Assessing the impact of exome sequencing on diagnostic yield in a large cohort of Brazilian patients

TL;DR

This study compares diagnostic success rates of exome sequencing versus multi-gene panels in Brazilian patients, finding exome sequencing more effective for certain conditions despite more uncertain results.

Contribution

The study provides a large-scale comparison of diagnostic yield between exome sequencing and multi-gene panels in a Brazilian cohort.

Findings

Exome sequencing had the highest detection rate (32.7%) compared to other tests.

Skeletal and hearing disorders showed the highest diagnostic yield (55% and 50%) with exome sequencing.

Exome sequencing had the highest rate of inconclusive results due to variants of uncertain significance.

Abstract

This study aimed to evaluate whether the increased use of exome sequencing as a primary next-generation sequencing test provides a higher diagnostic yield compared to multi-gene panels for various clinical indications within a Brazilian cohort.

We retrospectively analyzed test results from 3,025 patients who underwent single-gene tests, multi-gene panels, and exome sequencing in our laboratory. The results were categorized as positive, inconclusive, or negative, with clinical indications including neurodevelopmental, late-onset neurological, neuromuscular, syndromic, skin/hair, hematological/immunologic, ophthalmologic, inborn errors of metabolism, skeletal, cardiovascular, reproductive planning, cancer, genitourinary, gastrointestinal, and hearing disorders.

Of the 3,025 next-generation sequencing-based tests, 420 were single-gene tests, 1,158 were multi-gene panels, and 1,447 were exome sequencing. Although multi-gene panels were initially the most frequently ordered test, exome sequencing currently represents 62% of all next-generation sequencing-based tests performed in our laboratory. Exome sequencing had the highest detection rate (32.7%), but also the highest inconclusive rate. Among the clinical indications, when stratified by exome sequencing, skeletal and hearing disorders had the highest diagnostic yield, corresponding to 55 and 50%, respectively.

This study emphasizes the diagnostic usefulness of exome sequencing for complex genetic disorders in postnatal diagnosis. However, the expansion of exome sequencing also presents challenges, including an increased rate of inconclusive results due to variants of uncertain significance. Broader availability of exome sequencing must be accompanied by additional resources to address these challenges effectively.