Next-generation sequencing for diagnosis of rare diseases in the neonatal intensive care unit.

BACKGROUND: Rare diseases often present in the first days and weeks of life and may require complex management in the setting of a neonatal intensive care unit (NICU). Exhaustive consultations and traditional genetic or metabolic investigations are costly and often fail to arrive at a final diagnosis when no recognizable syndrome is suspected. For this pilot project, we assessed the feasibility of next-generation sequencing as a tool to improve the diagnosis of rare diseases in newborns in the NICU. METHODS: We retrospectively identified and prospectively recruited newborns and infants admitted to the NICU of the Children's Hospital of Eastern Ontario and the Ottawa Hospital, General Campus, who had been referred to the medical genetics or metabolics inpatient consult service and had features suggesting an underlying genetic or metabolic condition. DNA from the newborns and parents was enriched for a panel of clinically relevant genes and sequenced on a MiSeq sequencing platform (Illumina Inc.). The data were interpreted with a standard informatics pipeline and reported to care providers, who assessed the importance of genotype-phenotype correlations. RESULTS: Of 20 newborns studied, 8 received a diagnosis on the basis of next-generation sequencing (diagnostic rate 40%). The diagnoses were renal tubular dysgenesis, SCN1A-related encephalopathy syndrome, myotubular myopathy, FTO deficiency syndrome, cranioectodermal dysplasia, congenital myasthenic syndrome, autosomal dominant intellectual disability syndrome type 7 and Denys-Drash syndrome. INTERPRETATION: This pilot study highlighted the potential of next-generation sequencing to deliver molecular diagnoses rapidly with a high success rate. With broader use, this approach has the potential to alter health care delivery in the NICU.

Late diagnosis of cerebral folate deficiency: Fewer seizures with folinic acid in adult siblings.

Cerebral folate deficiency is a genetically heterogeneous condition.(1) Mutations in FOLR1 are responsible for a rare but treatable form of cerebral folate deficiency (OMIM #613068).(1) The gene codes for folate receptor alpha (FRα), a specific CNS folate transporter. Individuals with FOLR1-related folate deficiency present with ataxia, dyskinesia, spasticity, seizures, and regression in cognitive abilities and motor skills during early childhood.(2) Seizures commonly observed include generalized tonic-clonic, atonic, and myoclonic.(3) To date, there have been 18 individuals with FOLR1-related cerebral folate deficiency diagnosed in childhood and reported in the literature.(3-5) Early diagnosis is crucial, as high-dose folinic acid (2-5 mg/kg/day) has been reported to be an effective treatment that can ameliorate or even prevent further neurodegeneration, although no long-term treatment studies have been performed.(1,3,5,6) We present the late diagnosis of adult siblings with cerebral folate deficiency due to FOLR1 mutations and their subsequent treatment.

Case report of novel DYRK1A mutations in 2 individuals with syndromic intellectual disability and a review of the literature.

BACKGROUND: Chromosomal deletions encompassing DYRK1A have been associated with intellectual disability for several years. More recently, point mutations in DYRK1A have been shown to be responsible for a recognizable syndrome characterized by microcephaly, developmental delay and intellectual disability (ID) as well as characteristic facial features. Here we present 2 individuals with novel mutations in DYRK1A, and a review of the cases reported to date. CASE PRESENTATION: Both individuals presented with the well-known characteristic features, as well as rarer anomalies seen in a minority of patients. Patient 1 presented shortly after birth with an enlarged cisterna magna, distal contractures, and distinctive facies that included bitemporal narrowing and deep set eyes. A de novo splice site mutation in DYRK1A [c.951 + 4_951 + 7delAGTA; p.Val222Aspfs*22] was identified by next generation sequencing. Patient 2 presented at 7 months of age with microcephaly and dysmorphic features. She went several years without a diagnosis until a de novo DYRK1A nonsense mutation [c.787C>T; p.(Arg263*)] was identified at age 12. These individuals, and the 52 cases reviewed from the literature, show the characteristic features of the DYRK1A-related syndrome including global developmental delay, ID, microcephaly, feeding difficulties, and the facial gestalt. Other common findings include seizures, vision defects, brain abnormalities and skeletal abnormalities of the hands and feet. Less common features include optic nerve defects, contractures, ataxia, and cardiac anomalies. CONCLUSION: DYRK1A testing should be considered in individuals with the facial features, intellectual disability and post-natal microcephaly. Once diagnosed with DYRK1A-related intellectual disability, a cardiac and ophthalmologic assessment would be recommended as would routine surveillance by a pediatrician for psychomotor development, growth, and feeding.

Identification of a pathogenic FTO mutation by next-generation sequencing in a newborn with growth retardation and developmental delay.

BACKGROUND: A homozygous loss-of-function mutation p.(Arg316Gln) in the fat mass and obesity-associated (FTO) gene, which encodes for an iron and 2-oxoglutarate-dependent oxygenase, was previously identified in a large family in which nine affected individuals present with a lethal syndrome characterised by growth retardation and multiple malformations. To date, no other pathogenic mutation in FTO has been identified as a cause of multiple congenital malformations. METHODS: We investigated a 21-month-old girl who presented distinctive facial features, failure to thrive, global developmental delay, left ventricular cardiac hypertrophy, reduced vision and bilateral hearing loss. We performed targeted next-generation sequencing of 4813 clinically relevant genes in the patient and her parents. RESULTS: We identified a novel FTO homozygous missense mutation (c.956C>T; p.(Ser319Phe)) in the affected individual. This mutation affects a highly conserved residue located in the same functional domain as the previously characterised mutation p.(Arg316Gln). Biochemical studies reveal that p.(Ser319Phe) FTO has reduced 2-oxoglutarate turnover and N-methyl-nucleoside demethylase activity. CONCLUSION: Our findings are consistent with previous reports that homozygous mutations in FTO can lead to rare growth retardation and developmental delay syndrome, and further support the proposal that FTO plays an important role in early development of human central nervous and cardiovascular systems.

The evaluation of pre and post processing semen analysis parameters at the time of intrauterine insemination in couples diagnosed with male factor infertility and pregnancy rates based on stimulation agent. A retrospective cohort study.

OBJECTIVE: To identify pre or post processing semen analysis parameters that may be predictive of successful pregnancy in couples with male factor infertility undergoing intra uterine insemination (IUI). To evaluate the pregnancy rate based on ovulation inducing agent in couples with male factor infertility per the 2010 world health organization criteria treated with IUI. STUDY DESIGN: This retrospective study was performed at Stanford University medical center. All couples with male factor infertility fitting inclusion criteria were included over a 2 year period of time. 147 couples with male factor infertility were included and 356 IUIs were analyzed. All subjects in this study had Kruger strict analysis >4% normal forms. Logistic regression analysis was used to control for confounding effects and multiplicity. RESULTS: The overall pregnancy rate was 5.3%. No parameter in either the pre or post analysis predicted pregnancy. Furthermore, it was found that natural cycle and letrazole treatment had similar pregnancy rates (3% and 3%) p=ns. Similar outcomes were also observed between clomiphene citrate and gonadotropin stimulated cycles (7.5% and 6.0%) p=ns. CONCLUSIONS: Total motile sperm count which has been found to be a predictor of pregnancy when evaluated in isolation, may be due to a confounding effect. These low pregnancy rates should be considered when deciding whether to suggest IUI and when selecting a protocol for ovulation induction for couples with male factor infertility.