Use of genome sequencing to hunt for cryptic second-hit variants: analysis of 31 cases recruited to the 100 000 Genomes Project.

BACKGROUND: Current clinical testing methods used to uncover the genetic basis of rare disease have inherent limitations, which can lead to causative pathogenic variants being missed. Within the rare disease arm of the 100 000 Genomes Project (100kGP), families were recruited under the clinical indication 'single autosomal recessive mutation in rare disease'. These participants presented with strong clinical suspicion for a specific autosomal recessive disorder, but only one suspected pathogenic variant had been identified through standard-of-care testing. Whole genome sequencing (WGS) aimed to identify cryptic 'second-hit' variants. METHODS: To investigate the 31 families with available data that remained unsolved following formal review within the 100kGP, SVRare was used to aggregate structural variants present in <1% of 100kGP participants. Small variants were assessed using population allele frequency data and SpliceAI. Literature searches and publicly available online tools were used for further annotation of pathogenicity. RESULTS: Using these strategies, 8/31 cases were solved, increasing the overall diagnostic yield of this cohort from 10/41 (24.4%) to 18/41 (43.9%). Exemplar cases include a patient with cystic fibrosis harbouring a novel exonic LINE1 insertion in CFTR and a patient with generalised arterial calcification of infancy with complex interlinked duplications involving exons 2-6 of ENPP1. Although ambiguous by short-read WGS, the ENPP1 variant structure was resolved using optical genome mapping and RNA analysis. CONCLUSION: Systematic examination of cryptic variants across a multi-disease cohort successfully identifies additional pathogenic variants. WGS data analysis in autosomal recessive rare disease should consider complex structural and small intronic variants as potentially pathogenic second hits.

Sedaghatian spondylometaphyseal dysplasia in two siblings.

Sedaghatian type spondylometaphyseal dysplasia (SSMD) is a rare skeletal dysplasia with only 24 reported cases to date. Despite the limited literature available, evidence suggests this is a multi-system disorder, with neurological and cardiovascular abnormalities reported in addition to the skeletal features. We report a new family with two affected siblings and detailed phenotypic description of the affected proband. Diagnosis in the neonatal period led to retrospective genetic diagnosis of a previous affected pregnancy that was terminated due to severe ventriculomegaly. We suggest that a diagnosis of SSMD should be considered when shortened long bones are found in combination with significant brain abnormalities.

Kosaki Overgrowth Syndrome: Report of a Family with a Novel PDGFRB Variant.

Heterozygous activating missense variants of PDGFRB are associated with the phenotype of Kosaki overgrowth syndrome (KOGS). Here, we present a family including a father and 2 siblings with a novel variant, c.2567A>T (p.Asn856Ile), localized in the cytoplasmic tyrosine kinase domain, exhibiting a KOGS phenotype. The coarsening of the facial features, enlargement of the hands/feet, and progressive scoliosis started to appear after an average age of 6. There were no signs of thin/fragile skin, premature aging appearance, myofibroma, white matter findings, and intellectual disability in any of them. Corneal pterygium and evidence of cerebral vasculopathy were only detected in the father. One sibling exhibited café-au-lait spots. Posterior fossa enlargement was revealed only in one sibling. KOGS is an extremely rare overgrowth syndrome. No familial cases of KOGS have been reported so far. Hereby, we demonstrated that the features of KOGS can show mild intrafamilial variability, and the risk of vascular complications may arise with age.

Novel pathogenic variants and quantitative phenotypic analyses of Robinow syndrome: WNT signaling perturbation and phenotypic variability.

Robinow syndrome (RS) is a genetically heterogeneous disorder with six genes that converge on the WNT/planar cell polarity (PCP) signaling pathway implicated (DVL1, DVL3, FZD2, NXN, ROR2, and WNT5A). RS is characterized by skeletal dysplasia and distinctive facial and physical characteristics. To further explore the genetic heterogeneity, paralog contribution, and phenotypic variability of RS, we investigated a cohort of 22 individuals clinically diagnosed with RS from 18 unrelated families. Pathogenic or likely pathogenic variants in genes associated with RS or RS phenocopies were identified in all 22 individuals, including the first variant to be reported in DVL2. We retrospectively collected medical records of 16 individuals from this cohort and extracted clinical descriptions from 52 previously published cases. We performed Human Phenotype Ontology (HPO) based quantitative phenotypic analyses to dissect allele-specific phenotypic differences. Individuals with FZD2 variants clustered into two groups with demonstrable phenotypic differences between those with missense and truncating alleles. Probands with biallelic NXN variants clustered together with the majority of probands carrying DVL1, DVL2, and DVL3 variants, demonstrating no phenotypic distinction between the NXN-autosomal recessive and dominant forms of RS. While phenotypically similar diseases on the RS differential matched through HPO analysis, clustering using phenotype similarity score placed RS-associated phenotypes in a unique cluster containing WNT5A, FZD2, and ROR2 apart from non-RS-associated paralogs. Through human phenotype analyses of this RS cohort and OMIM clinical synopses of Mendelian disease, this study begins to tease apart specific biologic roles for non-canonical WNT-pathway proteins.

Diagnostic yield of rare skeletal dysplasia conditions in the radiogenomics era.

BACKGROUND: Skeletal dysplasia (SD) conditions are rare genetic diseases of the skeleton, encompassing a heterogeneous group of over 400 disorders, and represent approximately 5% of all congenital anomalies. Developments in genetic and treatment technologies are leading to unparalleled therapeutic advances; thus, it is more important than ever to molecularly confirm SD conditions. Data on 'rates-of-molecular yields' in SD conditions, through exome sequencing approaches, is limited. Figures of 39% and 52.5% have been reported in the USA (n = 54) and South Korea (n = 185) respectively. METHODS: We discuss a single-centre (in the UK) experience of whole-exome sequencing (WES) in a cohort of 15 paediatric patients (aged 5 months to 12 years) with SD disorders previously molecularly unconfirmed. Our cohort included patients with known clinical diagnoses and undiagnosed skeletal syndromes. Extensive phenotyping and expert radiological review by a panel of international SD radiology experts, coupled with a complex bioinformatics pipeline, allowed for both gene-targeted and gene-agnostic approaches. RESULTS: Significant variants leading to a likely or confirmed diagnosis were identified in 53.3% (n = 8/15) of patients; 46.7% (n = 7/15) having a definite molecular diagnosis and 6.7% (n = 1/15) having a likely molecular diagnosis. We discuss this in the context of a rare disease in general and specifically SD presentations. Of patients with known diagnoses pre-WES (n = 10), molecular confirmation occurred in 7/10 cases, as opposed to 1/5 where a diagnosis was unknown pre-test. Thus, diagnostic return is greatest where the diagnosis is known pre-test. For WGS (whole genome sequencing, the next iteration of WES), careful case selection (ideally of known diagnoses pre-test) will yield highest returns. CONCLUSIONS: Our results highlight the cost-effective use of WES-targeted bioinformatic analysis as a diagnostic tool for SD, particularly patients with presumed SD, where detailed phenotyping is essential. Thorough co-ordinated clinical evaluation between clinical, radiological, and molecular teams is essential for improved yield and clinical care. WES (and WGS) yields will increase with time, allowing faster diagnoses, avoiding needless investigations, ensuring individualised patient care and patient reassurance. Further diagnoses will lead to increased information on natural history/mechanistic details, and likely increased therapies and clinical trials.

AIFM1-associated X-linked spondylometaphyseal dysplasia with cerebral hypomyelination.

Spondylometaphyseal dysplasia with cerebral hypomyelination (SMD-H) is a very rare but distinctive phenotype, unusually combining spondylometaphyseal dysplasia with hypomyelinating leukodystrophy. Recently, SMD-H has been associated with variants confined to a specific intra-genic locus involving Exon 7, suggesting that AIFM1 plays an important role in bone development and metabolism as well as cerebral myelination. Here we describe two further affected boys, one with a novel intronic variant associated with skipping of Exon 7 of AIFM1 and the other a synonymous variant within Exon 7 of AIFM1. We describe their clinical course and radiological and genetic findings, providing further insight into the natural history of this condition.

Pediatric radiology in the diagnosis and management of skeletal dysplasias - welcome to the era of genomic medicine and modern drug pipelines.

Radiologists have long played a key role in the diagnosis and management of children with suspected skeletal dysplasia. Advancing molecular sciences, including the emergence of next generation sequencing and the development of modern rapid drug pipelines have the potential to transform this role.

Major skull manifestations of skeletal dysplasias - pictorial essay.

Skeletal dysplasias are a large group of rare conditions with widely heterogeneous manifestations and a reputation for being diagnostically difficult. Involvement of the brain and craniovertebral junction are features familiar to the paediatric neuroradiologist. Involvement of the skull itself represents an area of overlap between the domains of the neuroradiologist and the skeletal dysplasia radiologist. In this pictorial essay, we review the principal skull manifestations of skeletal dysplasias as they present to the neuroradiologist.

Juvenile Paget's disease with compound heterozygous mutations in TNFRSF11B presenting with recurrent clavicular fractures and a mild skeletal phenotype.

Juvenile Paget's disease (JPD) is a rare recessively-inherited bone dysplasia. The great majority of cases described to date have had homozygous mutations in TNFRSF11B, the gene encoding osteoprotegerin. We describe a boy who presented with recurrent clavicular fractures following minor trauma (8 fractures from age 2 to 11). He was of normal height and despite mild lateral bowing of the thighs and anterior bowing of the shins he remained physically active. Abnormal modelling was noted in ribs and humeri on clavicular radiographs, and a skeletal survey at the age of 7 showed generalised diaphyseal expansion of the long bones with thickening of the periosteal and endosteal surfaces of the cortices. On biochemical evaluation, serum alkaline phosphatase was noted to be persistently elevated. The diagnosis of JPD was confirmed by the finding of compound heterozygous mutations in TNFRSF11B: a maternally-inherited A>G missense mutation at position 1 of the first amino acid codon (previously reported) and a paternally-inherited splice acceptor site mutation in intron 3 at a highly conserved position (not previously reported). Bioinformatics analysis suggested both mutations were disease-causing. Compound heterozygote mutations in TNFRSF11B causing JPD have been previously reported only once - in a boy who also had a relatively mild skeletal phenotype. The milder features may lead to delay in diagnosis and diagnostic confusion with other entities, but the extraskeletal features of JPD may nonetheless develop.

A three-generation family with metaphyseal dysplasia, maxillary hypoplasia and brachydactyly (MDMHB) due to intragenic RUNX2 duplication.

Metaphyseal dysplasia with maxillary hypoplasia and brachydactyly (MDMHB) is an autosomal-dominant skeletal dysplasia characterised by metaphyseal flaring of the long bones, enlargement of the medial halves of the clavicles, maxillary hypoplasia, brachydactyly, dental anomalies and mild osteoporosis. To date, only one large French Canadian family and a Finnish woman have been reported with the condition. In both, intragenic duplication encompassing exons 3-5 of the RUNX2 gene was identified. We describe a new, three-generation family with clinical features of MDMHB and an intragenic tandem duplication of RUNX2 exons 3-6. Dental problems were the primary presenting feature in all four affected individuals. We compare the features in our family to those previously reported in MDMHB, review the natural history of this condition and highlight the importance of considering an underlying skeletal dysplasia in patients presenting with significant dental problems and other suggestive features, including disproportionate short stature and/or digital anomalies.

Metaphyseal dysplasia, Spahr type; missense MMP13 mutations in two Iraqi siblings.

We report on two siblings of Iraqi descent with clinical and radiographic features of metaphyseal dysplasia, Spahr type (MDST), born to consanguineous unaffected parents. Molecular testing confirmed pathogenic mutations in MMP13. We review the considerable overlap between MDST and other related disorders. These cases confirm the phenotypic variability and regressive nature of MDST in addition to suggesting bone fragility as a feature.

Achondroplasia: Really rhizomelic?

Achondroplasia is the most common form of short limb dwarfism in humans. The shortening of the limb lengths in achondroplasia is widely described as "rhizomelic." While this appearance may be convincing clinically, the description is not necessarily true or helpful radiologically. The aims of this study, were therefore, to determine whether rhizomelic shortening is a true feature of achondroplasia at diagnosis in infancy. Humeral, radial, femoral, and tibial diaphyseal lengths were recorded by two independent observers from 22 skeletal surveys of infants with achondroplasia and compared with 150 normal age-matched control subjects. Upper and lower limb bone length ratios (radial/humeral and tibial/femoral lengths, respectively) in both groups were compared using an unpaired t-test. Mean upper limb length ratios were statistically higher within the achondroplasia group at 0.87 ± 0.04 (n = 22, mean age 70 ± 94 days) compared to normal controls at 0.79 ± 0.02 (n = 150, mean age 113 days ± 88 days; P < 0.0001). Lower limb length ratios were not significantly different between groups (0.84 ± 0.04 vs. 0.83 ± 0.02, P = 0.46). There was good inter-observer agreement of limb length measurements, with an average measurement difference of 0.1 ± 1.4 mm. In conclusion, infants with achondroplasia demonstrate statistically significant rhizomelic shortening within the upper limbs, but not lower limbs at diagnosis, compared to normal controls. The term "rhizomelic shortening" in relation to achondroplasia should be reserved when describing upper limb proportions. © 2016 Wiley Periodicals, Inc.

Radiology of Osteogenesis Imperfecta, Rickets and Other Bony Fragility States.

This section gives an overview of radiological findings in bony fragility states, with a special focus on osteogenesis imperfecta (OI) and rickets. Conventional radiological assessment of bone density is inaccurate and imprecise and only reliably detects severe osteopaenia. However, other aspects of bone structure and morphology can be assessed, and it is possible to distinguish between osteopaenic and osteomalacic states. OI is a heterogeneous group of disorders of type 1 collagen formation and processing that are characterised by varying degrees of bony fragility, with presentations varying from perinatal lethality to asymptomatic. Radiological diagnosis of severe forms is usually straightforward, but that of milder disease may be challenging because specific features are often absent. However, a multidisciplinary approach is usually successful. Features of OI, including Wormian bones, skull base deformities, vertebral involvement and long bone fractures and deformities, are reviewed in this section. Rickets is best defined as a disorder of the growth plate characterised by the impaired apoptosis of hypertrophied chondrocytes. Vitamin D deficiency is a common cause of rickets. The patho-anatomical basis of radiological findings in rickets is reviewed and illustrated. Rickets is frequently accompanied by hyperparathyroidism and osteomalacia. Rickets used to be classified as calciopaenic or phosphopaenic but is now referred to as parathyroid hormone or fibroblast growth factor 23 mediated, respectively [1]. The radiological features of the two forms are reviewed.

A review of imaging protocols for suspected skeletal dysplasia and a proposal for standardisation.

Expert radiology opinions are often requested to aid diagnosis of skeletal dysplasias or dysostoses, but due to variability in the imaging protocols used at different centres the views presented may be considered inadequate or incomplete resulting in diagnostic delays and increased patient and family anxiety. We propose the introduction of a standardised protocol that may be adapted in certain specific situations.

Foetal radiography for suspected skeletal dysplasia: technique, normal appearances, diagnostic approach.

Despite advances in antenatal imaging and genetic techniques, post-delivery post-mortem foetal radiography remains the key investigation in accurate diagnosis of skeletal dysplasia manifesting in the foetus. Foetal radiography is best performed using pathology-specimen radiography equipment and is often carried out in the pathology department without involvement of the radiology unit. However, paediatric radiologists may be asked to interpret post-mortem foetal radiographs when an abnormality is suspected. Many foetal radiographs are carried out before 20 weeks' gestation, and the interpreting radiologist needs to be familiar with the range of normal post-mortem foetal appearances at different gestational ages, as well as the appearances of some of the more commonly presenting skeletal dysplasias, and will benefit from a systematic approach when assessing more challenging cases. In this pictorial essay, we illustrate various normal post-mortem foetal radiographic appearances, give examples of commonly occurring skeletal dysplasias, and describe an approach to establishing more difficult diagnoses.

Scoring of chest CT in children with cystic fibrosis: state of the art.

Chest CT has been proposed as a surrogate outcome measure in the evaluation of cystic fibrosis lung disease. Quantitative evaluation of chest CT findings requires application of a scoring system to derive numerical values. Several scoring systems are in use. These mostly rely on a subjective judgement of the severity and extent of various features of cystic fibrosis lung disease, including bronchiectasis, bronchial wall thickening, mucous plugging and air-trapping. Scores can subsequently be added to produce a total score. The precision or reproducibility of scoring systems has been assessed but with heterogeneous statistical approaches. Total scores appear to have high levels of reproducibility, but this might mask poorer levels of agreement for individual observations and component scores. It can also be questioned whether total scores are biologically meaningful, as compared to assessments of individual features. Various studies suggest that CT scores give an accurate indicator of the severity of disease, and CT scores might be the best predictors of long-term outcome, but data in this area are limited. CT scores are more sensitive than traditional lung-function indices such as FEV; however the lung clearance index, by multiple breath washout, appears to offer comparable sensitivity to CT. It is not clear whether CT scores are adequately responsive to changes in disease severity in the short to medium term; this is a challenge to the use of CT as a surrogate outcome measure for clinical trials of therapies specific to cystic fibrosis. Cystic fibrosis scoring would benefit from greater levels of standardisation in terms of CT techniques, scoring system, training of observers and measures of reproducibility. Automated approaches to quantifying CT parameters might also offer improved precision. The benefits of chest CT must be weighed against the principal drawback of radiation exposure. The case for more widespread use of chest CT would be strengthened if precision of CT scoring were improved.

Contrast-enhanced magnetic resonance angiography for the detection of crossing renal vessels in children with symptomatic ureteropelvic junction obstruction: comparison with operative findings.

BACKGROUND: Crossing renal vessels (CRV) are associated with ureteropelvic junction (UPJ) obstruction, particularly when presentation is beyond the neonatal period. Their presence may influence surgical management. OBJECTIVE: To evaluate the accuracy of contrast-enhanced magnetic resonance angiography (CE-MRA) in the identification of CRV in children requiring surgical treatment of symptomatic UPJ obstruction, against a gold standard of laparoscopic or open surgical findings. MATERIALS AND METHODS: We reviewed CE-MRA studies (3-D T2-weighted turbo spin-echo and multiphase 3-D spoiled gradient echo following intravenous gadolinium administration) of 14 children, age range 6-15 years, performed prior to surgery for suspected CRV-related UPJ obstruction. Consensus reviews of the CE-MRA studies were compared with surgical findings. RESULTS: CE-MRA demonstrated CRV at the level of the obstruction in nine and no crossing vessels in five children. These were all verified intraoperatively (chi2=14.0; P<0.001). In eight of the nine patients with CRV there was no evidence of intrinsic obstruction at surgery. In the remaining patient there was fibrosis of the upper ureter. CONCLUSION: CE-MRA is an accurate means of identifying CRV in children older than 6 years with symptomatic UPJ obstruction.