P-value Threshold Research Articles

A genome-wide association study identifies novel genetic loci associated with pulmonary embolism

Abstract Background Pulmonary embolism (PE) is a life-threatening cardiovascular condition. Studies showed that PE patients were associated with disorders of lipid metabolism and had higher triglyceride and lower HDL-C levels compared with healthy. We conducted the genome-wide association study to identify novel loci contributing to PE. Methods We conducted a large-scale GWAS of PE in 5,466 PE cases and 461,219 controls of European ancestry from the UK Biobank (466,685 participants total). We used genome-wide summary statistics to test for enrichment of functional annotations using ENRICHR. Example pathways included in Enrichr for testing include membership of genes in pathway databases such as the Kyoto Encyclopedia of Genes and Genomes (KEGG), Wikipathway, PANTHER, BioCarta or NCI-Nature pathways. We analyzed the pathways using combined score and p-values which were well validated by comparing to several methods. For pathway analyses, we considered a nominal P-value threshold of 0.05. Results We identified genome-wide significant genetic associations in 63 independent genetic loci for PE (P<5.0x10–7). Our findings for top pathways highlight that lipid metabolism (LIPC, LCAT, NPC2), caffeine metabolism (NAT2), and sudden cardiac death (ABCG8) related genetic loci play an important role in PE alongside genes already associated with coagulation-thrombosis pathway (VWF, THPO, PTPN11, INPP5D, UROS, HMBS) (all p-values p-values <0.05). Conclusion Our findings uncovered unexpected novel factors of PE etiology, suggesting novel mechanistic concepts of PE pathophysiology. Funding Acknowledgement Type of funding source: None

Artificial Image Objects for Classification of Schizophrenia with GWAS Selected SNVs and Convolutional Neural Network

Genome wide association studies (GWASs) had identified a large number of variants associated with schizophrenia. We proposed a new approach that considered individual variants as pixels and transformed a collection of variants into an artificial image object (AIO), which could be classified as regular image using advanced artificial intelligence algorithms such as convolutional neural networks (CNN). We selected two sets of SNVs by GWAS P-value threshold (≤ 5e-5), LD pruning and minor allele frequency (≥ 0.05) to create AIOs for the subjects in the MGS, SCCSS and CATIE datasets, and evaluated their performances using the binary diagnosis and a polygenic risk score (PRS) stratified 3 class phenotype. Trained with the combined MGS and SCCSS dataset, Set I SNVs, which consisted of 4,096 SNVs with pair-wise LD < 0.5, the CNN models achieved an accuracy of 0.678 ± 0.007 and an AUC of 0.738 ± 0.008 for the CATIE dataset for the diagnosis phenotype. Set II SNVs, which consisted of 44,100 SNVs with minor allele frequency ≥ 0.05, had similar performances (accuracy 0.685 ± 0.021; AUC 0.708 ± 0.030) for the same phenotype. The AIO approach performed about 10% better than PRS models that used the markers from the same GWAS P-value threshold. For the PRS stratified classes, Classes I and III were defined by the PRSmean ± 0.25 sd respectively. While the average performance for the 3 classes was similar to the diagnostic phenotype, the class specific performances for Classes I and III were much better (Set II SNVs, accuracy 0.806 ± 0.032 and 0.820 ± 0.049, and AUC 0.930 ± 0.017 and 0.867 ± 0.040 for Classes I and III respectively). These results suggested that if we could define schizophrenia with objective measures such as PRS, we would be able to predict schizophrenia with good confidence. Overall, we demonstrated that by transforming SNVs into AIOs and applying CNN algorithms, we could classify schizophrenia patients and controls with reasonable accuracy, opening a new window for using GWAS identified risk variants for risk assessment and diagnosis.

Factors Associated with Early Termination of Palliative Radiotherapy in a Hospitalized Patient Cohort

Patients receiving inpatient palliative radiotherapy (RT) for symptomatic metastases may not complete their treatment course, often due to declining functional status. Established tools estimating life expectancy have variable success in assessing whether patients are likely to complete a course of palliative RT, especially in a hospitalized setting where patients have other acute medical concerns. We report on a retrospective analysis of hospitalized patients initiated on palliative RT to determine predictive factors associated with early treatment termination. A retrospective analysis of 76 consecutive inpatient palliative RT treatments from August 2017 to September 2019 at a single academic institution was performed. Baseline characteristics including age, sex, Eastern Cooperative Oncology Group (ECOG) performance status, cancer diagnosis, and RT site were recorded. Treatment features reviewed included hospitalized days prior to consultation, time from consultation to treatment delivery, and delays (defined as 1+ hour from planned simulation/treatment). Univariable logistic regression was used to determine whether any variables were associated with incomplete treatment delivery. The Benjamini-Hochberg correction method was used to control for the false discovery rate (FDR) with an adjusted p-value threshold of 0.20 to address the multiple testing issue. Median age of the cohort was 61 years (interquartile range (IQR) 45-71). 74% and 26% of patients were ECOG 1-2 and 3-4, respectively. 80% completed treatment, while 20% did not complete palliative RT. Of those who terminated RT early, a median of 10 (IQR 10-12) fractions were planned, but a median of 4 (IQR 2-4) fractions were ultimately delivered. 9 of 15 (60%) patients who terminated RT early either rapidly declined in performance status or electively stopped to transition to hospice. Of the factors evaluated, only increased time from consultation to first treatment (odds ratio 1.01, unadjusted p = 0.02, adjusted p = 0.16) was significantly associated with early RT termination. Median time from consultation to first treatment was 2.9 (IQR 1.2 – 6.0) days. Patients who terminated RT early died after median of 23 (IQR 13–33) days from initial consultation. A fifth of hospitalized patients were unable to complete palliative RT, the majority of whom rapidly declined in ECOG status and/or transitioned to hospice. Increased time from consultation to initial treatment was related to early RT cessation, potentially due to ongoing deliberations about whether to initiate RT, or due to acute complications impacting medical stability for treatment. Implementing earlier goals-of-care discussions and prioritizing shorter fractionation schema would be helpful at reducing the number of initiated RT courses which are not completed, as these treatments have low therapeutic potential.

Obesity and ADHD: Exploring the role of body composition, BMI polygenic risk score, and reward system genes

The association between obesity and attention-deficit hyperactivity disorder (ADHD) has been extensively reported in the literature. However, the potential mechanisms underlying this association are not completely understood. This study aimed to evaluate the association between body composition and ADHD and explore the possible genetic mechanisms involved. We used data from the 1982 Pelotas (Brazil) Birth Cohort at age 30-year follow-up (N = 3630). We first used logistic regression analysis to test whether body mass index (BMI), fat mass (FM), and fat-free mass (FFM) were associated with ADHD. We further tested the association between BMI polygenic risk score (BMI-PRS) and ADHD and the role of the genes upregulated in the reward system using a gene-set association approach. BMI (odds ratio [OR] = 1.05; 95% confidence interval [CI], 1.00–1.09; p = 0.038) and FM (OR = 1.04; 95% CI, 1.00–1.07; p = 0.043) were associated with ADHD. The BMI-PRS was associated with ADHD (using p-value threshold (PT) = 0.4; OR = 1.65; 95% CI, 1.02–2.65) at a nominal level. In gene-set analysis, the reward system genes were associated with BMI in subjects with a high BMI-PRS score, considering PT = 0.4 (p = 0.014). The results suggest that BMI genetic components, especially those genes related to the reward system, may be involved in this association.

Interferon Beta-1b and Lopinavir–Ritonavir for Middle East Respiratory Syndrome

BackgroundWhether combined treatment with recombinant interferon beta-1b and lopinavir–ritonavir reduces mortality among patients hospitalized with Middle East respiratory syndrome (MERS) is unclear.MethodsWe conducted a randomized, adaptive, double-blind, placebo-controlled trial that enrolled patients at nine sites in Saudi Arabia. Hospitalized adults with laboratory-confirmed MERS were randomly assigned to receive recombinant interferon beta-1b plus lopinavir–ritonavir (intervention) or placebo for 14 days. The primary outcome was 90-day all-cause mortality, with a one-sided P-value threshold of 0.025. Prespecified subgroup analyses and safety analyses were conducted. Because of the pandemic of coronavirus disease 2019, the data and safety monitoring board requested an unplanned interim analysis and subsequently recommended the termination of enrollment and the reporting of the results.ResultsA total of 95 patients were enrolled; 43 patients were assigned to the intervention group and 52 to the placebo group. A total of 12 patients (28%) in the intervention group and 23 (44%) in the placebo group died by day 90. The analysis of the primary outcome, with accounting for the adaptive design, yielded a risk difference of −19 percentage points (upper boundary of the 97.5% confidence interval [CI], −3; one-sided P=0.024). In a prespecified subgroup analysis, treatment within 7 days after symptom onset led to lower 90-day mortality than use of placebo (relative risk, 0.19; 95% CI, 0.05 to 0.75), whereas later treatment did not. Serious adverse events occurred in 4 patients (9%) in the intervention group and in 10 (19%) in the placebo group.ConclusionsA combination of recombinant interferon beta-1b and lopinavir–ritonavir led to lower mortality than placebo among patients who had been hospitalized with laboratory-confirmed MERS. The effect was greatest when treatment was started within 7 days after symptom onset. (Funded by the King Abdullah International Medical Research Center; MIRACLE ClinicalTrials.gov number, NCT02845843.)

Genome-wide association study and genomic prediction of Fusarium ear rot resistance in tropical maize germplasm

Fusarium ear rot (FER) is a destructive maize fungal disease worldwide. In this study, three tropical maize populations consisting of 874 inbred lines were used to perform genome-wide association study (GWAS) and genomic prediction (GP) analyses of FER resistance. Broad phenotypic variation and high heritability for FER were observed, although it was highly influenced by large genotype-by-environment interactions. In the 874 inbred lines, GWAS with general linear model (GLM) identified 3034 single-nucleotide polymorphisms (SNPs) significantly associated with FER resistance at the P-value threshold of 1 × 10−5, the average phenotypic variation explained (PVE) by these associations was 3% with a range from 2.33% to 6.92%, and 49 of these associations had PVE values greater than 5%. The GWAS analysis with mixed linear model (MLM) identified 19 significantly associated SNPs at the P-value threshold of 1 × 10−4, the average PVE of these associations was 1.60% with a range from 1.39% to 2.04%. Within each of the three populations, the number of significantly associated SNPs identified by GLM and MLM ranged from 25 to 41, and from 5 to 22, respectively. Overlapping SNP associations across populations were rare. A few stable genomic regions conferring FER resistance were identified, which located in bins 3.04/05, 7.02/04, 9.00/01, 9.04, 9.06/07, and 10.03/04. The genomic regions in bins 9.00/01 and 9.04 are new. GP produced moderate accuracies with genome-wide markers, and relatively high accuracies with SNP associations detected from GWAS. Moderate prediction accuracies were observed when the training and validation sets were closely related. These results implied that FER resistance in maize is controlled by minor QTL with small effects, and highly influenced by the genetic background of the populations studied. Genomic selection (GS) by incorporating SNP associations detected from GWAS is a promising tool for improving FER resistance in maize.

Risk factors for hospital admission in patients undergoing outpatient anterior cruciate ligament reconstruction: A national database study

IntroductionAnterior Cruciate Ligament Reconstructions (ACLR) are routinely performed in an outpatient setting with low 90-day readmission rates (2.3%); however, admissions rates in the immediate perioperative period have been previously reported as high as 13.1%. Despite the surprisingly high number of patients requiring immediate perioperative admission, there has been a lack of recent literature specifically examining the associated risk factors for admission. MethodsUsing the American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) database, a query for patients who underwent ACLR from 2011 through 2018 was performed using Current Procedural Terminology codes. The following concomitant procedures were included: meniscectomy, meniscal repair, diagnostic arthroscopy, loose body removal, synovectomy, chondroplasty, abrasion chondroplasty, drilling for osteochondritis dissecans. Demographics including age, sex, race, body mass index (BMI) and comorbidities were collected. Perioperative factors collected were anesthesia type and operative times. Patient demographic and perioperative data were compared using Fisher's exact test and Pearson's chi-square test. Multivariate logistic regressions were used to calculate odds ratios (OR) and 95% confidence intervals (CI) of independent risk factors for postoperative admission. Holm-Bonferroni method yielded adjusted p-value thresholds for significance. ResultsOf the 20,819 patients undergoing ACLR with and without concomitant procedures, 3.8% of patients were admitted to the hospital in the immediate postoperative period. Following multivariate regression analysis, increased odds of admission were demonstrated with the use of regional anesthesia alone (OR = 2.77, 95%CI: 2.22–3.44; p < 0.001), increasing concurrent procedures (Table 1), and obesity classes II (OR = 1.62, 95%CI: 1.26–2.10; p < 0.001) and III (OR = 1.81, 95%CI: 1.33–2.47; p < 0.001). Subsequent subgroup analysis of the isolated ACLR procedures (N = 9,423) demonstrated a 3.3% postoperative admission rate. Multivariate regressions demonstrated increased odds of admission with regional anesthesia use only (OR = 2.62, 95%CI: 1.90–3.60; p < 0.001), obesity class II (OR = 2.22, 95%CI: 1.51–3.26; p < 0.001), and increasing minutes of operative time (OR = 1.01, 95%CI: 1.01–1.01; p < 0.001). Table 2 demonstrates increasing rates and odds of admission with increasing operative time in hours. ConclusionAnterior Cruciate Ligament Reconstructions are routinely performed in an outpatient setting; nevertheless, a subset of ACLR patients is admitted postoperatively. We found an increased risk of admission with the use of regional anesthesia alone, increasing concurrent procedures and obesity classes II and III. A further understanding of patient risk factors for those undergoing ACLR allows orthopedic surgeons to better develop a preoperative plan and discuss patient expectations, which will lead to more efficient resource allocation and improved patient satisfaction.

Interaction between adverse childhood experiences and polygenic risk in patients with bipolar disorder

The interaction between genes and environment often occurs when they depend on one another. We hypothesized that adverse childhood experiences (ACEs) would interact with genetic predispositions to bipolar disorder (BD), demonstrating earlier age at onset (AAO) and worse clinical outcomes. We aimed to clarify the effects of the interaction between ACEs and genetic susceptibility using polygenic risk score (PRS) on AAO and clinical outcomes. Single nucleotide polymorphisms and clinical data, including ACEs, were obtained from the Bipolar Genomic Study, which contains a large sample of BD participants. A total of 1615 subjects with BD I were obtained and divided into two groups according to the presence or absence of ACEs and an additional four groups based on the number of ACEs (none versus one versus two versus ≥ three types). ACEs was evaluated using the childhood life events scale (CLES). BD–PRS was obtained from the Psychiatric Genomics Consortium, which compared BD patients and healthy controls. The BD–PRS was higher in the group with ACEs than without ACEs at most p-value thresholds. In multivariate linear regression analyses, both groups with more ACEs and higher BD–PRS were independently and interactively associated with an earlier AAO of BD; however, only greater ACEs were associated with worsened clinical outcome. These findings highlight the clinical importance of evaluating ACEs and polygenic risk in research of the etiology of BD.

Polygenic risk for schizophrenia and subcortical brain anatomy in the UK Biobank cohort

Research has shown differences in subcortical brain volumes between participants with schizophrenia and healthy controls. However, none of these differences have been found to associate with schizophrenia polygenic risk. Here, in a large sample (n = 14,701) of unaffected participants from the UK Biobank, we test whether schizophrenia polygenic risk scores (PRS) limited to specific gene-sets predict subcortical brain volumes. We compare associations with schizophrenia PRS at the whole genome level (‘genomic’, including all SNPs associated with the disorder at a p-value threshold < 0.05) with ‘genic’ PRS (based on SNPs in the vicinity of known genes), ‘intergenic’ PRS (based on the remaining SNPs), and genic PRS limited to SNPs within 7 gene-sets previously found to be enriched for genetic association with schizophrenia (‘abnormal behaviour,’ ‘abnormal long-term potentiation,’ ‘abnormal nervous system electrophysiology,’ ‘FMRP targets,’ ‘5HT2C channels,’ ‘CaV2 channels’ and ‘loss-of-function intolerant genes’). We observe a negative association between the ‘abnormal behaviour’ gene-set PRS and volume of the right thalamus that survived correction for multiple testing (ß = −0.031, pFDR = 0.005) and was robust to different schizophrenia PRS p-value thresholds. In contrast, the only association with genomic PRS surviving correction for multiple testing was for right pallidum, which was observed using a schizophrenia PRS p-value threshold < 0.01 (ß = −0.032, p = 0.0003, pFDR = 0.02), but not when using other PRS P-value thresholds. We conclude that schizophrenia PRS limited to functional gene sets may provide a better means of capturing differences in subcortical brain volume than whole genome PRS approaches.

Early Childhood General Anesthesia and Neurodevelopmental Outcomes in the Avon Longitudinal Study of Parents and Children Birth Cohort.

Most common anesthetic agents have been implicated in causing neurodegeneration in the developing animal brain, leading to warnings regarding their use in children. The hypothesis of this study was that exposure to general anesthesia and surgery before 4 yr would associate with adverse neurodevelopmental outcomes at age 7 to 16 yr. This cohort study comprised 13,433 children enrolled in the Avon Longitudinal Study of Parents and Children, a prospective, population-based birth cohort born between 1991 and 1993 in southwest England. Children were grouped by none, single, or multiple exposures to general anesthesia and surgery by 4 yr. Motor, cognitive, linguistic, educational, social, and behavioral developmental outcomes were evaluated at 7 to 16 yr using school examination results, validated parent/teacher questionnaires, or clinic assessments. Continuous outcomes were z-scored. P-value thresholds were corrected using false discovery rate procedures. This study compared 46 neurodevelopmental outcomes in 13,433 children: 8.3% (1,110) exposed singly and 1.6% (212) exposed multiply to general anesthesia and surgery. Of these, the following reached predefined levels of statistical significance (corrected P < 0.00652): dynamic balance scores were 0.3 SD (95% CI, 0.1, 0.5; P < 0.001) lower in multiply exposed children; manual dexterity performance was 0.1 SD (95% CI, 0.0, 0.2; P = 0.006) lower in singly and 0.3 SD (95% CI, 0.1, 0.4; P < 0.001) lower in multiply exposed children; and social communication scores were 0.1 SD (95% CI, 0.0, 0.2; P = 0.001) and 0.4 SD (95% CI, 0.3, 0.5; P < 0.001) lower in singly and multiply exposed children, respectively. General anesthesia and surgery were not associated with impairments in the remaining neurodevelopmental measures including: general cognitive ability; attention; working memory; reading, spelling, verbal comprehension and expression; behavioral difficulties; or national English, mathematics, and science assessments (all ≤0.1 SD; corrected P ≥ 0.00652). Early childhood general anesthesia and surgery were not associated with a global picture of clinically and statistically significant neurodegenerative effects, providing reassurance about the neurotoxic potential of general anesthesia. Exposure to anesthesia and surgery was associated with significantly lower motor and social linguistic performance.

The polygenic risk for obsessive-compulsive disorder is associated with the personality trait harm avoidance.

Obsessive-compulsive disorder (OCD) is a complex psychiatric disorder with a substantial genetic contribution. While the specific variants underlying OCD's heritability are still unknown, findings from genome-wide association studies (GWAS) corroborate the importance of common SNPs explaining the phenotypic variance in OCD. Investigating associations between the genetic liability for OCD, as reflected by a polygenic risk score (PRS), and potential endophenotypes of the disorder, such as the personality trait harm avoidance, may aid the understanding of functional pathways from genes to diagnostic phenotypes. We derived PRS for OCD at several P-value thresholds based on the latest Psychiatric Genomics Consortium OCD GWAS (2688 cases, 7037 controls) in an independent sample of OCD patients (n=180), their unaffected first-degree relatives (n=108) and healthy controls (n=200). Using linear regression, we tested whether these PRS are associated with the personality trait harm avoidance. Results showed that OCD PRS significantly predicted OCD status, with patients having the highest scores and relatives having intermediate scores. Furthermore, the genetic risk for OCD was associated with harm avoidance across the entire sample, and among OCD patients. As indicated by mediation analyses, harm avoidance mediated the association between the OCD PRS and OCD caseness. These results were observed at multiple P-value thresholds and persisted after the exclusion of patients with a current comorbid major depressive or anxiety disorder. Our findings support the polygenic nature of OCD and further validate harm avoidance as a candidate endophenotype and diathesis of OCD.

Polygenic risk score analysis revealed shared genetic background in attention deficit hyperactivity disorder and narcolepsy

Attention deficit hyperactive disorder (ADHD) is a highly heritable neurodevelopmental disorder, and excessive daytime sleepiness is frequently observed in ADHD patients. Excessive daytime sleepiness is also a core symptom of narcolepsy and essential hypersomnia (EHS), which are also heritable conditions. Psychostimulants are effective for the symptomatic control of ADHD (primary recommended intervention) and the two sleep disorders (frequent off-label use). However, the common biological mechanism for these disorders has not been well understood. Using a previously collected genome-wide association study of narcolepsy and EHS, we calculated polygenic risk scores (PRS) for each individual. We investigated a possible genetic association between ADHD and narcolepsy traits in the Hamamatsu Birth Cohort for mothers and children (HBC study) (n = 876). Gene-set enrichment analyses were used to identify common pathways underlying these disorders. Narcolepsy PRS were significantly associated with ADHD traits both in the hyperactivity domain (e.g., P-value threshold < 0.05, β [SE], 5.815 [1.774]; P = 0.002) and inattention domain (e.g., P-value threshold < 0.05, β [SE], 5.734 [1.761]; P = 0.004). However, EHS PRS was not significantly associated with either domain of ADHD traits. Gene-set enrichment analyses revealed that pathways related to dopaminergic signaling, immune systems, iron metabolism, and glial cell function involved in both ADHD and narcolepsy. Findings indicate that ADHD and narcolepsy are genetically related, and there are possible common underlying biological mechanisms for this relationship. Future studies replicating these findings would be warranted to elucidate the genetic vulnerability for daytime sleepiness in individuals with ADHD.

Abstract 1193: Adult diffuse glioma GWAS by molecular subtype identifies variants in D2HGDH, FAM20C and GMEB2

Abstract Background: Genome-wide association studies (GWAS) revealed that 25 regions in 24 genes are associated with adult diffuse glioma development. These regions were identified by performing GWAS of glioma overall and by pathology (GBM and nonGBM). The 2016 WHO Classification of Tumors of the Central Nervous System utilizes two somatic alterations to molecularly-classify adult diffuse glioma: IDH mutation and 1p/19q codeletion. We hypothesized that germline variants may increase susceptibility to, or interact with, these somatic alterations to accelerate the development of specific molecular subtypes of glioma. We further hypothesize that germline variants associated with IDH-mutated glioma might be associated with other IDH-mutated tumors, namely, cholangiocarcinoma, acute myeloid leukemia (AML) and melanoma. Methods: We performed a GWAS by glioma molecular subtype - as defined by presence or absence of IDH somatic mutation and 1p/19q codeletion. A total of 1320 glioma cases and 1889 controls were used in the discovery set, and 799 glioma cases and 808 controls in the validation set. A meta-analysis was performed with a genome-wide p-value threshold of 5 × 10−8. GTEx data were used to perform an expression quantitative trait loci (eQTL) analysis. For germline variants that were significantly associated with IDH-mutated glioma, we evaluated pleiotropy with cholangiocarcinoma, AML and melanoma using TCGA and Mayo Biobank controls. Results: Variants in or near D2HGDH on chromosome 2 were genome-wide significant in IDH-mutated glioma (meta p-value = 2.82 × 10−10). TCGA reported that the D2HGDH region was commonly deleted in IDH-mutated gliomas that do not have 1p/19q codeletion. In TCGA data for IDH-mutated, non-codeleted glioma, we observed that the D2HGDH variant was inversely associated with tumor deletions of D2HGDH (odds ratio=0.57, p-value=0.015). The eQTL analyses demonstrated significant associations between D2HGDH germline variant and expression of D2HGDH (p=2.2 × 10−11). Further stratifying IDH-mutated glioma by 1p/19q codeletion status, one variant near FAM20C on chromosome 7 was genome-wide significant in gliomas that have IDH mutation and 1p/19q codeletion (meta p-value=9.56 × 10−9). Analyses are currently underway to evaluate pleiotropy of these IDH-mutated glioma germline variants with other IDH-mutated tumors including cholangiocarcinoma, AML and melanoma. Variants in or near GMEB2 on chromosome 20 were genome-wide significant in IDH wild-type glioma (meta p-value=2.60 × 10−10). The most significant variant in the GMEB2 region remained significant after adjustment for the known RTEL1 glioma risk variant nearby on chromosome 20 (p=0.029). Conclusions: We identified and validated novel germline variants in two genes that are associated with etiology of IDH-mutated and one gene that is associated with IDH wild-type adult diffuse glioma. Citation Format: Jeanette E. Eckel-Passow, Kristen L. Drucker, Thomas M. Kollmeyer, Matthew L. Kosel, Paul A. Decker, Annette M. Molinaro, Terri Rice, Corrine E. Praska, Lauren E. Clark, Alissa A. Caron, Alexej Abyzov, Anthony Batzler, Jun S. Song, Melike Pekmezci, Helen M. Hansen, Lucie S. McCoy, Paige M. Bracci, Joseph Wiemels, John K. Wiencke, Stephen Francis, Terence C. Burns, Caterina Giannini, Daniel H. Lachance, Margaret Wrensch, Robert B. Jenkins. Adult diffuse glioma GWAS by molecular subtype identifies variants in D2HGDH, FAM20C and GMEB2 [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1193.

Abstract 1327: Genome-wide loss-of-heterozygosity calling from low-pass sequencing of ligation-mediated whole genome amplified DNA in single tumor cells

Abstract Background: Genome-wide analysis of Loss-of-heterozygosity (LoH) has been shown to be important in several contexts, including the assessment of BRCAness signature, a marker of homologous repair deficiency in several cancer types associated with efficacy of platinum therapy and PARP inhibitors. Methods to infer genome-wide LoH status require high-coverage whole-genome sequencing or low-pass sequencing of a large number of single cells. We present a method to infer genome-wide LoH status of as low as one single-cell from low-pass sequencing of libraries produced by Ampli1™ LowPass kit, at a fraction of the cost of current NGS-based methods. Methods: We used low-pass sequencing data generated from 294 single Circulating Tumor Cells (CTCs) from prostate, multiple myeloma and lung cancer patients, and from 24 single cells from 8 cell lines. DNA amplified with Ampli1™ WGA kit (based on ligation-mediated PCR) combined with Ampli1 LowPass kit for Illumina generates a reduced genome representation, whereby a significant fraction of fragments is expected to be covered by more than one read. We reasoned that, even at a mean coverage insufficient for variant calling (≤0.05x), a statistically significant decrease in loci showing 2 alleles should be expected in LoH regions. A pileup of mapped sequences at dbSNP loci was obtained (minor allele frequency ≥5%; read depth ≥2). Mono- and bi-allelic loci (pileup containing 1 or 2 different alleles, respectively), were counted in each uniform copy-number (CN) genome segment within a single chromosome arm. Regions with CN equal to cell ploidy were used as internal reference. A one-sided Fisher test on biallelic sites depletion (multiplicity corrected p-value threshold of 0.05) was used to call LoH on each region. Results: Compared with libraries obtained using random shearing, Ampli1 LowPass single-cell libraries showed an increase in mean coverage of covered genome from 1.1 to 1.9 starting from the same number of reads (1M) thus increasing the number of loci for LoH calling. Analysis of 10 patients' single cells with known LoH events, corresponding to regions at copy number 1, detected 1006 events out of 1142. Several (492) copy neutral LoH events or LoHs in copy gained regions were also detected. Representatives of such events were verified successfully by high pass sequencing of the same library. Performance was confirmed by analysis of 24 single cells from cell lines whose LoH status was inferred from CCLE database. Conclusions: This innovative method leverages reduced genome representation inherent in Ampli1 LowPass libraries, to compute genome-wide LoH along with copy number (CN) status, meeting the need for LoH/CN analysis at single-cell level on rare-cells such as CTCs. Citation Format: Alberto Ferrarini, Claudio Forcato, Marianna Garonzi, Genny Buson, Massimiliano Pellicano, Francesca Fontana, Nicolò Manaresi. Genome-wide loss-of-heterozygosity calling from low-pass sequencing of ligation-mediated whole genome amplified DNA in single tumor cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1327.

Polygenic risk score-analysis of thromboembolism in patients with acute lymphoblastic leukemia

IntroductionThromboembolism (TE) is a common and serious toxicity of acute lymphoblastic leukemia (ALL) treatment, but studies of genetic predisposition have been underpowered with conflicting results. We tested whether TE in ALL and TE in the general adult population have a shared genetic etiology. Materials and methodsWe prospectively registered TE events and collected germline DNA in patients 1.0–45.9 years in the Nordic Society of Pediatric Hematology and Oncology (NOPHO) ALL2008 study (7/2008–7/2016). Based on summary statistics from two large genome-wide association studies (GWAS) on venous TE in adults (the International Network of VENous Thromboembolism Clinical Research Networks (INVENT) consortium and the UK Biobank), we performed polygenic risk score (PRS) analysis on TE development in the NOPHO cohort, progressively expanding the PRS by increasing the p-value threshold of single nucleotide polymorphism (SNP) inclusion. Results and conclusionEighty-nine of 1252 patients with ALL developed TE, 2.5 year cumulative incidence 7.2%. PRS of genome-wide significant SNPs from the INVENT and UK Biobank data were not significantly associated with TE, HR 1.16 (p 0.14) and 1.02 (p 0.86), respectively. Expanding PRS by increasing p-value threshold did not reveal polygenic overlap. However, subgroup analysis of adolescents 10.0–17.9 years (n = 231), revealed significant polygenic overlap with the INVENT GWAS. The best fit PRS, including 16,144 SNPs, was associated with TE with HR 1.76 (95% CI 1.23–2.52, empirical p-value 0.02). Our results support an underlying genetic predisposition for TE in adolescents with ALL and should be explored further in future TE risk prediction models.

Risk Factors Associated with External Ventricular Drain Associated Infections

<h3>Background</h3> The reduction of intracranial pressure using external ventricular drains (EVDs) is a life saving measure, but infection is a major complication of this procedure. Therefore, reducing procedural meningitis/ventriculitis is an important goal for healthcare infection prevention teams. This study determines the effectiveness of a newly implemented infection prevention bundle (IPB) and identifies possible risk factors increasing incidence of EVD-AIs. <h3>Methods</h3> This is a pre- and post-study performed at a single 440-bed academic medical center reviewing all EVD-AIs between January 2014 and October 2018 comparing the rates of EVD-AI before and after application of the IPB. Measured variables included procedure time, EVD placement location & duration, cerebrospinal fluid (CSF) specimen source, surgeon, and the presence of EVD-AI. Confirmed infection was defined as positive CSF culture, and possible infection was defined as high white blood cell count (>100 cells/ml) and/or low glucose levels (<40 mg/dL). Odds ratios (OR) of measured variables as related to EVD-AI presence were determined with a significance threshold of p-value <0.05. <h3>Results</h3> Out of 313 procedures, there were 105 unique patients eligible for analysis. Seventy patients had CSF analysis performed; 37 had possible EVD-AIs (31 pre-IPB and 6 post-IPB) and 7 were confirmed EVD-AIs (5 pre-IPB and 2 post-IPB) with no statistically significant difference pre- and post-IPB. The EVD duration (OR 1.20), EVD placement procedure (OR 2.38), and CSF specimen source (OR 7.00) were associated with increased risk of infection. <h3>Conclusions</h3> Multiple risk factors are associated with EVD-AIs, including longer EVD duration, EVDs placed at bedsides, and CSF drawn from EVD collection bags. The decrease in EVD-AIs is not conclusively linked to the implementation of the IPB due to the small number of procedures and short duration of follow up. The application of effective evidence-based infection prevention measures for EVD-related procedural meningitis/ventriculitis is an essential intervention to reduce morbidity and mortality.

A principal component approach to improve association testing with polygenic risk scores.

Polygenic risk scores (PRSs) have become an increasingly popular approach for demonstrating polygenic influences on complex traits and for establishing common polygenic signals between different traits. PRSs are typically constructed using pruning and thresholding (P+T), but the best choice of parameters is uncertain; thus multiple settings are used and the best is chosen. Optimization can lead to inflated Type I error. Permutation procedures can correct this, but they can be computationally intensive. Alternatively, a single parameter setting can be chosen a priori for the PRS, but choosing suboptimal settings results in loss of power. We propose computing PRSs under a range of parameter settings, performing principal component analysis (PCA) on the resulting set of PRSs, and using the first PRS-PC in association tests. The first PC reweights the variants included in the PRS to achieve maximum variation over all PRS settings used. Using simulations and a real data application to study PRS association with bipolar disorder and psychosis in bipolar disorder, we compare the performance of the proposed PRS-PCA approach with a permutation test and an a priori selected p-value threshold. The PRS-PCA approach is simple to implement, outperforms the other strategies in most scenarios, and provides an unbiased estimate of prediction performance.

Statistical inference of mass channel purity from Fisher ratio analysis using comprehensive two-dimensional gas chromatography with time of flight mass spectrometry data.

Tile-based Fisher ratio (F-ratio) analysis has recently been developed and validated for discovery-based studies of highly complex data collected using comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC×GC-TOFMS). In previous studies, interpretation and utilization of F-ratio hit lists has relied upon manual decomposition and quantification performed by chemometric methods such as parallel factor analysis (PARAFAC), or via manual translation of the F-ratio hit list information to peak table quantitative information provided by the instrument software (ChromaTOF). Both of these quantification approaches are bottlenecks in the overall workflow. In order to address this issue, a more automatable approach to provide accurate relative quantification for F-ratio analyses was investigated, based upon the mass spectral selectivity provided via the F-ratio spectral output. Diesel fuel spiked with 15 analytes at four concentration levels (80, 40, 20, and 10ppm) produced three sets of two class comparisons that were submitted to tile-based F-ratio analysis to obtain three hit lists, with an F-ratio spectrum for each hit. A novel algorithm which calculates the signal ratio (S-ratio) between two classes (eg., 80ppm versus 40ppm) was applied to all mass channels (m/z) in the F-ratio spectrum for each hit. A lack of fit (LOF) metric was utilized as a measure of peak purity and combined with F-ratio and p-values to study the relationship of each of these metrics with m/z purity. Application of a LOF threshold coupled with a p-value threshold yielded a subset of the most pure m/z for each of the 15 spiked analytes, evident by the low deviations (< 5%) in S-ratio relative to the true concentration ratio. A key outcome of this study was to demonstrate the isolation of pure m/z without the need for higher level signal decomposition algorithms.

Polygenic prediction of the risk of perinatal depressive symptoms.

Perinatal depression carries adverse effects on maternal health and child development, but genetic underpinnings remain unclear. We investigated the polygenic risk of perinatal depressive symptoms. About 742 women from the prospectivePrediction and Prevention of Pre-eclampsia and Intrauterine Growth Restriction cohort were genotyped and completed the Center for Epidemiologic Studies Depression scale 14 times during the prenatal period and twice up to 12 months postpartum. Polygenic risk scores for major depressive disorder, bipolar disorder, schizophrenia, and cross-disorder were calculated using multiple p-value thresholds. Polygenic risk scores for major depressive disorder, schizophrenia, and cross-disorder, but not bipolar disorder, were associated with higher prenatal and postpartum depressive symptoms (0.8%-1% increase per one standard deviation increase in polygenic risk scores). Prenatal depressive symptoms accounted for and mediated the associations between the polygenic risk scores and postpartum depressive symptoms (effect size proportions-mediated: 52.2%-88.0%). Further, the polygenic risk scores were associated with 1.24-1.45-fold odds to belong to the group displaying consistently high compared with consistently low depressive symptoms through out the prenatal and postpartum periods. Polygenic risk scores for major depressive disorder, schizophrenia, and cross-disorder in non-perinatal populations generalize to perinatal depressive symptoms and may afford to identify women for timely preventive interventions.

Statistics in scientific articles published in the European Annals of Otorhinolaryngology Head & Neck Diseases

ObjectivesTo evaluate biostatistics in scientific articles published in the European Annals of Otorhinolaryngology Head & Neck Diseases. Materials and methodsRetrospective analysis of 76 scientific articles published in 2018 and 2019. The main goal was to describe the percentage of articles using biostatistics and to explore for potential associations with the article's main characteristics. Secondary goals were, within the group of articles using statistical tests, to describe the type of statistics used, the assessment of normality in case of comparison of mean values, the p-value threshold for significance, the use of confidence intervals, and power analysis. ResultsStatistics were used in 73.7% of articles, without any significant association with main characteristics. Within the group of articles using statistics, the tests used were parametric, non-parametric and not specified in 77.7%, 51.4% and 1.8% of cases, respectively. Normality was checked in 14.2% of article using parametric tests to evaluate mean values. The p-value significance threshold was set at .05, .01, .005 levels and not defined in 60.7%, 1.8%, 1.8% and 35.7% of articles, respectively, while confidence intervals and power analyses were documented in 10.7% and 5.3%, respectively. ConclusionThis article underlines the need for better use of statistics in the European Annals of Otorhinolaryngology Head & Neck Diseases, to improve the quality of scientific articles published in the organ of written expression of the French and International French-speaking Societies of Otorhinolaryngology, and to support the ongoing move toward better medical science.