Phenotypic Associations Research Articles

Multiple genetic polymorphisms are associated with the risk of metabolic syndrome, fatty liver, and airflow limitation: A Taiwan Biobank study

BackgroundLinks have been reported between the airflow limitation and both metabolic syndrome (MetS) and fatty liver (FL). Additionally, associations between genetic factors and risks of MetS, FL, and airflow limitation have been identified separately in different studies. Our study aims to simultaneously explore the association between specific single nucleotide polymorphisms (SNPs) of certain genes and the risk of the three associated diseases. MethodsIn this retrospective cross-sectional nationwide study, 150,709 participants from the Taiwan Biobank (TWB) were enrolled. We conducted a genotype–phenotype association analysis of nine SNPs on seven genes (ApoE-rs429358, MBOAT7-rs641738, LEPR-rs1805096, APOC3-rs2854116, APOC3-rs2854117, PPP1R3B-rs4240624, PPP1R3B-rs4841132, TM6SF2-rs58542926, and IFNL4-rs368234815) using data from the TWB1.0 and TWB2.0 genotype dataset. Participants underwent a series of assessments including questionnaires, blood examinations, abdominal ultrasounds, and spirometry examinations. ResultsMetS was associated with FL and airflow limitation. ApoE-rs429358, LEPR-rs1805096, APOC3-rs2854116, APOC3-rs2854117, PPP1R3B-rs4240624, PPP1R3B-rs4841132, and TM6SF2-rs58542926 were significantly associated with the risk of MetS. The cumulative impact of T alleles of ApoE-rs429358 and TM6SF2-rs58542926 on the risk of FL was observed (p-value for trend < 0.001). Individuals without MetS and airflow limitation carrying LEPR-rs1805096 G_G genotype exhibited a reduction in the forced expiratory volume in 1 s percentage prediction (Coefficient −35, 95 % confidence interval (CI) −69.7– −0.4), low forced vital capacity percentage prediction (Coefficient −41.6, 95 % CI −82.6- −0.6), and low vital capacity percentage prediction (Coefficient −42.2, 95 % CI −84.2- −0.1). ConclusionsMetS significantly correlated with FL and airflow limitation. Multiple SNPs were notably associated with MetS. Specifically, T alleles of ApoE-rs429358 and TM6SF2-rs58542926 cumulatively increased the risk of FL. LEPR-rs1805096 shows a trend-wise association with pulmonary function, which is significant in patients without MetS or airflow limitation.

Whole exome sequencing analyses reveal novel genes in telomere length and their biomedical implications.

Telomere length is a putative biomarker of aging and is associated with multiple age-related diseases. There are limited data on the landscape of rare genetic variations in telomere length. Here, we systematically characterize the rare variant associations with leukocyte telomere length (LTL) through exome-wide association study (ExWAS) among 390,231 individuals in the UK Biobank. We identified 18 robust rare-variant genes for LTL, most of which estimated effects on LTL were significant (> 0.2 standard deviation per allele). The biological functions of the rare-variant genes were associated with telomere maintenance and capping and several genes were specifically expressed in the testis. Three novel genes (ASXL1, CFAP58, and TET2) associated with LTL were identified. Phenotypic association analyses indicated significant associations of ASXL1 and TET2 with cancers, age-related diseases, blood assays, and cardiovascular traits. Survival analyses suggested that carriers of ASXL1 or TET2 variants were at increased risk for cancers; diseases of the circulatory, respiratory, and genitourinary systems; and all-cause and cause-specific deaths. The CFAP58 carriers were at elevated risk of deaths due to cancers. Collectively, the present whole exome sequencing study provides novel insights into the genetic landscape of LTL, identifying novel genes associated with LTL and their implications on human health and facilitating a better understanding of aging, thus pinpointing the genetic relevance of LTL with clonal hematopoiesis, biomedical traits, and health-related outcomes.

Identification of RESP18 Gene Mutations Linked to Hereditary Non-Syndromic Cleft Lip and Palate in a Southern Chinese Family.

BACKGROUND Non-syndromic cleft lip with cleft palate (NSCLP) is one of the most common congenital birth defects worldwide; it causes lifelong problems and imposes burdens on patients and their families. This study aimed to describe the genomic analysis and identification of de novo regulated endocrine-specific protein 18 (RESP18) rs2385404 and rs2385405 gene polymorphisms associated with NSCLP in a southern Chinese family and to improve prevention, treatment, and prognosis of NSCLP. MATERIAL AND METHODS We performed a genome-wide association study (GWAS) to investigate the association of NSCLP phenotype with gene mutation. We investigated a 5-persons NSCLP family to screen the genetic variation of Han nationality in southern Chinese. Whole-genome sequencing (WGS) was used to detect all candidate genetic variants, and whole-exome sequencing (WES) was implemented to further verify mutations. The Clinical Variation Data Base (ClinVar) was employed for screening gene mutations. Finally, Sanger sequencing was applied to verify gene variations. RESULTS The combined analysis of WGS, WES, and ClinVar showed that a total of 9 variation positions overlapped among the 3 study cohorts. Sanger sequencing verified Glu amino acid variation in 2 mutation sites (rs2385404, rs2385405) from the RESP18 gene, which caused abnormal RESP18 function and was associated with hereditary NSCLP. CONCLUSIONS The combined genomic results showed that 2 mutations (rs2385404 and rs2385405) of the RESP18 gene were related to NSCLP in the family. The RESP18 gene may play an important role in the etiology and pathogenesis of cleft lip and palate.

Association of hypertriglyceridemic waist phenotype with metabolic syndrome traits and its diagnostic potential to predict metabolic syndrome in adults with excess body weight: A community-based cross-sectional study.

The hypertriglyceridemic waist (HTGW) phenotype is a simple measure to identify individuals at increased risk of metabolic syndrome (MetS) traits. The present study aimed to describe the HTGW prevalence, and its associations with MetS traits, and also determine the diagnostic potential of the mirror indices of HTGW phenotype to predict MetS and its components in community-dwelling adults with overweight or obesity in Southern, Sri Lanka. In a cross-sectional study, 300 adults with excess body weight (body mass index >23 kg/m2) were enrolled and examined for the HTGW phenotype (fasting plasma triglyceride concentration ≥1.695 mmol/L and waist circumference >90 and >85 cm in males and females, respectively). One in five adults with excess body weight had the HTGW phenotype. Phenotype-positive adults had significantly higher fasting plasma glucose (FPG) (p = 0.010), low-density lipoprotein cholesterol (HDL-C) (p < 0.001), total cholesterol (p < 0.001), atherogenic index (p < 0.001), coronary risk index (p = 0.001), triglyceride glucose index (p = 0.040), bioimpedance visceral fat (p = 0.041) and significantly lower HDL-C (p = 0.001) and cardioprotective index (p = 0.009) than those without the HTGW phenotype. Adults with excess body weight and the HTGW phenotype had an increased risk of FPG (odds ratio [OR] = 1.294; 95% confidence interval [CI] 1.051-1.594), atherogenic index (OR = 3.138; 95% CI = 1.559-6.317) and triglyceride glucose index (OR = 3.027; 95% CI = 1.111-8.249). The HTGW phenotype was strongly associated with MetS traits (OR = 16.584; 95% CI = 6.230-44.147). The cut-off values for the product of waist circumference × triglyceride, to identify the risk of having MetS and dyslipidemia among adults with excess body weight were 158.66 and 160.15 cm × mmol/L, respectively. The readily available and inexpensive measures of the HTGW phenotype could serve as a clinically useful marker to identify MetS traits in adults with excess body weight.

Pervasive loss of antigen presentation in solid tumors driven by loss of HLA class I expression.

e14654 Background: Human Leukocyte Antigens (HLA) play a key role in inducing responses to immune checkpoint inhibitor (ICI) therapy. HLA class I (HLA-I) expression is essential for antigen presentation in cancer cells and its loss leads to immune evasion. Expression of HLA-II shows presence of adaptive immune response via antigen presenting cells. To investigate the complex interplay of HLA class I/II in solid tumors, we study the landscape and association of several HLA phenotypes with biomarkers of tumor response and resistance to ICIs in a large pan-cancer cohort. Methods: A real-world cohort of 24,186 solid tumors was assessed by an immune expression profiling assay of 395 genes that were background subtracted, normalized, and ranked yielding a percentile rank value [0-100]. HLA Class I and class II expressions were estimated as average expression of HLA-A, HLA-B, HLA-C genes, and HLA HLA-DP, HLA-DQ, HLA-DR genes, respectively. Both HLA classes were labelled as high (≥66), moderate (≥33 &amp; &lt;66) or low (&lt;33). We studied the distribution of HLA I/II phenotype defined as Ihi/IIhi comprised hot tumors with no loss of HLA-I and Ilo/IIhi defines immune evasion via loss of HLA-I in hot tumors. Ihi/IIlo phenotype comprises less inflamed tumors with high HLA-I expression and Ilo/IIlo comprises of cold tumors. We also performed differential expression of ICI targets including PD-1, PD-L1, LAG-3, TIM3 and expression-based signatures of inflammation and cell proliferation. Results: Loss of HLA-I expression was observed in 44.1% (n= 10669) of all solid tumors with most frequent loss observed in prostate (55%, n=450) cancer. Similarly, loss of HLA-II expression was observed in 34.7% (n=8396) of solid tumors with highest loss observed in neuroendocrine (59%; n=345) cancers. 49% of all tumors presented with four HLA-phenotypes, where 17.9% (n=4332) were characterized by Ilo/IIlo phenotype. Ihi/IIlo was present in 13% (n=3127) of all tumors. Both Ihi/IIhi and Ilo/IIhi phenotypes were significantly (p&lt;0.001) associated with increased tumor inflammation. Other ICI targets such as PD-L1, TIM3, CTLA4 and LAG3 were significantly (p&lt;0.001) overexpressed in this immune evasion phenotype compared to other phenotypes. Conversely, Ilo/IIlo phenotype was significantly associated with cold tumors (p&lt;0.001), hinting at lack of adaptive immune response in these tumors. Conclusions: This study offers insight into pervasive loss of antigen presentation via HLA expression. Concurrent loss of HLA Class I expression with increased class II expression and additional ICI target co-expression is a potential immune escape mechanism in immunologically active solid tumors. Distinct and significant association of these MHC phenotypes with tumor inflammation, checkpoint markers and PD-L1 highlight the potential use of comprehensive immune profiling for further studying combination strategies to correct soft loss of HLA-I and ICI therapies.

Immune phenotype profiling based on anatomic origin of melanoma and impact on clinical outcomes of immune checkpoint inhibitor treatment.

9569 Background: The inflamed immune phenotype is associated with a favorable response to immunotherapy in metastatic malignant melanoma. Although variations in molecular features across melanoma subtypes and differing ethnic distributions have been well reported, studies investigating immune phenotypes across multiple institutions within the context of different melanoma subtypes are scarce. We examined the association of immune phenotypes with outcomes after immunotherapy, based on subtypes of malignant melanoma. Methods: Two institutional advanced melanoma cohortsrepresenting Asian and Western populations (YUHS, n = 123; Stanford University, n = 102) were included. H&amp;E-stained tumor slides were assessed using Lunit SCOPE IO, an AI-powered whole slide image analyzer, to define the inflamed score (IS, % of inflamed area) and the inflamed phenotype (&gt;33.3% IS). Clinical outcomes after immune checkpoint inhibitor (anti-PD-1/PD-L1) treatment, including progression-free survival (PFS) and overall-survival (OS), were assessed. Results: In the overall cohort (n = 225), the inflamed phenotype was associated with prolonged PFS (HR = 0.634, 95% CI: 0.453 – 0.887, p = 0.007) and OS (HR = 0.655, 95% CI: 0.432 – 0.992, p = 0.044). On analysis of melanoma subtypes, we identified non-acral cutaneous melanomas (CM, n = 94), acral melanomas (AM, n = 52), mucosal melanomas (n = 43), uveal melanomas (n = 16), and melanomas of unknown primary site (n = 20), with a disproportionate enrichment of AM (37.4%) and mucosal (29.3%) melanoma cases in the YUHS cohort and CM cases (68.6%) in the Stanford cohort. The IS varied across different melanoma subtypes, with the highest IS observed in CM (median, [IQR]; 34.0, [5.8–52.2]), and significantly lower scores in AM (22.3, [7.7–36.9]), mucosal (13.6, [0–31.4]), and uveal melanoma (5.5, [0–13.6]). Among CM patients, the inflamed phenotype was significantly associated with better post-immunotherapy PFS (HR = 0.476, 95% CI: 0.274 – 0.826, p = 0.007). In contrast, the inflamed phenotype did not correlate with survival in AM patients (p = 0.58), who exhibited universally poorer PFS compared to non-AM patients (HR = 2.124, 95% CI: 1.486 - 3.005). Conclusions: AI-powered immune phenotype assessment highlights a heterogeneity of immune phenotypes across specific melanoma subtypes, as well as differential association with outcomes after immune checkpoint inhibitor treatment. While CM patients were well-stratified by immune phenotype, the predictive value of immune phenotyping was less pronounced in acral melanomas, which demonstrated poorer outcomes following immunotherapy.

Cutaneous spectrum of lupus erythematosus: A cohort of patients from a referral-center in Colombia

IntroductionTo date, few epidemiological studies compare the incidence and prevalence of systemic lupus erythematosus (SLE) and isolated cutaneous lupus erythematosus (CLE). The information is even more scarce in Latin America. The aim of this study is to describe the phenotype of CLE in a reference center in Colombia. Materials and methodsA retrospective cross-sectional study was carried out. SLE was confirmed according to EULAR/ACR 2019 classification criteria and patients were simultaneously evaluated in the rheumatology and dermatology clinics. A descriptive and bivariate analysis was carried out. The institutional committee approved the study. ResultsThirty participants were diagnosed with SLE and CLE. Most patients were female (83.3%), with a mean age of 37±13 years. Chronic CLE was the most prevalent subtype (46.7%), followed by acute (30%) and subacute (16.7%) CLE. There were statistically significant differences when comparing acute CLE and reduced C4 (p=.032); in subacute CLE and interstitial lung disease (p=.010); and in lymphopenia (p=.012) and thrombocytopenia (p=.046). Finally, there was a difference in patients with chronic CLE and the use of topical corticosteroid (p=.026), methotrexate (p=.036), and SLEDAI>3 points (p=.025). ConclusionThis study provides valuable insights into the phenotypic characteristics and associations of CLE with systemic manifestations in the Colombian population, contributing to the understanding and managing of this complex autoimmune disease.

Genetic and phenotypic associations of frailty with cardiovascular indicators and behavioral characteristics

IntroductionFrailty Index (FI) is a common measure of frailty, which has been advocated as a routine clinical test by many guidelines. The genetic and phenotypic relationships of FI with cardiovascular indicators (CIs) and behavioral characteristics (BCs) are unclear, which has hampered ability to monitor FI using easily collected data. ObjectivesThis study is designed to investigate the genetic and phenotypic associations of frailty with CIs and BCs, and further to construct a model to predict FI. MethodGenetic relationships of FI with 288 CIs and 90 BCs were assessed by the cross-trait LD score regression (LDSC) and Mendelian randomization (MR). The phenotypic data of these CIs and BCs were integrated with a machine-learning model to predict FI of individuals in UK-biobank. The relationships of the predicted FI with risks of type 2 diabetes (T2D) and neurodegenerative diseases were tested by the Kaplan-Meier estimator and Cox proportional hazards model. ResultsMR revealed putative causal effects of seven CIs and eight BCs on FI. These CIs and BCs were integrated to establish a model for predicting FI. The predicted FI is significantly correlated with the observed FI (Pearson correlation coefficient = 0.660, P-value = 4.96 × 10-62). The prediction model indicated “usual walking pace” contributes the most to prediction. Patients who were predicted with high FI are in significantly higher risk of T2D (HR = 2.635, P < 2 × 10-16) and neurodegenerative diseases (HR = 2.307, P = 1.62 × 10-3) than other patients. ConclusionThis study supports associations of FI with CIs and BCs from genetic and phenotypic perspectives. The model that is developed by integrating easily collected CIs and BCs data in predicting FI has the potential to monitor disease risk.

Association of the muscle mass phenotype as assessed by a grading system with the quality of life of patients with incurable cancer in palliative care

BackgroundLoss of muscle mass (MM) is common in advanced stages of cancer, with an impact on worsening quality of life (QoL). In the current study the relationship of a previously proposed simple grade system to assess MM phenotypes with QoL was investigated to strengthen its clinical significance. AimTo verify whether the MM phenotypes, which were evaluated by using a grading system, are associated with the quality of life (QoL) of patients with incurable cancer. MethodsSecondary data from a cohort of patients with incurable cancer in palliative care, were analyzed. The grade system considers measurements of the muscle area arm and handgrip strength. Based on these measurements, patients are classified as probably non-sarcopenic (Nsarc), probably sarcopenic (PSarc), and sarcopenic (Sarc). The outcome measure was QoL domains assessed by the EORTC QoL Questionnaire Core-15. Logistic regression models were used to verify the association of the domains of QoL with the MM phenotypes. ResultsA total of 770 patients were included, median age 62 years and 56.6% females. The PSarc group had significantly worse scores in the QoL domains when compared to the Nsarc group (physical p= 0.001, emotional p= 0.018, fatigue p<0.001, nausea p= 0.017, insomnia p= 0.001, appetite loss p= 0.002, and global health p= 0.043). Adjusted logistic regression analysis showed an increased risk of worse QoL in the PSarc and Sarc, when compared to NSarc, respectively (Odds ratio [OR], 95% confidence interval [CI]): physical (OR: 2.54, CI: 1.78-3.62 and OR: 7.18, CI: 4.24-12.17), emotional (OR: 1.61, CI: 1.15-2.24 and OR: 1.49, CI: 1.01-2.20), fatigue (OR: 1.89, CI: 1.35-2.64 and OR: 1.83, CI: 1.23-2.71), insomnia (OR: 2.01, CI: 1.43-2.83 and OR: 3.11, CI: 2.04-4.75), while an appetite loss was associated with the PSarc (OR: 1.40, CI: 1.02-1.96), together with global health in the Sarc group (OR: 1.56, CI: 1.06-2.29). ConclusionThe severity of the MM phenotype was associated with a worse QoL domains. Our results highlight the importance of MM preserving to affecting QoL status. The grading system can be useful for predicting the QoL in those patients, and its usefulness can potentially impact clinical and therapeutic decision-making.

Cross-ancestry genome-wide association studies of brain imaging phenotypes.

Genome-wide association studies of brain imaging phenotypes are mainly performed in European populations, but other populations are severely under-represented. Here, we conducted Chinese-alone and cross-ancestry genome-wide association studies of 3,414 brain imaging phenotypes in 7,058 Chinese Han and 33,224 white British participants. We identified 38 new associations in Chinese-alone analyses and 486 additional new associations in cross-ancestry meta-analyses at P < 1.46 × 10-11 for discovery and P < 0.05 for replication. We pooled significant autosomal associations identified by single- or cross-ancestry analyses into 6,443 independent associations, which showed uneven distribution in the genome and the phenotype subgroups. We further divided them into 44 associations with different effect sizes and 3,557 associations with similar effect sizes between ancestries. Loci of these associations were shared with 15 brain-related non-imaging traits including cognition and neuropsychiatric disorders. Our results provide a valuable catalog of genetic associations for brain imaging phenotypes in more diverse populations.

The association of body composition phenotypes before chemotherapy with epithelial ovarian cancer mortality.

The association of body composition with epithelial ovarian carcinoma (EOC) mortality is poorly understood. To date, evidence suggests that high adiposity is associated with decreased mortality (an obesity paradox), but the impact of muscle on this association has not been investigated. Herein, we define associations of muscle and adiposity joint-exposure body composition phenotypes with EOC mortality. Body composition from 500 women in the Body Composition and Epithelial Ovarian Cancer Survival Study was dichotomized as normal or low skeletal muscle index (SMI), a proxy for sarcopenia, and high or low adiposity. Four phenotypes were classified as fit (normal SMI and low adiposity; reference; 16.2%), overweight or obese (normal SMI and high adiposity; 51.2%), sarcopenia and overweight or obese (low SMI and high adiposity; 15.6%), and sarcopenia or cachexia (low SMI and low adiposity; 17%). We used multivariable Cox models to estimate associations of each phenotype with mortality for EOC overall and high-grade serous ovarian carcinoma (HGSOC). Overweight or obesity was associated with up to 51% and 104% increased mortality in EOC and HGSOC [Hazard Ratio (HR)] = 1.51, 95% CI = 1.05 to 2.19 and HR = 2.04, 95% CI = 1.29 to 3.21). Sarcopenia and overweight or obesity was associated with up to 66% and 67% increased mortality in EOC and HGSOC (HR = 1.66, 95% CI = 1.13 to 2.45 and HR = 1.67, 95% CI = 1.05 to 2.68). Sarcopenia or cachexia was associated with up to 73% and 109% increased mortality in EOC and HGSOC (HR = 1.73, 95% CI = 1.14 to 2.63 and HR = 2.09, 95% CI = 1.25 to 3.50). Overweight or obesity, sarcopenia and overweight or obesity, and sarcopenia or cachexia phenotypes were each associated with increased mortality in EOC and HGSOC. Exercise and dietary interventions could be leveraged as ancillary treatment strategies for improving outcomes in the most fatal gynecological malignancy with no previously established modifiable prognostic factors.

#2613 Clinical spectrum and prognosis of the atypical polycystic kidney disease caused by monoallelic loss-of-function IFT140 variants

Abstract Background and Aims Monoallelic loss-of-function (LoF) variants in IFT140, which protein product is involved in retrograde ciliary trafficking and ciliary entry of membrane protein, have been recently linked to ADPKD spectrum, with 44 pedigrees reported so far [1]. The aim of this study was to characterize the disease presentation and renal outcome of individuals with monoallelic LoF variants of IFT140. Method Clinical information, family history and imaging data were collected for individuals with LoF IFT140-variants identified amongst 2800 individuals recruited in the Genkyst and Cystic ADPKD patients cohorts, and in different French, Spanish, and German centers. Targeted massive parallel sequencing of cystic genes or whole exome sequencing was performed. Newly identified and recently reported cases were combined to evaluate the influence of sex on eGFR using linear regression taking age into account. In addition, data of the Genome Aggregation (GnomAD) v4.0 and of the 100k Genomes project were respectively used to explore genetic prevalence and disease penetrance and expressivity. Results A total of 75 individuals from 61 pedigrees were identified (median age at last follow-up 56 years, 52% females). Forty-one different LoF IFT140-variants were identified: 14 nonsense, 7 splice-site, 14 frameshifting deletions or insertions and 6 large deletions, and no additional pathogenic variant was identified in any other gene. A majority of the individuals presented with large, exophytic cysts, median total kidney volume 688 (n = 35, range 201-4139) ml, and 90.9% were classified in Mayo Class 2A. Although 70.4% of the individuals had stage 1 or 2 chronic kidney disease (CKD) at the last follow up, proportion of CKD stage 3-5 was significantly higher (56.3% vs 7.7%, p &amp;lt; 0.00001) after 60 years of age. Adjusted for age, males exhibited lower eGFR (linear regression, p = 0.038, Fig. 1). Median age at diagnosis of hypertension was 63 years. Liver cysts were present in 12% of affected individuals with no case of symptomatic polycystic liver disease, and intracranial aneurysms in three of 10 screened patients. The genetic prevalence of monoallelic LoF IFT140 variants was estimated to be 19.56 (0.95 CI 18.60-20.53) per 10,000 in the entire GnomAD population (n = 280 in 807,162) and 29.4 (0.95 CI 25.4-33.8) per 10,000 in the 100kG (n = 190 in 64,185). Amongst the latter, kidney cysts were reported in 26.8% and diagnosis cystic kidney disease (Q61) was established in 18.4%. No obvious extra renal manifestations were identified, and out of total of 730 phenotype association tests conducted, only Q61 was associated with pLOF IFT140 variants (p = 2.9 × 10−9, OR = 5.6 (3.3-9.2)). Conclusion Individuals with monoallelic LoF variants of IFT140 are likely to develop kidney cysts and/or atypical forms of ADPKD. However, a large proportion may remain asymptomatic or undiagnosed. There is no evidence to recommend cascade screening using genetic testing in young at risk relatives. Follow-up of blood pressure and eGFR after 50 years of age should be advised.

Maladaptive personality traits and older adult relationship satisfaction: A co-twin control approach to understanding associations.

Maladaptive personality traits have been implicated in romantic relationship dissatisfaction, but the etiology of those links and the degree to which they extend to other types of relationships are unclear. The purpose of this study was to examine associations between maladaptive personality traits and satisfaction in various relationships using a co-twin control design to identify potential environmental contributions. The sample consisted of 1340 older adult twin participants from the Minnesota Twin Registry (Mage = 70.3) that completed the Personality Inventory for DSM-5 Faceted Brief Form and Network of Relationships Inventory (Revised for Older Adults). Several maladaptive personality traits were phenotypically associated with relationship dissatisfaction, with detachment and negative affect having the largest effects. Further, within twin pair differences in detachment and negative affect were associated with greater relationship dissatisfaction, suggesting that observed associations were mediated partly by the unique environment, not solely the result of genetic and familial confounding. Both phenotypic and co-twin associations were strongest overall in the romantic partner relationship. These findings support the notion that maladaptive personality traits are implicated in interpersonal dysfunction across multiple domains.

Association of Pharmacogenomic Phenotypes in CYP2D6, CYP2C9, CYP2C19, and CYP3A5 on Polypharmacy in Veterans.

The Department of Veterans Affairs (VA) utilizes a pharmacogenomic (PGx) program that analyzes specific "pharmacogenes." This study evaluates the effect that pharmacogenes may have on prevalence of polypharmacy. This retrospective cohort study included patients with VA prescriptions who underwent PGx testing. We quantified prescriptions active or recently expired at the time of PGx testing. We constructed two co-primary polypharmacy (≥10 medications) end points: (i) based on all medications and (ii) requiring that at least one medication was affected by a pharmacogene of interest. Pharmacogenes and actionable phenotypes of interest included poor and ultrarapid metabolizers for CYP2D6, CYP2C9, and CYP2C19 and intermediate and normal metabolizers for CYP3A5. Patients were classified as having 0, 1, and 2+ total phenotypes across all genes. Of the 15,144 patients screened, 13,116 met eligibility criteria. Across phenotype cohorts, there was no significant association with polypharmacy using all medications, number of total medications, or number of medications affected by phenotypes. However, there was a significant difference in patients with polypharmacy prescribed ≥1 medication impacted by PGx across phenotype groups: 2,514/4,949 (51%), 1,349/2,595 (52%), 204/350 (58%) (P = 0.03, OR 1.31, 95% CI 1.02-1.67). The median number of medications affected by PGx phenotypes with ≥1 PGx-impacted medication across phenotype groups was a median of 0 (IQR 0, 0), 0 (IQR 0, 0), and 1 (IQR 0, 1) (P < 0.001). In patients prescribed ≥1 medication impacted by PGx, those with more actionable pharmacogenomic phenotypes were more likely to meet polypharmacy criteria.

Seedling root system adaptation to water availability during maize domestication and global expansion.

The maize root system has been reshaped by indirect selection during global adaptation to new agricultural environments. In this study, we characterized the root systems of more than 9,000 global maize accessions and its wild relatives, defining the geographical signature and genomic basis of variation in seminal root number. We demonstrate that seminal root number has increased during maize domestication followed by a decrease in response to limited water availability in locally adapted varieties. By combining environmental and phenotypic association analyses with linkage mapping, we identified genes linking environmental variation and seminal root number. Functional characterization of the transcription factor ZmHb77 and in silico root modeling provides evidence that reshaping root system architecture by reducing the number of seminal roots and promoting lateral root density is beneficial for the resilience of maize seedlings to drought.

Assessment of gene–disease associations and recommendations for genetic testing for somatic variants in vascular anomalies by VASCERN-VASCA

BackgroundVascular anomalies caused by somatic (postzygotic) variants are clinically and genetically heterogeneous diseases with overlapping or distinct entities. The genetic knowledge in this field is rapidly growing, and genetic testing is now part of the diagnostic workup alongside the clinical, radiological and histopathological data. Nonetheless, access to genetic testing is still limited, and there is significant heterogeneity across the approaches used by the diagnostic laboratories, with direct consequences on test sensitivity and accuracy. The clinical utility of genetic testing is expected to increase progressively with improved theragnostics, which will be based on information about the efficacy and safety of the emerging drugs and future molecules. The aim of this study was to make recommendations for optimising and guiding the diagnostic genetic testing for somatic variants in patients with vascular malformations.ResultsPhysicians and lab specialists from 11 multidisciplinary European centres for vascular anomalies reviewed the genes identified to date as being involved in non-hereditary vascular malformations, evaluated gene–disease associations, and made recommendations about the technical aspects for identification of low-level mosaicism and variant interpretation. A core list of 24 genes were selected based on the current practices in the participating laboratories, the ISSVA classification and the literature. In total 45 gene–phenotype associations were evaluated: 16 were considered definitive, 16 strong, 3 moderate, 7 limited and 3 with no evidence.ConclusionsThis work provides a detailed evidence-based view of the gene–disease associations in the field of vascular malformations caused by somatic variants. Knowing both the gene–phenotype relationships and the strength of the associations greatly help laboratories in data interpretation and eventually in the clinical diagnosis. This study reflects the state of knowledge as of mid-2023 and will be regularly updated on the VASCERN-VASCA website (VASCERN-VASCA, https://vascern.eu/groupe/vascular-anomalies/).

Causal association of sleep traits with the risk of thyroid cancer: A mendelian randomization study.

This study was to explore the causal associations of sleep traits including sleep duration, snoring, chronotype, sleep disorders, getting up in the morning, sleeplessness/insomnia and nap during day with the risk of thyroid cancer based on Mendelian randomization (MR) analysis. Summary single nucleotide polymorphism (SNP)-phenotype association data were obtained from published genome-wide association studies (GWASs) using the FinnGen and UK Biobank databases. A series of screening processes were performed to select qualified SNPs strongly related to exposure. We applied the inverse variance weighted (IVW), the Mendelian Randomization robust adjusted profile score (MR-RAPS), the Mendelian randomization pleiotropy residual sum and outlier (MR-PRESSO), and the Weighted Median to estimate the causal links between sleep traits and the risk of thyroid cancer. Odds ratio (OR) and 95% confidence interval (CI) were calculated. The IVW results showed that getting up in the morning (OR = 0.055, 95%CI: 0.004-0.741) and napping during day (OR = 0.031, 95%CI: 0.002-0.462) were associated with decreased risk of thyroid cancer in the Italian population. A 1.30-h decrease of sleep duration was associated with 7.307-fold of thyroid cancer risk in the Finnish population (OR = 7.307, 95%CI: 1.642-32.519). Cronotype could decrease the risk of thyroid cancer in the Finnish population (OR = 0.282, 95%CI: 0.085-0.939). Sleep disorders increased the risk of thyroid cancer in the Finnish population (OR = 2.298, 95%CI: 1.194-4.422). The combined results revealed that sleep duration was correlated with increased risk of thyroid cancer (OR = 5.600, 95%CI: 1.458-21.486). Decreased sleep duration was associated with increased risk of thyroid cancer, which indicated the importance of adequate sleep for the prevention of thyroid cancer.

Transcriptome Analysis of Sesame (Sesamum indicum L.) Reveals the LncRNA and mRNA Regulatory Network Responding to Low Nitrogen Stress.

Nitrogen is one of the important factors restricting the development of sesame planting and industry in China. Cultivating sesame varieties tolerant to low nitrogen is an effective way to solve the problem of crop nitrogen deficiency. To date, the mechanism of low nitrogen tolerance in sesame has not been elucidated at the transcriptional level. In this study, two sesame varieties Zhengzhi HL05 (ZZ, nitrogen efficient) and Burmese prolific (MD, nitrogen inefficient) in low nitrogen were used for RNA-sequencing. A total of 3964 DEGs (differentially expressed genes) and 221 DELs (differentially expressed lncRNAs) were identified in two sesame varieties at 3d and 9d after low nitrogen stress. Among them, 1227 genes related to low nitrogen tolerance are mainly located in amino acid metabolism, starch and sucrose metabolism and secondary metabolism, and participate in the process of transporter activity and antioxidant activity. In addition, a total of 209 pairs of lncRNA-mRNA were detected, including 21 pairs of trans and 188 cis. WGCNA (weighted gene co-expression network analysis) analysis divided the obtained genes into 29 modules; phenotypic association analysis identified three low-nitrogen response modules; through lncRNA-mRNA co-expression network, a number of hub genes and cis/trans-regulatory factors were identified in response to low-nitrogen stress including GS1-2 (glutamine synthetase 1-2), PAL (phenylalanine ammonia-lyase), CHS (chalcone synthase, CHS), CAB21 (chlorophyll a-b binding protein 21) and transcription factors MYB54, MYB88 and NAC75 and so on. As a trans regulator, lncRNA MSTRG.13854.1 affects the expression of some genes related to low nitrogen response by regulating the expression of MYB54, thus responding to low nitrogen stress. Our research is the first to provide a more comprehensive understanding of DEGs involved in the low nitrogen stress of sesame at the transcriptome level. These results may reveal insights into the molecular mechanisms of low nitrogen tolerance in sesame and provide diverse genetic resources involved in low nitrogen tolerance research.

Causal association and shared genetics between telomere length and COVID-19 outcomes: New evidence from the latest large-scale summary statistics

BackgroundObservational studies suggested that leukocyte telomere length (LTL) is shortened in COVID-19 patients. However, the genetic association and causality remained unknown. MethodsBased on the genome-wide association of LTL (N = 472,174) and COVID-19 phenotypes (N = 1086,211–2597,856), LDSC and SUPERGNOVA were used to estimate the genetic correlation. Cross-trait GWAS meta-analysis, colocalization, fine-mapping analysis, and transcriptome-wide association study were conducted to explore the shared genetic etiology. Mendelian randomization (MR) was utilized to infer the causality. Upstream and downstream two-step MR was performed to investigate the potential mediating effects. ResultsLDSC identified a significant genetic association between LTL and all COVID-19 phenotypes (rG < 0, p < 0.05). Six significant regions were observed for LTL and COVID-19 susceptibility and hospitalization, respectively. Colocalization analysis found rs144204502, rs34517439, and rs56255908 were shared causal variants between LTL and COVID-19 phenotypes. Numerous biological pathways associated with LTL and COVID-19 outcomes were identified, primarily involving immune-related pathways. MR showed that longer LTL was significantly associated with a lower risk of COVID-19 severity (OR [95% CI] = 0.81 [0.71–0.92], p = 1.24 ×10-3) and suggestively associated with lower risks of COVID-19 susceptibility (OR [95% CI] = 0.96 [0.92–1.00], p = 3.44 ×10-2) and COVID-19 hospitalization (OR [95% CI] = 0.89 [0.80–0.98], p = 1.89 ×10-2). LTL partially mediated the effects of BMI, smoking, and education on COVID-19 outcomes. Furthermore, six proteins partially mediated the causality of LTL on COVID-19 outcomes, including BNDF, QPCT, FAS, MPO, SFTPB, and APOF. ConclusionsOur findings suggested that shorter LTL was genetically associated with a higher risk of COVID-19 phenotypes, with shared genetic etiology and potential causality.

A novel method for multiple phenotype association studies based on genotype and phenotype network.

Joint analysis of multiple correlated phenotypes for genome-wide association studies (GWAS) can identify and interpret pleiotropic loci which are essential to understand pleiotropy in diseases and complex traits. Meanwhile, constructing a network based on associations between phenotypes and genotypes provides a new insight to analyze multiple phenotypes, which can explore whether phenotypes and genotypes might be related to each other at a higher level of cellular and organismal organization. In this paper, we first develop a bipartite signed network by linking phenotypes and genotypes into a Genotype and Phenotype Network (GPN). The GPN can be constructed by a mixture of quantitative and qualitative phenotypes and is applicable to binary phenotypes with extremely unbalanced case-control ratios in large-scale biobank datasets. We then apply a powerful community detection method to partition phenotypes into disjoint network modules based on GPN. Finally, we jointly test the association between multiple phenotypes in a network module and a single nucleotide polymorphism (SNP). Simulations and analyses of 72 complex traits in the UK Biobank show that multiple phenotype association tests based on network modules detected by GPN are much more powerful than those without considering network modules. The newly proposed GPN provides a new insight to investigate the genetic architecture among different types of phenotypes. Multiple phenotypes association studies based on GPN are improved by incorporating the genetic information into the phenotype clustering. Notably, it might broaden the understanding of genetic architecture that exists between diagnoses, genes, and pleiotropy.