The phenotype-genotype reference map: Improving biobank data science through replication

Population-scale biobanks linked to electronic health record data provide vast opportunities to extend our knowledge of human genetics and discover new phenotype-genotype associations. Given their dense phenotype data, biobanks can also facilitate replication studies on a phenome-wide scale. Here, we introduce the phenotype-genotype reference map (PGRM), a set of 5,879 genetic associations from 523 GWAS publications that can be used for high-throughput replication experiments. PGRM phenotypes are standardized as phecodes, ensuring interoperability between biobanks. We applied the PGRM to five ancestry-specific cohorts from four independent biobanks and found evidence of robust replications across a wide array of phenotypes. We show how the PGRM can be used to detect data corruption and to empirically assess parameters for phenome-wide studies. Finally, we use the PGRM to explore factors associated with replicability of GWAS results.

Accuracy of Ultrasound Elastography and Fibrosis-4 Index (FIB-4) in Ruling Out Cirrhosis in Obese Non-Alcoholic Fatty Liver Disease (NAFLD) Patients

Introduction: Non-alcoholic fatty liver disease (NAFLD) is the most common cause of advanced liver disease in the USA. Liver biopsy, the gold standard diagnostic test for evaluating liver fibrosis, is associated with significant risk and expense. The accuracy of ultrasound elastography and Fibrosis-4 index (FIB-4) in the obese NAFLD population is unknown. We aimed to compare the accuracy of ultrasound elastography and FIB-4 to liver biopsy in ruling out cirrhosis in NAFLD patients at a tertiary, transplant referral center in the US.

Methods: We retrospectively evaluated 93 patients with a mean age of 53 years (SD: 13 years) who underwent liver ultrasound elastography and liver biopsy, and additionally calculated their FIB-4 at the time of biopsy. We compared the liver stiffness measurement (LSM) obtained from ultrasound elastography and FIB-4 with the pathology results for ruling out cirrhosis.

Results: 85% of the patients were white, 53% were female, average BMI was 34.7 (SD: 6.7), 52% had diabetes, and 53% had hypertension. For biopsy-proven cirrhosis (prevalence 15%), a cut-off value of 12.5 kilopascals (kPa) for F4 had a sensitivity of 92% and a specificity of 54%. Values below this threshold excluded cirrhosis with 98% certainty. Compared to FIB-4, ultrasound elastography showed higher accuracy in ruling out cirrhosis (92% vs. 80% sensitivity, 98% vs. 95% negative predictive value (NPV), respectively).

Conclusion: To our knowledge, this is the first study in a tertiary transplant referral center in the USA to show that ultrasound elastography was superior to FIB-4 and can be used as a reliable screening test to rule out cirrhosis in obese NAFLD patients at a 12.5 kPa cut-off. Therefore, helping to avoid the risk and expense associated with liver biopsy.

Abstract WP201: Increasing Mortality From Ischemic Stroke In The US, Racial And Etiological Analysis

Background: Ischemic stroke is the fifth leading cause of death in the United States. In spite of the recent advances in the management of ischemic stroke, mortality rates remain high and have increased in recent years. Importantly, mortality differs by race, with African Americans more likely to die from stroke. To better understand stroke mortality we examined data from 1999 through 2018 with respect to both race and stroke subtype.

Methods: Using the Multiple Cause Of Death Database, we identified all patients who died of cerebral infarction (CI) using the International Classification of Diseases, 10th revision code I63. Age-adjusted mortality rates (AAMR) standardized to the 2000 US census data were used. Data for continuous variables were examined using simple linear regression models and multivariable linear regression models controlling for relevant covariates. All tests were two-tailed and p < 0.05 was considered significant.

Results: A total of 201,157 CI deaths were identified between 1999 and 2018. AAMR showed a U-shaped trend, such that compared to 1999-2004 (4.52±0.60) AAMR decreased from 2005-2014 (2.06±0.20), p < 0.001, and increased from 2015-2018 (3.63±1.32), p < 0.001. AAMR differed significantly by race, p = 0.045. Rates were 3.05+1.26 for Caucasians and 4.04+1.74 for African Americans. AAMR decreased between 1999 and 2018 for thrombotic strokes, p < 0.001, while AAMR increased over this time for embolic stroke, p < 0.001. Amongst Caucasians, there was no significant differences in AAMR for each stroke subtype from 1999 to 2018, p = 0.081. However, for African Americans, there was a significantly higher AAMR for thrombotic strokes (0.56±0.33) compared to embolic strokes (0.33±0.15), p = 0.006.

Conclusion: Despite recent advances in ischemic stroke management, AAMR has increased in the last 4 years by 1.8 times. AAMR in African Americans is 1.3 times that of Caucasians with African American mortality from thrombotic stroke being 1.7 times higher than from embolic stroke. Mortality from CI caused by embolism increased by 2.8 times over the study period while that due to thrombosis decreased by 5 times. Further studies are needed to clarify the reasons behind the recent increase in AAMR.

Pediatric Patients with SARS-CoV-2 Infection: Clinical Characteristics in the United States from a Large Global Health Research Network

Background Few reports have been published on the clinical presentation of pediatric patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aim to shed more light on the clinical presentation of pediatric patients infected with coronavirus disease 2019 (COVID-19), and also potential risk factors for more severe clinical case presentation. Methods We used a large global health research network to gather clinical data extracted from the electronic medical records of pediatric patients aged < 18 years with confirmed SARS-CoV-2 from January 1, 2020 to May 7, 2020. Clinical symptoms at presentation, hospitalization status, associated co-morbidities, and treatments received were reviewed. Results A total of 627 patients with COVID-19 diagnosis (334 were outpatient, 293 were inpatient) were included from a total of 20 organizations across the United States. The mean age of patients was seven years, 48% were females. Inpatients were younger than outpatients (mean age of 5.6 years vs 8.2 years, p<0.001). Sixty-one percent of patients in the inpatient group were < 5 years of age vs. 44% in the outpatient group. Amongst 293 inpatients, 90% (n=265) were non-severe and 10% (n=28) were classified as severe. The percentage of patients <5 years was higher in severe inpatients vs. non-severe (71% vs 60%.) Significantly more patients with a severe illness vs. non-severe illness had a history of co-morbidity including non-congenital heart disease (50% vs 11%, p<0.001) and disease of the respiratory system (86% vs 53%, p< 0.001). Conclusion Clinicians should closely monitor young children with underlying conditions and COVID-19, as they may be more likely to be hospitalized and have a higher severity of the disease.

Do repeat ultrasounds affect orchiectomy rate in patients with testicular torsion treated at a pediatric institution?

INTRODUCTION

Testicular torsion is a urological emergency; as the testicular salvage rate decreases with time, prompt intervention is required to restore the blood flow. Interhospital transfers and ultrasound examinations, while clinically essential to proper treatment and diagnosis, may adversely affect outcomes by delaying surgical intervention. Patients transferred to another institution for treatment of testicular torsion may experience a further time delay by undergoing two ultrasound examinations: one at the initial admitting institution and one at the receiving institution. To the knowledge of the authors, no study has yet explored the time delays and outcomes associated with these repeat ultrasounds.

OBJECTIVE

The objective was to investigate the impact of repeat ultrasound imaging on time to treatment and patient outcomes in patients with testicular torsion.

STUDY DESIGN

A retrospective chart review of 133 patients, aged 0-20 years, treated at the authors' institution for testicular torsion was conducted. Neonate patients and patients who did not receive ultrasound were excluded. Demographic and clinical variables were collected from the electronic medical record. Pearson Chi-squared and t-tests were used for univariate comparisons, and multivariate logistic regression analysis was performed to measure the relationships between variables.

RESULTS

Forty-nine percent of patients were primary patients, and 51% were transfer patients. Fifty-two percent of transfer patients received repeat ultrasounds. In comparison to salvaged patients, those who underwent orchiectomy experienced a greater delay between presentation at the institution and surgical intervention (229 min vs 177 min, p = 0.048). The transfer status does not appear to be related to the outcome, i.e. orchiectomy versus salvage. Patients who underwent orchiectomy were more likely than salvaged patients to have received repeat ultrasounds (p = 0.008). Repeat ultrasound patients had three times the likelihood of orchiectomy of single ultrasound patients. In a subset analysis of transfer patients, repeat ultrasound patients were more likely than single ultrasound patients to receive an orchiectomy (p = 0.03).

DISCUSSION

In agreement with previous studies, patients who underwent orchiectomy were found to experience greater treatment delays and trend toward transfer. Specifically, repeat ultrasound and time between presentation and intervention appear to influence patient outcomes. The effect of repeat ultrasound on outcomes appears to be independent of the transfer status. The study was limited by its retrospective nature and small sample size.

CONCLUSION

The analysis suggests that efforts to prevent repeat ultrasounds and minimize the time between presentation and intervention would improve patient outcomes. It is proposed that standardized clinical decision-making procedures, such as the TWIST scoring system, be incorporated into hospital protocols.