Genome Association Research Articles

Peripheral Anomalies in USH2A Cause Central Auditory Anomalies in a Mouse Model of Usher Syndrome and CAPD.

Central auditory processing disorder (CAPD) is associated with difficulties hearing and processing acoustic information, as well as subsequent impacts on the development of higher-order cognitive processes (i.e., attention and language). Yet CAPD also lacks clear and consistent diagnostic criteria, with widespread clinical disagreement on this matter. As such, identification of biological markers for CAPD would be useful. A recent genome association study identified a potential CAPD risk gene, USH2A. In a homozygous state, this gene is associated with Usher syndrome type 2 (USH2), a recessive disorder resulting in bilateral, high-frequency hearing loss due to atypical cochlear hair cell development. However, children with heterozygous USH2A mutations have also been found to show unexpected low-frequency hearing loss and reduced early vocabulary, contradicting assumptions that the heterozygous (carrier) state is “phenotype free”. Parallel evidence has confirmed that heterozygous Ush2a mutations in a transgenic mouse model also cause low-frequency hearing loss (Perrino et al., 2020). Importantly, these auditory processing anomalies were still evident after covariance for hearing loss, suggesting a CAPD profile. Since usherin anomalies occur in the peripheral cochlea and not central auditory structures, these findings point to upstream developmental feedback effects of peripheral sensory loss on high-level processing characteristic of CAPD. In this study, we aimed to expand upon the mouse behavioral battery used in Perrino et al. (2020) by evaluating central auditory brain structures, including the superior olivary complex (SOC) and medial geniculate nucleus (MGN), in heterozygous and homozygous Ush2a mice. We found that heterozygous Ush2a mice had significantly larger SOC volumes while homozygous Ush2a had significantly smaller SOC volumes. Heterozygous mutations did not affect the MGN; however, homozygous Ush2a mutations resulted in a significant shift towards more smaller neurons. These findings suggest that alterations in cochlear development due to USH2A variation can secondarily impact the development of brain regions important for auditory processing ability.

Multi-Parental Populations Suitable for Identifying Sources of Resistance to Powdery Mildew in Winter Wheat.

Wheat (Triticum aestivum L.) is one of the world’s staple food crops and one of the most devastating foliar diseases attacking wheat is powdery mildew (PM). In Denmark only a few specific fungicides are available for controlling PM and the use of resistant cultivars is often recommended. In this study, two Chinese wheat landraces and two synthetic hexaploid wheat lines were used as donors for creating four multi-parental populations with a total of 717 individual lines to identify new PM resistance genetic variants. These lines and the nine parental lines (including the elite cultivars used to create the populations) were genotyped using a 20 K Illumina SNP chip, which resulted in 8,902 segregating single nucleotide polymorphisms for assessment of the population structure and whole genome association study. The largest genetic difference among the lines was between the donors and the elite cultivars, the second largest genetic difference was between the different donors; a difference that was also reflected in differences between the four multi-parental populations. The 726 lines were phenotyped for PM resistance in 2017 and 2018. A high PM disease pressure was observed in both seasons, with severities ranging from 0 to >50%. Whole genome association studies for genetic variation in PM resistance in the populations revealed significant markers mapped to either chromosome 2A, B, or D in each of the four populations. However, linkage disequilibrium between these putative quantitative trait loci (QTL) were all above 0.80, probably representing a single QTL. A combined analysis of all the populations confirmed this result and the most associated marker explained 42% of the variation in PM resistance. This study gives both knowledge about the resistance as well as molecular tools and plant material that can be utilised in marker-assisted selection. Additionally, the four populations produced in this study are highly suitable for association studies of other traits than PM resistance.

Efficient multiplexed genome engineering with a polycistronic tRNA and CRISPR guide-RNA reveals an important role of detonator in reproduction of Drosophila melanogaster.

Genome association studies in human and genetic studies in mouse implicated members of the transmembrane protein 132 (TMEM132) family in multiple conditions including panic disorder, hearing loss, limb and kidney malformation. However, the presence of five TMEM132 paralogs in mammalian genomes makes it extremely challenging to reveal the full requirement for these proteins in vivo. In contrast, there is only one TMEM132 homolog, detonator (dtn), in the genome of fruit fly Drosophila melanogaster, enabling straightforward research into its in vivo function. In the current study, we generate multiple loss-of-function dtn mutant fly strains through a polycistronic tRNA-gRNA approach, and show that most embryos lacking both maternal and paternal dtn fail to hatch into larvae, indicating an essential role of dtn in Drosophila reproduction.

Almond diversity and homozygosity define structure, kinship, inbreeding, and linkage disequilibrium in cultivated germplasm, and reveal genomic associations with nut and seed weight

Almond [Prunus dulcis Miller (D.A. Webb)] is the main tree nut species worldwide. Here, genotyping-by-sequencing (GBS) was applied to 149 almond cultivars from the ex situ collections of the Italian Council for Agricultural Research (CREA) and the Spanish National Research Council (CSIC), leading to the detection of 93,119 single-nucleotide polymorphisms (SNPs). The study of population structure outlined four distinct genetic groups and highlighted diversification between the Mediterranean and Californian gene pools. Data on SNP diversity and runs of homozygosity (ROHs) allowed the definition of kinship, inbreeding, and linkage disequilibrium (LD) decay in almond cultivated germplasm. Four-year phenotypic observations, gathered on 98 cultivars of the CREA collection, were used to perform a genome-wide association study (GWAS) and, for the first time in a crop species, homozygosity mapping (HM), resulting in the identification of genomic associations with nut, shell, and seed weight. Both GWAS and HM suggested that loci controlling nut and seed weight are mostly independent. Overall, this study provides insights on the almond cultivation history and delivers information of major interest for almond genetics and breeding. In a broader perspective, our results encourage the use of ROHs in crop science to estimate inbreeding, choose parental combinations minimizing the risk of inbreeding depression, and identify genomic footprints of selection for specific traits.

The Mutational Landscape of Metastatic Castration-sensitive Prostate Cancer: The Spectrum Theory Revisited

BackgroundEmerging data suggest that metastasis is a spectrum of disease burden rather than a binary state, and local therapies, such as radiation, might improve outcomes in oligometastasis. However, current definitions of oligometastasis are solely numerical. ObjectiveTo characterize the somatic mutational landscape across the disease spectrum of metastatic castration-sensitive prostate cancer (mCSPC) to elucidate a biological definition of oligometastatic CSPC. Design, setting, and participantsThis was a retrospective study of men with mCSPC who underwent clinical-grade sequencing of their tumors (269 primary tumor, 25 metastatic sites). Patients were classified as having biochemically recurrent (ie, micrometastatic), metachronous oligometastatic (≤5 lesions), metachronous polymetastatic (>5 lesions), or de novo metastatic (metastasis at diagnosis) disease. Outcome measurements and statistical analysisWe measured the frequency of driver mutations across metastatic classifications and the genomic associations with radiographic progression-free survival (rPFS) and time to castrate-resistant prostate cancer (CRPC). Results and limitationsThe frequency of driver mutations in TP53 (p = 0.01), WNT (p = 0.08), and cell cycle (p = 0.04) genes increased across the mCSPC spectrum. TP53 mutation was associated with shorter rPFS (26.7 vs 48.6 mo; p = 0.002), and time to CRPC (95.6 vs 155.8 mo; p = 0.02) in men with oligometastasis, and identified men with polymetastasis with better rPFS (TP53 wild-type, 42.7 mo; TP53 mutated, 18.5 mo; p = 0.01). Mutations in TP53 (incidence rate ratio [IRR] 1.45; p = 0.004) and DNA double-strand break repair (IRR 1.61; p < 0.001) were associated with a higher number of metastases. Mutations in TP53 were also independently associated with shorter rPFS (hazard ratio [HR] 1.59; p = 0.03) and the development of CRPC (HR 1.71; p = 0.01) on multivariable analysis. This study was limited by its retrospective nature, sample size, and the use of commercially available sequencing platforms, resulting in a limited predefined set of genes examined. ConclusionsSomatic mutational profiles reveal a spectrum of metastatic biology that helps in redefining oligometastasis beyond a simple binary state of lesion enumeration. Patient summaryOligometastatic prostate cancer is typically defined as less than three to five metastatic lesions and evidence suggests that using radiation or surgery to treat these sites improves clinical outcomes. As of now, treatment decisions for oligometastasis are solely defined according to the number of lesions. However, this study suggests that tumor mutational profiles can provide a biological definition of oligometastasis and complement currently used numerical definitions.

Identification and Verification of Molecular Subtypes with Enhanced Immune Infiltration Based on m6A Regulators in Cutaneous Melanoma.

Background As the most aggressive type of skin cancer, cutaneous melanoma (CM) is experiencing a rapidly rising mortality in recent years. Exploring potential prognostic biomarkers or mechanisms of disease progression therefore has a great significance for CM. The purpose of this study was to identify genetic markers and prognostic performance of N6-methyladenosine (m6A) regulators in CM. Method Gene expression profiles, copy number variation (CNV), and single nucleotide polymorphism (SNP) data of patients were obtained from The Cancer Genome Atlas (TCGA) database. Results Genomic variation and association analysis of gene expressions revealed a high degree of genomic variation in the presence of m6A-regulated genes. m6A patients with high-frequency genomic variants in the regulatory gene tended to develop a worse prognosis (p < 0.01). Unsupervised cluster analysis of the expression profiles of m6A-regulated genes identified three clinically distinct molecular subtypes, including degradation-enhanced subgroup and immune-enhanced subgroup, with significant prognostic differences (p = 0.046). A novel prognostic signature, which was established according to m6A-related characteristic genes identified through genome-wide expression spectrum, could effectively identify samples with poor prognosis and enhanced immune infiltration, and the effectiveness was also verified in the dataset of the chip. Conclusion We identified genetic changes in the m6A regulatory gene in CM and related survival outcomes. The findings of this study provide new insights into the epigenetic understanding of m6A in CM.

Exploring the clinical significance of serous tubal intraepithelial carcinoma associated with advanced high-grade serous ovarian cancer: A Memorial Sloan Kettering Team Ovary Study

ObjectiveTo evaluate the clinical significance and genomic associations of concurrent serous tubal intraepithelial carcinoma (STIC) with high-grade serous carcinoma (HGSC) of the ovary in women undergoing primary debulking surgery (PDS). MethodsAll patients who underwent PDS for HGSC between 01/2015 and 12/2018 were captured in a prospectively maintained institutional database. Patients were categorized based on the presence or absence of concurrent STIC noted on final pathology. Demographic, perioperative, and outcomes data were collected, and groups were compared using standard statistical tests. Progression-free survival (PFS) and overall survival (OS) were evaluated using the Kaplan-Meier method. For comparison of differences in somatic alterations between the two cohorts, specimens were sequenced using MSK-IMPACT. ResultsOf 306 eligible patients, 87 (28%) had a concurrent STIC lesion (+STIC) and 219 (72%) did not (no-STIC). Demographics and clinicopathological factors were similar between the two cohorts, except for a significantly higher median preoperative CA-125 level in the no-STIC group (423 U/mL vs. 321 U/mL; p=0.029). There were no significant differences in median PFS (22.7 months [95%CI: 18.9-28.4] vs. 27.7 months [95%CI: 25.5-30.5]; p=0.126) and 3- year OS rate (81% [95%CI: 70-88%] vs. 85% [95%CI: 78-90%]; p=0.392) between +STIC and no-STIC patients, respectively. Targeted DNA-sequencing via MSK-IMPACT showed a similar distribution of driver mutations or structural genetic alterations, and affected genetic signaling pathways were similar between the cohorts. ConclusionsThere were no identifiable clinical and genetic differences in patients with HGSC and concurrent STIC. These data suggest a comparable, if not identical, disease process.

Multiple-Race Stem Rust Resistance Loci Identified in Durum Wheat Using Genome-Wide Association Mapping.

Stem rust of wheat caused by Puccinia graminis Pers. f.sp. trtici Eriks and E. Henn., is the most damaging fungal disease of both common (Triticum aestivum L.) and durum (Triticum turgidum L., ssp. Durum) wheat. Continuously emerging races virulent to many of the commercially deployed qualitative resistance genes have caused remarkable loss worldwide and threaten global wheat production. The objectives of this study were to evaluate the response of a panel of 283 durum wheat lines assembled by the International Maize and Wheat Improvement Center (CIMMYT) to multiple races of stem rust in East Africa at the adult plant stage and map loci associated with field resistance. The lines were evaluated in Debre Zeit, Ethiopia and Njoro, Kenya from 2018 to 2019 in five environments (year × season). The panel was genotyped using genotyping-by-sequencing. After filtering, 26,439 Single Nucleotide Polymorphism (SNP) markers and 280 lines and three checks were retained for analysis. Population structure was assessed using principal component analysis. Genome-wide association analysis (GWAS) was conducted using Genomic Association and Prediction Integrated Tool (GAPIT). The broad-sense heritability of the phenotype data revealed that 64–83% of the variation in stem rust response explained by the genotypes and lines with multiple race resistance were identified. GWAS analysis detected a total of 160 significant marker trait associations representing 42 quantitative trait loci. Of those, 21 were potentially novel and 21 were mapped to the same regions as previously reported loci. Known stem rust resistance genes/alleles were postulated including Sr8a, Sr8155B1, SrWeb/Sr9h, Sr11, Sr12, Sr13/Sr13 alleles, Sr17, Sr28/Sr16, Sr22, and Sr49. Lines resistant to multiple races in East Africa can be utilized as parents in durum wheat breeding programs. Further studies are needed to determine if there are new alleles at the Sr13 locus and potential markers for the known Sr13 alleles.

Genomic Association of Single Nucleotide Polymorphisms with Blood Pressure Response to Hydrochlorothiazide among South African Adults with Hypertension.

This study described single nucleotide polymorphisms (SNPs) in hydrochlorothiazide-associated genes and further assessed their correlation with blood pressure control among South African adults living with hypertension. A total of 291 participants belonging to the Nguni tribes of South Africa on treatment for hypertension were recruited. Nineteen SNPs in hydrochlorothiazide pharmacogenes were selected and genotyped using MassArray. Uncontrolled hypertension was defined as blood pressure ≥140/90 mmHg. The association between genotypes, alleles and blood pressure response to treatment was determined by conducting multivariate logistic regression model analysis. The majority of the study participants were female (73.19%), Xhosa (54.98%) and had blood pressure ≥140/90 mmHg (68.73%). Seventeen SNPs were observed among the Xhosa tribe, and two (rs2070744 and rs7297610) were detected among Swati and Zulu participants. Furthermore, alleles T of rs2107614 (AOR = 6.69; 95%CI 1.42–31.55; p = 0.016) and C of rs2776546 (AOR = 3.78; 95%CI 1.04–13.74; p = 0.043) were independently associated with uncontrolled hypertension, whilst rs2070744 TC (AOR = 38.76; 95%CI 5.54–270.76; p = 0.00023), CC (AOR = 10.44; 95%CI 2.16–50.29; p = 0.003) and allele T of rs7297610 (AOR = 1.86; 95%CI 1.09–3.14; p = 0.023) were significantly associated with uncontrolled hypertension among Zulu and Swati participants. We confirmed the presence of SNPs associated with hydrochlorothiazide, some of which were significantly associated with uncontrolled hypertension in the study sample. Findings open doors for further studies on personalized therapy for hypertension in the country.

Identification of Novel Genomic Associations and Gene Candidates for Grain Starch Content in Sorghum.

Starch accumulated in the endosperm of cereal grains as reserve energy for germination serves as a staple in human and animal nutrition. Unraveling genetic control for starch metabolism is important for breeding grains with high starch content. In this study, we used a sorghum association panel with 389 individuals and 141,557 single nucleotide polymorphisms (SNPs) to fit linear mixed models (LMM) for identifying genomic regions and potential candidate genes associated with starch content. Three associated genomic regions, one in chromosome (chr) 1 and two novel associations in chr-8, were identified using combination of LMM and Bayesian sparse LMM. All significant SNPs were located within protein coding genes, with SNPs ∼ 52 Mb of chr-8 encoding a Casperian strip membrane protein (CASP)-like protein (Sobic.008G111500) and a heat shock protein (HSP) 90 (Sobic.008G111600) that were highly expressed in reproductive tissues including within the embryo and endosperm. The HSP90 is a potential hub gene with gene network of 75 high-confidence first interactors that is enriched for five biochemical pathways including protein processing. The first interactors of HSP90 also showed high transcript abundance in reproductive tissues. The candidates of this study are likely involved in intricate metabolic pathways and represent candidate gene targets for source-sink activities and drought and heat stress tolerance during grain filling.

Genome-Wide Association Study for Flowering Time in Korean Cowpea Germplasm

Cowpea is an annual legume crop; although it is an essential food in developing countries, cowpea is now grown worldwide. For the genetic improvement of plants, flowering time is one of the major selection criteria. In general, flowering is regulated by photoperiod and temperature, along with the interaction between environmental factors. In this study, we aimed to investigate the candidate genes associated with flowering time using genome-wide association study (GWAS). To investigate the flowering time-related genes, 384 cowpea germplasms were genotyped with 51,128 single nucleotide polymorphisms (SNPs). The main genetic component of days to flowering (DTF) was analyzed using genome association and prediction integrated tool (GAPIT) and elastic-net analyses. From the GAPIT and elastic-net analyses, a total of 23 SNPs were significantly associated with DTF among five (chr. 2, 3, 7, 9, and 11) and seven (chr. 1, 2, 3, 4, 5, 8, and 9) different chromosomes, respectively. Based on our analysis, Vigun01g084000, Vigun01g227200, Vigun02g062600, and Vigun03g296800 were considered the major candidate genes that were significantly associated with DTF in cowpea. These results confirmed that DTF might be controlled by multiple genes affecting early flowering, delaying flowering time, repressing the transition to flowering, etc. This study will potentially contribute to effective DTF genomic selection in plant breeding to better understand the genetic basis and explore the mechanism of flowering time.

NIA genetics of Alzheimer’s disease data storage site (NIAGADS): Update 2020

AbstractBackgroundNIAGADS is a national genetics data repository that facilitates access of genotypic data to qualified investigators for the study of the genetics of late‐onset Alzheimer’s disease (AD) and other neurological diseases. Collaborations with large consortia and centers such as the Alzheimer’s Disease Genetics Consortium (ADGC), Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium, the Alzheimer’s Disease Genome Sequencing Project (ADSP), and the Genome Center for Alzheimer’s Disease (GCAD) allow NIAGADS to lead the effort in managing large AD datasets that can be easily accessed by the research community and utilized to their fullest extent.MethodNIAGADS is supported by National Institute on Aging (NIA) under a cooperative agreement (U24 AG041689). All data derived from NIA funded AD genetics studies are expected to be deposited in NIAGADS or another NIA approved site. NIAGADS manages a Data Sharing Service (DSS) that facilitates the deposition and sharing of genomic data and association results with approved users in the neurodegenerative research community. In addition, researchers are able to freely use the NIAGADS Genomics Database to search annotation resources that link published AD studies to AD‐relevant sequence features and genome‐wide annotations.ResultAs of January 2020, NIAGADS houses 67 datasets (23 added in 2019) with &gt;59,000 samples and nearly 34 billion genotypes. Qualified investigators can retrieve ADSP sequencing data with ease and flexibility through the NIAGADS DSS. The ADSP and other contributing studies have completed whole exome sequencing (WES) of 20,630 subjects and whole‐genome sequencing (WGS) of 4,750 subjects. Raw WES and WGS files, quality controlled VCF files, and phenotype data files are available via qualified access. The next planned dataset release will occur in late 2020 and will contain an additional 13,136 genomes jointly genotype called with the first release of 4,750 genomes, totaling about 17,886 genomes.ConclusionNIAGADS is a rich resource for AD researchers, with the goal of facilitating advances in Alzheimer’s genetics research. By housing datasets from multiple projects and institutions, NIAGADS enables AD researchers to be more efficient in meeting their research goals. Datasets, guidelines, and new features are available on our website at https://www.niagads.org.

ANÁLISIS DE SECUENCIAS GENÓMICAS SUGIEREN QUE EL GEN DE LA PRODINORFINA ESTÁ BAJO SELECCIÓN POSITIVA EN BOVINOS

Dynorphin A is an endogenous opioid peptide that is part of the KNDy system in the hypothalamus of mammals. This peptide acts as an inhibitor of the GnRH pulse generation, thus regulating the onset of puberty and reproductive cycles. The PDYN gene encodes the propeptide Prodynorphin, the precursor of Dynorphin A. Despite its physiological relevance, PDYN has not emerged as a candidate gene associated with puberty in genomic association studies conducted in cattle. The present work aimed to search for signatures of selection on the PDYN gene among cattle breeds. To this, the whole genome sequences from 57 samples of ten cattle breeds were used. The samples were grouped based on breed selection history and their productive differences, particularly in terms of sexual precocity. The population structure was analyzed using Principal Component Analyses. To evidence recent selection processes, neutrality tests, such as Tajima’s D and Fu &amp; Li’s F* and D* were performed in defined functional regions of PDYN. The putative promoter of PDYN showed a population structure that is in agreement with the criteria considered to make the groups. In that region, neutrality tests were consistently negative and resulted in statistically significant for the dairy breeds. Also, these breeds exhibited less variability in the haplotype analyses than the others. The results presented here suggest that regulatory regions of PDYN could be under positive selection, particularly in dairy breeds. Key words: reproduction; KNDy neurons; Dynorphin; signatures of selection.

Whole genome sequence association analyses of brain volumes in the TOPMed program

AbstractBackgroundGenome‐wide association studies (GWAS) of brain volumes have identified common genetic variants with modest effect sizes that lie mainly in non‐coding regions. We sought to identify low frequency and rare variants influencing brain volumes by performing whole genome association analyses using sequence data from the Trans‐Omics for Precision Medicine (TOPMed) Program.MethodsWe analyzed up to 3,975 participants (58% women; 78% Europeans, 22% African‐Americans), mean age of 62.5 (13.9), from four TOPMed population‐ or family‐based studies (FHS, GENESTAR, CHS, and GENOA). We excluded participants with dementia, stroke, presence of large brain infarcts, tumor or any other finding affecting the scan. We tested the association of hippocampal (HV), total brain (TBV), lateral ventricular (LVV) and intracranial (ICV) volumes with individual genetic variants using mixed‐effect linear regression models adjusted for age, age2, sex, study and principal components. Models including HV, TBV and LVV were adjusted for ICV. We accounted for relatedness using a kinship matrix and trait variance variability using a random effects model. We retained variants with a minor allele count greater than 40.ResultsWe detected new genome‐wide significant (P &lt; 5 × 10−8) low frequency or rare variants in five regions associated with HV (5q31, P = 10−9) and TBV (2p22, P = 10−8; 17q25, P = 4 × 10−9; Xp11, P = 2 × 10−10; Xq21, P = 4 × 10−8). We also confirmed previously observed common variants in GWAS loci for HV (12q14 &amp; 12q24), LVV (3q28, 12q23 &amp; 16q24) and ICV (6q21, 6q22 &amp; 17q21). The top 5q31 hit for HV (rs246587) lies at 19kb from the PCDHAC2 gene, encoding neural cadherin‐like cell adhesion proteins that most likely play a critical role in the establishment and maintenance of specific neuronal connections in the brain.ConclusionsOur whole genome analysis revealed intriguing new loci associated with brain volumes. Future work will include ancestry‐specific and conditional analyses, gene‐based and burden tests as well as the inclusion of additional TOPMed cohorts. Supported by: U01s AG058589, AG052409, R01s AG054076, AG033040 AG049607, HL112064, NS062059, FHS contracts HHSN268201500001I and 75N92019D00031, R01HL131136 (Analysis Commons).

Sexual Dimorphic Role of CD14 (Cluster of Differentiation 14) in Salt-Sensitive Hypertension and Renal Injury.

Genomic sequence and gene expression association studies in animals and humans have identified genes that may be integral in the pathogenesis of various diseases. CD14 (cluster of differentiation 14)-a cell surface protein involved in innate immune system activation-is one such gene associated with cardiovascular and hypertensive disease. We previously showed that this gene is upregulated in renal macrophages of Dahl salt-sensitive animals fed a high-salt diet; here we test the hypothesis that CD14 contributes to the elevated pressure and renal injury observed in salt-sensitive hypertension. Using CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeat-associated 9), we created a targeted mutation in the CD14 gene on the Dahl SS (SS/JrHSDMcwi) background and validated the absence of CD14 peptides via mass spectrometry. Radiotelemetry was used to monitor blood pressure in wild-type and CD14-/- animals challenged with high salt and identified infiltrating renal immune cells via flow cytometry. Germline knockout of CD14 exacerbated salt-sensitive hypertension and renal injury in female animals but not males. CD14-/- females demonstrated increased infiltrating macrophages but no difference in infiltrating lymphocytes. Transplant of CD14+/+ or CD14-/- bone marrow was used to isolate the effects of CD14 knockout to hematopoietic cells and confirmed that the differential phenotype observed was due to knockout of CD14 in hematopoietic cells. Ovariectomy was used to remove the influence of female sex hormones, which completely abrogated the effect of CD14 knockout. These studies provide a novel treatment target and evidence of a new dichotomy in immune activation between sexes within the context of hypertensive disease where CD14 regulates immune cell activation and renal injury.

14 Genome-wide association study of frozen sperm quality in cocks

Abstract Preservation of the genetic material of unique breeds of hens involves the use of semen cryobanks. The aim of the study was to search for genomic associations with rooster sperm quality after freezing. We took into account the decrease in sperm motility after thawing. Genotyping of 96 individuals (roosters) using the Affymetrix Axiom®600k Array chip was performed. Genomic data were obtained using the Plink 1.9 software. DNA samples were taken with genotyping quality at SNP loci more than 95%, SNP with MAF &amp;gt; 0.01. GWAS was performed using EMMAX. SNP information in the corresponding genes was determined using the genomic browsers NCBI and Ensembl. Assessment of rooster sperm quality showed high individual variability in total motility before freezing (20–95%), and after freezing (5–70%). Significant SNPs were detected on the chromosomes GGA1 (rs315598192, rs316943858), GGA2 (rs312981435), GGA3 (rs13694743), GGA11 (rs314024471), GGA19 (rs316346648), GGA22 (rs31797024248, rga31780824824, gga22 (rs3178082424). Candidate genes ZC3HC1, CACNA2D1, BCKDHB, AMFR, and GOSR1 were identified. The annotated genes were associated with cell cycle regulation, the formation of calcium cytoskeleton, and the formation of a multienzyme complex associated with the inner membrane of mitochondria, glycosylated transmembrane receptor. The experimental data and results can be used to study the localization of regions and genes associated with phenotypic traits of frozen sperm quality. Authors acknowledge financial support from Russian Science Foundation № 18-16-00071.

Expression-based analysis of genes related to single nucleotide polymorphism hits associated with bovine leukemia virus proviral load in Argentinean dairy cattle

In dairy cattle infected with bovine leukemia virus (BLV), the proviral load (PVL) level is directly related to the viral transmission from infected animals to their healthy herdmates. Two contrasting phenotypic groups can be identified when assessing PVL in peripheral blood of infected cows. A large number of reports point to bovine genetic variants (single nucleotide polymorphisms) as one of the key determinants underlying PVL level. However, biological mechanisms driving BLV PVL profiles and infection progression in cattle have not yet been elucidated. In this study, we evaluated whether a set of candidate genes affecting BLV PVL level according to whole genome association studies are differentially expressed in peripheral blood mononuclear cells derived from phenotypically contrasting groups of BLV-infected cows. During a 10-mo-long sampling scheme, 129 Holstein cows were phenotyped measuring anti-BLV antibody levels, PVL quantification, and white blood cell subpopulation counts. Finally, the expression of 8 genes (BOLA-DRB3, PRRC2A, ABT1, TNF, BAG6, BOLA-A, LY6G5B, and IER3) located within the bovine major histocompatibility complex region harboring whole genome association SNP hits was evaluated in 2 phenotypic groups: high PVL (n = 7) and low PVL (n = 8). The log2 initial fluorescence value (N0) transformed mean expression values for the ABT1 transcription factor were statistically different in high- and low-PVL groups, showing a higher expression of the ABT1 gene in low-PVL cows. The PRRC2A and IER3 genes had a significant positive (correlation coefficient = 0.61) and negative (correlation coefficient = -0.45) correlation with the lymphocyte counts, respectively. Additionally, the relationships between gene expression values and lymphocyte counts were modeled using linear regressions. Lymphocyte levels in infected cows were better explained (coefficient of determination = 0.56) when fitted a multiple linear regression model using both PRRC2A and IER3 expression values as independent variables. The present study showed evidence of differential gene expression between contrasting BLV infection phenotypes. These genes have not been previously related to BLV pathobiology. This valuable information represents a step forward in understanding the BLV biology and the immune response of naturally infected cows under a commercial milk production system. Efforts to elucidate biological mechanisms leading to BLV infection progression in cows are valuable for BLV control programs. Further studies integrating genotypic data, global transcriptome analysis, and BLV progression phenotypes are needed to better understand the BLV-host interaction.

Race, Ethnicity, Ancestry, and Genomics in Hawai‘i

This paper examines how populations in a multiethnic cohort project used to study environmental causes of cancer in Hawai‘i have been reorganized in ways that have contributed to the racialization of the human genome. We examine the development of two central genomic data infrastructures, the multiethnic cohort (MEC) and a collection of reference DNA called the HapMap. The MEC study populations were initially designed to examine differences in nutrition as risk factors for disease, and then were repurposed to search for potential genomic risk factors for disease. The biomaterials collected from these populations became institutionalized in a data repository that later became a major source of “diverse” DNA for other studies of genomic risk factors for disease. We examine what happened when the MEC biorepository and dataset, organized by ethnic labels, came to be used, in conjunction with the data from the HapMap reference populations, to construct human population genetic categories. Developing theory on genomic racialization, we examine (1) how and why Hawai‘i became sited as a “virtual natural laboratory” for collecting and examining biomaterials from different ethnic groups, and the consequences of the transformation of those local Hawaiian ethnic groups into five racial and ethnic OMB categories meant to represent global continental groups for genomic studies. We then discuss (2) how this transformation, via the geneticists’ effort to standardize the study of genomic risk for disease around the globe, led to the construction of humans as statistical genetic resources and entities for genomic biomedicine and the human population genetics discipline. Through this transformation of populations and biorepositories, we argue (3) that the twenty-first century has seen the intertwining of “race,” “population,” and “genome” via large-scale genomic association studies. We show how “race” has become imbricated in human population genetics and genomic biomedicine. This essay is part of a special issue entitled Pacific Biologies: How Humans Become Genetic, edited by Warwick Anderson and M. Susan Lindee.

Mastermind: A Comprehensive Genomic Association Search Engine for Empirical Evidence Curation and Genetic Variant Interpretation.

Design and interpretation of genome sequencing assays in clinical diagnostics and research labs is complicated by an inability to identify information from the medical literature and related databases quickly, comprehensively and reproducibly. This challenge is compounded by the complexity and heterogeneity of nomenclatures used to describe diseases, genes and genetic variants. Mastermind is a widely-used bioinformatic platform of genomic associations that has indexed more than 7.5 M full-text articles and 2.5 M supplemental datasets. It has automatically identified, disambiguated and annotated >6.1 M genetic variants and identified >50 K disease-gene associations. Here, we describe how Mastermind improves the sensitivity and reproducibility of clinical variant interpretation and produces comprehensive genomic landscapes of genetic variants driving pharmaceutical research. We demonstrate an alarmingly high degree of heterogeneity across commercially available panels for hereditary cancer that is resolved by evidence from Mastermind. We further examined the sensitivity of Mastermind for variant interpretation by examining 108 clinically-encountered variants and comparing the results to alternate methods. Mastermind demonstrated a sensitivity of 98.4% compared to 4.4, 45.6, and 37.4% for alternatives PubMed, Google Scholar, and ClinVar, respectively, and a specificity of 98.5% compared to 45.1, 57.6, and 68.8% as well as an increase in content yield of 22.6-, 2.2-, and 2.6-fold. When curated for clinical significance, Mastermind identified more than 4.9-fold more pathogenic variants than ClinVar for representative genes. For structural variants, we compared Mastermind’s ability to sensitively identify evidence for 10 representative disease-causing CNVs versus results identified in PubMed, as well as its ability to identify evidence for fusion events compared to COSMIC. Mastermind demonstrated a 4.0- to 43.9-fold increase in references for specific CNVs compared to PubMed, as well as 5.4-fold more fusion genes when compared with COSMIC’s curated database. Additionally, Mastermind produced an 8.0-fold increase in reference citations for fusion events common to Mastermind and outside databases. Taken together, these results demonstrate the utility and superiority of Mastermind in terms of both sensitivity and specificity of automated results for clinical diagnostic variant interpretation for multiple genetic variant types and highlight the potential benefit in informing pharmaceutical research.

Considering Cell Proliferation to Optimize Detection of Radiation-Induced 53BP1 Positive Foci in 15 Mouse Strains Ex Vivo.

Due to high metabolic activity, proliferating cells continuously generate free radicals, which induce DNA double-strand breaks (DSB). Fluorescently tagged nuclear foci of DNA repair protein 53 binding protein-1 (53BP1) are used as a standard metric for measuring DSB formation at baseline and in response to environmental insults such as radiation. Here we demonstrate that the background level of spontaneous 53BP1+ foci formation can be modeled mathematically as a function of cell confluence, which is a metric of their proliferation rate. This model was validated using spontaneous 53BP1+ foci data from 72 cultures of primary skin fibroblasts derived from 15 different strains of mice, showing a ∼10-fold decrease from low to full confluence that is independent of mouse strain. On the other hand, the baseline level of spontaneous 53BP1+ foci in a fully confluent cell population was strain-dependent, suggesting genomic associations, and correlated with radiation sensitivity based on previous measurements in the same cell lines. Finally, we have developed an online open-access tool to correct for the effect of cell confluence on 53BP1+ foci-based quantification of DSB. This tool provides guidelines for the number of cells required to reach statistical significance for the detection of DSB induced by low doses of ionizing radiation as a function of confluence and time postirradiation.