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BackgroundCongenital diaphragmatic hernia (CDH) is a life-threatening birth defect that often co-occurs with non-hernia-related anomalies (CDH+). While copy number variant (CNV) analysis is often employed as a diagnostic test for CDH+, clinical exome sequencing (ES) has not been universally adopted.MethodsWe analysed a clinical database of ~12 000 test results to determine the diagnostic yields of ES in CDH+ and to identify new phenotypic expansions.ResultsAmong the 76 cases with an indication of CDH+, a molecular diagnosis was made in 28 cases for a diagnostic yield of 37% (28/76). A provisional diagnosis was made in seven other cases (9%; 7/76). Four individuals had a diagnosis of Kabuki syndrome caused by frameshift variants in KMT2D. Putatively deleterious variants in ALG12and EP300were each found in two individuals, supporting their role in CDH development. We also identified individuals with de novo pathogenic variants in FOXP1and SMARCA4, and compound heterozygous pathogenic variants in BRCA2. The role of these genes in CDH development is supported by the expression of their mouse homologs in the developing diaphragm, their high CDH-specific pathogenicity scores generated using a previously validated algorithm for genome-scale knowledge synthesis and previously published case reports.ConclusionWe conclude that ES should be ordered in cases of CDH+ when a specific diagnosis is not suspected and CNV analyses are negative. Our results also provide evidence in favour of phenotypic expansions involving CDH for genes associated with ALG12-congenital disorder of glycosylation, Rubinstein-Taybi syndrome, Fanconi anaemia, Coffin-Siris syndrome and FOXP1-related disorders.

Aluelements, the short interspersed element numbering more than 1 million copies per human genome, can mediate the formation of copy number variants (CNVs) between substrate pairs. These Alu/Alu-mediated rearrangements (AAMRs) can result in pathogenic variants that cause diseases. To investigate the impact of AAMR on gene variation and human health, we first characterized Alus that are involved in mediating CNVs (CNV-Alus) and observed that these Alus tend to be evolutionarily younger. We then computationally generated, with the assistance of a supercomputer, a test data set consisting of 78 million Alupairs and predicted ∼18% of them are potentially susceptible to AAMR. We further determined the relative risk of AAMR in 12,074 OMIM genes using the count of predicted CNV-Alupairs and experimentally validated the predictions with 89 samples selected by correlating predicted hotspots with a database of CNVs identified by clinical chromosomal microarrays (CMAs) on the genomes of approximately 54,000 subjects. We fine-mapped 47 duplications, 40 deletions, and two complex rearrangements and examined a total of 52 breakpoint junctions of simple CNVs. Overall, 94% of the candidate breakpoints were at least partially Alumediated. We successfully predicted all (100%) of Alupairs that mediated deletions (n= 21) and achieved an 87% positive predictive value overall when including AAMR-generated deletions and duplications. We provided a tool, AluAluCNVpredictor, for assessing AAMR hotspots and their role in human disease. These results demonstrate the utility of our predictive model and provide insights into the genomic features and molecular mechanisms underlying AAMR.

IMPORTANCE Patients with rare diseases and complex clinical presentations represent a challenge for clinical diagnostics. Genomic approaches are allowing the identification of novel variants in genes for very rare disorders, enabling a molecular diagnosis. Genomics is also revealing a phenotypic expansion whereby the full spectrum of clinical expression conveyed by mutant alleles at a locus can be better appreciated. OBJECTIVE To elucidate the molecular cause of a complex neuropathy phenotype in 3 patients by applying genomic sequencing strategies. DESIGN, SETTING, AND PARTICIPANTS Three affected individuals from 2 unrelated families presented with a complex neuropathy phenotype characterized by axonal sensorimotor neuropathy and microcephaly. They were recruited into the Centers for Mendelian Genomics research program to identify the molecular cause of their phenotype. Whole-genome, targeted whole-exome sequencing, and high-resolution single-nucleotide polymorphism arrays were performed in genetics clinics of tertiary care pediatric hospitals and biomedical research institutions. MAIN OUTCOMES AND MEASURES Whole-genome and whole-exome sequencing identified the variants responsible for the patients’ clinical phenotype. RESULTS We identified compound heterozygous alleles in 2 affected siblings from 1 family and a homozygous nonsense variant in the third unrelated patient in the vaccinia-related kinase 1 gene (VRK1). In the latter subject, we found a common haplotype on which the nonsense mutation occurred and that segregates in the Ashkenazi Jewish population. CONCLUSIONS AND RELEVANCE We report the identification of disease-causing alleles in 3 children from 2 unrelated families with a previously uncharacterized complex axonal motor and sensory neuropathy accompanied by severe nonprogressive microcephaly and cerebral dysgenesis. Our data raise the question of whether VRK1 mutations disturb cell cycle progression and may result in apoptosis of cells in the nervous system. The application of unbiased genomic approaches allows the identification of potentially pathogenic mutations in unsuspected genes in highly genetically heterogeneous and uncharacterized neurological diseases.

Mendelian disease genomic research has undergone a massive transformation over the past decade. With increasing availability of exome and genome sequencing, the role of Mendelian research has expanded beyond data collection, sequencing, and analysis to worldwide data sharing and collaboration.

Purpose:Mutational load of susceptibility variants has not been studied on a genomic scale in a clinical population, nor has the potential to identify these mutations as incidental findings during clinical testing been systematically ascertained.Methods:Array comparative genomic hybridization, a method for genome-wide detection of DNA copy-number variants, was performed clinically on DNA from 9,005 individuals. Copy-number variants encompassing or disrupting single genes were identified and analyzed for their potential to confer predisposition to dominant, adult-onset disease. Multigene copy-number variants affecting dominant, adult-onset cancer syndrome genes were also assessed.Results:In our cohort, 83 single-gene copy-number variants affected 40 unique genes associated with dominant, adult-onset disorders and unrelated to the patients’ referring diagnoses (i.e., incidental) were found. Fourteen of these copy-number variants are likely disease-predisposing, 25 are likely benign, and 44 are of unknown clinical consequence. When incidental copy-number variants spanning up to 20 genes were considered, 27 copy-number variants affected 17 unique genes associated with dominant, adult-onset cancer predisposition.Conclusion:Copy-number variants potentially conferring susceptibility to adult-onset disease can be identified as incidental findings during routine genome-wide testing. Some of these mutations may be medically actionable, enabling disease surveillance or prevention; however, most incidentally observed single-gene copy-number variants are currently of unclear significance to the patient.Genet Med 2013:15(1):45–54

Purpose:A number of genes in the 9q34.11 region may be haploinsufficient. However, studies analyzing genotype–phenotype correlations of deletions encompassing multiple dosage-sensitive genes in the region are lacking.Methods:We mapped breakpoints of 10 patients with 9q34.11 deletions using high-resolution 9q34-specific array comparative genomic hybridization (CGH) to determine deletion size and gene content.Results:The 9q34.11 deletions range in size from 67?kb to 2.8?Mb. Six patients exhibit intellectual disability and share a common deleted region including STXBP1; four manifest variable epilepsy. In five subjects, deletions include SPTAN1, previously associated with early infantile epileptic encephalopathy, infantile spasms, intellectual disability, and hypomyelination. In four patients, the deletion includes endoglin (ENG), causative of hereditary hemorrhagic telangiectasia. Finally, in four patients, deletions involve TOR1A, of which molecular defects lead to early-onset primary dystonia. Ninety-four other RefSeq genes also map to the genomic intervals investigated.Conclusion:STXBP1 haploinsufficiency results in progressive encephalopathy characterized by intellectual disability and may be accompanied by epilepsy, movement disorders, and autism. We propose that 9q34.11 genomic deletions involving ENG, TOR1A, STXBP1, and SPTAN1 are responsible for multisystemic vascular dysplasia, early-onset primary dystonia, epilepsy, and intellectual disability, therefore revealing cis-genetic effects leading to complex phenotypes.Genet Med 2012:14(10):868–876

A number of genes in the 9q34.11 region may be haploinsufficient. However, studies analyzing genotype–phenotype correlations of deletions encompassing multiple dosage-sensitive genes in the region are lacking.

The rates of decay of O(3P) atoms in H2/CO/N2mixtures in a discharge flow system have been measured, using O + CO chemiluminescence. The mechanism is: O + H2→ OH + H (1), O + OH → O2+ H (2), CO + OH → CO2+ H (3). At 425 K, k2/k3= 260 ± 20; literature values of k3combine to yield k2= (2.65 ± 0.52) × 1010dm3mol−1s−1.

The present study examined the impact of rational emotive education (REE) on locus of control, rationality and anxiety in order to evaluate REE's potential in promoting the psychological adjustment and growth of Year 4 primary school children. Individual differences in the external-internal dimension of locus of control were considered a possible predictor of intervention outcome. The sample consisted of two regular Year 4 classes in a private girls school in metropolitan Melbourne which were randomly assigned to either REE or attention control condition. Results indicated that REE was effective in increasing children's perception of internal control and rationality and that program effectiveness in increasing children's rationality was not associated with their pre-intervention locus of control orientation. No evidence was found for REE's efficacy in producing significant changes in trait anxiety.

Responses on the 31-item Gender Dysphoria (Gd) scale of the MMPI of 104 primary gender-dysphoric males who had undergone or were about to undergo gender-reassignment surgery, 25 secondary gender-dysphoric patients from the same clinics, and 563 male psychiatric outpatients were tabulated and specificities and sensitivities calculated. The scale had satisfactory specificity, correctly identifying 98.1% of subjects. Sensitivity was unsatisfactory (40%) in distinguishing secondary gender-dysphorics in the Gender Clinic samples but adequate (88.4%) in the combined psychiatric outpatient and Gender Clinic samples. Factor analysis yielded 8 dimensions, but only 2 of these were easily interpretable or had sufficient items to ensure reliability, suggesting that there was little possibility of utilizing subscales. It is concluded that the Gdscale is an appropriate instrument for excluding primary gender dysphoria when used in conjunction with conventional diagnostic assessments.

The hypothesis that annual climatic variation can affect the nutritive value of host-plant tissue for a herbivore was tested. Larvae of a single generation of western spruce budworm, Choristoneura occidentalis Free., were fed foliages that had been collected on five consecutive springs from a stand of balsam fir Abies balsamea (L.) Mill. Budworm of both sexes were about 20 percent heavier at pupation when fed folages that had been produced in early rather than later spring seasons. This could result in an estimated 25 percent difference in the reproductive rate of females. It is concluded that annual variations in spring climate can affect the nutritive value of forage.