Exploring the perioptome: the role of genomics in thoracic surgery and anaesthesia

iGAS: A framework for using electronic intraoperative medical records for genomic discovery

OBJECTIVE

Design and implement a HIPAA and Integrating the Healthcare Enterprise (IHE) profile compliant automated pipeline, the integrated Genomics Anesthesia System (iGAS), linking genomic data from the Mount Sinai Health System (MSHS) BioMe biobank to electronic anesthesia records, including physiological data collected during the perioperative period. The resulting repository of multi-dimensional data can be used for precision medicine analysis of physiological readouts, acute medical conditions, and adverse events that can occur during surgery.

MATERIALS AND METHODS

A structured pipeline was developed atop our existing anesthesia data warehouse using open-source tools. The pipeline is automated using scheduled tasks. The pipeline runs weekly, and finds and identifies all new and existing anesthetic records for BioMe participants.

RESULTS

The pipeline went live in June 2015 with 49.2% (n=15,673) of BioMe participants linked to 40,947 anesthetics. The pipeline runs weekly in minimal time. After eighteen months, an additional 3671 participants were enrolled in BioMe and the number of matched anesthetic records grew 21% to 49,545. Overall percentage of BioMe patients with anesthetics remained similar at 51.1% (n=18,128). Seven patients opted out during this time. The median number of anesthetics per participant was 2 (range 1-144). Collectively, there were over 35 million physiologic data points and 480,000 medication administrations linked to genomic data. To date, two projects are using the pipeline at MSHS.

CONCLUSION

Automated integration of biobank and anesthetic data sources is feasible and practical. This integration enables large-scale genomic analyses that might inform variable physiological response to anesthetic and surgical stress, and examine genetic factors underlying adverse outcomes during and after surgery.

Genetics and epigenetics in perioperative medicine

PURPOSE OF REVIEW

To summarize is to review recent progress in 'genomic' science and how this may be applied to the perioperative environment. Although investigations that relate genetic variation to perioperative outcomes continue, it is increasingly apparent that epigenetic mechanisms may contribute to much of the observed variation in complex outcomes not otherwise explained by differences in genetic sequence.

RECENT FINDINGS

Examples of recent findings relating to the role of epigenetic modifications in complex disease and outcomes are derived from research into type 1 diabetes, pain, and the hypoxic response. These studies provide models for future cohort study design, potential perioperative drug targets, and hypothesis development. Genetic and epigenetic factors combine to alter both gene expression and drug responses at both pharmacokinetic and pharmacodynamic levels. These factors impact on the efficacy and safety of multiple drug classes used in perioperative medicine.

SUMMARY

Enhancing our understanding of the way in which patients as genomic organisms interact with the perioperative environment requires a more sophisticated appreciation of the factors governing gene expression than has been the case to date. Epigenetic mechanisms are sure to play a pivotal role in what is essentially an acquired phenotype.