Polygenic Contribution Research Articles

Contribution of common and rare damaging variants in familial forms of bipolar disorder and phenotypic outcome

Genome-wide association studies on bipolar disorders (BD) have revealed an additive polygenic contribution of common single-nucleotide polymorphisms (SNPs). However, these SNPs explain only 25% of the overall genetic variance and suggest a role of rare variants in BD vulnerability. Here, we combined high-throughput genotyping data and whole-exome sequencing in cohorts of individuals with BD as well as in multiplex families with a high density of affected individuals in order to determine the contribution of both common and rare variants to BD genetic vulnerability. Using polygenic risk scores (PRS), we showed a strong contribution of common polymorphisms previously associated with BD and schizophrenia (SZ) and noticed that those specifically associated with SZ contributed more in familial forms of BD than in non-familial ones. The analysis of rare damaging variants shared by affected individuals in multiplex families with BD revealed a single interaction network enriched in neuronal and developmental biological pathways, as well as in the regulation of gene expression. We identified four genes with a higher mutation rate in individuals with BD than in the general population and showed that mutations in two of them were associated with specific clinical manifestations. In addition, we showed a significant negative correlation between PRS and the number of rare damaging variants specifically in unaffected individuals of multiplex families. Altogether, our results suggest that common and rare genetic variants both contribute to the familial aggregation of BD and this genetic architecture may explain the heterogeneity of clinical manifestations in multiplex families.

Heritable cancer risk in the genomic era

Traditional family history based identification of heritable cancer predisposition is giving way to genomic technologies applied to well annotated clinical cohorts, yielding a complex landscape of disease. The International Sarcoma Kindred Study was formed to investigate the heritable aspects of sarcoma. We have previously identified not only monogenic drivers but also polygenic contributions to sarcoma. Most recently we have completed whole genome sequencing (WGS) of 1700 sarcoma probands. A rare variant burden analysis showed the greatest enrichment in pathogenic variation was in TP53, NF1 and POT1. Heritable risk correlates with early age at diagnosis. The Genetic Cancer Risk in the Young Study is a cohort of 1100 young (0–40 years) cancer patients. Using WGS we aim to investigate further the heritable drivers of disease. Translation of genetic insights into better management of risk is pivotal to the value proposition for genomics, most likely through early cancer detection. In 2012 we began a surveillance study utilising whole body MRI. There are currently 76 participants and we have detected 14 new primary malignancies that have been treated with curative intent. We aim to inform identification of those at greatest heritable risk and influence clinical risk management in the genomic era of personalised medicine.

Polygenic contributions to alcohol use and alcohol use disorders across population-based and clinically ascertained samples.

Studies suggest that alcohol consumption and alcohol use disorders have distinct genetic backgrounds. We examined whether polygenic risk scores (PRS) for consumption and problem subscales of the Alcohol Use Disorders Identification Test (AUDIT-C, AUDIT-P) in the UK Biobank (UKB; N = 121 630) correlate with alcohol outcomes in four independent samples: an ascertained cohort, the Collaborative Study on the Genetics of Alcoholism (COGA; N = 6850), and population-based cohorts: Avon Longitudinal Study of Parents and Children (ALSPAC; N = 5911), Generation Scotland (GS; N = 17 461), and an independent subset of UKB (N = 245 947). Regression models and survival analyses tested whether the PRS were associated with the alcohol-related outcomes. In COGA, AUDIT-P PRS was associated with alcohol dependence, AUD symptom count, maximum drinks (R2 = 0.47-0.68%, p = 2.0 × 10-8-1.0 × 10-10), and increased likelihood of onset of alcohol dependence (hazard ratio = 1.15, p = 4.7 × 10-8); AUDIT-C PRS was not an independent predictor of any phenotype. In ALSPAC, the AUDIT-C PRS was associated with alcohol dependence (R2 = 0.96%, p = 4.8 × 10-6). In GS, AUDIT-C PRS was a better predictor of weekly alcohol use (R2 = 0.27%, p = 5.5 × 10-11), while AUDIT-P PRS was more associated with problem drinking (R2 = 0.40%, p = 9.0 × 10-7). Lastly, AUDIT-P PRS was associated with ICD-based alcohol-related disorders in the UKB subset (R2 = 0.18%, p < 2.0 × 10-16). AUDIT-P PRS was associated with a range of alcohol-related phenotypes across population-based and ascertained cohorts, while AUDIT-C PRS showed less utility in the ascertained cohort. We show that AUDIT-P is genetically correlated with both use and misuse and demonstrate the influence of ascertainment schemes on PRS analyses.

In This Issue

HomeCirculation ResearchVol. 126, No. 2In This Issue Free AccessIn BriefPDF/EPUBAboutView PDFView EPUBSections ToolsAdd to favoritesDownload citationsTrack citationsPermissions ShareShare onFacebookTwitterLinked InMendeleyReddit Jump toFree AccessIn BriefPDF/EPUBIn This Issue Ruth Williams Ruth WilliamsRuth Williams Search for more papers by this author Originally published16 Jan 2020https://doi.org/10.1161/RES.0000000000000321Circulation Research. 2020;126:159is related toMonogenic and Polygenic Contributions to Atrial Fibrillation RiskMetabolic Remodeling Promotes Cardiac Hypertrophy by Directing Glucose to Aspartate Biosynthesisis related toActivated Endothelial TGFβ1 Signaling Promotes Venous Thrombus Nonresolution in Mice Via Endothelin-1TGFβ Signaling and Defective Thrombus Resolution (p 162)Aberrant TGFβ1 signaling is a likely driver of chronic thromboembolic pulmonary hypertension, say Bochenek et al.Download figureDownload PowerPointChronic thromboembolic pulmonary hypertension (CTEPH) is a rare, life-threatening form of pulmonary hypertension characterized by persistent blood clots in the lung arteries that ultimately result in the formation of fibrotic lesions containing irregular vasculature. The mechanisms underlying CTEPH are largely unknown, but because the cytokine TGFβ1 regulates fibrosis and angiogenesis, and because mutations affecting TGFβ1 signaling have been implicated in another form of pulmonary hypertension, Bochenek and colleagues hypothesized this factor’s involvement. Sure enough, they found that, in CTEPH patient tissue, components of the TGFβ1 pathway were upregulated, including TGFβ1 itself and endothelin-1—a vasoconstrictor and promoter of fibrosis. The team also showed that mice engineered to lack TGFβ1 in platelet cells had faster resolution of experimental thrombosis than did control animals. Furthermore, inhibition of endothelin-1 activity prevented human and mouse endothelial cells converting to a fibrotic phenotype. The results suggest the TGFβ1-to-endothelin-1 pathway plays a pathological role in CTEPH and lends supporting evidence that the clinical use of endothelin-1 receptor blockers—prescribed to some patients with CTEPH—is a worthwhile therapy.ACC2 Deletion Prevents Aspartate Synthesis(p 182)Boosting fatty acid oxidation prevents aspartate synthesis and cardiac hypertrophy, report Ritterhoff et al.Download figureDownload PowerPointCardiac hypertrophy, in which the heart and its component cells become enlarged, can be a normal physiological process to cope with increased demand—for example, in pregnancy or elite athletes—but can also be pathological—caused by high blood pressure and other cardiovascular conditions. Pathological hypertrophy is associated with a metabolic switch in the heart from primarily fatty acid-based to glucose-based. And, boosting fatty acid oxidation (FAO) can protect against hypertrophy in cultured cardiomyocytes and animals. The mechanism underlying this protection is unknown, however. Now, Ritterhoff and colleagues show that in addition to increased glucose consumption, hypertrophic rat cardiomyocytes ramp up their levels of aspartate—a molecule involved in cell growth via synthesis of nucleic acids, RNAs, and proteins. And, boosting FAO (by genetic manipulation) prevents both the aspartate rise and hypertrophy in the cells as well as in live mice. Adding aspartate to such FAO-boosted cells could reinstate the hypertrophic phenotype. The discovery of this relationship between glucose metabolism, aspartate, and FAO may inform the design of new therapies aimed at manipulating heart cell metabolism to manage hypertrophy, say the authors.Genetic Basis of Atrial Fibrillation (p 200)Choi et al examine poly-and mono-genetic predisposition to atrial fibrillation.Download figureDownload PowerPointAffecting ≈30 million individuals worldwide, atrial fibrillation (AF) is a common cardiac arrhythmia associated with an increased risk of heart failure, stroke, dementia, and death. While the condition can be idiopathic, there is also evidence of inheritance. Indeed, a quarter of patients have a parent, sibling, or child with the condition. Genome-wide association studies have identified numerous common genetic variants linked to AF, and the more of these variants a person carries, the greater the risk—referred to as their polygenic risk score (PRS). Studies of families with AF have also revealed rarer monogenic variants, such as loss-of-function (LOF) mutations in the sarcomeric gene titin (TTN). Now, Choi and colleagues look at these common polygenic and rare monogenic variants together to examine their relative contributions. Studying the genomes of 1546 AF patients and more than 41 000 controls, the team discovered a significant association between AF and rare LOF variants at TTN. Indeed, 14% of individuals with such variants had AF. However, the team also showed that while TTN variants were highly penetrant, PRS scores accounted for considerably more of the variance in AF susceptibility. Thus, the study indicates that, generally speaking, a person’s PRS is a better indicator of overall AF risk. Previous Back to top Next FiguresReferencesRelatedDetailsRelated articlesMonogenic and Polygenic Contributions to Atrial Fibrillation RiskSeung Hoan Choi, et al. Circulation Research. 2020;126:200-209Metabolic Remodeling Promotes Cardiac Hypertrophy by Directing Glucose to Aspartate BiosynthesisJulia Ritterhoff, et al. Circulation Research. 2020;126:182-196Activated Endothelial TGFβ1 Signaling Promotes Venous Thrombus Nonresolution in Mice Via Endothelin-1Magdalena L. Bochenek, et al. Circulation Research. 2020;126:162-181 January 17, 2020Vol 126, Issue 2 Advertisement Article InformationMetrics © 2020 American Heart Association, Inc.https://doi.org/10.1161/RES.0000000000000321 Originally publishedJanuary 16, 2020 PDF download Advertisement

Increased Burden of Common Risk Alleles in Children With a Significant Fracture History.

Extreme presentations of common disease in children are often presumed to be of Mendelian etiology, but their polygenic basis has not been fully explored. We tested whether children with significant fracture history and no osteogenesis imperfecta (OI) are at increased polygenic risk for fracture. A childhood significant fracture history was defined as the presence of low-trauma vertebral fractures or multiple long bone fractures. We generated a polygenic score of heel ultrasound-derived speed of sound, termed "gSOS," which predicts risk of osteoporotic fracture. We tested if individuals from three cohorts with significant childhood fracture history had lower gSOS. A Canadian cohort included 94 children with suspected Mendelian osteoporosis, of which 68 had negative OI gene panel. Two Finnish cohorts included 59 children with significant fracture history and 22 with suspected Mendelian osteoporosis, among which 18 had no OI. After excluding individuals with OI and ancestral outliers, we generated gSOS estimates and compared their mean to that of a UK Biobank subset, representing the general population. The average gSOS across all three cohorts (n = 131) was -0.47 SD lower than that in UK Biobank (n = 80,027, p = 1.1 × 10-5 ). The gSOS of 78 individuals with suspected Mendelian osteoporosis was even lower (-0.76 SD, p = 5.3 × 10-10 ). Among the 131 individuals with a significant fracture history, we observed 8 individuals with gSOS below minus 2 SD from the mean; their mean lumbar spine DXA-derived bone mineral density Z-score was -1.7 (SD 0.8). In summary, children with significant fracture history but no OI have an increased burden of common risk alleles. This suggests that a polygenic contribution to disease should be considered in children with extreme presentations of fracture. © 2020 American Society for Bone and Mineral Research.

Polygenic risk for Alzheimer's disease shapes hippocampal scene-selectivity

Preclinical models of Alzheimer’s disease (AD) suggest APOE modulates brain function in structures vulnerable to AD pathophysiology. However, genome-wide association studies now demonstrate that AD risk is shaped by a broader polygenic architecture, estimated via polygenic risk scoring (AD-PRS). Despite this breakthrough, the effect of AD-PRS on brain function in young individuals remains unknown. In a large sample (N = 608) of young, asymptomatic individuals, we measure the impact of both (i) APOE and (ii) AD-PRS on a vulnerable cortico-limbic scene-processing network heavily implicated in AD pathophysiology. Integrity of this network, which includes the hippocampus (HC), is fundamental for maintaining cognitive function during ageing. We show that AD-PRS, not APOE, selectively influences activity within the HC in response to scenes, while other perceptual nodes remained intact. This work highlights the impact of polygenic contributions to brain function beyond APOE, which could aid potential therapeutic/interventional strategies in the detection and prevention of AD.

Monogenic and Polygenic Contributions to Atrial Fibrillation Risk

Genome-wide association studies have identified over 100 genetic loci for atrial fibrillation (AF); recent work described an association between loss-of-function (LOF) variants in TTN and early-onset AF. We sought to determine the contribution of rare and common genetic variation to AF risk in the general population. The UK Biobank is a population-based study of 500 000 individuals including a subset with genome-wide genotyping and exome sequencing. In this case-control study, we included AF cases and controls of genetically determined white-European ancestry; analyses were performed using a logistic mixed-effects model adjusting for age, sex, the first 4 principal components of ancestry, empirical relationships, and case-control imbalance. An exome-wide, gene-based burden analysis was performed to examine the relationship between AF and rare, high-confidence LOF variants in genes with ≥10 LOF carriers. A polygenic risk score for AF was estimated using the LDpred algorithm. We then compared the contribution of AF polygenic risk score and LOF variants to AF risk. The study included 1546 AF cases and 41 593 controls. In an analysis of 9099 genes with sufficient LOF variant carriers, a significant association between AF and rare LOF variants was observed in a single gene, TTN (odds ratio, 2.71, P=2.50×10-8). The association with AF was more significant (odds ratio, 6.15, P=3.26×10-14) when restricting to LOF variants located in exons highly expressed in cardiac tissue (TTNLOF). Overall, 0.44% of individuals carried TTNLOF variants, of whom 14% had AF. Among individuals in the highest 0.44% of the AF polygenic risk score only 9.3% had AF. In contrast, the AF polygenic risk score explained 4.7% of the variance in AF susceptibility, while TTNLOF variants only accounted for 0.2%. Both monogenic and polygenic factors contribute to AF risk in the general population. While rare TTNLOF variants confer a substantial AF penetrance, the additive effect of many common variants explains a larger proportion of genetic susceptibility to AF.

Quantifying the polygenic contribution to variable expressivity in eleven rare genetic disorders

Rare genetic disorders (RGDs) often exhibit significant clinical variability among affected individuals, a disease characteristic termed variable expressivity. Recently, the aggregate effect of common variation, quantified as polygenic scores (PGSs), has emerged as an effective tool for predictions of disease risk and trait variation in the general population. Here, we measure the effect of PGSs on 11 RGDs including four sex-chromosome aneuploidies (47,XXX; 47,XXY; 47,XYY; 45,X) that affect height; two copy-number variant (CNV) disorders (16p11.2 deletions and duplications) and a Mendelian disease (melanocortin 4 receptor deficiency (MC4R)) that affect BMI; and two Mendelian diseases affecting cholesterol: familial hypercholesterolemia (FH; LDLR and APOB) and familial hypobetalipoproteinemia (FHBL; PCSK9 and APOB). Our results demonstrate that common, polygenic factors of relevant complex traits frequently contribute to variable expressivity of RGDs and that PGSs may be a useful metric for predicting clinical severity in affected individuals and for risk stratification.

Genetic Architecture of Human Obesity Traits in the Rhesus Macaque

Objective:While the metabolic consequences of obesity have been studied extensively in the rhesus macaque, corollary genetic studies of obesity are non-existent. Here, we assess genetic contributions to spontaneous adiposity in this species.Methods:We assessed phenotypic variation by age-class and sex for body mass index, waist-to-height ratio, waist-to-thigh ratio, and waist circumference in 583 macaques. We estimated total and sex-specific heritability for all traits, including waist-to-thigh ratio adjusted for BMI, as well as genotypic and phenotypic correlations. We also assessed functional genetic variation at BDNF, FTO, LEP, LEPR, MC4R, PCSK1, POMC, and SIM1 in 4 animals with extreme spontaneous adiposity.Results:Trait heritability in the combined sample was low-to-moderate (0.14–0.32), while sex-specific heritability was more substantial (0.20–0.67). Heritability was greater in females for all traits except BMI. All traits were robustly correlated, with genetic correlations of 0.63–0.93 indicating substantial pleiotropy. We discovered likely functional variants in the 4 macaques at all 8 human obesity genes, including 6 missense mutations in BDNF, FTO, LEP, LEPR, and PCSK1, and notably, 1 nonsense mutation in LEPR.Conclusions:We find a moderate polygenic contribution to adiposity in rhesus macaques, and mutations with potentially larger effects in multiple genes that influence obesity in humans.

SA27 - EXOME SEQUENCING OF MULTIPLY AFFECTED BIPOLAR DISORDER FAMILIES AND FOLLOW-UP RESEQUENCING IMPLICATE RARE VARIANTS IN NEURONAL GENES CONTRIBUTING TO DISEASE ETIOLOGY

Background Bipolar Disorder (BD) is a complex neuropsychiatric disorder characterized by recurrent episodes of mania and depression. It is a severe disorder of mood with a lifetime prevalence of about 1% and a high heritability of about 70%. Models of illness are most consistent with a polygenic contribution of common and rare variants to disease susceptibility. As the cumulative impact of common alleles with small effect may only explain around 25–38% of the phenotypic variance for BD, rare variants of high penetrance have been suggested to contribute to BD susceptibility. One way to evaluate this hypothesis is to investigate large pedigrees densely affected with BD, in which the existence of a genetic variant of strong effect inherited from a common ancestor may be more likely. Methods In the present study, we investigated 226 individuals of 68 large multiply affected families of European origin using Whole Exome Sequencing (WES). In each family, two to five affected individuals with BD or recurrent major depression were selected for sequencing. WES was performed on the Illumina HiSeq. 2500 platform and the Varbank pipeline of the Cologne Center for Genomics was used for data analysis. All identified variants shared within each family were filtered for a minor allele frequency Results We identified a total of 1214 rare, segregating and functional variants implicating 1122 different genes, of which 903 were brain expressed. Subsequently, we applied the Residual Variation Intolerance Scores (Petrovski et al., 2013) and identified 294 genes that were ranked among the 20% most “intolerant” genes in the genome. Gene enrichment analysis of these genes showed a significant enrichment for 18 pathways (p We prioritized genes that were (i) found in at least two unrelated families in the present study, (ii) previously reported in next generation sequencing or GWAS studies of BD, or (iii) predominantly driving the significant pathways in our gene enrichment analysis. The different approaches of prioritization yielded 42 promising candidate genes including CDH22 which encodes a calcium-dependent cell adhesion protein that plays an important role in the morphogenesis of neural cells during brain development. Discussion Our preliminary results strongly suggest that rare and highly-penetrant variants in neuronal and cell adhesion genes contribute to BD etiology. The 42 prioritized candidate genes are currently being followed up by resequencing in cohorts of about 2500 independent BD cases and 2500 controls of European ancestry. For resequencing, we use the single molecule molecular inversion probes (smMIPs) technology that enables multiplex targeted resequencing in large cohorts. The smMIPs sequences have been designed with the empirically trained design algorithm MIPgen (Boyle et al., 2014) and sequencing is currently performed on the Illumina HiSeq. 2500 platform. The resequencing results will provide further insights into the particular genes and pathways which are involved in BD development.

Genetic determinants of glucose levels in pregnancy: genetic risk scores analysis and GWAS in the Norwegian STORK cohort.

Objective Hyperglycaemia during pregnancy increases the risk of adverse health outcomes in mother and child, but the genetic aetiology is scarcely studied. Our aims were to (1) assess the overlapping genetic aetiology between the pregnant and non-pregnant population and (2) assess the importance of genome-wide polygenic contributions to glucose traits during pregnancy, by exploring whether genetic risk scores (GRSs) for fasting glucose (FG), 2-h glucose (2hG), type 2 diabetes (T2D) and BMI in non-pregnant individuals were associated with glucose measures in pregnant women. Methods We genotyped 529 Norwegian pregnant women and constructed GRS from known genome-wide significant variants and SNPs weakly associated (p > 5 × 10-8) with FG, 2hG, BMI and T2D from external genome-wide association studies (GWAS) and examined the association between these scores and glucose measures at gestational weeks 14-16 and 30-32. We also performed GWAS of FG, 2hG and shape information from the glucose curve during an oral glucose tolerance test (OGTT). Results GRSFG explained similar variance during pregnancy as in the non-pregnant population (~5%). GRSBMI and GRST2D explained up to 1.3% of the variation in the glucose traits in pregnancy. If we included variants more weakly associated with these traits, GRS2hG and GRST2D explained up to 2.4% of the variation in the glucose traits in pregnancy, highlighting the importance of polygenic contributions. Conclusions Our results suggest overlap in the genetic aetiology of FG in pregnant and non-pregnant individuals. This was less apparent with 2hG, suggesting potential differences in postprandial glucose metabolism inside and outside of pregnancy.

Identifying SNPs and candidate genes for three litter traits using single-step GWAS across six parities in Landrace and Large White pigs

Total number born (TNB), number born alive (NBA), and litter weight born alive (LWB) are critically important traits in pig production. The sow's parity is one of the major factors influencing litter traits. Because of monogenic or polygenic contributions and the presence of temporal gene effects in different sows' parities, it is difficult to clarify the biological and genetic background. To systematically explore the genetic mechanism of litter traits, we conducted 18 GWASs using single-step GWAS (ssGWAS) based on two breeds (908 Landrace and 1,130 Large White sow litter records) for each litter trait in different parities. A total of 300 Landrace and 300 Large White sows were genotyped by sequencing (GBS). ssGWAS was performed separately for each breed and each parity due to population stratification and temporal gene effect. In summary, we identified 80 (15 for Landrace and 65 for Large White), 227 (52 for Landrace, 175 for Large White), and 187 (34 for Landrace, 153 for Large White) single nucleotide polymorphisms (SNPs) affecting TNB, NBA, and LWB, respectively. Of them, we suggest that a total of 22 loci (SSC1: 125098202, SSC1: 117560058, SSC14: 147794697, SSC8: 84823302, SSC9: 143554876, and SSC9: 138766097 for Landrace; SSC1: 4023577, SSC1: 3859573, SSC1: 4891063, SSC16: 5197665, SSC10: 32050819, SSC13: 13552924, SSC13: 92819, SSC17: 3579607, SSC13: 196698221, SSC7: 30918403, SSC16: 46221484, SSC16: 46169204, SSC2: 41988642, SSC2: 44475457, SSC2: 42521875, and SSC7: 58411951 for Large White) are shared by TNB, NBA, and LWB. These results indicate the existence of gene temporal effect in each parity. Furthermore, our findings suggest four interesting candidate genes (FBXL7, ALDH1A2, LEPR, and DDX1) associated with litter traits in different parities that have a major effect on embryonic development progression. In conclusion, 22 crucial SNPs and four interesting candidate genes were identified for three litter traits across six parities. These findings advance our understanding of the genetic architecture of litter traits and confirm the presence of temporal gene effects in different parities. Importantly, functional validation studies for findings of particular interest are recommended in litter traits.

Polygenic risk score for schizophrenia is more strongly associated with ancestry than with schizophrenia.

The polygenic risk score (PRS) for schizophrenia, derived from very large numbers of weakly associated genetic markers, has been repeatedly shown to be robustly associated with schizophrenia in independent samples and also with other diseases and traits. This study aims to explore the distribution of the schizophrenia PRS in subjects of different ancestry. The schizophrenia PRS derived from the large genome-wide association study carried out by the Psychiatric Genetics Consortium was calculated using the downloaded genotypes of HapMap subjects from 11 different ancestral groups. It was also calculated using downloaded genotypes of European schizophrenia cases and controls from the CommonMind Consortium. The PRS for schizophrenia varied significantly between ancestral groups (P<2×10(-16)) and was much higher in African than European HapMap subjects. The mean difference between these groups was 10 times as high as the mean difference between European schizophrenia cases and controls. The distributions of scores for African and European subjects hardly overlapped. The PRS cannot be regarded as simply a measure of the polygenic contribution to risk of schizophrenia and clearly contains a strong ancestry component. It is possible that this could be controlled to some extent by incorporating principal components as covariates, but doubts remain as to how it should be interpreted. The PRS derived from European subjects cannot be applied to non-Europeans, limiting its potential usefulness in clinical settings and raising issues of inequity in health provision. Previous studies that have used the PRS should be re-examined in the light of these findings.

Quantifying the Polygenic Contribution to Cutaneous Squamous Cell Carcinoma Risk

Genetic factors play an important role in cutaneous squamous cell carcinoma risk. Genome-wide association studies have identified 21 single nucleotide polymorphisms associated with cutaneous squamous cell carcinoma risk. Yet no studies have attempted to quantify the contribution of heritability to cutaneous squamous cell carcinoma risk by calculating the population attributable risk using a combination of all discovered genetic variants. Using an additive multi-locus linear logistic model, we determined the cumulative association of these 21 genetic regions to cutaneous squamous cell carcinoma population attributable risk. We computed a multi-locus population attributable risk of 62%, suggesting that if the effects of all the risk alleles were removed from a population, the cutaneous squamous cell carcinoma risk would drop by 62%. Using stratified analysis, we also examined the impact of sex on polygenic risk score, and found that men have an increased relative risk throughout the spectrum of the polygenic risk score. Quantifying the impact of genetic predisposition on the proportion of cancer cases can guide future research decisions and public health policy planning.

Genetic Modifiers in Neurodegeneration.

To review the evidence for genetic modifier effects in the neurodegenerative diseases Huntington's Disease (HD), Frontotemporal Lobar Degeneration (FTLD), Alzheimer's Disease (AD), and Parkinson's Disease (PD). Increasingly, we understand human disease genetics less through the lens of single-locus/single-trait effects, and more through that of polygenic contributions to disease risk. In addition, specific examples of genetic modifier effects of the chromosome 7 gene TMEM106B on various target genes including those causal for Mendelian classes of FTLD - GRN and c9orf72 - have emerged from both genetic cohort studies and mechanistic examinations of biological pathways. Here, we summarize the literature reporting genetic modifier effects in HD, FTLD, AD, and PD. We further contextualize reported genetic modifier effects in these diseases in terms of insight they may lend to the concept of a polygenic landscape for the major neurodegenerative diseases.

Characterization of the Cry1Ah resistance in Asian corn Borer and its cross-resistance to other Bacillus thuringiensis toxins

Transgenic crops producing insecticidal proteins are effective to manage lepidopteran pests. Development of insect-resistance is the major threat to Bacillus thuringiensis (Bt) crops such as Cry1Ah-Maize. Laboratory selection with Bt-Cry1Ah toxin incorporated in artificial diet, during 48 generations of Asian corn borer (ACB) Ostrinia furnacalis produced 200-fold resistance. This resistant colony ACB-AhR readily consumed and survived on Cry1Ah-expressing Bt-maize. Cross-resistance analysis showed high cross-resistance to Cry1F (464-fold), moderate cross-resistance to Cry1Ab (28.38-fold), Cry1Ac (22.11-fold) and no cross-resistance to Cry1Ie toxin. This ACB-AhR cross-resistant phenotype is different from ACB-Cry1Fa resistant population that showed no cross resistance to Cry1Ah, suggesting that different mechanisms of resistance were selected in these two populations. Bioassays of reciprocal F1 crosses-progeny suggested autosomal inheritance of Cry1Ah resistance with no maternal effects. The dominance of resistance increased as concentration decreased. In Cry1Ah-maize tissues the progeny of reciprocal F1 crosses behaved as functionally recessive. Progenies analysis from backcrosses (F1 × resistant strain) suggested polygenic contribution to Cry1Ah- resistance in ACB-AhR. The use of multiple toxins is an imperative factor for delaying evolution of resistance to Cry1Ah-corn in ACB. However, the fact that ACB-AhR showed cross resistance to Cry1Fa indicates that selection of toxins for pyramided plants should be carefully done.

Polygenic Contribution in Individuals With Early-Onset Coronary Artery Disease.

Despite evidence of high heritability, monogenic disorders are identified in a minor fraction of individuals with early-onset coronary artery disease (EOCAD). We hypothesized that some individuals with EOCAD carry a high number of common genetic risk variants, with a combined effect similar to Mendelian forms of coronary artery disease, such as familial hypercholesterolemia. To confirm the polygenic contribution to EOCAD (age of ≤40 years for men and ≤45 years for women), we calculated in 111 418 British participants from the UK Biobank cohort a genetic risk score (GRS) based on the presence of 182 independent variants associated with coronary artery disease (GRS182). Participants with a diagnosis of EOCAD who underwent a revascularization procedure (n=96) had a significantly higher GRS182 (P=3.21×10-9) than those without EOCAD. An increase of 1 SD in GRS182 corresponded to an odds ratio of 1.84 (1.52-2.24) for EOCAD. The prevalence of a polygenic contribution that increased EOCAD risk similar to what is observed in heterozygous familial hypercholesterolemia was estimated at 1 in 53. In a local cohort of individuals with EOCAD (n=30), GRS182 was significantly increased compared with UK Biobank controls (P=0.001). Seven participants (23%) had a GRS182 corresponding to an estimated 2-fold increase in EOCAD risk; none had a rare mutation involved in monogenic dyslipidemia or EOCAD. These results suggest a significant polygenic contribution in individuals presenting with EOCAD, which could be more prevalent than familial hypercholesterolemia. Determination of the polygenic risk component could be included in the diagnostic workup of patients with EOCAD.

Genetics of body fat mass and related traits in a pig population selected for leanness

Obesity is characterized as the excessive accumulation of body fat and has a complex genetic foundation in humans including monogenic high-risk mutations and polygenic contributions. Domestic pigs represent a valuable model on an obesity-promoting high-caloric diet while constantly evaluated for body characteristics. As such, we investigated the genetics of obesity-related traits, comprising subcutaneous fat thickness, lean mass percentage, and growth rate, in a pig population. We conducted genome-wide association analyses using an integrative approach of single-marker regression models and multi-marker Bayesian analyses. Thus, we identified 30 genomic regions distributed over 14 different chromosomes contributing to the variation in obesity-related traits. In these regions, we validated the association of four candidate genes that are functionally connected to the regulation of appetite, processes of adipogenesis, and extracellular matrix formation. Our findings revealed fundamental genetic factors which deserves closer attention regarding their roles in the etiology of obesity.

Genetic testing of familial hypercholesterolemia: Monogenic form and polygenic contribution to cardiovascular risk

Aim: Cascade screening of Familial Hypercholesterolemia (FH) using genetic testing has been recommended but polygenic origin could reduce the efficiency of such approach. A polyGenic Score (GS) has been described helping to identify polygenic form of FH. We have developed a genetic test combining detection of monogenic form as well as polygenic contribution in FH.

Polygenic burdens on cell-specific pathways underlie the risk of rheumatoid arthritis

Recent evidence suggests that a substantial portion of complex disease risk alleles modify gene expression in a cell-specific manner. To identify candidate causal genes and biological pathways of immune-related complex diseases, we conducted expression quantitative trait loci (eQTL) analysis on five subsets of immune cells (CD4+ T cells, CD8+ T cells, B cells, natural killer (NK) cells and monocytes) and unfractionated peripheral blood from 105 healthy Japanese volunteers. We developed a three-step analytical pipeline comprising (i) prediction of individual gene expression using our eQTL database and public epigenomic data, (ii) gene-level association analysis and (iii) prediction of cell-specific pathway activity by integrating the direction of eQTL effects. By applying this pipeline to rheumatoid arthritis data sets, we identified candidate causal genes and a cytokine pathway (upregulation of tumor necrosis factor (TNF) in CD4+ T cells). Our approach is an efficient way to characterize the polygenic contributions and potential biological mechanisms of complex diseases.