Standard Quality Control Procedures Research Articles

AAPM Task Group Report 299: Quality control in multi-energy computed tomography.

Multi-energy computed tomography (MECT) offers the opportunity for advanced visualization, detection, and quantification of select elements (e.g., iodine) or materials (e.g., fat) beyond the capability of standard single-energy computed tomography (CT). However, the use of MECT requires careful consideration as substantially different hardware and software approaches have been used by manufacturers, including different sets of user-selected or hidden parameters that affect the performance and radiation dose of MECT. Another important consideration when designing MECT protocols is appreciation of the specific tasks being performed; for instance, differentiating between two different materials or quantifying a specific element. For a given task, it is imperative to consider both the radiation dose and task-specific image quality requirements. Development of a quality control (QC) program is essential to ensure the accuracy and reproducibility of these MECT applications. Although standard QC procedures have been well established for conventional single-energy CT, the substantial differences between single-energy CT and MECT in terms of system implementations, imaging protocols, and clinical tasks warrant QC tests specific to MECT. This task group was therefore charged with developing a systematic QC program designed to meet the needs of MECT applications. In this report, we review the various MECT approaches that are commercially available, including information about hardware implementation, MECT image types, image reconstruction, and postprocessing techniques that are unique to MECT. We address the requirements for MECT phantoms, review representative commercial MECT phantoms, and offer guidance regarding homemade MECT phantoms. We discuss the development of MECT protocols, which must be designed carefully with proper consideration of MECT technology, imaging task, and radiation dose. We then outline specific recommended QC tests in terms of general image quality, radiation dose, differentiation and quantification tasks, and diagnostic and therapeutic applications.

Longevity study of a triple-GEM chamber for the HL-LHC upgrade

As part of the high-luminosity LHC (HL-LHC) upgrade, the CMS muon spectrometer will extend its coverage in the very forward region with triple-GEM detectors. These detectors will cope with a harsh environment with expected background fluxes up to 150 kHz/cm (Sauli, 2016) [2]. At the end of HL-LHC operation, the total accumulated charge at the hottest point is expected to reach 7.9 C/cm (Sauli, 2016) [2]. This accumulated charge is unprecedented for a GEM detector.A full-size triple-GEM chamber was built using the design planned for the most forward CMS muon station using GEM foils produced at CERN. While operated with a gas mixture of Ar/CO2 (70/30)%, the chamber was irradiated with photons from a silver-target X-ray source over 1.5 years to reach an accumulated charge of 8 C/cm2. Before and after irradiation the chamber was validated using the standard quality control procedures; gas gain and energy resolution were measured. During irradiation the gain was monitored weekly. The irradiation was interrupted only for the certification measurements. A non-irradiated sector was monitored for comparison. Temperature and pressure in the lab were continuously measured to derive correction factors to calibrate the gas gain. No degradation in gas gain was observed when reaching 8 C/cm2. Irradiated and non-irradiated chamber components were inspected for potential impacts from irradiation.

The genetic risk architecture of mucosal melanoma.

10595 Background: Mucosal melanoma (MM) is a rare and aggressive subtype of melanoma. Outcomes for MM are significantly worse than for cutaneous melanoma (CM). While somatic mutations induced by UV radiation are known to cause CM, less is known about environmental and genetic alterations associated with MM. High penetrance alleles have been identified in familial cases of CM but the contribution of germline mutations to development of MM is not understood. Further, whilst population-based risk has been elaborated in CM, little is known for MM. The aim of this study is to characterize the germline genetic architecture of MM from high penetrance alleles to patient population genetics. Methods: A large retrospective cohort of MM patients (n=247) seen at MD Anderson Cancer Center were identified. Demographics, primary tumor sites, and presence of somatic mutations in BRAF, NRAS and KIT were extracted. Germline sequencing was performed on PBMC derived genomic DNA from the cohort using a gene panel of 322 major cancer genes. Frequency of identified germline alleles were compared to expected population control rate based on TOPMED using Fisher’s exact test. For genome wide association analysis (GWAS), genotyping will be performed on the MM cohort and the control group using the Infinium Global Screening Array. Cancer-free controls matched 3:1 based on MM cohort demographics have been assembled from existing case-control studies at MD Anderson. Following standard quality control procedures, we will impute variants from TOPMed using the Michigan Imputation Server. SNPtest v2.5.268 software will be utilized to perform association tests, using a multivariate logistic regression model incorporating gender and principal components. In addition to variants that may surpass a genome-wide significance score, we will inspect results for an enrichment of cancer genes. Results: Median age of MM cohort is 63, female predominant (60%), primarily White (84.6%), with gastrointestinal (36%), genitourinary (34%) and head & neck (30%) being the most common MM subtypes. Characteristics of the cohort were representative of the US MM population. Somatic mutations in KIT (26%) were most common. Germline mutations were found in 10.9% of the cohort, with most common detected variations in MITF (c.G952A:p.E318K) (2.4%) at OR of 13.9 (95%CI 5.0, 30.9), and CHEK2 (c.1100delC:p.T367fs) (1.6%) at OR of 16.4 (4.4, 42.9) compared to population control rate. Conclusions: Our study is the first to demonstrate the distribution of germline mutations in the largest cohort of MM patients. The MITF E318K allele is a known risk factor for CM, while CHEK2 1100delC allele has mixed evidence for conferring CM risk. GWAS data are currently being analyzed and these updated results will be presented in the context of the comprehensive analyses of germline risk alleles in MM patients.

Identification of sex‐specific genetic variants associated with tau‐PET

AbstractBackgroundAbnormal tau deposition is an important pathological feature of AD. Important sex differences exist, with women showing greater tau deposition along the AD continuum compared to men. Our group has previously shown sex differences in the genetic risk associated with AD. However, whether specific genetic variants are associated with sex differences in tau aggregation remains unknown. This study aims to identify sex‐specific genetic variants associated with tau deposition.MethodWe included 493 subjects (women n = 246, men n = 247) from the ADNI‐3 study with genotyping data and [18F]Flortaucipir tau PET data. Genetic data underwent standard quality control procedures to remove single nucleotide polymorphisms (SNPs) with more than 5% missingness, failing the Hardy–Weinberg equilibrium test at p = 1 × 10−6 and minor allele frequency < 1%. Participants were all white and included irrespective of clinical diagnosis (CN, MCI and AD). We focused our analysis on genetic variants within 10 genes previously shown to have sex‐dependent effects in AD to reduce the burden of multiple comparisons: BIN1, MS4A6A, DNAJA2, FERMT2, APOC1, APOC1P1, FAM193B, C2orf47, TYW5, CR1. One‐way multivariate analysis of variance (MANOVA) was applied to identify genetic variants associated with tau PET data in three ROIs (composite regions of Braak1, Braak34 and Braak56 stages) in women and men separately. We controlled for age, scanner, amyloid status, APOE ε4 carriership, diagnosis (CN vs MCI vs AD), and the first 20 genetic principal components to adjust for population stratification. Bonferroni correction was applied within each gene based on the number of SNPs tested.ResultTable 1 shows the significant genetic variants associated with tau PET. We identified three novel genetic loci associated with tau deposition specifically in women: DNAJA2 rs79711283, FERMT2 rs113357081 and TYW5rs74614106. In men, three loci within CR1: rs115096248, rs113698814, rs78150633 were found significantly associated with tau burden.ConclusionOur findings discovered sex‐specific genetic variants associated with tau deposition independent of APOE ε4, amyloid and clinical diagnosis. These results provide potential gene targets for understanding the mechanism of sex‐specific tau aggregation and developing sex‐specific gene‐guided precision prevention or therapeutic interventions for AD.

Gamma counting protocols for the accurate quantification of 225Ac and 213Bi without the need for a secular equilibrium between parent and gamma-emitting daughter

BackgroundQuantification of actinium-225 through gamma counter measurements, when there is no secular equilibrium between actinium-225 and its gamma emitting daughters bismuth-213 and/or francium-221, can provide valuable information regarding the possible relocation of recoiled daughters such that related radiotoxicity effects can be evaluated. This study proposes a multiple time-point protocol using the bismuth-213 photopeak with measurements before secular equilibrium between actinium-225 and bismuth-213, and a single time-point protocol using both the francium-221 and bismuth-213 photopeak while assuming secular equilibrium between actinium-225 and francium-221 but not between bismuth-213 and actinium-225.ResultsGood agreement (i.e. 3% accuracy) was obtained when relying on a multiple time-points measurement of bismuth-213 to quantify both actinium-225 and excess of bismuth-213. Following scatter correction, actinium-225 can be accurately quantified using the francium-221 in a single time-point measurement within 3% of accuracy. The analysis performed on the stability data of [225Ac]Ac-DEPA and [225Ac]Ac-DOTA complexes, before secular equilibrium between bismuth-213 and actinium-225 was formed, revealed considerable amounts of unbound bismuth-213 (i.e. more than 90%) after 24 h of the radiolabeling most likely due to the recoiled daughter effect.ConclusionBoth protocols were able to accurately estimate 225Ac-activities provided the francium-221 energy window was corrected for the down scatter of the higher-energy gamma-emissions by bismuth-213. This could prove beneficial to study the recoiled daughter effect and redistribution of free bismuth-213 by monitoring the accumulation or clearance of bismuth-213 in different tissues during biodistribution studies or in patient samples during clinical studies. On the other hand, the single gamma counter measurement protocol, although required a 30 min waiting time, is more time and cost efficient and therefore more appropriate for standardized quality control procedures of 225Ac-labeled radiopharmaceuticals.

Use of multiple polygenic risk scores for distinguishing schizophrenia-spectrum disorder and affective psychosis categories in a first-episode sample; the EU-GEI study.

Schizophrenia (SZ), bipolar disorder (BD) and depression (D) run in families. This susceptibility is partly due to hundreds or thousands of common genetic variants, each conferring a fractional risk. The cumulative effects of the associated variants can be summarised as a polygenic risk score (PRS). Using data from the EUropean Network of national schizophrenia networks studying Gene-Environment Interactions (EU-GEI) first episode case-control study, we aimed to test whether PRSs for three major psychiatric disorders (SZ, BD, D) and for intelligent quotient (IQ) as a neurodevelopmental proxy, can discriminate affective psychosis (AP) from schizophrenia-spectrum disorder (SSD). Participants (842 cases, 1284 controls) from 16 European EU-GEI sites were successfully genotyped following standard quality control procedures. The sample was stratified based on genomic ancestry and analyses were done only on the subsample representing the European population (573 cases, 1005 controls). Using PRS for SZ, BD, D, and IQ built from the latest available summary statistics, we performed simple or multinomial logistic regression models adjusted for 10 principal components for the different clinical comparisons. In case-control comparisons PRS-SZ, PRS-BD and PRS-D distributed differentially across psychotic subcategories. In case-case comparisons, both PRS-SZ [odds ratio (OR) = 0.7, 95% confidence interval (CI) 0.54-0.92] and PRS-D (OR = 1.31, 95% CI 1.06-1.61) differentiated AP from SSD; and within AP categories, only PRS-SZ differentiated BD from psychotic depression (OR = 2.14, 95% CI 1.23-3.74). Combining PRS for severe psychiatric disorders in prediction models for psychosis phenotypes can increase discriminative ability and improve our understanding of these phenotypes. Our results point towards the potential usefulness of PRSs in specific populations such as high-risk or early psychosis phases.

Abstract 13039: Putative Protective Effects Of Caffeine And Its Metabolites On Coronary Heart Disease In The Middle East

Introduction: Protective association between coronary heart disease (CHD) and caffeine intake and its metabolism has been reported. Some of the caffeine’s beneficial actions may be attributed to its direct effect on the endothelial cell, stimulating the production of nitric oxide (NO), as well as its role as an adenosine receptor antagonist. In the Middle East and Gulf region CHD is rampant, and caffeine consumption is also relatively high. The interaction of the two is of interest and will be investigated in this study. Hypothesis: Caffeine is a protective factor for CHD in the Middle East. Methods: The Qatar Cardiovascular Biorepository provided 1,001 CHD patients and the Qatar Biobank provided 2,999 control subjects. Metabolites in the caffeine pathway (KEGG, hsa00232) were quantified and curated via liquid chromatography-mass spectrometry by Metabolon Inc. We then subjected data to standard quality control procedures. Association between metabolite levels and CHD was tested by logistic univariate regression, controlling for age, BMI, and sex. Results: The caffeine KEGG pathway contains 22 compounds. Eleven were present in our cleaned metabolomics panel, and all of them were reduced in CHD patients (Figure 1). Five were significant at P <0.05: caffeine ( P =5.26x10 -3 ), 1,7-dimethyluric acid ( P =2.96x10 -4 ), paraxanthine ( P =8.67x10 -3 ), theobromine ( P =2.33x10 -5 ), and 1-methylxanthine ( P =1.17x10 -2 ). Through pathway enrichment analysis, caffeine metabolism pathway was found to be significantly enriched with an FDR P =4.59x10 -34 and an enrichment ratio of 44.23. Conclusions: The finding of lower levels of caffeine and several of its metabolites in CHD patients in this study suggests a potential protective effect for this stimulant. However, this is a cross-sectional cohort study, so we are observing only association at a slice in time.

A Visual Support of Standard Procedures for Solar Radiation Quality Control

Solar irradiance data from high-quality ground-based measurements are primordial for different solar energy applications. In order to achieve the required accuracy, quality control procedures are of great benefit. A variety of approaches have been proposed. In this sense, some approaches propose a visual representation of the routine, while others only provide a time series of binary flag values, and do not propose any specific visualization of the flagged data as opposed to non-flagged ones. In this regard, the present paper puts forward a complete routine including several quality control procedures for solar irradiance measurements by providing visual support for these different approaches. The visual tool in question was validated using five years research data with 10 minutes resolution of the global, diffuse and direct components of solar irradiation collected from three ground-based weather stations in Morocco. This visual tool puts forth a more precise idea of the measurement quality by detecting various errors, such as time shifts, outliers identification; either with one or two components, or consistency tests between the three components of solar radiation when available. The proposed tool can be regarded as a means of improving the detection rate of abnormal data as a first step in diagnosing the prominent causes of error.

DNA methylation mediates the effect of maternal smoking on offspring birthweight: a birth cohort study of multi-ethnic US mother\u2013newborn pairs

BackgroundMaternal smoking affects more than half a million pregnancies each year in the US and is known to result in fetal growth restriction as measured by lower birthweight and its associated long-term consequences. Maternal smoking also has been linked to altered fetal DNA methylation (DNAm). However, what remains largely unexplored is whether these DNAm alterations are merely markers of smoking exposure or if they also have implications for health outcomes. This study tested the hypothesis that fetal DNAm mediates the effect of maternal smoking on newborn birthweight.MethodsThis study included mother–newborn pairs from a US predominantly urban, low-income multi-ethnic birth cohort. DNAm in cord blood were determined using the Illumina Infinium MethylationEPIC BeadChip. After standard quality control and normalization procedures, an epigenome-wide association study (EWAS) of maternal smoking was performed using linear regression models, controlling for maternal age, education, race, parity, pre-pregnancy body mass index, alcohol consumption, gestational age, maternal pregestational/gestational diabetes, child sex, cord blood cell compositions and batch effects. To quantify the degree to which cord DNAm mediates the smoking-birthweight association, the VanderWeele-Vansteelandt approach for single mediator and structural equational model for multiple mediators were used, adjusting for pertinent covariates.ResultsThe study included 954 mother–newborn pairs. Among mothers, 165 (17.3%) ever smoked before or during pregnancy. Newborns with smoking exposure had on average 258 g lower birthweight than newborns without exposure (P < 0.001). Using a false discovery rate (FDR) < 0.05 as the significance cutoff, the EWAS identified 38 differentially methylated CpG sites associated with maternal smoking. Of those, 17 CpG sites were mapped to previously reported genes: GFI1, AHRR, CYP1A1, and CNTNAP2; 8 of those, located in the first three genes, were Bonferroni significantly associated with newborn birthweight and mediated the smoking-birthweight association. The combined mediation effect of the three genes explained 67.8% of the smoking-birthweight association.ConclusionsOur study not only lends further support that maternal smoking alters fetal DNAm in a multiethnic population, but also suggests that fetal DNAm substantially mediates the maternal smoking–birthweight association. Our findings, if further validated, indicate that DNAm modification is likely an important pathway by which maternal smoking impairs fetal growth and, perhaps, even long-term health outcomes.

Identification of a novel genetic locus associated with immune-mediated thrombotic thrombocytopenic purpura.

Immune thrombotic thrombocytopenic purpura (iTTP) is an ultra-rare, life-threatening disorder, mediated through severe ADAMTS13 deficiency causing multi-system micro-thrombi formation, and has specific human leukocyte antigen associations. We undertook a large genome-wide association study to investigate additional genetically distinct associations in iTTP. We compared two iTTP patient cohorts with controls, following standardized genome-wide quality control procedures for single-nucleotide polymorphisms and imputed HLA types. Associations were functionally investigated using expression quantitative trait loci (eQTL), and motif binding prediction software. Independent associations consistent with previous findings in iTTP were detected at the HLA locus and in addition a novel association was detected on chromosome 3 (rs9884090, P=5.22x10-10, odds ratio 0.40) in the UK discovery cohort. Meta-analysis, including the French replication cohort, strengthened the associations. The haploblock containing rs9884090 is associated with reduced protein O-glycosyltransferase 1 (POGLUT1) expression (eQTL P<0.05), and functional annotation suggested a potential causative variant (rs71767581). This work implicates POGLUT1 in iTTP pathophysiology and suggests altered post-translational modification of its targets may influence disease susceptibility.

Genome-wide association study of patients with a severe major depressive episode treated with electroconvulsive therapy

Although large genome-wide association studies (GWAS) of major depressive disorder (MDD) have identified many significant loci, the SNP-based heritability remains notably low, which might be due to etiological heterogeneity in existing samples. Here, we test the utility of targeting the severe end of the MDD spectrum through genome-wide SNP genotyping of 2725 cases who received electroconvulsive therapy (ECT) for a major depressive episode (MDE) and 4035 controls. A subset of cases (n = 1796) met a narrow case definition (MDE occurring in the context of MDD). Standard GWAS quality control procedures and imputation were conducted. SNP heritability and genetic correlations with other traits were estimated using linkage disequilibrium score regression. Results were compared with MDD cases of mild-moderate severity receiving internet-based cognitive behavioral therapy (iCBT) and summary results from the Psychiatric Genomics Consortium (PGC). The SNP-based heritability was estimated at 29–34% (SE: 6%) for the narrow case definition, considerably higher than the 6.5–8.0% estimate in the most recent PGC MDD study. Our severe MDE cases had smaller genetic correlations with neurodevelopmental disorders and neuroticism than PGC MDD cases but higher genetic risk scores for bipolar disorder than iCBT MDD cases. One genome-wide significant locus was identified (rs114583506, P = 5e−8) in an intron of HLA-B in the major histocompatibility locus on chr6. These results indicate that individuals receiving ECT for an MDE have higher burden of common variant risk loci than individuals with mild-moderate MDD. Furthermore, severe MDE shows stronger relations with other severe adult-onset psychiatric disorders but weaker relations with personality and stress-related traits than mild-moderate MDD. These findings suggest a different genetic architecture at the severest end of the spectrum, and support further study of the severest MDD cases as an extreme phenotype approach to understand the etiology of MDD.

A likelihood ratio approach for identifying three-quarter siblings in genetic databases

The detection of family relationships in genetic databases is of interest in various scientific disciplines such as genetic epidemiology, population and conservation genetics, forensic science, and genealogical research. Nowadays, screening genetic databases for related individuals forms an important aspect of standard quality control procedures. Relatedness research is usually based on an allele sharing analysis of identity by state (IBS) or identity by descent (IBD) alleles. Existing IBS/IBD methods mainly aim to identify first-degree relationships (parent–offspring or full siblings) and second degree (half-siblings, avuncular, or grandparent–grandchild) pairs. Little attention has been paid to the detection of in-between first and second-degree relationships such as three-quarter siblings (3/4S) who share fewer alleles than first-degree relationships but more alleles than second-degree relationships. With the progressively increasing sample sizes used in genetic research, it becomes more likely that such relationships are present in the database under study. In this paper, we extend existing likelihood ratio (LR) methodology to accurately infer the existence of 3/4S, distinguishing them from full siblings and second-degree relatives. We use bootstrap confidence intervals to express uncertainty in the LRs. Our proposal accounts for linkage disequilibrium (LD) by using marker pruning, and we validate our methodology with a pedigree-based simulation study accounting for both LD and recombination. An empirical genome-wide array data set from the GCAT Genomes for Life cohort project is used to illustrate the method.

The Quality Assurance and Quality Control Protocol for Neuropsychological Data Collection and Curation in the Ontario Neurodegenerative Disease Research Initiative (ONDRI) Study.

As large research initiatives designed to generate big data on clinical cohorts become more common, there is an increasing need to establish standard quality assurance (QA; preventing errors) and quality control (QC; identifying and correcting errors) procedures for critical outcome measures. The present article describes the QA and QC approach developed and implemented for the neuropsychology data collected as part of the Ontario Neurodegenerative Disease Research Initiative study. We report on the efficacy of our approach and provide data quality metrics. Our findings demonstrate that even with a comprehensive QA protocol, the proportion of data errors still can be high. Additionally, we show that several widely used neuropsychological measures are particularly susceptible to error. These findings highlight the need for large research programs to put into place active, comprehensive, and separate QA and QC procedures before, during, and after protocol deployment. Detailed recommendations and considerations for future studies are provided.

Genome-wide association study of panic disorder reveals genetic overlap with neuroticism and depression.

Panic disorder (PD) has a lifetime prevalence of 2-4% and heritability estimates of 40%. The contributory genetic variants remain largely unknown, with few and inconsistent loci having been reported. The present report describes the largest genome-wide association study (GWAS) of PD to date comprising genome-wide genotype data of 2248 clinically well-characterized PD patients and 7992 ethnically matched controls. The samples originated from four European countries (Denmark, Estonia, Germany, and Sweden). Standard GWAS quality control procedures were conducted on each individual dataset, and imputation was performed using the 1000 Genomes Project reference panel. A meta-analysis was then performed using the Ricopili pipeline. No genome-wide significant locus was identified. Leave-one-out analyses generated highly significant polygenic risk scores (PRS) (explained variance of up to 2.6%). Linkage disequilibrium (LD) score regression analysis of the GWAS data showed that the estimated heritability for PD was 28.0-34.2%. After correction for multiple testing, a significant genetic correlation was found between PD and major depressive disorder, depressive symptoms, and neuroticism. A total of 255 single-nucleotide polymorphisms (SNPs) with p < 1 × 10-4 were followed up in an independent sample of 2408 PD patients and 228,470 controls from Denmark, Iceland and the Netherlands. In the combined analysis, SNP rs144783209 showed the strongest association with PD (pcomb = 3.10 × 10-7). Sign tests revealed a significant enrichment of SNPs with a discovery p-value of <0.0001 in the combined follow up cohort (p = 0.048). The present integrative analysis represents a major step towards the elucidation of the genetic susceptibility to PD.

Familial Alzheimer\u2019s Disease and Recessive Modifiers

Alzheimer’s disease (AD) is progressive brain disorder that affects ~ 50 million people worldwide and has no current effective treatment. AD age of onset (ADAOO) has shown to be critical for the identification of genes that modify the appearance of AD signs and symptoms in a specific population. We clinically characterized and whole-exome genotyped 71 individuals with AD from the Paisa genetic isolate, segregating the (PSEN1) E280A dominant fully penetrant mutation, and analyzed the potential recessive effects of ~ 50,000 common functional genomic variants to the ADAOO. Standard quality control and filtering procedures were applied, and recessive single- and multi-locus linear mixed-effects models were used. We identified genetic variants in the SLC9C1, CSN1S1, and LOXL4 acting recessively to delay ADAOO up to ~ 11, ~ 6, and ~ 9 years on average, respectively. In contrast, the CC recessive genotype in marker DHRS4L2-rs2273946 accelerates ADAOO by ~ 8 years. This study, reports new recessive variants modifying ADAOO in PSEN1 E280A mutation carriers. This set of genes are implicated in important biological processes and molecular functions commonly affected by genes associated with the etiology of AD such as APP, APOE, and CLU. Future functional studies using modern techniques such as induced pluripotent stem cells will allow a better understanding of the over expression and down regulation of these recessive modifier variants and hence the pathogenesis of AD. These results are important for prediction of AD and ultimately, substantial to develop new therapeutic strategies for individuals at risk or affected by AD.

Genome-Wide Association Study of Panic Disorder

BackgroundPanic Disorder (PD) is one of the most common anxiety disorders with a lifetime prevalence of about 4%. The disorder is characterized by recurrent episodes of abrupt intense fear accompanied by additional physiological or cognitive symptoms. Although PD shows moderate heritability estimates of 30-54%, the genetic variants contributing to PD are largely unknown, with only few and inconsistent loci reported to date. To address the challenge of underpowered individual studies, we conducted the largest genome-wide association study of PD to date comprising more than 9,900 individuals. MethodsIn our study, we generated genome-wide SNP data from 2,147 clinically well-characterized patients with PD and 7,760 ethnically matched controls. The samples originate from four different European countries (Denmark, Estonia, Germany and Sweden). Standard GWAS quality control procedures were performed on each dataset individually. Imputation was performed using the 1000 Genomes Project reference panel. Then a meta-analysis was performed using the Ricopili pipeline (https://sites.google.com/a/broadinstitute.org/ricopili/). ResultsIn our meta-analysis, we did not identify any genome-wide significant locus. 36 linkage disequilibrium independent SNPs had a p-value < 1e-05. Leave-one-out analyses demonstrated highly significant polygenetic risk scores with an explained variance of up to 3%. Using the recently published LD Score regression method on our GWAS data the estimated heritability for PD was 0.2923. DiscussionIn this collaborative study with sample sizes being larger than any other PD GWAS published to date, we did not identify any genome-wide significant locus. However, our PD meta-analysis shows highly similar characteristics as similar sized GWAS previously conducted in schizophrenia. LD Score regression analysis provides the first SNP-based heritability estimate for PD based on genotype data of more than 9,900 individuals. Replication of our top findings in independent European datasets as well as further pathway analyses are currently underway and will be presented.

DNA Repair Genes May Influence Cognitive Outcomes in Adult Patients with Hematologic Malignancies (HM) Treated with Blood or Marrow Transplantation (BMT)

Introduction: We recently demonstrated that cognitive impairment (CI) is prevalent and persistent in HM patients treated with BMT (Sharafeldin et al., J Clin Oncol, 2018). While the impact of genetic factors on cognition in the non-oncology realm is well-recognized, limited information exists in HM patients treated with BMT. We tested the hypothesis that genetic variants in blood-brain barrier (BBB), drug transporter, telomere homeostasis, neurotransmission, neural repair and DNA repair are associated with CI in HM patients treated with BMT. We previously presented preliminary results of the Discovery cohort (Sharafeldin et al., Blood, 2016); here we present additional analyses (at the gene level) on the Discovery cohort, and replication of salient findings in an independent Validation cohort.Methods: The Discovery cohort consisted of prospective, longitudinally-assessed patients undergoing autologous or allogeneic BMT for HM at a single center. Cognitive function was assessed objectively using a battery of standardized tests prior to BMT, and at 6mo, 1y, 2y, and 3y post-BMT; germline DNA was collected pre-BMT. Global Deficit Score (GDS) was used as an indicator of CI (GDS ≥0.5 indicated CI). We employed a candidate gene approach, relying on biologically-plausible hypotheses for gene selection. Standard quality control procedures yielded 985 SNPs in 68 genes with a total genotyping call rate of 99% in 277 BMT recipients. Generalized estimating equation models were fitted to examine association of individual SNPs with CI. Linkage disequilibrium-based pruning yielded 326 independent tests, with an overall p-value threshold of 1.53x10-4 using Bonferroni correction for multiple testing. We also conducted gene-level analysis considering each gene as a SNP-set using the machine learning approach of logic regression, with cross-validation, to identify SNP-SNP interactions at the gene-level (Bonferroni p ≤ 7.94x10-4). An independent Validation case-control set from the BMT Survivor Study was used to replicate significant findings from the Discovery cohort, using conditional logistic regression models. Cases (n=141) were BMT survivors who reported: i) presence of memory/learning problems; and ii) severity of memory/learning problems. Controls (n=258) were BMT survivors without cognitive problems, matched (1-2/case) on race/ethnicity, HM, and time from BMT.Results:Discovery: Among the 277 patients in the Discovery cohort, mean age at BMT was 50y, 59% were males, 69% were non-Hispanic whites and 47% received an allogeneic BMT. Male sex (OR=3.2, 95%CI, 1.5-6.7, p=0.002) and lower pre-BMT cognitive reserve (OR=4.6, 95%CI, 2.2-9.6, p <0.0001) were associated with CI. Risk of CI was increased in the younger patients (<50y) if they received TBI (age*TBI interaction OR=3.86, 95%CI, 1.0-15.1, p=0.05). Final genetic models were adjusted for relevant variables with significant independent main effects including BMT type, age at BMT, sex, race/ethnicity, and cognitive reserve. We identified significant associations between CI and BBB, telomere homeostasis and DNA repair SNPs using the single-SNP (Fig 1) and gene-level analyses. Replication: The mean age at BMT was 44y, 54% were males, 88% were non-Hispanic whites and 5% received an allogeneic BMT. Replication models were adjusted for age at BMT, sex, race, and education and income levels. Of the 69 SNPs identified for replication, DNA repair SNPs from the single-SNP analysis rs13006837 on XRCC5 (OR=5.8, 95%CI, 2.7-12.3, p=2.0 x 10-5) and rs293796 on OGG1 gene (OR=11.4, 95%CI, 4.6-28.5, p-value=1.08 x 10-6) were successfully replicated. Five SNPs on DNA repair genes from the gene-level analysis showed individual statistically-significant associations in the Validation cohort: rs238417 on ERCC2 (OR=0.48, 95%CI, 0.25-0.91, p=0.03); rs2526698 on EXO1 (OR=0.57, 95%CI: 0.33-0.98, p=0·04); rs3793906 on MGMT (OR=1.96, 95%CI: 1.2-3.3, p=0.01); rs4725016 on RPA3 (OR=0.20, 95%CI, 0.05-0.92, p=0.04); and rs1479569 on XRCC4 (OR=2.3, 95%CI, 1.3-4.1, p=0.005).Conclusion: Our study provides genetic characterization of adult HM patients at increased risk of cognitive impairment following BMT; associations with DNA repair variants were independently replicated. These findings could have implications towards the personalized management of patients undergoing BMT. DisclosuresForman:Mustang Therapeutics: Other: Licensing Agreement, Patents & Royalties, Research Funding.

Targeting Neuroplasticity, Cardiovascular, and Cognitive-Associated Genomic Variants in Familial Alzheimer\u2019s Disease

The identification of novel genetic variants contributing to the widespread in the age of onset (AOO) of Alzheimer’s disease (AD) could aid in the prognosis and/or development of new therapeutic strategies focused on early interventions. We recruited 78 individuals with AD from the Paisa genetic isolate in Antioquia, Colombia. These individuals belong to the world largest multigenerational and extended pedigree segregating AD as a consequence of a dominant fully penetrant mutation in the PSEN1 gene and exhibit an AOO ranging from the early 1930s to the late 1970s. To shed light on the genetic underpinning that could explain the large spread of the age of onset (AOO) of AD, 64 single nucleotide polymorphisms (SNP) associated with neuroanatomical, cardiovascular, and cognitive measures in AD were genotyped. Standard quality control and filtering procedures were applied, and single- and multi-locus linear mixed-effects models were used to identify AOO-associated SNPs. A full two-locus interaction model was fitted to define how identified SNPs interact to modulate AOO. We identified two key epistatic interactions between the APOE*E2 allele and SNPs ASTN2-rs7852878 and SNTG1-rs16914781 that delay AOO by up to ~ 8 years (95% CI 3.2–12.7, P = 1.83 × 10−3) and ~ 7.6 years (95% CI 3.3–11.8, P = 8.69 × 10−4), respectively, and validated our previous finding indicating that APOE*E2 delays AOO of AD in PSEN1 E280 mutation carriers. This new evidence involving APOE*E2 as an AOO delayer could be used for developing precision medicine approaches and predictive genomics models to potentially determine AOO in individuals genetically predisposed to AD.

Placental DNA Methylation of miR-548 and WWTR1 Genes Influence Insulin Sensitivity during Pregnancy

Insulin sensitivity decrease in pregnancy is a physiologic adaptation to derive nutrients for the growing fetus. The placenta has a major role in this phenomenon, but exact mechanisms remain unknown. A better understanding of the placental role in maternal insulin sensitivity regulation could help us reveal pathophysiologic pathways of gestational diabetes. We tested associations between insulin sensitivity and DNA methylation (DNAm) across the genome in 439 placenta samples from our prospective cohort Gen3G using Illumina EPIC arrays. Women were recruited at 1st trimester of pregnancy and performed a 2-hour 75g oral glucose tolerance test (OGTT) at 24-28 weeks: we measured glucose and insulin levels at each OGTT point to calculate Matsuda insulin sensitivity index. We applied standard quality control procedures for DNAm arrays analyses and adjusted for technical batch effects. We tested 720,077 individual CpGs using robust linear regression on M-values (adjusted for maternal age, BMI, smoking, parity, gestational age at birth, and child sex) and used Bonferroni to account for multiple testing. We found that maternal insulin sensitivity was associated with DNAm in placenta at 318 CpGs across the genome (P&amp;lt;6.94 x10-8). Among these, we found differentially methylated CpGs at loci well known for their role in diabetes (TCF7L2, SPRY2), brown adipose tissue regulation (PRDM16), and near the Prolactin Receptor. Mendelian Randomization (MR) analyses supported that placental DNAm causally influence maternal insulin sensitivity at 28 CpGs (P&amp;lt;0.05). Among these, our two strongest MR associations (FDR adjusted P&amp;lt;0.05) pointed at CpGs near miR-548 (P=5.6x10-5) and WWTR1 (P=9.8x10-5), a gene implicated in PPARalpha regulation and previously associated with preeclampsia. Our findings highlight the role of placenta epigenetic regulation in insulin sensitivity during pregnancy and reveal novel potential biologic targets implicated in gestational metabolic disorders. Disclosure M. Hivert: None. C.M. Briggs: None. A. Cardenas: None. P. Perron: Research Support; Self; Merck &amp; Co., Inc., Pfizer Inc., Novo Nordisk Inc.. Speaker's Bureau; Self; Sanofi. Research Support; Self; AstraZeneca. L. Bouchard: None.

Effects of Reheating Procedure and Oven Type on Performance Testing Results of Asphalt Mixtures

Reheating and oven-aging procedures of plant-produced asphalt mixtures in laboratories are important topics to consider as performance testing of mixtures becomes more popular among agencies. Differences between laboratory equipment and procedure could significantly affect performance properties. The objective of this study is to investigate the influence of sample size, oven type, and variation in reheating/aging temperatures on the results of two performance tests on plant-produced mixtures. A selected mixture was tested for volumetric properties and performance using Hamburg wheel-tracking (HWT) and semi-circular bending (SCB-IFIT) tests. Results show that reheating mixtures uncovered and in smaller containers could significantly reduce the time to achieve aging temperature, and could make the process more efficient and consistent. In addition, aging using three different oven types showed that temperature within ovens can vary significantly depending on the location of the sample inside the oven, which affects the time required to reach the target temperature, and thus may also influence the aging of the sample. The mixture volumetric properties show that the effect of various heating conditions is marginal. Using the developed reheating/aging procedure of this study, the results of the HWT and SCB-IFIT tests showed no substantial effect of oven type on rutting and cracking resistance. The overall results indicate that there is a need to standardize the conditions of reheating, sample geometry, and to verify uniformity of temperature in ovens. Such standardization can further reduce variability and thus should be part of the AASHTO/ASTM standard procedures for quality control, or of laboratory equipment calibration procedures.