Delivering high throughput urgent exome sequencing at a diagnostic laboratory

Abstract

Background: The clinical utility and feasibility of urgent exome sequencing established by the MRFF Acute Care Flagship (ACF)1 resulted in an increase in expedited referrals. Managing this demand while managing turnaround times (TAT) required implementation of a high throughput workflow and increased resourcing. Method: Retrospective audit of exome referrals at a public diagnostic genetics laboratory, NSW Health Pathology Randwick Genomics. Primary outcome was TAT for expedited exomes, measured from receipt to report issued. A referrer satisfaction survey was conducted. Results: Annual expedited and total exome referral numbers have grown from 0 expedited/56 total exomes in 2017 to 18/292 in 2018 to 48/430 in 2019 to 96/548 in 2020 to 234/1005 in 2021 (1/1/21–18/11/21). The median TAT for expedited exomes outside the ACF was 26 days in 2018, 24 days in 2019, 19 days in 2020 and 14 days in 2021. ACF TAT was 5, 6, and 9 days for 2018, 2019 and 2020 respectively. Referrers reported satisfaction with this service. Discussion: This study demonstrates that urgent/expedited exome reports can be provided in clinically relevant TAT, despite increasing referral numbers, using laboratory process redesign and modest staffing increases. Maintaining this level of service is essential for prenatal and acute inpatient/ICU testing. Reference 1. Australian Genomics Health Alliance Acute Care Flagship. Feasibility of ultra-rapid exome sequencing in critically ill infants and children with suspected monogenic conditions in the Australian public health care system. JAMA 2020; 323: 2503–11.