Differences In Allele Frequencies Research Articles

A population-aware retrospective regression to detect genome-wide variants with sex difference in allele frequency

A population-aware retrospective regression to detect genome-wide variants with sex difference in allele frequency

Neuregulin 2 Is a Candidate Gene for Autism Spectrum Disorder.

Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with heterogeneous and complex genetic underpinnings. Our previous microarray gene expression profiling identified significantly different neuregulin-2 gene (NRG2) expression between ASD patients and controls. Thus, we aimed to clarify whether NRG2 is a candidate gene associated with ASD. The study consisted of two stages. First, we used real-time quantitative PCR in 20 ASDs and 20 controls to confirm the microarray gene expression profiling results. The average NRG2 gene expression level in patients with ASD (3.23 ± 2.80) was significantly lower than that in the controls (9.27 ± 4.78, p < 0.001). Next, we conducted resequencing of all the exons of NRG2 in a sample of 349 individuals with ASD, aiming to identify variants of the NRG2 associated with ASD. We identified three variants, including two single nucleotide variants (SNVs), IVS3 + 13A > G (rs889022) and IVS10 + 32T > A (rs182642591), and one small deletion at exon 11 of NRG2 (delGCCCGG, rs933769137). Using data from the Taiwan Biobank as the controls, we found no significant differences in allele frequencies of rs889022 and rs182642591 between two groups. However, there is a significant difference in the genotype and allele frequency distribution of rs933769137 between ASDs and controls (p < 0.0001). The small deletion is located in the EGF-like domain at the C-terminal of the NRG2 precursor protein. Our findings suggest that NRG2 might be a susceptibility gene for ASD.

Pharmacogenetic landscape of pain management variants among Mediterranean populations.

Chronic pain is a major socioeconomic burden in the Mediterranean region. However, we noticed an under-representation of these populations in the pharmacogenetics of pain management studies. In this context, we aimed 1) to decipher the pharmacogenetic variant landscape among Mediterranean populations compared to worldwide populations in order to identify therapeutic biomarkers for personalized pain management and 2) to better understand the biological process of pain management through in silico investigation of pharmacogenes pathways. We collected genes and variants implicated in pain response using the Prisma guidelines from literature and PharmGK database. Next, we extracted these genes from genotyping data of 829 individuals. Then, we determined the variant distribution among the studied populations using multivariate (MDS) and admixture analysis with R and STRUCTURE software. We conducted a Chi2 test to compare the interethnic frequencies of the identified variants. We used SNPinfo web server, miRdSNP database to identify miRNA-binding sites. In addition, we investigated the functions of the identified genes and variants using pathway enrichment analysis and annotation tools. Finally, we performed docking analysis to assess the impact of variations on drug interactions. We identified 63 variants implicated in pain management. MDS analysis revealed that Mediterranean populations are genetically similar to Mexican populations and divergent from other populations. STRUCTURE analysis showed that Mediterranean populations are mainly composed of European ancestry. We highlighted differences in the minor allele frequencies of three variants (rs633, rs4680, and rs165728) located in the COMT gene. Moreover, variant annotation revealed ten variants with potential miRNA-binding sites. Finally, protein structure and docking analysis revealed that two missense variants (rs4680 and rs6267) induced a decrease in COMT protein activity and affinity for dopamine. Our findings revealed that Mediterranean populations diverge from other ethnic groups. Furthermore, we emphasize the importance of pain-related pathways and miRNAs to better implement these markers as predictors of analgesic responses in the Mediterranean region.

Understanding the determinants of sweet taste liking in the African and East Asian ancestry groups in the U.S.-A study protocol.

The liking for sweet taste is a powerful driver for consuming added sugars, and therefore, understanding how sweet liking is formed is a critical step in devising strategies to lower added sugars consumption. However, current research on the influence of genetic and environmental factors on sweet liking is mostly based on research conducted with individuals of European ancestry. Whether these results can be generalized to people of other ancestry groups warrants investigation. We will determine the differences in allele frequencies in sweet-related genetic variants and their effects on sweet liking in 426 adults of either African or East Asian ancestry, who have the highest and lowest average added sugars intake, respectively, among ancestry groups in the U.S. We will collect information on participants' sweet-liking phenotype, added sugars intake (sweetness exposure), anthropometric measures, place-of-birth, and for immigrants, duration of time living in the U.S. and age when immigrated. Ancestry-specific polygenic scores of sweet liking will be computed based on the effect sizes of the sweet-related genetic variants on the sweet-liking phenotype for each ancestry group. The predictive validity of the polygenic scores will be tested using individuals of African and East Asian ancestry from the UK Biobank. We will also compare sweet liking between U.S.-born individuals and immigrants within each ancestry group to test whether differences in environmental sweetness exposure during childhood affect sweet liking in adulthood. Expanding genetic research on taste to individuals from ancestry groups traditionally underrepresented in such research is consistent with equity goals in sensory and nutrition science. Findings from this study will help in the development of a more personalized nutrition approach for diverse populations. This protocol has been preregistered with the Center for Open Science (https://doi.org/10.17605/OSF.IO/WPR9E).

MMP-1, MMP-8, and MMP-13 Gene Polymorphisms and Haplotype Is a Risk Factor for Dupuytren Contracture: A Case-Control Study.

There is an increased tissue expression of matrix metalloproteinases (MMPs) on Dupuytren contracture (DC). Genetic polymorphisms (single nucleotide polymorphism [SNPs]) in genes of these enzymes may individually influence these transcriptions. Haplotype analysis, which is the observation of a group of alleles, could be more useful to identify the association between SNPs and DC. The purpose of this study was to evaluate the influence of MMP-1 g.-1607 G>GG (rs1799750), MMP-8 g.-799 C>T (rs11225395), and MMP-13 g.-77 A>G (rs2252070) SNPs individually and in haplotype on DC. A total of 60 patients with a clinical diagnosis of DC were evaluated and matched, according to age and gender, with the control group of 100 patients without this clinical diagnosis. Genomic DNA was extracted from saliva samples, and genotypes were obtained by polymerase chain reaction-restriction fragment length polymorphism. Statistical analysis of the results included Mann-Whitney U test, Chi-squared test, and PHASE and R software, with a significance level of 5%. The 3 SNPs studied showed significant differences in allele and genotype frequencies between the groups: 2G in MMP-1 (P = .018; odds ratio [OR] 1.80 (95% confidence interval [CI], 1.13-2.88)), T in MMP-8 (P = .015; OR 0.53 (95% CI, 0.33-0.88)), and A in MMP-13 (rs2252070) SNPs (P = .040, OR 0.54 (95% CI, 0.33-0.90)) are risk alleles. The global haplotype analysis indicated a significant difference between both groups. In conclusion, MMP-1 g.-1607 G>GG (rs1799750), MMP-8 g.-799 C>T (rs11225395), and MMP-13 g.-77 A>G (rs2252070) SNPs, individually and in haplotype, are a risk factor for DC, indicating that these SNPs may be a potential diagnostic and prognostic factor for DC.

Association of KLOTHO gene variants with metabolic and renal function parameters in Mexican patients living with type 2 diabetes.

Type 2 diabetes (T2D) and high blood pressure are the main causes of chronic kidney disease (CKD) in adulthood. Both metabolic and oxidative stresses driven by hyperglycemia as well as genetic factors have been suggested as pathogenic causes of renal failure. Some single nucleotide variants (SNVs) on gene coding KLOTHO (KL) have been implicated in several clinical scenarios including hypertension, diabetes, and cardiovascular disease. The aim of this study was to analyze the association of rs1207568 (-395G > A), rs953614 (+ 1062T > G) and rs564481 (+ 1818C > T) SNVs with metabolic and renal function parameters in Mexican patients living with type 2 diabetes. A cross-sectional study was conducted in 637 Mexican patients with T2D, and/or hypertension without previous diagnosis of CKD. Anthropometric, metabolic, and renal function parameters were determined. Patients were genotyped for rs1207568, rs953614 and rs564481 SNVs and associations under a dominant genetic model were analyzed by logistic regression. For rs9536314, G-allele showed to be protective for hypo-HDL-C, albuminuria, and CKD. Carriers of minor allele of rs564481 had low odds for high glucose levels. No differences in genotype nor allele frequencies between the patients and the reference population were observed. In Mexican patients living with type 2 diabetes, KL variant rs9536314 was found associated with low odds of hypo-HDL cholesterol, albuminuria and presence of CKD. Meanwhile the consensus of soluble KLOTHO measurement is reached, genetic variants in the KL gene could be considered as genetic markers for CKD susceptibility in patients at high-risk of vascular complications.

The Relationship Between CYP46A1 Polymorphism and Suicide Risk: A Preliminary Investigation.

Suicide is a global public health issue, with a particularly high incidence in individuals suffering from Major Depressive Disorder (MDD). The role of cholesterol in suicide risk remains controversial, prompting investigations into genetic markers that may be implicated. This study examines the association between CYP46A1 polymorphisms, specifically SNPs rs754203 and rs4900442, and suicide risk in a Mexican MDD patient cohort. Our study involved 188 unrelated suicide death victims, 126 MDD patients, and 144 non-suicidal controls. Genotypic and allelic frequencies were assessed using the Real Time-polymerase chain reaction method, and associations with suicide risk were evaluated using chi-square tests. The study revealed significant differences in allelic and genotypic frequencies in rs754203 SNP between suicide death and controls. The CYP46A1 rs754203 genotype G/G was significantly linked with suicide, and the G allele was associated with a higher risk of suicide (OR = 1.370, 95% CI = 1.002-1.873). However, we did not observe any significant differences in genotype distribution or allele frequencies of CYP46A1 rs4900442. Our study suggests that carriers of the CYP46A1 rs754203 G allele (A/G + G/G) may play a role in suicidal behavior, especially in males. Our findings support that the CYP46A1 gene may be involved in susceptibility to suicide, which has not been investigated previously. These results underscore the importance of further research in different populations to elucidate the genetic underpinnings of the role of CYP46A1 in suicide risk and to develop targeted interventions for at-risk populations.

CYP2C8 rs11572080 and CYP3A4 rs2740574 risk genotypes in paclitaxel-treated premenopausal breast cancer patients

Breast cancer (BC) is the most prevalent malignancy in women globally. At time of diagnosis, premenopausal BC is considered more aggressive and harder to treat than postmenopausal cases. Cytochrome P450 (CYP) enzymes are responsible for phase I of estrogen metabolism and thus, they are prominently involved in the pathogenesis of BC. Moreover, CYP subfamily 2C and 3A play a pivotal role in the metabolism of taxane anticancer agents. To understand genetic risk factors that may have a role in pre-menopausal BC we studied the genotypic variants of CYP2C8, rs11572080 and CYP3A4, rs2740574 in female BC patients on taxane-based therapy and their association with menopausal status. Our study comprised 105 female patients with histologically proven BC on paclitaxel-therapy. They were stratified into pre-menopausal (n = 52, 49.5%) and post-menopausal (n = 53, 50.5%) groups. Genotyping was done using TaqMan assays and employed on Quantstudio 12 K flex real-time platform. Significant increased frequencies of rs11572080 heterozygous CT genotype and variant T allele were established in pre-menopausal group compared to post-menopausal group (p = 0.023, 0.01, respectively). Moreover, logistic regression analysis revealed a significant association between rs11572080 CT genotype and premenopausal BC. However, regarding rs2740574, no significant differences in genotypes and allele frequencies between both groups were detected. We reported a significant association between CYP2C8 genotypic variants and premenopausal BC risk in Egyptian females. Further studies on larger sample sizes are still needed to evaluate its importance in early prediction of BC in young women and its effect on treatment outcome.

Footprints of Stress in Vitiligo: Association of the 5-HTR2C rs6318 Variant

Abstract Vitiligo is a chronic, progressive autoimmune dermatological disease, and stress is known to have an impact on the development of vitiligo. However, the effect of the serotonin pathway and its impact have not been clearly explained for disease progression. Thus, this study aimed to clarify the stress induced serotonin receptor 5-HTR2C rs6318 variant and its association with vitiligo pathogenesis. Case-control study was conducted with 108 vitiligo patients and 107 age-sex matched, unrelated healthy control group. Real Time-PCR analysis was used for genotyping the 5-HTR2C variation. Genotype and allele frequencies, genotype distributions, Hardy-Weinberg Equilibrium (HWE) and vitiligo-related risk measurements were examined. Genotype correlations of the variant were also analyzed based on gender difference, age onset, Koebner phenomenon history, triggered with stress, clinical subgroups, treatment types, the presence of other autoimmune diseases, vitiligo presence in family members and other auto-immune diseases in relatives. Statistical differences in 5HT-R2C receptor genotypes and allele frequencies between patients and controls were not detected. Genotype frequencies were not in agreement with Hardy-Weinberg Equilibrium in the patients’ group (p&lt;0.00001). The frequency of the risk allele (allele C) was not significantly different between the patient and control groups (p=0.1392). However, in the clinical subgroup analysis, the risk allele presence was detected to be significantly higher for early age onset (&lt;40 years) vitiligo development (p=0.035, OR=Infinity, RR=1.391) and lower in Koebner phenomenon history (p=0.0276, OR= 0.219, RR=0.325). In conclusion, although there was no association between the 5-HTR2C variant rs6318 and vitiligo, current results indicate that there is an association between the 5HTR2C rs6318 variant C allele and early onset vitiligo development.

Genetic control of DNA methylation is largely shared across European and East Asian populations

DNA methylation is an ideal trait to study the extent of the shared genetic control across ancestries, effectively providing hundreds of thousands of model molecular traits with large QTL effect sizes. We investigate cis DNAm QTLs in three European (n = 3701) and two East Asian (n = 2099) cohorts to quantify the similarities and differences in the genetic architecture across populations. We observe 80,394 associated mQTLs (62.2% of DNAm probes with significant mQTL) to be significant in both ancestries, while 28,925 mQTLs (22.4%) are identified in only a single ancestry. mQTL effect sizes are highly conserved across populations, with differences in mQTL discovery likely due to differences in allele frequency of associated variants and differing linkage disequilibrium between causal variants and assayed SNPs. This study highlights the overall similarity of genetic control across ancestries and the value of ancestral diversity in increasing the power to detect associations and enhancing fine mapping resolution.

Abstract 774: Genetic architecture, evolutionary genomics, and genomic risk of prostate cancer in sub-Saharan Africa

Abstract Men of African descent have the highest prostate cancer (CaP) incidence and mortality rates, yet the genetic basis of CaP in African men has been understudied. We performed the first large-scale genomic analysis of CaP across sub-Saharan Africa (SSA). We evaluated the evolutionary history of CaP-associated loci, generated a novel genomic risk score, inferred ancestry-specific genetic architectures, and fine-mapped disease associations using in 3,963 CaP cases and 3,509 controls recruited in Ghana, Nigeria, Senegal, South Africa, and Uganda through the Men of African Descent and Carcinoma of the Prostate (MADCaP) Network. Fifteen independent associations at 8q24.21, 6q22.1, and 11q13.3 reached genome-wide significance, including four novel associations. Multiple lead SNPs were private alleles in SSA, a pattern arising from recent mutations and the out-of-Africa bottleneck. These SSA-specific alleles contribute to haplotypes with odds ratios for CaP above 2.4. The genetic architecture of CaP differs across SSA, with effect size differences contributing more to this heterogeneity than allele frequency differences. Population genetic analyses reveal that SSA CaP associations are largely governed by neutral evolution, as opposed to natural selection. This finding is consistent with the late onset of this disease. Focusing on 2,502 age-matched cases and 2,222 non-cancer controls, we generated a novel genomic predictor of CaP. We then assessed the extent to which this polygenic risk score was correlated with age of onset, PSA levels, genetic ancestry, and family history of study participants. The performance of this novel polygenic risk score was tested on other populations of African descent, as well as populations with non-African ancestry. Our findings emphasize the utility of conducting genetic studies in diverse populations. Citation Format: Timothy R. Rebbeck, Rohini Janivara, Wenlong C. Chen, Ujani Hazra, MADCaP Network, Joseph Lachance. Genetic architecture, evolutionary genomics, and genomic risk of prostate cancer in sub-Saharan Africa [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 774.

Patterns of genetic variation and local adaptation of a native herbivore to a lethal invasive plant.

Understanding the evolutionary processes that influence fitness is critical to predicting species' responses to selection. Interactions among evolutionary processes including gene flow, drift and the strength of selection can lead to either local adaptation or maladaptation, especially in heterogenous landscapes. Populations experiencing novel environments or resources are ideal for understanding the mechanisms underlying adaptation or maladaptation, specifically in locally co-evolved interactions. We used the interaction between a native herbivore that oviposits on a patchily distributed introduced plant that in turn causes significant mortality to the larvae to test for signatures of local adaptation in areas where the two co-occurred. We used whole-genome sequencing to explore population structure, patterns of gene flow and signatures of local adaptation. We found signatures of local adaptation in response to the introduced plant in the absence of strong population structure with no genetic differentiation and low genetic variation. Additionally, we found localized allele frequency differences within a single population between habitats with and without the lethal plant, highlighting the effects of strong selection. Finally, we identified that selection was acting on larval ability to feed on the plant rather than on females' ability to avoid oviposition, thus uncovering the specific ontogenetic target of selection. Our work highlights the potential for adaptation to occur in a fine-grained landscape in the presence of gene flow and low genetic variation.

The Association of Leptin Receptor Gene Q223R Polymorphism with Obesity in the Yakut Population

Background: This study aimed to compare the frequencies of alleles and genotypes of the LEPR Q223R SNP in the Yakut population in samples with normal BMI and obesity and compare the data obtained with other populations worldwide. Methods and Results: The study included 336 DNA samples from volunteers of Yakut nationality (117 women and 219 men) without chronic diseases, whose average age was 47.4±0.06 years. All volunteers were divided into two groups: Group 1 (n=151) with normal BMI and Group 2 (n=185) with obesity. Group 2 was divided into two subgroups: Group 2A (n=156) with BMI ≥30 kg/m2 plus OA and Group 2B (n=29) with BMI ≥30 kg/m2 and without abdominal obesity.The study of the LEPR Q223R SNP was performed using the PCR-RFLP method. The frequency of the G allele of the LEPR Q223R SNP was 79.5% in Group 1 and 82.7% in Group 2. Analysis showed a high frequency of genotype GG: 64.2% and 69.7% in Group 1 and Group 2, respectively. The frequency of the GA genotype was 30.5% in Group 1 and 25.9% in Group 2.The frequency of alleles and genotypes does not differ in the sample of Yakuts with normal BMI and those with obesity. There are also no differences in the frequency of alleles and genotypes based on gender and the presence of abdominal obesity.The high frequency of the G allele in the Yakut population is close to that observed in East Asian populations (86.9%). There was no statistical difference in allele frequencies in comparison with the populations of Han Chinese from Beijing, Japanese from Tokyo, and Vietnamese from Ho Chi Minh City. In European, African, American, and South Asian populations, the G allele occurs with a frequency of 43.7% to 59.2%. Conclusion: The LEPR Q223R SNP does not affect BMI in the Yakut population. In this study, Q223R allele frequencies were like allele frequencies in East Asian populations but not in Caucasians, reflecting racial diversity in the allele distribution of this polymorphism.

Expected values for the accuracy of predicted breeding values accounting for genetic differences between reference and target populations

BackgroundGenetic merit, or breeding values as referred to in livestock and crop breeding programs, is one of the keys to the successful selection of animals in commercial farming systems. The developments in statistical methods during the twentieth century and single nucleotide polymorphism (SNP) chip technologies in the twenty-first century have revolutionized agricultural production, by allowing highly accurate predictions of breeding values for selection candidates at a very early age. Nonetheless, for many breeding populations, realized accuracies of predicted breeding values (PBV) remain below the theoretical maximum, even when the reference population is sufficiently large, and SNPs included in the model are in sufficient linkage disequilibrium (LD) with the quantitative trait locus (QTL). This is particularly noticeable over generations, as we observe the so-called erosion of the effects of SNPs due to recombinations, accompanied by the erosion of the accuracy of prediction. While accurately quantifying the erosion at the individual SNP level is a difficult and unresolved task, quantifying the erosion of the accuracy of prediction is a more tractable problem. In this paper, we describe a method that uses the relationship between reference and target populations to calculate expected values for the accuracies of predicted breeding values for non-phenotyped individuals accounting for erosion. The accuracy of the expected values was evaluated through simulations, and a further evaluation was performed on real data.ResultsUsing simulations, we empirically confirmed that our expected values for the accuracy of PBV accounting for erosion were able to correctly determine the prediction accuracy of breeding values for non-phenotyped individuals. When comparing the expected to the realized accuracies of PBV with real data, only one out of the four traits evaluated presented accuracies that were significantly higher than the expected, approaching h2\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\sqrt{{{\ ext{h}}}^{2}}$$\\end{document}.ConclusionsWe defined an index of genetic correlation between reference and target populations, which summarizes the expected overall erosion due to differences in allele frequencies and LD patterns between populations. We used this correlation along with a trait’s heritability to derive expected values for the accuracy (R\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\ ext{R}}$$\\end{document}) of PBV accounting for the erosion, and demonstrated that our derived ER|erosion\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\ ext{E}}\\left[{\ ext{R}}|{\ ext{erosion}}\\right]$$\\end{document} is a reliable metric.

Research on the Correlation Between rs2110385 Polymorphisms of the Visfatin Gene and Nonproliferative Diabetic Retinopathy

Objective: To investigate the association between rs2110385 polymorphisms of the visfatin gene and the risk of type 2 diabetic retinopathy (DR). Methods: 172 Han subjects were selected from Xi’an Shaanxi Province；140 patients with type 2 diabetes mellitus (T2DM) and 32 normal controls (NC) were selected from our hospital. Patients with diabetes were divided into a non-DR group (T2DM) (n = 69) and a nonproliferative diabetic retinopathy Group (DR) (n =71) after dilated fundus photography and fundus fluorescein angiography. rs2110385/Alu Ⅰ genotypes were detected by standardized polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and the differences in the detection rates of different genotypes in the above populations were compared. Results: 1) The visfatin level in the DR Group was significantly higher than that in the NC and T2DM groups (P &lt; 0.05). 2) The frequency of GG genotype and G allele of rs2110385 in the DR Group were higher than those in the T2DM and NC groups (80.3, 69.6, 50.0, 86.6, 79, 65.6, P &lt; 0.05). 3) There were significant differences in allele frequency and genotype frequency distribution of rs2110385 between the DR Group and the NC group (P &lt; 0.01). Conclusion: Visfatin increased in the nonproliferative diabetic retinopathy group and could be a potential indicator for the clinical prediction of DR. The G allele of the rs2110385 polymorphic site may be related to the risk of DR.

Abstract A016: The breast cancer genome and its association with the breast tissue bacteriome

Abstract BC is the most prevalent and leading fatal cancer type in women, yet the causes of most cases are unknown, indicating the necessity of deciphering contributing factors to quicken detection and inform therapeutic options. This research explores the relationship between the breast cancer (BC) genome and breast tissue bacteriome. BC forms in microenvironments in which genes and bacteria are in close proximity and research evidences gene-bacteria communication, but the relationship between the BC genome and the changing breast tissue bacteriome is not well understood. We hypothesized that genetic variation in the top ten genes commonly linked to BC: BRCA1, BRCA2, PTEN, TP53, PALB2, CHEK2, ATM, BRIP1, BARD1 , and STK11 would be associated with variations in the breast tissue bacteriome. We conducted 30X whole genome sequencing on 60 breast tissue samples (healthy, H (n=15), pre-diagnostic, PD (n=15), tumor, T (n=15), and adjacent normal, AN (n=15)) donated to the Susan G. Komen and Indiana University Simon Cancer Center Tissue Banks. These same samples were previously analyzed for microbiome composition and function using 16S rRNA sequencing (published in mSystems, 2022). Following sequence pre-processing, variant calling, and alternate allele frequency calculation by the UC Davis Bioinformatics Core, we selected only high and moderate variants for these genes with a quality score ≥ 55 for further analysis. Of the ten we intended to analyze, only 8 met these criteria within our data set: BRCA1, BRCA2, PTEN, TP53, PALB2, CHEK2, ATM , and BRIP1 . We ran generalized linear models to select variants with differences in alternate allele frequency among the tissue types (H, PD, AN, T, p ≤ 0.2). Alternate allele frequencies and genotypes of these variants that passed this filter were then associated with bacterial ASVs deemed differentially abundant relative to the H tissue type (mSystems, 2022) using MaAsLin2. Three BC-linked genes BRCA1, TP53 , and ATM show significant associations with the taxa, Muribaculaceae, Alcaligenes faecalis, Oceanobacillus, Romboutsia, Pseudomonas , and Pseudomonas fragi , at a p-value ≤ 0.01 and q-value ≤ 0.25. These genera belong to phyla (Bacteroides, Firmicutes, and Actinobacteria) which have been shown to either interact directly with the genome to produce cancer-causing DNA damage, or to be associated with other types of cancer, suggesting their likely role in tumorigenesis. The discovered associations further our understanding of the genetic and microbial determinants of breast cancer and may highlight the breast tissue bacteriome as a biomarker of BC. Citation Format: Ariana McCaw, Rachel Jiang, Lindsey Marian, Leah Stiemsma. The breast cancer genome and its association with the breast tissue bacteriome [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A016.

Analysis of CHIP-Related Mutation and Risk of Cardio-Cerebrovasculars Events in Patients with Myeloproliferative Neoplasms

To analyze the mutant spectrum of clonal hematopoiesis of indeterminate potential (CHIP) related mutations and clinical characteristics and to explore the correlation and the possible mechanism between CHIP-related mutations and cardio-cerebrovasculars events (CCEs) in patients with myeloproliferative neoplasms (MPNs). The clinical data and next-generation sequencing results of 73 MPN patients in Beijing Anzhen Hospital from August 2019 to July 2022 were retrospectively analyzed. Statistical analyses were conducted by multivariate logistic regression for the effects of CHIP-related mutations and inflammatory cytokines on CCEs for MPNs patients. Fifty-five cases of MPN (75.3%) showed positive in CHIP-related genes. There was no significant difference in variant allele frequency of CHIP-related gene between essential thrombocythemia (ET) and polycythemia vera (PV). CHIP-related gene mutations were mainly single gene mutations, with mutation rate from high to low as JAK2V617F (63.0%, 46/73), ASXL1 (16.4%, 12/73), TET2 (11.0%, 8/73), DNMT3A (9.6%, 7/73), SRSF2 (6.9%, 5/73), SF3B1 (4.1%, 3/73), TP53(1.4%, 1/73) and PPM1D (1.4%, 1/73). The mutation rate of CHIP-related genes in MPN patients >60 years old was significantly higher than that in the patients ≤60 years old ［91.7%(33/36) vs 59.5%(22/37)］. CCEs occurred in 27 MPNs patients (37.0%, MPNs/CCEs), and 5 had recurrent CCEs, all of which were arterial events. Age (62.8±12.8 years vs 53.9±15.8 years, P =0.015), IL-1β level (17.7±26.0 vs 4.3±8.6, P =0.012), IL-8 level (360.7±598.6 vs 108.3±317.0, P =0.045), the proportion of the patients with thrombosis history (29.6% vs 2.2%, P =0.020), and the detection rate of CHIP-related mutations (88.9% vs 67.4%, P =0.040) in the group with CCEs were higher than those in the group without CCEs. Multivariate Logistic regression analysis showed that age（OR =0.917， 95%CI ：0.843-0.999, P =0.047）, thrombosis history (OR =34.148， 95%CI ：2.392-487.535, P =0.009), any CHIP-related mutations(OR =16.065， 95%CI ：1.217-212.024， P =0.035), and elevated level of IL-1β (OR =0.929， 95%CI ：0.870-0.992， P =0.027) were independent risk factors for MPNs/CCEs. CHIP-related gene mutations were not associated with CCEs in MPN patients, but DNMT3A (OR =88.717， 95%CI ：2.690-292.482， P =0.012) and ASXL1 (OR =7.941， 95%CI ：1.045-60.353， P =0.045) were independent risk factors for CCEs in PV. There is a higher mutation rate of CHIP-related genes in MPN patients, especially those over 60 years old. Older age, thrombosis history, CHIP-related mutations and IL-1β elevated levels are independent risk factors for CCEs in MPN. DNMT3A and ASXL1 mutations are independent risk factors for CCEs in PV patients. CHIP-related gene mutations and inflammatory cytokine IL-1 β elevated levels may be the novel risk factors for CCEs in MPN.

Mass-Rearing Conditions Do Not Always Reduce Genetic Diversity: The Case of the Mexican Fruit Fly, Anastrepha ludens (Diptera: Tephritidae).

The application of the sterile insect technique (SIT) requires the adaptation of insects to mass-rearing conditions. It is generally accepted that this adaptation may include a reduction in genetic diversity and an associated loss of desirable characteristics for the effective performance of sterile insects in the field. Here, we compare the genetic diversity of two mass-reared strains of the Mexican fruit fly, Anastrepha ludens, and a wild (WIL) population collected near Tapachula, Mexico, using seven DNA microsatellites as molecular genetic markers. The mass-reared strains were a bisexual laboratory strain (LAB) with approximately 130 generations under mass-rearing and a genetic sexing strain, Tapachula-7 (TA7), also under mass-rearing for 100 generations. Our results revealed an overall low level of genetic differentiation (approximately 15%) among the three strains, with the LAB and WIL populations being genetically most similar and TA7 most genetically differentiated. Although there were some differences in allele frequencies between strains, our results show that overall, the adaptation to mass-rearing conditions did not reduce genetic variability compared to the wild sample in terms of heterozygosity or allelic richness, nor did it appear to alter the level of inbreeding with respect to the wild populations. These results are contrary to the general idea that mass-rearing always results in a reduction in genetic diversity. Overall, our findings can contribute to a better understanding of the impact that adaptation to mass-rearing conditions may have on the genetic make-up of strains.

Association of polymorphism (RS1800896) of IL-10 gene and IL-10 gene expression in ovarian cancer patients from Georgia

Background/Aim: Ovarian cancer is one of the most important causes of tumour-associated mortality and morbidity in women. Some genetic alterations, determining predisposition to ovarian cancer have already been identified, but these are mostly syndrome-associated cases, most ovarian tumours are still regarded as sporadic. The aim of this research was to identify new predisposing factors that might increase ovarian cancer risk. Genetic variants of IL-10 gene in patients with ovarian cancer was analysed. Methods: Forty-eight patients with ovarian cancer along with 48 agematched controls were included in the study. Single nucleotide polymorphism (SNP) genotyping and gene expression assays for IL-10 were performed using TaqMan assay (Thermo Scientific, USA). The selected SNP was rs1800896 upstream of IL-10 gene (IL-10-1082). All statistical analyses were performed by GraphPad Prism 9.3.1 for Mac. Results: The genotype distributions of IL-10 gene polymorphisms among cancer and control groups were all according to the expected Hardy-Weinberg equilibrium. There was no statistically significant difference in frequency of genotypes and alleles between the two study groups (p &gt; 0.05). In another analysis, the samples were grouped according to the polymorphic variant IL-10 (-1082) A/G. Subjects having the homozygous variant (A/A) had lower IL-10 mRNA levels than those with the homozygous wild (G/G) genotype in both, ovarian cancer patients and controls, p &lt; 0.05. mRNA levels on IL-10 were different among cases and controls (p &lt; 0.05). Patients with ovarian cancer had higher level of mRNA for IL-10. Conclusions: These results support the theory that IL-10 gene expression levels differ in patients with and without ovarian cancer. Polymorphic variant IL-10 (-1082) A/G couldn't be confirmed to explain this difference in gene expression levels.

Identification of Breed-Specific SNPs in Ethiopian Indigenous and European Beef Cattle Breeds and how they May Influence Adaptation and Selection Signatures

Background: Understanding the genetic foundation of locally adapted indigenous cattle breeds is critical information for developing appropriate genetic improvement and conservation initiatives. To investigate breed-specific SNPs, and minor allele frequency of three Ethiopian cattle breeds Begait, (n = 40), Boran (n = 40), and Fogera (n = 43) were genotyped with 80K SNP array. Three European beef cattle breeds (Angus, n = 42), Hereford (n = 35), and Charolais (n = 37) were also used for comparison. Results: The average minor allele frequency was 0.19 ± 0.17, 0.20 ± 0.17, 0.21± 0.17, 0.31 ± 0.13, 0.32 ± 0.12, 0.32 ± 0.13 for Angus, Herford, Charolais, Boran, Fogera, and Begait cattle, respectively. Minor allele frequency difference was observed between Ethiopian indigenous and European beef cattle breeds. Across the Ethiopian and European cattle breeds, a common variant minor allele frequency (≥0.10 and ≤ 0.5) accounted 94% and 62%, respectively. A total of 7759 and 48 SNPs were identified as breed-specific in Ethiopian cattle breeds and European beef cattle breeds respectively. These SNPs resided with 3364 genes for Ethiopian cattle breeds and 17 genes for European beef cattle breeds. Interestingly important biological processes and pathways related to tropical adaptation in Ethiopian cattle populations were identified through gene Ontology analysis. Conclusions: The higher minor allele frequency and breed-specific SNPs detected in Ethiopian indigenous breeds show the presence of high genetic variability. This genetic variation in Ethiopian cattle breeds is used as a potential source for future breeding programs.