Variation In Allele Frequencies Research Articles

Human genetic diversity regulating the TLR10/TLR1/TLR6 locus confers increased cytokines in response to Chlamydia trachomatis.

SummaryHuman genetic diversity can have profound effects on health outcomes upon exposure to infectious agents. For infections with Chlamydia trachomatis (C. trachomatis), the wide range of genital and ocular disease manifestations are likely influenced by human genetic differences that regulate interactions between C. trachomatis and host cells. We leveraged this diversity in cellular responses to demonstrate the importance of variation at the Toll-like receptor 1 (TLR1), TLR6, and TLR10 locus to cytokine production in response to C. trachomatis. We determined that a single-nucleotide polymorphism (SNP) (rs1057807), located in a region that forms a loop with the TLR6 promoter, is associated with increased expression of TLR1, TLR6, and TLR10 and secreted levels of ten C. trachomatis-induced cytokines. Production of these C. trachomatis-induced cytokines is primarily dependent on MyD88 and TLR6 based on experiments using inhibitors, blocking antibodies, RNAi, and protein overexpression. Population genetic analyses further demonstrated that the mean IL-6 response of cells from two European populations were higher than the mean response of cells from three African populations and that this difference was partially attributable to variation in rs1057807 allele frequency. In contrast, a SNP associated with a different pro-inflammatory cytokine (rs2869462 associated with the chemokine CXCL10) exhibited an opposite response, underscoring the complexity of how different genetic variants contribute to an individual’s immune response. This multidisciplinary study has identified a long-range chromatin interaction and genetic variation that regulates TLR6 to broaden our understanding of how human genetic variation affects the C. trachomatis-induced immune response.

Genetic diversity of 'Very Important Pharmacogenes' in two South-Asian populations.

ObjectivesReliable identification of population-specific variants is important for building the single nucleotide polymorphism (SNP) profile. In this study, genomic variation using allele frequency differences of pharmacologically important genes for Gujarati Indians in Houston (GIH) and Indian Telugu in the U.K. (ITU) from the 1000 Genomes Project vis-à-vis global population data was studied to understand its role in drug response.MethodsJoint genotyping approach was used to derive variants of GIH and ITU independently. SNPs of both these populations with significant allele frequency variation (minor allele frequency ≥ 0.05) with super-populations from the 1000 Genomes Project and gnomAD based on Chi-square distribution with p-value of ≤ 0.05 and Bonferroni’s multiple adjustment tests were identified. Population stratification and fixation index analysis was carried out to understand genetic differentiation. Functional annotation of variants was carried out using SnpEff, VEP and CADD score.ResultsPopulation stratification of VIP genes revealed four clusters viz., single cluster of GIH and ITU, one cluster each of East Asian, European, African populations and Admixed American was found to be admixed. A total of 13 SNPs belonging to ten pharmacogenes were identified to have significant allele frequency variation in both GIH and ITU populations as compared to one or more super-populations. These SNPs belong to VKORC1 (rs17708472, rs2359612, rs8050894) involved in Vitamin K cycle, cytochrome P450 isoforms CYP2C9 (rs1057910), CYP2B6 (rs3211371), CYP2A2 (rs4646425) and CYP2A4 (rs4646440); ATP-binding cassette (ABC) transporter ABCB1 (rs12720067), DPYD1 (rs12119882, rs56160474) involved in pyrimidine metabolism, methyltransferase COMT (rs9332377) and transcriptional factor NR1I2 (rs6785049). SNPs rs1544410 (VDR), rs2725264 (ABCG2), rs5215 and rs5219 (KCNJ11) share high fixation index (≥ 0.5) with either EAS/AFR populations. Missense variants rs1057910 (CYP2C9), rs1801028 (DRD2) and rs1138272 (GSTP1), rs116855232 (NUDT15); intronic variants rs1131341 (NQO1) and rs115349832 (DPYD) are identified to be ‘deleterious’.ConclusionsAnalysis of SNPs pertaining to pharmacogenes in GIH and ITU populations using population structure, fixation index and allele frequency variation provides a premise for understanding the role of genetic diversity in drug response in Asian Indians.

BRAFV600E Mutant Allele Frequency (MAF) Influences Melanoma Clinicopathologic Characteristics.

Simple SummaryThe mutational load of BRAFV600E in melanomas has been described as a possible prognostic biomarker but there is no information about the mutant allele frequency (MAF) variability of BRAFV600E within cutaneous melanomas and its potential prognostic implications. Our study suggests that the variation degree of BRAFV600E MAF within primary cutaneous melanoma could act as a determinant in the location of primary melanomas as well as their first metastases and could influence prognostic indicators such as Breslow and mitotic indexes. BRAFV600E MAF variation is also related to the neoplastic cell phenotype and tumor lymphocytic infiltrate of primary tumors. For all these reasons, detection of BRAFV600E MAF variation could be a useful prognostic biomarker. It is worth exploring the role of BRAFV600E MAF variation with regards to the response of melanoma to targeted therapies.Background: Cutaneous melanoma shows high variability regarding clinicopathological presentation, evolution and prognosis. Methods: Next generation sequencing was performed to analyze hotspot mutations in different areas of primary melanomas (MMp) and their paired metastases. Clinicopathological features were evaluated depending on the degree of variation of the BRAFV600E mutant allele frequency (MAF) in MMp. Results: In our cohort of 14 superficial spreading, 10 nodular melanomas and 52 metastases, 17/24 (71%) melanomas had a BRAFV600E mutation and 5/24 (21%) had a NRASQ61 mutation. We observed a high variation of BRAFV600E MAF (H-BRAFV600E) in 7/17 (41%) MMp. The H-BRAFV600E MMp were all located on the trunk, had lower Breslow and mitotic indexes and predominantly, a first nodal metastasis. Regions with spindled tumor cells (Spin) and high lymphocytic infiltrate (HInf) were more frequent in the H-BRAFV600E patients (4/7; 57%), whereas regions with epithelial tumor cells (Epit) and low lymphocytic infiltrate (LInf) were predominant (6/10; 60%) and exclusive in the low BRAFV600E MAF variation tumors (L-BRAFV600E). The H-BRAFV600E/Spin/HInf MMp patients had better prognostic features and nodal first metastasis. Conclusions: The H-BRAFV600E MMp were located on the trunk, had better prognostic characteristics, such as lower Breslow and mitotic indexes as well as high lymphocytic infiltrate.

Allele frequency divergence reveals ubiquitous influence of positive selection in Drosophila.

Resolving the role of natural selection is a basic objective of evolutionary biology. It is generally difficult to detect the influence of selection because ubiquitous non-selective stochastic change in allele frequencies (genetic drift) degrades evidence of selection. As a result, selection scans typically only identify genomic regions that have undergone episodes of intense selection. Yet it seems likely such episodes are the exception; the norm is more likely to involve subtle, concurrent selective changes at a large number of loci. We develop a new theoretical approach that uncovers a previously undocumented genome-wide signature of selection in the collective divergence of allele frequencies over time. Applying our approach to temporally resolved allele frequency measurements from laboratory and wild Drosophila populations, we quantify the selective contribution to allele frequency divergence and find that selection has substantial effects on much of the genome. We further quantify the magnitude of the total selection coefficient (a measure of the combined effects of direct and linked selection) at a typical polymorphic locus, and find this to be large (of order 1%) even though most mutations are not directly under selection. We find that selective allele frequency divergence is substantially elevated at intermediate allele frequencies, which we argue is most parsimoniously explained by positive-not negative-selection. Thus, in these populations most mutations are far from evolving neutrally in the short term (tens of generations), including mutations with neutral fitness effects, and the result cannot be explained simply as an ongoing purging of deleterious mutations.

Genotypes of informative loci from 1000 Genomes data allude evolution and mixing of human populations

Principal Component Analysis (PCA) projects high-dimensional genotype data into a few components that discern populations. Ancestry Informative Markers (AIMs) are a small subset of SNPs capable of distinguishing populations. We integrate these two approaches by proposing an algorithm to identify necessary informative loci whose removal from the data deteriorates the PCA structure. Unlike classical AIMs, necessary informative loci densely cover the genome, hence can illuminate the evolution and mixing history of populations. We conduct a comprehensive analysis to the genotype data of the 1000 Genomes Project using necessary informative loci. Projections along the top seven principal components demarcate populations at distinct geographic levels. Millions of necessary informative loci along each PC are identified. Population identities along each PC are approximately determined by weighted sums of minor (or major) alleles over the informative loci. Variations of allele frequencies are aligned with the history and direction of population evolution. The population distribution of projections along the top three PCs is recapitulated by a simple demographic model based on several waves of founder population separation and mixing. Informative loci possess locational concentration in the genome and functional enrichment. Genes at two hot spots encompassing dense PC 7 informative loci exhibit differential expressions among European populations. The mosaic of local ancestry in the genome of a mixed descendant from multiple populations can be inferred from partial PCA projections of informative loci. Finally, informative loci derived from the 1000 Genomes data well predict the projections of an independent genotype data of South Asians. These results demonstrate the utility and relevance of informative loci to investigate human evolution.

Statistical Modelling of Population-Level Exonic Variant Frequency Data with an Emphasis on Rare Variants

Introduction & Objective: Rare variants with allele frequency smaller than 1% are postulated to be associated with disease susceptibility. Since allele frequencies vary globally, the use of population control data that does not match the study population can produce bias. The research question is to identify factors that explain variation in allele frequency across populations. The secondary question is to evaluate the potential bias in using population as control data when studying variants. We use data from gnomAD (Genome Aggregation Database) to answer these questions.
 Methods: We apply each of three model formulations: Linear, Logistic, and Poisson to explain how the frequency or count of variants depends on population subgroup/ancestry, functional annotation, sex, and disease status. We also evaluate interactions between population subgroups and functional annotation.
 Results: For very rare variants (allele frequency < 0.1%), likelihood ratio testing (LRT) provides evidence that allele frequencies vary with functional annotation and population in all three model formulations. By LRT, interactions of population and functional annotation are significant in the Logistic model and the Poisson model. The goodness-of-fit statistics show a better fit in the linear model compared to low frequency variants.
 Conclusion: We observe that population & functional annotation affect variant frequencies, and conclude that detection of differences across populations and annotations is model scale-dependent, especially for different degrees of rareness. Therefore, statisticians need to carefully consider the potential for bias when using gnomAD as control data. Moreover, gnomAD is a great resource for studies dealing with rare variants.

Comparative analysis of allele variation using allele frequencies according to sample size in Korean population

BackgroundAllele frequency using short tandem repeats (STRs) is used to calculate likelihood ratio for database match, to interpret DNA mixture and to estimate ethnic groups in forensic genetics. In Korea, three population studies for 23 STR loci have been conducted with different sample size for forensic purposes.ObjectiveWe performed comparative analysis to determine how the difference of sample size affects the allele frequency and allele variation within same ethnic population (i.e. Korean). Furthermore, this study was conducted to check how the sampling group and multiplex kit also affect allele variation such as rare alleles and population specific alleles.MethodsTo compare allele variation, we used allele frequencies of three population data published from three Korean forensic research groups. Allele frequencies were calculated using different sample sizes and multiplex kits: 526, 1000, and 2000 individuals, respectively.ResultsThe results showed the different distribution of allele frequencies in some loci. There was also a difference in the number of rare alleles observed by the sample size and sampling bias. In particular, an allele of 9.1 in the D2S441 locus was not observed in population study with 526 individuals due to multiplex kits.ConclusionBecause the allele frequencies play an important role in forensic genetics, even if the samples are derived from the same population, it is important to consider the effects of sample size, sampling bias, and selection of multiplex kits in population studies.

Generation of unequal nuclear genotype proportions in Rhizophagus irregularis progeny causes allelic imbalance in gene transcription.

Summary Arbuscular mycorrhizal fungi (AMF) form mutualisms with most plant species. The model AMF Rhizophagus irregularis is common in many ecosystems and naturally forms homokaryons and dikaryons. Quantitative variation in allele frequencies in clonally dikaryon offspring suggests they disproportionately inherit two distinct nuclear genotypes from their parent. This is interesting, because such progeny strongly and differentially affect plant growth. Neither the frequency and magnitude of this occurrence nor its effect on gene transcription are known.Using reduced representation genome sequencing, transcriptomics, and quantitative analysis tools, we show that progeny of homokaryons and dikaryons are qualitatively genetically identical to the parent. However, dikaryon progeny differ quantitatively due to unequal inheritance of nuclear genotypes. Allele frequencies of actively transcribed biallelic genes resembled the frequencies of the two nuclear genotypes.More biallelic genes showed transcription of both alleles than monoallelic transcription, but biallelic transcription was less likely with greater allelic divergence. Monoallelic transcription levels of biallelic genes were reduced compared with biallelic gene transcription, a finding consistent with genomic conflict.Given that genetic variation in R. irregularis is associated with plant growth, our results establish quantitative genetic variation as a future consideration when selecting AMF lines to improve plant production.

Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus

Understanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics. Based on genome-wide Fst (pairwise fixation index) and Vst analyses, which compared the variance in allele frequencies of single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), respectively, we found a high level of genetic differentiation between two populations. CNV patterns revealed population-specific expansions and contractions. Interestingly, we identified a ~20 kbp genomic island of high divergence with a strong sign of positive selection. This region contains a melanin-biosynthetic polyketide synthase gene cluster linked to six additional genes likely involved in biosynthesis, membrane trafficking, regulation, and localization of melanin. Differences in growth yield and melanin biosynthesis between the two populations grown under 2% NaCl stress suggested that this genomic island contributes to the observed differences in melanin accumulation. Our findings provide a better understanding of the genetic and evolutionary mechanisms underlying the adaptation to saline conditions of the L. rhizohalophila–S. salsa symbiosis.

Association of Vitamin D, Zinc and Selenium Related Genetic Variants With COVID-19 Disease Severity.

Background: COVID-19 pandemic has proved to be an unrelenting health threat for more than a year now. The emerging amount of data indicates that vitamin D, zinc and selenium could be important for clinical presentation of COVID-19. Here, we investigated association of genetic variants related to the altered level and bioavailability of vitamin D, zinc and selenium with clinical severity of COVID-19.Methods: We analyzed variants in genes significant for the status of vitamin D (DHCR7/NADSYN1 rs12785878, GC rs2282679, CYP2R1 rs10741657, and VDR rs2228570), zinc (PPCDC rs2120019) and selenium (DMGDH rs17823744) in 120 Serbian adult and pediatric COVID-19 patients using allelic discrimination. Furthermore, we carried out comparative population genetic analysis among European and other worldwide populations to investigate variation in allelic frequencies of selected variants.Results: Study showed that DHCR7/NADSYN rs12785878 and CYP2R1 rs10741657 variants were associated with severe COVID-19 in adults (p = 0.03, p = 0.017, respectively); carriers of DHCR7/NADSYN TG+GG and CYP2R1 GG genotypes had 0.21 and 5.9 the odds for developing severe disease, OR 0.21 (0.05–0.9) and OR 5.9 (1.4–25.2), respectively. There were no associations between selected genetic variants and disease severity in pediatric patients. Comparative population genetic analysis revealed that Serbian population had the lowest frequency of CYP2R1 rs10741657 G allele compared to other non-Finish Europeans (0.58 compared to 0.69 and 0.66 in Spanish and Italian population, respectively), suggesting that other populations should also investigate the relationship of CYP2R1 variant and the COVID-19 disease course.Conclusion: The results of the study indicated that vitamin D related genetic variants were implicated in severe COVID-19 in adults. This could direct prevention strategies based on population specific nutrigenetic profiles.

Genetic diversity and effective population sizes of thirteen Indian cattle breeds

BackgroundThe genetic structure of a diverse set of 15 Indian indigenous breeds and non-descript indigenous cattle sampled from eight states was examined, based on 777 k single nucleotide polymorphism (SNP) genotypes obtained on 699 animals, with sample sizes ranging from 17 to 140 animals per breed. To date, this is the largest and most detailed assessment of the genetic diversity of Indian cattle breeds.ResultsAdmixture analyses revealed that 109 of the indigenous animals analyzed had more than 1% Bos taurus admixture of relatively recent origin. Pure indigenous animals were defined as having more than 99% Bos indicus ancestry. Assessment of the genetic diversity within and between breeds using principal component analyses, F statistics, runs of homozygosity, the genomic relationship matrix, and maximum likelihood clustering based on allele frequencies revealed a low level of genetic diversity among the indigenous breeds compared to that of Bos taurus breeds. Correlations of SNP allele frequencies between breeds indicated that the genetic variation among the Bos indicus breeds was remarkably low. In addition, the variance in allele frequencies represented less than 1.5% between the Indian indigenous breeds compared to about 40% between Bos taurus dairy breeds. Effective population sizes (Ne) increased during a period post-domestication, notably for Ongole cattle, and then declined during the last 100 generations. Although we found that most of the identified runs of homozygosity are short in the Indian indigenous breeds, indicating no recent inbreeding, the high FROH coefficients and low FIS values point towards small population sizes. Nonetheless, the Ne of the Indian indigenous breeds is currently still larger than that of Bos taurus dairy breeds.ConclusionsThe changes in the estimates of effective population size are consistent with domestication from a large native population followed by consolidation into breeds with a more limited population size. The surprisingly low genetic diversity among Indian indigenous cattle breeds might be due to their large Ne since their domestication, which started to decline only 100 generations ago, compared to approximately 250 to 500 generations for Bos taurus dairy cattle.

Experimental evolution supports signatures of sexual selection in genomic divergence.

Comparative genomics has contributed to the growing evidence that sexual selection is an important component of evolutionary divergence and speciation. Divergence by sexual selection is implicated in faster rates of divergence of the X chromosome and of genes thought to underlie sexually selected traits, including genes that are sex biased in expression. However, accurately inferring the relative importance of complex and interacting forms of natural selection, demography, and neutral processes that occurred in the evolutionary past is challenging. Experimental evolution provides an opportunity to apply controlled treatments for multiple generations and examine the consequent genomic divergence. Here, we altered sexual selection intensity, elevating sexual selection in polyandrous lines and eliminating it in monogamous lines, and examined patterns of allele frequency divergence in the genome of Drosophila pseudoobscura after more than 160 generations of experimental evolution. Divergence is not uniform across the genome but concentrated in “islands,” many of which contain candidate genes implicated in mating behaviors and other sexually selected phenotypes. These are more often seen on the X chromosome, which also shows greater divergence in F ST than neutral expectations. There are characteristic signatures of selection seen in these regions, with lower diversity on the X chromosome than the autosomes, and differences in diversity on the autosomes between selection regimes. Reduced Tajima's D within some of the divergent regions may imply that selective sweeps have occurred, despite considerable recombination. These changes are associated with both differential gene expression between the lines and sex‐biased gene expression within the lines. Our results are very similar to those thought to implicate sexual selection in divergence between species and natural populations, and hence provide experimental support for the likely role of sexual selection in driving such types of genetic divergence, but also illustrate how variable outcomes can be for different genomic regions.

Accurately estimating the homologous recombination deficiency based on low-pass whole-genome sequencing and target sequencing.

e15077 Background: Homologous recombination deficiency (HRD) is a promising biomarker for poly ADP-ribose polymerase (PARP) inhibitors. In the past, the HRD status was mainly estimated by summing the loss of heterozygosity (LOH), telomeric allelic imbalance (TAI), and large-scale state transition (LST) based on target sequencing. However, the heterozygous loci coverage and probe number are closely correlated to B allele frequency and copy number variations (CNVs). Here we developed a novel method to combine the data from low-pass whole-genome sequencing (WGS) and target sequencing to accurately estimate the genome-wide CNVs and allelic imbalance. Methods: We first performed low-pass WGS and target sequencing on 30 healthy controls, formalin-fixed and paraffin-embedded (FFPE) samples, and matched blood cell samples for 29 patients with breast cancer or ovarian cancer. Two HRD positive samples were diluted to 40%, 30%, 20%, and 10% tumor purity with matched blood cell samples, respectively. Each diluted sample was sequenced 20 times. The baseline for CNVs was built based on the sequencing data of healthy donors. To eliminate the artifacts resulted from the sequencing platform, models for each candidate single nucleotide polymorphism (SNP) in target regions were trained using the data from healthy donors. The mutations of BRCA1/BRCA2 of 29 patients were used to define the threshold of the HRD score. The numbers of LOH, LST, and TAI were evaluated by CNVs and B allele frequency. Results: We defined a cutoff of 42 for the HRD status based on the low-pass WGS and target sequencing data of 29 patients. Specifically, the original HRD scores for two selected HRD positive samples were 68 and 89. The median HRD scores for 40%, 30%, 20%, and 10% tumor purity samples were 69 and 88, 66.5 and 90, 61 and 68, 52 and 34.5, respectively. Conclusions: We developed a novel method for robustly inferring the HRD status using low-pass WGS and target sequencing with a limit of detection of 20%.

Geographical and linguistic structure in the people of Kenya demonstrated using 21 autosomal STRs

Kenya is a diverse and populous nation that employs DNA evidence in its criminal justice system, and therefore requires reliable information on autosomal STR allele frequency variation across the country and in its many ethnic groups. In order to provide reference data and to assess population structure, we analysed the 21 autosomal STRs in the GlobalFiler multiplex in a sample of 510 indigenous Kenyans representing the country’s eight former provinces, 43 of its 47 counties, three main linguistic families and all 29 ethnic groups that each comprise >0.5% of the 2019 census population. The indigenous population originated from successive migrations of Cushitic, Nilotic and Bantu speaking groups who settled in regions that suited their distinctive sustenance lifestyles. Consequently, they now largely reside in a patchwork of communities with strong associations with particular counties and provinces and limited degrees of inter-group marriage, as shown by DNA donors’ ancestry details. We found significant genetic differentiation between the three Nilotic language sub-families, with Western Nilotes (the Luo ethnic group) showing greater similarity to the Bantu than the Southern and Eastern Nilotes which themselves showed closer affinity to the Cushitic speakers. This concurs with previous genetic, linguistic and social studies. Comparisons with other African populations also showed that linguistic affiliation is a stronger factor than geography. This study revealed several rare off-ladder alleles whose structure was determined by Sanger sequencing. Among the unusual features that could affect profile interpretation were a deletion of Amelogenin Y but no other forensic marker (autosomal or Y-chromosomal), a triallelic pattern at TPOX and an extremely short SE33 allele falling within the expected size range of D7S820. Compared with the currently implemented Identifiler multiplex, Random Match Probabilities decreased from 6.4 × 10–19 to 3.9 × 10–27. The appreciation of local population structure provided by the geographically and ethnically representative sample in this study highlights the structured genetic landscape of Kenya.

Identification of ANXA2 as a Potential Susceptibility Gene for Diabetic Retinopathy in a Genome-Wide Association Analysis in Chinese Patients With Type 2 Diabetes Mellitus

Background: Diabetic retinopathy (DR) is the most frequent microvascular complication of type 2 diabetes mellitus (T2DM). Variation in allele frequencies between different ethnic groups may influence the detectability of the risk variants in different populations. It is therefore important to conduct ethnic-specific association analysis to discover novel loci. The major objective of this study was to conduct a 2-stage genome-wide association study (GWAS) to identify novel susceptibility single nucleotide polymorphisms (SNPs) for sight-threatening DR in Chinese patients with T2DM. Methods and Materials: The discovery stage consisted of 681 STDR cases and 758 non-STDR controls of Southern Chinese ancestry. The Illumina Infinium Asian Screening Array (ASA) was used for genotyping of the subjects. Imputation was performed using the TOPMed Imputation Server. SNPs with minor allele frequency (MAF) <0.01 and INFO score <0.3 were excluded. Single variant association analysis was performed in SNPTEST using the multiple logistic regression model with adjustment for age, gender, duration of diabetes, hypertension, hemoglobin A1c (HbA1c), and the first five principal components. The replication cohort was comprised of an independent sample set of 278 STDR cases and 834 non-STDR controls. Meta-analysis of the association results of the discovery and replication stages was conducted using the “GWAMA” software. The inverse variance fixed-effect method was used to meta-analyze the summary statistics of the two stages. Results: In the discovery stage, the strongest association was detected at an intronic variant of ANXA2 (P=1.87x10-7; OR[95%CI]:1.59[1.31–1.96]). Ninety-three SNPs showing suggestive associations (P<5x10-5) with STDR in the discovery stage were selected for replication. In the meta-analysis of the two stages, the ANXA2 SNP again showed the strongest association with STDR (P=2.18x10-6; OR[95%CI]: 1.45[1.24–1.70]). ANXA2 encodes the annexin A2 which has been shown to play an important role in promoting angiogenesis. An intronic SNP of DOC2B, a tumor suppressor gene that exhibits functions in cell proliferation and migration, also demonstrated a marginal association with STDR (P=5.17x10-6; OR[95%CI]: 1.41[1.22–1.63]). Two intergenic variants located at the RPL31P11-FCRLA (P=7.25x10-6; OR[95%CI]: 1.54[1.27–1.85]) and COL6A1-COL6A2 (P=9.60x10-6; OR[95%CI]: 0.73[0.63–0.84]) loci also showed suggestive associations with STDR. Conclusion: Several novel STDR-associated genetic variants were identified in this genome-wide association study. Our findings have shed new lights on the genetic basis of STDR in Chinese patients with T2DM. Further validation in independent cohorts to validate our findings are warranted. Acknowledgements: This study was supported by the Research Grant Council – General Research Fund of Hong Kong (Ref no.: 17118119).

Cross-ancestry genome-wide association studies identified heterogeneous loci associated with differences of allele frequency and regulome tagging between participants of European descent and other ancestry groups from the UK Biobank.

To investigate cross-ancestry genetics of complex traits, we conducted a phenome-wide analysis of loci with heterogeneous effects across African, Admixed-American, Central/South Asian, East Asian, European and Middle Eastern participants of the UK Biobank (N = 441 331). Testing 843 phenotypes, we identified 82 independent genomic regions mapping variants showing genome-wide significant (GWS) associations (P < 5 × 10-8) in the trans-ancestry meta-analysis and GWS heterogeneity among the ancestry-specific effects. These included (i) loci with GWS association in one ancestry and concordant but heterogeneous effects among the other ancestries and (ii) loci with a GWS association in one ancestry group and an experiment-wide significant discordant effect (P < 6.1 × 10-4) in at least another ancestry. Since the trans-ancestry GWS associations were mostly driven by the European ancestry sample size, we investigated the differences of the allele frequency (ΔAF) and linkage disequilibrium regulome tagging (ΔLD) between European populations and the other ancestries. Within loci with concordant effects, the degree of heterogeneity was associated with European-Middle Eastern ΔAF (P = 9.04 × 10-6) and ΔLD of European populations with respect to African, Admixed-American and Central/South Asian groups (P = 8.21 × 10-4, P = 7.17 × 10-4 and P = 2.16 × 10-3, respectively). Within loci with discordant effects, ΔAF and ΔLD of European populations with respect to African and Central/South Asian ancestries were associated with the degree of heterogeneity (ΔAF: P = 7.69 × 10-3 and P = 5.31 × 10-3, ΔLD: P = 0.016 and P = 2.65 × 10-4, respectively). Considering the traits associated with cross-ancestry heterogeneous loci, we observed enrichments for blood biomarkers (P = 5.7 × 10-35) and physical appearance (P = 1.38 × 10-4). This suggests that these specific phenotypic classes may present considerable cross-ancestry heterogeneity owing to large allele frequency and LD variation among worldwide populations.

The protective effects of the methylenetetrahydrofolate reductase rs1801131 variant among Saudi smokers.

Methylenetetrahydrofolate reductase (MTHFR) polymorphism plays a fundamental role in susceptibility to various diseases, including cancers and autoimmune diseases. In the current study, we aimed to compare genotype and allele frequency variations of rs1801131, one of the most common variants found in the MTHFR gene, among Saudi smokers and non-smokers. We hypothesized that genetic variations of this gene are responsible for many diseases, particularly those caused by cigarette smoking (CS) such as pulmonary diseases, oral cancer and lung cancer. We performed a case-control study on a sample of 235 healthy smokers and 239 healthy non-smokers in Saudi Arabia. The rs1801131 SNP genotypes were determined using a genotyping assay and multiple in silico algorithmic software programs were used to identify the effects and structural functions of the rs1801131 (Glu429Ala) mutation. Using chi-squared tests, we found that, among smokers, TG and GG genotype carriers had 0.209-fold (OR = 0.209, P < 0.005) and 0.427-fold (OR = 0.427, P = 0.003) lower risks of CS-related disease compared to TT reference genotypes. In addition, this protective effect was observed in Saudi smokers independent of age, gender, types of smoking, duration, and average daily smoking consumption. Filling a research gap by exploring this topic in the Saudi population, the current findings indicate that genotype and allele distributions of MTHFR rs1801131 polymorphism present fundamental protective effects against the risk of CS-related disease. These findings should be verified in future studies with larger sample sizes, different ethnicities, and patients suffering from CS-related diseases, such as oral cancer and lung cancer.

Leveraging genomics to understand threats to migratory birds.

Understanding how risk factors affect populations across their annual cycle is a major challenge for conserving migratory birds. For example, disease outbreaks may happen on the breeding grounds, the wintering grounds, or during migration and are expected to accelerate under climate change. The ability to identify the geographic origins of impacted individuals, especially outside of breeding areas, might make it possible to predict demographic trends and inform conservation decision‐making. However, such an effort is made more challenging by the degraded state of carcasses and resulting low quality of DNA available. Here, we describe a rapid and low‐cost approach for identifying the origins of birds sampled across their annual cycle that is robust even when DNA quality is poor. We illustrate the approach in the common loon (Gavia immer), an iconic migratory aquatic bird that is under increasing threat on both its breeding and wintering areas. Using 300 samples collected from across the breeding range, we develop a panel of 158 single‐nucleotide polymorphisms (SNP) loci with divergent allele frequencies across six genetic subpopulations. We use this SNP panel to identify the breeding grounds for 142 live nonbreeding individuals and carcasses. For example, genetic assignment of loons sampled during botulism outbreaks in parts of the Great Lakes provides evidence for the significant role the lakes play as migratory stopover areas for loons that breed across wide swaths of Canada, and highlights the vulnerability of a large segment of the breeding population to botulism outbreaks that are occurring in the Great Lakes with increasing frequency. Our results illustrate that the use of SNP panels to identify breeding origins of carcasses collected during the nonbreeding season can improve our understanding of the population‐specific impacts of mortality from disease and anthropogenic stressors, ultimately allowing more effective management.

Genetic and morphological relationships of fieldwrens (Calamanthus): implications for conservation status and management

ABSTRACT Sound taxonomy is important for providing a scientific basis for the listing of threatened taxa and allowing informed decisions for conservation management. The Australian fieldwrens (Acanthizidae: Calamanthus spp.), small passerines of shrublands across mesic to arid southern Australia, have been challenging in this respect. Difficulties in interpreting the variation in morphology and colouration across their geographic range have resulted in taxonomic controversy for a century; multiple arrangements of species and subspecies have been proposed, including a prevailing view that there are two species and seven subspecies in the Rufous Fieldwren, Calamanthus campestris complex. Two island subspecies (C. campestris hartogi and C. c. dorrie) are currently listed as Vulnerable. We hypothesised that C. campestris is monotypic (including C. montanellus) and that variation is clinal across mainland populations. Results of our genetic, morphological and colour pattern analyses are largely consistent with this hypothesis. However, we did find evidence of genetic divergence between eastern and western populations and some genetic support for recognition of C. c. hartogi (Dirk Hartog Island) based on divergence in nuclear allele frequencies. Together, our results provide a strong case for the hypotheses that C. montanellus is a synonym of C. campestris, and that rather than consisting of seven subspecies, C. campestris comprises two mainland subspecies C. c. campestris and C. c. rubiginosus east and west, respectively, of 133 degrees longitude, and only one island subspecies, C. c. hartogi. In this regard, the currently recognised C. c. dorrie is nominated for removal from threatened species lists.

Islands of runs of homozygosity indicate selection signatures in Ovis aries 6 (OAR6) of French dairy sheep

Runs of homozygosity (ROH) are contiguous homozygous segments of the genome where the haplotypes inherited from each parent are identical. The occurrence of ROH is not randomly distributed across the genome, and ROH islands across many animals may be the result of selective pressure. The objective of this study was to demonstrate that the presence of ROH islands may be indicative of selection signatures in French dairy sheep breeds and subpopulations. The data set available included animals (artificial insemination males) from various breeds and subpopulations: Basco-Béarnaise breed (321 individuals), Manech Tête Noire breed (329 individuals), Manech Tête Rousse breed (1,906 individuals), Lacaune Confederation subpopulation (3,030 individuals), and Lacaune Ovitest subpopulation (3,114 individuals). Animals were genotyped with the Illumina OvineSNP50 BeadChip. After applying filtering criteria, the genomic data included 38,287 autosomal SNP distributed across 26 chromosomes and 8,700 individuals. One island of ROH was detected on OAR6 in the same genomic position across animals (between 30 and 40 Mb). Global Wright's differentiation coefficients for 2 SNP within this ROH island were high (0.67–0.68). The linkage disequilibrium between both SNP was also elevated (0.98). The divergence in allele frequencies in those SNP grouped Basco-Béarnaise, Manech Tête Noire, and Manech Tête Rousse breeds in one cluster and Lacaune Confederation and Lacaune Ovitest subpopulations in another cluster. The closest candidate genes are NCAPG and LCORL, which have been reported to be under positive selection and suggested to control weight and height in sheep. The preliminary identification of ROH suggests the presence of selection. However, for the identification of potential candidate genes, ROH detection should be combined with other approaches to improve mapping accuracy.