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Case-control studies have shown that patients with Crohn's disease (CD) have a microbial composition different from healthy individuals. Although the causes of CD are unknown, epidemiologic studies suggest that diet is an important contributor to CD risk, potentially via modulation of bacterial composition and gut inflammation. We hypothesized that long-term dietary clusters (DCs) are associated with gut microbiome compositions and gut inflammation. Our objectives were to identify dietary patterns and assess whether they are associated with alterations in specific gut microbial compositions and subclinical levels of gut inflammation in a cohort of healthy first-degree relatives (FDRs) of patients with CD.As part of the Genetic, Environmental, Microbial (GEM) Project, we recruited a cohort of 2289 healthy FDRs of patients with CD. Individuals provided stool samples and answered a validated food frequency questionnaire reflecting their habitual diet during the year before sample collection. Unsupervised analysis identified 3 dietary and 3 microbial composition clusters.DC3, resembling the Mediterranean diet, was strongly associated with a defined microbial composition, with an increased abundance of fiber-degrading bacteria, such as Ruminococcus, as well as taxa such as Faecalibacterium. The DC3 diet was also significantly associated with lower levels of subclinical gut inflammation, defined by fecal calprotectin, compared with other dietary patterns. No significant associations were found between individual food items and fecal calprotectin, suggesting that long-term dietary patterns rather than individual food items contribute to subclinical gut inflammation. Additionally, mediation analysis demonstrated that DC3 had a direct effect on subclinical inflammation that was partially mediated by the microbiota.Overall, these results indicated that Mediterranean-like dietary patterns are associated with microbiome and lower intestinal inflammation. This study will help guide future dietary strategies that affect microbial composition and host gut inflammation to prevent diseases.

In Table 2 of the article cited above, the univariable MR analyses for microalbuminuria were erroneously cited as inverse variance weighted analyses. The row headings in Table 2 have been revised to show the correct analyses performed: MR-Egger, weighted median and mode, and simple mode analyses. In Fig. 3, the confidence intervals were erroneously plotted as error bars. Fig. 3 has been updated with the correct confidence intervals from the text. The revised online version of the article can be accessed at https://doi.org/10.2337/db22-0696.

Contains fulltext : 292919.pdf (Publisher’s version ) (Open Access) BACKGROUND: High myopia (HM), defined as a spherical equivalent refractive error (SER) ≤ -6.00 diopters (D), is a leading cause of sight impairment, through myopic macular degeneration (MMD). We aimed to derive an improved polygenic score (PGS) for predicting children at risk of HM and to test if a PGS is predictive of MMD after accounting for SER. METHODS: The PGS was derived from genome-wide association studies in participants of UK Biobank, CREAM Consortium, and Genetic Epidemiology Research on Adult Health and Aging. MMD severity was quantified by a deep learning algorithm. Prediction of HM was quantified as the area under the receiver operating curve (AUROC). Prediction of severe MMD was assessed by logistic regression. FINDINGS: In independent samples of European, African, South Asian and East Asian ancestry, the PGS explained 19% (95% confidence interval 17-21%), 2% (1-3%), 8% (7-10%) and 6% (3-9%) of the variation in SER, respectively. The AUROC for HM in these samples was 0.78 (0.75-0.81), 0.58 (0.53-0.64), 0.71 (0.69-0.74) and 0.67 (0.62-0.72), respectively. The PGS was not associated with the risk of MMD after accounting for SER: OR = 1.07 (0.92-1.24). INTERPRETATION: Performance of the PGS approached the level required for clinical utility in Europeans but not in other ancestries. A PGS for refractive error was not predictive of MMD risk once SER was accounted for. FUNDING: Supported by the Welsh Government and Fight for Sight (24WG201).

PDF file - 275K, Significance of the mammographic breast density polygenic risk score (PRS) for the prediction of breast cancer risk, according to percent cut-off of SNPs used in the PRS: sensitivity analysis using imputed case:control genotype dosages.

IntroductionAdiposity, particularly centripetal adiposity/reduced gluteofemoral adiposity, increases dyslipidemia, type 2 diabetes (T2D) and coronary artery disease (CAD). Genome-wide association studies (GWAS) to date have identified 12 loci associated with body fat percentage (BFP). Biological sex influences both overall adiposity and fat distribution. Further, testosterone and sex hormone binding globulin (SHBG) influence adiposity and metabolic function, with differential effects of testosterone in men and women.MethodsWe performed sex-stratified GWAS of BFP in white British individuals from the UK biobank adjusting for SHBG and testosterone. We further investigated association of the identified loci with high density cholesterol (HDL), triglyceride (TG), T2D, CAD, and MRI-derived abdominal subcutaneous adipose tissue (ASAT), visceral adipose tissue (VAT) and gluteofemoral adipose tissue (GFAT) using publicly available data from large GWAS. We also performed 2-sample Mendelian Randomization (MR) using identified BFP variants as instruments to investigate causal effect of BFP on HDL, TG, T2D and CAD in males and females separately.ResultsWe identified 193 and 174 autosomal loci explaining 3.35% and 2.60% of the variation in BFP in males and females, respectively. In addition, we identified 2 Chr X loci in men. Only 38 of these loci associated with BFP in both males and females. Seven loci in men including the 2 loci on Chr X and ten loci in females have not been associated with any adiposity or cardiometabolic traits previously. The majority of BFP loci did not associate with cardiometabolic traits. Of the BFP loci associated with cardiometabolic traits several had paradoxically beneficial cardiometabolic effects with favourable fat distribution. Consistent with that sex-stratified MR analyses using identified BFP variants as instruments did not find convincing supportive evidence that increased BFP has deleterious cardiometabolic effects in either sex with highly significant heterogeneity.ConclusionsAdjusting for testosterone and SHBG with sex-stratified analyses substantially increased the number of BFP associated loci. Despite this adjustment, there was limited genetic overlap in BFP in males and females. Further identified loci in general did not have adverse cardiometabolic effects which may reflect the protective effect of favourable fat distribution and the modulation of cardiometabolic risk by testosterone and SHBG.

Next-generation sequencing has led to an explosion of genetic findings for many rare diseases. However, most of the variants identified are very rare and were identified in small pedigrees, which creates challenges in terms of penetrance estimation and translation into genetic counselling in the setting of cascade testing. We use simulations to show that for a rare (dominant) disorder where a variant is identified in a small number of small pedigrees, the penetrance estimate can both have large uncertainty and be drastically inflated, due to underlying ascertainment bias. We have developed PenEst, an app that allows users to investigate the phenomenon across ranges of parameter settings. We also illustrate robust ascertainment corrections via the LOD score, and recommend a LOD-based approach to assessing pathogenicity of rare variants in the presence of reduced penetrance.

SummaryTen years ago, a detailed analysis of genome-wide association studies showed that only 33% of the studies included the X chromosome. Multiple recommendations were made to combat eXclusion. Here we re-surveyed the research landscape to determine if these earlier recommendations had been translated. Unfortunately, among the summary statistics reported in 2021 in the NHGRI-EBI GWAS catalog, only 25% provided results for the X chromosome and 3% for the Y chromosome, suggesting that the eXclusion phenomenon documented earlier not only persists but has also expanded into an eXclusionarY problem. Normalizing by physical length of the chromosome, the average number of studies published until 11/29/22 with genome-wide significant findings on the X chromosome is ~1 study/Mb. In contrast, it ranges from ~6 to ~16 studies/Mb for chromosomes 4 and 19, respectively. Compared with the autosomal growth rate of ~0.086 studies/Mb/year over the last decade, studies of the X chromosome grew at less than one-seventh that rate, only ~0.012 studies/Mb/year. Among the studies that reported significant association on the X chromosome, there were extreme heterogeneities in how they analyzed the data and documented the results, suggesting the need for guidelines. Not surprisingly, among the 430 scores sampled from the PolyGenic Score catalog, 0% contained weights for sex chromosomal SNPs. To overcome the dearth of sex chromosome analyses, we provide five sets of recommendations and future directions. Finally, until the sex chromosomes are included in a whole-genome study, instead of GWAS, we propose they be more properly referred to as “AWAS” for “autosome-wide scan”.

Obesity is postulated to independently increase chronic kidney disease (CKD), even after adjusting for type 2 diabetes (T2D) and hypertension. Dysglycemia below T2D thresholds, frequently seen with obesity, also increases CKD risk. Whether obesity increases CKD independent of dysglycemia and hypertension is unknown and likely influences the optimal weight loss (WL) needed to reduce CKD. T2D remission rates plateau with 20–25% WL after bariatric surgery (BS), but further WL increases normoglycemia and normotension. We undertook bidirectional inverse variance weighted Mendelian randomization (IVWMR) to investigate potential independent causal associations between increased BMI and estimated glomerular filtration rate (eGFR) in CKD (CKD(eGFR)) (50% decline in eGFR (primary outcome) or CKD hospitalization (secondary outcome), using

Objectives Genetics plays an important role in SLE risk, as well as osteonecrosis (ON), a significant and often debilitating complication of SLE. We aimed to identify genetic risk loci for ON in people with childhood-onset (cSLE) and adult-onset (aSLE) SLE. Methods We enrolled participants from two tertiary care centres who met classification criteria for SLE. Participants had prospectively collected clinical data and were genotyped on a multiethnic array. Un-genotyped single nucleotide polymorphisms (SNPs) were imputed, and ancestry was inferred using principal components (PCs). Our outcome was symptomatic ON confirmed by imaging. We completed time-to-ON and logistic regression of ON genome-wide association studies (GWASs) with covariates for sex, age of SLE diagnosis, five PCs for ancestry, corticosteroid use and selected SLE manifestations. We conducted separate analyses for cSLE and aSLE and meta-analysed results using inverse-variance weighting. Genome-wide significance was P Results The study included 940 participants with SLE, 87% female and 56% with cSLE. ON was present in 7.6% (n = 71). Median age of SLE diagnosis was 16.9 years (interquartile range [IQR]: 13.5, 29.3), with median follow-up of 8.0 years (IQR: 4.2, 15.7). Meta-GWAS of cSLE and aSLE time-to-ON of 4 431 911 SNPs identified a significant Chr.2 SNP, rs34118383 (minor allele frequency = 0.18), intronic to WIPF1 (hazard ratio = 3.2 [95% CI: 2.2, 4.8]; P = 1.0 × 10−8). Conclusion We identified an intronic WIPF1 variant associated with a 3.2 times increased hazard for ON (95% CI: 2.2, 4.8; P = 1.0 × 10−8) during SLE follow-up, independent of corticosteroid exposure. The effect of the SNP on time-to-ON was similar in cSLE and aSLE. This novel discovery represents a potential ON risk locus. Our results warrant replication.

BackgroundInsulin resistance (IR) with associated compensatory hyperinsulinemia (HI) are early abnormalities in the etiology of prediabetes (preT2D) and type 2 diabetes (T2D). IR and HI also associate with increased erythrocytosis. Hemoglobin A1c (HbA1c) is commonly used to diagnose and monitor preT2D and T2D, but can be influenced by erythrocytosis independent of glycemia.MethodsWe undertook bidirectional Mendelian randomization (MR) in individuals of European ancestry to investigate potential causal associations between increased fasting insulin adjusted for BMI (FI), erythrocytosis and its non-glycemic impact on HbA1c. We investigated the association between the triglyceride-glucose index (TGI), a surrogate measure of IR and HI, and glycation gap (difference between measured HbA1c and predicted HbA1c derived from linear regression of fasting glucose) in people with normoglycemia and preT2D.ResultsInverse variance weighted MR (IVWMR) suggested that increased FI increases hemoglobin (Hb, b=0.54 ± 0.09, p=2.7 x 10-10), red cell count (RCC, b=0.54 ± 0.12, p=5.38x10-6) and reticulocyte (RETIC, b=0.70 ± 0.15, p=2.18x10-6). Multivariable MR indicated that increased FI did not impact HbA1c (b=0.23 ± 0.16, p=0.162) but reduced HbA1c after adjustment for T2D (b=0.31 ± 0.13, p=0.016). Increased Hb (b=0.03 ± 0.01, p=0.02), RCC (b=0.02 ± 0.01, p=0.04) and RETIC (b=0.03 ± 0.01, p=0.002) might modestly increase FI. In the observational cohort, increased TGI associated with decreased glycation gap, (i.e., measured HbA1c was lower than expected based on fasting glucose, (b=-0.09 ± 0.009, pConclusionsMR suggests increased FI increases erythrocytosis and might potentially decrease HbA1c by non-glycemic effects. Increased TGI, a surrogate measure of increased FI, associates with lower-than-expected HbA1c in people with preT2D. These findings merit confirmatory studies to evaluate their clinical significance.

Background Skin autofluorescence (SAF) is a non-invasive measure reflecting accumulation of advanced glycation endproducts (AGEs) in the skin. Higher SAF levels are associated with an increased risk of developing type 2 diabetes and cardiovascular disease. An earlier genome-wide association study (GWAS) revealed a strong association between NAT2 variants and SAF. The aim of this study was to calculate SAF heritability and to identify additional genetic variants associated with SAF through genome-wide association studies (GWAS). Results In 27,534 participants without diabetes the heritability estimate of lnSAF was 33% ± 2.0% (SE) in a model adjusted for covariates. In meta-GWAS for lnSAF five SNPs, on chromosomes 8, 11, 15 and 16 were associated with lnSAF (P –8): 1. rs2846707 (Chr11:102,576,358,C > T), which results in a Met30Val missense variant in MMP27 exon 1 (NM_022122.3); 2. rs2470893 (Chr15:75,019,449,C > T), in intergenic region between CYP1A1 and CYP1A2; with attenuation of the SNP-effect when coffee consumption was included as a covariate; 3. rs12931267 (Chr16:89,818,732,C > G) in intron 30 of FANCA and near MC1R; and following conditional analysis 4. rs3764257 (Chr16:89,800,887,C > G) an intronic variant in ZNF276, 17.8 kb upstream from rs12931267; finally, 30 kb downstream from NAT2 5. rs576201050 (Chr8:18,288,053,G > A). Conclusions This large meta-GWAS revealed five SNPs at four loci associated with SAF in the non-diabetes population. Further unravelling of the genetic architecture of SAF will help in improving its utility as a tool for screening and early detection of diseases and disease complications.

Teaching statistics through engaging applications to contemporary large-scale datasets is essential to attracting students to the field. To this end, we developed a hands-on, week-long workshop for senior high-school or junior undergraduate students, without prior knowledge in statistical genetics but with some basic knowledge in data science, to conduct their own genome-wide association studies (GWAS). The GWAS was performed for open source gene expression data, using publicly-available human genetics data. Assisted by a detailed instruction manual, students were able to obtain ∼1.4 million p-values from a real scientific study, within several days. This early motivation kept students engaged in learning the theories that support their results, including regression, data visualization, results interpretation, and large-scale multiple hypothesis testing. To further their learning motivation by emphasizing the personal connection to this type of data analysis, students were encouraged to make short presentations about how GWAS has provided insights into the genetic basis of diseases that are present in their friends and/or families. The appended open source, step-by-step instruction manual includes descriptions of the datasets used, the software needed, and results from the workshop. Additionally, scripts used in the workshop are archived on Zenodo to further enhance reproducible research and training.

Rationale & Objective: Pathogenic variants in type IV collagen have been reported to account for a significant proportion of chronic kidney disease. Accordingly, genetic testing is increasingly used to diagnose kidney diseases, but testing also may reveal rare missense variants that are of uncertain clinical significance. To aid in interpretation, computational prediction (called in silico) programs may be used to predict whether a variant is clinically important. We evaluate the performance of in silico programs for COL4A3/A4/A5 variants. Study Design, Setting, & Participants: Rare missense variants in COL4A3/A4/A5 were identified in disease cohorts, including a local focal segmental glomerulosclerosis (FSGS) cohort and publicly available disease databases, in which they are categorized as pathogenic or benign based on clinical criteria. Tests Compared & Outcomes: All rare missense variants identified in the 4 disease cohorts were subjected to in silico predictions using 12 different programs. Comparisons between the predictions were compared with: (1) variant classification (pathogenic or benign) in the cohorts and (2) functional characterization in a randomly selected smaller number (17) of pathogenic or uncertain significance variants obtained from the local FSGS cohort. Results: In silico predictions correctly classified 75% to 97% of pathogenic and 57% to 100% of benign COL4A3/A4/A5 variants in public disease databases. The congruency of in silico predictions was similar for variants categorized as pathogenic and benign, with the exception of benign COL4A5 variants, in which disease effects were overestimated. By contrast, in silico predictions and functional characterization classified all 9 pathogenic COL4A3/A4/A5 variants correctly that were obtained from a local FSGS cohort. However, these programs also overestimated the effects of genomic variants of uncertain significance when compared with functional characterization. Each of the 12 in silico programs used yielded similar results. Limitations: Overestimation of in silico program sensitivity given that they may have been used in the categorization of variants labeled as pathogenic in disease repositories. Conclusions: Our results suggest that in silico predictions are sensitive but not specific to assign COL4A3/A4/A5 variant pathogenicity, with misclassification of benign variants and variants of uncertain significance. Thus, we do not recommend in silico programs but instead recommend pursuing more objective levels of evidence suggested by medical genetics guidelines.

Mendelian randomization (MR) suggests post-prandial hyperinsulinemia (unadjusted for plasma glucose) increases body mass index (BMI) but its impact on cardiometabolic disease (CMD), a leading cause for mortality and morbidity in people with obesity is not established. Fat distribution i.e. increased centripetal and/or reduced femoro-gluteal adiposity is causally associated with and better predicts CMD than BMI. We therefore undertook bi-directional MR to assess the effect of corrected insulin response (CIR, insulin 30 minutes after a glucose challenge adjusted for plasma glucose) on BMI, waist-to-hip ratio (WHR), leg fat, type 2 diabetes (T2D), triglyceride (TG), high-density lipoprotein (HDL), liver fat, hypertension and CAD in people of European descent. Inverse variance weighted MR suggests a potential causal association between increased CIR and increased BMI (b= 0.048±0.02, p=0.03), increased leg fat (b=0.029±0.012, p=0.01), reduced T2D (b=-0.73±0.15, p=6x10-7, OR 0.48 (0.36-0.64), reduced TG (b=-0.07±0.02, p=0.003) and increased HDL (b=0.04±0.01, p=0.006) with some evidence of horizontal pleiotropy. CIR had neutral effects on WHR (b=0.009±0.02, p=0.69), liver fat (b=-0.08±0.04, p=0.06), hypertension (b=-0.001±0.004, p=0.7, odds ratio (OR) (95% confidence interval (CI)) OR 1.00 (0.99-1.01) and coronary artery disease (b=-0.002±0.002, p=0.48, OR 0.99 (0.81-1.21). T2D decreased CIR (b-0.22±0.04, p=1.3x10-7), with no evidence that BMI, TG, HDL, liver fat, hypertension and CAD modulate CIR. In conclusion, we did not find evidence that increased CIR increases CMD. It might increase BMI with favorable fat distribution, reduce T2D and improve lipids.

Specific variants in genes that encode the α3α4α5 chains of type IV collagen cause Alport syndrome (AS), which encompass a clinical spectrum from isolated hematuria to multisystem disease affecting sight, hearing and kidney function. The commonest form is X-linked Alport syndrome (XLAS; COL4A5) with autosomal AS (COL4A3 and COL4A4) comprising a minority of cases. While historic data estimates the frequency of AS at 1:5000-10,000, recent population-based genetic studies suggest the prevalence is considerably higher. Genome-wide association studies (GWAS) have been performed in the Icelandic (deCODE) and UK (UK Biobank) populations, demonstrating an association of type IV collagen gene variants with AS relevant kidney traits. In the Icelandic population, 1 in 600 carries a 2.5-kb COL4A3 coding deletion or a COL4A3 missense variant (rs200287952[A], Gly695Arg), both of which are strongly associated with hematuria and albuminuria (P values = 1.9 × 10-5 to 2.5 × 10-20). In the UK Biobank, COL4A4 rs35138315 (Ser969X; carrier frequency 0.13%) is strongly associated with both hematuria and albuminuria (P = 1.5 × 10-73). Thus, the frequency for autosomal AS is 5-16 times higher than the historic prevalence of all forms of the disorder. Furthermore, COL4A4 rs3518315 (Ser969X) is also a reported founder mutation in families with autosomal dominant focal and segmental glomerulosclerosis and autosomal recessive forms of AS. This supports an additive mode of inheritance for specific variants, wherein a number of copies of a mutation influence disease severity in a cumulative fashion. These studies did not include the X chromosome, excluding analysis of COL4A5, which represents an area for future study.

Background and objectives Progression of autosomal dominant polycystic kidney disease (ADPKD) is highly variable. On average, protein-truncating PKD1 mutations are associated with the most severe kidney disease among all mutation classes. Here, we report that patients with protein-truncating PKD1 mutations may also have mild kidney disease, a finding not previously well recognized. Design, setting, participants, & measurements From the extended Toronto Genetic Epidemiologic Study of Polycystic Kidney Disease, 487 patients had PKD1 and PKD2 sequencing and typical ADPKD imaging patterns by magnetic resonance imaging or computed tomography. Mayo Clinic Imaging Classification on the basis of age- and height-adjusted total kidney volume was used to assess their cystic disease severity; classes 1A or 1B were used as a proxy to define mild disease. Multivariable linear regression was performed to test the effects of age, sex, and mutation classes on log-transformed height-adjusted total kidney volume and eGFR. Results Among 174 study patients with typical imaging patterns and protein-truncating PKD1 mutations, 32 (18%) were found to have mild disease on the basis of imaging results (i.e., Mayo Clinic Imaging class 1A–1B), with their mutations spanning the entire gene. By multivariable analyses of age, sex, and mutation class, they displayed mild disease similar to patients with PKD2 mutations and Mayo Clinic Imaging class 1A–1B. Most of these mildly affected patients with protein-truncating PKD1 mutations reported a positive family history of ADPKD in preceding generations and displayed significant intrafamilial disease variability. Conclusions Despite having the most severe mutation class, 18% of patients with protein-truncating PKD1 mutations had mild disease on the basis of clinical and imaging assessment. Podcast This article contains a podcast at https://www.asn-online.org/media/podcast/CJASN/2021_02_18_CJN11100720_final.mp3

The identification of genetic variation that directly impacts infection susceptibility to SARS-CoV-2 and disease severity of COVID-19 is an important step towards risk stratification, personalized treatment plans, therapeutic, and vaccine development and deployment. Given the importance of study design in infectious disease genetic epidemiology, we use simulation and draw on current estimates of exposure, infectivity, and test accuracy of COVID-19 to demonstrate the feasibility of detecting host genetic factors associated with susceptibility and severity in published COVID-19 study designs. We demonstrate that limited phenotypic data and exposure/infection information in the early stages of the pandemic significantly impact the ability to detect most genetic variants with moderate effect sizes, especially when studying susceptibility to SARS-CoV-2 infection. Our insights can aid in the interpretation of genetic findings emerging in the literature and guide the design of future host genetic studies. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-020-00818-2.

Strabismus is a common condition, affecting 1-4% of individuals. Isolated strabismus has been studied in families with Mendelian inheritance patterns. Despite the identification of multiple loci via linkage analyses, no specific genes have been identified from these studies. The current study is based on a seven-generation family with isolated strabismus inherited in an autosomal dominant manner. A total of 13 individuals from a common ancestor have been included for linkage analysis, and a single linkage signal has been identified at chromosome 14q12 with a multipoint LOD score of 4.69. Disruption of this locus is known to cause FOXG1 syndrome (or congenital Rett syndrome; OMIM #613454 and *164874), in which 84% of affected individuals present with strabismus. With the incorporation of next generation sequencing and in-depth bioinformatic analyses, a 4bp non-coding deletion was prioritized as the top candidate for the observed strabismus phenotype. The deletion is predicted to disrupt regulation of FOXG1, which encodes a transcription factor of the Forkhead family. Suggestive of an auto-regulation effect, the disrupted sequence matches the consensus FOXG1 and Forkhead family transcription factor binding site and has been observed in previous ChIP-seq studies to be bound by Foxg1 in early mouse brain development. The findings of this study indicate that the strabismus phenotype commonly observed within FOXG1 syndrome is separable from the more severe syndromic characteristics. Future study of this specific deletion may shed light on the regulation of FOXG1 expression and may enhance our understanding of the mechanisms contributing to strabismus and FOXG1 syndrome.Author summaryEye misalignment, or strabismus, can affect up to 4% of individuals. When strabismus is detected early, intervention in young children based on eye patching and/or corrective lenses can be beneficial. In some cases, corrective surgeries are used to align the eyes, with many individuals requiring multiple surgeries over a lifetime. A better understanding of the causes of strabismus may lead to earlier detection as well as improved treatment options. Hippocrates observed that strabismus runs in families over 2,400 years ago, an early recognition of what we now recognize as a portion of cases arising from genetic causes. We describe a large family affected by strabismus and identify a single region on chromosome 14 that may be responsible. The region contains FOXG1, in which mutations are known to cause a severe syndrome, with 84% of affected individuals also having strabismus. We identify a 4bp deletion in the region that appears to auto-regulate when FOXG1 is active. Future study of this genetic alteration may enhance our understanding of the mechanisms of strabismus.

Metabolic memory, the persistent benefits of early glycaemic control on preventing and/or delaying the development of diabetic complications, has been observed in the Diabetes Control and Complications Trial (DCCT) and in the Epidemiology of Diabetes Interventions and Complications (EDIC) follow-up study, but the underlying mechanisms remain unclear. Here, we show the involvement of epigenetic DNA methylation (DNAme) in metabolic memory by examining its associations with preceding glycaemic history, and with subsequent development of complications over an 18-yr period in the blood DNA of 499 randomly selected DCCT participants with type 1 diabetes who are also followed up in EDIC. We demonstrate the associations between DNAme near the closeout of DCCT and mean HbA1c during DCCT (mean-DCCT HbA1c) at 186 cytosine-guanine dinucleotides (CpGs) (FDR < 15%, including 43 at FDR < 5%), many of which were located in genes related to complications. Exploration studies into biological function reveal that these CpGs are enriched in binding sites for the C/EBP transcription factor, as well as enhancer/transcription regions in blood cells and haematopoietic stem cells, and open chromatin states in myeloid cells. Mediation analyses show that, remarkably, several CpGs in combination explain 68-97% of the association of mean-DCCT HbA1c with the risk of complications during EDIC. In summary, DNAme at key CpGs appears to mediate the association between hyperglycaemia and complications in metabolic memory, through modifying enhancer activity at myeloid and other cells.

Background The bleeding risks for nonsyndromic platelet function disorders (PFDs) that impair aggregation responses and/or cause dense granule deficiency (DGD) are uncertain. Objectives Our goal was to quantify bleeding risks for a cohort of consecutive cases with uncharacterized PFD. Methods Sequential cases with uncharacterized PFDs that had reduced maximal aggregation (MA) with multiple agonists and/or nonsyndromic DGD were invited to participate along with additional family members to reduce bias. Index cases were further evaluated by exome sequencing, with analysis of RUNX1‐dependent genes for cases with RUNX1 sequence variants. Bleeding assessment tools were used to estimate bleeding scores, with bleeding risks estimated as odds ratios (ORs) relative to general population controls. Relationships between symptoms and laboratory findings were also explored. Results Participants with uncharacterized PFD (n = 37; 23 index cases) had impaired aggregation function (70%), nonsyndromic DGD (19%) or both (11%), unlike unaffected relatives. Probable pathogenic RUNX1 variants were found in 2 (9%) index cases/families, whereas others had PFD of unknown cause. Participants with PFD had increased bleeding scores compared to unaffected family members and general population controls, and increased risks for mucocutaneous (OR, 4‐207) and challenge‐related bleeding (OR, 12‐43), and for receiving transfusions for bleeding (OR, 100). Reduced MA with collagen was associated with wound healing problems and bruising, and more severe DGD was associated with surgical bleeding (P

Background & Aims: A proportion of infants and young children with inflammatory bowel diseases (IBDs) have subtypes associated with a single gene variant (monogenic IBD). We aimed to determine the prevalence of monogenic disease in a cohort of pediatric patients with IBD. Methods: We performed whole-exome sequencing analyses of blood samples from an unselected cohort of 1005 children with IBD, aged 0–18 years (median age at diagnosis, 11.96 years) at a single center in Canada and their family members (2305 samples total). Variants believed to cause IBD were validated using Sanger sequencing. Biopsies from patients were analyzed by immunofluorescence and histochemical analyses. Results: We identified 40 rare variants associated with 21 monogenic genes among 31 of the 1005 children with IBD (including 5 variants in XIAP, 3 in DOCK8, and 2 each in FOXP3, GUCY2C, and LRBA). These variants occurred in 7.8% of children younger than 6 years and 2.3% of children aged 6–18 years. Of the 17 patients with monogenic Crohn’s disease, 35% had abdominal pain, 24% had nonbloody loose stool, 18% had vomiting, 18% had weight loss, and 5% had intermittent bloody loose stool. The 14 patients with monogenic ulcerative colitis or IBD-unclassified received their diagnosis at a younger age, and their most predominant feature was bloody loose stool (78%). Features associated with monogenic IBD, compared to cases of IBD not associated with a single variant, were age of onset younger than 2 years (odds ratio [OR], 6.30; P = .020), family history of autoimmune disease (OR, 5.12; P = .002), extra-intestinal manifestations (OR, 15.36; P < .0001), and surgery (OR, 3.42; P = .042). Seventeen patients had variants in genes that could be corrected with allogeneic hematopoietic stem cell transplantation. Conclusions: In whole-exome sequencing analyses of more than 1000 children with IBD at a single center, we found that 3% had rare variants in genes previously associated with pediatric IBD. These were associated with different IBD phenotypes, and 1% of the patients had variants that could be potentially corrected with allogeneic hematopoietic stem cell transplantation. Monogenic IBD is rare, but should be considered in analysis of all patients with pediatric onset of IBD.

The genetic contribution to different aspects of empathy is now established, although the exact loci are unknown. We undertook a genome-wide association study of emotional empathy (EE) as measured by emotion recognition skills in 4,780 8-year old children from the ALSPAC cohort who were genotyped and imputed to Phase 1 version 3 of the 1000 Genomes Project. We failed to find any genome-wide significant signal in either our unstratified analysis or analysis stratified according to sex. A gene-based association analysis similarly failed to find any significant loci. In contrast, our transcriptome-wide association study (TWAS) with a whole blood reference panel identified two significant loci in the unstratified analysis, residualised for the effects of age, sex and IQ. One signal was for CD93 on chromosome 20; this gene is not strongly expressed in the brain, however. The other signal was for AL118508, a non-protein coding pseudogene, which completely lies within CD93’s genomic coordinates, thereby explaining its signal. Neither are obvious candidates for involvement in the brain processes that underlie emotion recognition and its developmental pathways.

BACKGROUND AND OBJECTIVES: Glomerular hematuria has varied causes but can have a genetic basis, including Alport syndrome and IgA nephropathy. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: We used summary statistics to identify genetic variants associated with hematuria in White British UK Biobank participants. Individuals with glomerular hematuria were enriched by excluding participants with genitourinary conditions. A strongly associated locus on chromosome 2 (COL4A4-COL4A3) was identified. The region was reimputed using the Trans-Omics for Precision Medicine Program followed by sequential rounds of regional conditional analysis, conditioning on previous genetic signals. Similarly, we applied conditional analysis to identify independent variants in the MHC region on chromosome 6 using imputed HLA haplotypes. RESULTS: In total, 16,866 hematuria cases and 391,420 controls were included. Cases had higher urinary albumin-creatinine compared with controls (women: 13.01 mg/g [8.05–21.33] versus 12.12 mg/g [7.61–19.29]; P

Functional annotations have the potential to increase power of genome-wide association studies (GWAS) by prioritizing variants according to their biological function, but this potential has not been well studied. We comprehensively evaluated all 1132 traits in the UK Biobank whose SNP-heritability estimates were given “medium” or “high” labels by Neale’s lab. For each trait, we integrated GWAS summary statistics of close to 8 million common variants (minor allele frequency $$>1\%$$ > 1 % ) with either their 75 individual functional scores or their meta-scores, using three different data-integration methods. Overall, the number of new genome-wide significant findings after data-integration increases as a trait SNP-heritability estimate increases. However, there is a trade-off between new findings and loss of baseline GWAS findings, resulting in similar total numbers of significant findings between using GWAS alone and integrating GWAS with functional scores, across all 1132 traits analyzed and all three data-integration methods considered. Our findings suggest that, even with the current biobank-level sample size, more informative functional scores and/or new data-integration methods are needed to further improve the power of GWAS of common variants. For example, studying variants in coding sequence and obtaining cell-type-specific scores are potential future directions.

Meta-GWAS report numerous variants associated with type 2 diabetes (T2D), however, for diabetic retinopathy (DR) no loci achieved genome-wide significance. There are limited candidate gene analyses for T2D and/or DR reported from the Pakistani population. Therefore, the current study was designed to evaluate the genetic association of 10 loci with T2D, non-proliferative DR (NPDR), and proliferative DR (PDR). In total 375 T2D cases and 205 controls were collected. The T2D cases included diabetic no retinopathy (n = 196), NPDR (n = 95), and PDR (n = 84). Genomic DNA was isolated, and 19 SNPs were genotyped. To determine association of SNPs with T2D, logistic regression analyses were performed adjusting for age and sex. Moreover, for association of SNPs with NPDR and PDR logistic regression analyses adjusting for diabetes duration and age of T2D onset were performed. In multivariate analysis, the minor alleles of rs1043618 [G C, odds ratio (OR) 95% confidence interval (CI) = 1.45 (1.13-1.87), p = 4.00E-3], rs3807987 [G A, 1.87 (1.22-2.94), p = 0.01], rs12672038 [G A, 1.53 (1.04-2.30), p = 0.03] and rs2055858 [G C, 1.70 (1.20-2.43), p = 3.00E-3] were associated with higher risk while rs1801133 (C T, 0.59 (0.42-0.83), p = 2.28E-3) was associated with a lower risk of T2D. Moreover, minor alleles of rs2055858 [G C, 1.77 (1.17-2.68), p = 0.02], and rs3759890 [C G, 2.17 (1.39-3.39), p = 4.00E-3] showed an association with PDR when compared with DNR. However, only the association of rs1801133 survived multiple test correction. Hence, we report that rs1801133 is associated with T2D in the Pakistani population. In addition, out of studied 10 genes 8 proteins had higher interactions among themselves that are predicted to be partially biologically connected, as a group.

An unexpectedly high proportion of SNPs on the X chromosome in the 1000 Genomes Project phase 3 data were identified with significant sex differences in minor allele frequencies (sdMAF). sdMAF persisted for many of these SNPs in the recently released high coverage whole genome sequence of the 1000 Genomes Project that was aligned to GRCh38, and it was consistent between the five super-populations. Among the 245,825 common (MAF>5%) biallelic X-chromosomal SNPs in the phase 3 data presumed to be of high quality, 2,039 have genome-wide significant sdMAF (p-value

Oral disease continues to be a public health burden, affecting almost half of the global population, and disproportionately affecting the most vulnerable communities.1 Development organisations use different approaches to tackle this through short-term volunteering programmes in low- and middle-income countries, to address oral health needs in a variety of ways. There is evidence that volunteering requires a high level of cultural competence to avoid negatively impacting on local healthcare systems.2-4 The oral health care needs of communities in Sub-Saharan Africa (SSA) differ markedly from those in the developed world, posing challenges for volunteering organisations to provide effective programmes in circumstances where there is a lack of resources, equipment and infrastructure.

An unexpectedly high proportion of SNPs on the X chromosome in the 1000 Genomes Project phase 3 data were identified with significant sex differences in minor allele frequencies (sdMAF). sdMAF persisted for many of these SNPs in the recently released high coverage whole genome sequence, and it was consistent between the five super-populations. Among the 245,825 common biallelic SNPs in phase 3 data presumed to be high quality, 2,039 have genome-wide significant sdMAF (p-value

Background Rare variants in gene coding regions likely have a greater impact on disease-related phenotypes than common variants through disruption of their encoded protein. We searched for rare variants associated with onset of end stage kidney disease (ESKD) in individuals with type 1 diabetes at advanced kidney disease stage. Methods Gene-based exome array analysis of 15,449 genes in 5 large incidence cohorts of individuals with type 1 diabetes and proteinuria were analyzed for survival time-to-ESKD, testing the top gene in a 6th cohort (N=2,372/1,115 events all cohorts) and replicating in two retrospective case-control studies (N=1,072 cases, 752 controls). Deep resequencing of the top associated gene in 5 cohorts confirmed the findings. We performed immunohistochemistry and gene expression experiments in human control and diseased cells, and in mouse ischemia reperfusion and aristolochic acid nephropathy models. Results Protein coding variants in the hydroxysteroid 17-beta dehydrogenase 14 gene (HSD17B14), predicted to affect protein structure, had a net protective effect against development of ESKD at exome-wide significance (N=4,196; p-value=3.3x10-7). The HSD17B14 gene and encoded enzyme were robustly expressed in healthy human kidney, maximally in proximal tubular cells. Paradoxically, gene and protein expression were attenuated in human diabetic proximal tubules and in mouse kidney injury models. Expressed HSD17B14 gene and protein levels remained low without recovery after 21 days in a murine ischemic reperfusion injury model. Decreased gene expression was found in other chronic kidney disease-associated renal pathologies. Conclusions HSD17B14 gene is mechanistically involved in diabetic kidney disease. The encoded sex steroid enzyme is a druggable target, potentially opening a new avenue for therapeutic development.

Introduction & Objective: Cumulated advanced glycation end products (AGEs) in the bloodstream and tissues contribute to the pathogenesis of diabetes complications. The skin intrinsic fluorescence (SIF) is a non-invasive measurement of dermal AGEs level using spectrometer, and it can be used as a biomarker in AGEs-related diseases. Previously, specific epigenomic factor has been found to be associated with haemoglobin A1c (HbA1c). HbA1c is a type of glycated haemoglobin – the HbA1c test measures the average glycemic control over the period of 3 months. However, the effect of epigenetic factors on the level of AGEs in the skin remains unknown. We hypothesize that some cytosine-guanine dinucleotides (CpGs) are associated with SIF. An epigenome-wide associations study (EWAS) was performed to identify CpG sites associated with SIF in people with type 1 diabetes. Methods: 499 people with type 1 diabetes that have both methylation and SIF from the Diabetes Control Complications Trial/Epidemiology of Diabetes Interventions and Complications (DCCT/EDIC) study were included. We fit linear regression models for SIF with each CpG site one at a time. The epigenome-wide significance level (p=5e-8) was applied. Then the result is compared with the null hypothesis where CpGs are not associated with SIF to check the inflation. In order to check the assumptions of the multiple linear models at a single CpG, we use diagnostic plots. Results: We did not identify a specific CpG that is significantly associated with neither skin intrinsic fluorescence 1 (SIF1) nor skin intrinsic fluorescence 12 (SIF 12).The CpG site with strongest effect is cg06538183 ([SE] -2.73 [0.61], p = 8.72e-6) on SIF1 and cg12871967 ([SE] 2.52, 0.53, p = 2.71e-6) on SIF12. Conclusion: We did not find any specific CpG that was significantly associated with either SIF 1 or SIF12. In general, the result suggests that DNA methylation does not impact the accumulation of AGEs in skin cells. DNA methylation data has a unique pattern of distribution that drives the non-uniform distribution of the p-values. The group of 275,301 CpGs that have means above the median and standard deviations below the median has the expected uniform p-value distribution.

Background Focal and segmental glomerulosclerosis (FSGS) is a histologic pattern of injury that characterizes a wide spectrum of diseases. Many genetic causes have been identified in FSGS but even in families with comprehensive testing, a significant proportion remain unexplained. Methods In a family with adult-onset autosomal dominant FSGS, linkage analysis was performed in 11 family members followed by whole exome sequencing (WES) in 3 affected relatives to identify candidate genes. Results Pathogenic variants in known nephropathy genes were excluded. Subsequently, linkage analysis was performed and narrowed the disease gene(s) to within 3% of the genome. WES identified 5 heterozygous rare variants, which were sequenced in 11 relatives where DNA was available. Two of these variants, in LAMA2 and LOXL4, remained as candidates after segregation analysis and encode extracellular matrix proteins of the glomerulus. Renal biopsies showed classic segmental sclerosis/hyalinosis lesion on a background of mild mesangial hypercellularity. Examination of basement membranes with electron microscopy showed regions of dense mesangial matrix in one individual and wider glomerular basement membrane (GBM) thickness in two individuals compared to historic control averages. Conclusions Based on our findings, we postulate that the additive effect of digenic inheritance of heterozygous variants in LAMA2 and LOXL4 leads to adult-onset FSGS. Limitations to our study includes the absence of functional characterization to support pathogenicity. Alternatively, identification of additional FSGS cases with suspected deleterious variants in LAMA2 and LOXL4 will provide more evidence for disease causality. Thus, our report will be of benefit to the renal community as sequencing in renal disease becomes more widespread.

GWAS have identified thousands of loci associated with human complex diseases and traits. How these loci are distributed through the genome has not been systematically evaluated. We hypothesised that the location of GWAS loci differ between ancestral linkage groups (ALGs) related to the paralogy and function of genes. We used data from the NHGRI-EBI GWAS catalog to determine whether the density of GWAS loci relative to HapMap variants in each ALG differed, and whether ALG’s were enriched for experimental factor ontological (EFO) terms assigned to the GWAS traits. In a gene-level analyses we explored the characteristics of genes linked to GWAS loci and those mapping to the ALG’s. We find that GWAS loci were enriched or deficient in 9 and 7 of the 17 ALG’s respectively, while there was no difference in the number of GWAS loci in regions of the human genome unassigned to an ALG. All but 2 ALG’s were significantly enriched or deficient for one or more EFO terms. Lastly, we find that genes assigned to an ALG are under higher levels of selective constraint, have longer coding sequences and higher median expression in the tissue of highest expression than genes not mapping to an ALG. On the other hand, genes associated with GWAS loci have longer genomic length and exhibit higher levels of selective constraint relative to non-GWAS genes.Collectively, this suggests that understanding the location and ancestral origins of GWAS signals may be informative for the development of tools for variant prioritization and interpretation.

Most replicated genetic determinants for type 1 diabetes are common (minor allele frequency [MAF] >5%). We aimed to identify novel rare or low-frequency (MAF