A general approach for haplotype phasing across the full spectrum of relatedness

Exploring the genetic influence on hair cortisol concentration: Genetic association of rs11621961 on SERPINA6/1 locus in the 2004 Pelotas Birth Cohort (Brazil)

Genetics plays a critical role in regulating cortisol, as demonstrated by the association of the SERPINA6/1 locus with plasma cortisol concentrations in a genome-wide association meta-analysis (GWAMA). These genes are integral to glucocorticoid transport and regulation, highlighting a direct genetic influence on cortisol availability. This study examines the genetic contribution to hair cortisol concentration (HCC) in adolescents from the 2004 Pelotas (Brazil) Birth Cohort at age 15, employing three distinct approaches: 1) polygenic score (PGS), 2) gene-based analysis, and 3) candidate variations analysis. A total of 1667 individuals were included. The cortisol-PGS was derived from the most recent morning plasma cortisol GWAMA study, and gene-based analyses were performed using MAGMA. For the analysis of candidate variants in the SERPINA6/1 locus, we selected SNPs with P-values ≤ 5 × 10-8 from the cortisol GWAMA and conducted in silico analyses to assess potential regulatory functions. Nineteen SNPs were tested. Our results revealed a significant association between rs11621961 and HCC after multiple testing correction. This intergenic SNP, located 1.1 kb from the 3'-untranslated region (UTR) of SERPINA6, showed that the T allele was associated with higher HCC (β=0.05, FDR-P = 0.038). Functional in silico analyses suggested that rs11621961 might influence gene expression and chromatin structure by altering motifs and acting as an expression quantitative trait locus (eQTL) in lymphoblastoid cell lines. However, neither the cortisol-PGS nor gene-based analyses showed an association with HCC. This study offers important contributions to the understanding of the genetic determinants of HCC, advancing the knowledge of the relationship between genetics and cortisol regulation in adolescents.

Body mass index modifies genetic susceptibility to high systolic blood pressure in adolescents and young adults: results from an 18-year longitudinal study

Genome-wide association studies (GWAS) in adults have identified single nucleotide polymorphisms (SNPs) associated with systolic blood pressure (SBP), but it is unclear whether the findings apply in youth. Further, the role of body mass index (BMI) in these associations is understudied. Our objective was to determine whether BMI modifies genetic susceptibility to high SBP in young people. The sample comprised 714 participants of European ancestry recruited in 1999-2000 from 10 Montreal-area high schools for a longitudinal study. SBP was measured at ages 12, 15, 17, 24, and 30. Blood and saliva samples were collected at ages 14, 20, and 25. Two evidence-based genetic risk scores (GRS) were constructed based on GWAS results in adults: GRS22 used 22 SNPs and GRS182 added 160 additional SNPs to GRS22. Sex-specific associations between each GRS and repeated measures of SBP were estimated using linear mixed models including BMI and a GRS*BMI product term. GRS182 explained a greater proportion of SBP variance than GRS22, and a greater proportion in females than males. The associations increased monotonically with BMI values between 22 kg/m2 and 35 kg/m2. Results indicate that BMI modifies the association between a GRS and SBP levels from adolescence to adulthood.

Genetic effects on gestational diabetes mellitus and their interactions with environmental factors among Japanese women

Gestational diabetes mellitus (GDM) is common in Japanese women, posing serious risks to mothers and offspring. This study investigated the influence of maternal genotypes on the risk of GDM and examined how these genotypes modify the effects of psychological and dietary factors during pregnancy. We analyzed data from 20,399 women in the Tohoku Medical Megabank Project Birth and Three-Generation Cohort. Utilizing two customized SNP arrays for the Japanese population (Affymetrix Axiom Japonica Array v2 and NEO), we performed a meta-analysis to combine the datasets. Gene-environment interactions were assessed by modeling interaction terms between genome-wide significant single nucleotide polymorphisms (SNPs) and psychological and dietary factors. Our analysis identified two SNP variants, rs7643571 (p = 9.14 × 10-9) and rs140353742 (p = 1.24 × 10-8), located in an intron of the MDFIC2 gene, as being associated with an increased risk of GDM. Additionally, although there were suggestive patterns for interactions between these SNPs and both dietary factors (e.g., carbohydrate and fruit intake) and psychological distress, none of the interaction terms remained significant after Bonferroni correction (p < 0.05/8). While nominal significance was observed in some models (e.g., psychological distress, p = 0.04), the data did not provide robust evidence of effect modification on GDM risk once adjusted for multiple comparisons. These findings reveal novel genetic associations with GDM in Japanese women and highlight the importance of gene-environment interactions in its etiology. Given that previous genome-wide association studies (GWAS) on GDM have primarily focused on Western populations, our study provides new insights by examining an Asian population using a population-specific array.

Machine Learning on Prediagnostic Metabolite Data Identifies Etiologic Endotypes of Exfoliation Glaucoma in United States Health Professionals

Purpose

Exfoliation glaucoma (XFG) etiology is poorly understood. Metabolomics-based etiologic endotypes of XFG may provide novel etiologic insights. We aimed to use unsupervised machine learning on prediagnostic plasma metabolites to characterize etiologic XFG endotypes.

Design

Prospective case-only analysis.

Participants

Among Nurses' Health Study and Health Professionals Follow-up Study participants, 205 (174 female and 31 male) incident XFG cases diagnosed with an average of 11.8 years following blood collection (1989-1995) were included.

Methods

We identified and confirmed incident cases of XFG or XFG suspect (collectively called "XFG" henceforth) through 2016 with medical record review. Liquid chromatography-mass spectrometry was used to profile 341 plasma metabolites. After preprocessing prediagnostic metabolites with adjustment for season, time of blood draw, and fasting status, we computed a distance matrix using Pearson distance and computed gap statistics to identify distinct endotypes.

Main Outcome Measures

Metabolomics-based XFG etiologic endotypes. Metabolomic profiles were compared across endotypes; false discovery rate (FDR) was used to account for multiple comparisons in Metabolite Set Enrichment Analyses. Exfoliation glaucoma environmental risk factors (e.g., lifetime ultraviolet (UV) exposure, folate consumption), a genetic risk score incorporating 8 major single nucleotide polymorphisms for exfoliation syndrome, and clinical presentations were compared across endotypes.

Results

We identified 3 distinct XFG metabolomic endotypes. Compared with the most common endotype 2 (reference group [n = 90; 43.9%]), endotype 1 (n = 56; 27.3%) tended to include more male southern US residents with greater UV exposure and were the least likely to have cardiovascular disease; among women, a higher percentage were postmenopausal. Endotype 3 (n = 59; 28.8%) was associated with being a male northern US resident; a higher prevalence of cardiovascular disease and risk factors such as higher body mass index, diabetes, hypertension, and dyslipidemia; and the lowest genetic susceptibility score. There were no differences in ophthalmic characteristics (e.g., maximum intraocular pressure, bilaterality, age at diagnosis) across endotypes (P ≥ 0.6). In metabolite class analyses, compared with endotype 2, organic acids and carnitines were positively associated with endotype 1, whereas diacylglycerols and triacylglycerols were positively associated with endotype 3 (FDR <0.05).

Conclusions

Integrated metabolomic profiling can identify distinct XFG etiologic endotypes, suggesting different pathobiological mechanisms.

Financial Disclosures

Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

A neuronal Slit1-dependent program rescues oligodendrocyte differentiation and myelination under chronic hypoxic conditions

Oligodendrocyte maturation arrest in hypoxia-induced white matter injury (WMI) results in long-term neurofunctional disabilities of preterm infants. Although neurons are closely linked to myelination regulation, how neurons respond to the above process remains elusive. Here, we identify a compensatory role of neuronal Slit1-dependent signaling in protecting against hypoxia-induced hypomyelination and ameliorating motor and cognitive disabilities. Conditional ablation of Slit1 in neurons exacerbates hypoxia-induced hypomyelination but is negligible for developmental myelination. Secreted Slit1 from hypoxic neurons directly targets oligodendrocyte, acting through Robo2-srGAP1-RhoA signaling. Pharmacological inhibition of RhoA restores myelination and promotes neurofunctional recovery in adolescent mice. Notably, natural selection analysis and functional validation indicate an adaptive variant with higher Slit1 gene expression in the Tibetan population, which has low oxygen availability. Collectively, these findings show a neuronal Slit1-dependent program of OL differentiation and suggest that targeting the Slit1-Robo2 signaling axis may have therapeutic potential for treatment of preterm infants with hypoxic WMI.

Preeclampsia prediction with maternal and paternal polygenic risk scores: the TMM BirThree Cohort Study

Genomic information from pregnant women and the paternal parent of their fetuses may provide effective biomarkers for preeclampsia (PE). This study investigated the association of parental polygenic risk scores (PRSs) for blood pressure (BP) and PE with PE onset and evaluated predictive performances of PRSs using clinical predictive variables. In the Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study, 19,836 participants were genotyped using either Affymetrix Axiom Japonica Array v2 (further divided into two cohorts-the PRS training cohort and the internal-validation cohort-at a ratio of 1:2) or Japonica Array NEO (external-validation cohort). PRSs were calculated for systolic BP (SBP), diastolic BP (DBP), and PE and hyperparameters for PRS calculation were optimized in the training cohort. PE onset was associated with maternal SBP-, DBP-, and PE-PRSs and paternal SBP- and DBP-PRSs only in the external-validation cohort. Meta-analysis revealed overall associations with maternal PRSs but highlighted significant heterogeneity between cohorts. Maternal DBP-PRS calculated using "LDpred2" presented the most improvement in prediction models and provided additional predictive information on clinical predictive variables. Paternal DBP-PRS improved prediction models in the internal-validation cohort. In conclusion, Parental PRS, along with clinical predictive variables, is potentially useful for predicting PE.

Common variation in meiosis genes shapes human recombination phenotypes and aneuploidy risk

The leading cause of human pregnancy loss is aneuploidy, often tracing to errors in chromosome segregation during female meiosis. While abnormal crossover recombination is known to confer risk for aneuploidy, limited data have hindered understanding of the potential shared genetic basis of these key molecular phenotypes. To address this gap, we performed retrospective analysis of preimplantation genetic testing data from 139,416 in vitro fertilized embryos from 22,850 sets of biological parents. By tracing transmission of haplotypes, we identified 3,656,198 crossovers, as well as 92,485 aneuploid chromosomes. Counts of crossovers were lower in aneuploid versus euploid embryos, consistent with their role in chromosome pairing and segregation. Our analyses further revealed that a common haplotype spanning the meiotic cohesin SMC1B is significantly associated with both crossover count and maternal meiotic aneuploidy, with evidence supporting a non-coding cis-regulatory mechanism. Transcriptome- and phenome-wide association tests also implicated variation in the synaptonemal complex component C14orf39 and crossover-regulating ubiquitin ligases CCNB1IP1 and RNF212 in meiotic aneuploidy risk. More broadly, recombination and aneuploidy possess a partially shared genetic basis that also overlaps with reproductive aging traits. Our findings highlight the dual role of recombination in generating genetic diversity, while ensuring meiotic fidelity.

Genomic Exploration of Essential Hypertension in African-Brazilian Quilombo Populations: A Comprehensive Approach With Pedigree Analysis and Family-Based Association Studies

BACKGROUND

Essential hypertension (EH) is a global health issue. Despite extensive research, much of EH heritability remains unexplained. We investigated the genetic basis of EH in African-derived individuals from partially isolated quilombo populations in Vale do Ribeira (São Paulo, Brazil).

METHODS AND RESULTS

Samples from 431 individuals (167 affected, 261 unaffected, 3 unknown) were genotyped using a 650 000 single-nucleotide polymorphism array. Estimated global ancestry proportions were 47% African, 36% European, and 16% Native American. We constructed 6 pedigrees using additional data from 673 individuals and created 3 nonoverlapping single-nucleotide polymorphism subpanels. We phased haplotypes and performed local ancestry analysis to account for admixture. Genome-wide linkage analysis and fine-mapping via family-based association studies were conducted, prioritizing EH-associated genes through a systematic approach involving databases like PubMed, ClinVar, and GWAS (Genome-Wide Association Studies) Catalog. Linkage analysis identified 22 regions of interest with logarithm of the odds scores ranging from 1.45 to 3.03, encompassing 2363 genes. Fine-mapping (family-based association studies) identified 60 EH-related candidate genes and 117 suggestive/significant variants. Among these, 14 genes, including PHGDH, S100A10, MFN2, and RYR2, were strongly related to hypertension harboring 29 suggestive/significant single-nucleotide polymorphisms.

CONCLUSIONS

Through a complementary approach combining admixture-adjusted Genome-wide linkage analysis based on Markov chain Monte Carlo methods, family-based association studies on known and imputed data, and gene prioritizing, new loci, variants, and candidate genes were identified. These findings provide targets for future research, replication in other populations, facilitate personalized treatments, and improve public health toward African-derived underrepresented populations. Limitations include restricted single-nucleotide polymorphism coverage, self-reported pedigree data, and lack of available EH genomic studies on admixed populations for independent validation, despite the performed genetic correlation analyses using summary statistics.

Canine genome-wide association study identifies DENND1B as an obesity gene in dogs and humans

Obesity is a heritable disease, but its genetic basis is incompletely understood. Canine population history facilitates trait mapping. We performed a canine genome-wide association study for body condition score-a measure of obesity-in 241 Labrador retrievers. Using a cross-species approach, we showed that canine obesity genes are also associated with rare and common forms of obesity in humans. The lead canine association was within the gene DENN domain containing 1B (DENND1B). Each copy of the alternate allele was associated with ~7.5% greater body fat. We demonstrate a role for this gene in regulating signaling and trafficking of melanocortin 4 receptor, a critical controller of energy homeostasis. Thus, canine genetics identified obesity genes and mechanisms relevant to both dogs and humans.

Missense variants in FRS3 affect body mass index in populations of diverse ancestries

Obesity is associated with adverse effects on health and quality of life. Improved understanding of its underlying pathophysiology is essential for developing counteractive measures. To search for sequence variants with large effects on BMI, we perform a multi-ancestry meta-analysis of 13 genome-wide association studies on BMI, including data derived from 1,534,555 individuals of European ancestry, 339,657 of Asian ancestry, and 130,968 of African ancestry. We identify an intergenic 262,760 base pair deletion at the MC4R locus that associates with 4.11 kg/m2 higher BMI per allele, likely through downregulation of MC4R. Moreover, a rare FRS3 missense variant, p.Glu115Lys, only found in individuals from Finland, associates with 1.09 kg/m2 lower BMI per allele. We also detect three other low-frequency FRS3 missense variants that associate with BMI with smaller effects and are enriched in different ancestries. We characterize FRS3 as a BMI-associated gene, encoding an adaptor protein known to act downstream of BDNF and TrkB, which regulate appetite, food intake, and energy expenditure through unknown signaling pathways. The work presented here contributes to the biological foundation of obesity by providing a convincing downstream component of the BDNF-TrkB pathway, which could potentially be targeted for obesity treatment.

iModEst: disentangling -omic impacts on gene expression variation across genes and tissues

Many regulatory factors impact the expression of individual genes including, but not limited, to microRNA, long non-coding RNA (lncRNA), transcription factors (TFs), cis-methylation, copy number variation (CNV), and single-nucleotide polymorphisms (SNPs). While each mechanism can influence gene expression substantially, the relative importance of each mechanism at the level of individual genes and tissues is poorly understood. Here, we present the integrative Models of Estimated gene expression (iModEst), which details the relative contribution of different regulators to the gene expression of 16,000 genes and 21 tissues within The Cancer Genome Atlas (TCGA). Specifically, we derive predictive models of gene expression using tumour data and test their predictive accuracy in cancerous and tumour-adjacent tissues. Our models can explain up to 70% of the variance in gene expression across 43% of the genes within both tumour and tumour-adjacent tissues. We confirm that TF expression best predicts gene expression in both tumour and tumour-adjacent tissue whereas methylation predictive models in tumour tissues does not transfer well to tumour adjacent tissues. We find new patterns and recapitulate previously reported relationships between regulator and gene-expression, such as CNV-predicted FGFR2 expression and SNP-predicted TP63 expression. Together, iModEst offers an interactive, comprehensive atlas of individual regulator-gene-tissue expression relationships as well as relationships between regulators.

Mini-review of clinical data service platforms in the era of artificial intelligence: A case study of the iHi data platform

In the past two decades, healthcare organizations have transitioned from the early stages of digitization and digitalization to a more comprehensive process of digital transformation, a shift significantly accelerated by the advent of artificial intelligence (AI). Consequently, the development of high-quality clinical data warehouses, derived from electronic health records (EHRs) and enriched with multidomain data, such as genomics, proteomics, and Internet of Things (IoT) information, has become essential for the creation of the modern patient digital twin (PDT). This approach is critical for leveraging AI in the evolving landscape of clinical practice. Leading medical centers and healthcare institutions have adopted this model, as summarized in this review. Since 2020, China Medical University Hospital (CMUH) has been constructing its data ecosystem by integrating EHRs with extensive genomic databases. This initiative has led to the development of a data service platform, the ignite Hyper-intelligence (iHi®) platform. The iHi platform serves as a case study exemplifying the workflow of the smart data chip, which facilitates the deep cleaning and reliable de-identification of clinical data while incorporating analytical platforms related to genomics and the microbiome to enhance insight extraction processes. The ability to predict complex interactions and disease trajectories among PDTs, digital counterparts of healthcare professionals, and virtual socioeconomic environments will be pivotal in advancing personalized healthcare and optimizing patient outcomes. Future challenges will involve the unification of cross-institutional data platforms and ensuring the interoperability of AI inferences-key factors that will define the next era of AI-driven healthcare.

Fine-mapping the CYP2A6 regional association with nicotine metabolism among African American smokers

The nicotine metabolite ratio (NMR; 3'hydroxycotinine/cotinine) is a stable biomarker for CYP2A6 enzyme activity and nicotine clearance, with demonstrated clinical utility in personalizing smoking cessation treatment. Common genetic variation in the CYP2A6 region is strongly associated with NMR in smokers. Here, we investigated this regional association in more detail. We evaluated the association of CYP2A6 single-nucleotide polymorphisms (SNPs) and * alleles with NMR among African American smokers (N = 953) from two clinical trials of smoking cessation. Stepwise conditional analysis and Bayesian fine-mapping were undertaken. Putative causal variants were incorporated into an existing African ancestry-specific genetic risk score (GRS) for NMR, and the performance of the updated GRS was evaluated in both African American (n = 953) and European ancestry smokers (n = 933) from these clinical trials. Five independent associations with NMR in the CYP2A6 region were identified using stepwise conditional analysis, including the deletion variant CYP2A6*4 (beta = -0.90, p = 1.55 × 10-11). Six putative causal variants were identified using Bayesian fine-mapping (posterior probability, PP = 0.67), with the top causal configuration including CYP2A6*4, rs116670633, CYP2A6*9, rs28399451, rs8192720, and rs10853742 (PP = 0.09). Incorporating these putative causal variants into an existing ancestry-specific GRS resulted in comparable prediction of NMR within African American smokers, and improved trans-ancestry portability of the GRS to European smokers. Our findings suggest that both * alleles and SNPs underlie the association of the CYP2A6 region with NMR among African American smokers, identify a shortlist of variants that may causally influence nicotine clearance, and suggest that portability of GRSs across populations can be improved through inclusion of putative causal variants.

Increasing specificity in ADHD genetic association studies during childhood: use of the oxytocin-vasopressin pathway in attentional processes suggests specific mechanism for endophenotypes in the 2004 Pelotas birth (Brazil) cohort

Attentional executive functions, representing a set of self-regulatory cognitive skills, can be a potential Attention-Deficit/Hyperactivity Disorder (ADHD) endophenotype useful for exploring the huge heterogeneity associated to the disorder. Specific biological pathways like the oxytocin-vasopressin pathway (OT-AVP) can unreel ADHD polygenicity. Here, we test the association between genome-wide ADHD polygenic score (PGS) (ADHD-PGS) and both ADHD symptoms and attentional executive functions in the participants of the 2004 Pelotas (Brazil) birth cohort study (N = 4231). We also investigated whether the OT-AVP genomic pathway (OT/AVPADHD-PGS) is involved in the etiology of ADHD and whether it influences the specificity of attentional functions. ADHD symptoms were assessed through the Strength and Difficulties Questionnaire (SDQ) and the attentional executive functions were evaluated by the Test-of-Everyday-Attention-for-Children (TEA-Ch) at 11 years follow-up. The ADHD-PGS and OT/AVPADHD-PGS were constructed based on the most recent ADHD GWAS meta-analytic statistics. The OT/AVPADHD-PGS included only functional relevant genes for the pathway using KEGG repository. ADHD-PGS was associated with ADHD symptoms and attentional control/switching domain. OT/AVPADHD-PGS showed an enrichment for selective attention domain [number of targets (β = - 0.09, 95% CI = - 0.17; - 0.02, competitive-P = 0.025); attention score (β = 0.11, 95% CI = 0.001; 0.23, competitive-P = 0.050), and in attentional control/switching domain [verbal processing speed (β = 0.27, 95% CI = 0.05; 0.50, competitive-P = 0.041); attentional control (β = 0.42, 95% CI = 0.12; 0.73, competitive-P = 0.033). Our results show a specific role of the OT/AVP pathway in attentional executive functions and suggest that increasing both phenotypic and genetic specificity is of great value. These findings have clinical relevance since OT/AVP have a role in attention toward social cues and shared attentions, which are impaired in children with ADHD.

The Evolutionary Forest of Pancreatic Cancer

SIGNIFICANCE

Although the pancreatic cancer genome has been described, it has not been explored with respect to stages of diagnosis or treatment bottlenecks. We now describe and quantify the genomic features of PDAC in the context of evolutionary metrics and in doing so have identified a novel prognostic biomarker.

Genomic Exploration of Essential Hypertension in African-Brazilian Quilombo Populations: A Comprehensive Approach with Pedigree Analysis and Family-Based Association Studies

Background

Essential Hypertension (EH) is a global health issue. Despite extensive research, much of EH heritability remains unexplained. We investigated the genetic basis of EH in African-derived individuals from partially isolated quilombo populations in Vale do Ribeira (SP-Brazil).

Methods

Samples from 431 individuals (167 affected, 261 unaffected, 3 unknown) were genotyped using a 650k SNP array. Estimated global ancestry proportions were 47% African, 36% European, and 16% Native American. We constructed six pedigrees using additional data from 673 individuals and created three non-overlapping SNP subpanels. We phased haplotypes and performed local ancestry analysis to account for admixture. Genome-wide linkage analysis (GWLA) and fine-mapping via family-based association studies (FBAS) were conducted, prioritizing EH-associated genes through systematic approach involving databases like PubMed, ClinVar, and GWAS Catalog.

Results

Linkage analysis identified 22 regions of interest (ROIs) with LOD scores ranging 1.45-3.03, encompassing 2,363 genes. Fine-mapping (FBAS) identified 60 EH-related candidate genes and 117 suggestive/significant variants. Among these, 14 genes, including PHGDH, S100A10, MFN2, and RYR2, were strongly related to hypertension harboring 29 suggestive/significant SNPs.

Conclusions

Through a complementary approach - combining admixture-adjusted GWLA based on Markov chain Monte Carlo methods, FBAS on known and imputed data, and gene prioritizing - new loci, variants, and candidate genes were identified. These findings provide targets for future research, replication in other populations, facilitate personalized treatments, and improve public health towards African-derived underrepresented populations. Limitations include restricted SNP coverage, self-reported pedigree data, and lack of available EH genomic studies on admixed populations for independent validation, despite the performed genetic correlation analyses using summary statistics.

The influence of fetal sex on maternal blood pressure in pregnancy

Background

Pregnancy with a male fetus carries a higher risk of term pre-eclampsia than pregnancy with a female fetus. Based on evidence that maternal blood pressure (BP) may be raised in pregnancies with Beckwith-Wiedemann syndrome (fetal overgrowth), a possible contributing factor to the association between male sex and term pre-eclampsia is that males grow faster, reaching ~130 g higher birth weight, on average, than females. The association between fetal sex and maternal BP in healthy pregnancies is not known. We hypothesized that male sex would be associated with higher maternal BP in healthy pregnancies, and that this association would be explained by birth weight differences between males and females.

Methods and findings

We tested the association between fetal sex and maternal systolic (SBP) and diastolic blood pressure (DBP), measured at ~28 weeks of gestation, in a meta-analysis of five different cohorts of mother-child pairs (n up to 109,842). Maternal BP was analyzed as both a continuous and dichotomized (high BP: yes or no) outcome. Linear regression models were constructed with and without adjustment for birth weight to assess whether any difference in maternal BP was explained by the difference in birth weight between male and female babies. Lastly, we constructed a fetal genetic score for birth weight using 186 own-birth-weight-associated single-nucleotide polymorphisms (SNPs) to test whether birth-weight-raising-alleles in the fetus were associated with maternal BP in pregnancy (n up to 32,232). Both maternal SBP and DBP were higher in pregnancy when carrying a male fetus compared to a female fetus (mean difference 0.35 mmHg [95%CI: 0.15-0.55] and 0.35 mmHg [95%CI: 0.21-0.49], for SBP and DBP, respectively). An independent effect of fetal sex remained when including birth weight but attenuated slightly (0.22 mmHg [95%CI: 0.02-0.42] and 0.31 mmHg [95%CI: 0.17-0.45], for SBP and DBP respectively). A positive effect estimate was found for odds of experiencing high maternal BP given pregnancy with a male fetus, but confidence intervals were wide (OR 1.05 [95%CI: 0.98-1.12]). No evidence for an association was found between a fetal birth weight genetic score and SBP or DBP when conditioned on maternal genotype.

Conclusions

We found strong evidence to support a small effect of male fetal sex on higher maternal BP in pregnancy and that larger fetal size at birth does not contribute to a substantial part of this association. Our findings do not indicate a difference in maternal BP that would warrant changes to routine monitoring in clinical practice but do suggest that male sex may be a contributing risk factor for BP-related complications.

Accelerometer-derived sleep metrics in adolescents reveal shared genetic influences with obesity and stress in a Brazilian birth cohort study

We aimed to test the association between sleep-related polygenic scores (PGSs) and accelerometer-based sleep metrics among Brazilian adolescents and to evaluate potential mechanisms underlying the association through the enrichment of obesity, and cortisol pathway-specific polygenic scores (PRSet). Utilizing data from The 2004 Pelotas (Brazil) Birth Cohort, sleep time window and sleep efficiency were measured at the 11-year-old follow-up using ActiGraph accelerometers. Three sleep PGSs were developed based on the most recent genome-wide association study of accelerometer-based sleep measures. PRSet, calculated using variants linked to body mass index (BMI) and plasmatic cortisol concentration, aimed to assess pleiotropic effects. Linear regression models, adjusted for sex and the first 10 principal components of ancestry, were employed to explore the impact of sleep PGS and specific-PRSet on sleep phenotypes. The number of nocturnal sleep episodes-PGS was positively associated with sleep time window (β = 2.306, SE: 0.92, p = .011). Nocturnal sleep episodes were also associated with sleep time window when restricted to BMI-PRSet (β = 2.682, SE: 0.912, competitive p = .003). Both the number of sleep episodes and sleep time window cortisol-PRSets were associated (β = .002, SE: 0.001, p = .013; β = .003, SE: 0.001, p = .003, respectively) and exhibited enrichment in molecular pathways (competitive p = .011; competitive p = .003, respectively) with sleep efficiency. Sleep polygenetic components observed in European adults may partially explain the accelerometer-based sleep time window in Brazilian adolescents. Specific BMI molecular pathways strengthened the association between sleep PGS and sleep time window, while the cortisol concentration pathway had a significant impact on the genetic liability for sleep efficiency. Our results suggest genetic overlap as a potential etiological pathway for sleep-related comorbidities, emphasizing common genetic mechanisms.

A genome-wide association study for recurrent laryngeal neuropathy in the Thoroughbred horse identifies a candidate gene that regulates myelin structure

BACKGROUND

Equine recurrent laryngeal neuropathy (RLN) is an economically important upper respiratory tract (URT) disease with a genetic contribution to risk, but genetic variants independent of height have not been identified for Thoroughbreds. The method of clinical assessment for RLN is critical to accurately phenotype groups for genetic studies.

OBJECTIVES

To identify genetic risk loci for RLN in Thoroughbreds in a genome-wide association study (GWAS) following high-resolution phenotyping.

STUDY DESIGN

Case-control.

METHODS

Thoroughbred horses were characterised as RLN cases and controls using resting and exercising URT endoscopic examinations and laryngeal ultrasonography, with the case-cohort supplemented using a questionnaire. Genotypes for 43 831 autosomal single-nucleotide polymorphisms (SNPs) from n = 235 horses (n = 110 cases; n = 125 controls) were used to estimate trait heritability and identify significantly associated SNPs in a GWAS. Haplotypes were examined in cases and controls and risk allele frequencies were examined in a population cohort (n = 3126).

RESULTS

Heritability was h2 = 0.30 including sex and 5PCs as covariates. A SNP on ECA20 located between candidate genes, DAAM2 and LRFN2, was significantly associated with RLN. Six index SNPs with allelic effect sizes OR = 1.5-2.9 were identified on ECA1, ECA14, and ECA20 close to candidate genes ATPA10, KCNN2, and TFAP2A. Eleven ECA20 SNPs defined seven haplotypes with homozygous H2/H2 horses having a 3.1× higher risk of RLN. Risk alleles segregate in the population, and stallions are carriers.

MAIN LIMITATIONS

The main study population was young. Horses in the control group had no evidence of RLN as 2- or 3-year olds but may have developed RLN later.

CONCLUSIONS

Genetic markers for RLN were identified which may be useful for the development of a polygenic risk score. Candidate genes with functions in neuropathies may further the understanding of RLN pathobiology.

PITX2 expression and Neanderthal introgression in HS3ST3A1 contribute to variation in tooth dimensions in modern humans

Dental morphology varies greatly throughout evolution, including in the human lineage, but little is known about the biology of this variation. Here, we use multiomics analyses to examine the genetics of variation in tooth crown dimensions. In a human cohort with mixed continental ancestry, we detected genome-wide significant associations at 18 genome regions. One region includes EDAR, a gene known to impact dental features in East Asians. Furthermore, we find that EDAR variants increase the mesiodistal diameter of all teeth, following an anterior-posterior gradient of decreasing strength. Among the 17 novel-associated regions, we replicate 7/13 in an independent human cohort and find that 4/12 orthologous regions affect molar size in mice. Two association signals point to compelling candidate genes. One is ∼61 kb from PITX2, a major determinant of tooth development. Another overlaps HS3ST3A1, a paralogous neighbor of HS3ST3B1, a tooth enamel knot factor. We document the expression of Pitx2 and Hs3st3a1 in enamel knot and dental epithelial cells of developing mouse incisors. Furthermore, associated SNPs in PITX2 and HS3ST3A1 overlap enhancers active in these cells, suggesting a role for these SNPs in gene regulation during dental development. In addition, we document that Pitx2 and Hs3st3a1/Hs3st3b1 knockout mice show alterations in dental morphology. Finally, we find that associated SNPs in HS3ST3A1 are in a DNA tract introgressed from Neanderthals, consistent with an involvement of HS3ST3A1 in tooth size variation during human evolution.

Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations

Bos taurus (taurine) and Bos indicus (indicine) cattle diverged at least 150,000 years ago and, since that time, substantial genomic differences have evolved between the two lineages. During the last two millennia, genetic exchange in Africa has resulted in a complex tapestry of taurine-indicine ancestry, with most cattle populations exhibiting varying levels of admixture. Similarly, there are several Southern European cattle populations that also show evidence for historical gene flow from indicine cattle, the highest levels of which are found in the Central Italian White breeds. Here we use two different software tools (MOSAIC and ELAI) for local ancestry inference (LAI) with genome-wide high- and low-density SNP array data sets in hybrid African and residually admixed Southern European cattle populations and obtained broadly similar results despite critical differences in the two LAI methodologies used. Our analyses identified genomic regions with elevated levels of retained or introgressed ancestry from the African taurine, European taurine, and Asian indicine lineages. Functional enrichment of genes underlying these ancestry peaks highlighted biological processes relating to immunobiology and olfaction, some of which may relate to differing susceptibilities to infectious diseases, including bovine tuberculosis, East Coast fever, and tropical theileriosis. Notably, for retained African taurine ancestry in admixed trypanotolerant cattle we observed enrichment of genes associated with haemoglobin and oxygen transport. This may reflect positive selection of genomic variants that enhance control of severe anaemia, a debilitating feature of trypanosomiasis disease, which severely constrains cattle agriculture across much of sub-Saharan Africa.

Two founder variants account for over 90% of pathogenic BRCA alleles in the Orkney and Shetland Isles in Scotland

For breast and ovarian cancer risk assessment in the isolated populations of the Northern Isles of Orkney and Shetland (in Scotland, UK) and their diasporas, quantifying genetically drifted BRCA1 and BRCA2 pathogenic variants is important. Two actionable variants in these genes have reached much higher frequencies than in cosmopolitan UK populations. Here, we report a BRCA2 splice acceptor variant, c.517-2A>G, found in breast and ovarian cancer families from Shetland. We investigated the frequency and origin of this variant in a population-based research cohort of people of Shetland ancestry, VIKING I. The variant segregates with female breast and ovarian cancer in diagnosed cases and is classified as pathogenic. Exome sequence data from 2108 VIKING I participants with three or more Shetlandic grandparents was used to estimate the population prevalence of c.517-2A>G in Shetlanders. Nine VIKING I research volunteers carry this variant, on a shared haplotype (carrier frequency 0.4%). This frequency is ~130-fold higher than in UK Biobank, where the small group of carriers has a different haplotype. Records of birth, marriage and death indicate genealogical linkage of VIKING I carriers to a founder from the Isle of Whalsay, Shetland, similar to our observations for the BRCA1 founder variant c.5207T>C from Westray, Orkney. In total, 93.5% of pathogenic BRCA variant carriers in Northern Isles exomes are accounted for by these two drifted variants. We thus provide the scientific evidence of an opportunity for screening people of Orcadian and Shetlandic origins for each drifted pathogenic variant, particularly women with Westray or Whalsay ancestry.

Analysis of the winter oilseed rape recombination landscape suggests maternal-paternal bias

Recombination, the reciprocal exchange of DNA between homologous chromosomes, is a mandatory step necessary for meiosis progression. Crossovers between homologous chromosomes generate new combinations of alleles and maintain genetic diversity. Due to genetic, epigenetic, and environmental factors, the recombination landscape is highly heterogeneous along the chromosomes and it also differs between populations and between sexes. Here, we investigated recombination characteristics across the 19 chromosomes of the model allopolyploid crop species oilseed rape (Brassica napus L.), using two unique multiparental populations derived from two genetically divergent founder pools, each of which comprised 50 genetically diverse founder accessions. A fully balanced, pairwise chain-crossing scheme was utilized to create each of the two populations. A total of 3213 individuals, spanning five successive generations, were genotyped using a 15K SNP array. We observed uneven distribution of recombination along chromosomes, with some genomic regions undergoing substantially more frequent recombination in both populations. In both populations, maternal recombination events were more frequent than paternal recombination. This study provides unique insight into the recombination landscape at chromosomal level and reveals a maternal-paternal bias for recombination number with implications for breeding.

Genome-wide association analysis of cystatin c and creatinine kidney function in Chinese women

BACKGROUND

With increasing incidence and treatment costs, chronic kidney disease (CKD) has become an important public health problem in China, especially in females. However, the genetic determinants are very limited. The estimated glomerular filtration rate (eGFR) based on creatinine is commonly used as a measure of renal function but can be easily affected by other factors. In contrast, eGFR based on both creatinine and cystatin C (eGFRcr-cys) improved the diagnostic accuracy of CKD. To our knowledge, no genome-wide association analysis of eGFRcr-cys has been conducted in the Chinese population.

METHODS

By conducting a Genome-Wide association study(GWAS), a method used to identify associations between genetic regions (genomes) and traits/diseases, we examined the relationship between genetic factors and eGFRcr-cys in Chinese women, with 1983 participants and 3,838,121 variants included in the final analysis.

RESULT

One significant locus (20p11.21) was identified in the Chinese female population, which has been reported to be associated with eGFR based on cystatin C (eGFRcys) in the European population. More importantly, we found two new suggestive loci (1p31.1 and 11q24.2), which have not yet been reported. A total of three single nucleotide polymorphisms were identified as the most important variants in these regions, including rs2405367 (CST3), rs66588571(KRT8P21), and rs626995 (OR8B2).

CONCLUSION

We identified 3 loci 20p11.21, 1p31.1, and 11q24.2 to be significantly associated with eGFRcr-cys. These findings and subsequent functional analysis describe new biological clues related to renal function in Chinese women and provide new ideas for the diagnosis and treatment development of CKD.

Gene - maltreatment interplay in adult ADHD symptoms: main role of a gene-environment correlation effect in a Brazilian population longitudinal study

Childhood maltreatment correlates with attention-deficit/hyperactivity disorder (ADHD) in previous research. The interaction between ADHD genetic predisposition and maltreatment's impact on ADHD symptom risk remains unclear. We aimed to elucidate this relationship by examining the interplay between a polygenic score for ADHD (ADHD-PGS) and childhood maltreatment in predicting ADHD symptoms during young adulthood. Using data from the 2004 Pelotas (Brazil) birth cohort comprising 4231 participants, we analyzed gene-environment interaction (GxE) and correlation (rGE). We further explored rGE mechanisms through mediation models. ADHD symptoms were assessed at age 18 via self-report (Adult Self Report Scale - ASRS) and mother-reports (Strength and Difficulties Questionnaire - SDQ). The ADHD-PGS was derived from published ADHD GWAS meta-analysis. Physical and psychological child maltreatment was gauged using the Parent-Child Conflict Tactics Scale (CTSPC) at ages 6 and 11, with a mean score utilized as a variable. The ADHD-PGS exhibited associations with ADHD symptoms on both ASRS (β = 0.53; 95% CI: 0.03; 1.03, p = 0.036), and SDQ (β = 0.20; 95% CI: 0.08; 0.32, p = 0.001) scales. The total mean maltreatment score was associated with ADHD symptoms using both scales [(βASRS = 0.51; 95% CI: 0.26;0.77) and (βSDQ = 0.24; 95% CI: 0.18;0.29)]. The ADHD-PGS was associated with total mean maltreatment scores (β = 0.09; 95% CI: 0.01; 0.17; p = 0.030). Approximately 47% of the total effect of ADHD-PGS on maltreatment was mediated by ADHD symptoms at age 6. No evidence supported gene-environment interaction in predicting ADHD symptoms. Our findings underscore the significant roles of genetics and childhood maltreatment as predictors for ADHD symptoms in adulthood, while also indicating a potential evocative mechanism through gene-environment correlation.

Identification of risk loci for postpartum depression in a genome-wide association study

AIM

Genome-wide association studies (GWAS) of postpartum depression (PPD) based on accumulated cohorts with multiple ethnic backgrounds have failed to identify significantly associated loci. Herein, we conducted a GWAS of Japanese perinatal women along with detailed confounding information to uncover PPD-associated loci.

METHODS

The first and second cohorts (n = 9260 and n = 8582 perinatal women enrolled in the Tohoku Medical Megabank Project) and the third cohort (n = 997), recruited at Nagoya University, underwent genotyping. Of them, 1421, 1264, and 225 were classified as PPD based on the Edinburgh Postnatal Depression Scale 1 month after delivery. The most influential confounding factors of genetic liability to PPD were selected, and logistic regression analyses were performed to evaluate genetic associations with PPD after adjusting for confounders.

RESULTS

A meta-analysis of GWAS results from the three cohorts identified significant associations between PPD and the following loci (P < 5 × 10-8) by integrating the number of deliveries and the number of family members living together as the most influential confounders: rs377546683 at DAB1, rs11940752 near UGT8, rs141172317, rs117928019, rs76631412, rs118131805 at DOCK2, rs188907279 near ZNF572, rs504378, rs690150, rs491868, rs689917, rs474978, rs690118, rs690253 near DIRAS2, rs1435984417 at ZNF618, rs57705782 near PTPRM, and rs185293917 near PDGFB. Pathway analyses indicated that SNPs suggestively associated with PPD were mostly over-represented in categories including long-term depression, GnRH signaling, glutamatergic synapse, oxytocin signaling, and Rap1 signaling.

CONCLUSION

The current GWAS study identified eight loci significantly associated with PPD, which may clarify the genetic structure underlying its pathogenesis.

Gut microbial and human genetic signatures of inflammatory bowel disease increase risk of comorbid mental disorders

The high prevalence of comorbid mental disorders (CMDs) in patients with inflammatory bowel disease (IBD) is well-documented. This study delves into the intricate CMD-IBD relationship through comprehensive analyses using human variants, gut microbiome, and anxiety/depression estimates from a cohort of 507 IBD patients and 75 controls. Notably, patients with IBD, especially those with CMD, exhibited lower diversity than controls. We identified 106 differentially abundant taxa (DATs) in IBD patients compared to controls and 21 DATs distinguishing CMD-affected from CMD-free IBD patients. Microbial IBD-risk scores, reflecting an individual's microbial burden for IBD, revealed a significant enrichment of IBD-risk signatures in CMD-affected patients compared to CMD-free patients. Additionally, there was an IBD-risk variant potentially regulating the abundance of an IBD/CMD-associated DAT, suggesting an interplay between IBD-risk variants and dysbiosis in CMD. Our investigation underscores the pivotal role of IBD-associated gut dysbiosis in predisposing IBD patients to CMD, partially through genetic variant-mediated mechanisms.

Discovery and prioritization of genetic determinants of kidney function in 297,355 individuals from Taiwan and Japan

Current genome-wide association studies (GWAS) for kidney function lack ancestral diversity, limiting the applicability to broader populations. The East-Asian population is especially under-represented, despite having the highest global burden of end-stage kidney disease. We conducted a meta-analysis of multiple GWASs (n = 244,952) on estimated glomerular filtration rate and a replication dataset (n = 27,058) from Taiwan and Japan. This study identified 111 lead SNPs in 97 genomic risk loci. Functional enrichment analyses revealed that variants associated with F12 gene and a missense mutation in ABCG2 may contribute to chronic kidney disease (CKD) through influencing inflammation, coagulation, and urate metabolism pathways. In independent cohorts from Taiwan (n = 25,345) and the United Kingdom (n = 260,245), polygenic risk scores (PRSs) for CKD significantly stratified the risk of CKD (p < 0.0001). Further research is required to evaluate the clinical effectiveness of PRSCKD in the early prevention of kidney disease.

Interpretation of SNP combination effects on schizophrenia etiology based on stepwise deep learning with multi-precision data

Schizophrenia genome-wide association studies (GWAS) have reported many genomic risk loci, but it is unclear how they affect schizophrenia susceptibility through interactions of multiple SNPs. We propose a stepwise deep learning technique with multi-precision data (SLEM) to explore the SNP combination effects on schizophrenia through intermediate molecular and cellular functions. The SLEM technique utilizes two levels of precision data for learning. It constructs initial backbone networks with more precise but small amount of multilevel assay data. Then, it learns strengths of intermediate interactions with the less precise but massive amount of GWAS data. The learned networks facilitate identifying effective SNP interactions from the intractably large space of all possible SNP combinations. We have shown that the extracted SNP combinations show higher accuracy than any single SNPs and preserve the accuracy in an independent dataset. The learned networks also provide interpretations of molecular and cellular interactions of SNP combinations toward schizophrenia etiology.

Diversity in Recombination Hotspot Characteristics and Gene Structure Shape Fine-Scale Recombination Patterns in Plant Genomes

During the meiosis of many eukaryote species, crossovers tend to occur within narrow regions called recombination hotspots. In plants, it is generally thought that gene regulatory sequences, especially promoters and 5' to 3' untranslated regions, are enriched in hotspots, but this has been characterized in a handful of species only. We also lack a clear description of fine-scale variation in recombination rates within genic regions and little is known about hotspot position and intensity in plants. To address this question, we constructed fine-scale recombination maps from genetic polymorphism data and inferred recombination hotspots in 11 plant species. We detected gradients of recombination in genic regions in most species, yet gradients varied in intensity and shape depending on specific hotspot locations and gene structure. To further characterize recombination gradients, we decomposed them according to gene structure by rank and number of exons. We generalized the previously observed pattern that recombination hotspots are organized around the boundaries of coding sequences, especially 5' promoters. However, our results also provided new insight into the relative importance of the 3' end of genes in some species and the possible location of hotspots away from genic regions in some species. Variation among species seemed driven more by hotspot location among and within genes than by differences in size or intensity among species. Our results shed light on the variation in recombination rates at a very fine scale, revealing the diversity and complexity of genic recombination gradients emerging from the interaction between hotspot location and gene structure.

A fine-scale genetic map of the Japanese population

Genetic maps are fundamental resources for linkage and association studies. A fine-scale genetic map can be constructed by inferring historical recombination events from the genome-wide structure of linkage disequilibrium-a non-random association of alleles among loci-by using population-scale sequencing data. We constructed a fine-scale genetic map and identified recombination hotspots from 10 092 551 bi-allelic high-quality autosomal markers segregating among 150 unrelated Japanese individuals whose genotypes were determined by high-coverage (30×) whole-genome sequencing, and the genotype quality was carefully controlled by using their parents' and offspring's genotypes. The pedigree information was also utilized for haplotype phasing. The resulting genome-wide recombination rate profiles were concordant with those of the worldwide population on a broad scale, and the resolution was much improved. We identified 9487 recombination hotspots and confirmed the enrichment of previously known motifs in the hotspots. Moreover, we demonstrated that the Japanese genetic map improved the haplotype phasing and genotype imputation accuracy for the Japanese population. The construction of a population-specific genetic map will help make genetics research more accurate.

Genome-wide analyses of neonatal jaundice reveal a marked departure from adult bilirubin metabolism

Jaundice affects almost all neonates in their first days of life and is caused by the accumulation of bilirubin. Although the core biochemistry of bilirubin metabolism is well understood, it is not clear why some neonates experience more severe jaundice and require treatment with phototherapy. Here, we present the first genome-wide association study of neonatal jaundice to date in nearly 30,000 parent-offspring trios from Norway (cases ≈ 2000). The alternate allele of a common missense variant affecting the sequence of UGT1A4 reduces the susceptibility to jaundice five-fold, which replicated in separate cohorts of neonates of African American and European ancestries. eQTL colocalization analyses indicate that the association may be driven by regulation of UGT1A1 in the intestines, but not in the liver. Our results reveal marked differences in the genetic variants involved in neonatal jaundice compared to those regulating bilirubin levels in adults, suggesting distinct genetic mechanisms for the same biological pathways.

Genome-wide association study based on clustering by obesity-related variables uncovers a genetic architecture of obesity in the Japanese and the UK populations

Whether all obesity-related variants contribute to the onset of obesity or one or a few variants cause obesity in genetically heterogeneous populations remains obscure. Here, we investigated the genetic architecture of obesity by clustering the Japanese and British populations with obesity using obesity-related factors. In Step-1, we conducted a genome-wide association study (GWAS) with body mass index (BMI) as the outcome for eligible participants. In Step-2, we assigned participants with obesity (BMI ≥25 kg/m2) to five clusters based on obesity-related factors. Subsequently, participants from each cluster and those with a BMI <25 kg/m2 were combined. A GWAS was conducted for each cluster. Several previously identified obesity-related genes were verified in Step-1. Of the genes detected in Step-1, unique obesity-related genes were detected separately for each cluster in Step-2. Our novel findings suggest that a smaller sample size with increased homogeneity may provide insights into the genetic architecture of obesity.

Bayesian Estimation of Allele-Specific Expression in the Presence of Phasing Uncertainty

Motivation

Allele-specific expression (ASE) analyses aim to detect imbalanced expression of maternal versus paternal copies of an autosomal gene. Such allelic imbalance can result from a variety of cis-acting causes, including disruptive mutations within one copy of a gene that impact the stability of transcripts, as well as regulatory variants outside the gene that impact transcription initiation. Current methods for ASE estimation suffer from a number of shortcomings, such as relying on only one variant within a gene, assuming perfect phasing information across multiple variants within a gene, or failing to account for alignment biases and possible genotyping errors.

Results

We developed BEASTIE, a Bayesian hierarchical model designed for precise ASE quantification at the gene level, based on given genotypes and RNA-Seq data. BEASTIE addresses the complexities of allelic mapping bias, genotyping error, and phasing errors by incorporating empirical phasing error rates derived from Genome-in-a-Bottle individual NA12878. BEASTIE surpasses existing methods in accuracy, especially in scenarios with high phasing errors. This improvement is critical for identifying rare genetic variants often obscured by such errors. Through rigorous validation on simulated data and application to real data from the 1000 Genomes Project, we establish the robustness of BEASTIE. These findings underscore the value of BEASTIE in revealing patterns of ASE across gene sets and pathways.

Availability and Implementation

The software is freely available from https://github.com/x811zou/BEASTIE . BEASTIE is available as Python source code and as a Docker image.

Supplementary information

Additional information is available online.

haploMAGIC: accurate phasing and detection of recombination in multiparental populations despite genotyping errors

Recombination is a key mechanism in breeding for promoting genetic variability. Multiparental populations (MPPs) constitute an excellent platform for precise genotype phasing, identification of genome-wide crossovers (COs), estimation of recombination frequencies, and construction of recombination maps. Here, we introduce haploMAGIC, a pipeline to detect COs in MPPs with single-nucleotide polymorphism (SNP) data by exploiting the pedigree relationships for accurate genotype phasing and inference of grandparental haplotypes. haploMAGIC applies filtering to prevent false-positive COs due to genotyping errors (GEs), a common problem in high-throughput SNP analysis of complex plant genomes. Hence, it discards haploblocks not reaching a specified minimum number of informative alleles. A performance analysis using populations simulated with AlphaSimR revealed that haploMAGIC improves upon existing methods of CO detection in terms of recall and precision, most notably when GE rates are high. Furthermore, we constructed recombination maps using haploMAGIC with high-resolution genotype data from 2 large multiparental populations of winter rapeseed (Brassica napus). The results demonstrate the applicability of the pipeline in real-world scenarios and showed good correlations in recombination frequency compared with alternative software. Therefore, we propose haploMAGIC as an accurate tool at CO detection with MPPs that shows robustness against GEs.

Genetic Ancestry and Self-Reported "Skin Color/Race" in the Urban Admixed Population of São Paulo City, Brazil

Epidemiological studies frequently classify groups based on phenotypes like self-reported skin color/race, which inaccurately represent genetic ancestry and may lead to misclassification, particularly among individuals of multiracial backgrounds. This study aimed to characterize both global and local genome-wide genetic ancestries and to assess their relationship with self-reported skin color/race in an admixed population of Sao Paulo city. We analyzed 226,346 single-nucleotide polymorphisms from 841 individuals participating in the population-based ISA-Nutrition study. Our findings confirmed the admixed nature of the population, demonstrating substantial European, significant Sub-Saharan African, and minor Native American ancestries, irrespective of skin color. A correlation was observed between global genetic ancestry and self-reported color-race, which was more evident in the extreme proportions of African and European ancestries. Individuals with higher African ancestry tended to identify as Black, those with higher European ancestry tended to identify as White, and individuals with higher Native American ancestry were more likely to self-identify as Mixed, a group with diverse ancestral compositions. However, at the individual level, this correlation was notably weak, and no deviations were observed for specific regions throughout the individual's genome. Our findings emphasize the significance of accurately defining and thoroughly analyzing race and ancestry, especially within admixed populations.

The great tit HapMap project: A continental-scale analysis of genomic variation in a songbird

A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.

Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish

Despite deep evolutionary conservation, recombination rates vary greatly across the genome and among individuals, sexes and populations. Yet the impact of this variation on adaptively diverging populations is not well understood. Here we characterized fine-scale recombination landscapes in an adaptively divergent pair of marine and freshwater populations of threespine stickleback from River Tyne, Scotland. Through whole-genome sequencing of large nuclear families, we identified the genomic locations of almost 50,000 crossovers and built recombination maps for marine, freshwater and hybrid individuals at a resolution of 3.8 kb. We used these maps to quantify the factors driving variation in recombination rates. We found strong heterochiasmy between sexes but also differences in recombination rates among ecotypes. Hybrids showed evidence of significant recombination suppression in overall map length and in individual loci. Recombination rates were lower not only within individual marine-freshwater-adaptive loci, but also between loci on the same chromosome, suggesting selection on linked gene 'cassettes'. Through temporal sampling along a natural hybrid zone, we found that recombinants showed traits associated with reduced fitness. Our results support predictions that divergence in cis-acting recombination modifiers, whose functions are disrupted in hybrids, may play an important role in maintaining differences among adaptively diverging populations.

Tracing the fine-scale demographic history and recent admixture in Hmong-Mien speakers

The linguistic, historical, and subsistent uniqueness of Hmong-Mien (HM) speakers offers a wonderful opportunity to investigate how these factors impact the genetic structure. The genetic differentiation among HM speakers and their population history are not well characterized. Here, we generate genome-wide data from 65 Yao ethnicity samples and analyze them with published data, particularly by leveraging haplotype-based methods. We determined that the fine-scale genetic substructure of HM speakers corresponds better with linguistic classification than with geography. Particularly, parallels between serial founder events and language differentiations can be observed in West Hmongic speakers. Multiple lines of evidence indicate that ~500-year-old GaoHuaHua individuals are most closely related to West Hmongic-speaking Bunu. The strong genetic bottleneck of some HM-speaking groups, especially Bunu, could potentially be associated with their long-term practice of swidden agriculture to some degree. The inferred admixture dates for most of the HM speakers overlap with the reign of the Ming dynasty (1368-1644 CE). Besides a common genetic origin for HM speakers, their genetic ancestry is shared primarily with neighboring Han Chinese and Tai-Kadai speakers in south China. In conclusion, our analyses reveal that recent isolation and admixture events have contributed to the genetic population history of present-day HM speakers.

Cancer risks among first-degree relatives of women with a genetic predisposition to breast cancer

BACKGROUND

Associations between germline alterations in women and cancer risks among their relatives are largely unknown.

METHODS

We identified women from 2 Swedish cohorts Karolinska Mammography Project for Risk Prediction of Breast Cancer (KARMA) and prevalent KARMA (pKARMA), including 28 362 women with genotyping data and 13 226 with sequencing data. Using Swedish Multi-Generation Register, we linked these women to 133 389 first-degree relatives. Associations between protein-truncating variants in 8 risk genes and breast cancer polygenic risk score in index women and cancer risks among their relatives were modeled via Cox regression.

RESULTS

Female relatives of index women who were protein-truncating variant carriers in any of the 8 risk genes had an increased breast cancer risk compared with those of noncarriers (hazard ratio [HR] = 1.85, 95% confidence interval [CI] = 1.52 to 2.27), with the strongest association found for protein-truncating variants in BRCA1 and 2. These relatives had a statistically higher risk of early onset than late-onset breast cancer (P = .001). Elevated breast cancer risk was also observed in female relatives of index women with higher polygenic risk score (HR per SD = 1.28, 95% CI = 1.23 to 1.32). The estimated lifetime risk was 22.3% for female relatives of protein-truncating variant carriers and 14.4% for those related to women in the top polygenic risk score quartile. Moreover, relatives of index women with protein-truncating variant presence (HR = 1.30, 95% CI = 1.06 to 1.59) or higher polygenic risk score (HR per SD = 1.04, 95% CI = 1.01 to 1.07) were also at higher risk of nonbreast hereditary breast and ovary cancer syndrome-related cancers.

CONCLUSIONS

Protein-truncating variants of risk genes and higher polygenic risk score in index women are associated with an increased risk of breast and other hereditary breast and ovary syndrome-related cancers among relatives.

History of tuberculosis disease is associated with genetic regulatory variation in Peruvians

A quarter of humanity is estimated to have been exposed to Mycobacterium tuberculosis (Mtb) with a 5-10% risk of developing tuberculosis (TB) disease. Variability in responses to Mtb infection could be due to host or pathogen heterogeneity. Here, we focused on host genetic variation in a Peruvian population and its associations with gene regulation in monocyte-derived macrophages and dendritic cells (DCs). We recruited former household contacts of TB patients who previously progressed to TB (cases, n = 63) or did not progress to TB (controls, n = 63). Transcriptomic profiling of monocyte-derived DCs and macrophages measured the impact of genetic variants on gene expression by identifying expression quantitative trait loci (eQTL). We identified 330 and 257 eQTL genes in DCs and macrophages (False Discovery Rate (FDR) < 0.05), respectively. Four genes in DCs showed interaction between eQTL variants and TB progression status. The top eQTL interaction for a protein-coding gene was with FAH, the gene encoding fumarylacetoacetate hydrolase, which mediates the last step in mammalian tyrosine catabolism. FAH expression was associated with genetic regulatory variation in cases but not controls. Using public transcriptomic and epigenomic data of Mtb-infected monocyte-derived dendritic cells, we found that Mtb infection results in FAH downregulation and DNA methylation changes in the locus. Overall, this study demonstrates effects of genetic variation on gene expression levels that are dependent on history of infectious disease and highlights a candidate pathogenic mechanism through pathogen-response genes. Furthermore, our results point to tyrosine metabolism and related candidate TB progression pathways for further investigation.

Understanding the genomic heterogeneity of North African Imazighen: from broad to microgeographical perspectives

The strategic location of North Africa has led to cultural and demographic shifts, shaping its genetic structure. Historical migrations brought different genetic components that are evident in present-day North African genomes, along with autochthonous components. The Imazighen (plural of Amazigh) are believed to be the descendants of autochthonous North Africans and speak various Amazigh languages, which belong to the Afro-Asiatic language family. However, the arrival of different human groups, especially during the Arab conquest, caused cultural and linguistic changes in local populations, increasing their heterogeneity. We aim to characterize the genetic structure of the region, using the largest Amazigh dataset to date and other reference samples. Our findings indicate microgeographical genetic heterogeneity among Amazigh populations, modeled by various admixture waves and different effective population sizes. A first admixture wave is detected group-wide around the twelfth century, whereas a second wave appears in some Amazigh groups around the nineteenth century. These events involved populations with higher genetic ancestry from south of the Sahara compared to the current North Africans. A plausible explanation would be the historical trans-Saharan slave trade, which lasted from the Roman times to the nineteenth century. Furthermore, our investigation shows that assortative mating in North Africa has been rare.

Selection signatures and landscape genomics analysis to reveal climate adaptation of goat breeds

Goats have achieved global prominence as essential livestock since their initial domestication, primarily owing to their remarkable adaptability to diverse environmental and production systems. Differential selection pressures influenced by climate have led to variations in their physical attributes, leaving genetic imprints within the genomes of goat breeds raised in diverse agroecological settings. In light of this, our study pursued a comprehensive analysis, merging environmental data with single nucleotide polymorphism (SNP) variations, to unearth indications of selection shaped by climate-mediated forces in goats. Through the examination of 43,300 SNPs from 51 indigenous goat breeds adapting to different climatic conditions using four analytical methods: latent factor mixed models (LFMM), F-statistics (Fst), Extended haplotype homozygosity across populations (XPEHH), and spatial analysis method (SAM), A total of 74 genes were revealed to display clear signs of selection, which are believed to be influenced by climatic conditions. Among these genes, 32 were consistently identified by at least two of the applied methods, and three genes (DENND1A, PLCB1, and ITPR2) were confirmed by all four approaches. Moreover, our investigation yielded 148 Gene Ontology (GO) terms based on these 74 genes, underlining pivotal biological pathways crucial for environmental adaptation. These pathways encompass functions like vascular smooth muscle contraction, cellular response to heat, GTPase regulator activity, rhythmic processes, and responses to temperature stimuli. Of significance, GO terms about endocrine regulation and energy metabolic responses, key for local adaptation were also uncovered, including biological processes, such as cell differentiation, regulation of peptide hormone secretion, and lipid metabolism. These findings contribute to our knowledge of the genetic structure of climate-triggered adaptation across the goat genome and have practical implications for marker-assisted breeding in goats.

Whole-genome resequencing of Chinese indigenous sheep provides insight into the genetic basis underlying climate adaptation

BACKGROUND

Chinese indigenous sheep are valuable resources with unique features and characteristics. They are distributed across regions with different climates in mainland China; however, few reports have analyzed the environmental adaptability of sheep based on their genome. We examined the variants and signatures of selection involved in adaptation to extreme humidity, altitude, and temperature conditions in 173 sheep genomes from 41 phenotypically and geographically representative Chinese indigenous sheep breeds to characterize the genetic basis underlying environmental adaptation in these populations.

RESULTS

Based on the analysis of population structure, we inferred that Chinese indigenous sheep are divided into four groups: Kazakh (KAZ), Mongolian (MON), Tibetan (TIB), and Yunnan (YUN). We also detected a set of candidate genes that are relevant to adaptation to extreme environmental conditions, such as drought-prone regions (TBXT, TG, and HOXA1), high-altitude regions (DYSF, EPAS1, JAZF1, PDGFD, and NF1) and warm-temperature regions (TSHR, ABCD4, and TEX11). Among all these candidate genes, eight ABCD4, CNTN4, DOCK10, LOC105608545, LOC121816479, SEM3A, SVIL, and TSHR overlap between extreme environmental conditions. The TSHR gene shows a strong signature for positive selection in the warm-temperature group and harbors a single nucleotide polymorphism (SNP) missense mutation located between positions 90,600,001 and 90,650,001 on chromosome 7, which leads to a change in the protein structure of TSHR and influences its stability.

CONCLUSIONS

Analysis of the signatures of selection uncovered genes that are likely related to environmental adaptation and a SNP missense mutation in the TSHR gene that affects the protein structure and stability. It also provides information on the evolution of the phylogeographic structure of Chinese indigenous sheep populations. These results provide important genetic resources for future breeding studies and new perspectives on how animals can adapt to climate change.

Persistent DNA Methylation Changes across the First Year of Life and Prenatal NO2 Exposure in a Canadian Prospective Birth Study

BACKGROUND

Evidence suggests that prenatal air pollution exposure alters DNA methylation (DNAm), which could go on to affect long-term health. It remains unclear whether DNAm alterations present at birth persist through early life. Identifying persistent DNAm changes would provide greater insight into the molecular mechanisms contributing to the association of prenatal air pollution exposure with atopic diseases.

OBJECTIVES

This study investigated DNAm differences associated with prenatal nitrogen dioxide (NO 2 ) exposure (a surrogate measure of traffic-related air pollution) at birth and 1 y of age and examined their role in atopic disease. We focused on regions showing persistent DNAm differences from birth to 1 y of age and regions uniquely associated with postnatal NO 2 exposure.

METHODS

Microarrays measured DNAm at birth and at 1 y of age for an atopy-enriched subset of Canadian Health Infant Longitudinal Development (CHILD) study participants. Individual and regional DNAm differences associated with prenatal NO 2 (n = 128 ) were identified, and their persistence at age 1 y were investigated using linear mixed effects models (n = 124 ). Postnatal-specific DNAm differences (n = 125 ) were isolated, and their association with NO 2 in the first year of life was examined. Causal mediation investigated whether DNAm differences mediated associations between NO 2 and age 1 y atopy or wheeze. Analyses were repeated using biological sex-stratified data.

RESULTS

At birth (n = 128 ), 18 regions of DNAm were associated with NO 2 , with several annotated to HOX genes. Some of these regions were specifically identified in males (n = 73 ), but not females (n = 55 ). The effect of prenatal NO 2 across CpGs within altered regions persisted at 1 y of age. No significant mediation effects were identified. Sex-stratified analyses identified postnatal-specific DNAm alterations.

DISCUSSION

Regional cord blood DNAm differences associated with prenatal NO 2 persisted through at least the first year of life in CHILD participants. Some differences may represent sex-specific alterations, but replication in larger cohorts is needed. The early postnatal period remained a sensitive window to DNAm perturbations. https://doi.org/10.1289/EHP13034.

Genome-wide association study of nausea and vomiting during pregnancy in Japan: the TMM BirThree Cohort Study

BACKGROUND

Nausea and vomiting during pregnancy (NVP) and hyperemesis gravidarum (HG), common conditions affecting most pregnant women, are highly heritable and associated with maternal and fetal morbidity. However, the pathologies underlying NVP and HG and their associated loci are scarce.

METHODS

We performed genome-wide association studies (GWAS) of NVP in pregnant women (n = 23,040) who participated in the Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study in Japan from July 2013 to March 2017. Participants were divided into discovery (n = 9,464) and replication (n = 10,051) stages based on the platform used for their genotyping. Loci that achieved the genome-wide significance level (p < 5.0 × 10- 8) in the discovery stage were selected for genotyping in the replication stage. A meta-analysis integrating the discovery and replication stage results (n = 19,515) was conducted. NVP-related variables were identified as categorical or continuous.

RESULTS

GWAS analysis in the discovery phase revealed loci linked to NVP in two gene regions, 11q22.1 (rs77775955) and 19p13.11 (rs749451 and rs28568614). Loci in these two gene regions have also been shown to be associated with HG in a White European population, indicating the generalizability of the GWAS analyses conducted in this study. Of these, only rs749451 and rs28568614 at 19p13.11 reached the genome-wide suggestive level (p < 1.0 × 10- 5) in the replication stage; however, both loci were significant in the meta-analysis.

CONCLUSIONS

NVP-related loci were identified in the Japanese population at 11q22.1 and 19p13.11, as reported in previous GWAS. This study contributes new evidence on the generalizability of previous GWAS on the association between genetic background and NVP.

Genomic Analyses Capture the Human-Induced Demographic Collapse and Recovery in a Wide-Ranging Cervid

The glacial cycles of the Quaternary heavily impacted species through successions of population contractions and expansions. Similarly, populations have been intensely shaped by human pressures such as unregulated hunting and land use changes. White-tailed and mule deer survived in different refugia through the Last Glacial Maximum, and their populations were severely reduced after the European colonization. Here, we analyzed 73 resequenced deer genomes from across their North American range to understand the consequences of climatic and anthropogenic pressures on deer demographic and adaptive history. We found strong signals of climate-induced vicariance and demographic decline; notably, multiple sequentially Markovian coalescent recovers a severe decline in mainland white-tailed deer effective population size (Ne) at the end of the Last Glacial Maximum. We found robust evidence for colonial overharvest in the form of a recent and dramatic drop in Ne in all analyzed populations. Historical census size and restocking data show a clear parallel to historical Ne estimates, and temporal Ne/Nc ratio shows patterns of conservation concern for mule deer. Signatures of selection highlight genes related to temperature, including a cold receptor previously highlighted in woolly mammoth. We also detected immune genes that we surmise reflect the changing land use patterns in North America. Our study provides a detailed picture of anthropogenic and climatic-induced decline in deer diversity and clues to understanding the conservation concerns of mule deer and the successful demographic recovery of white-tailed deer.

Comparing feature selection and machine learning approaches for predicting CYP2D6 methylation from genetic variation

Introduction

Pharmacogenetics currently supports clinical decision-making on the basis of a limited number of variants in a few genes and may benefit paediatric prescribing where there is a need for more precise dosing. Integrating genomic information such as methylation into pharmacogenetic models holds the potential to improve their accuracy and consequently prescribing decisions. Cytochrome P450 2D6 (CYP2D6) is a highly polymorphic gene conventionally associated with the metabolism of commonly used drugs and endogenous substrates. We thus sought to predict epigenetic loci from single nucleotide polymorphisms (SNPs) related to CYP2D6 in children from the GUSTO cohort.

Methods

Buffy coat DNA methylation was quantified using the Illumina Infinium Methylation EPIC beadchip. CpG sites associated with CYP2D6 were used as outcome variables in Linear Regression, Elastic Net and XGBoost models. We compared feature selection of SNPs from GWAS mQTLs, GTEx eQTLs and SNPs within 2 MB of the CYP2D6 gene and the impact of adding demographic data. The samples were split into training (75%) sets and test (25%) sets for validation. In Elastic Net model and XGBoost models, optimal hyperparameter search was done using 10-fold cross validation. Root Mean Square Error and R-squared values were obtained to investigate each models' performance. When GWAS was performed to determine SNPs associated with CpG sites, a total of 15 SNPs were identified where several SNPs appeared to influence multiple CpG sites.

Results

Overall, Elastic Net models of genetic features appeared to perform marginally better than heritability estimates and substantially better than Linear Regression and XGBoost models. The addition of nongenetic features appeared to improve performance for some but not all feature sets and probes. The best feature set and Machine Learning (ML) approach differed substantially between CpG sites and a number of top variables were identified for each model.

Discussion

The development of SNP-based prediction models for CYP2D6 CpG methylation in Singaporean children of varying ethnicities in this study has clinical application. With further validation, they may add to the set of tools available to improve precision medicine and pharmacogenetics-based dosing.

Differences in polygenic score distributions in European ancestry populations: implications for breast cancer risk prediction

The 313-variant polygenic risk score (PRS313) provides a promising tool for breast cancer risk prediction. However, evaluation of the PRS313 across different European populations which could influence risk estimation has not been performed. Here, we explored the distribution of PRS313 across European populations using genotype data from 94,072 females without breast cancer, of European-ancestry from 21 countries participating in the Breast Cancer Association Consortium (BCAC) and 225,105 female participants from the UK Biobank. The mean PRS313 differed markedly across European countries, being highest in south-eastern Europe and lowest in north-western Europe. Using the overall European PRS313 distribution to categorise individuals leads to overestimation and underestimation of risk in some individuals from south-eastern and north-western countries, respectively. Adjustment for principal components explained most of the observed heterogeneity in mean PRS. Country-specific PRS distributions may be used to calibrate risk categories in individuals from different countries.

Star allele search: a pharmacogenetic annotation database and user-friendly search tool of publicly available 1000 Genomes Project biospecimens

Here we describe a new public pharmacogenetic (PGx) annotation database of a large (n = 3,202) and diverse biospecimen collection of 1000 Genomes Project cell lines and DNAs. The database is searchable with a user friendly, web-based tool ( www.coriell.org/StarAllele/Search ). This resource leverages existing whole genome sequencing data and PharmVar annotations to characterize *alleles for each biospecimen in the collection. This new tool is designed to facilitate in vitro functional characterization of *allele haplotypes and diplotypes as well as support clinical PGx assay development, validation, and implementation.