Cross-reactive probes on Illumina DNA methylation arrays: a large study on ALS shows that a cautionary approach is warranted in interpreting epigenome-wide association studies

Illumina DNA methylation arrays are a widely used tool for performing genome-wide DNA methylation analyses. However, measurements obtained from these arrays may be affected by technical artefacts that result in spurious associations if left unchecked. Cross-reactivity represents one of the major challenges, meaning that probes may map to multiple regions in the genome. Although several studies have reported on this issue, few studies have empirically examined the impact of cross-reactivity in an epigenome-wide association study (EWAS). In this paper, we report on cross-reactivity issues that we discovered in a large EWAS on the presence of the C9orf72 repeat expansion in ALS patients. Specifically, we found that that the majority of the significant probes inadvertently cross-hybridized to the C9orf72 locus. Importantly, these probes were not flagged as cross-reactive in previous studies, leading to novel insights into the extent to which cross-reactivity can impact EWAS. Our findings are particularly relevant for epigenetic studies into diseases associated with repeat expansions and other types of structural variation. More generally however, considering that most spurious associations were not excluded based on pre-defined sets of cross-reactive probes, we believe that the presented data-driven flag and consider approach is relevant for any type of EWAS

Genetic variability in sporadic amyotrophic lateral sclerosis

With the advent of gene therapies for amyotrophic lateral sclerosis (ALS), there is a surge in gene testing for this disease. Although there is ample experience with gene testing for C9orf72, SOD1, FUS and TARDBP in familial ALS, large studies exploring genetic variation in all ALS-associated genes in sporadic ALS (sALS) are still scarce. Gene testing in a diagnostic setting is challenging, given the complex genetic architecture of sALS, for which there are genetic variants with large and small effect sizes. Guidelines for the interpretation of genetic variants in gene panels and for counselling of patients are lacking. We aimed to provide a thorough characterization of genetic variability in ALS genes by applying the American College of Medical Genetics and Genomics (ACMG) criteria on whole genome sequencing data from a large cohort of 6013 sporadic ALS patients and 2411 matched controls from Project MinE. We studied genetic variation in 90 ALS-associated genes and applied customized ACMG-criteria to identify pathogenic and likely pathogenic variants. Variants of unknown significance were collected as well. In addition, we determined the length of repeat expansions in C9orf72, ATXN1, ATXN2 and NIPA1 using the ExpansionHunter tool. We found C9orf72 repeat expansions in 5.21% of sALS patients. In 50 ALS-associated genes, we did not identify any pathogenic or likely pathogenic variants. In 5.89%, a pathogenic or likely pathogenic variant was found, most commonly in SOD1, TARDBP, FUS, NEK1, OPTN or TBK1. Significantly more cases carried at least one pathogenic or likely pathogenic variant compared to controls (odds ratio 1.75; P-value 1.64 × 10−5). Isolated risk factors in ATXN1, ATXN2, NIPA1 and/or UNC13A were detected in 17.33% of cases. In 71.83%, we did not find any genetic clues. A combination of variants was found in 2.88%. This study provides an inventory of pathogenic and likely pathogenic genetic variation in a large cohort of sALS patients. Overall, we identified pathogenic and likely pathogenic variants in 11.13% of ALS patients in 38 known ALS genes. In line with the oligogenic hypothesis, we found significantly more combinations of variants in cases compared to controls. Many variants of unknown significance may contribute to ALS risk, but diagnostic algorithms to reliably identify and weigh them are lacking. This work can serve as a resource for counselling and for the assembly of gene panels for ALS. Further characterization of the genetic architecture of sALS is necessary given the growing interest in gene testing in ALS

Structural variation analysis of 6,500 whole genome sequences in amyotrophic lateral sclerosis

There is a strong genetic contribution to Amyotrophic lateral sclerosis (ALS) risk, with heritability estimates of up to 60%. Both Mendelian and small effect variants have been identified, but in common with other conditions, such variants only explain a little of the heritability. Genomic structural variation might account for some of this otherwise unexplained heritability. We therefore investigated association between structural variation in a set of 25 ALS genes, and ALS risk and phenotype. As expected, the repeat expansion in the C9orf72 gene was identified as associated with ALS. Two other ALS-associated structural variants were identified: inversion in the VCP gene and insertion in the ERBB4 gene. All three variants were associated both with increased risk of ALS and specific phenotypic patterns of disease expression. More than 70% of people with respiratory onset ALS harboured ERBB4 insertion compared with 25% of the general population, suggesting respiratory onset ALS may be a distinct genetic subtype

Telomere length analysis in amyotrophic lateral sclerosis using large-scale whole genome sequence data

Background: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the loss of upper and lower motor neurons, leading to progressive weakness of voluntary muscles, with death following from neuromuscular respiratory failure, typically within 3 to 5 years. There is a strong genetic contribution to ALS risk. In 10% or more, a family history of ALS or frontotemporal dementia is obtained, and the Mendelian genes responsible for ALS in such families have now been identified in about 50% of cases. Only about 14% of apparently sporadic ALS is explained by known genetic variation, suggesting that other forms of genetic variation are important. Telomeres maintain DNA integrity during cellular replication, differ between sexes, and shorten naturally with age. Sex and age are risk factors for ALS and we therefore investigated telomere length in ALS. Methods: Samples were from Project MinE, an international ALS whole genome sequencing consortium that includes phenotype data. For validation we used donated brain samples from motor cortex from people with ALS and controls. Ancestry and relatedness were evaluated by principal components analysis and relationship matrices of DNA microarray data. Whole genome sequence data were from Illumina HiSeq platforms and aligned using the Isaac pipeline. TelSeq was used to quantify telomere length using whole genome sequence data. We tested the association of telomere length with ALS and ALS survival using Cox regression. Results: There were 6,580 whole genome sequences, reducing to 6,195 samples (4,315 from people with ALS and 1,880 controls) after quality control, and 159 brain samples (106 ALS, 53 controls). Accounting for age and sex, there was a 20% (95% CI 14%, 25%) increase of telomere length in people with ALS compared to controls (p = 1.1 × 10−12), validated in the brain samples (p = 0.03). Those with shorter telomeres had a 10% increase in median survival (p = 5.0×10−7). Although there was no difference in telomere length between sporadic ALS and familial ALS (p=0.64), telomere length in 334 people with ALS due to expanded C9orf72 repeats was shorter than in those without expanded C9orf72 repeats (p = 5.0×10−4). Discussion: Although telomeres shorten with age, longer telomeres are a risk factor for ALS and worsen prognosis. Longer telomeres are associated with ALS

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo

Predicting morphologies of solution processed polymer: Fullerene blends

The performance of solution processed polymer:fullerene thin film photovoltaic cells is largely determined by the nanoscopic and mesoscopic morphology of these blends that is formed during the drying of the layer. Although blend morphologies have been studied in detail using a variety of microscopic, spectroscopic, and scattering techniques and a large degree of control has been obtained, the current understanding of the processes involved is limited. Hence, predicting the optimized processing conditions and the corresponding device performance remains a challenge. We present an experimental and modeling study on blends of a small band gap diketopyrrolopyrrole- quinquethiophene alternating copolymer (PDPP5T) and [6,6]-phenyl-C 71-butyric acid methyl ester ([70]PCBM) cast from chloroform solution. The model uses the homogeneous Flory-Huggins free energy of the multicomponent blend and accounts for interfacial interactions between (locally) separated phases, based on physical properties of the polymer, fullerene, and solvent. We show that the spinodal liquid-liquid demixing that occurs during drying is responsible for the observed morphologies. The model predicts an increasing feature size and decreasing fullerene concentration in the polymer matrix with increasing drying time in accordance with experimental observations and device performance. The results represent a first step toward a predictive model for morphology formation. © 2013 American Chemical Society

Predicting morphologies of solution processed polymer : fullerene blends

The performance of solution processed polymer:fullerene thin film photovoltaic cells is largely determined by the nanoscopic and mesoscopic morphology of these blends that is formed during the drying of the layer. Although blend morphologies have been studied in detail using a variety of microscopic, spectroscopic, and scattering techniques and a large degree of control has been obtained, the current understanding of the processes involved is limited. Hence, predicting the optimized processing conditions and the corresponding device performance remains a challenge. We present an experimental and modeling study on blends of a small band gap diketopyrrolopyrrole-quinquethiophene alternating copolymer (PDPP5T) and [6,6]-phenyl-C71-butyric acid methyl ester ([70]PCBM) cast from chloroform solution. The model uses the homogeneous Flory–Huggins free energy of the multicomponent blend and accounts for interfacial interactions between (locally) separated phases, based on physical properties of the polymer, fullerene, and solvent. We show that the spinodal liquid–liquid demixing that occurs during drying is responsible for the observed morphologies. The model predicts an increasing feature size and decreasing fullerene concentration in the polymer matrix with increasing drying time in accordance with experimental observations and device performance. The results represent a first step toward a predictive model for morphology formation

Sensing platform based on micro-ring resonator and on-chip reference sensors in SOI

This article presents work on a Silicon-On-Insulator (SOI) compact sensing platform based on Micro Ring Resonators (MRRs). In order to enable correction for variations in environmental conditions (temperature, mechanical stress etc), a study has been performed on the performance of uncoated sensing MRRs, and of SU8- and SiO2-covered reference MRRs. Excellent shielding for both cover materials has been obtained, however, water permeation into the SU8 causes a slow drift in sensor response. We believe that a user-friendly, low-cost and robust way for optical interfacing to MRR sensor chips is required for practical application in Point-Of-Care diagnostics, and that the cost and complexity of optical-electrical read-out systems must decrease. We have taken first steps to realize that vision, by building a prototype free-space optical coupling set-up, which enables non-photonic experts to characterize surface activation processes using MRRs. Moreover, we present our first steps towards on-chip read-out systems. © 2014 SPIE