Defining the role of common variation in the genomic and biological architecture of adult human height

Causal effect of body mass index on herpes zoster and postherpetic neuralgia: A Mendelian randomization study

Although observational studies have reported the relationship between body mass index (BMI), herpes zoster (HZ), and postherpetic neuralgia (PHN), the impacts of BMI on the incidence of HZ and PHN are still controversial. Our study aimed to explore the causal effect of BMI on HZ and PHN by a 2-sample Mendelian randomization (MR) approach. Genome-wide association studies data on BMI, HZ, and PHN were derived from publicly available genetic summary datasets. A total of 28 phenotypic single-nucleotide polymorphisms were selected as instrumental variables for BMI. Inverse-variance weighted (IVW) method was conducted as the primary MR analysis method to explore the causal effect of BMI on HZ and PHN. Several sensitivity analyses were performed to test the robustness of the MR results. Our study found no strong evidence for an effect of BMI on HZ incidence (IVW: OR = 1.018, 95% CI = 0.964-1.075, P = .524). However, it demonstrated that increased BMI was related to a higher risk of PHN (IVW: OR = 1.234, 95% CI = 1.002-1.520, P = .048). Besides, no significant heterogeneity or horizontal pleiotropy was observed in our study, and sensitivity analysis was consistent with the results. There is no causal effect of BMI on HZ risk, but it may be causally associated with a risk of PHN.

Short Stature for the General Pediatrician

Short stature (SS) is among the most common reasons for referral to a pediatric endocrinology clinic, particularly in urban areas. An appropriate medical history, including family history with measurement of the parents, an evaluation of the growth chart, an appropriate review of systems and physical exam, and determining the bone age, will allow the clinician to have a clear understanding of the reason(s) why the child is short. Familial SS and constitutional delay of growth are the most common causes of short stature. Children who are small for gestational age, whose height are not normal by age 2 years, and have dysmorphic features or abnormal body proportions should have an evaluation for genetic causes of SS. Children with abnormal growth velocity should be evaluated for endocrinopathies, inflammatory conditions, intestinal malabsorption, environmental factors, and/or chromosome mosaicism. Treatment of the identified cause should restore normal growth. Growth hormone treatment is only required by a minority of patients with SS.

The GWAS candidate far upstream element binding protein 3 (FUBP3) is required for normal skeletal growth, and adult bone mass and strength in mice

Bone mineral density (BMD) and height are highly heritable traits for which hundreds of genetic loci have been linked through genome wide association studies (GWAS). FUBP3 is a DNA and RNA binding protein best characterised as a transcriptional regulator of c-Myc, but little is known about its role in vivo. Single nucleotide polymorphisms in FUBP3 at the 9q34.11 locus have been associated with BMD, fracture and height in multiple GWAS, but FUBP3 has no previously established role in the skeleton. We analysed Fubp3-deficient mice to determine the consequence of FUBP3 deficiency in vivo. Mice lacking Fubp3 had reduced survival to adulthood and impaired skeletal growth. Bone mass was decreased, most strikingly in the vertebrae, with altered trabecular micro-architecture. Fubp3 deficient bones were also weak. These data provide the first functional demonstration that Fubp3 is required for normal skeletal growth and development and maintenance of adult bone structure and strength, indicating that FUBP3 contributes to the GWAS association of 9q34.11 with variation in height, BMD and fracture.

Landscape of rare-allele variants in cultivated and wild soybean genomes

Rare-allele variants are important for crop improvement because they can be linked to important traits. However, genome-wide distribution and annotation of rare-allele variants have not been reported. We analyzed sequencing data from 1556 soybean accessions and found 6,533,419 rare-allele variants in Glycine max and 941,274 in Glycine soja populations. Although the total number of variants was 20% less in G. max than G. soja, the number of rare-allele variants in G. max was six times that in G. soja. Among the rare-allele variants in G. max, 19.16% were novel mutations that did not exist in G. soja. Domestication and artificial selection have not only reduced overall genetic diversity but also the frequency of variants of cultivated soybean. Rare-allele variants were mainly located in intergenic and noncoding regions rather than coding regions, and in heterochromatin regions rather than euchromatic regions. There were 121,450 rare-allele variations in 36,213 G. max genes and 20,645 in 12,332 G. soja genes, resulting in nonsynonymous, stop gain or stop loss mutations. This study provided the first comprehensive understanding of rare-allele variants in wild and cultivated soybean genomes and its potential impact on gene functions. This information will be valuable for future studies aimed at improving soybean varieties, as these variants may help reveal the underlying mechanisms controlling traits and have the potential to improve stress resistance, yield, and adaptability to environments.

Characterizing differences in the muscle transcriptome between cattle with alternative LCORL-NCAPG haplotypes

BACKGROUND

The LCORL-NCAPG locus is a major quantitative trait locus (QTL) on bovine chromosome 6 (BTA6) that influences growth and carcass composition in cattle. To further understand the molecular mechanism responsible for the phenotypic changes associated with this locus, twenty-four Charolais-sired calves were selected for muscle transcriptome analysis based on alternative homozygous LCORL-NCAPG haplotypes (i.e., 12 "QQ" and 12 "qq", where "Q" is a haplotype harboring variation associated with increased growth). At 300 days of age, a biopsy of the longissimus dorsi muscle was collected from each animal for RNA sequencing.

RESULTS

Gene expression analysis identified 733 genes as differentially expressed between QQ and qq animals (q-value < 0.05). Notably, LCORL and genes known to be important regulators of growth such as IGF2 were upregulated in QQ individuals, while genes associated with adiposity such as FASN and LEP were downregulated, reflecting the increase in lean growth associated with this locus. Gene set enrichment analysis demonstrated QQ individuals had downregulation of pathways associated with adipogenesis, alongside upregulation of transcripts for cellular machinery essential for protein synthesis and energy metabolism, particularly ribosomal and mitochondrial components.

CONCLUSIONS

The differences in the muscle transcriptome between QQ and qq animals imply that muscle hypertrophy may be metabolically favored over accumulation of fat in animals with the QQ haplotype. Our findings also suggest this haplotype could be linked to a difference in LCORL expression that potentially influences the downstream transcriptional effects observed, though further research will be needed to confirm the molecular mechanisms underlying the associated changes in phenotype.

Development and validation of a polygenic risk score for height in a Greek cohort: Association with blood pressure measurements

Human height is a highly heritable trait. Genome-wide association studies have identified thousands of genetic variants linked to height, some of which exhibit pleiotropic effects. However, population-specific genome-wide Polygenic Risk Scores (PRSs) for height for specific populations remain limited. In this study, we developed a PRS for height tailored to Greek individuals using a dataset of 1970 adults. We applied a robust, iterative PRS construction pipeline based on previously published methods to capture the unique genetic architecture of height in this population. Our analysis identified multiple significant heightassociated SNPs specific to the Greek population and the constructed Greek-specific PRS accounted for 10.8% of height variability. A significant overlap of height-associated SNPs with those of generalized PRSs from other European populations constitutes a positive marker for our methodology. Additionally, the PRS was associated with blood pressure, aligning with evidence from other studies. These results highlight the importance of applying a rigorous methodology in PRS derivation. This is the first genome-wide height-PRS for Greek adults, which may serve as a foundation for further studies on genetic risk prediction and personalized healthcare in underrepresented populations.

JointPRS: A data-adaptive framework for multi-population genetic risk prediction incorporating genetic correlation

Genetic risk prediction for non-European populations is hindered by limited Genome-Wide Association Study (GWAS) sample sizes and small tuning datasets. We propose JointPRS, a data-adaptive framework that leverages genetic correlations across multiple populations using GWAS summary statistics. It achieves accurate predictions without individual-level tuning data and remains effective in the presence of a small tuning set thanks to its data-adaptive approach. Through extensive simulations and real data applications to 22 quantitative and four binary traits in five continental populations evaluated using the UK Biobank (UKBB) and All of Us (AoU), JointPRS consistently outperforms six state-of-the-art methods across three data scenarios: no tuning data, same-cohort tuning and testing, and cross-cohort tuning and testing. Notably, in the Admixed American population, JointPRS improves lipid trait prediction in AoU by 6.46%-172.00% compared to the other existing methods.

A Bayesian approach to correcting the attenuation bias of regression using polygenic risk score

Polygenic risk score has become increasingly popular for predicting the value of complex traits. In many settings, polygenic risk score is used as a covariate in regression analysis to study the association between different phenotypes. However, measurement error in polygenic risk score causes attenuation bias in the estimation of regression coefficients. In this paper, we employ a Bayesian approach to accounting for the measurement error of polygenic risk score and correcting the attenuation bias in linear and logistic regression. Through simulation, we show that our approach is able to obtain approximately unbiased estimation of coefficients and credible intervals with correct coverage probability. We also empirically compare our Bayesian measurement error model with the conventional regression model by analyzing real traits in the UK Biobank. The results demonstrate the effectiveness of our approach as it significantly reduces the error in coefficient estimates.

Evaluating ARG-estimation methods in the context of estimating population-mean polygenic score histories

Scalable methods for estimating marginal coalescent trees across the genome present new opportunities for studying evolution and have generated considerable excitement, with new methods extending scalability to thousands of samples. Benchmarking of the available methods has revealed general tradeoffs between accuracy and scalability, but performance in downstream applications has not always been easily predictable from general performance measures, suggesting that specific features of the ancestral recombination graph (ARG) may be important for specific downstream applications of estimated ARGs. To exemplify this point, we benchmark ARG estimation methods with respect to a specific set of methods for estimating the historical time course of a population-mean polygenic score (PGS) using the marginal coalescent trees encoded by the ARG. Here, we examine the performance in simulation of seven ARG estimation methods: ARGweaver, RENT+, Relate, tsinfer+tsdate, ARG-Needle, ASMC-clust, and SINGER, using their estimated coalescent trees and examining bias, mean squared error, confidence interval coverage, and Type I and II error rates of the downstream methods. Although it does not scale to the sample sizes attainable by other new methods, SINGER produced the most accurate estimated PGS histories in many instances, even when Relate, tsinfer+tsdate, ARG-Needle, and ASMC-clust used samples 10 or more times as large as those used by SINGER. In general, the best choice of method depends on the number of samples available and the historical time period of interest. In particular, the unprecedented sample sizes allowed by Relate, tsinfer+tsdate, ARG-Needle, and ASMC-clust are of greatest importance when the recent past is of interest-further back in time, most of the tree has coalesced, and differences in contemporary sample size are less salient.

Polygenic overlap between subjective well-being and psychiatric disorders and cross-ancestry validation

Subjective well-being (SWB) is important for understanding human behaviour and health. Although the connection between SWB and psychiatric disorders has been studied, common genetic mechanisms remain unclear. This study aimed to explore the genetic relationship between SWB and psychiatric disorders. Bivariate causal mixture modelling (MiXeR), polygenic risk score (PRS) and Mendelian randomization (MR) analyses showed substantial polygenic overlap and associations between SWB and the psychiatric disorders. Subsequent replication studies in East Asian populations confirmed the polygenic overlap between schizophrenia and SWB. The conditional and conjunctional false discovery rate analyses identified additional or shared genetic loci associated with SWB or psychiatric disorders. Functional annotation revealed enrichment of specific brain tissues and genes associated with SWB. The identified genetic loci showed cross-ancestry transferability between the European and Korean populations. Our findings provide valuable insights into the common genetic mechanisms underlying SWB and psychiatric disorders.

Population genomics of sika deer reveals recent speciation and genetic selective signatures during evolution and domestication

BACKGROUND

Population genomic analysis can reconstruct the phylogenetic relationship and demographic history, and identify genomic selective signatures of a species. To date, fundamental aspects of population genomic analyses, such as intraspecies taxonomy, evolutionary history, and adaptive evolution, of sika deer have not been systematically investigated. Furthermore, accumulating lines of evidences have illustrated that incorrect species delimitation will mislead conservation decisions, and even lead to irreversible mistakes in threatened species.

RESULTS

In this study, we resequenced 81 wild and 71 domesticated sika deer representing 10 main geographic populations and two farms to clarify the species delimitation, demographic and divergence histories, and adaptive evolution of this species. First, our analyses of whole genomes, Y chromosomes and mitochondrial genomes revealed substantial genetic differentiation between the continental and Japanese lineages of sika deer, representing two phylogenetically distinct species. Second, sika deer in Japan were inferred to have experienced a "divergence-mixing-isolation" evolutionary scenario. Third, we identified four candidate genes (XKR4, NPAS3, CTNNA3, and CNTNAP5) possibly involved in body size regulation of sika deer by selective sweep analysis. Furthermore, we also detected two candidate genes (NRP2 and EDIL3) that may be associated with an important economic trait (antler weight) were under selection during the process of domestication.

CONCLUSION

Population genomic analyses revealed that the continental and Japanese lineages represent distinct phylogenetic species. Moreover, our results provide insights into the genetic selection signatures related to body size differences and a valuable genomic resource for future genetic studies and genomics-informed breeding of sika deer.

Genetic causal effects of multi-site chronic pain on post-traumatic stress disorder: Evidence from a two-sample, two-step Mendelian randomization study

BACKGROUND

Existing evidence supports a correlation between multi-site chronic pain and post-traumatic stress disorder (PTSD), but it is yet to be determined if this correlation is causal and in what direction the causation works.

METHODS

Applying two-sample Mendelian randomization (MR) analysis to data from available genome-wide association studies in populations of European ancestry, we estimated the causal association between multi-site chronic pain and no pain versus PTSD. Moreover, we used multivariable and mediation MR analysis to assess the mediating effects of 13 lifestyle factors or diseases on the causal relationship between multi-site chronic pain and PTSD. The MR analyses were mainly conducted with the inverse variance weighted (IVW) method, followed by various sensitivity and validation analyses.

RESULTS

Multi-site chronic pain dramatically increases the risk of developing PTSD (odds ratio [OR]IVW = 2.39, 95 % confidence interval [CI] = 1.72-3.31, p = 2.10 × 10-7), and no pain significantly reduces the risk of developing PTSD (ORIVW = 0.12, 95 % CI = 0.05-0.30, p = 3.14 × 10-6). Multivariable MR found that 13 potential confounding factors do not influence the causal effect of multi-site chronic pain on PTSD. Moreover, body mass index (BMI) (6.98 %), educational attainment (8.79 %), major depressive disorder (MDD) (36.98 %) and insomnia (27.25 %) mediate the causal connection between multi-site chronic pain and PTSD.

CONCLUSION

Overall, individuals with multi-site chronic pain may be at a higher risk of developing PTSD, and this risk is partially influenced by the pathways involving BMI, educational attainment, MDD, and insomnia. These factors offer potential targets for therapeutic interventions.

Effect of the thinking healthy programme-based internet intervention model for maternal perinatal depression: A pilot study

BACKGROUND

Thinking Healthy Programme (THP) is an evidence-based psychosocial intervention that can be delivered by non-psychologists and does not require the implementer to have a mental health background or field experience. The THP has been tested in maternal health in many countries. However, the application of the THP model in Chinese maternal and child health has not been reported.

OBJECTIVE

This study aimed to explore the feasibility of the Thinking Healthy Programme (THP) model for improving perinatal depressive symptoms and infant growth when implemented by non-psychologists (e.g., nurses) for Chinese pregnant women.

METHODS

122 pregnant women with Edinburgh Postnatal Depression Scale (EPDS) ≥ 10 were selected from a tertiary hospital in Fujian Province between January 2022 to May 2022. Participants were randomly assigned to the intervention group (n = 61) and the control group (n = 61). The intervention group received the THP-based online delivery intervention and enhanced usual care (EUC), while the control group only received EUC. The outcomes were maternal depressive symptoms, infant growth, and other maternal and infant outcomes. Outcomes were assessed at baseline (during pregnancy), 3 months postpartum, and 6 months postpartum.

RESULTS

The Generalized Linear Mixed Model (GLMM) showed that there were significant time effects for EPDS scores and PHQ-9 scores between the two groups over time (p < 0.001, p = 0.040). The depression subscale of EPDS and PHQ-9 scores decreased significantly only within the intervention group between 6 months postpartum and baseline (p = 0.003, p = 0.023), the comparison group did not. Compared with the control group, the intervention group had a statistically significantly longer breastfeeding time (5.52 ± 1.25 vs. 4.50 ± 1.69, p = 0.012) at 6 months postpartum, and a lower absolute value of BMI-for-age z-score at post intervention and follow up post intervention (3 and 6 months post-delivery) (-0.87 ± 1.41 vs. -1.41 ± 2.53, p = 0.229; -0.14 ± 1.19 vs. -0.29 ± 1.11, p = 0.539) although no statistically significant difference.

LIMITATIONS

This study had several limitations. First, it was a single-center study and the sample size was small, which may limit the results. This finding needs to be confirmed by further large multicenter studies. Second, the outcomes were based on maternal self-report alone, which was subjected to social desirability and recall bias. Third, the study only monitored the effects up to the 6-month endpoint. Future studies should incorporate a longer-term evaluation of its effects on infant behavioral and temperament outcomes.

CONCLUSION

The THP-based online delivery intervention model helped to improve maternal perinatal depressive symptoms, with important benefits for improving maternal and infant health. This suggested the feasibility for non-psychologists to implement the THP model.

Mendelian Randomization Analysis Identifies Causal Effects of Multi-Site Chronic Pain on Obstructive Sleep Apnea

Background

Observational studies have suggested an association between obstructive sleep apnea (OSA) and chronic pain disorders, but causal evidence have not been confirmed.

Methods

Here we performed Mendelian randomization (MR) study to explore the potential causal association and mediating roles of modifiable factors between multi-site chronic pain (MCP) and OSA. Independent single nucleotide polymorphisms (SNPs) (N=26) from MCP GWAS (n=387,649) in the UK Biobank were used as instrumental variables to test associations with OSA from the FinnGen consortium, which encompassed 16,761 individuals with OSA cases and 201,194 individuals without OSA.

Results

MR analyses provide genetic evidence to predict MCP on the risk of OSA. Specifically, a per-site increase in multi-site chronic pain was linked to a 184% higher risk of OSA (ORIVW = 1.84, 95% CI = 1.29-2.63, p = 7.24×10-4). However, we also performed reverse association analyses and found no significant casual effect of OSA on MCP. MR estimates were in agreement regardless of the method used, such as MR-egger, weighted median and weighted mode, thereby demonstrating the accuracy of the causal associations. Through mediation analyses, we found that body mass index (BMI), waist circumference, and educational attainment explained a substantial proportion of the association between MCP and OSA (proportion mediated=21.13%; 26.57% and 9.66% respectively).

Conclusion

Our findings suggest that both pain management interventions, prevention of obesity and health education are likely to be effective strategies to reduce OSA risk in individuals with MCP.

Immune-developmental processes contribute to schizophrenia risk: insights from a genetic overlap study with height

BACKGROUND

Shorter stature has been phenotypically linked to increased prevalence of schizophrenia (SCZ), but the nature of this association is unknown.

METHODS

Using genome-wide genetic data, we studied the SCZ-height relationship on a genetic level. Applying novel genetic methods and tools, we analyzed gene-sets, tissue-types, cell-types, local genetic correlation, conditional genetic analyses, and fine-mapping of effector-genes to scrutinize the SCZ-height relationship.

RESULTS

We identified 142 genes statistically associated with both SCZ and height and found enrichment in 3 functional gene-sets. Genetic annotations implicated the pituitary and specifically mesenchymal stem cells for height and thyrotropic cells for SCZ. While the global SCZ-height genetic correlation was nonsignificant, 9 genomic regions showed robust local genetic correlations (7 negative, 6 in the MHC-region). The shared genetic signal for SCZ and height within the 6 MHC-regions was partially explained by mutual genetic overlap with white blood cell count, particularly lymphocytes. Fine-mapping prioritized 3 shared effector-genes (GIGYF2, HLA-C, and LIN28B) involved in immune response sensitivity and development of immune and pituitary cell-types.

CONCLUSIONS

Overall, our findings suggest an involvement during height-development of thyrotropic cells and immune response sensitivity contributing towards risk of SCZ.

Novel homozygous SPAG17 variants cause human male infertility through multiple morphological abnormalities of spermatozoal flagella related to axonemal microtubule doublets

ABSTRACT

Male infertility can result from impaired sperm motility caused by multiple morphological abnormalities of the flagella (MMAF). Distinct projections encircling the central microtubules of the spermatozoal axoneme play pivotal roles in flagellar bending and spermatozoal movement. Mammalian sperm-associated antigen 17 ( SPAG17 ) encodes a conserved axonemal protein of cilia and flagella, forming part of the C1a projection of the central apparatus, with functions related to ciliary/flagellar motility, skeletal growth, and male fertility. This study investigated two novel homozygous SPAG17 mutations (M1: NM_206996.2, c.829+1G>T, p.Asp212_Glu276del; and M2: c.2120del, p.Leu707*) identified in four infertile patients from two consanguineous Pakistani families. These patients displayed the MMAF phenotype confirmed by Papanicolaou staining and scanning electron microscopy assays of spermatozoa. Quantitative real-time polymerase chain reaction (PCR) of patients' spermatozoa also revealed a significant decrease in SPAG17 mRNA expression, and immunofluorescence staining showed the absence of SPAG17 protein signals along the flagella. However, no apparent ciliary-related symptoms or skeletal malformations were observed in the chest X-rays of any of the patients. Transmission electron microscopy of axoneme cross-sections from the patients showed incomplete C1a projection and a higher frequency of missing microtubule doublets 1 and 9 compared with those from fertile controls. Immunofluorescence staining and Western blot analyses of spermatogenesis-associated protein 17 (SPATA17), a component of the C1a projection, and sperm-associated antigen 6 (SPAG6), a marker of the spring layer, revealed disrupted expression of both proteins in the patients' spermatozoa. Altogether, these findings demonstrated that SPAG17 maintains the integrity of spermatozoal flagellar axoneme, expanding the phenotypic spectrum of SPAG17 mutations in humans.

Genome-wide association study on chronic postsurgical pain in the UK Biobank

BACKGROUND

Chronic postsurgical pain (CPSP) persists beyond the expected healing period after surgery, imposing a substantial burden on overall patient well-being. Unfortunately, CPSP often remains underdiagnosed and undertreated. To better understand the mechanism of CPSP development, we aimed to identify genetic variants associated with CPSP.

METHODS

A genome-wide association study was conducted in a cohort of 95,931 individuals from the UK Biobank who had undergone different surgical procedures. Three analyses were performed: (1) case-control analysis (2923 cases with CPSP and 93,008 controls), (2) ordinal analysis in three groups based on time of analgesics use (n=95,931), and (3) a meta-analysis combining our dataset with a recent publication (n=97,281).

RESULTS

In the case-control analysis, one genetic locus within GLRA3 displayed a genome-wide significant (P<2.5×10-8) association with CPSP, and nine loci displayed suggestively significant associations (P<1×10-6). The ordinal analysis aligned with the case-control analysis, with an additional locus (rs140330443) reaching genome-wide significance. In the meta-analysis with the recently published dataset, the single nucleotide polymorphism (SNP) rs17298280 in the GLRA3 gene remained significant (P=2.19×10-9).

CONCLUSIONS

This study contributes new insights into the genetic factors associated with CPSP. The top hit GLRA3 is known for involvement in prostaglandin E2-induced pain processing pathways. Our study provides a foundation for future investigations into the function of these risk variants and the mechanisms underlying CPSP by offering summary statistics. However, further validation in other cohorts is required to confirm these findings.

Insights from the largest diverse ancestry sex-specific disease map for genetically predicted height

We performed ancestry and sex specific Phenome Wide Association Studies (PheWAS) to explore disease related outcomes associated with genetically predicted height. This is the largest PheWAS on genetically predicted height involving up to 840,000 individuals of diverse ancestry. We explored European, African, East Asian ancestries and Hispanic population groups. Increased genetically predicted height is associated with hyperpotassemia and autism in the male cross-ancestry analysis. We report male-only European ancestry associations with anxiety disorders, post-traumatic stress and substance addiction and disorders. We identify a signal with benign neoplasm of other parts of digestive system in females. We report associations with a series of disorders, several with no prior evidence of association with height, involving mental disorders and the endocrine system. Our study suggests that increased genetically predicted height is associated with higher prevalence of many clinically relevant traits which has important implications for epidemiological and clinical disease surveillance and risk stratification.

Sox8: a multifaceted transcription factor in development and disease

Sox8 is a transcription factor that belongs to the Sox family of high-mobility-group domain containing proteins and is closely related to Sox9 and Sox10. During prenatal development, Sox8 is expressed in several ectoderm-, endoderm- and mesoderm-derived tissues and has been implicated in processes of organogenesis and differentiation. Sox8 expression is found in several important cells such as Sertoli cells in the male gonad, glial cells, satellite cells, and chondrocytes. However, Sox8 is not essential for the proper development of any of the involved systems, as it functions redundantly with Sox9 or Sox10 and no major developmental disturbances have been noticed in its absence. Despite its perceived limited importance as a developmental regulator, Sox8 exhibits a more significant role in late development and adult tissues. Several studies highlight the importance of Sox8 for the homeostasis of adipose tissue, Sertoli cells and the blood-testis-barrier functioning, and the maintenance of myelin in the central nervous system. Emerging evidence points to SOX8 as a promising candidate for a disease-causing gene in humans and suggests that changes in SOX8 function or expression could contribute to pathological states. For instance, genetic variants of SOX8 have been linked to multiple sclerosis and familial essential tremor, while SOX8 alterations have been related to poor cancer prognosis and infertility. This Review provides an overview of Sox8's versatile role in development and adult tissues as well as its lesser-known contributions to various diseases, and its potential as a therapeutic target.

A 5' Promoter Region SNP in CTSC Leads to Increased Hypoxia Tolerance in Changfeng Silver Carp (Hypophthalmichthys molitrix)

Silver carp is a critically significant species in freshwater aquaculture in China, characterized by its limited tolerance to hypoxia. In this study, a significant SNP locus at Chr8: 29647765 (T/C) associated with hypoxia tolerance traits was identified in Changfeng silver carp, and the homozygotic CC genotype exhibited higher hypoxic tolerance than the homozygotic TT and heterozygotic TC genotypes. Under hypoxic conditions, the hemoglobin concentration increased, with the CC genotype demonstrating a significantly higher level compared with the TT genotype; the activities of antioxidant enzymes including catalase and superoxide dismutase were significantly higher in the CC genotype than in the other genotypes; the area of the gill lamellae was significantly smaller in the CC genotype than in the TT and TC genotypes; and the number of apoptotic cells in the brain was significantly lower in the CC genotype than in the TT and TC genotypes. Sequence analysis showed that this SNP was located in the promoter region of the cathepsin C (CTSC) gene. The expression levels of the CTSC gene were analyzed across the three genotypes, revealing that the CC genotype exhibited significantly lower expression compared with the TT and TC genotypes under hypoxia. This finding suggests that the SNP associated with the CC genotype leads to reduced CTSC expression, which may facilitate better physiological adaptation to hypoxia. Analysis of the promoter region of CTSC found a unique predicted hypoxia-inducible factor 1-alpha (HIF-1α) binding site (CGTG) in the T genotype, implying that the differential expression of CTSC among the three genotypes under hypoxic stress may be regulated by HIF-1α, a transcription factor integral to hypoxia adaptation, thereby affecting hypoxia tolerance, which further affects the immune response of the Changfeng silver carp in response to the hypoxic environment. Although SNPs represent significant genetic determinants, their phenotypic effects are predominantly mediated through complex interactions within gene regulatory networks and environmental influences. This study identified an effective SNP site in Changfeng silver carp, providing valuable guidance for future selective breeding and the development of new hypoxia-tolerant varieties.

A Litmus Test for Confounding in Polygenic Scores

Polygenic scores (PGSs) are being rapidly adopted for trait prediction in the clinic and beyond. PGSs are often thought of as capturing the direct genetic effect of one's genotype on their phenotype. However, because PGSs are constructed from population-level associations, they are influenced by factors other than direct genetic effects, including stratification, assortative mating, and dynastic effects ("SAD effects"). Our interpretation and application of PGSs may hinge on the relative impact of SAD effects, since they may often be environmentally or culturally mediated. We developed a method that estimates the proportion of variance in a PGS (in a given sample) that is driven by direct effects, SAD effects, and their covariance. We leverage a comparison of a PGS of interest based on a standard GWAS with a PGS based on a sibling GWAS-which is largely immune to SAD effects-to quantify the relative contribution of each type of effect to variance in the PGS of interest. Our method, Partitioning Genetic Scores Using Siblings (PGSUS, pron. "Pegasus"), breaks down variance components further by axes of genetic ancestry, allowing for a nuanced interpretation of SAD effects. In particular, PGSUS can detect stratification along major axes of ancestry as well as SAD variance that is "isotropic" with respect to axes of ancestry. Applying PGSUS, we found evidence of stratification in PGSs constructed using large meta-analyses of height and educational attainment as well as in a range of PGSs constructed using the UK Biobank. In some instances, a given PGS appears to be stratified along a major axis of ancestry in one prediction sample but not in another (for example, in comparisons of prediction in samples from different countries, or in ancient DNA vs. contemporary samples). Finally, we show that different approaches for adjustment for population structure in GWASs have distinct advantages with respect to mitigation of ancestry-axis-specific and isotropic SAD variance in PGS. Our study illustrates how family-based designs can be combined with standard population-based designs to guide the interpretation and application of genomic predictors.

Association and mediation pathways of maternal hyperglycaemia and liability to gestational diabetes with neonatal outcomes: A two-sample Mendelian randomization study

AIMS

Maternal hyperglycemia is linked to adverse neonatal outcomes. However, current evidence was insufficient for mechanistic pathways. We aim to use two-sample Mendelian randomization (MR) to obtain a comprehensive understanding of the causal association and mediation pathways.

MATERIALS AND METHODS

Genetic variants of fasting glucose (FG), insulin sensitivity index (ISI), glycated haemoglobin (HbA1c), gestational diabetes mellitus (GDM) and type 2 diabetes (T2D) were used as instruments (N = 50 404-898 130). The associations with offspring birthweight, gestational duration, spontaneous preterm and post-term birth were assessed by the inverse-variance weighted method, using summary statistics of European genome-wide association studies (N = 131 279-210 248). Sensitivity analyses, including multivariable MR removing pleiotropic effect from maternal body mass index (BMI), assessed the robustness. Mediation via placental weight and maternal hypertension were assessed via a two-step MR design.

RESULTS

FG (0.46 SD per mmol/L, 95% confidence interval [95% CI]: 0.32, 0.61) and GDM liability (0.18 SD per log odds, 95% CI: 0.08, 0.18) were positively associated with birthweight, with consistent findings for HbA1c, T2D liability and ISI. These associations were mediated by placental weight (proportion mediated: 32.8% to 77.7%). Higher HbA1c, GDM and T2D liability were associated with preterm birth (odds ratios for GDM: 1.07, 95% CI: 1.01, 1.14) and shorter gestational duration, whilst the association for T2D attenuated after adjusted for maternal BMI and gestational hypertension.

CONCLUSION

Maternal hyperglycemia is associated with higher birthweight (possibly indicating macrosomia), mediated via increased placental growth. GDM and T2D liability are related to preterm birth, whilst the association for T2D liability is driven by maternal adiposity.

Effects of childhood and adult height on later life cardiovascular disease risk estimated through Mendelian randomization

Taller individuals are at elevated and protected risk of various cardiovascular disease endpoints. Whether this is due to a direct consequence of their height during childhood, a long-term effect of remaining tall throughout the lifecourse, or confounding by other factors, is unknown. We sought to address this by harnessing human genetic data from the UK Biobank to separate the independent effects of childhood and adulthood height using an approach known as lifecourse Mendelian randomization (MR). Protective effects of taller childhood height on risk of later life coronary artery disease (OR = 0.78 per change in height category, 95% CI = 0.70 to 0.86, P = 4 × 10- 10) and stroke (OR = 0.93, 95% CI = 0.86 to 1.00, P = 0.03) using data from large-scale consortia were found using a univariable model, although evidence of these effects attenuated in a multivariable setting upon accounting for adulthood height. In contrast, direct effects of taller childhood height on increased risk of later life atrial fibrillation (OR = 1.61, 95% CI = 1.42 to 1.79, P = 5 × 10- 7) and thoracic aortic aneurysm (OR = 1.55, 95% CI = 1.16 to 1.95, P = 0.03) were found even after accounting for adulthood height. Evidence for both of these direct effects was replicated in the Million Veterans Program. The protective effect of childhood height on risk of coronary artery disease and stroke can be largely explained by taller children typically becoming taller individuals in later life. Conversely, the independent effect of childhood height on increased risk of atrial fibrillation and thoracic aortic aneurysm may point towards developmental mechanisms in early life which confer a lifelong risk on these disease outcomes.

Short-term evolutionary implications of an introgressed size-determining supergene in a vulnerable population

The Thorny Skate (Amblyraja radiata) is a vulnerable species displaying a discrete size-polymorphism in the northwest Atlantic Ocean (NWA). We conducted whole genome sequencing of samples collected across its range. Genetic diversity was similar at all sampled sites, but we discovered a ~ 31 megabase bi-allelic supergene associated with the size polymorphism, with the larger size allele having introgressed in the last ~160,000 years B.P. While both Gulf of Maine (GoM) and Canadian (CAN) populations exhibit the size polymorphism, we detected a significant deficit of heterozygotes at the supergene and longer stretches of homozygosity in GoM population. This suggests inbreeding driven by assortative mating for size in GoM but not in CAN. Coalescent-based demographic modelling reveals strong migration between regions maintaining genetic variability in the recombining genome, preventing speciation between morphs. This study highlights short-term context-dependent evolutionary consequences of a size-determining supergene providing new insights for the management of vulnerable species.

Modeling gene interactions in polygenic prediction via geometric deep learning

Polygenic risk score (PRS) is a widely used approach for predicting individuals' genetic risk of complex diseases, playing a pivotal role in advancing precision medicine. Traditional PRS methods, predominantly following a linear structure, often fall short in capturing the intricate relationships between genotype and phenotype. In this study, we present PRS-Net, an interpretable geometric deep learning-based framework that effectively models the nonlinearity of biological systems for enhanced disease prediction and biological discovery. PRS-Net begins by deconvoluting the genome-wide PRS at the single-gene resolution and then explicitly encapsulates gene-gene interactions leveraging a graph neural network (GNN) for genetic risk prediction, enabling a systematic characterization of molecular interplay underpinning diseases. An attentive readout module is introduced to facilitate model interpretation. Extensive tests across multiple complex traits and diseases demonstrate the superior prediction performance of PRS-Net compared with a wide range of conventional PRS methods. The interpretability of PRS-Net further enhances the identification of disease-relevant genes and gene programs. PRS-Net provides a potent tool for concurrent genetic risk prediction and biological discovery for complex diseases.

Unravelling the Relationship Between Height, Lean Mass, Alzheimer's Disease and Cognition Through Mendelian Randomization

BACKGROUND

Genetic evidence from Mendelian randomization (MR) analyses suggests that higher lean mass causally protects against Alzheimer's disease (AD) and enhances cognitive function. However, the potential confounding role of height, which shares genetic etiology with lean mass, has not been fully examined.

METHODS

Genetic predictors of whole-body lean mass were obtained from a genome-wide association study (GWAS) performed in the UK Biobank cohort (UKB; n = 448,322). Genetic predictors of height were also obtained from UKB (height0.5M = 455,332) and from a GWAS meta-analysis (height1.5Mn = 1,578,425). The study outcomes included clinically diagnosed AD (21,982 cases and 41,944 controls) and cognitive performance (n = 269,867). All study participants were of European ancestry. We conducted univariable and multivariable MR analyses to examine the total and independent effects of lean mass and height on the specified outcomes under different statistical adjustment strategies.

RESULTS

In univariable MR analyses, genetically proxied lean mass (odds ratio [OR] per 1-standard deviation [SD] increase 0.81, 95% confidence interval [CI] 0.72-0.91, p = 3.8 × 10-4) and height (OR 0.90, 95% CI 0.84-0.96, p = 0.001) were associated with reduced risk of AD. Genetically proxied lean mass (β 0.10, 95% CI 0.08-0.12, p = 6.24 × 10-6) and height (β 0.07, 95% CI 0.05-0.08, p = 1.16 × 10-15) were further associated with improved cognitive performance. In multivariable MR analyses, adjustment for height1.5M partially attenuated the lean mass association with AD (OR 0.91, 95% CI 0.74-1.12, p = 0.40), whereas the height1.5M-AD association remained similar after adjusting for lean mass (OR 0.89, 95% CI 0.79-1.00, p = 0.04). Adjustment for height also attenuated the association of lean mass with cognitive performance (β 0.00, 95% CI -0.07-0.06, p = 0.94), whereas height maintained a similar association with improved cognitive performance after adjustment for lean mass (β 0.07, 95% CI 0.03-0.10, p = 0.001).

CONCLUSIONS

Height may confound the genetic associations between lean mass and both cognitive performance and AD risk. Residual direct effects of lean mass on AD risk cannot be excluded due to limitations in statistical power and genetic instrument strength in MVMR. These findings emphasize the necessity of adjusting for height when using MR to investigate the clinical effects of lean mass.

The extent of the hip bone sexual dimorphism in two Italian coeval modern skeletal samples

The rate of sexual dimorphism in the human hip bone is primarily due to the structural demands of childbirth. Genetic, environmental, and socio-cultural factors can also influence pelvic shape variations across populations. This study examines intra-population sex variation within the Italian population based on regional differences of 280 coxal bones from two documented human osteological collections (Bologna and Sassari) coming from different geographical areas, the northern continental and island regions. Nineteen metric variables were used to evaluate sexual dimorphism and population differences. Most of the variables showed sexual dimorphism, particularly the hip height and ischio-pubic measures within both populations, and accurately predicted sex for each population (Bologna: 100%; Sassari: 91.2%). Results show the Bologna sample have larger dimensions for most of the measurements than the Sassari one, especially when considering the longitudinal ones. Some female traits of the Bologna sample are larger than the correspondent ones in the Sassari males. The rate of sexual dimorphism between the populations shows significant differences, with better sex distinction for Bologna than Sassari. This study aims at interpreting these intra-population differences, considering the effect of environmental (physical and social milieu) and genetic factors, underscoring the importance of this local differences for accurate diagnostic criteria.

Functional genomics of human skeletal development and the patterning of height heritability

Underlying variation in height are regulatory changes to chondrocytes, cartilage cells comprising long-bone growth plates. Currently, we lack knowledge on epigenetic regulation and gene expression of chondrocytes sampled across the human skeleton, and therefore we cannot understand basic regulatory mechanisms controlling height biology. We first rectify this issue by generating extensive epigenetic and transcriptomic maps from chondrocytes sampled from different growth plates across developing human skeletons, discovering novel regulatory networks shaping human bone/joint development. Next, using these maps in tandem with height genome-wide association study (GWAS) signals, we disentangle the regulatory impacts that skeletal element-specific versus global-acting variants have on skeletal growth, revealing the prime importance of regulatory pleiotropy in controlling height variation. Finally, as height is highly heritable, and thus often the test case for complex-trait genetics, we leverage these datasets within a testable omnigenic model framework to discover novel chondrocyte developmental modules and peripheral-acting factors shaping height biology and skeletal growth.

Cross-species analysis of genetic architecture and polygenic risk scores for non-contact ACL rupture in dogs and humans

Non-contact anterior cruciate ligament (ACL) rupture is a common serious orthopaedic disease in humans and dogs. Familial risk has been recognized in both species but interactions between genetic effects and environmental risk are not understood. We investigated ACL rupture heritability, genetic architecture, selection pressure, sharing of risk genes and biological pathways, and polygenic risk score (PRS) prediction of disease risk. In both species, ACL rupture has moderate heritability, is likely under negative selection, and has a highly polygenic architecture where thousands of variant effects act together to influence disease risk. In dogs, we found hotspots of regional heritability. We also confirmed sharing of multiple risk genes. Our findings challenge the dogma that non-contact ACL rupture is predominantly due to a single overload injury event. Our results also suggest that accurate PRS prediction of ACL rupture risk is an achievable goal in both species, enabling identification of individuals for personalized medical care.

Monogenic causes of familial short stature

Genetic factors play a crucial role in determining human height. Short stature commonly affects multiple family members and therefore, familial short stature (FSS) represents a significant proportion of growth disorders. Traditionally, FSS was considered a benign polygenic condition representing a subcategory of idiopathic short stature (ISS). However, advancements in genetic research have revealed that FSS can also be monogenic, inherited in an autosomal dominant manner and can result from different mechanisms including primary growth plate disorders, growth hormone deficiency/insensitivity or by the disruption of fundamental intracellular pathways. These discoveries have highlighted a broader phenotypic spectrum for monogenic forms of short stature, which may exhibit mild manifestations indistinguishable from ISS. Given the overlapping features and the difficulty in differentiating polygenic from monogenic FSS without genetic testing, some researchers redefine FSS as a descriptive term that encompasses any familial occurrence of short stature, regardless of the underlying cause. This shift emphasizes the complexity of diagnosing and managing short stature within families, reflecting the diverse genetic landscape that influences human growth.

Variants in WASHC3, a component of the WASH complex, cause short stature, variable neurodevelopmental abnormalities, and distinctive facial dysmorphism

Purpose

Genetic defects that impair growth plate chondrogenesis cause a phenotype that varies from skeletal dysplasia to mild short stature with or without other syndromic features. In many individuals with impaired skeletal growth, the genetic causes remain unknown.

Method

Exome sequence was performed in 3 unrelated families with short stature, distinctive facies, and neurodevelopmental abnormalities. The impact of identified variants was studied in vitro.

Results

Exome sequencing identified variants in WASHC3, a component of the WASH complex. In the first family, a de-novo-dominant missense variant (p.L69F) impaired WASHC3 participation in the WASH complex, altered PTH1R endosomal trafficking, diminished PTH1R signaling, and affected growth plate chondrocyte hypertrophic differentiation, providing a likely explanation for the short stature. Knockdown of other WASH complex components also diminished PTH1R signaling. In the second and third families, a homozygous variant in the start codon (p.M1?) markedly reduced WASHC3 protein expression.

Conclusion

In combination with prior studies of WASH complex proteins, our findings provide evidence that the WASH complex is required for normal skeletal growth and that, consequently, genetic abnormalities impairing the function of the WASH complex (WASHopathy) cause short stature, as well as distinctive facies and variable neurodevelopmental abnormalities.

Accelerating Heritability, Genetic Correlation, and Genome-Wide Association Imaging Genetic Analyses in Complex Pedigrees

National and international biobanking efforts led to the collection of large and inclusive imaging genetics datasets that enable examination of the contribution of genetic and environmental factors to human brains in illness and health. High-resolution neuroimaging (~104-6 voxels) and genetic (106-8 single nucleotide polymorphic [SNP] variants) data are available in statistically powerful (N = 103-5) epidemiological and disorder-focused samples. Performing imaging genetics analyses at full resolution afforded in these datasets is a formidable computational task even under the assumption of unrelatedness among the subjects. The computational complexity rises as ~N2-3 (where N is the sample size), when accounting for relatedness among subjects. We describe fast, non-iterative simplifications to accelerate classical variance component (VC) methods including heritability, genetic correlation, and genome-wide association in dense and complex empirical pedigrees. These approaches linearize (from N2-3 to N~1) computational effort while maintaining fidelity (r ~ 0.95) with the VC results and take advantage of parallel computing provided by central and graphics processing units (CPU and GPU). We show that the new approaches lead to a 104- to 106-fold reduction in computational complexity-making voxel-wise heritability, genetic correlation, and genome-wide association studies (GWAS) analysis practical for large and complex samples such as those provided by the Amish and Human Connectome Projects (N = 406 and 1052 subjects, respectively) and UK Biobank (N = 31,681). These developments are shared in open-source, SOLAR-Eclipse software.

Genome-wide Mendelian randomization identifies drugs associated with body height

Background

Mendelian randomization (MR) has been used to identify drug targets in many conditions. Height is a classic complex trait affected by genetic and early-life environmental factors. No systematic screening has been conducted to identify drugs that interact with height. We investigated the causal relationship between genes and height, and systematically screened for interactive drugs that may promote or delay growth.

Methods

We performed MR using summary statistics from the Genetic Investigation of ANthropometric Traits consortium (N=253,288), the UK Biobank (N=461,950), and the BioBank Japan Project (N=159,095). Gene expression-single-nucleotide polymorphism associations represented by cis-expression quantitative trait loci data were obtained from the Genotype-Tissue Expression study and were used as genetic instruments. We performed annotation and enrichment analyses of the genes. Interactive drugs were identified through drug-gene interactions.

Results

Of the 27,094 genes screened, 209 had causal associations with height, including genes associated with height and short stature phenotypes (AMZ1, GNA12, NPPC, UQCC1, and ZBTB38), genes associated with height in a few studies (ANKIB1, CEP250, DCAF16, HIST1H4E, and HLA-C), and genes without previous evidence (BTN2A2 and RBMS1P1). Enrichment analysis showed that transcriptional regulation by RUNX1 was the most enriched pathway. Interactive drugs were identified, including amoxicillin, atenolol, infliximab, colchicine, propionyl-L-carnitine, BMN-111, and tamoxifen, which were known to have a positive effect on height. We also identified drugs that had a negative effect on height, including antineoplastic drugs, corticosteroids, and antiepileptic drugs. Moreover, many interactive drugs have not been previously reported to be associated with height.

Conclusions

Our results suggest that many genes have causal effects on height. By interrogating drug-gene interactions, interactive drugs have been identified as having both positive and negative effects on growth, which would help make clinical decisions.

Multimodal analysis of RNA sequencing data powers discovery of complex trait genetics

RNA sequencing has the potential to reveal many modalities of transcriptional regulation, such as various splicing phenotypes, but studies on gene regulation are often limited to gene expression due to the complexity of extracting and analyzing multiple RNA phenotypes. Here, we present Pantry, a framework to efficiently generate diverse RNA phenotypes from RNA sequencing data and perform downstream integrative analyses with genetic data. Pantry generates phenotypes from six modalities of transcriptional regulation (gene expression, isoform ratios, splice junction usage, alternative TSS/polyA usage, and RNA stability) and integrates them with genetic data via QTL mapping, TWAS, and colocalization testing. We apply Pantry to Geuvadis and GTEx data, finding that 4768 of the genes with no identified eQTL in Geuvadis have QTL in at least one other transcriptional modality, resulting in a 66% increase in genes over eQTL mapping. We further found that the QTL exhibit modality-specific functional properties that are further reinforced by joint analysis of different RNA modalities. We also show that generalizing TWAS to multiple RNA modalities approximately doubles the discovery of unique gene-trait associations, and enhances identification of regulatory mechanisms underlying GWAS signal in 42% of previously associated gene-trait pairs.

A multi-regional human brain atlas of chromatin accessibility and gene expression facilitates promoter-isoform resolution genetic fine-mapping

Brain region- and cell-specific transcriptomic and epigenomic features are associated with heritability for neuropsychiatric traits, but a systematic view, considering cortical and subcortical regions, is lacking. Here, we provide an atlas of chromatin accessibility and gene expression profiles in neuronal and non-neuronal nuclei across 25 distinct human cortical and subcortical brain regions from 6 neurotypical controls. We identified extensive gene expression and chromatin accessibility differences across brain regions, including variation in alternative promoter-isoform usage and enhancer-promoter interactions. Genes with distinct promoter-isoform usage across brain regions were strongly enriched for neuropsychiatric disease risk variants. Moreover, we built enhancer-promoter interactions at promoter-isoform resolution across different brain regions and highlighted the contribution of brain region-specific and promoter-isoform-specific regulation to neuropsychiatric disorders. Including promoter-isoform resolution uncovers additional distal elements implicated in the heritability of diseases, thereby increasing the power to fine-map risk genes. Our results provide a valuable resource for studying molecular regulation across multiple regions of the human brain and underscore the importance of considering isoform information in gene regulation.

Empirical versus estimated accuracy of imputation: optimising filtering thresholds for sequence imputation

BACKGROUND

Genotype imputation is a cost-effective method for obtaining sequence genotypes for downstream analyses such as genome-wide association studies (GWAS). However, low imputation accuracy can increase the risk of false positives, so it is important to pre-filter data or at least assess the potential limitations due to imputation accuracy. In this study, we benchmarked three different imputation programs (Beagle 5.2, Minimac4 and IMPUTE5) and compared the empirical accuracy of imputation with the software estimated accuracy of imputation (Rsqsoft). We also tested the accuracy of imputation in cattle for autosomal and X chromosomes, SNP and INDEL, when imputing from either low-density or high-density genotypes.

RESULTS

The accuracy of imputing sequence variants from real high-density genotypes was higher than from low-density genotypes. In our software benchmark, all programs performed well with only minor differences in accuracy. While there was a close relationship between empirical imputation accuracy and the imputation Rsqsoft, this differed considerably for Minimac4 compared to Beagle 5.2 and IMPUTE5. We found that the Rsqsoft threshold for removing poorly imputed variants must be customised according to the software and this should be accounted for when merging data from multiple studies, such as in meta-GWAS studies. We also found that imposing an Rsqsoft filter has a positive impact on genomic regions with poor imputation accuracy due to large segmental duplications that are susceptible to error-prone alignment. Overall, our results showed that on average the imputation accuracy for INDEL was approximately 6% lower than SNP for all software programs. Importantly, the imputation accuracy for the non-PAR (non-Pseudo-Autosomal Region) of the X chromosome was comparable to autosomal imputation accuracy, while for the PAR it was substantially lower, particularly when starting from low-density genotypes.

CONCLUSIONS

This study provides an empirically derived approach to apply customised software-specific Rsqsoft thresholds for downstream analyses of imputed variants, such as needed for a meta-GWAS. The very poor empirical imputation accuracy for variants on the PAR when starting from low density genotypes demonstrates that this region should be imputed starting from a higher density of real genotypes.

Lung development genes, adult lung function and cognitive traits

Lower lung function is associated with lower cognitive function and an increased risk of dementia. This has not been adequately explained and may partly reflect shared developmental pathways. In UK Biobank participants of European ancestry, we tested the association between lung function measures (forced vital capacity and forced expiratory volume in 1 s to forced vital capacity ratio; n = 306 476) and cognitive traits including nine cognitive function test scores (n = 32 321-428 609), all-cause dementia, Alzheimer's disease and vascular dementia (6805, 2859 and 1544 cases, respectively, and ∼421 241 controls). In the same population, we derived summary statistics for associations between common genetic variants in 55 lung development genes and lung function measures and cognitive traits using adjusted linear/logistic regression models. Using a hypothesis-driven Bayesian co-localization analysis, we finally investigated the presence of shared genetic signals between lung function measures and cognitive traits at each of these 55 genes. Higher lung function measures were generally associated with higher scores of cognitive function tests as well as lower risk of dementia. The strongest association was between forced vital capacity and vascular dementia (adjusted hazard ratio 0.74 per standard deviation increase, 95% confidence interval 0.67-0.83). Of the 55 genes of interest, we found shared variants in four genes, namely: CSNK2B rs9267531 (forced vital capacity and forced expiratory volume in 1 s to forced vital capacity ratio with fluid intelligence and pairs matching), NFATC3 rs548092276 & rs11275011 (forced expiratory volume in 1 s to forced vital capacity ratio with fluid intelligence), PTCH1 rs2297086 & rs539078574 (forced expiratory volume in 1 s to forced vital capacity ratio with reaction time) and KAT8 rs138259061 (forced vital capacity with pairs matching). However, the direction of effects was not in keeping with our hypothesis, i.e. variants associated with lower lung function were associated with better cognitive function or vice versa. We also found distinct variants associated with lung function and cognitive function in KAT8 (forced vital capacity and Alzheimer's disease) and PTCH1 (forced vital capacity and forced expiratory volume in 1 s to forced vital capacity ratio with fluid intelligence and reaction time). The links between CSNK2B and NFATC3 and cognitive traits have not been previously reported by genome-wide association studies. Despite shared genes and variants, our findings do not support the hypothesis that shared developmental signalling pathways explain the association of lower adult lung function with poorer cognitive function.

MR Corge: sensitivity analysis of Mendelian randomization based on the core gene hypothesis for polygenic exposures

SUMMARY

Mendelian randomization is being utilized to assess causal effects of polygenic exposures, where many genetic instruments are subject to horizontal pleiotropy. Existing methods for detecting and correcting for horizontal pleiotropy have important assumptions that may not be fulfilled. Built upon the core gene hypothesis, we developed MR Corge for performing sensitivity analysis of Mendelian randomization. MR Corge identifies a small number of putative core instruments that are more likely to affect genes with a direct biological role in an exposure and obtains causal effect estimates based on these instruments, thereby reducing the risk of horizontal pleiotropy. Using positive and negative controls, we demonstrated that MR Corge estimates aligned with established biomedical knowledge and the results of randomized controlled trials. MR Corge may be widely applied to investigate polygenic exposure-outcome relationships.

AVAILABILITY AND IMPLEMENTATION

An open-sourced R package is available at https://github.com/zhwm/MRCorge.

Analyses of GWAS signal using GRIN identify additional genes contributing to suicidal behavior

Genome-wide association studies (GWAS) identify genetic variants underlying complex traits but are limited by stringent genome-wide significance thresholds. We present GRIN (Gene set Refinement through Interacting Networks), which increases confidence in the expanded gene set by retaining genes strongly connected by biological networks when GWAS thresholds are relaxed. GRIN was validated on both simulated interrelated gene sets as well as multiple GWAS traits. From multiple GWAS summary statistics of suicide attempt, a complex phenotype, GRIN identified additional genes that replicated across independent cohorts and retained biologically interrelated genes despite a relaxed significance threshold. We present a conceptual model of how these retained genes interact through neurobiological pathways that may influence suicidal behavior, and identify existing drugs associated with these pathways that would not have been identified under traditional GWAS thresholds. We demonstrate GRIN's utility in boosting GWAS results by increasing the number of true positive genes identified from GWAS results.

[Single nucleotide polymorphism heritability of non-syndromic cleft lip with or without cleft palate in Chinese population]

OBJECTIVE

To delve into the intricate relationship between common genetic variations across the entire genome and the risk of non-syndromic cleft lip with or without cleft palate (NSCL/P).

METHODS

Utilizing summary statistics data from genome-wide association studies (GWAS), a thorough investigation to evaluate the impact of common variations on the genome were undertook. This involved assessing single nucleotide polymorphism (SNP) heritability across the entire genome, as well as within specific genomic regions. To ensure the robustness of our analysis, stringent quality control measures were applied to the GWAS summary statistics data. Criteria for inclusion encompassed the absence of missing values, a minor allele frequency ≥1%, P-values falling within the range of 0 to 1, and clear SNP strand orientation. SNP meeting these stringent criteria were then meticulously included in our analysis. The SNP heritability of NSCL/P was calculated using linkage disequilibrium score regression. Additionally, hierarchical linkage disequilibrium score regression to partition SNP heritability within coding regions, promoters, introns, enhancers, and super enhancers were employed, and the enrichment levels within different genomic regions using LDSC (v1.0.1) software were further elucidated.

RESULTS

Our study drew upon GWAS summary statistics data obtained from 806 NSCL/P trios, comprising a total of 2 418 individuals from the Chinese population. Following rigorous quality control procedures, 490 593 out of 492 993 SNP were deemed suitable for inclusion in SNP heritability calculations. The observed SNP heritability of NSCL/P was 0.55 (95%CI: 0.28-0.82). Adjusting for the elevated disease pre-valence within our sample, the SNP heritability scaled down to 0.37 (95%CI: 0.19-0.55) based on the prevalence observed in the general Chinese population. Notably, our enrichment analysis unveiled significant enrichment of SNP heritability within enhancer regions (15.70, P=0.04) and super enhancer regions (3.18, P=0.03).

CONCLUSION

Our study sheds light on the intricate interplay between common genetic variations and the risk of NSCL/P in the Chinese population. By elucidating the SNP heritability landscape across different genomic regions, we contribute valuable insights into the genetic basis of NSCL/P. The significant enrichment of SNP heritability within enhancer and super enhancer regions underscores the potential role of these regulatory elements in shaping the genetic susceptibility to NSCL/P. This paves the way for further research aimed at uncovering novel genetic pathogenic factors underlying NSCL/P pathogenesis.

Genetically inferred birthweight, height, and puberty timing and risk of osteosarcoma

INTRODUCTION

Several studies have linked increased risk of osteosarcoma with tall stature, high birthweight, and early puberty, although evidence is inconsistent. We used genetic risk scores (GRS) based on established genetic loci for these traits and evaluated associations between genetically inferred birthweight, height, and puberty timing with osteosarcoma.

METHODS

Using genotype data from two genome-wide association studies, totaling 1039 cases and 2923 controls of European ancestry, association analyses were conducted using logistic regression for each study and meta-analyzed to estimate pooled odds ratios (ORs) and 95% confidence intervals (CIs). Subgroup analyses were conducted by case diagnosis age, metastasis status, tumor location, tumor histology, and presence of a known pathogenic variant in a cancer susceptibility gene.

RESULTS

Genetically inferred higher birthweight was associated with an increased risk of osteosarcoma (OR =1.59, 95% CI 1.07-2.38, P = 0.02). This association was strongest in cases without metastatic disease (OR =2.46, 95% CI 1.44-4.19, P = 9.5 ×10-04). Although there was no overall association between osteosarcoma and genetically inferred taller stature (OR=1.06, 95% CI 0.96-1.17, P = 0.28), the GRS for taller stature was associated with an increased risk of osteosarcoma in 154 cases with a known pathogenic cancer susceptibility gene variant (OR=1.29, 95% CI 1.03-1.63, P = 0.03). There were no significant associations between the GRS for puberty timing and osteosarcoma.

CONCLUSION

A genetic propensity to higher birthweight was associated with increased osteosarcoma risk, suggesting that shared genetic factors or biological pathways that affect birthweight may contribute to osteosarcoma pathogenesis.

Comparison of genomic prediction accuracy using different models for egg production traits in Taiwan country chicken

In local chickens targeted for niche markets, genotyping costs are relatively high due to the small population size and diverse breeding goals. The single-step genomic best linear unbiased prediction (ssGBLUP) model, which combines pedigree and genomic information, has been introduced to increase the accuracy of genomic estimated breeding value (GEBV). Therefore, this model may be more beneficial than the genomic BLUP (GBLUP) model for genomic selection in local chickens. Additionally, the single-step genome-wide association study (ssGWAS) can be used to extend the ssGBLUP model results to animals with available phenotypic information but without genotypic data. In this study, we compared the accuracy of (G)EBVs using the pedigree-based BLUP (PBLUP), GBLUP, and ssGBLUP models. Moreover, we conducted single-SNP GWAS (SNP-GWAS), GBLUP-GWAS, and ssGWAS methods to identify genes associated with egg production traits in the NCHU-G101 chicken to understand the feasibility of using genomic selection in a small population. The average prediction accuracy of (G)EBV for egg production traits using the PBLUP, GBLUP, and ssGBLUP models is 0.536, 0.531, and 0.555, respectively. In total, 22 suggestive- and 5% Bonferroni genome-wide significant-level SNPs for total egg number (EN), average laying rate (LR), average clutch length, and total clutch number are detected using 3 GWAS methods. These SNPs are mapped onto Gallus gallus chromosomes (GGA) 4, 6, 10, 18, and 25 in NCHU-G101 chicken. Furthermore, through SNP-GWAS and ssGWAS methods, we identify 2 genes on GGA4 associated with EN and LR: ENSGALG00000023172 and PPARGC1A. In conclusion, the ssGBLUP model demonstrates superior prediction accuracy, performing on average 3.41% than the PBLUP model. The implications of our gene results may guide future selection strategies for Taiwan Country chickens. Our results highlight the applicability of the ssGBLUP model for egg production traits selection in a small population, specifically NCHU-G101 chicken in Taiwan.

In search of the genetic variants of human sex ratio at birth: was Fisher wrong about sex ratio evolution?

The human sex ratio (fraction of males) at birth is close to 0.5 at the population level, an observation commonly explained by Fisher's principle. However, past human studies yielded conflicting results regarding the existence of sex ratio-influencing mutations-a prerequisite to Fisher's principle, raising the question of whether the nearly even population sex ratio is instead dictated by the random X/Y chromosome segregation in male meiosis. Here we show that, because a person's offspring sex ratio (OSR) has an enormous measurement error, a gigantic sample is required to detect OSR-influencing genetic variants. Conducting a UK Biobank-based genome-wide association study that is more powerful than previous studies, we detect an OSR-associated genetic variant, which awaits verification in independent samples. Given the abysmal precision in measuring OSR, it is unsurprising that the estimated heritability of OSR is effectively zero. We further show that OSR's estimated heritability would remain virtually zero even if OSR is as genetically variable as the highly heritable human standing height. These analyses, along with simulations of human sex ratio evolution under selection, demonstrate the compatibility of the observed genetic architecture of human OSR with Fisher's principle and render it plausible that multiple OSR-influencing genetic variants segregate among humans.

Genome-Wide Association Study on Body Conformation Traits in Xinjiang Brown Cattle

Body conformation traits are linked to the health, longevity, reproductivity, and production performance of cattle. These traits are also crucial for herd selection and developing new breeds. This study utilized pedigree information and phenotypic (1185 records) and genomic (The resequencing of 496 Xinjiang Brown cattle generated approximately 74.9 billion reads.) data of Xinjiang Brown cattle to estimate the genetic parameters, perform factor analysis, and conduct a genome-wide association study (GWAS) for these traits. Our results indicated that most traits exhibit moderate to high heritability. The principal factors, which explained 59.12% of the total variance, effectively represented body frame, muscularity, rump, feet and legs, and mammary system traits. Their heritability estimates range from 0.17 to 0.73, with genetic correlations ranging from -0.53 to 0.33. The GWAS identified 102 significant SNPs associated with 12 body conformation traits. A few of the SNPs were located near previously reported genes and quantitative trait loci (QTLs), while others were novel. The key candidate genes such as LCORL, NCAPG, and FAM184B were annotated within 500 Kb upstream and downstream of the significant SNPs. Therefore, factor analysis can be used to simplify multidimensional conformation traits into new variables, thus reducing the computational burden. The identified candidate genes from GWAS can be incorporated into the genomic selection of Xinjiang Brown cattle, enhancing the reliability of breeding programs.

Improving on polygenic scores across complex traits using select and shrink with summary statistics (S4) and LDpred2

BACKGROUND

As precision medicine advances, polygenic scores (PGS) have become increasingly important for clinical risk assessment. Many methods have been developed to create polygenic models with increased accuracy for risk prediction. Our select and shrink with summary statistics (S4) PGS method has previously been shown to accurately predict the polygenic risk of epithelial ovarian cancer. Here, we applied S4 PGS to 12 phenotypes for UK Biobank participants, and compared it with the LDpred2 and a combined S4 + LDpred2 method.

RESULTS

The S4 + LDpred2 method provided overall improved PGS accuracy across a variety of phenotypes for UK Biobank participants. Additionally, the S4 + LDpred2 method had the best estimated PGS accuracy in Finnish and Japanese populations. We also addressed the challenge of limited genotype level data by developing the PGS models using only GWAS summary statistics.

CONCLUSIONS

Taken together, the S4 + LDpred2 method represents an improvement in overall PGS accuracy across multiple phenotypes and populations.

JointPRS: A Data-Adaptive Framework for Multi-Population Genetic Risk Prediction Incorporating Genetic Correlation

Genetic prediction accuracy for non-European populations is hindered by the limited sample size of Genome-wide association studies (GWAS) data in these populations. Additionally, it is challenging to tune model parameters with a small tuning dataset for methods that require tuning data, which is often the case for non-European samples. To address these challenges, we propose JointPRS, a novel, data-adaptive framework that simultaneously models multiple populations using GWAS summary statistics. JointPRS incorporates genetic correlation structures into the prediction framework, enabling accurate performance even without individual-level tuning data. Additionally, it uniquely employs a data-adaptive approach, providing a robust solution when only a small tuning dataset is available. Through extensive simulations and real data applications to 22 quantitative traits and four binary traits in five continental populations (European (EUR); East Asian (EAS); African (AFR); South Asian (SAS); and Admixed American (AMR)) evaluated using the UK Biobank (UKBB) and All of Us (AoU), we demonstrate that JointPRS outperforms six other state-of-art methods across three different data scenarios (no tuning data, tuning and testing data from the same cohort, and tuning and testing data from different cohorts) for most traits in non-European populations, while maintaining model simplicity and computational efficiency.

Fast and scalable ensemble learning method for versatile polygenic risk prediction

Polygenic risk scores (PRS) enhance population risk stratification and advance personalized medicine, but existing methods face several limitations, encompassing issues related to computational burden, predictive accuracy, and adaptability to a wide range of genetic architectures. To address these issues, we propose Aggregated L0Learn using Summary-level data (ALL-Sum), a fast and scalable ensemble learning method for computing PRS using summary statistics from genome-wide association studies (GWAS). ALL-Sum leverages a L0L2 penalized regression and ensemble learning across tuning parameters to flexibly model traits with diverse genetic architectures. In extensive large-scale simulations across a wide range of polygenicity and GWAS sample sizes, ALL-Sum consistently outperformed popular alternative methods in terms of prediction accuracy, runtime, and memory usage by 10%, 20-fold, and threefold, respectively, and demonstrated robustness to diverse genetic architectures. We validated the performance of ALL-Sum in real data analysis of 11 complex traits using GWAS summary statistics from nine data sources, including the Global Lipids Genetics Consortium, Breast Cancer Association Consortium, and FinnGen Biobank, with validation in the UK Biobank. Our results show that on average, ALL-Sum obtained PRS with 25% higher accuracy on average, with 15 times faster computation and half the memory than the current state-of-the-art methods, and had robust performance across a wide range of traits and diseases. Furthermore, our method demonstrates stable prediction when using linkage disequilibrium computed from different data sources. ALL-Sum is available as a user-friendly R software package with publicly available reference data for streamlined analysis.

Forensic height estimation using polygenic score in Korean population

Height is known to be a classically heritable trait controlled by complex polygenic factors. Numerous height-associated genetic variants across the genome have been identified so far. It is also a representative of externally visible characteristics (EVC) for predicting appearance in forensic science. When biological evidence at a crime scene is deficient in identifying an individual, the examination of forensic DNA phenotyping using some genetic variants could be considered. In this study, we aimed to predict 'height', a representative forensic phenotype, by using a small number of genetic variants when short tandem repeat (STR) analysis is hard with insufficient biological samples. Our results not only replicated previous genetic signals but also indicated an upward trend in polygenic score (PGS) with increasing height in the validation and replication stages for both genders. These results demonstrate that the established SNP sets in this study could be used for height estimation in the Korean population. Specifically, since the PGS model constructed in this study targets only a small number of SNPs, it contributes to enabling forensic DNA phenotyping even at crime scenes with a minimal amount of biological evidence. To the best of our knowledge, this was the first study to evaluate a PGS model for height estimation in the Korean population using GWAS signals. Our study offers insight into the polygenic effect of height in East Asians, incorporating genetic variants from non-Asian populations.

Large changes in detected selection signatures after a selection limit in mice bred for voluntary wheel-running behavior

In various organisms, sequencing of selectively bred lines at apparent selection limits has demonstrated that genetic variation can remain at many loci, implying that evolution at the genetic level may continue even if the population mean phenotype remains constant. We compared selection signatures at generations 22 and 61 of the "High Runner" mouse experiment, which includes 4 replicate lines bred for voluntary wheel-running behavior (HR) and 4 non-selected control (C) lines. Previously, we reported multiple regions of differentiation between the HR and C lines, based on whole-genome sequence data for 10 mice from each line at generation 61, which was >31 generations after selection limits had been reached in all HR lines. Here, we analyzed pooled sequencing data from ~20 mice for each of the 8 lines at generation 22, around when HR lines were reaching limits. Differentiation analyses of allele frequencies at ~4.4 million SNP loci used the regularized T-test and detected 258 differentiated regions with FDR = 0.01. Comparable analyses involving pooling generation 61 individual mouse genotypes into allele frequencies by line produced only 11 such regions, with almost no overlap among the largest and most statistically significant peaks between the two generations. These results implicate a sort of "genetic churn" that continues at loci relevant for running. Simulations indicate that loss of statistical power due to random genetic drift and sampling error are insufficient to explain the differences in selection signatures. The 13 differentiated regions at generation 22 with strict culling measures include 79 genes related to a wide variety of functions. Gene ontology identified pathways related to olfaction and vomeronasal pathways as being overrepresented, consistent with generation 61 analyses, despite those specific regions differing between generations. Genes Dspp and Rbm24 are also identified as potentially explaining known bone and skeletal muscle differences, respectively, between the linetypes.