The main distinction between BGM and other programs aimed at clinical diagnosis of suspected monogenic disease is that our main focus is on discovering novel disease–gene associations, most typically in undiagnosed disease states. For this reason, cases with recognizable or known phenotypes are either directed elsewhere or are initially screened for the extant disease-causing variants linked to those phenotypes. Therefore, the majority of cases that come to the attention of the program described here are non-routine, high-complexity cases, and often referred from other programs, where they were deemed intractable.

To date, we have enrolled 244 families, sequenced DNA from 122 patients, along with additional samples from informative family members, analyzed 106 of these cases (Supp. Table 1), and elucidated a genetic etiology for 30 cases (Table 1). Another 48 cases (not listed here) have been resolved to the level of a potentially pathologic variant in one or a very small number of candidate genes, but require identification of additional related cases or functional experiments to demonstrate causality. Of the 30 cases solved by our program and listed in Table 1, 6 were referred to us with prior negative WES or gene panel sequencing, while at least 10 of the solved cases, or one third, afforded a genetic etiology for a previously unknown medical condition (Table 1). In addition, several of the families that were solved by this program had only one affected proband, and therefore required a more complicated disease gene discovery analysis than would otherwise be the case. Since our program’s primary focus is on novel disease–gene discovery, and since cases for which a known genetic variant is strongly suspected in advance of WES/WGS are excluded from our pipeline, it is notable that our ~28% (30/106) rate of gene identification is nominally equivalent to the 17–25% diagnostic yield reported by clinical genome sequencing programs.24,25,26,27,28

Additional examples of significant disease-associated gene identifications, summarized in Table 1, further illustrate specific features of the program. These cases include PIEZO2 (a subtype of distal arthrogryposis, a musculoskeletal contracture and respiratory disease),23 LOX (familial aortic dissection),29 WISP3 (precocious arthritis),30 CHST11 (T cell lymphoma with limb abnormalities),31 complement factor C3 gene (Chopra et al., manuscript in preparation), several cases of undiagnosed craniofacial dysmorphoses, and a gene that causes a rare form of lung cancer (Frank et al., manuscript in preparation) among others.

Table 1 also depicts a ratio of 21 WES to 9 WGS cases under “Sequencing strategy,” which is consistent with the ratio for all 122 patients, which includes 91 analyzed by WES and 43 by WGS. A total of 251 samples were submitted for WES, or ~2.8 samples per case, while 108 samples were submitted for WGS, or ~2.5 samples per case. While the majority of solved cases identify non-synonymous variants that should be captured by WES, the advantages of WGS include more uniform coverage, precise detection of regions of identity by descent, genome-wide data to call structural variants, and the opportunity to call potential non-coding regulatory variants within linkage disequilibrium peaks around disease-associated genes. For example, in a case with craniofacial anomalies and hypotonia we detected a translocation that disrupts intron 2 of CAPZB (Table 1, case 12). Also, in a novel syndrome of skeletal malformation and malignant lymphoproliferative disease (Table 1, case 1), a partial deletion of CHST11 was detected which might have been difficult to detect with WES capture methodology. Finally, a progressive pseudorheumatoid arthropathy of childhood (PPAC) case (Table 1, case 2) benefited from careful detection of autozygous segments by WGS, which reduced the analysis to only 6% of the genome given the consanguineous family structure.

Some of our cases were diagnosed by identification of a novel variant in a known disease-associated gene, despite our selection criteria for gene discovery. Several reasons account for this circumstance. First, some referred disorders are misdiagnosed or undiagnosed simply because they are relatively rare and have not been previously seen by the referring clinical team. An example of such a case is PPAC, with a WISP3 variant (Table 1, case 2). Second, some cases have had prior research grade WES and novel variants in known genes have been missed by the referring research team due to limitations of available WES interpretation tools. For example, this was the case in infantile-onset IBD with a variant in the disease-causing gene32,33 DOCK8 (Table 1, case 4). Lastly, some patients have had WES or gene panels performed in clinical laboratories that do not follow-up with functional studies on reported variants of uncertain significance. This is illustrated by the MED12 variant identified in a patient with congenital anomalies, polydactyly, and developmental delay. Thus, WES/WGS holds considerable value in rendering a definitive diagnosis in undiagnosed genetic cases. Even if deep re-analysis does not lead to the discovery of a novel disease-causing gene, clarification of the etiology of atypical, ambiguous, or challenging cases often expands our knowledge of the range of phenotypic states associated with specific genes and provides a definitive diagnosis for the patient and family.

In addition to providing insights into disease biology, the identification of disease-causing genes has broader medical ramifications. For example, once Mendelian disease-causing variants are validated through functional studies, the role of these genes in more common, related diseases states can be explored. For example, a newly discovered gene for Mendelian IBD may have immediate relevance to understanding the etiology of more common adult forms of IBD, such as Crohn’s disease or ulcerative colitis. As one approach to pursue such potential connections, gene-centric PheWAS34,35 statistical analysis can be performed across all phenotypic categories within available large-scale sequencing datasets. Such analyses can validate specific Mendelian disease gene findings in the context of common disease, and explore the broader value of the genetic information.

Other successful case analyses illustrate the potential of a modern genomic medicine service to provide insight into disease-causing pathways of direct therapeutic importance. For example, a 35-year-old Caucasian male presented to the hospital for evaluation of a personal and family history of thoracic aortic aneurysm and dissection (TAAD). He had undergone surgical repair of pectus excavatum at 2 years of age and was diagnosed with a large ascending aortic aneurysm at age 19. Based on these anomalies and other physical features including tall stature, high arched palate, and dental crowding, as well as a family history consistent with an autosomal dominant mode of inheritance, he was diagnosed of Marfan syndrome. However, genetic testing identified no variants in FBN1, TGFBR1, and TGFBR2, the genes that are associated with Marfan syndrome. Genetic testing performed in the proband’s affected mother also failed to reveal any causal variants in a larger collection of genes associated with connective tissue disorders: ACTA2, COL3A1, MYH11, SLC2A10, SMAD3, or MYLK. Therefore, WGS was performed for the proband and his affected cousin and identified a p.Met298Arg missense variant in the elastin and collagen cross-linking enzyme, Lysyl oxidase, encoded by the LOX gene.29 This variant would place a repulsive positive charge from Arg in the Cu2+ binding active site of the enzyme. Lysyl oxidase activity in skin declines with low dietary Cu2+ and increases with repletion.36 Taken together, these findings suggest the hypothesis that Cu2+ supplementation, within US Department of Agriculture (USDA) safety guidelines, might augment the Cu2+-dependent enzymatic function of LOX and therefore help protect against aortic disease in individuals carrying this variant. This hypothesis is now directly testable in a murine model where the specific genetic variant has been knocked-in to the endogenous Lox locus. In addition, family members carrying the p.Met298Arg variant are now being serially monitored by echocardiography and by magnetic resonance angiography for aortic dilatation, which may prevent significant morbidity and mortality when identified early in the course of disease rather than at the time of rupture.