Sex-Specific Developmental Scales for Surveillance

BACKGROUND

Developmental surveillance, conducted routinely worldwide, is fundamental for early detection of children at risk for developmental delay. We aimed to explore sex-related difference in attainment rates of developmental milestones and to evaluate the clinical need for separate sex-specific scales.

METHODS

This is a cross-sectional, natiowide retrospective study, utilizing data from a national child surveillance program of ∼1000 maternal child health clinics. The main cohort, used for constructing sex-specific developmental scales, included all children born between January 2014 to September 2020, who visited maternal child health clinics from birth to 6 years of age (n = 839 574). Children with abnormal developmental potential were excluded (n = 195 616). A validation cohort included all visits between 2020 and 2021 (n = 309 181). The sex-differences in normative attainment age of 59 developmental milestones from 4 domains were evaluated. The milestones with a significant gap between males and females were identified, and the projected error rates when conducting unified versus sex-specific surveillance were calculated.

RESULTS

A new sex-specific developmental scale was constructed. In total, females preceded males in most milestones of all developmental domains, mainly at older ages. Conducting routine developmental surveillance using a unified scale, compared with sex-specific scales, resulted in potential missing of females at risk for developmental delay (19.3% of failed assessments) and over-diagnosis of males not requiring further evaluation (5.9% of failed assessments).

CONCLUSIONS

There are sex-related differences in the normative attainment rates of developmental milestones, indicating possible distortion of the currently used unified scales. These findings suggest that using sex-specific scales may improve the accuracy of early childhood developmental surveillance.

Early Prediction of Autistic Spectrum Disorder Using Developmental Surveillance Data

Importance

With the continuous increase in the prevalence of autistic spectrum disorder (ASD), effective early screening is crucial for initiating timely interventions and improving outcomes.

Objective

To develop predictive models for ASD using routinely collected developmental surveillance data and to assess their performance in predicting ASD at different ages and in different clinical scenarios.

Design, Setting, and Participants

This retrospective cohort study used nationwide data of developmental assessments conducted between January 1, 2014, and January 17, 2023, with minimal follow-up of 4 years and outcome collection in March 2023. Data were from a national program of approximately 1000 maternal child health clinics that perform routine developmental surveillance of children from birth to 6 years of age, serving 70% of children in Israel. The study included all children who were assessed at the maternal child health clinics (N = 1 187 397). Children were excluded if they were born at a gestational age of 33 weeks or earlier, had no record of gestational age, or were followed up for less than 4 years without an ASD outcome. The data set was partitioned at random into a development set (80% of the children) and a holdout evaluation set (20% of the children), both with the same prevalence of ASD outcome.

Exposures

For each child, demographic and birth-related covariates were extracted, as were per-visit growth measurements, quantified developmental milestone assessments, and referral summary covariates. Only information that was available before the prediction age was used for training and evaluating the models.

Main Outcome and Measure

The main outcome was eligibility for a governmental disabled child allowance due to ASD, according to administrative data of the National Insurance Institute of Israel. The performance of the models that predict the outcome was evaluated and compared with previous work on the Modified Checklist for Autism in Toddlers (M-CHAT).

Results

The study included 1 187 397 children (610 588 [51.4%] male). The performance of the ASD prediction models improved with prediction age, with fair accuracy already at 12 months of age. A model that combined longitudinal measures of developmental milestone assessments with a minimal set of demographic variables, which was applied at 18 to 24 months of age, achieved an area under the receiver operating characteristic curve of 0.83, with a sensitivity of 45.1% at a specificity of 95.0%. A model using single-visit assessments achieved an area under the receiver operating characteristic curve of 0.81 and a sensitivity of 41.2% at a specificity of 95.0%. The best performing prediction models surpassed the pooled performance of M-CHAT (sensitivity, 40%; specificity, 95%) reported in studies with a similar design.

Conclusions and Relevance

This cohort study found that ASD can be predicted from routine developmental surveillance data at an accuracy surpassing M-CHAT screening. This tool may be seamlessly integrated in the clinical workflow to improve early identification of children who may benefit from timely interventions.

Increased rates of unattained developmental milestones among Israeli children between 2016 and 2020: a national report

BACKGROUND

The early years of children's lives are critical for their healthy development. Although children's growth and development rates may vary, a significant delay during early childhood could indicate a medical or a developmental disorder. Developmental surveillance is used worldwide by healthcare providers in routine encounters, as well as by educators and parents, to elicit concerns about child development. In this work, we used a national dataset of developmental assessments to describe temporal trends of milestone attainment rates and associations between milestone attainment and various sociodemographic factors.

METHODS

The study included 1,002,700 children ages birth until 6 years with 4,441,689 developmental visits between the years 2016 and 2020. We used the Israeli developmental scale to assess the annual rates of failure to attain language, social and motoric milestones by the entire population, as well as by subgroups stratified by sociodemographic factors. In addition, we evaluated the rates of parental concern for child development and of the nurse's report of development inadequate for age. We used multivariable logistic regression to analyze the impact of different sociodemographic factors on the odds of failure to attain milestones, while controlling for confounding.

RESULTS

Milestone failure rates progressively increased over the examined years in all developmental domains, and most prominently in the language domain. Conversely, the rates of parental concern for developmental delay remained constant. In multivariable analysis, higher risk of milestone attainment failure was observed in children whose mothers were divorced, unemployed, immigrant, had lower education, of Bedouin origin or were over 40 years old when giving birth.

CONCLUSIONS

This report describes national trends of child development in the gross motor, fine motor, language, and social domains. A periodic report of these trends should be published to objectively evaluate subgroups in need for intervention, and to assess the effectiveness of intervention programs in attempt to maximize the developmental potential of children in Israel.

Youth Mental Health Outcomes up to Two Years After SARS-CoV-2 Infection Long-COVID or Long-Pandemic Syndrome: A Retrospective Cohort Study

PURPOSE

Youth mental distress has substantially increased during the COVID-19 pandemic. However, it is unclear if mental symptoms are directly related to SARS-CoV-2 infection or to social restrictions. We aimed to investigate mental health outcomes in infected versus uninfected adolescents, for up to two years after an index polymerase chain reaction (PCR) test.

METHODS

A retrospective cohort study, based on electronic health records from a large nationally representative Israeli health fund, among adolescents aged 12-17 years with a PCR test for SARS-CoV-2 between March 1, 2020 and March 1, 2021. Infected and uninfected individuals were matched by age, sex, test date, sector, and socioeconomic status. Cox regression was used to derive hazard ratios (HRs) for mental health outcomes within two years from PCR test for infected versus uninfected individuals, while accounting for pre-existing psychiatric history. External validation was performed on UK primary care data.

RESULTS

Among 146,067 PCR-tested adolescents, 24,009 were positive and 22,354 were matched with negative adolescents. SARS-CoV-2 infection was significantly associated with reduced risks for dispensation of antidepressants (HR 0.74, 95% confidence interval [CI] 0.66-0.83), diagnoses of anxiety (HR 0.82, 95% CI 0.71-0.95), depression (HR 0.65, 95% CI 0.53-0.80), and stress (HR 0.80, 95% CI 0.69-0.92). Similar results were obtained in the validation dataset.

DISCUSSION

This large, population-based study suggests that SARS-CoV-2 infection is not associated with elevated risk for mental distress in adolescents. Our findings highlight the importance of taking a holistic view on adolescents' mental health during the pandemic, with consideration of both SARS-CoV-2 infection and response measures.

A Developmental Surveillance Score for Quantitative Monitoring of Early Childhood Milestone Attainment: Algorithm Development and Validation

BACKGROUND

Developmental surveillance, conducted routinely worldwide, is fundamental for timely identification of children at risk of developmental delays. It is typically executed by assessing age-appropriate milestone attainment and applying clinical judgment during health supervision visits. Unlike developmental screening and evaluation tools, surveillance typically lacks standardized quantitative measures, and consequently, its interpretation is often qualitative and subjective.

OBJECTIVE

Herein, we suggested a novel method for aggregating developmental surveillance assessments into a single score that coherently depicts and monitors child development. We described the procedure for calculating the score and demonstrated its ability to effectively capture known population-level associations. Additionally, we showed that the score can be used to describe longitudinal patterns of development that may facilitate tracking and classifying developmental trajectories of children.

METHODS

We described the Developmental Surveillance Score (DSS), a simple-to-use tool that quantifies the age-dependent severity level of a failure at attaining developmental milestones based on the recently introduced Israeli developmental surveillance program. We evaluated the DSS using a nationwide cohort of >1 million Israeli children from birth to 36 months of age, assessed between July 1, 2014, and September 1, 2021. We measured the score's ability to capture known associations between developmental delays and characteristics of the mother and child. Additionally, we computed series of the DSS in consecutive visits to describe a child's longitudinal development and applied cluster analysis to identify distinct patterns of these developmental trajectories.

RESULTS

The analyzed cohort included 1,130,005 children. The evaluation of the DSS on subpopulations of the cohort, stratified by known risk factors of developmental delays, revealed expected relations between developmental delay and characteristics of the child and mother, including demographics and obstetrics-related variables. On average, the score was worse for preterm children compared to full-term children and for male children compared to female children, and it was correspondingly worse for lower levels of maternal education. The trajectories of scores in 6 consecutive visits were available for 294,000 children. The clustering of these trajectories revealed 3 main types of developmental patterns that are consistent with clinical experience: children who successfully attain milestones, children who initially tend to fail but improve over time, and children whose failures tend to increase over time.

CONCLUSIONS

The suggested score is straightforward to compute in its basic form and can be easily implemented as a web-based tool in its more elaborate form. It highlights known and novel relations between developmental delay and characteristics of the mother and child, demonstrating its potential usefulness for surveillance and research. Additionally, it can monitor the developmental trajectory of a child and characterize it. Future work is needed to calibrate the score vis-a-vis other screening tools, validate it worldwide, and integrate it into the clinical workflow of developmental surveillance.

Predicting future onset of depression among middle-aged adults with no psychiatric history

BACKGROUND

Depression is a major cause of disability worldwide. Recent data suggest that, in industrialised countries, the prevalence of depression peaks in middle age. Identifying factors predictive of future depressive episodes is crucial for developing prevention strategies for this age group.

AIMS

We aimed to identify future depression in middle-aged adults with no previous psychiatric history.

METHOD

To predict a diagnosis of depression 1 year or more following a comprehensive baseline assessment, we used a data-driven, machine-learning methodology. Our data-set was the UK Biobank of middle-aged participants (N = 245 036) with no psychiatric history.

RESULTS

Overall, 2.18% of the study population developed a depressive episode at least 1 year following baseline. Basing predictions on a single mental health questionnaire led to an area under the curve of the receiver operating characteristic of 0.66, and a predictive model leveraging the combined results of 100 UK Biobank questionnaires and measurements improved this to 0.79. Our findings were robust to demographic variations (place of birth, gender) and variations in methods of depression assessment. Thus, machine-learning-based models best predict diagnoses of depression when allowing the inclusion of multiple features.

CONCLUSIONS

Machine-learning approaches show potential for being beneficial for the identification of clinically relevant predictors of depression. Specifically, we can identify, with moderate success, people with no recorded psychiatric history as at risk for depression by using a relatively small number of features. More work is required to improve these models and evaluate their cost-effectiveness before integrating them into the clinical workflow.

Data-Driven Assessment of Adolescents' Mental Health During the COVID-19 Pandemic

OBJECTIVE

Adolescents' mental health was severely compromised during the COVID-19 pandemic. Longitudinal real-world studies on changes in the mental health of adolescents during the later phase of the pandemic are limited. We aimed to quantify the effect of COVID-19 pandemic on adolescents' mental health outcomes based on electronic health records.

METHOD

This was a retrospective cohort study using the computerized database of a 2.5 million members, state-mandated health organization in Israel. Rates of mental health diagnoses and psychiatric drug dispensations were measured among adolescents 12 to 17 years of age with and without pre-existing mental history, for the years 2017 to 2021. Relative risks were computed between the years, and interrupted time series (ITS) analyses evaluated changes in monthly incidence rates of psychiatric outcomes.

RESULTS

The average population size was 218,146 in 2021. During the COVID-19 period, a 36% increase was observed in the incidence of depression (95% CI = 25-47), 31% in anxiety (95% CI = 23-39), 20% in stress (95% CI = 13-27), 50% in eating disorders (95% CI = 35-67), 25% in antidepressant use (95% CI = 25-33), and 28% in antipsychotic use (95% CI = 18-40). A decreased rate of 26% (95% CI = 0.80-0.88) was observed in ADHD diagnoses. The increase of the examined outcomes was most prominent among youth without psychiatric history, female youth, general secular Jewish population, youth with medium-high socioeconomic status, and those 14 to 15 years of age. ITS analysis confirmed a significantly higher growth in the incidence of psychiatric outcomes during the COVID-19 period, compared to those in previous years.

CONCLUSION

This real-world study highlights the deterioration of adolescents' mental health during the COVID-19 pandemic and suggests that youth mental health should be considered during health policy decision making.

DIVERSITY & INCLUSION STATEMENT

We worked to ensure sex and gender balance in the recruitment of human participants. We worked to ensure race, ethnic, and/or other types of diversity in the recruitment of human participants. We actively worked to promote sex and gender balance in our author group. The author list of this paper includes contributors from the location and/or community where the research was conducted who participated in the data collection, design, analysis, and/or interpretation of the work.

Long covid outcomes at one year after mild SARS-CoV-2 infection: nationwide cohort study

OBJECTIVES

To determine the clinical sequelae of long covid for a year after infection in patients with mild disease and to evaluate its association with age, sex, SARS-CoV-2 variants, and vaccination status.

DESIGN

Retrospective nationwide cohort study.

SETTING

Electronic medical records from an Israeli nationwide healthcare organisation.

POPULATION

1 913 234 Maccabi Healthcare Services members of all ages who did a polymerase chain reaction test for SARS-CoV-2 between 1 March 2020 and 1 October 2021.

MAIN OUTCOME MEASURES

Risk of an evidence based list of 70 reported long covid outcomes in unvaccinated patients infected with SARS-CoV-2 matched to uninfected people, adjusted for age and sex and stratified by SARS-CoV-2 variants, and risk in patients with a breakthrough SARS-CoV-2 infection compared with unvaccinated infected controls. Risks were compared using hazard ratios and risk differences per 10 000 patients measured during the early (30-180 days) and late (180-360 days) time periods after infection.

RESULTS

Covid-19 infection was significantly associated with increased risks in early and late periods for anosmia and dysgeusia (hazard ratio 4.59 (95% confidence interval 3.63 to 5.80), risk difference 19.6 (95% confidence interval 16.9 to 22.4) in early period; 2.96 (2.29 to 3.82), 11.0 (8.5 to 13.6) in late period), cognitive impairment (1.85 (1.58 to 2.17), 12.8, (9.6 to 16.1); 1.69 (1.45 to 1.96), 13.3 (9.4 to 17.3)), dyspnoea (1.79 (1.68 to 1.90), 85.7 (76.9 to 94.5); 1.30 (1.22 to 1.38), 35.4 (26.3 to 44.6)), weakness (1.78 (1.69 to 1.88), 108.5, 98.4 to 118.6; 1.30 (1.22 to 1.37), 50.2 (39.4 to 61.1)), and palpitations (1.49 (1.35 to 1.64), 22.1 (16.8 to 27.4); 1.16 (1.05 to 1.27), 8.3 (2.4 to 14.1)) and with significant but lower excess risk for streptococcal tonsillitis and dizziness. Hair loss, chest pain, cough, myalgia, and respiratory disorders were significantly increased only during the early phase. Male and female patients showed minor differences, and children had fewer outcomes than adults during the early phase of covid-19, which mostly resolved in the late period. Findings remained consistent across SARS-CoV-2 variants. Vaccinated patients with a breakthrough SARS-CoV-2 infection had a lower risk for dyspnoea and similar risk for other outcomes compared with unvaccinated infected patients.

CONCLUSIONS

This nationwide study suggests that patients with mild covid-19 are at risk for a small number of health outcomes, most of which are resolved within a year from diagnosis.

Assessing the Attainment Rates of Updated CDC Milestones Using a New Israeli Developmental Scale

OBJECTIVES

Developmental milestones norms are widely used worldwide and are fundamental for early childhood developmental surveillance. We compared a new Israeli evidence-based national developmental scale with the recently updated Centers for Disease Control and Prevention (CDC) checklists.

METHODS

We used a cohort of nearly 4.5 million developmental assessments of 758 300 full-term born children aged 0 to 6 years (ALL-FT cohort), who visited maternal child health clinics in Israel for routine developmental surveillance. Among the assessed milestones of 4 developmental domains (gross motor, fine motor, language, and personal-social) we identified milestones that had equivalents on the CDC checklists and assessed the attainment rates of the Israeli children at the ages recommended by the CDC, at which ≥75% of the children would be expected to achieve the milestone. The analysis was repeated on a subgroup of 658 958 children who were considered healthy, typically developing by their birth and growth characteristics (NORMAL-FT cohort).

RESULTS

There were 29 milestones, across all developmental domains and assessment ages, whose definitions by both tools were compatible, and could be compared. The attainment rate at the CDC-recommended age was >90% for 22 (76%) and 23 (79%) milestones, and the median attainment rates were 95.2% and 96.3% in the ALL-FT and NORMAL-FT cohorts, respectively.

CONCLUSIONS

For almost all comparable milestones of all domains and all ages, children of the Israeli cohorts achieved the milestones earlier than expected by the CDC-defined threshold age. Evidence-based analysis of milestone norms among different populations may enable adjustments of developmental scales and facilitate more personalized developmental surveillance.

Estimating the effect of cesarean delivery on long-term childhood health across two countries

Assessing the impact of cesarean delivery (CD) on long-term childhood outcomes is challenging as conducting a randomized controlled trial is rarely feasible and inferring it from observational data may be confounded. Utilizing data from electronic health records of 737,904 births, we defined and emulated a target trial to estimate the effect of CD on predefined long-term pediatric outcomes. Causal effects were estimated using pooled logistic regression and standardized survival curves, leveraging data breadth to account for potential confounders. Diverse sensitivity analyses were performed including replication of results in an external validation set from the UK including 625,044 births. Children born in CD had an increased risk to develop asthma (10-year risk differences (95% CI) 0.64% (0.31, 0.98)), an average treatment effect of 0.10 (0.07-0.12) on body mass index (BMI) z-scores at age 5 years old and 0.92 (0.68-1.14) on the number of respiratory infection events until 5 years of age. A positive 10-year risk difference was also observed for atopy (10-year risk differences (95% CI) 0.74% (-0.06, 1.52)) and allergy 0.47% (-0.32, 1.28)). Increased risk for these outcomes was also observed in the UK cohort. Our findings add to a growing body of evidence on the long-term effects of CD on pediatric morbidity, may assist in the decision to perform CD when not medically indicated and paves the way to future research on the mechanisms underlying these effects and intervention strategies targeting them.

Standardization of a Developmental Milestone Scale Using Data From Children in Israel

IMPORTANCE

Routine developmental screening tests for children are used worldwide for early detection of developmental delays. However, assessment of developmental milestone norms lacks strong normative data, and there are inconsistencies among different screening tools.

OBJECTIVE

To establish milestone norms and build an updated developmental scale.

DESIGN, SETTING, AND PARTICIPANTS

This is a cross-sectional, population-based study conducted between 2014 and 2020. Developmental assessments were conducted by trained public health nurses, documented in national maternal child health clinics, known as Tipat Halav, which serve all children in Israel. Participants included all children born between January 2014 and September 2020, who were followed at the maternal child health clinics from birth to age 6 years. Exclusion criteria were preterm birth, missing gestational age, low birth weight (<2.5 kg), abnormal weight measurement (<3% according to standardized child growth charts), abnormal head circumference measurement (<3% or >97% according to standardized child growth charts), and visits without developmental data or without the child's age. Data analysis was performed from September 2020 to June 2021.

EXPOSURES

In total, 59 milestones in 4 developmental domains were evaluated, and the achievement rate per child's age was calculated for each milestone.

MAIN OUTCOMES AND MEASURES

A contemporary developmental scale, the Tipat Halav Israel Screening (THIS) Developmental Scale, was built, presenting the 75%, 90%, and 95% achievement rates for each milestone. The THIS scale was compared with other commonly used screening tests, including the Denver Developmental Screening Test II (Denver II), the Alberta Infant Motor Scale (AIMS), and the Centers for Disease Control and Prevention (CDC) Developmental Assessment.

RESULTS

A total of 839 574 children were followed in the maternal child health clinics between January 2014 and September 2020 in Israel, and 195 616 children were excluded. A total of 3 774 517 developmental assessments were performed for the remaining 643 958 children aged 0 to 6 years (319 562 female children [49.6%]), resulting in the establishment of new developmental norms. In terms of the comparable milestones, THIS milestones had a match of 18 of 27 (67%) with the Denver II, 7 of 7 (100%) with AIMS, and 10 of 19 (53%) with the CDC Developmental Assessment. The remaining unmatched milestones were achieved earlier in the THIS scale compared with other screening tools.

CONCLUSIONS AND RELEVANCE

The THIS developmental scale is based on the largest population evaluated to date for developmental performance, representing the heterogeneous, multicultural population comprising this cohort. It is recommended for further evaluation worldwide.

Results of an early second PCR test performed on SARS-CoV-2 positive patients may support risk assessment for severe COVID-19

Identifying patients at increased risk for severe COVID-19 is of high priority during the pandemic as it could affect clinical management and shape public health guidelines. In this study we assessed whether a second PCR test conducted 2–7 days after a SARS-CoV-2 positive test could identify patients at risk for severe illness. Analysis of a nationwide electronic health records data of 1683 SARS-CoV-2 positive individuals indicated that a second negative PCR test result was associated with lower risk for severe illness compared to a positive result. This association was seen across different age groups and clinical settings. More importantly, it was not limited to recovering patients but also observed in patients who still had evidence of COVID-19 as determined by a subsequent positive PCR test. Our study suggests that an early second PCR test may be used as a supportive risk-assessment tool to improve disease management and patient care.

Estimation of postpartum depression risk from electronic health records using machine learning

BACKGROUND

Postpartum depression is a widespread disorder, adversely affecting the well-being of mothers and their newborns. We aim to utilize machine learning for predicting risk of postpartum depression (PPD) using primary care electronic health records (EHR) data, and to evaluate the potential value of EHR-based prediction in improving the accuracy of PPD screening and in early identification of women at risk.

METHODS

We analyzed EHR data of 266,544 women from the UK who gave first live birth between 2000 and 2017. We extracted a multitude of socio-demographic and medical variables and constructed a machine learning model that predicts the risk of PPD during the year following childbirth. We evaluated the model's performance using multiple validation methodologies and measured its accuracy as a stand-alone tool and as an adjunct to the standard questionnaire-based screening by Edinburgh postnatal depression scale (EPDS).

RESULTS

The prevalence of PPD in the analyzed cohort was 13.4%. Combing EHR-based prediction with EPDS score increased the area under the receiver operator characteristics curve (AUC) from 0.805 to 0.844 and the sensitivity from 0.72 to 0.76, at specificity of 0.80. The AUC of the EHR-based prediction model alone varied from 0.72 to 0.74 and decreased by only 0.01-0.02 when applied as early as before the beginning of pregnancy.

CONCLUSIONS

PPD risk prediction using EHR data may provide a complementary quantitative and objective tool for PPD screening, allowing earlier (pre-pregnancy) and more accurate identification of women at risk, timely interventions and potentially improved outcomes for the mother and child.

What Factors Increase the Risk of Complications in SARS-CoV-2-Infected Patients? A Cohort Study in a Nationwide Israeli Health Organization

BACKGROUND

Reliably identifying patients at increased risk for coronavirus disease (COVID-19) complications could guide clinical decisions, public health policies, and preparedness efforts. Multiple studies have attempted to characterize at-risk patients, using various data sources and methodologies. Most of these studies, however, explored condition-specific patient cohorts (eg, hospitalized patients) or had limited access to patients' medical history, thus, investigating related questions and, potentially, obtaining biased results.

OBJECTIVE

This study aimed to identify factors associated with COVID-19 complications from the complete medical records of a nationally representative cohort of patients, with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.

METHODS

We studied a cohort of all SARS-CoV-2-positive individuals, confirmed by polymerase chain reaction testing of either nasopharyngeal or saliva samples, in a nationwide health organization (covering 2.3 million individuals) and identified those who suffered from serious complications (ie, experienced moderate or severe symptoms of COVID-19, admitted to the intensive care unit, or died). We then compared the prevalence of pre-existing conditions, extracted from electronic health records, between complicated and noncomplicated COVID-19 patient cohorts to identify the conditions that significantly increase the risk of disease complications, in various age and sex strata.

RESULTS

Of the 4353 SARS-CoV-2-positive individuals, 173 (4%) patients suffered from COVID-19 complications (all age ≥18 years). Our analysis suggests that cardiovascular and kidney diseases, obesity, and hypertension are significant risk factors for COVID-19 complications. It also indicates that depression (eg, males ≥65 years: odds ratio [OR] 2.94, 95% CI 1.55-5.58; P=.01) as well as cognitive and neurological disorders (eg, individuals ≥65 years old: OR 2.65, 95% CI 1.69-4.17; P<.001) are significant risk factors. Smoking and presence of respiratory diseases do not significantly increase the risk of complications.

CONCLUSIONS

Our analysis agrees with previous studies on multiple risk factors, including hypertension and obesity. It also finds depression as well as cognitive and neurological disorders, but not smoking and respiratory diseases, to be significantly associated with COVID-19 complications. Adjusting existing risk definitions following these observations may improve their accuracy and impact the global pandemic containment and recovery efforts.

Performance analysis of a machine learning flagging system used to identify a group of individuals at a high risk for colorectal cancer

Individuals with colorectal cancer (CRC) have a tendency to intestinal bleeding which may result in mild to severe iron deficiency anemia, but for many colon cancer patients hematological abnormalities are subtle. The fecal occult blood test (FOBT) is used as a pre-screening test whereby those with a positive FOBT are referred to colonscopy. We sought to determine if information contained in the complete blood count (CBC) report coud be processed automatically and used to predict the presence of occult colorectal cancer (CRC) in the setting of a large health services plan. Using the health records of the Maccabi Health Services (MHS) we reviewed CBC reports for 112,584 study subjects of whom 133 were diagnosed with CRC in 2008 and analysed these with the MeScore tool. The odds ratio for being diagnosed with CRC in 2008 was calculated with regards to the MeScore, using cutoff levels of 97% and 99% percentiles. For individuals in the highest one percentile, the odds ratio for CRC was 21.8 (95% CI 13.8 to 34.2). For the majority of the individuals with cancer, CRC was not suspected at the time of the blood draw. Frequent use of anticoagulants, the presence of other gastrointestinal pathologies and non-GI malignancies were assocaitged with false positive MeScores. The MeScore can help identify individuals in the population who would benefit most from CRC screening, including those with no clinical signs or symptoms of CRC.

Development and validation of a predictive model for detection of colorectal cancer in primary care by analysis of complete blood counts: a binational retrospective study

OBJECTIVE

The use of risk prediction models grows as electronic medical records become widely available. Here, we develop and validate a model to identify individuals at increased risk for colorectal cancer (CRC) by analyzing blood counts, age, and sex, then determine the model's value when used to supplement conventional screening.

MATERIALS AND METHODS

Primary care data were collected from a cohort of 606 403 Israelis (of whom 3135 were diagnosed with CRC) and a case control UK dataset of 5061 CRC cases and 25 613 controls. The model was developed on 80% of the Israeli dataset and validated using the remaining Israeli and UK datasets. Performance was evaluated according to the area under the curve, specificity, and odds ratio at several working points.

RESULTS

Using blood counts obtained 3-6 months before diagnosis, the area under the curve for detecting CRC was 0.82 ± 0.01 for the Israeli validation set. The specificity was 88 ± 2% in the Israeli validation set and 94 ± 1% in the UK dataset. Detecting 50% of CRC cases, the odds ratio was 26 ± 5 and 40 ± 6, respectively, for a false-positive rate of 0.5%. Specificity for 50% detection was 87 ± 2% a year before diagnosis and 85 ± 2% for localized cancers. When used in addition to the fecal occult blood test, our model enabled more than a 2-fold increase in CRC detection.

DISCUSSION

Comparable results in 2 unrelated populations suggest that the model should generally apply to the detection of CRC in other groups. The model's performance is superior to current iron deficiency anemia management guidelines, and may help physicians to identify individuals requiring additional clinical evaluation.

CONCLUSIONS

Our model may help to detect CRC earlier in clinical practice.

Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR)

Alternative mRNA splicing is a major mechanism for gene regulation and transcriptome diversity. Despite the extent of the phenomenon, the regulation and specificity of the splicing machinery are only partially understood. Adenosine-to-inosine (A-to-I) RNA editing of pre-mRNA by ADAR enzymes has been linked to splicing regulation in several cases. Here we used bioinformatics approaches, RNA-seq and exon-specific microarray of ADAR knockdown cells to globally examine how ADAR and its A-to-I RNA editing activity influence alternative mRNA splicing. Although A-to-I RNA editing only rarely targets canonical splicing acceptor, donor, and branch sites, it was found to affect splicing regulatory elements (SREs) within exons. Cassette exons were found to be significantly enriched with A-to-I RNA editing sites compared with constitutive exons. RNA-seq and exon-specific microarray revealed that ADAR knockdown in hepatocarcinoma and myelogenous leukemia cell lines leads to global changes in gene expression, with hundreds of genes changing their splicing patterns in both cell lines. This global change in splicing pattern cannot be explained by putative editing sites alone. Genes showing significant changes in their splicing pattern are frequently involved in RNA processing and splicing activity. Analysis of recently published RNA-seq data from glioblastoma cell lines showed similar results. Our global analysis reveals that ADAR plays a major role in splicing regulation. Although direct editing of the splicing motifs does occur, we suggest it is not likely to be the primary mechanism for ADAR-mediated regulation of alternative splicing. Rather, this regulation is achieved by modulating trans-acting factors involved in the splicing machinery.

CD6 and syntaxin binding protein 6 variants and response to tumor necrosis factor alpha inhibitors in Danish patients with rheumatoid arthritis

BACKGROUND

TNFα inhibitor therapy has greatly improved the treatment of patients with rheumatoid arthritis, however at least 30% do not respond. We aimed to investigate insertions and deletions (INDELS) associated with response to TNFα inhibitors in patients with rheumatoid arthritis (RA).

METHODOLOGY AND PRINCIPAL FINDINGS

In the DANBIO Registry we identified 237 TNFα inhibitor naïve patients with RA (81% women; median age 56 years; disease duration 6 years) who initiated treatment with infliximab (n=160), adalimumab (n=56) or etanercept (n=21) between 1999 and 2008 according to national treatment guidelines. Clinical response was assessed at week 26 using EULAR response criteria. Based on literature, we selected 213 INDELS potentially related to RA and treatment response using the GeneVa® (Compugen) in silico database of 350,000 genetic variations in the human genome. Genomic segments were amplified by polymerase chain reaction (PCR), and genotyped by Sanger sequencing or fragment analysis. We tested the association between genotypes and EULAR good response versus no response, and EULAR good response versus moderate/no response using Fisher's exact test. At baseline the median DAS28 was 5.1. At week 26, 68 (29%) patients were EULAR good responders, while 81 (34%) and 88 (37%) patients were moderate and non-responders, respectively. A 19 base pair insertion within the CD6 gene was associated with EULAR good response vs. no response (OR=4.43, 95% CI: 1.99-10.09, p=7.211×10(-5)) and with EULAR good response vs. moderate/no response (OR=4.54, 95% CI: 2.29-8.99, p=3.336×10(-6)). A microsatellite within the syntaxin binding protein 6 (STXBP6) was associated with EULAR good response vs. no response (OR=4.01, 95% CI: 1.92-8.49, p=5.067×10(-5)).

CONCLUSION

Genetic variations within CD6 and STXBP6 may influence response to TNFα inhibitors in patients with RA.

A case-control study of a sex-specific association between a 15q25 variant and lung cancer risk

BACKGROUND

Genetic variants located at 15q25, including those in the cholinergic receptor nicotinic cluster (CHRNA5) have been implicated in both lung cancer risk and nicotine dependence in recent genome-wide association studies. Among these variants, a 22-bp insertion/deletion, rs3841324 showed the strongest association with CHRNA5 mRNA expression levels. However the influence of rs3841324 on lung cancer risk has not been studied in depth.

METHODS

We have, therefore, evaluated the association of rs3841324 genotypes with lung cancer risk in a case-control study of 624 Caucasian subjects with lung cancer and 766 age- and sex-matched cancer-free Caucasian controls. We also evaluated the joint effects of rs3841324 with single-nucleotide polymorphisms (SNP) rs16969968 and rs8034191 in the 15q25 region that have been consistently implicated in lung cancer risk.

RESULTS

We found that the homozygous genotype with both short alleles (SS) of rs3841324 was associated with a decreased lung cancer risk in female ever smokers relative to the homozygous wild-type (LL) and heterozygous (LS) genotypes combined in a recessive model [OR(adjusted) = 0.55, 95% confidence interval (CI), 0.31-0.89, P = 0.0168]. There was no evidence for a sex difference in the association between this variant and cigarettes smoked per day (CPD). Diplotype analysis of rs3841324 with either rs16969968 or rs8034191 showed that these polymorphisms influenced the lung cancer risk independently.

CONCLUSIONS AND IMPACT

This study has shown a sex difference in the association between the 15q25 variant rs3841324 and lung cancers. Further research is warranted to elucidate the mechanisms underlying these observations.

Transcription-mediated gene fusion in the human genome

Transcription of a gene usually ends at a regulated termination point, preventing the RNA-polymerase from reading through the next gene. However, sporadic reports suggest that chimeric transcripts, formed by transcription of two consecutive genes into one RNA, can occur in human. The splicing and translation of such RNAs can lead to a new, fused protein, having domains from both original proteins. Here, we systematically identified over 200 cases of intergenic splicing in the human genome (involving 421 genes), and experimentally demonstrated that at least half of these fusions exist in human tissues. We showed that unique splicing patterns dominate the functional and regulatory nature of the resulting transcripts, and found intergenic distance bias in fused compared with nonfused genes. We demonstrate that the hundreds of fused genes we identified are only a subset of the actual number of fused genes in human. We describe a novel evolutionary mechanism where transcription-induced chimerism followed by retroposition results in a new, active fused gene. Finally, we provide evidence that transcription-induced chimerism can be a mechanism contributing to the evolution of protein complexes.