Clinical efficacy of a next-generation sequencing gene panel for primary immunodeficiency diagnostics.

Primary immunodeficiencies (PIDs) are rare monogenic inborn errors of immunity that result in impairment of functions of the human immune system. PIDs have a broad phenotype with increased morbidity and mortality, and treatment choices are often complex. With increased accessibility of next-generation sequencing (NGS), the rate of discovery of genetic causes for PID has increased exponentially. Identification of an underlying monogenic diagnosis provides important clinical benefits for patients with the potential to alter treatments, facilitate genetic counselling, and pre-implantation diagnostics. We investigated a NGS PID panel of 242 genes within clinical care across a range of PID phenotypes. We also evaluated Phenomizer to predict causal genes from human phenotype ontology (HPO) terms. Twenty-seven participants were recruited, and a total of 15 reportable variants were identified in 48% (13/27) of the participants. The panel results had implications for treatment in 37% (10/27) of participants. Phenomizer identified the genes harbouring variants from HPO terms in 33% (9/27) of participants. This study shows the clinical efficacy that genetic testing has in the care of PID. However, it also highlights some of the disadvantages of gene panels in the rapidly moving field of PID genomics and current challenges in HPO term assignment for PID.

Habitual levels of vigorous, but not moderate or light, physical activity is positively related to cortical bone mass in adolescents.

CONTEXT: The intensity of habitual physical activity (PA) needed to affect skeletal development in childhood is currently unclear. OBJECTIVE: To examine associations between light PA, moderate PA, and vigorous PA (as assessed by accelerometry), and tibial cortical bone mass (BMC(C)) as measured by peripheral quantitative computed tomography. DESIGN/SETTING: Cross-sectional analysis based on the Avon Longitudinal Study of Parents and Children. PARTICIPANTS: A total of 1748 boys and girls (mean age 15.5 yr) participated in the study. OUTCOME MEASURES: We measured BMC(C), cortical bone mineral density, periosteal circumference, and endosteal circumference by tibial peripheral quantitative computed tomography. RESULTS: Multivariable models, adjusted for height and other activity levels, indicated vigorous PA was positively related to BMC(C) (P = 0.0001). There was little evidence of a relationship with light PA or moderate PA (both P ≥ 0.7). In path analyses, the relationship between vigorous PA and BMC(C) [0.082 (95% confidence interval [CI]: 0.037, 0.128), P = 0.0004] (SD change per doubling of vigorous PA) was minimally attenuated by adjusting for body composition [0.070 (95% CI: 0.026, 0.115), P = 0.002]. In analyses adjusted for body composition, the relationship between vigorous PA and BMC(C) was explained by the periosteal circumference pathway [0.043 (95% CI: 0.004, 0.082), P = 0.03] and the endosteal circumference adjusted for periosteal circumference pathway [0.031 (95% CI: 0.011, 0.050), P = 0.002], while there was little contribution from the cortical bone mineral density pathway (P = 0.3). CONCLUSIONS: Vigorous day-to-day PA is associated with indices of BMC(C) and geometry in adolescents, whereas light or moderate PA has no detectable association. Therefore, promoting PA in childhood is unlikely to benefit skeletal development unless high-impact activities are also increased.

Further refinement of the critical minimal genetic region for the imprinting disorder 6q24 transient neonatal diabetes.

AIMS/HYPOTHESIS: Transient neonatal diabetes (TND) is associated with overexpression of genes within a critical region on 6q24. This study aims to refine the boundaries of this region to reduce the number of potential candidate genes for 6q24 TND. METHODS: Fifteen patients with transient neonatal diabetes and submicroscopic chromosome 6 duplications were investigated. The duplications were confirmed by microsatellite analysis and subsequently mapped using tiled chromosome 6 array Comparative Genomic Hybridisation (aCGH) and MLPA. Duplication boundaries were compared to identify the minimal shared region of duplication. These data were then used with available clinical data to identify associations between size of 6q24 duplication and severity of TND phenotype. RESULTS: Alignment of the minimal region of duplication to the human genome reduced the minimal TND critical region, formerly estimated at 440 kb, to 160-173 kb, revealing PLAGL1 (pleiomorphic adenoma gene-like 1) and HYMAI (imprinted in hydatidiform mole) to be the only genes wholly included therein. Additionally, the complete paternal duplication of a region containing the theoretical protein FAM164B was associated with the severe growth restriction observed in 6q24 duplication patients. CONCLUSIONS/INTERPRETATION: This study has significantly reduced the critical region associated with 6q24 TND. It has eliminated several previous TND candidate genes, leaving the overlapping imprinted genes PLAGL1 and HYMAI as the only remaining complete candidate genes for 6q24 TND. Moreover, these data provide the first evidence that an additional region, encompassing the theoretical protein FAM164B, may have a critical role in the growth restriction phenotype observed in many 6q24 TND patients.

Obesogenic diet and physical activity: independent or associated behaviours in adolescents?

OBJECTIVE: Associations between diet and physical activity may identify behaviours that could be changed together to prevent childhood obesity. The present study examines associations between physical activity and obesogenic dietary behaviours in a large UK adolescent cohort. DESIGN: Cross-sectional analysis of a UK cohort. Adolescents aged 10-11 years completed three 1 d diet diaries. Average daily energy consumption, percentage energy from fat and carbohydrate, energy density and grams of fruit and vegetables were estimated. To assess physical activity participants wore an accelerometer for three or more days. Regression models were run by sex to examine the extent to which dietary variables predicted physical activity before and after controlling for pubertal status, maternal education and adiposity. SETTING: The Avon Longitudinal Study of Parents and Children (ALSPAC), south-west England. SUBJECTS: Adolescents who provided diet data at age 10 years and physical activity data at age 11 years. RESULTS: Among boys, percentage energy from fat was consistently negatively associated with accelerometer-determined indicators of physical activity (standardized beta (beta) = -0.055 to -0.101, P < 0.05) while total energy (beta = 0.066 to 0.091, P < 0.05) and percentage energy from carbohydrate (beta = 0.054 to 0.106, P < 0.05) were positively associated before and after adjustment for confounders. For girls fruit and vegetable intake was consistently positively associated with physical activity (beta = 0.056 to 0.074, P < 0.005). However all associations were weak. Associations were broadly comparable when participants with non-plausible dietary reports were included or excluded from the analyses. CONCLUSIONS: Obesogenic diet and physical activity behaviours were weakly associated, suggesting that interventions should focus on implementing strategies that are independently successful at changing diet or physical activity behaviours either separately or in combination.

Myopia and later physical activity in adolescence: a prospective study.

OBJECTIVES: To investigate associations between objectively measured physical activity (PA) and myopia in children. METHODS: Children from the Avon Longitudinal Study of Parents and Children (ALSPAC) were asked to wear a uniaxial accelerometer for 7 days. Measures of counts per minute (cpm), minutes spent in moderate to vigorous activity (MVPA) and minutes of sedentary behaviour (msed) were derived from the accelerometer worn at age 12. Children were also examined, at age 10, using an autorefractor to estimate myopia. Social and parental factors were collected from pregnancy and physical measures of the child were recorded at age 12. RESULTS: 4880 children had valid PA and autorefraction data. In minimally adjusted models (age and gender) myopic children were less active than the other children: beta = -49.9 cpm (95% CI -73.5 to -26.4, p = <0.001). The myopic group spent less time in MVPA than the other children: beta = -3.2 minutes MVPA (95% CI -5.2 to -1.1, p = 0.003) and more time sedentary: beta = 15.8 minutes (95% CI 5.8 to 25.8, p = 0.002). The effect sizes were attenuated by adjustment for social and behavioural confounders although myopia status in the better (less myopic on autorefraction) eye remained strongly associated with cpm and MVPA but less so for sedentary behaviour: beta = -36.8 cpm (95% CI -67.8 to -5.8, p = 0.02), beta = -2.7 MVPA (95% CI -5.3 to -0.1, p = 0.04), beta = 10.1 msed (95% CI -2.9 to 23.1, p = 0.13). CONCLUSION: Myopic children may be more at risk of having lower levels of PA than their non-myopic peers, although the difference was modest.

Association of duration of television viewing in early childhood with the subsequent development of asthma.

OBJECTIVE: To investigate whether duration of television (TV) viewing in young children is associated with subsequent development of asthma. METHODS: Children taking part in the Avon Longitudinal Study of Parents and Children (ALSPAC) with no wheeze up to the age of 3.5 years and follow-up data at 11.5 years of age took part in a prospective longitudinal cohort study. The main outcome measure was asthma, defined as doctor-diagnosed asthma by 7.5 years of age with symptoms and/or treatment in the previous 12 months at 11.5 years of age. Parental report of hours of TV viewing per day by the children was ascertained at 39 months. RESULTS: In children with no symptoms of wheeze at 3.5 years of age and follow-up data at 11.5 years of age, the prevalence of asthma was 6% (185/3065). Increased TV viewing at 3.5 years was associated with increased prevalence of asthma at 11.5 years of age (p for linear trend = 0.0003). Children who watched television for >2 h/day were almost twice as likely to develop asthma by 11.5 years of age as those watching TV for 1-2 h/day (adjusted odds ratio 1.8 (95% CI 1.2 to 2.6)). CONCLUSION: Longer duration of TV viewing in children with no symptoms of wheeze at 3.5 years of age was associated with the development of asthma in later childhood.

AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes.

UNLABELLED: The undertaking of large-scale DNA sequencing screens for somatic variants in human cancers requires accurate and rapid processing of traces for variants. Due to their often aneuploid nature and admixed normal tissue, heterozygous variants found in primary cancers are often subtle and difficult to detect. To address these issues, we have developed a mutation detection algorithm, AutoCSA, specifically optimized for the high throughput screening of cancer samples. AVAILABILITY: http://www.sanger.ac.uk/genetics/CGP/Software/AutoCSA.

Comparative sequence analysis (CSA): a new sequence-based method for the identification and characterization of mutations in DNA.

Direct sequencing analysis is largely used to confirm and characterize mutations previously detected by more rapid tests. We have developed a method-Comparative Sequence Analysis (CSA)-that simplifies the analysis of sequencing data facilitating its use as a first screen for mutation detection. Sequence data were split into their component electrophoretograms and the use of a size standard enabled equivalent traces from different individuals to be overlaid. This allowed simple and rapid visual analysis of the results. Using this technique in a blind study, we tested 576 samples for mutations in the Von Hippel-Lindau tumor suppressor gene, VHL. We were able to identify and characterize all 78 known mutations present within the sample set (100% sensitivity and specificity).