Differences In Minor Allele Frequencies Research Articles

Comprehensive whole-genome analyses of the UK Biobank reveal significant sex differences in both genotype missingness and allele frequency on the X chromosome.

The UK Biobank is the most used dataset for genome-wide association studies (GWAS). GWAS of sex, essentially sex differences in minor allele frequencies (sdMAF), has identified autosomal SNPs with significant sdMAF, including in the UK Biobank, but the X chromosome was excluded. Our recent report identified multiple regions on the X chromosome with significant sdMAF, using short-read sequencing of other datasets. We performed a whole genome sdMAF analysis, with ~410k white British individuals from the UK Biobank, using array genotyped, imputed or exome sequencing data. We observed marked sdMAF on the X chromosome, particularly at the boundaries between the pseudo-autosomal regions (PAR) and the non-PAR (NPR), as well as throughout the NPR, consistent with our earlier report. A small fraction of autosomal SNPs also showed significant sdMAF. Using the centrally imputed data, which relied mostly on low-coverage whole genome sequence, resulted in 2.1% of NPR SNPs with significant sdMAF. The whole exome sequencing also displays sdMAF on the X chromosome, including some NPR SNPs with heterozygous genotype calls in males. Genotyping, sequencing and imputation of X chromosomal SNPs requires further attention to ensure the integrity for downstream association analysis.

Genetic Variants in WNT16 and PKD2L1 Locus Affect Heel Ultrasound Bone Stiffness: Analyses from the General Population and Patients Evaluated for Osteoporosis.

Osteoporosis, a complex chronic disease with increasing prevalence, is characterised by reduced bone mineral density (BMD) and increased fracture risk. The high heritability of BMD suggests substantial impact of the individual genetic disposition on bone phenotypes and the development of osteoporosis. In the past years, genome-wide association studies (GWAS) identified hundreds of genetic variants associated with BMD or osteoporosis. Here, we analysed 1103 single nucleotide polymorphisms (SNPs), previously identified as associated with estimated BMD (eBMD) in the UK Biobank. We assessed whether these SNPs are related to heel stiffness index obtained by quantitative ultrasound in 5665 adult participants of the Study of Health in Pomerania (SHIP). We confirmed 45 significant associations after correction for multiple testing. Next, we analysed six selected SNPs in 631 patients evaluated for osteoporosis [rs2707518 (CPED1/WNT16), rs3779381 (WNT16), rs115242848 (LOC101927709/EN1), rs10239787 (JAZF1), rs603424 (PKD2L1) and rs6968704 (JAZF1)]. Differences in minor allele frequencies (MAF) of rs2707518 and rs3779381 between SHIP participants (higher MAF) and patients evaluated for osteoporosis (lower MAF) indicated a protective effect of the minor allele on bone integrity. In contrast, differences in MAF of rs603424 indicated a harmful effect. Co-localisation analyses indicated that the rs603424 effect may be mediated via stearoyl-CoA desaturase (SCD) expression, an enzyme highly expressed in adipose tissue with a crucial role in lipogenesis. Taken together, our results support the role of the WNT16 pathway in the regulation of bone properties and indicate a novel causal role of SCD expression in adipose tissue on bone integrity.

MAP3K19 regulatory variation in populations with African ancestry may increase COVID-19 severity

To identify ancestry-linked genetic risk variants associated with COVID-19 hospitalization, we performed an integrative analysis of two genome-wide association studies and resolved four single nucleotide polymorphisms more frequent in COVID-19-hospitalized patients with non-European ancestry. Among them, the COVID-19 risk SNP rs16831827 shows the largest difference in minor allele frequency (MAF) between populations with African and European ancestry and also shows higher MAF in hospitalized COVID-19 patients among cohorts of mixed ancestry (odds ratio [OR]= 1.20, 95% CI: 1.10-1.30) and entirely African ancestry (OR= 1.30, 95% CI: 1.02-1.67). rs16831827 is an expression quantitative trait locus of MAP3K19. MAP3K19 expression is induced during ciliogenesis and most abundant in ciliated tissues including lungs. Single-cell RNA sequencing analyses revealed that MAP3K19 is highly expressed in multiple ciliated cell types. As rs16831827∗T is associated with reduced MAP3K19 expression, it may increase the risk of severe COVID-19 by reducing MAP3K19 expression.

The impact of QTL sharing and properties on multi-breed GWAS in cattle: a simulation study

Context Genome-wide association studies (GWAS) and meta-analyses can be used to detect variants that affect quantitative traits. Multi-breed GWAS may lead to increased power and precision compared with within-breed GWAS. However, not all causal variants segregate in all breeds, and variants that segregate in multiple breeds may have different allele frequencies in different breeds. It is not known how differences in minor allele frequency (MAF) affect multi-breed GWAS and meta-analyses. Aims Our aim was to study the impact of differences in MAF at causal variants on mapping power and precision. Methods We used real imputed sequence data to simulate quantitative traits in three dairy cattle breeds. Causal variants (QTN) were simulated according to the following three scenarios: variants with a similar MAF in all breeds, variants with a lower MAF in one breed than the other, and variants that each only segregated in one of the breeds. We analysed the simulated quantitative traits with three methods to compare mapping power and precision: within-breed GWAS, multi-breed GWAS and meta-analysis. Key results Our results indicated that the multi-breed analyses (multi-breed GWAS or meta-analysis) detected similar or more QTN than did within-breed GWAS, with improved mapping precision in most scenarios. However, when MAF differed between breeds, or variants were breed specific, the advantage of the multi-breed analyses over within breed GWAS decreased. Regardless of the type of QTN (similar MAF in all breeds, different MAF in different breeds, or only segregating in one breed), multi-breed GWAS and meta-analyses performed similar or better than did within-breed GWAS, demonstrating the benefits of multi-breed GWAS. We did not find large differences between the results obtained with the meta-analysis and multi-breed GWAS, confirming that a meta-analysis can be a suitable approximation of a multi-breed GWAS. Conclusions Our results showed that multi-breed GWAS and meta-analysis generally detect more QTN with improved precision than does within-breed GWAS, and that even with differences in MAF, multi-breed analyses did not perform worse than within-breed GWAS. Implications Our study confirmed the benefits of multi-breed GWAS and meta-analysis.

Frequency of functional exonic single-nucleotide polymorphisms and haplotype distribution in the SLCO1B1 gene across genetic ancestry groups in the Qatari population

Organic anion transporting polypeptides (OATP), which are encoded by SLCO genes, participate in the hepatic elimination of drugs and xenobiotics. SLCO1B1 is an important pharmacogenomic gene (encoding OATP1B1) associated with response to the uptake of endogenous compounds, such as statin and bilirubin. Ethnicity of the patient modulates the response to these drugs; the frequency and haplotype data for SLCO1B1 genetic variants in the Arab population is lacking. Therefore, we determined the frequencies of two well-characterized SLCO1B1 single nucleotide polymorphisms (SNP) and haplotypes that affect the OATP1B1 drugs transportation activity in Qatari population. Genotyping data for two SLCO1B1 SNPs (c.388A > G, c.521 T > C) were extracted from whole exome data of 1050 Qatari individuals, who were divided into three ancestry groups, namely Bedouins, Persians/South Asians, and Africans. By way of using Fisher's exact and Chi-square tests, we evaluated the differences in minor allele frequency (MAF) of the two functional SNPs and haplotype frequencies (HF) among the three ancestry groups. The OATP1B1 phenotypes were assigned according to their function by following the guidelines from the Clinical Pharmacogenetics Implementation Consortium for SLCO1B1 and Simvastatin-Induced Myopathy.The MAF of SLCO1B1:c.388A > G was higher compared to that of SLCO1B1:c.521 T > C in the study cohort. It was significantly high in the African ancestry group compared with the other two groups, whereas SLCO1B1:c.521 T > C was significantly low in the African ancestry group compared with the other two groups. The SLCO1B1 *15 haplotype had the highest HF, followed by *1b, *1a, and *5. Only the SLCO1B1 *5 haplotype showed no significant difference in frequency across the three ancestry groups. Furthermore, we observed that the OATP1B1 normal function phenotype accounted for 58% of the Qatari individuals, the intermediate function phenotype accounted for 35% with significant differences across the ancestry groups, and the low function phenotype accounted for 6% of the total Qatari individuals with a higher trend observed in the Bedouin group.The results indicate that the phenotype frequencies of the OATP1B1 intermediate and low function in the Qatari population appear at the higher end of the frequency range seen worldwide. Thus, a pharmacogenetic screening program for SLCO1B1 variants may be necessary for the Qatari population.

Major sex differences in allele frequencies for X chromosomal variants in both the 1000 Genomes Project and gnomAD.

An unexpectedly high proportion of SNPs on the X chromosome in the 1000 Genomes Project phase 3 data were identified with significant sex differences in minor allele frequencies (sdMAF). sdMAF persisted for many of these SNPs in the recently released high coverage whole genome sequence of the 1000 Genomes Project that was aligned to GRCh38, and it was consistent between the five super-populations. Among the 245,825 common (MAF>5%) biallelic X-chromosomal SNPs in the phase 3 data presumed to be of high quality, 2,039 have genome-wide significant sdMAF (p-value <5e-8). sdMAF varied by location: non-pseudo-autosomal region (NPR) = 0.83%, pseudo-autosomal regions (PAR1) = 0.29%, PAR2 = 13.1%, and X-transposed region (XTR)/PAR3 = 0.85% of SNPs had sdMAF, and they were clustered at the NPR-PAR boundaries, among others. sdMAF at the NPR-PAR boundaries are biologically expected due to sex-linkage, but have generally been ignored in association studies. For comparison, similar analyses found only 6, 1 and 0 SNPs with significant sdMAF on chromosomes 1, 7 and 22, respectively. Similar sdMAF results for the X chromosome were obtained from the high coverage whole genome sequence data from gnomAD V 3.1.2 for both the non-Finnish European and African/African American samples. Future X chromosome analyses need to take sdMAF into account.

Ethnic Diversity and Warfarin Pharmacogenomics.

Warfarin has remained the most commonly prescribed vitamin K oral anticoagulant worldwide since its approval in 1954. Dosing challenges including having a narrow therapeutic window and a wide interpatient variability in dosing requirements have contributed to making it the most studied drug in terms of genotype-phenotype relationships. However, most of these studies have been conducted in Whites or Asians which means the current pharmacogenomics evidence-base does not reflect ethnic diversity. Due to differences in minor allele frequencies of key genetic variants, studies conducted in Whites/Asians may not be applicable to underrepresented populations such as Blacks, Hispanics/Latinos, American Indians/Alaska Natives and Native Hawaiians/other Pacific Islanders. This may exacerbate health inequalities when Whites/Asians have better anticoagulation profiles due to the existence of validated pharmacogenomic dosing algorithms which fail to perform similarly in the underrepresented populations. To examine the extent to which individual races/ethnicities are represented in the existing body of pharmacogenomic evidence, we review evidence pertaining to published pharmacogenomic dosing algorithms, including clinical utility studies, cost-effectiveness studies and clinical implementation guidelines that have been published in the warfarin field.

Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations

BackgroundStructural variants (SV) are causative for some prominent phenotypic traits of livestock as different comb types in chickens or color patterns in pigs. Their effects on production traits are also increasingly studied. Nevertheless, accurately calling SV remains challenging. It is therefore of interest, whether close-by single nucleotide polymorphisms (SNPs) are in strong linkage disequilibrium (LD) with SVs and can serve as markers. Literature comes to different conclusions on whether SVs are in LD to SNPs on the same level as SNPs to other SNPs. The present study aimed to generate a precise SV callset from whole-genome short-read sequencing (WGS) data for three commercial chicken populations and to evaluate LD patterns between the called SVs and surrounding SNPs. It is thereby the first study that assessed LD between SVs and SNPs in chickens.ResultsThe final callset consisted of 12,294,329 bivariate SNPs, 4,301 deletions (DEL), 224 duplications (DUP), 218 inversions (INV) and 117 translocation breakpoints (BND). While average LD between DELs and SNPs was at the same level as between SNPs and SNPs, LD between other SVs and SNPs was strongly reduced (DUP: 40%, INV: 27%, BND: 19% of between-SNP LD). A main factor for the reduced LD was the presence of local minor allele frequency differences, which accounted for 50% of the difference between SNP – SNP and DUP – SNP LD. This was potentially accompanied by lower genotyping accuracies for DUP, INV and BND compared with SNPs and DELs. An evaluation of the presence of tag SNPs (SNP in highest LD to the variant of interest) further revealed DELs to be slightly less tagged by WGS SNPs than WGS SNPs by other SNPs. This difference, however, was no longer present when reducing the pool of potential tag SNPs to SNPs located on four different chicken genotyping arrays.ConclusionsThe results implied that genomic variance due to DELs in the chicken populations studied can be captured by different SNP marker sets as good as variance from WGS SNPs, whereas separate SV calling might be advisable for DUP, INV, and BND effects.

SAT-310 Analysis of the Influence of Glucocorticoid Receptor Gene Polymorphism BCL-1 on Clinical and Psychiatric Manifestations in Brazilian Patients with Cushing’s Disease

In Cushing’s disease (CD), the spectrum of clinical manifestations is considerably wide, and the intensity of symptoms does not correlate with the magnitude of cortisol hypersecretion or with pituitary tumor size. Polymorphisms in the gene that encodes the glucocorticoid receptor (GR), an essential regulator of the hypothalamic-pituitary-adrenal axis, have been linked to some psychiatric disorders. Considering that psychiatric manifestations are present in nearly all patients with hypercortisolism, we hypothesized a possible correlation of polymorphisms in the GR gene and clinical and psychiatric manifestations, in CD. To investigate the frequency and clinical implications of the GR gene polymorphism Bcl-1 in patients with CD, we conducted a cross-sectional, case-controlled study. Fifty-three Brazilian patients with CD aged between 12 and 75 years and one hundred healthy controls aged between 42 and 67 years, of both genders, who provided written informed consent, were enrolled. Blood samples were collected from patients for DNA extraction and sequencing for analysis of the GR gene polymorphism Bcl-1. Clinical data (obesity, skin lesions, muscle weakness, hypertension, diabetes, hypokalemia, and sex-related disorders) were obtained through retrospective analysis of medical records, appointment with endocrinologist and with psychiatrist. Mini International Neuropsychiatric Interview, scales self-applicable of anxiety and depression were used to address psychiatric conditions. From the 53 patients studied, 48 were women (90,56%), and 16 patients had macroadenoma (2 of them had tumors larger than 4 cm). Overall frequencies of the Minor Allele for Bcl-1 polymorphism, which corresponds to the risk allele for psychiatric illness in the normal population, did not significantly differ between CD patients (67.92%) and controls (74.00%). Similarly, differences in Minor Allele Frequencies among subgroups of patients presenting with psychiatric and clinical manifestations of CD were not statistically significant. Although data from the literature strongly suggests a correlation between Bcl-1 polymorphism with psychiatric disorders (especially depression) in the normal population, this association was not observed in our cohort of patients with CD. More studies are needed to better clarify a possible role for GR gene polymorphisms as modifiers of the spectrum of psychiatric and clinical manifestations of CD.

Association of Genetic Variants of Dopamine and Serotonin In Schizophrenia

Several studies indicated that antipsychotic treatment response and side effect manifestation can be different due to inter-individual variability in genetic variations. Here we perform a case-control study to explore a potential association between schizophrenia and variants within the antipsychotic drug molecular targets (DRD1, DRD2, DRD3, HTR2A, HTR6) and metabolizing enzymes (CYP2D6, COMT) genes in Armenian population including also analysis of their possible relationship with disease clinical symptoms. A total of 18 SNPs was studied in patients with schizophrenia (n=78) and healthy control subjects (n=77) using MassARRAY genotyping. We found that two studied genetic variants, namely DRD2 rs4436578*C and HTR2A rs6314*A are underrepresented in the group of patients compared to healthy subjects. After the correction for multiple testing, the rs4436578*C variant remained significant while the rs6314*A reported borderline significance. No significant differences in minor allele frequencies for other studied variants were identified. Also, a relationship between the genotypes and age of onset as well as disease duration has been detected. The DRD2 rs4436578*C genetic variant might have protective role against schizophrenia, at least in Armenians.

The Cancer Prevention Project of Philadelphia: preliminary findings examining diversity among the African diaspora

ABSTRACT Objective: Cancer mortality inequity among persons of African Ancestry is remarkable. Yet, Black inclusion in cancer biology research is sorely lacking and warrants urgent attention. Epidemiologic research linking African Ancestry and the African Diaspora to disease susceptibility and outcomes is critical for understanding the significant and troubling health disparities among Blacks. Therefore, in a cohort of diverse Blacks, this study examined differences in genetic ancestry informative markers (AIMs) in the DNA repair pathway and the cancer related biomarker 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL). Methods: Participants completed a questionnaire and provided bio-specimens. AIMs in or around DNA repair pathway genes were analyzed to assess differences in minor allele frequency (MAF) across the 3 ethnic subgroups. NNAL concentration in urine was measured among current smokers. Results: To date the cohort includes 852 participants, 88.3% being Black. Of the 752 Blacks, 51.3% were US-born, 27.8% were Caribbean-born, and 19.6% were Africa-born. Current and former smokers represented 14.9% and 10.0%, respectively. US-born Blacks were more likely to be smokers and poor metabolizers of NNAL. Two-way hierarchical clustering revealed MAF of AIMs differed across the 3 ethnic subgroups. Conclusion: Our findings are consistent with the emerging literature demonstrating Black heterogeneity underscoring African Ancestry genetic subgroup differences – specifically relevant to cancer. Further investigations, with data harmonization and sharing, are urgently needed to begin to map African Ancestry cancer biomarkers as well as race, and race by place\\region comparative biomarkers to inform cancer prevention and treatment in the era of precision medicine.

Abstract 228: Association analysis across different populations identifies 26 new cutaneous melanoma risk loci

Abstract Heritability of cutaneous melanoma is among the highest across cancer types and is mostly determined by common, noncoding genetic variants. Previous genome-wide association studies (GWAS), mostly including subjects from Australia and Northern European countries, had identified twenty genetic loci associated with melanoma risk. To characterize the genetic landscape of cutaneous melanoma across different populations, we conducted a new association study in Southern European countries including 6,043 melanoma cases and 10,383 controls from the MelaNostrum Consortium. Moreover, we largely expanded the analyses of melanoma cases and controls from other populations, for a total of 27,450 histologically confirmed melanoma cases and 49,888 controls from Northern Europe, Southern Europe, USA and Australia. Imputation was done using the Haplotype Reference Consortium as a reference panel. We assessed the association between cutaneous melanoma risk and single-nucleotide polymorphisms (SNPs) adjusting for country and ancestry-informative principal components. We identified 26 new genetic loci associated with melanoma risk achieving genome-wide significance. The pigmentation pathway, with TYRP1 and MITF, and the telomere-related pathway with RTEL1, TERC, and POT1 among the candidate genes, continued to show an important role for melanoma susceptibility. Additional candidate pathways emerged, including signaling (with GPRC5A and DOCK8), cell-cell junction (with CDH1), immune-related functions (with DCST2, involved in antigen processing), transcriptional regulation (with FOXD3, which represses MITF expression), or tumor-suppressor genes (TP53). Adding genotype data from 6,130 self-reported melanoma cases in a sensitivity analysis identified eight additional novel genetic loci involved in the HLA region, signaling transduction and transcription factor functions. A combined analysis of the melanoma GWAS with the GWAS of pigmentation characteristics from the UK Biobank including 500,000 UK persons, and with a GWAS of nevus density including over 52,000 persons, revealed substantial overlap across phenotypes. Although the effect size of the SNPs on melanoma risk was consistent across populations, substantial differences in minor allele frequency (MAF) were observed in pigmentation-related genes between Northern and Southern European populations; for example, MC1R, SLC45A2, and ASIP SNP MAF was 8.2, 3.1 and 14.2 in Northern and 2.6, 8.8, and 5.5 in Southern European subjects, respectively. Additional analyses based on melanoma histologic subtypes and body site distribution are ongoing. These results provide further insight into genetic susceptibility to cutaneous melanoma and provide the opportunity for genetic risk scores in risk-prediction models for early detection and targeted prevention of the disease. Citation Format: Cristina Pellegrini, Matthew Law, Mark Iles, Mitch Machiela, Alex Stratigos, Tongwu Zhang, Kevin Brown, Julia Newton-Bishop, Nick Hayward, Nick Martin, Alisa Goldstein, Rose Yang, Stephen Chanock, Florence Demenais, Susana Puig, Eduardo Nagore, Jianxin Shi, Tim Bishop, Stuart McGregor, Maria Teresa Landi, GenoMEL Consortium, MelaNostrum Consortium. Association analysis across different populations identifies 26 new cutaneous melanoma risk loci [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 228.

Age-Related Hearing Impairment Associated NAT2, GRM7, GRHL2 Susceptibility Gene Polymorphisms and Haplotypes in Roma and Hungarian Populations.

Age-related hearing impairment (ARHI) is the most frequent sensory disease in the elderly, which is caused by an interaction between genetic and environmental factors. Here we examined the ethnic differences, allele and genotype frequencies of the NAT2, GRM7, and GRHL2 genes pooled samples of healthy Hungarian and healthy and hearing impaired Roma people. Study populations of healthy Hungarian and Roma subjects were characterized for the rs1799930 NAT2, rs11928865 GRM7, rs10955255, rs13263539, and rs1981361 GRHL2 polymorphisms and deaf Roma subjects were characterized for the rs1799930 NAT2, rs13263539, and rs1981361 GRHL2 using a PCR-RFLP method. We found significant differences in minor allele frequencies for GRHL2 rs13263539 and rs1981361 polymorphism between healthy Roma and Hungarian samples (37.9% vs. 51.0% and 43.6% vs. 56.2%, respectively; p < 0.05). The differences of homozygous genotype of GRHL2 rs13263539 and rs1981361 variants, values were also significantly different (13.0% vs. 25.3% and 16.5 vs. 32.3%; p < 0.05). The NAT2 rs1799930 homozygous genotype was 14.0% in healthy Romas and 7.7% in Hungarians, while the minor A allele frequency was 38.0% and 26.7% in Roma and Hungarian population, respectively (p < 0.05). Furthermore, the frequency of GGT, GAC and GAT haplotypes was significantly higher in the Hungarian population than in healthy Roma (1.87 vs. 4.47%, 0.91 vs. 2.07% and 1.15 vs. 5.51%, respectively; p < 0.008). Present study revealed significant interethnic differences in allele polymorphisms of NAT2, GRM7 and GRHL2 exhibit quite marked ethnic differences in Roma populations that might have important implications for the preventive and therapeutic treatments in this population.

Abstract 13051: Unbiased Estimate of Heritability of CAD Before and After Adjustment for Traditional Risk Factors in Five NHLBI Cohorts

Introduction: The relative contribution of traditional risk factors (TRFs) to the genesis of CAD remains uncertain. Cohort studies report a high population attributable risk for TRFs, but only a third of the GWAS loci for CAD mediate risk through TRFs. Furthermore, these loci explain a small fraction of the overall heritability of CAD based on twin studies making it unclear whether these patterns will persist and whether estimates from twin studies are inflated. Hypothesis: Unbiased estimates of narrow sense heritability ( h 2 ) of CAD using contemporary analytic techniques applied to very distantly related individuals prior to and after adjustment of TRFs have not yet been reported. We hypothesized that such estimates would confirm a high heritability of CAD and that a substantial proportion of the genetic variance would be independent of TRFs. Methods: We used ~7 million genome wide imputed single nucleotide polymorphisms (SNPs) and a mixed linear model implemented in Genome-wide Complex Trait Analysis to estimate the h 2 of CAD from genomic relatedness among participants of five prospective NHLBI cohorts - ARIC, CHS, FHS, MESA, and WHI. To guard against bias from differences in minor allele frequencies (MAF) as well as region-specific heterogeneity in linkage disequilibrium (LD) between variants used in our analyses and causal variants, we used MAF and LD stratified multicomponent genetic restricted maximum likelihood. We ran 2 models assuming a population prevalence of 8%. The first model was not adjusted for any covariates and the second was adjusted for all TRFs as well as use of antihypertensive and statin drugs. Results: We analyzed a total of 23,522 participants including 3520 that developed incident clinical CAD during follow up. CAD h 2 was 39% (±3.1%) in our unadjusted model and 32% (±3.2%) in our fully adjusted model. A large majority (~95%) of the heritability in both models was derived from common SNPs with MAF &gt;1%. Conclusions: CAD is a moderately heritable trait with a large fraction of its genetic variance being a result of processes unrelated to TRFs. Prior family based estimates of the h 2 of CAD do not appear biased upwards. Consistent with many other complex traits, a majority of the genetic variance can be explained by common SNPs with very modest effects.

Identifying Genetic Variants in Adolescents With Oppositional Defiant Disorders and/or Conduct Disorders: A Brief Report

To add to diversity in our state biobank, we explored the feasibility of collecting genetic material from adolescents with oppositional defiant disorder (ODD) and/or conduct disorder (CD) and their family members. We also preliminarily explored genetic factors associated with ODD and/or CD by comparing participant data to 1000 Genome Project data on minor allele frequencies. Adolescents with ODD and/or CD and family members provided saliva samples for genetic testing. We evaluated five single-nucleotide polymorphisms (SNPs), respectively, in the dopamine receptor subtype D2, dopamine receptor subtype D3, dopamine beta-hydroxylase, dopamine transporter gene SLC6A3, and alpha-2-adrenergic receptor genes. Fisher's exact tests were used to examine differences in minor allele frequencies for each SNP. Thirty-one viable samples were genotyped from 15 affected adolescents and 16 unaffected family members; the 60% consent rate reflected high feasibility. Compared with the 1000 Genome Project frequencies, affected adolescents had higher frequencies of the genetic variant in the dopamine receptor subtype D2 (p = .05) and dopamine beta-hydroxylase (p = 0.03), but not of the other three SNPs examined. Collecting genetic materials from an ethnically diverse sample of affected adolescents and their families is feasible. We offer practical suggestions to strengthen the integrity of future research studies.

Increasing the number of single nucleotide polymorphisms used in genomic evaluation of dairy cattle

GeneSeek (Neogen Corp., Lexington, KY) designed a new version of the GeneSeek Genomic Profiler HD BeadChip for Dairy Cattle, which originally had >77,000 single nucleotide polymorphisms (SNP). A set of >140,000 SNP was selected that included all SNP on the existing GeneSeek chip, all SNP used in US national genomic evaluations, SNP that were possible functional mutations, and other informative SNP. Because SNP with a lower minor allele frequency might track causative variants better, 30,000 more SNP were selected from the Illumina BovineHD Genotyping BeadChip (Illumina Inc., San Diego, CA) by choosing SNP to maximize differences in minor allele frequency between a SNP being considered for the new chip and the 2 SNP that flanked it. Single-gene tests were included if their location was known and bioinformatics indicated relevance for dairy cattle. To determine which SNP from the new chip should be included in genomic evaluations, genotypes available from chips already in use were used to impute and evaluate the SNP set. Effects for 134,511 usable SNP were estimated for all breed–trait combinations; SNP with the largest absolute values for effects were selected (5,000 for Holsteins, 1,000 for Jerseys, and 500 each for Brown Swiss and Ayrshires for each trait). To increase overlap with the 60,671 SNP currently used for genomic evaluation, 12,094 more SNP with the largest effects were added. After removing SNP with many parent–progeny conflicts, 84,937 SNP remained. Three cutoff studies were conducted with 3 SNP sets to determine reliability gain over that for parent average when evaluations based on August 2011 data were used to predict December 2014 performance. Across all traits, mean Holstein reliability gains were 32.5, 33.4, and 32.0 percentage points for 60,671, 84,937, and 134,511 SNP, respectively. After genotypes from the new chip became available, the proposed set was reduced from 84,937 to 77,321 SNP to remove SNP that were not included during manufacture, reduce computing time, and improve imputation performance. The set of 77,321 SNP was evaluated using August 2011 data to predict April 2015 performance. Reliability gain over 60,671 SNP was 1.4 percentage points across traits for Holsteins. Improvement over 84,937 SNP was partially the result of 4mo of additional data and genotypes from the new chip. Revision of the SNP set used for genomic evaluation is expected to be an ongoing process to increase evaluation accuracy.

Genetic variations in GPSM3 associated with protection from rheumatoid arthritis affect its transcript abundance.

G protein signaling modulator 3 (GPSM3) is a regulator of G protein-coupled receptor signaling, with expression restricted to leukocytes and lymphoid organs. Previous genome-wide association studies have highlighted single-nucleotide polymorphisms (SNPs rs204989, rs204991) in a region upstream of the GPSM3 transcription start site as being inversely correlated to the prevalence of rheumatoid arthritis (RA) -- this association is supported by the protection afforded to Gpsm3-deficient mice in models of inflammatory arthritis. Here, we assessed the functional consequences of these polymorphisms. We collected biospecimens from 50 volunteers with RA diagnoses, 50 RA-free volunteers matched to the aforementioned group, and 100 unmatched healthy young volunteers. We genotyped these individuals for GPSM3 (rs204989, rs204991), CCL21 (rs2812378), and HLA gene region (rs6457620) polymorphisms, and found no significant differences in minor allele frequencies between the RA and disease-free cohorts. However, we identified that individuals homozygous for SNPs rs204989 and rs204991 had decreased GPSM3 transcript abundance relative to individuals homozygous for the major allele. In vitro promoter activity studies suggest that SNP rs204989 is the primary cause of this decrease in transcript levels. Knockdown of GPSM3 in THP-1 cells, a human monocytic cell line, was found to disrupt ex vivo migration to the chemokine MCP-1.

Genetic predisposition in patients with hypertension and normal ejection fraction to oxidative stress

The role of oxidative stress (OXS) due to myocardial nitric oxide synthase (NOS) uncoupling related to oxidative depletion of its cofactor tetrahydrobiopterin (BH4) emerged in the pathogenesis of heart failure with preserved ejection fraction. We determined the prevalence of six single nucleotide polymorphisms (SNPs) of genes encoding enzymes related to OXS, BH4 metabolism, and NOS function in ≥60-year-old 94 patients with hypertension and 18 age-matched controls with normal ejection fraction. Using echocardiography, 56/94 (60%) patients with hypertension had left ventricular (LV) diastolic dysfunction (HTDD+ group) and 38/94 (40%) patients had normal LV diastolic function (HTDD− group). Four SNPs (rs841, rs3783641, rs10483639, and rs807267) of guanosine triphosphate cyclohydrolase-1, the rate-limiting enzyme in BH4 synthesis, one (rs4880) of manganese superoxide dismutase, and one (rs1799983) of endothelial NOS genes were genotyped using real-time polymerase chain reaction method and Taqman probes. Protein carbonylation, BH4, and total biopterin levels were measured from plasma samples. No between-groups difference in minor allele frequency of SNPs was found. We calculated a genetic score indicating risk for OXS based on the minor allele frequencies of the SNPs. A high genetic risk for OXS was significantly associated with HTDD+ even after adjustment for confounding variables (odds ratio [95% confidence interval]:4.79 [1.12–20.54]; P = .035). In both patient groups protein carbonylation (P < .05 for both), plasma BH4 (P < .01 for both) and in the HTDD+ group total biopterin (P < .05) increased versus controls. In conclusion, in patients with hypertension and normal ejection fraction, a potential precursor of heart failure with preserved ejection fraction, a partly genetically determined increased OXS, seems to be associated with the presence of LV diastolic dysfunction.

Erratum to: Inter-ethnic differences in genetic variants within the transmembrane protease, serine 6 (TMPRSS6) gene associated with iron status indicators: a systematic review with meta-analyses.

Transmembrane protease, serine 6 (TMPRSS6), is likely to be involved in iron metabolism through its pleiotropic effect on hepcidin concentrations. Recently, genome-wide association studies have identified common variants in the TMPRSS6 gene to be linked to anaemia and low iron status. To get a more precise evaluation of identified TMPRSS6 single nucleotide polymorphism associations with iron status in cohorts of differing continental ancestry, we conducted a systematic review with meta-analyses. We searched the literature using HuGE Navigator, Pubmed and Scopus databases for primarily genome-wide association studies using TMPRSS6 as a free term. Fixed-effects meta-analysis was used to obtain summary estimates of associations. Eleven studies comprised Caucasian populations, four included an Asian population and one study included an African-American population. Differences in minor allele frequencies of 8 TMPRSS6 SNPs (rs855791, rs4820268, rs2111833, rs1421312, rs228921, rs228918, rs228919 and rs575620) across ethnic groups were observed, with the MAF of rs855791 significantly higher in Asian populations than in Caucasians (0.55 vs 0.42, P < 0.0001). In the meta-analysis, the A allele of rs855791 was associated with lower Hb and ferritin concentrations in all populations. This allele was also associated with increased serum transferrin receptor and transferrin concentrations. We observed similar associations for the G allele in rs4820268. Clear disparities in associations were found for the African-American population, although not statistically significant. Associations between TMPRSS6 SNPs and anaemia are consistent across Caucasian and Asian populations. This study highlights the need to conduct studies in African populations where iron deficiency is of utmost public health significance.

Inter-ethnic differences in genetic variants within the transmembrane protease, serine 6 (TMPRSS6) gene associated with iron status indicators: a systematic review with meta-analyses.

Transmembrane protease, serine 6 (TMPRSS6), is likely to be involved in iron metabolism through its pleiotropic effect on hepcidin concentrations. Recently, genome-wide association studies have identified common variants in the TMPRSS6 gene to be linked to anaemia and low iron status. To get a more precise evaluation of identified TMPRSS6 single nucleotide polymorphism associations with iron status in cohorts of differing continental ancestry, we conducted a systematic review with meta-analyses. We searched the literature using HuGE Navigator, Pubmed and Scopus databases for primarily genome-wide association studies using TMPRSS6 as a free term. Fixed-effects meta-analysis was used to obtain summary estimates of associations. Eleven studies comprised Caucasian populations, four included an Asian population and one study included an African-American population. Differences in minor allele frequencies of 8 TMPRSS6 SNPs (rs855791, rs4820268, rs2111833, rs1421312, rs228921, rs228918, rs228919 and rs575620) across ethnic groups were observed, with the MAF of rs855791 significantly higher in Asian populations than in Caucasians (0.55 vs 0.42, P<0.0001). In the meta-analysis, the A allele of rs855791 was associated with lower Hb and ferritin concentrations in all populations. This allele was also associated with increased serum transferrin receptor and transferrin concentrations. We observed similar associations for the G allele in rs4820268. Clear disparities in associations were found for the African-American population, although not statistically significant. Associations between TMPRSS6 SNPs and anaemia are consistent across Caucasian and Asian populations. This study highlights the need to conduct studies in African populations where iron deficiency is of utmost public health significance.