(Un)standardized testing: the diagnostic odyssey of children with rare genetic disorders in Alberta, Canada.

PURPOSE: We provide a description of the diagnostic odyssey for a cohort of children seeking diagnosis of a rare genetic disorder in terms of the time from initial consultation to most recent visit or receipt of diagnosis, the number of tests per patient, and the types of tests received. METHODS: Retrospective chart review of 299 children seen at the Alberta Children's Hospital (ACH) Genetics Clinic (GC) for whom the result of at least one single-gene test, gene panel, or chromosome microarray analysis (CMA) was recorded. RESULTS: Of 299 patients, 90 (30%) received a diagnosis in the period of the review. Patients had an average of 5.4 tests each; 236 (79%) patients received CMA; 172 (58%) patients received single-gene tests and 34 (11%) received gene panels; 167 (56%) underwent imaging/electrical activity studies. The mean observation period was 898 days (95% confidence interval [CI] 791, 1004). Among patients with visits recorded prior to visiting ACH GC, 43% of the total observation time occurred prior to the GC. CONCLUSION: As genomic technologies expand, the nature of the diagnostic odyssey will change. This study has outlined the current standard of care in the ACH GC, providing a baseline against which future changes can be assessed.

Alternative genomic diagnoses for individuals with a clinical diagnosis of Dubowitz syndrome.

Dubowitz syndrome (DubS) is considered a recognizable syndrome characterized by a distinctive facial appearance and deficits in growth and development. There have been over 200 individuals reported with Dubowitz or a "Dubowitz-like" condition, although no single gene has been implicated as responsible for its cause. We have performed exome (ES) or genome sequencing (GS) for 31 individuals clinically diagnosed with DubS. After genome-wide sequencing, rare variant filtering and computational and Mendelian genomic analyses, a presumptive molecular diagnosis was made in 13/27 (48%) families. The molecular diagnoses included biallelic variants in SKIV2L, SLC35C1, BRCA1, NSUN2; de novo variants in ARID1B, ARID1A, CREBBP, POGZ, TAF1, HDAC8, and copy-number variation at1p36.11(ARID1A), 8q22.2(VPS13B), Xp22, and Xq13(HDAC8). Variants of unknown significance in known disease genes, and also in genes of uncertain significance, were observed in 7/27 (26%) additional families. Only one gene, HDAC8, could explain the phenotype in more than one family (N = 2). All but two of the genomic diagnoses were for genes discovered, or for conditions recognized, since the introduction of next-generation sequencing. Overall, the DubS-like clinical phenotype is associated with extensive locus heterogeneity and the molecular diagnoses made are for emerging clinical conditions sharing characteristic features that overlap the DubS phenotype.

Automated syndrome diagnosis by three-dimensional facial imaging.

PURPOSE: Deep phenotyping is an emerging trend in precision medicine for genetic disease. The shape of the face is affected in 30-40% of known genetic syndromes. Here, we determine whether syndromes can be diagnosed from 3D images of human faces. METHODS: We analyzed variation in three-dimensional (3D) facial images of 7057 subjects: 3327 with 396 different syndromes, 727 of their relatives, and 3003 unrelated, unaffected subjects. We developed and tested machine learning and parametric approaches to automated syndrome diagnosis using 3D facial images. RESULTS: Unrelated, unaffected subjects were correctly classified with 96% accuracy. Considering both syndromic and unrelated, unaffected subjects together, balanced accuracy was 73% and mean sensitivity 49%. Excluding unrelated, unaffected subjects substantially improved both balanced accuracy (78.1%) and sensitivity (56.9%) of syndrome diagnosis. The best predictors of classification accuracy were phenotypic severity and facial distinctiveness of syndromes. Surprisingly, unaffected relatives of syndromic subjects were frequently classified as syndromic, often to the syndrome of their affected relative. CONCLUSION: Deep phenotyping by quantitative 3D facial imaging has considerable potential to facilitate syndrome diagnosis. Furthermore, 3D facial imaging of "unaffected" relatives may identify unrecognized cases or may reveal novel examples of semidominant inheritance.

Correction: The value of diagnostic testing for parents of children with rare genetic diseases.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The value of diagnostic testing for parents of children with rare genetic diseases.

PURPOSE: Exome sequencing (ES) can rapidly identify disease-causing variants responsible for rare, single-gene diseases, and potentially reduce the duration of the diagnostic odyssey. Our study examines how parents and families value ES. METHODS: We developed a discrete choice experiment (DCE) survey that was administered to parents of children with rare diseases. The DCE included 14 choice tasks with 6 attributes and 3 alternatives. A valuation-space model was used to estimate willingness to pay, willingness to wait for test results, and minimum acceptable chance of a diagnosis for changes in each attribute. RESULTS: There were n = 319 respondents of whom 89% reported their child had genetic testing, and 66% reported their child had a diagnosis. Twenty-six percent reported that their child had been offered ES. Parents were willing to pay CAD$6590 (US$4943), wait 5.2 years to obtain diagnostic test results, and accept a reduction of 3.1% in the chance of a diagnosis for ES compared with operative procedures. CONCLUSION: Timely access to ES could reduce the diagnostic odyssey and associated costs. Before ES is incorporated routinely into care for patients with rare diseases in Canada and more broadly, there must be a clear understanding of its value to patients and families.

Clinical and genetic heterogeneity in Dubowitz syndrome: Implications for diagnosis, management and further research.

Dubowitz syndrome was described in 1965 as a recognizable syndrome characterized by microcephaly, short stature, eczema, mild developmental delays, and an increased risk of malignancy. Since its original description, there have been over 200 reported cases though no single gene has been identified to explain a significant proportion of affected individuals. Since the last definitive review of Dubowitz syndrome in 1996, there have been 63 individuals with a clinical, or suspected, diagnosis of Dubowitz syndrome reported in 51 publications. These individuals show a markedly wide spectrum with respect to growth, facial gestalt, psychomotor development, and risk of malignancy; genetic causes were identified in 33% (21/63). Seven individuals had deleterious copy number variants, in particular deletions at 14q32 and 17q24 were reported and showed overlap with the Dubowitz phenotype. Several cases were shown to have single gene disorders that included de novo or biallelic pathogenic variants in several genes including NSUN2 and LIG4 frequently identified by next-generation sequencing methods. It appears that the inability to identify a single gene responsible for Dubowitz syndrome reflects its extreme clinical and genetic heterogeneity. However, detailed phenotyping combined with careful grouping of subsets of unsolved cases and in conjunction with data-sharing will identify novel disease genes responsible for additional cases. In the interim, for those clinically diagnosed with a Dubowitz phenotype, we recommend assessment by a Medical Geneticist, a microarray and, if available, clinical or research based genome-wide sequencing. Management suggestions, including decisions regarding malignancy screening in select patients will be discussed.

Longer term survival of a child with autosomal recessive cutis laxa due to a mutation in FBLN4.

Autosomal recessive cutis laxa (ARCL) is a clinically and genetically heterogeneous group of disorders characterized by loose, inelastic skin and variable systemic involvement and severity. Mutations in the FBLN4 gene are associated with ARCL1B. Fibulin-4 is important in elastic fiber formation and smooth muscle cell differentiation. We describe herein an 8-year-old boy who presented with severe aortic root dilatation and arterial tortuosity at 1 year of age which required surgical repair. His parents were consanguineous and there was a family history of three brothers who died early in life with an unknown type of connective tissue disorder in the 1960s. Both parents of the patient reported here were related to these three boys. We used a homozygosity mapping strategy with a 900K SNP array and identified FBLN4 as a candidate gene in an extended region of homozygosity. We sequenced this gene in the patient and identified a homozygous non-synonymous mutation at c.376G>A (p.Glu126Lys) in exon 5 that was predicted to be damaging. ARCL1B has most typically been associated with early demise but our report suggests that long-term survival is possible. With this longer term survival we are learning more about the natural history of this disorder, which includes baroreceptor reflex failure and low bone mineral density in this patient.

Cytogenetic and molecular characterization of a de-novo cryptic deletion of 7p21 associated with an apparently balanced translocation and complex craniosynostosis.

We describe a female infant with complex craniosynostosis, significant craniofacial dysmorphism and developmental delay in which a de-novo apparently balanced translocation between chromosomes 7 and 18 [46,XX,t(7;18)(p15.3;q11.2)] was identified. Additional cytogenetic and molecular investigations identified a cryptic interstitial 7.6-10.6-Mb deletion of the region between bands 7p21.2 and 7p21.3 on the derivative chromosome 18. The deletion was of paternal origin and contained the TWIST1 gene, although her features were not completely characteristic of Saethre-Chotzen syndrome. The phenotype of this patient is likely further complicated by loss of other genes within the deleted region and/or disruption of a critical gene(s) at the sites of the breakpoints on chromosomes 7 and 18. This case illustrates the need for a systematic molecular study of breakpoints and the surrounding chromosomal regions in patients with apparently balanced rearrangements and phenotypic abnormalities.

Frontometaphyseal dysplasia: mutations in FLNA and phenotypic diversity.

Frontometaphyseal dysplasia is an X-linked trait primarily characterized by a skeletal dysplasia comprising hyperostosis of the skull and modeling anomalies of the tubular bones. Extraskeletal features include tracheobronchial, cardiac, and urological malformations. A proportion of individuals have missense mutations or small deletions in the X-linked gene, FLNA. We report here our experience with comprehensive screening of the FLNA gene in a group of 23 unrelated probands (11 familial instances, 12 simplex cases; total affected individuals 32) with FMD. We found missense mutations leading to substitutions in the actin-binding domain and within filamin repeats 9, 10, 14, 16, 22, and 23 of filamin A in 13/23 (57%) of individuals in this cohort. Some mutations present with a male phenotype that is characterized by a severe skeletal dysplasia, cardiac, and genitourinary malformations that leads to perinatal death. Although no phenotypic feature consistently discriminates between females with FMD who are heterozygous for FLNA mutations and those in whom no FLNA mutation can be identified, there is a difference in the degree of skewing of X-inactivation between these two groups. This observation suggests that locus heterogeneity may exist for this disorder.