Exome/Genome Sequencing in Undiagnosed Syndromes

Abstract

Exome sequencing (ES) and genome sequencing (GS) have radically transformed the diagnostic approach to undiagnosed rare/ultrarare Mendelian diseases. Next-generation sequencing (NGS), the technology integral for ES, GS, and most large (100+) gene panels, has enabled previously unimaginable diagnoses, changes in medical management, new treatments, and accurate reproductive risk assessments for patients, as well as new disease gene discoveries. Yet, challenges remain, as most individuals remain undiagnosed with current NGS. Improved NGS technology has resulted in long-read sequencing, which may resolve diagnoses in some patients who do not obtain a diagnosis with current short-read ES and GS, but its effectiveness is unclear, and it is expensive. Other challenges that persist include the resolution of variants of uncertain significance, the urgent need for patients with ultrarare disorders to have access to therapeutics, the need for equity in patient access to NGS-based testing, and the study of ethical concerns. However, the outlook for undiagnosed disease resolution is bright, due to continual advancements in the field.

Keywords: Mendelian diseases; exome sequencing; genome sequencing; next-generation sequencing; rare/ultrarare diseases; undiagnosed diseases.

Figure 1

Next-generation sequencing with Illumina technology. (a) Library preparation and sequencing. DNA is fragmented and adapters ligated to create a sequencing library. Samples are then reassembled in the genetic sequence used for data analysis. (b) Alignment and variant calling. Short-read DNA fragments are aligned to the reference genome for variant calling. Examples of variants of interest include findings such as identification of a heterozygous missense variant (yellow arrow), a homozygous missense variant (blue-green arrow), and/or a two-base-pair heterozygous deletion (pink arrow).