Abstract
Sequencing the first human genome in 2003 took 15 years and cost $2.7 billion. Advances in sequencing technologies have since decreased costs to the point where it is now feasible to resequence a whole human genome for $1000 in a single day. These advances have allowed the generation of huge volumes of high-quality human sequence data used to construct increasingly large catalogs of both population-level and disease-causing variation. The existence of such databases, coupled with a high-quality human reference genome, means we are able to interrogate and annotate all types of genetic variation and identify pathogenic variants for many diseases. Increasingly, sequencing-based approaches are being used to elucidate the underlying genetic cause of autoimmune diseases, a group of roughly 80 polygenic diseases characterized by abnormal immune responses where healthy tissue is attacked. Although sequence data generation has become routine and affordable, significant challenges remain with no gold-standard methodology to identify pathogenic variants currently available. This review examines the latest methodologies used to identify pathogenic variants in autoimmune diseases and considers available sequencing options and subsequent bioinformatic methodologies and strategies. The development of reliable and robust sequencing and analytic workflows to detect pathogenic variants is critical to realize the potential of precision medicine programs where patient variant information is used to inform clinical practice.