A phenome-wide association study of tandem repeat variation in 168,554 individuals from the UK Biobank.

Most genetic association studies focus on binary variants. To identify the effects of multi-allelic variation of tandem repeats (TRs) on human traits, we performed direct TR genotyping and phenome-wide association studies in 168,554 individuals from the UK Biobank, identifying 47 TRs showing causal associations with 73 traits. We replicated 23 of 31 (74%) of these causal associations in the All of Us cohort. While this set included several known repeat expansion disorders, novel associations we found were attributable to common polymorphic variation in TR length rather than rare expansions and include e.g. a coding polyhistidine motif in HRCT1 influencing risk of hypertension and a poly(CGC) in the 5'UTR of GNB2 influencing heart rate. Causal TRs were strongly enriched for associations with local gene expression and DNA methylation. Our study highlights the contribution of multi-allelic TRs to the "missing heritability" of the human genome.

POPULATION FREQUENCY OF REPEAT EXPANSIONS INDICATES INCREASED DISEASE PREVALENCE ESTIMATES ACROSS DIFFERENT POPULATIONS.

Repeat expansion disorders (REDs) are a devastating group of predominantly neurological diseases. Together they are common, affecting 1 in 3,000 people worldwide with population-specific differences. However, prevalence estimates of REDs are hampered by heterogeneous clinical presentation, variable geographic distributions, and technological limitations leading to under-ascertainment. Here, leveraging whole genome sequencing data from 82,176 individuals from different populations we found an overall carrier frequency of REDs of 1 in 340 individuals. Modelling disease prevalence using genetic data, age at onset and survival, we show that REDs are up to 3-fold more prevalent than currently reported figures. While some REDs are population-specific, e.g. Huntington's disease type 2, most REDs are represented in all broad genetic ancestries, including Africans and Asians, challenging the notion that some REDs are found only in European populations. These results have worldwide implications for local and global health communities in the diagnosis and management of REDs both at local and global levels.

A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 as a significant cause of intellectual disability.

GC-rich tandem repeat expansions (TREs) are often associated with DNA methylation, gene silencing and folate-sensitive fragile sites and underlie several congenital and late-onset disorders. Through a combination of DNA methylation profiling and tandem repeat genotyping, we identified 24 methylated TREs and investigated their effects on human traits using PheWAS in 168,641 individuals from the UK Biobank, identifying 156 significant TRE:trait associations involving 17 different TREs. Of these, a GCC expansion in the promoter of AFF3 was linked with a 2.4-fold reduced probability of completing secondary education, an effect size comparable to several recurrent pathogenic microdeletions. In a cohort of 6,371 probands with neurodevelopmental problems of suspected genetic etiology, we observed a significant enrichment of AFF3 expansions compared to controls. With a population prevalence that is at least 5-fold higher than the TRE that causes fragile X syndrome, AFF3 expansions represent a significant cause of neurodevelopmental delay.

Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation.

Short tandem repeats (STRs) contribute significantly to genetic diversity in humans, including disease-causing variation. Although the effect of STR variation on gene expression has been extensively assessed, their impact on epigenetics has been poorly studied and limited to specific genomic regions. Here, we investigated the hypothesis that some STRs act as independent regulators of local DNA methylation in the human genome and modify risk of common human traits. To address these questions, we first analyzed two independent data sets comprising PCR-free whole-genome sequencing (WGS) and genome-wide DNA methylation levels derived from whole-blood samples in 245 (discovery cohort) and 484 individuals (replication cohort). Using genotypes for 131,635 polymorphic STRs derived from WGS using HipSTR, we identified 11,870 STRs that associated with DNA methylation levels (mSTRs) of 11,774 CpGs (Bonferroni P < 0.001) in our discovery cohort, with 90% successfully replicating in our second cohort. Subsequently, through fine-mapping using CAVIAR we defined 585 of these mSTRs as the likely causal variants underlying the observed associations (fm-mSTRs) and linked a fraction of these to previously reported genome-wide association study signals, providing insights into the mechanisms underlying complex human traits. Furthermore, by integrating gene expression data, we observed that 12.5% of the tested fm-mSTRs also modulate expression levels of nearby genes, reinforcing their regulatory potential. Overall, our findings expand the catalog of functional sequence variants that affect genome regulation, highlighting the importance of incorporating STRs in future genetic association analysis and epigenetics data for the interpretation of trait-associated variants.

A phenome-wide association study identifies effects of copy-number variation of VNTRs and multicopy genes on multiple human traits.

The human genome contains tens of thousands of large tandem repeats and hundreds of genes that show common and highly variable copy-number changes. Due to their large size and repetitive nature, these variable number tandem repeats (VNTRs) and multicopy genes are generally recalcitrant to standard genotyping approaches and, as a result, this class of variation is poorly characterized. However, several recent studies have demonstrated that copy-number variation of VNTRs can modify local gene expression, epigenetics, and human traits, indicating that many have a functional role. Here, using read depth from whole-genome sequencing to profile copy number, we report results of a phenome-wide association study (PheWAS) of VNTRs and multicopy genes in a discovery cohort of ∼35,000 samples, identifying 32 traits associated with copy number of 38 VNTRs and multicopy genes at 1% FDR. We replicated many of these signals in an independent cohort and observed that VNTRs showing trait associations were significantly enriched for expression QTLs with nearby genes, providing strong support for our results. Fine-mapping studies indicated that in the majority (∼90%) of cases, the VNTRs and multicopy genes we identified represent the causal variants underlying the observed associations. Furthermore, several lie in regions where prior SNV-based GWASs have failed to identify any significant associations with these traits. Our study indicates that copy number of VNTRs and multicopy genes contributes to diverse human traits and suggests that complex structural variants potentially explain some of the so-called "missing heritability" of SNV-based GWASs.

Automated Bone Marrow Cell Classification for Haematological Disease Diagnosis Using Siamese Neural Network.

The critical structure and nature of different bone marrow cells which form a base in the diagnosis of haematological ailments requires a high-grade classification which is a very prolonged approach and accounts for human error if performed manually, even by field experts. Therefore, the aim of this research is to automate the process to study and accurately classify the structure of bone marrow cells which will help in the diagnosis of haematological ailments at a much faster and better rate. Various machine learning algorithms and models, such as CNN + SVM, CNN + XGB Boost and Siamese network, were trained and tested across a dataset of 170,000 expert-annotated cell images from 945 patients' bone marrow smears with haematological disorders. The metrics used for evaluation of this research are accuracy of model, precision and recall of all the different classes of cells. Based on these performance metrics the CNN + SVM, CNN + XGB, resulted in 32%, 28% accuracy, respectively, and therefore these models were discarded. Siamese neural resulted in 91% accuracy and 84% validation accuracy. Moreover, the weighted average recall values of the Siamese neural network were 92% for training and 91% for validation. Hence, the final results are based on Siamese neural network model as it was outperforming all the other algorithms used in this research.

A comparison of intravenous methylprednisolone and hydrocortisone for the treatment of acute inflammatory bowel disease.

BACKGROUND AND AIM: Despite widespread recommendations and use of intravenous corticosteroids (IVCS) for the treatment of acute flares of ulcerative colitis and Crohn's disease, limited evidence exists comparing outcomes of the two most common regimens, intravenous methylprednisolone (IVMP) and intravenous hydrocortisone (IVHC). IVHC has stronger mineralocorticoid effects compared with IVMP and may cause higher rates of hypokalemia. We aimed to determine differences in clinical outcomes including requirement for inpatient rescue therapy, bowel resection, and rates of hypokalemia. METHODS: We conducted a multicenter cohort study of all adult patients admitted with an acute flare of inflammatory bowel disease (IBD) to the three tertiary hospitals in Auckland, New Zealand, where the protocol at each institution is either IVMP 60 mg daily or IVHC 100 mg four times daily. All patients requiring IVCS between 20 June 2016 and 30 June 2018 were included. The IVCS protocol was then changed at one hospital, where further data were collected for a further 12 months from 30 January 2019 until 30 December 2019. RESULTS: There were 359 patients, including 129 (35.9%) patients receiving IVMP and 230 (64.1%) patients receiving IVHC. IVMP treatment was associated with a greater requirement for rescue therapy than IVHC (36.4% vs 19.6%, P = 0.001; odds ratio [OR] = 2.79; 95% confidence interval [CI], 1.64-4.75, P < 0.001), but also reduced rates of hypokalemia (55.8% vs 67.0%, P = 0.04; OR = 0.49; 95% CI, 0.30-0.81, P = 0.005). There was no difference between treatment groups for the median length of admission (5 days, interquartile range [IQR] 3-8), median duration of IVCS treatment (3 days, IQR 2-5), or bowel resection within 30 days of admission (12.4% vs 11.7%; OR = 1.04). CONCLUSION: For the treatment of an acute flare of IBD, treatment with IVMP results in significantly more requirement for inpatient rescue biologic or cyclosporin. In addition, it causes statistically significant less hypokalemia than IVHC, although in practice differences are negligible.

Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression.

Variable number tandem repeats (VNTRs) are composed of large tandemly repeated motifs, many of which are highly polymorphic in copy number. However, because of their large size and repetitive nature, they remain poorly studied. To investigate the regulatory potential of VNTRs, we used read-depth data from Illumina whole-genome sequencing to perform association analysis between copy number of ∼70,000 VNTRs (motif size ≥ 10 bp) with both gene expression (404 samples in 48 tissues) and DNA methylation (235 samples in peripheral blood), identifying thousands of VNTRs that are associated with local gene expression (eVNTRs) and DNA methylation levels (mVNTRs). Using an independent cohort, we validated 73%-80% of signals observed in the two discovery cohorts, while allelic analysis of VNTR length and CpG methylation in 30 Oxford Nanopore genomes gave additional support for mVNTR loci, thus providing robust evidence to support that these represent genuine associations. Further, conditional analysis indicated that many eVNTRs and mVNTRs act as QTLs independently of other local variation. We also observed strong enrichments of eVNTRs and mVNTRs for regulatory features such as enhancers and promoters. Using the Human Genome Diversity Panel, we define sets of VNTRs that show highly divergent copy numbers among human populations and show that these are enriched for regulatory effects and preferentially associate with genes that have been linked with human phenotypes through GWASs. Our study provides strong evidence supporting functional variation at thousands of VNTRs and defines candidate sets of VNTRs, copy number variation of which potentially plays a role in numerous human phenotypes.

Rare genetic variation at transcription factor binding sites modulates local DNA methylation profiles.

Although DNA methylation is the best characterized epigenetic mark, the mechanism by which it is targeted to specific regions in the genome remains unclear. Recent studies have revealed that local DNA methylation profiles might be dictated by cis-regulatory DNA sequences that mainly operate via DNA-binding factors. Consistent with this finding, we have recently shown that disruption of CTCF-binding sites by rare single nucleotide variants (SNVs) can underlie cis-linked DNA methylation changes in patients with congenital anomalies. These data raise the hypothesis that rare genetic variation at transcription factor binding sites (TFBSs) might contribute to local DNA methylation patterning. In this work, by combining blood genome-wide DNA methylation profiles, whole genome sequencing-derived SNVs from 247 unrelated individuals along with 133 predicted TFBS motifs derived from ENCODE ChIP-Seq data, we observed an association between the disruption of binding sites for multiple TFs by rare SNVs and extreme DNA methylation values at both local and, to a lesser extent, distant CpGs. While the majority of these changes affected only single CpGs, 24% were associated with multiple outlier CpGs within ±1kb of the disrupted TFBS. Interestingly, disruption of functionally constrained sites within TF motifs lead to larger DNA methylation changes at nearby CpG sites. Altogether, these findings suggest that rare SNVs at TFBS negatively influence TF-DNA binding, which can lead to an altered local DNA methylation profile. Furthermore, subsequent integration of DNA methylation and RNA-Seq profiles from cardiac tissues enabled us to observe an association between rare SNV-directed DNA methylation and outlier expression of nearby genes. In conclusion, our findings not only provide insights into the effect of rare genetic variation at TFBS on shaping local DNA methylation and its consequences on genome regulation, but also provide a rationale to incorporate DNA methylation data to interpret the functional role of rare variants.

A Survey of Rare Epigenetic Variation in 23,116 Human Genomes Identifies Disease-Relevant Epivariations and CGG Expansions.

There is growing recognition that epivariations, most often recognized as promoter hypermethylation events that lead to gene silencing, are associated with a number of human diseases. However, little information exists on the prevalence and distribution of rare epigenetic variation in the human population. In order to address this, we performed a survey of methylation profiles from 23,116 individuals using the Illumina 450k array. Using a robust outlier approach, we identified 4,452 unique autosomal epivariations, including potentially inactivating promoter methylation events at 384 genes linked to human disease. For example, we observed promoter hypermethylation of BRCA1 and LDLR at population frequencies of ∼1 in 3,000 and ∼1 in 6,000, respectively, suggesting that epivariations may underlie a fraction of human disease which would be missed by purely sequence-based approaches. Using expression data, we confirmed that many epivariations are associated with outlier gene expression. Analysis of variation data and monozygous twin pairs suggests that approximately two-thirds of epivariations segregate in the population secondary to underlying sequence mutations, while one-third are likely sporadic events that occur post-zygotically. We identified 25 loci where rare hypermethylation coincided with the presence of an unstable CGG tandem repeat, validated the presence of CGG expansions at several loci, and identified the putative molecular defect underlying most of the known folate-sensitive fragile sites in the genome. Our study provides a catalog of rare epigenetic changes in the human genome, gives insight into the underlying origins and consequences of epivariations, and identifies many hypermethylated CGG repeat expansions.

Episignatures Stratifying Helsmoortel-Van Der Aa Syndrome Show Modest Correlation with Phenotype.

Helsmoortel-Van der Aa syndrome (HVDAS) is a neurodevelopmental condition associated with intellectual disability/developmental delay, autism spectrum disorder, and multiple medical comorbidities. HVDAS is caused by mutations in activity-dependent neuroprotective protein (ADNP). A recent study identified genome-wide DNA methylation changes in 22 individuals with HVDAS, adding to the group of neurodevelopmental disorders with an epigenetic signature. This methylation signature segregated those with HVDAS into two groups based on the location of the mutations. Here, we conducted an independent study on 24 individuals with HVDAS and replicated the existence of the two mutation-dependent episignatures. To probe whether the two distinct episignatures correlate with clinical outcomes, we used deep behavioral and neurobiological data from two prospective cohorts of individuals with a genetic diagnosis of HVDAS. We found limited phenotypic differences between the two HVDAS-affected groups and no evidence that individuals with more widespread methylation changes are more severely affected. Moreover, in spite of the methylation changes, we observed no profound alterations in the blood transcriptome of individuals with HVDAS. Our data warrant caution in harnessing methylation signatures in HVDAS as a tool for clinical stratification, at least with regard to behavioral phenotypes.

Is evaluation of non-HDL-C better than calculated LDL-C in CAD patients? MMIMSR experiences.

OBJECTIVE: The present study aimed to establish a better marker for the assessment of coronary artery disease (CAD). METHODS: One hundred patients of CAD (aged 20-60 years) of both sex and patients of hypertension with symptoms of CAD were selected for the study.50 age and sex matched healthy controls were chosen for the present study. Serum total cholesterol, triglycerides and HDL-C were estimated in Simens Dimensions RxL. LDL-C, VLDL-C were calculated by Friedwald Formula while non-HDL-C was calculated by subtracting HDL-C level from total cholesterol level. The comparison of non-HDL-C and friedwald calculated LDL-C was made in terms of independent't' test, serum TG levels (TG ≤ 200 mg/dl and TG > 200 mg/dl) and area under receiver operating characteristic (AUROC) curve. RESULTS & CONCLUSION: The non-HDL-C levels (mean ± S.D) were higher in both test and control groups to that of the levels of friedwald calculated LDL-C. The area under receiver operating characteristic (AUROC) curve was significantly higher for non-HDL-C than for friedwald calculated LDL-C. The predictive value of non-HDL-C and friedwald calculated LDL-C were also compared in group A (serum TG ≤ 200 mg/dl) and group B (serum TG > 200 mg/dl). Non-HDL-C levels showed a significant difference in both the groups while the results were non-significant to that of friedwald calculated LDL. Thus, non-HDL-C is much specific and sensitive parameter for assessment of CAD risk. Moreover, non-HDL-C levels can also be done in non-fasting state with accuracy, thereby, it is patient friendly parameter. Therefore, the authors strongly suggest the incorporation of non-HDL-C in routine lipid profile panel.

Virtual Reality Use for Symptom Management in Palliative Care: A Pilot Study to Assess User Perceptions.

In the past two decades, virtual reality (VR) technology has found use in a variety of clinical settings including pain management, physical medicine and rehabilitation, psychiatry, and neurology. However, little is known about the utility of VR in the palliative care setting. Moreover, previous investigations have not explored user perceptions of the VR experience in this population. Understanding user perceptions of the VR intervention will be critical for the development and delivery of effective VR therapies. To examine the utility of VR for palliative care patients, a pilot study of VR use was conducted with 12 adult patients diagnosed with life-limiting illness who were residents at a free-standing hospice facility. The intervention consisted of a one-time 30-minute VR experience. User perceptions were assessed through both quantitative and qualitative means, including participant responses to open-ended questions after the VR intervention. Acute changes in symptom burden were assessed using the revised Edmonton Symptom Assessment Scale. Participants found the VR experience to be both enjoyable and useful, and the intervention was well-tolerated overall. This study provides support for VR as a promising new therapeutic modality for patients undergoing palliative care.

Predictors of non-attendance at outpatient endoscopy: a five-year multi-centre observational study from New Zealand.

AIMS: Outpatient endoscopy non-attendance leads to diagnostic delay and increasing wait times. We aimed to analyse endoscopy non-attendance rates and factors associated with it at the Canterbury and Auckland District Health Boards during a five-year period. METHODS: Consecutive appointments between April 2012 and March 2017 were assessed. The following procedures were included: gastroscopy, colonoscopy and endoscopic retrograde cholangiopancreatography. Predictors of non-attendance were assessed using univariate and multivariate binary logistic regression. RESULTS: A total of 58,434 appointments were offered (Canterbury-33,697, Auckland-24,737), of which 2,694 (4.6%) were not attended. Maori (OR 3.0, 95%CI 2.63-3.42) and Pacific Peoples (OR 3.1, 95%CI 2.7-3.55) were significantly more likely to miss appointments compared with Europeans. Patients from socioeconomically most deprived areas (NZDep10) had higher rates of non-attendance (OR 2.13, 95%CI 1.72-2.63) compared with NZDep1. Males (OR 1.43, 95%CI 1.32-1.56) and the Auckland District Health Board patients (OR 2.28, 95%CI 2.08-2.50) had higher non-attendance rates. CONCLUSION: Overall, 4.6% patients did not attend endoscopy appointments. Maori, Pacific Peoples and patients from socioeconomically deprived areas had higher non-attendance rates. Targeted interventions for at-risk groups would potentially lessen health inequalities and optimise utilisation of endoscopy resources.

Screening for rare epigenetic variations in autism and schizophrenia.

While many studies have led to the identification of rare sequence variants linked with susceptibility to autism and schizophrenia, the contribution of rare epigenetic variations (epivariations) in these disorders remains largely unexplored. Previously we presented evidence that epivariations occur relatively frequently in the human genome, and likely contribute to a subset of congenital and neurodevelopmental disorders through the disruption of dosage-sensitive genes. Here we extend this approach, studying methylation profiles from 297 samples with autism and 767 cases with schizophrenia, identifying 84 and 268 rare epivariations in these two cohorts, respectively, that were absent from 4,860 population controls. We observed multiple features associated with these epivariations that support their pathogenic relevance, including (a) a significant enrichment for epivariations in schizophrenic individuals at genes previously linked with schizophrenia, (b) increased brain expression of genes associated with epivariations found in autism cases compared with controls, (c) in autism families, a significant excess of epivariations found specifically in affected versus unaffected sibs, (d) Gene Ontology terms linked with epivariations found in autism, including "D1 dopamine receptor binding." Our study provides additional evidence that rare epivariations likely contribute to the mutational spectra underlying neurodevelopmental disorders.

A survey of inter-individual variation in DNA methylation identifies environmentally responsive co-regulated networks of epigenetic variation in the human genome.

While population studies have resulted in detailed maps of genetic variation in humans, to date there are few robust maps of epigenetic variation. We identified sites containing clusters of CpGs with high inter-individual epigenetic variation, termed Variably Methylated Regions (VMRs) in five purified cell types. We observed that VMRs occur preferentially at enhancers and 3' UTRs. While the majority of VMRs have high heritability, a subset of VMRs within the genome show highly correlated variation in trans, forming co-regulated networks that have low heritability, differ between cell types and are enriched for specific transcription factor binding sites and biological pathways of functional relevance to each tissue. For example, in T cells we defined a network of 95 co-regulated VMRs enriched for genes with roles in T-cell activation; in fibroblasts a network of 34 co-regulated VMRs comprising all four HOX gene clusters enriched for control of tissue growth; and in neurons a network of 18 VMRs enriched for roles in synaptic signaling. By culturing genetically-identical fibroblasts under varying environmental conditions, we experimentally demonstrated that some VMR networks are responsive to the environment, with methylation levels at these loci changing in a coordinated fashion in trans dependent on cellular growth. Intriguingly these environmentally-responsive VMRs showed a strong enrichment for imprinted loci (p<10-80), suggesting that these are particularly sensitive to environmental conditions. Our study provides a detailed map of common epigenetic variation in the human genome, showing that both genetic and environmental causes underlie this variation.

Identification of rare de novo epigenetic variations in congenital disorders.

Certain human traits such as neurodevelopmental disorders (NDs) and congenital anomalies (CAs) are believed to be primarily genetic in origin. However, even after whole-genome sequencing (WGS), a substantial fraction of such disorders remain unexplained. We hypothesize that some cases of ND-CA are caused by aberrant DNA methylation leading to dysregulated genome function. Comparing DNA methylation profiles from 489 individuals with ND-CAs against 1534 controls, we identify epivariations as a frequent occurrence in the human genome. De novo epivariations are significantly enriched in cases, while RNAseq analysis shows that epivariations often have an impact on gene expression comparable to loss-of-function mutations. Additionally, we detect and replicate an enrichment of rare sequence mutations overlapping CTCF binding sites close to epivariations, providing a rationale for interpreting non-coding variation. We propose that epivariations contribute to the pathogenesis of some patients with unexplained ND-CAs, and as such likely have diagnostic relevance.

DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome.

Genomic imprinting is a mechanism in which gene expression varies depending on parental origin. Imprinting occurs through differential epigenetic marks on the two parental alleles, with most imprinted loci marked by the presence of differentially methylated regions (DMRs). To identify sites of parental epigenetic bias, here we have profiled DNA methylation patterns in a cohort of 57 individuals with uniparental disomy (UPD) for 19 different chromosomes, defining imprinted DMRs as sites where the maternal and paternal methylation levels diverge significantly from the biparental mean. Using this approach we identified 77 DMRs, including nearly all those described in previous studies, in addition to 34 DMRs not previously reported. These include a DMR at TUBGCP5 within the recurrent 15q11.2 microdeletion region, suggesting potential parent-of-origin effects associated with this genomic disorder. We also observed a modest parental bias in DNA methylation levels at every CpG analyzed across ∼1.9 Mb of the 15q11-q13 Prader-Willi/Angelman syndrome region, demonstrating that the influence of imprinting is not limited to individual regulatory elements such as CpG islands, but can extend across entire chromosomal domains. Using RNA-seq data, we detected signatures consistent with imprinted expression associated with nine novel DMRs. Finally, using a population sample of 4,004 blood methylomes, we define patterns of epigenetic variation at DMRs, identifying rare individuals with global gain or loss of methylation across multiple imprinted loci. Our data provide a detailed map of parental epigenetic bias in the human genome, providing insights into potential parent-of-origin effects.

DNA Methylation Signatures of Early Childhood Malnutrition Associated With Impairments in Attention and Cognition.

BACKGROUND: Early childhood malnutrition affects 113 million children worldwide, impacting health and increasing vulnerability for cognitive and behavioral disorders later in life. Molecular signatures after childhood malnutrition, including the potential for intergenerational transmission, remain unexplored. METHODS: We surveyed blood DNA methylomes (~483,000 individual CpG sites) in 168 subjects across two generations, including 50 generation 1 individuals hospitalized during the first year of life for moderate to severe protein-energy malnutrition, then followed up to 48 years in the Barbados Nutrition Study. Attention deficits and cognitive performance were evaluated with the Connors Adult Attention Rating Scale and Wechsler Abbreviated Scale of Intelligence. Expression of nutrition-sensitive genes was explored by quantitative reverse transcriptase polymerase chain reaction in rat prefrontal cortex. RESULTS: We identified 134 nutrition-sensitive, differentially methylated genomic regions, with most (87%) specific for generation 1. Multiple neuropsychiatric risk genes, including COMT, IFNG, MIR200B, SYNGAP1, and VIPR2 showed associations of specific methyl-CpGs with attention and IQ. IFNG expression was decreased in prefrontal cortex of rats showing attention deficits after developmental malnutrition. CONCLUSIONS: Early childhood malnutrition entails long-lasting epigenetic signatures associated with liability for attention and cognition, and limited potential for intergenerational transmission.

Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans.

Despite representing an important source of genetic variation, tandem repeats (TRs) remain poorly studied due to technical difficulties. We hypothesized that TRs can operate as expression (eQTLs) and methylation (mQTLs) quantitative trait loci. To test this we analyzed the effect of variation at 4849 promoter-associated TRs, genotyped in 120 individuals, on neighboring gene expression and DNA methylation. Polymorphic promoter TRs were associated with increased variance in local gene expression and DNA methylation, suggesting functional consequences related to TR variation. We identified >100 TRs associated with expression/methylation levels of adjacent genes. These potential eQTL/mQTL TRs were enriched for overlaps with transcription factor binding and DNaseI hypersensitivity sites, providing a rationale for their effects. Moreover, we showed that most TR variants are poorly tagged by nearby single nucleotide polymorphisms (SNPs) markers, indicating that many functional TR variants are not effectively assayed by SNP-based approaches. Our study assigns biological significance to TR variations in the human genome, and suggests that a significant fraction of TR variations exert functional effects via alterations of local gene expression or epigenetics. We conclude that targeted studies that focus on genotyping TR variants are required to fully ascertain functional variation in the genome.