Genome Sequencing in the Intensive Care Unit Population

Overview

The purpose of this study is to understand how the use of whole genome sequencing (WGS) may be able to increase the speed with which a diagnosis is made for patients in an intensive care unit population. This is not an assessment of a new device, test, or technology. This project is an investigation of the utility of this technology in clinical care when compared to standard of care testing. The study will look at the ability to more quickly diagnose a patient (time to diagnosis and efficacy of testing) as compared to standard of care testing. The study will also look at the impact of WGS on patient outcomes and cost of clinical care.

This is an observational study to understand if the use of whole genome sequencing (WGS) increases the speed to diagnosis and how clinical management is changed in an intensive care population of neonates. This project utilizes approved genome sequencing methods at CLIA-certified facilities. 1. Neonate subjects who are eligible and whose parents consent to the study will undergo blood sample which will be sent for WGS and bioinformatics analysis, filtering first with a targeted panel of 1722 genes most likely to cause genetic disorders in the first year of life, and then with a whole exome filter if no obvious diagnosis is determined using the 1722 gene panel filter. Testing is completed in a CLIA-certified laboratory. Pathogenic, likely-pathogenic, and variants of uncertain significance in genes related the child's clinical features will be returned to the care team and to the parents in the setting of genetic counseling for use in clinical decision making about management. A report is added to the neonates EMR. Consent will include permission to access financial records of the hospitalization, to compare costs and length-of-stay to matched controls. 2. Parents of identified neonates who consent to the study for the for the purpose of trio analysis will have samples collected which will undergo concurrent analysis with the child to assist in determining the pathogenicity of variants in genomic sequencing. Pathogenic and likely-pathogenic secondary findings in the ACMG 59 later-onset medically actionable genes will be reported to the parents in the setting of genetic counseling ONLY if the parents opt in to learn these results AND they are identified in the child. 3. Siblings of participating neonates, if needed for interpretation of the neonate's genetic studies, will have samples collected for use in the genetic analysis. Pathogenic and likely-pathogenic results in childhood-onset disorders will be reported to the parents in the setting of genetic counseling. 4. Historical controls will be identified and matched to study participants. Historical controls will include infants in the ICU having a genetics consult ordered during their initial admission over the prior 24 months. Matching between study participants and matched controls will be performed using Propensity Scores. We will fit a logistical regression model to the combined treatment and control groups, and will then use the nearest neighbor matching to create matched pairs. The matching will help reduce bias and increase power to detect true effects. These controls will only be used for the fiscal and length of stay analyses; no genetic testing will be done on this cohort.