, associated to a massive influx of Africans. Other migratory flows introduced into the Brazilian population genetic components from Asia and the Middle East. Currently, Brazil has a highly admixed population and, therefore, the study of genetic factors in the context of health or disease in Brazil is a challenging and remarkably interesting subject. This phenomenon is exemplified by the genetic variant CCR5Δ32, a 32 base-pair deletion in the CCR5 gene. CCR5Δ32 originated in Europe, but the time of origin as well as the selective pressures that allowed the maintenance of this variant and the establishment of its current frequencies in the different human populations is still a field of debates. Due to its origin, the CCR5Δ32 allele frequency is high in European-derived populations (~10%) and low in Asian and African native human populations. In Brazil, the CCR5Δ32 allele frequency is intermediate (4-6%) and varies on the Brazilian States, depending on the migratory history of each region. CCR5 is a protein that regulates the activity of several immune cells, also acting as the main HIV-1 co-receptor. The CCR5 expression is influenced by CCR5Δ32 genotypes. No CCR5 expression is observed in CCR5Δ32 homozygous individuals. Thus, the CCR5Δ32 has particular effects on different diseases. At the population level, the effect that CCR5Δ32 has on European populations may be different than that observed in highly admixed populations. Besides less evident due to its low frequency in admixed groups, the effect of the CCR5Δ32 variant may be affected by other genetic traits. Understanding the effects of CCR5Δ32 on Brazilians is essential to predict the potential use of pharmacological CCR5 modulators in Brazil. Therefore, this study reviews the impacts of the CCR5Δ32 on the Brazilian population, considering infectious diseases, inflammatory conditions, and cancer. Finally, this article provides a general discussion concerning the impacts of a European-derived variant, the CCR5Δ32, on a highly admixed population.


2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Agata Kostro-Ambroziak ◽  
Anna Siekiera ◽  
Magdalena Czajkowska ◽  
Jan J. Pomorski ◽  
Hanna Panagiotopoulou

Abstract Microsatellite loci are commonly used markers in population genetic studies. In this study, we present 40 novel and polymorphic microsatellite loci elaborated for the ichneumonid parasitoid Latibulus argiolus (Rossi, 1790). Reaction condition optimisation procedures allowed 14 of these loci to be co-amplified in two PCRs and loaded in two multiplex panels onto a genetic analyser. The assay was tested on 197 individuals of L. argiolus originating from ten natural populations obtained from the host nests of paper wasps. The validated loci were polymorphic with high allele numbers ranging from eight to 27 (average 17.6 alleles per locus). Both observed and expected heterozygosity values were high, ranging between 0.75 and 0.92 for HO (mean 0.83) and from 0.70 to 0.90 for HE (mean 0.85). The optimized assay showed low genotyping error rate and negligible null allele frequency. The designed multiplex panels could be successfully applied in relatedness analyses and genetic variability studies of L. argiolus populations, which would be particularly interesting considering the coevolutionary context of this species with its social host.


2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Robert Fragoza ◽  
Jishnu Das ◽  
Shayne D. Wierbowski ◽  
Jin Liang ◽  
Tina N. Tran ◽  
...  

Abstract Each human genome carries tens of thousands of coding variants. The extent to which this variation is functional and the mechanisms by which they exert their influence remains largely unexplored. To address this gap, we leverage the ExAC database of 60,706 human exomes to investigate experimentally the impact of 2009 missense single nucleotide variants (SNVs) across 2185 protein-protein interactions, generating interaction profiles for 4797 SNV-interaction pairs, of which 421 SNVs segregate at > 1% allele frequency in human populations. We find that interaction-disruptive SNVs are prevalent at both rare and common allele frequencies. Furthermore, these results suggest that 10.5% of missense variants carried per individual are disruptive, a higher proportion than previously reported; this indicates that each individual’s genetic makeup may be significantly more complex than expected. Finally, we demonstrate that candidate disease-associated mutations can be identified through shared interaction perturbations between variants of interest and known disease mutations.


2018 ◽  
Author(s):  
Ryan K Waples ◽  
Anders Albrechtsen ◽  
Ida Moltke

AbstractKnowledge of how individuals are related is important in many areas of research and numerous methods for inferring pairwise relatedness from genetic data have been developed. However, the majority of these methods were not developed for situations where data is limited. Specifically, most methods rely on the availability of population allele frequencies, the relative genomic position of variants, and accurate genotype data. But in studies of non-model organisms or ancient human samples, such data is not always available. Motivated by this, we present a new method for pairwise relatedness inference, which requires neither allele frequency information nor information on genomic position. Furthermore, it can be applied to both genotype data and to low-depth sequencing data where genotypes cannot be accurately called. We evaluate it using data from SNP arrays and low-depth sequencing from a range of human populations and show that it can be used to infer close familial relationships with a similar accuracy as a widely used method that relies on population allele frequencies. Additionally, we show that our method is robust to SNP ascertainment, which is important for application to a diverse range of populations and species.


2016 ◽  
Author(s):  
Fernando Racimo ◽  
Davide Marnetto ◽  
Emilia Huerta-Sánchez

AbstractComparisons of DNA from archaic and modern humans show that these groups interbred, and in some cases received an evolutionary advantage from doing so. This process - adaptive introgression - may lead to a faster rate of adaptation than is predicted from models with mutation and selection alone. Within the last couple of years, a series of studies have identified regions of the genome that are likely examples of adaptive introgression. In many cases, once a region was ascertained as being introgressed, commonly used statistics based on both haplotype as well as allele frequency information were employed to test for positive selection. Introgression by itself, however, changes both the haplotype structure and the distribution of allele frequencies, thus confounding traditional tests for detecting positive selection. Therefore, patterns generated by introgression alone may lead to false inferences of positive selection. Here we explore models involving both introgression and positive selection to investigate the behavior of various statistics under adaptive introgression. In particular, we find that the number and allelic frequencies of sites that are uniquely shared between archaic humans and specific present-day populations are particularly useful for detecting adaptive introgression. We then examine the 1000 Genomes dataset to characterize the landscape of uniquely shared archaic alleles in human populations. Finally, we identify regions that were likely subject to adaptive introgression and discuss some of the most promising candidate genes located in these regions.


2009 ◽  
Vol 58 (1-6) ◽  
pp. 276-279 ◽  
Author(s):  
S. Cavers ◽  
R. C. Munro ◽  
◽  

Abstract Using databases of previously published primers, we optimised six nuclear microsatellite markers for Prunus africana for the purposes of studying spatial genetic structure and gene flow. To assess variability, these and three previously transferred loci were screened in populations from Kenya and South Africa. Across both populations most loci were polymorphic, with the exception of a single locus which failed to amplify in the South African samples, exhibiting between 2 and 22 alleles and levels of expected heterozygosity (He) ranged from 0.059 to 0.932. Departures from Hardy-Weinberg equilibrium were detected for all loci but not for all populations. The estimated null allele frequency was very low to moderate and no evidence for linkage disequilibrium was detected.


2018 ◽  
Author(s):  
M. Saitou ◽  
Y. Satta ◽  
O. Gokcumen

ABSTRACTThe deletion of the metabolizing Glutathione S-transferase Mu 1 (GSTM1) gene was previously associated with multiple cancers, metabolic and autoimmune disorders, as well as drug response. It is unusually common, with allele frequency reaching up to 75% in some human populations. Such high allele frequency of a derived allele with apparent impact on an otherwise conserved gene is a rare phenomenon. To investigate the evolutionary history of this locus, we analyzed 310 genomes using population genetics tools. Our analysis revealed a surprising lack of linkage disequilibrium between the deletion and the flanking single nucleotide variants in this locus, indicating gene conversion events. Tests that measure extended homozygosity and rapid change in allele frequency identified signatures of an incomplete soft-sweep in the locus. Using empirical approaches, we identified the Tanuki haplogroup, which carries the GSTM1 deletion and is found in approximately 70% of East Asian chromosomes. This haplogroup has rapidly increased its frequency in East Asian populations, contributing to a high population differentiation among continental human populations. We showed that extended homozygosity and population differentiation for this haplogroup is incompatible with simulated neutral expectations in East Asian populations. In parallel, we revealed that the Tanuki haplogroup is significantly associated with the expression levels of other GSTM genes. Collectively, our results suggest that the Tanuki haplogroup has likely undergone a soft sweep in East Asia with multiple functional consequences. Our study provides the necessary framework for further studies to elucidate the evolutionary reasons that maintain disease-susceptibility variants in the GSTM1 locus.Lay summaryHere, we describe the evolutionary forces that shape the variation in a genomic region, which has been associated with bladder cancer, metabolic and autoimmune disorders and response to different drugs. Our results reveal a new genetic type common in Asian populations that may have important evolutionary and biomedical implications.


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