Short-read genome sequencing (GS) holds the promise of becoming the
primary diagnostic approach for the assessment of autism spectrum disorder
(ASD) and fetal structural anomalies (FSAs). However, few studies have
comprehensively evaluated its performance against current standard-of-care
diagnostic tests: karyotype, chromosomal microarray (CMA), and exome
sequencing (ES). To assess the clinical utility of GS, we compared its
diagnostic yield against these three tests in 1,612 quartet families
including an individual with ASD and in 295 prenatal families. Our GS
analytic framework identified a diagnostic variant in 7.8% of ASD probands,
almost 2-fold more than CMA (4.3%) and 3-fold more than ES (2.7%). However,
when we systematically captured copy-number variants (CNVs) from the exome
data, the diagnostic yield of ES (7.4%) was brought much closer to, but did
not surpass, GS. Similarly, we estimated that GS could achieve an overall
diagnostic yield of 46.1% in unselected FSAs, representing a 17.2%
increased yield over karyotype, 14.1% over CMA, and 4.1% over ES with CNV
calling or 36.1% increase without CNV discovery. Overall, GS provided an
added diagnostic yield of 0.4% and 0.8% beyond the combination of all three
standard-of-care tests in ASD and FSAs, respectively. This corresponded to
nine GS unique diagnostic variants, including sequence variants in exons
not captured by ES, structural variants (SVs) inaccessible to existing
standard-of-care tests, and SVs where the resolution of GS changed variant
classification. Overall, this large-scale evaluation demonstrated that GS
significantly outperforms each individual standard-of-care test while also
outperforming the combination of all three tests, thus warranting
consideration as the first-tier diagnostic approach for the assessment of
ASD and FSAs.