Common single-base insertions in the VNTR of the carboxyl ester lipase (CEL) gene are benign and also likely to arise somatically in the exocrine pancreas.

The CEL gene encodes carboxyl ester lipase, a pancreatic digestive enzyme. CEL is extremely polymorphic due to a variable number tandem repeat (VNTR) located in the last exon. Single-base deletions within this VNTR cause the inherited disorder MODY8, whereas little is known about VNTR single-base insertions in pancreatic disease. We therefore mapped CEL insertion variants (CEL-INS) in 200 Norwegian patients with pancreatic neoplastic disorders. Twenty-eight samples (14.0%) carried CEL-INS alleles. Most common were insertions in repeat 9 (9.5%), which always associated with a VNTR length of 13 repeats. The combined INS allele frequency (0.078) was similar to that observed in a control material of 416 subjects (0.075). We performed functional testing in HEK293T cells of a set of CEL-INS variants, in which the insertion site varied from the first to the 12th VNTR repeat. Lipase activity showed little difference among the variants. However, CEL-INS variants with insertions occurring in the most proximal repeats led to protein aggregation and endoplasmic reticulum stress, which upregulated the unfolded protein response. Moreover, by using a CEL-INS-specific antibody, we observed patchy signals in pancreatic tissue from humans without any CEL-INS variant in the germline. Similar pancreatic staining was seen in knock-in mice expressing the most common human CEL VNTR with 16 repeats. CEL-INS proteins may therefore be constantly produced from somatic events in the normal pancreatic parenchyma. This observation along with the high population frequency of CEL-INS alleles strongly suggests that these variants are benign, with a possible exception for insertions in VNTR repeats 1-4.

Extending protein interaction networks using proteoforms and small molecules.

MOTIVATION: Biological network analysis for high-throughput biomedical data interpretation relies heavily on topological characteristics. Networks are commonly composed of nodes representing genes or proteins that are connected by edges when interacting. In this study, we use the rich information available in the Reactome pathway database to build biological networks accounting for small molecules and proteoforms modeled using protein isoforms and post-translational modifications to study the topological changes induced by this refinement of the network representation. RESULTS: We find that improving the interactome modeling increases the number of nodes and interactions, but that isoform and post-translational modification annotation is still limited compared to what can be expected biologically. We also note that small molecule information can distort the topology of the network due to the high connectedness of these molecules, which does not necessarily represent the reality of biology. However, by restricting the connections of small molecules to the context of biochemical reactions, we find that these improve the overall connectedness of the network and reduce the prevalence of isolated components and nodes. Overall, changing the representation of the network alters the prevalence of articulation points and bridges globally but also within and across pathways. Hence, some molecules can gain or lose in biological importance depending on the level of detail of the representation of the biological system, which might in turn impact network-based studies of diseases or druggability. AVAILABILITY AND IMPLEMENTATION: Networks are constructed based on data publicly available in the Reactome Pathway knowledgebase: reactome.org.

Dominant Mutations in the Autoimmune Regulator AIRE Are Associated with Common Organ-Specific Autoimmune Diseases.

The autoimmune regulator (AIRE) gene is crucial for establishing central immunological tolerance and preventing autoimmunity. Mutations in AIRE cause a rare autosomal-recessive disease, autoimmune polyendocrine syndrome type 1 (APS-1), distinguished by multi-organ autoimmunity. We have identified multiple cases and families with mono-allelic mutations in the first plant homeodomain (PHD1) zinc finger of AIRE that followed dominant inheritance, typically characterized by later onset, milder phenotypes, and reduced penetrance compared to classical APS-1. These missense PHD1 mutations suppressed gene expression driven by wild-type AIRE in a dominant-negative manner, unlike CARD or truncated AIRE mutants that lacked such dominant capacity. Exome array analysis revealed that the PHD1 dominant mutants were found with relatively high frequency (>0.0008) in mixed populations. Our results provide insight into the molecular action of AIRE and demonstrate that disease-causing mutations in the AIRE locus are more common than previously appreciated and cause more variable autoimmune phenotypes.

Smoking during pregnancy and its effect on placental weight: a Mendelian randomization study.

BACKGROUND: The causal relationship between maternal smoking in pregnancy and reduced offspring birth weight is well established and is likely due to impaired placental function. However, observational studies have given conflicting results on the association between smoking and placental weight. We aimed to estimate the causal effect of newly pregnant mothers quitting smoking on their placental weight at the time of delivery. METHODS: We used one-sample Mendelian randomization, drawing data from the Avon Longitudinal Study of Parents and Children (ALSPAC) (N = 690 to 804) and the Norwegian Mother, Father and Child Cohort Study (MoBa) (N = 4267 to 4606). The sample size depends on the smoking definition used for different analyses. The analysis was performed in pre-pregnancy smokers only, due to the specific role of the single-nucleotide polymorphism (SNP) rs1051730 (CHRNA5 - CHRNA3 - CHRNB4) in affecting smoking cessation but not initiation. RESULTS: Fixed effect meta-analysis showed a 182 g [95%CI: 29,335] higher placental weight for pre-pregnancy smoking mothers who continued smoking at the beginning of pregnancy, compared with those who stopped smoking. Using the number of cigarettes smoked per day in the first trimester as the exposure, the causal effect on placental weight was 11 g [95%CI: 1,21] per cigarette per day. Similarly, smoking at the end of pregnancy was causally associated with higher placental weight. Using the residuals of birth weight regressed on placental weight as the outcome, we showed evidence of lower offspring birth weight relative to the placental weight, both for continuing smoking at the start of pregnancy as well as continuing smoking throughout pregnancy (change in z-score birth weight adjusted for z-score placental weight: -0.8 [95%CI: -1.6,-0.1]). CONCLUSION: Our results suggest that continued smoking during pregnancy causes higher placental weights.

Acetaminophen Use During Pregnancy and Children's Risk of Autism, ADHD, and Intellectual Disability.

Importance: Several studies suggest that acetaminophen (paracetamol) use during pregnancy may increase risk of neurodevelopmental disorders in children. If true, this would have substantial implications for management of pain and fever during pregnancy. Objective: To examine the associations of acetaminophen use during pregnancy with children's risk of autism, attention-deficit/hyperactivity disorder (ADHD), and intellectual disability. Design, Setting, and Participants: This nationwide cohort study with sibling control analysis included a population-based sample of 2 480 797 children born in 1995 to 2019 in Sweden, with follow-up through December 31, 2021. Exposure: Use of acetaminophen during pregnancy prospectively recorded from antenatal and prescription records. Main Outcomes and Measures: Autism, ADHD, and intellectual disability based on International Classification of Diseases, Ninth Revision and International Classification of Diseases, Tenth Revision codes in health registers. Results: In total, 185 909 children (7.49%) were exposed to acetaminophen during pregnancy. Crude absolute risks at 10 years of age for those not exposed vs those exposed to acetaminophen were 1.33% vs 1.53% for autism, 2.46% vs 2.87% for ADHD, and 0.70% vs 0.82% for intellectual disability. In models without sibling control, ever-use vs no use of acetaminophen during pregnancy was associated with marginally increased risk of autism (hazard ratio [HR], 1.05 [95% CI, 1.02-1.08]; risk difference [RD] at 10 years of age, 0.09% [95% CI, -0.01% to 0.20%]), ADHD (HR, 1.07 [95% CI, 1.05-1.10]; RD, 0.21% [95% CI, 0.08%-0.34%]), and intellectual disability (HR, 1.05 [95% CI, 1.00-1.10]; RD, 0.04% [95% CI, -0.04% to 0.12%]). To address unobserved confounding, matched full sibling pairs were also analyzed. Sibling control analyses found no evidence that acetaminophen use during pregnancy was associated with autism (HR, 0.98 [95% CI, 0.93-1.04]; RD, 0.02% [95% CI, -0.14% to 0.18%]), ADHD (HR, 0.98 [95% CI, 0.94-1.02]; RD, -0.02% [95% CI, -0.21% to 0.15%]), or intellectual disability (HR, 1.01 [95% CI, 0.92-1.10]; RD, 0% [95% CI, -0.10% to 0.13%]). Similarly, there was no evidence of a dose-response pattern in sibling control analyses. For example, for autism, compared with no use of acetaminophen, persons with low (<25th percentile), medium (25th-75th percentile), and high (>75th percentile) mean daily acetaminophen use had HRs of 0.85, 0.96, and 0.88, respectively. Conclusions and Relevance: Acetaminophen use during pregnancy was not associated with children's risk of autism, ADHD, or intellectual disability in sibling control analysis. This suggests that associations observed in other models may have been attributable to familial confounding.

Characterisation of HNF1A variants in paediatric diabetes in Norway using functional and clinical investigations to unmask phenotype and monogenic diabetes.

AIMS/HYPOTHESIS: Correctly diagnosing MODY is important, as individuals with this diagnosis can discontinue insulin injections; however, many people are misdiagnosed. We aimed to develop a robust approach for determining the pathogenicity of variants of uncertain significance in hepatocyte nuclear factor-1 alpha (HNF1A)-MODY and to obtain an accurate estimate of the prevalence of HNF1A-MODY in paediatric cases of diabetes. METHODS: We extended our previous screening of the Norwegian Childhood Diabetes Registry by 830 additional samples and comprehensively genotyped HNF1A variants in autoantibody-negative participants using next-generation sequencing. Carriers of pathogenic variants were treated by local healthcare providers, and participants with novel likely pathogenic variants and variants of uncertain significance were enrolled in an investigator-initiated, non-randomised, open-label pilot study (ClinicalTrials.gov registration no. NCT04239586). To identify variants associated with HNF1A-MODY, we functionally characterised their pathogenicity and assessed the carriers' phenotype and treatment response to sulfonylurea. RESULTS: In total, 615 autoantibody-negative participants among 4712 cases of paediatric diabetes underwent genetic sequencing, revealing 19 with HNF1A variants. We identified nine carriers with novel variants classified as variants of uncertain significance or likely to be pathogenic, while the remaining ten participants carried five pathogenic variants previously reported. Of the nine carriers with novel variants, six responded favourably to sulfonylurea. Functional investigations revealed their variants to be dysfunctional and demonstrated a correlation with the resulting phenotype, providing evidence for reclassifying these variants as pathogenic. CONCLUSIONS/INTERPRETATION: Based on this robust classification, we estimate that the prevalence of HNF1A-MODY is 0.3% in paediatric diabetes. Clinical phenotyping is challenging and functional investigations provide a strong complementary line of evidence. We demonstrate here that combining clinical phenotyping with functional protein studies provides a powerful tool to obtain a precise diagnosis of HNF1A-MODY.

Autozygosity mapping and time-to-spontaneous delivery in Norwegian parent-offspring trios.

Parental genetic relatedness may lead to adverse health and fitness outcomes in the offspring. However, the degree to which it affects human delivery timing is unknown. We use genotype data from ≃25 000 parent-offspring trios from the Norwegian Mother, Father and Child Cohort Study to optimize runs of homozygosity (ROH) calling by maximizing the correlation between parental genetic relatedness and offspring ROHs. We then estimate the effect of maternal, paternal and fetal autozygosity and that of autozygosity mapping (common segments and gene burden test) on the timing of spontaneous onset of delivery. The correlation between offspring ROH using a variety of parameters and parental genetic relatedness ranged between -0.2 and 0.6, revealing the importance of the minimum number of genetic variants included in an ROH and the use of genetic distance. The optimized compared to predefined parameters showed a ≃45% higher correlation between parental genetic relatedness and offspring ROH. We found no evidence of an effect of maternal, paternal nor fetal overall autozygosity on spontaneous delivery timing. Yet, through autozygosity mapping, we identified three maternal loci TBC1D1, SIGLECs and EDN1 gene regions reducing the median time-to-spontaneous onset of delivery by ≃2-5% (P-value < 2.3 × 10-6). We also found suggestive evidence of a fetal locus at 3q22.2, near the RYK gene region (P-value = 2.0 × 10-6). Autozygosity mapping may provide new insights on the genetic determinants of delivery timing beyond traditional genome-wide association studies, but particular and rigorous attention should be given to ROH calling parameter selection.

Apgar Score and Risk of Neonatal Death among Preterm Infants.

BACKGROUND: Gestational age is the major determinant of neonatal death (death within the first 28 days of life) in preterm infants. The joint effect of gestational age and Apgar score on the risk of neonatal death is unknown. METHODS: Using data from the Swedish Medical Birth Register, we identified 113,300 preterm infants (22 weeks 0 days to 36 weeks 6 days of gestation) born from 1992 through 2016. In analyses stratified according to gestational age (22 to 24 weeks, 25 to 27 weeks, 28 to 31 weeks, 32 to 34 weeks, and 35 or 36 weeks), we estimated adjusted relative risks of neonatal death and absolute rate differences in neonatal mortality (i.e., the excess number of neonatal deaths per 100 births) according to the Apgar scores at 5 and 10 minutes and according to the change in the Apgar score between 5 minutes and 10 minutes. Scores range from 0 to 10, with higher scores indicating a better physical condition of the newborn. RESULTS: There were 1986 neonatal deaths (1.8%). The incidence of neonatal death ranged from 0.2% (at 36 weeks of gestation) to 76.5% (at 22 weeks of gestation). Lower Apgar scores were associated with higher relative risks of neonatal death and greater absolute rate differences in neonatal mortality in all gestational-age strata. For example, among infants born at 28 to 31 weeks, the adjusted absolute rate differences according to the 5-minute Apgar score, with those who had a score of 9 or 10 serving as the reference group, were 51.7 (95% confidence interval [CI], 38.1 to 65.4) for a score of 0 or 1, 25.5 (95% CI, 18.3 to 32.8) for a score of 2 or 3, 7.1 (95% CI, 5.1 to 9.1) for a score of 4 to 6, and 1.2 (95% CI, 0.5 to 1.9) for a score of 7 or 8. An increase in the Apgar score between 5 minutes and 10 minutes was associated with lower neonatal mortality than a stable Apgar score. CONCLUSIONS: In this study, Apgar scores at 5 and 10 minutes provided prognostic information about neonatal survival among preterm infants across gestational-age strata. (Funded by the Swedish Research Council for Health, Working Life, and Welfare and Karolinska Institutet.).

A polygenic risk score to help discriminate primary adrenal insufficiency of different etiologies.

BACKGROUND: Autoimmune Addison's disease (AAD) is the most common cause of primary adrenal insufficiency (PAI). Despite its exceptionally high heritability, tools to estimate disease susceptibility in individual patients are lacking. We hypothesized that polygenic risk score (PRS) for AAD could help investigate PAI pathogenesis in pediatric patients. METHODS: We here constructed and evaluated a PRS for AAD in 1223 seropositive cases and 4097 controls. To test its clinical utility, we reevaluated 18 pediatric patients, whose whole genome we also sequenced. We next explored the individual PRS in more than 120 seronegative patients with idiopathic PAI. RESULTS: The genetic susceptibility to AAD-quantified using PRS-was on average 1.5 standard deviations (SD) higher in patients compared with healthy controls (p < 2e - 16), and 1.2 SD higher in the young patients compared with the old (p = 3e - 4). Using the novel PRS, we searched for pediatric patients with strikingly low AAD susceptibility and identified cases of monogenic PAI, previously misdiagnosed as AAD. By stratifying seronegative adult patients by autoimmune comorbidities and disease duration we could delineate subgroups of PRS suggesting various disease etiologies. CONCLUSIONS: The PRS performed well for case-control differentiation and susceptibility estimation in individual patients. Remarkably, a PRS for AAD holds promise as a means to detect disease etiologies other than autoimmunity.

Severity of preterm birth and the risk of pulmonary hypertension in childhood: A population-based cohort study in Sweden.

BACKGROUND: Preterm birth (<37 completed gestational weeks) has been linked to pulmonary hypertension (PH), but the relationship to severity of preterm birth has not been studied. OBJECTIVES: We investigated associations between extremely (<28 weeks), very (28-31 weeks), moderately (32-36 weeks) preterm birth, early-term birth (37-38 weeks) and later PH. Additionally, we explored associations between birthweight for gestational age and PH. METHODS: This registry-based cohort study followed 3.1 million individuals born in Sweden (1987-2016) from 1 up to a maximum of 30 years of age. The outcome was diagnosis or death from PH in national health registers. Adjusted hazard ratios (HR) were estimated using Cox regression analysis. Unadjusted and confounder-adjusted incidence rate differences were also calculated. RESULTS: Of 3,142,812 individuals, there were 543 cases of PH (1.2 per 100,000 person-years), 153 of which in individuals without malformations. Compared with individuals born at 39 weeks, adjusted HRs with 95% confidence interval (CI) for PH for extremely, moderately, and very preterm birth were 68.78 (95% CI 49.49, 95.57), 13.86 (95% CI 9.27, 20.72) and 3.42 (95% CI 2.46, 4.74), respectively, and for early-term birth 1.74 (1.31, 2.32). HRs were higher in subjects without malformations. There were 90 additional cases of PH per 100,000 person-years in the extremely preterm group (50 after excluding malformations). Very small for gestational age (below 2 SD from estimated birthweight for gestational age and sex) was also associated with increased risk of PH (adjusted HR 2.02, 95% CI 1.14, 3.57). CONCLUSIONS: We found an inverse association between gestational age and later PH, but the incidence and absolute risks are low. The severity of preterm birth adds clinically relevant information to the assessment of cardiovascular risks in childhood.

Disability digital divide: survey of accessibility of eHealth services as perceived by people with and without impairment.

BACKGROUND: Sustainable and effective eHealth requires accessibility for everyone. Little is known about how accessibility of eHealth is perceived among people with various impairments. The aim of this study was to compare use and perceived difficulty in the use of eHealth among people with and without impairment, and how different types of impairment were associated with perceived difficulty in the use of eHealth. METHODS: This study used data collected in a nationwide survey in Sweden. Snowball sampling was used to recruit participants with self-reported impairment, from June to October 2019. In February 2020, the survey was posted to people in the general population who were matched to the participants with impairment by age, gender and county of residence. Multiple logistic regression was used to analyse the use of four eHealth services, and perceived difficulty in the use of six eHealth services. RESULTS: In total, 1631 participants with, and 1084 participants without impairment responded to the survey. Participants with impairment reported less use and more difficulty in the use of all eHealth services as compared to participants without impairment. When comparing types of impairment, booking healthcare appointments online was least used and most avoided by participants with communication, language and calculation impairments (adjusted odds ratio (aOR) use 0.64, 95% confidence interval (95%CI) 0.49-0.83; aOR avoid 1.64, 95%CI 1.19-2.27), and intellectual impairments (aOR use 0.28, 95%CI 0.20-0.39; aOR avoid 2.88, 95%CI 1.86-4.45). The Swedish national web-portal for health information and services, 1177.se, was reported difficult to use the most among participants with communication, language and calculation impairments (aOR 2.24, 95%CI 1.50-3.36), deaf-blindness (aOR 11.24, 95%CI 3.49-36.23) and hearing impairment (aOR 2.50, 95%CI 1.17-5.35). CONCLUSIONS: The results confirm the existence of an eHealth disability digital divide. People with impairment were not one homogeneous group, but differed in perceived difficulties in regard to eHealth. Based on a purposeful subgrouping of impairments, we showed that people with communication, language and calculation impairments, and intellectual impairments, reported least use and most difficulty in using eHealth. The findings can guide further research in creating eHealth that is accessible for all, including those with the most significant difficulties.

Low Apgar score and need for resuscitation increased the probability of receiving therapeutic hypothermia more strongly than acidosis at birth.

AIM: The aim of this study was to investigate how individual markers for birth asphyxia, so-called A criteria, were associated with the probability of receiving therapeutic hypothermia. METHODS: This population-based cohort study included 1336 live-born singleton term infants with any A criterion in the Stockholm-Gotland Region, Sweden during 2008 to 2014. The Swedish Neonatal Quality Register and National Patient Register were used for data collection. Results were presented as adjusted odds ratios (aORs) with 95% confidence intervals (CIs). RESULTS: There were 89 infants, 44 boys and 45 girls with mean gestational age 40.5 weeks, who received therapeutic hypothermia. Low Apgar score, aOR 12.44 (95% CI 5.99-25.86), and resuscitation, aOR 9.18 (95% CI 3.77-22.34), were strongly associated with therapeutic hypothermia. A pH <7.0 was less associated with the outcome, aOR 2.02 (95% CI 1.02-4.0). No infant who received therapeutic hypothermia fulfilled the criteria of base deficit ≥16 mmol/L only. CONCLUSION: A low Apgar score of and/or a need for resuscitation is more relevant for identifying infants eligible for therapeutic hypothermia, compared to other A criteria. This knowledge could be used clinically to identify cases for review and avoid unnecessary monitoring of infants.

Development and Evaluation of eHealth Services Regarding Accessibility: Scoping Literature Review.

BACKGROUND: Accessibility is acknowledged as a key to inclusion in the Convention of Rights for People with Disabilities. An inaccessible design can result in exclusion from eHealth and cause disability among people who have impairments. OBJECTIVE: This scoping literature review aimed to investigate how eHealth services have been developed and evaluated regarding accessibility for people with impairments. METHODS: In line with Arksey and O'Malley's framework for scoping studies and using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR), we conducted a search in 4 databases (PubMed, Scopus, IEEE, and Web of Science) in October 2020 and an update of the search in June 2022. The search strategy was structured according to the PICO model as follows: Population/Problem, digital accessibility for users with impairment; Intervention, health care delivered by any digital solution; Comparison, not applicable; Outcome, use of and adherence to (1) Web Content Accessibility Guidelines (WCAG), (2) other accessibility guidelines, and (3) other means, for designing or evaluating accessibility in eHealth services. A Boolean search was conducted by combining terms related to accessibility and eHealth. All authors participated in screening abstracts according to the eligibility criteria. Each publication, containing a potentially relevant abstract, was read (full text) and assessed for eligibility by 2 authors independently and pairwise. Publications deemed eligible were read by all authors and discussed for consensus. RESULTS: A total of 8643 publications were identified. After abstract screening, 131 publications remained for full-text reading. Of those, 116 publications were excluded as they did not meet the eligibility criteria. Fifteen publications involving studies of 12 eHealth services were included in the study. Of the 15 publications, 2 provided a definition of accessibility, 5 provided an explanation of accessibility, and 8 did not provide any explanation. Five publications used the WCAG to evaluate accessibility when developing eHealth services. One publication used International Organization for Standardization (ISO) 29138, ISO 2941, and ISO/International Electrotechnical Commission (IEC) 30071-1 standards together with the Spanish Association for Standardization (UNE) 139803 standard. Eleven publications used other means to address accessibility, including text-level grading; literature review about accessibility; user tests, focus groups, interviews, and design workshops with target groups of patients, relatives, and health care professionals; and comparative analysis of existing technical solutions to provide information about useful requirements. CONCLUSIONS: Although a clear definition of accessibility can enhance operationalization and thus measurability when evaluating accessibility in eHealth services, accessibility was insufficiently defined in most of the included studies. Further, accessibility guidelines and standards were used to a very limited extent in the development and evaluation of eHealth services. Guidelines for developing complex interventions that include guidance for accessibility are motivated to ensure that accessibility will be considered systematically in eHealth services.

The position of single-base deletions in the VNTR sequence of the carboxyl ester lipase (CEL) gene determines proteotoxicity.

Variable number of tandem repeat (VNTR) sequences in the genome can have functional consequences that contribute to human disease. This is the case for the CEL gene, which is specifically expressed in pancreatic acinar cells and encodes the digestive enzyme carboxyl ester lipase. Rare single-base deletions (DELs) within the first (DEL1) or fourth (DEL4) VNTR segment of CEL cause maturity-onset diabetes of the young, type 8 (MODY8), an inherited disorder characterized by exocrine pancreatic dysfunction and diabetes. Studies on the DEL1 variant have suggested that MODY8 is initiated by CEL protein misfolding and aggregation. However, it is unclear how the position of single-base deletions within the CEL VNTR affects pathogenic properties of the protein. Here, we investigated four naturally occurring CEL variants, arising from single-base deletions in different VNTR segments (DEL1, DEL4, DEL9, and DEL13). When the four variants were expressed in human embryonic kidney 293 cells, only DEL1 and DEL4 led to significantly reduced secretion, increased intracellular aggregation, and increased endoplasmic reticulum stress compared with normal CEL protein. The level of O-glycosylation was affected in all DEL variants. Moreover, all variants had enzymatic activity comparable with that of normal CEL. We conclude that the longest aberrant protein tails, resulting from single-base deletions in the proximal VNTR segments, have highest pathogenic potential, explaining why DEL1 and DEL4 but not DEL9 and DEL13 have been observed in patients with MODY8. These findings further support the view that CEL mutations cause pancreatic disease through protein misfolding and proteotoxicity, leading to endoplasmic reticulum stress and activation of the unfolded protein response.

SeeCiTe: a method to assess CNV calls from SNP arrays using trio data.

MOTIVATION: Single nucleotide polymorphism (SNP) genotyping arrays remain an attractive platform for assaying copy number variants (CNVs) in large population-wide cohorts. However, current tools for calling CNVs are still prone to extensive false positive calls when applied to biobank scale arrays. Moreover, there is a lack of methods exploiting cohorts with trios available (e.g. nuclear family) to assist in quality control and downstream analyses following the calling. RESULTS: We developed SeeCiTe (Seeing CNVs in Trios), a novel CNV-quality control tool that postprocesses output from current CNV-calling tools exploiting child-parent trio data to classify calls in quality categories and provide a set of visualizations for each putative CNV call in the offspring. We apply it to the Norwegian Mother, Father and Child Cohort Study (MoBa) and show that SeeCiTe improves the specificity and sensitivity compared to the common empiric filtering strategies. To our knowledge, it is the first tool that utilizes probe-level CNV data in trios (and singletons) to systematically highlight potential artifacts and visualize signal intensities in a streamlined fashion suitable for biobank scale studies. AVAILABILITY AND IMPLEMENTATION: The software is implemented in R with the source code freely available at https://github.com/aksenia/SeeCiTe. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Association of sweetened carbonated beverage consumption during pregnancy and ADHD symptoms in the offspring: a study from the Norwegian Mother, Father and Child Cohort Study (MoBa).

PURPOSE: Intrauterine exposures influence offspring health and development. Here we investigated maternal intake of sweetened carbonated beverages (SCB) during pregnancy and its association with ADHD symptoms in the offspring. METHODS: This study was based on the Norwegian Mother, Father and Child Cohort Study (MoBa) and the Medical Birth Registry of Norway. Maternal diet mid-pregnancy was assessed using a food frequency questionnaire (FFQ). All mothers who responded to the FFQ and a questionnaire when their child was 8 years of age were included (n = 39,870). The exposure was defined as maternal intake (daily servings) of SCB, using no daily intake as reference. Outcome was offspring ADHD symptoms, evaluated as a continuous standardized ADHD score and as a binary outcome of six or more ADHD symptoms vs. five symptoms or less. Associations were analysed using log-binomial regression and linear mixed regression models with adjustment for covariates. RESULTS: The adjusted regression coefficients for the standardized ADHD offspring symptom score were 0.31 [95% confidence intervals (0.001, 0.62)] and 0.46 (0.15, 0.77) for maternal daily intake of ≥ 1 glasses of SCB, when the models included adjustments for total energy intake or energy intake from other sources than SCBs and sweet drinks, respectively. The corresponding adjusted relative risks were 1.16 (1.004, 1.34) and 1.21. (1.05, 1.39) for drinking ≥ 1 glasses daily. CONCLUSION: In a large pregnancy cohort with offspring followed until 8 years of age, we found an association between maternal daily intake of SCB and offspring ADHD symptoms. These results suggest a weak positive relationship between prenatal exposure to SCB and offspring ADHD.

Maternal Obesity and Risk of Early-onset Neonatal Bacterial Sepsis: Nationwide Cohort and Sibling-controlled Studies.

BACKGROUND: Maternal overweight and obesity are related to risks of pregnancy and delivery complications that, in turn, are associated with newborn infections. We examined the associations between early pregnancy body mass index (BMI; kg/m2) and risk of early-onset neonatal bacterial sepsis (EOS). METHODS: We conducted a nationwide population-based retrospective cohort study of 1 971 346 live singleton infants born in Sweden between 1997 and 2016. Outcome was a culture-confirmed EOS diagnosis. We estimated hazard ratios (HR) of EOS according to BMI using proportional hazard models, and identified potential mediators. Among term infants, we conducted sibling-controlled analyses. RESULTS: EOS risk per 1000 live births was 1.48; 0.76 in term and 15.52 in preterm infants. Compared with infants of normal-weight mothers (BMI, 18.5-24.9), the adjusted HR (95% confidence interval [CI]) of EOS for BMI categories <18.5, 25.0-29.9, 30.0-34.9, 35.0-39.9, and ≥40.0 were, respectively, 1.07 (.83-1.40), 1.19 (1.08-1.32), 1.70 (1.49-1.94), 2.11 (1.73-2.58), and 2.50 (1.86-3.38). Maternal overweight and obesity increased the risk of EOS by group B Streptococcus, Staphylococcus aureus, and Escherichia coli. Half of the association was mediated through preeclampsia, cesarean section delivery, and preterm delivery. A dose-response association was consistently apparent in term infants only. In sibling-controlled analyses, every kilogram per meter squared interpregnancy BMI change was associated with a mean 8.3% increase in EOS risk (95% CI, 1.7%-15.3%; P = .01). CONCLUSIONS: Risk of EOS increases with maternal overweight and obesity severity, particularly in term infants.

Comprehensive characterization of copy number variation (CNV) called from array, long- and short-read data.

BACKGROUND: SNP arrays, short- and long-read genome sequencing are genome-wide high-throughput technologies that may be used to assay copy number variants (CNVs) in a personal genome. Each of these technologies comes with its own limitations and biases, many of which are well-known, but not all of them are thoroughly quantified. RESULTS: We assembled an ensemble of public datasets of published CNV calls and raw data for the well-studied Genome in a Bottle individual NA12878. This assembly represents a variety of methods and pipelines used for CNV calling from array, short- and long-read technologies. We then performed cross-technology comparisons regarding their ability to call CNVs. Different from other studies, we refrained from using the golden standard. Instead, we attempted to validate the CNV calls by the raw data of each technology. CONCLUSIONS: Our study confirms that long-read platforms enable recalling CNVs in genomic regions inaccessible to arrays or short reads. We also found that the reproducibility of a CNV by different pipelines within each technology is strongly linked to other CNV evidence measures. Importantly, the three technologies show distinct public database frequency profiles, which differ depending on what technology the database was built on.

Neonatal Morbidities in Infants Born Late Preterm at 35-36 Weeks of Gestation: A Swedish Nationwide Population-based Study.

OBJECTIVE: To assess risk for neonatal morbidities among infants born late preterm at 35-36 gestational weeks, early term (37-38 weeks), and late-term (41 weeks) infants, compared with full-term (39-40 weeks) infants. STUDY DESIGN: This nationwide population-based cohort study included 1 650 450 non-malformed liveborn singleton infants born at 35-41 weeks between 1998 and 2016 in Sweden. The relative risks for low Apgar score (0-3) at 5 minutes; respiratory, metabolic, infectious, and neurologic morbidities; and severe neonatal morbidity (composite outcome) were adjusted for maternal, pregnancy, delivery, and infant characteristics. RESULTS: Compared with infants born at 39-40 weeks, the adjusted relative risks and proportions of infants born at 35-36 weeks were higher for metabolic morbidity 7.79 (95%, 7.61 to 7.97; 33.75% vs 3.11%), respiratory morbidity 5.54 (95% CI, 5.24 to 5.85; 5.49% vs 0.75%), severe neonatal morbidity 2.42 (95% CI, 2.27 to 2.59; 3.40% versus 1.03%), infectious morbidity 1.98 (95% CI, 1.83 to 2.14; 2.53% vs 0.95%), neurologic morbidity 1.74 (95% CI, 1.48 to 2.03; 0.54% vs 0.23%), and low Apgar score 2.07 (95% CI, 1.72 to 2.51; 0.42% vs 0.12%). The risks for respiratory, severe neonatal morbidity, infectious, neurologic morbidities, and low Apgar score were highest at 35 weeks, gradually decreased until 39 weeks, and increased during 39-41 weeks. CONCLUSIONS: Infants born late preterm at 35-36 weeks of gestation are at increased risk of neonatal morbidities, although the absolute risks for severe neonatal morbidities are low. Our findings reinforce the need of preventing late preterm delivery to decrease the burden of neonatal morbidity and help professionals and families with a better risk assessment.

Identification of ADHD risk genes in extended pedigrees by combining linkage analysis and whole-exome sequencing.

Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder with a complex genetic background, hampering identification of underlying genetic risk factors. We hypothesized that combining linkage analysis and whole-exome sequencing (WES) in multi-generation pedigrees with multiple affected individuals can point toward novel ADHD genes. Three families with multiple ADHD-affected members (Ntotal = 70) and apparent dominant inheritance pattern were included in this study. Genotyping was performed in 37 family members, and WES was additionally carried out in 10 of those. Linkage analysis was performed using multi-point analysis in Superlink Online SNP 1.1. From prioritized linkage regions with a LOD score ≥ 2, a total of 24 genes harboring rare variants were selected. Those genes were taken forward and were jointly analyzed in gene-set analyses of exome-chip data using the MAGMA software in an independent sample of patients with persistent ADHD and healthy controls (N = 9365). The gene-set including all 24 genes together, and particularly the gene-set from one of the three families (12 genes), were significantly associated with persistent ADHD in this sample. Among the latter, gene-wide analysis for the AAED1 gene reached significance. A rare variant (rs151326868) within AAED1 segregated with ADHD in one of the families. The analytic strategy followed here is an effective approach for identifying novel ADHD risk genes. Additionally, this study suggests that both rare and more frequent variants in multiple genes act together in contributing to ADHD risk, even in individual multi-case families.