Combining exome/genome sequencing with data repository analysis reveals novel gene-disease associations for a wide range of genetic disorders

Abstract

Purpose: Within this study, we aimed to discover novel gene-disease associations in patients with no genetic diagnosis after exome/genome sequencing (ES/GS).

Methods: We followed two approaches: (1) a patient-centered approach, which after routine diagnostic analysis systematically interrogates variants in genes not yet associated to human diseases; and (2) a gene variant centered approach. For the latter, we focused on de novo variants in patients that presented with neurodevelopmental delay (NDD) and/or intellectual disability (ID), which are the most common reasons for genetic testing referrals. Gene-disease association was assessed using our data repository that combines ES/GS data and Human Phenotype Ontology terms from over 33,000 patients.

Results: We propose six novel gene-disease associations based on 38 patients with variants in the BLOC1S1, IPO8, MMP15, PLK1, RAP1GDS1, and ZNF699 genes. Furthermore, our results support causality of 31 additional candidate genes that had little published evidence and no registered OMIM phenotype (56 patients). The phenotypes included syndromic/nonsyndromic NDD/ID, oral-facial-digital syndrome, cardiomyopathies, malformation syndrome, short stature, skeletal dysplasia, and ciliary dyskinesia.

Conclusion: Our results demonstrate the value of data repositories which combine clinical and genetic data for discovering and confirming gene-disease associations. Genetic laboratories should be encouraged to pursue such analyses for the benefit of undiagnosed patients and their families.

Fig. 1. Summary of the applied strategies for identification of novel gene–disease associations.

a Patient-centered approach to systematically interrogate variants in genes not yet associated to human diseases in patients with no genetic diagnosis after exome/genome sequencing (ES/GS). b Gene variant centered approach to analyze de novo variants in cases with ES/GS performed and no genetic diagnosis. DP depth of reads, pLI probability of loss-of-function intolerance.

Fig. 2. The phenotype associated with IPO8 homozygous loss-of-function (LoF) variants.

Upper panel: photographs illustrating clinical features. Patient 7, with umbilical hernia, brachydactyly of hands, proximal placement of the thumbs, short nails, genus varus, pes planus, brachydactyly of foot, and short toenails. Patient 9 with low-set ears, sparse scalp hair, broad and sparse eyebrows, hypertelorism, long palpebral fissures, and depressed nasal bridge. Patient 13 with frontal bossing, wide, sparse eyebrows, hypertelorism, large palpebral fissures (downslanted), deep philtrum, and thin vermilion of the upper lip. Joint hypermobility (wrist and thumb), as well as long foot, long toes, hindfoot valgus, and pes planus. Lower panel: family trees of patients with IPO8 homozygous LoF variants and clinical abnormalities. Patients presented with a complex phenotype that included abnormalities of the cardiovascular system (congenital heart defects, cardiomyopathy, engorged brain vasculature), the skeletal system (joint hypermobility, pectus deformities, genus valgus/varus, scoliosis), and the skin (cutis laxa). Most patients presented hypotonia, neurodevelopmental delay (NDD), and failure to thrive. Other features included intestinal malrotation, Gastroesophageal reflux (GER), and hydronephrosis.

Fig. 3. The phenotype associated with ZNF699 homozygous loss-of-function (LoF) variants.

Upper panel: photographs showing phenotypic features of two patients (patients 27 and 35, Table 1). Patient 27, male index has low anterior hairline, thick scalp hair, thick eyebrows, synophrys, long eyelashes, long palpebral fissures, proptosis, strabismus, bulbous nose, low hanging columella, smooth philtrum, wide mouth, micrognathia, short neck, brachydactyly, right preaxial polydactyly, and bilateral syndactyly of the second and third toes. Patient 35, male index with coarse face, broad eyebrows, long palpebral fissures, wide mouth, thin vermilion of the upper lip, and bilateral absent thumbs. He presented generalized hypotonia and was severely emaciated. The patient deceased at 9 months old. Lower panel: summarized family trees of patients with ZNF699 homozygous LoF variants and clinical features. Patients presented with a severe phenotype that included congenital heart defects, gastrointestinal (intestinal atresia, pyloric stenosis, GER, hepatosplenomegaly), genitourinary (renal hypoplasia, cryptorchidism, chordee, hypospadias, ambiguous genitalia), and skeletal abnormalities (preaxial polydactyly, absent thumbs, syndactyly). Other recurrent features were generalized hypotonia, sensorineural hearing impairment, and premature hair graying. All patients have severe neurodevelopmental delay (NDD).