Mathematical constraints on FST: multiallelic markers in arbitrarily many populations

Interpretations of values of the FST measure of genetic differentiation rely on an understanding of its mathematical constraints. Previously, it has been shown that FST values computed from a biallelic locus in a set of multiple populations and FST values computed from a multiallelic locus in a pair of populations are mathematically constrained by the frequency of the allele that is most frequent across populations. We report here the mathematical constraint on FST given the frequency M of the most frequent allele at a multiallelic locus in a set of multiple populations, providing the most general description to date of mathematical constraints on FST in terms of M. Using coalescent simulations of an island model of migration with an infinitely-many-alleles mutation model, we argue that the joint distribution of FST and M helps in disentangling the separate influences of mutation and migration on FST. Finally, we show that our results explain puzzling patterns of microsatellite differentiation, such as the lower FST values in interspecific comparisons between humans and chimpanzees than in the intraspecific comparison of chimpanzee populations. We discuss the implications of our results for the use of FST.

Is There Any Influence of TBP CAG / CAA Repeats on Huntington's Disease Age at Onset?

Huntington's disease (HD) is a genetic neurodegenerative progressive and fatal disease characterized by motor disorder, cognitive impairment and behavioral problems, caused by expanded repeats of CAG trinucleotides in the HTT gene. The aim of this study was to investigate the influence of TBP gene CAG/CAA repeats in conjunction with HTT gene CAG repeats, on the age of HD onset in Brazilian individuals. Individuals diagnosed as molecularly negative for HD, presented 29-39 TBP CAG/CAA (mean = 36 ± 2; median = 36). The most frequent allele had 36 repeats. The heterozygosity was 84%. In individuals diagnosed as molecularly positive for HD, a range of 25-40 TBP CAG/ CAA was found (mean = 36 ± 2; median = 36). The most frequent TBP allele had 38 repeats and the heterozygosity was 81%. We also conducted TBP direct Sanger sequencing of some samples which demonstrated other TBP structures different from the wild-type. The HTT expanded CAG and TBP CAG/CAA repeat sizes jointly explained 66% of the age at onset (AO) in our HD patients. The strongest variable in the model associated to AO was the number of expanded HTT CAG repeats. The difference between the association of HD AO with HTT expanded CAG together with TBP CAG / CAA and the association of HD AO with HTT expanded CAG was 0.001 (∆R2). Therefore, we found a weak association (0.1%) of TBP CAG/CAA repeats on HD AO, if any.

Multi Locus Sequence Typing and spa Typing of Staphylococcus Aureus Isolated from the Milk of Cows with Subclinical Mastitis in Croatia

Background: The bacterial species S. aureus is the most common causative agent of mastitis in cows in most countries with a dairy industry. The prevalence of infection caused by S. aureus ranges from 2% to more than 50%, and it causes 10–12% of all cases of clinical mastitis. Aim: The objective was to analyze 237 strains of S. aureus isolated from the milk of cows with subclinical mastitis regarding the spa, mecA, mecC and pvl genes and to perform spa and multi-locus sequence typing (MLST). Methods: Sequencing amplified gene sequences was conducted at Macrogen Europe. Ridom StaphType and BioNumerics software was used to analyze obtained sequences of spa and seven housekeeping genes. Results: The spa fragment was present in 204 (86.1%) of strains, while mecA and mecC gene were detected in 10 strains, and the pvl gene was not detected. Spa typing successfully analyzed 153 tested isolates (64.3%), confirming 53 spa types, four of which were new types. The most frequent spa type was t2678 (14%). MLST typed 198 (83.5%) tested strains and defined 32 different allele profiles, of which three were new. The most frequent allele profile was ST133 (20.7%). Six groups (G) and 15 singletons were defined. Conclusion: Taking the number of confirmed spa types and sequence types (STs) into account, it can be concluded that the strains of S. aureus isolated from the milk of cows with subclinical mastitis form a heterogenous group. To check the possible zoonotic potential of isolates it would be necessary to test the persons and other livestock on the farms.

Major CYP450 polymorphism Among Saudi Patients

Background: Cytochrome P450 (CYP) contributes to a huge collection of medicinal products' Phase I metabolization. We aimed to summarize and investigate the current evidence regarding the frequency of CYP2D6, CYP2C9, CYP2C19, MDR1 in Saudi Arabia. Methods: A computerized search in four databases was done using the relevant keywords. Screening process was done in two steps; title and abstract screening and full-text screening. Data of demographic and characteristics of included studies and patients was extracted and tabulated. Results: Ten studies were eligible for our criteria and were included in this systematic review. Age of participants ranged between 17-65 years. Only two subjects showed PM phenotype of CYP2C19 in Saudi population. The most frequent alleles were CYP2C19*1 (62.9%), CYP2C19*2 (11.2%-32%), and CYP2C19*17 (25.7%). The CYP2C19m1 was observed in 97 cases of extensive metabolizing (EM) phenotype CYP2C19. Concerning the CYP2C9, the most frequent alleles were CYP2C9*1 and CYP2C9*2, and the most frequent genotype was CYP2C9*1*1. The CYP2D6*41 allele and C1236T MDR1 were the most frequent allele in this population. Conclusion: The current evidence suggests that Saudi Arabians resembled European in the frequency of CYP2C19, Caucasians in both the incidence of CYP2C9 and CYP2C19m1 and absence of CYP2C19m2. The CYP2D6*41 allele frequency in Saudi Arabians is relatively high. We recommend a further research to evaluate the basic and clinical relevance of gene polymorphism in such ethnicity.

Frequency distribution of IL-17A G197A (rs2275913) and IL-17F A7488G (rs763780) polymorphisms among healthy Sudanese population

Objectives: IL-17A G197A and IL-17F A7488G polymorphisms has been identified to be associated with the susceptibility to many diseases. This study aimed to investigate the frequency distribution of IL-17A G197A and IL-17F A7488G polymorphisms among healthy Sudanese population. A descriptive cross-sectional hospital-based molecular study conducted in different sites throughout Sudan. Two ml blood samples were collected from 717 healthy participants. Demographic data and the medical history of the participants were collected.Results: Of the 717 participants, 355 (49.5%) were males and 362 (50.5%) were females, their mean age was 30.2±17.2 and 32.2±16.5, respectively. For IL-17A, the most frequent genotype detected among males and females was IL-17A heterozygote allele (AG); 215 (60.6%) and 194 (53.6%), respectively. Whereas, for IL-17F, the most frequent allele among males and females was the homozygote allele (AA); 298 (83.9%) for males and 322 (89.0%) for females. HWE for genotype distributions of IL-17A was showing statistical insignificance for IL-17A among males and females, P value 0.614. While HWE for IL-17F reached the equilibrium level, P value 0.048. The most frequent age group was those aged between 21 to 40 years; 281 (39.2%). Arab constituted the major ethnicity of the study participants; 418 (58.3%), P value 0.034.

Frequency distribution of IL-17A G197A (rs2275913) and IL-17F A7488G (rs763780) polymorphisms among healthy Sudanese population

Objectives: IL-17A G197A and IL-17F A7488G polymorphisms has been identified to be associated with the susceptibility to many diseases. This study aimed to investigate the frequency distribution of IL-17A G197A and IL-17F A7488G polymorphisms among healthy Sudanese population. A descriptive cross-sectional hospital-based molecular study conducted in different sites throughout Sudan. Two ml blood samples were collected from 717 healthy participants. Demographic data and the medical history of the participants were collected.Results: Of the 717 participants, 355 (49.5%) were males and 362 (50.5%) were females, their mean age was 30.2±17.2 and 32.2±16.5, respectively. For IL-17A, the most frequent genotype detected among males and females was IL-17A heterozygote allele (AG); 215 (60.6%) and 194 (53.6%), respectively. Whereas, for IL-17F, the most frequent allele among males and females was the homozygote allele (AA); 298 (83.9%) for males and 322 (89.0%) for females. HWE for genotype distributions of IL-17A was showing statistical insignificance for IL-17A among males and females, P value 0.614. While HWE for IL-17F reached the equilibrium level, P value 0.048. The most frequent age group was those aged between 21 to 40 years; 281 (39.2%). Arab constituted the major ethnicity of the study participants; 418 (58.3%), P value 0.034.

Frequency Distribution of IL-17A G197A (rs2275913) and IL-17F A7488G (rs763780) Polymorphisms Among Healthy Sudanese Population

Objectives IL-17A G197A and IL-17F A7488G polymorphisms has been identified to be associated with the susceptibility to many diseases. This study aimed to investigate the frequency distribution of IL-17A G197A and IL-17F A7488G polymorphisms among healthy Sudanese population. A descriptive cross-sectional hospital-based molecular study conducted in different sites throughout Sudan. Two ml blood samples were collected from 717 healthy participants. Demographic data and the medical history of the participants were collected.Results Of the 717 participants, 355 (49.5%) were males and 362 (50.5%) were females, their mean age was 30.2 ± 17.2 and 32.2 ± 16.5, respectively. For IL-17A, the most frequent genotype detected among males and females was IL-17A heterozygote allele (AG); 215 (60.6%) and 194 (53.6%), respectively. Whereas, for IL-17F, the most frequent allele among males and females was the homozygote allele (AA); 298 (83.9%) for males and 322 (89.0%) for females. HWE for genotype distributions of IL-17A was showing statistical insignificance for IL-17A among males and females, P value 0.614. While HWE for IL-17F reached the equilibrium level, P value 0.048. The most frequent age group was those aged between 21 to 40 years; 281 (39.2%). Arab constituted the major ethnicity of the study participants; 418 (58.3%), P value 0.034.

N-acetyltransferase 2 genotypes amongst Zulu Speaking South Africans and isoniazid / N-acetyl-isoniazid pharmacokinetics during anti-tuberculosis treatment

BackgroundDistribution of N-acetyltransferase2 (NAT2) polymorphisms varies considerably among different ethnic groups. Information on NAT2 single-nucleotide polymorphisms in South African population is limited. We investigated NAT2 polymorphisms and their effect on isoniazid pharmacokinetics in Zulu black HIV-infected South Africans in Durban, South Africa. Methods: HIV-infected participants with culture-confirmed pulmonary tuberculosis (TB) were enrolled from two unrelated studies. Culture-confirmed participants were genotyped for NAT2 polymorphisms 282C>T, 341T>C, 481C>T, 857G>A, 590G>A and 803A>G using Life Technologies pre-validated Taqman assays (Life Technologies, Paisley, UK). Participants underwent sampling for determination of plasma isoniazid and N-acetylisoniazid concentrations.ResultsAmongst the 120 patients, 63/120 (52.5%) were slow metabolisers (NAT2*5/*5), 43/120 (35.8%) had intermediate (NAT2*5/12), and 12/120 (11.7%) had rapid genotype (NAT2*4/*11, NAT2*11/12 and NAT2*12/12). NAT2 alleles in this study were *4, *5C, *5D, *5E, *5J, *5K, *5KA, *5T, *11A, *12A/12C and *12M. NAT2*5 was the most frequent allele (70.4%) followed by NAT2*12 (27.9%). 34/40 had both PK results and NAT2 genotyping results. The median area under the concentration-time-curve to infinity (AUC0-∞) interquartile range (IQR) was 7.81 (5.87 – 16.83) μg/ml/hr and maximum concentration (Cmax) 3.14 μg/ml (2.42 – 4.36) μg/mL. Individual polymorphisms were not equally distributed, with some represented in small numbers. Genotype did not correlate with phenotype, rapid genotype showing higher AUC0-∞ than slow but not significant, p=0.43.ConclusionThere was high prevalence of slow followed by intermediate then rapid acetylator genotypes. The poor concordance between genotype and phenotype suggests that other factors or genetic loci influence INH metabolism, and warrants further investigation in this population.

Analysis of the UGT1A1 Genotype in Hyperbilirubinemia Patients: Differences in Allele Frequency and Distribution

Objective. The spectrum of UDP-glucuronyl transferase A1 (UGT1A1) variants in hereditary unconjugated hyperbilirubinemia varies markedly between different ethnic populations. This study evaluated the UGT1A1 genotypes in hyperbilirubinemia patients from southeastern China. Methods. We enrolled 60 patients from southeastern China (44 men and 16 women; age range: 3–76 years) with unconjugated hyperbilirubinemia and performed genetic analysis of the UGT1A1 gene by direct sequencing. Results. For patients with Gilbert syndrome, 85% (47/55) harbored pathogenic variants of UGT1A1⁎60. Both UGT1A1⁎28 and UGT1A1⁎81 were detected in the promoter region of UGT1A1. Additionally, 83% (20/24) of patients with Gilbert syndrome heterozygous for UGT1A1⁎60 had an association with heterozygous variation of UGT1A1⁎28 or UGT1A1⁎81, while 91% (21/23) of Gilbert syndrome patients homozygous for UGT1A1⁎60 had biallelic variations of UGT1A1⁎28 and UGT1A1⁎81. We detected 213 UGT1A1 allelic variants, including six novel variations, with the most frequent allele being the UGT1A1⁎60, followed by UGT1A1⁎28 and UGT1A1⁎6. All of the patients showed multiple sites of variants in UGT1A1; however, variation number was not associated with bilirubin levels (P>0.05). Conclusions. The spectrum of UGT1A1 variants in southeastern Chinese patients was distinct from other ethnic populations. Our findings broaden the knowledge concerning traits associated with UGT1A1 variants and help profile genotype–phenotype correlations in hyperbilirubinemia patients.

EGFR L858R mutation as a possible target for individual-independent immunotherapy in Chinese population.

8538 Background: Neoantigens arise from tumor-specific mutations and potentially provoke immune responses. General vaccines targeting these peptides could be beneficial for patients suffering from common cancers, like lung cancer. Therefore, a retrospective analysis was performed on 799 non-small cell lung cancer (NSCLC) tissue samples previously profiled using our 1021-gene panel. Each sample was collected from a unique patient, from whom peripheral blood or normal tissue was also obtained as control. Methods: Sequencing data were generated and pre-analyzed according to our in-house procedures. HLA typing was done using OptiType v1.0 (required sequences were captured by 1021-gene panel) and neoantigens were predicted by netMHCpan v4.0 based on typed HLA alleles and curated non-frameshift somatic mutations with frequency > 5%, which were called in pre-analysis. A neoantigen is considered mutant-specific if IC50 mut is < 500 nM and IC50 wild is > 500 nM, and especially, it is considered a strong-binder if IC50 mut is < 50 nM. Results: HLA typing returned 141 unique alleles, with the top 3 by carrier frequency being A*1101 (39%), C*0102 (33%) and A*2402 (28%). A further investigation into HLA alleles, mutations and neoantigens revealed two mutations on EGFR as candidates for off-the-shelf vaccine development: (1) L858R mutation (19%, 151 out of 799) and (2) E746_A750del mutation (13%, 106 out of 799). Among the four neoantigens derived from EGFR L858R mutation is HVKITDFGR, which can be recognized by A*3303 (IC50 mut = 22.93 nM and IC50 wild = 12,733.96 nM) and the combination is shared by 3% of the patients (23 out of 799), despite that A*3303 is not a very frequent allele in this population (16%, 127 out of 799). Two neoantigens were derived from EGFR E746_A750del mutation, including IPVAIKTSPK, which is mainly recognized by A*1101 (IC50 mut = 158.16 nM and IC50 wild = 31,132.66 nM). This combination is shared by 5% of the patients (41 out of 799). Conclusions: (1) EGFR L858R mutation and HLA-A*3303 could be a good target for individual-independent vaccine development. (2) HLA-A*1101 is the most frequent allele in this population. However, HLA-A*1101 and E746_A750del mutation is not so ideal for off-the-shelf vaccine development.