Combinatorial batching of DNA for ultralow-cost detection of pathogenic variants.

BACKGROUND: Next-generation sequencing (NGS) based population screening holds great promise for disease prevention and earlier diagnosis, but the costs associated with screening millions of humans remain prohibitive. New methods for population genetic testing that lower the costs of NGS without compromising diagnostic power are needed. METHODS: We developed double batched sequencing where DNA samples are batch-sequenced twice - directly pinpointing individuals with rare variants. We sequenced batches of at-birth blood spot DNA using a commercial 113-gene panel in an explorative (n = 100) and a validation (n = 100) cohort of children who went on to develop pediatric cancers. All results were benchmarked against individual whole genome sequencing data. RESULTS: We demonstrated fully replicable detection of cancer-causing germline variants, with positive and negative predictive values of 100% (95% CI, 0.91-1.00 and 95% CI, 0.98-1.00, respectively). Pathogenic and clinically actionable variants were detected in RB1, TP53, BRCA2, APC, and 19 other genes. Analyses of larger batches indicated that our approach is highly scalable, yielding more than 95% cost reduction or less than 3 cents per gene screened for rare disease-causing mutations. We also show that double batched sequencing could cost-effectively prevent childhood cancer deaths through broad genomic testing. CONCLUSIONS: Our ultracheap genetic diagnostic method, which uses existing sequencing hardware and standard newborn blood spots, should readily open up opportunities for population-wide risk stratification using genetic screening across many fields of clinical genetics and genomics.

Assessment of Seasonality and Extremely Preterm Birth in Denmark.

Importance: Preterm birth, particularly extremely preterm birth, has been associated with substantial morbidity and mortality. Research during SARS-CoV-2-related lockdowns revealed reductions in the more severe subtypes of preterm birth in some countries, suggesting the presence of preventable risk factors, such as infectious diseases or social behavior. Seasonality may provide a similar means of assessing natural changes in the daily life of pregnant individuals that were similar to those experienced during the COVID-19 lockdown period. Objective: To evaluate the association between seasonality and extremely preterm birth. Design, Setting, and Participants: This nationwide cohort study included 1 136 143 pregnancies in Denmark with onset between January 1, 1997, and December 31, 2016, in which the fetuses survived 21 completed weeks of gestation. Pregnancies were followed up until preterm birth, fetal death, or 37 completed weeks of gestation. Data were analyzed from September 2020 to September 2021. Exposures: Season during gestation (primary exposure) and season of pregnancy onset. Main Outcomes and Measures: The main outcome of extremely preterm birth was defined as a live birth occurring between 22 weeks, 0 days' gestation and 27 weeks, 6 days' gestation. Cox regression analyses were used to estimate hazard ratios (HRs) for season during gestation and season of pregnancy onset, with adjustment for socioeconomic and demographic factors. Results: Among 662 338 pregnant individuals, the median age at pregnancy onset was 30.0 years (IQR, 6.0 years). Of 1 136 143 pregnancies, 2009 extremely preterm births (cumulative incidence, 0.18%) were identified during follow-up. Season during gestation was associated with extremely preterm birth, with cumulative incidences of 0.17% (95% CI, 0.16%-0.19%) in spring, 0.18% (95% CI, 0.17%-0.20%) in summer, 0.20% (95% CI, 0.18%-0.21%) in autumn, and 0.16% (95% CI, 0.14%-0.17%) in winter. Compared with winter, the adjusted HRs (AHRs) for the risk of extremely preterm birth were 1.11 (95% CI, 0.97-1.26) for spring, 1.15 (95% CI, 1.02-1.31) for summer, and 1.25 (95% CI, 1.10-1.42) for autumn. The number of extremely preterm births associated with the increased risk in the spring, summer, and autumn was 56.1 (95% CI, 18.2-99.7), representing 2.8% (95% CI, 0.9%-5.0%) of all extremely preterm births in the study. Season of pregnancy onset was not associated with the risk of extremely preterm birth in spring (AHR, 0.98; 95% CI, 0.95-1.01) or summer (AHR, 1.00; 95% CI, 0.96-1.03) compared with winter, but a slight increase in risk was observed in autumn (AHR, 1.05; 95% CI, 1.02-1.09) compared with winter. Conclusions and Relevance: In this large, national cohort study, seasonality was associated with 2.8% of all extremely preterm births. Season during gestation was associated with the rate of extremely preterm birth, suggesting the presence of potential risk factors associated with season that may be preventable. Further research to identify risk factors for extremely preterm birth associated with seasonality is warranted.

Frequent blood donation and offspring scholastic attainment: an assessment of long-term consequences of prenatal iron deficiency.

BACKGROUND: Due to physiological demands, children and premenopausal women are at risk of developing iron deficiency. In premenopausal women, the risk may be further increased by repeated whole blood donations. Short-term consequences of iron deficiency in infancy include impaired cognitive development and lower IQ scores. This prompts concern that maternal iron deficiency before or during pregnancy may have long-term consequences for the offspring, for example, by affecting scholastic attainment. The aim of this study was to evaluate if prepregnancy donation intensity is associated with offspring scholastic attainment measured as grade averages in standardized national written examinations in Denmark. STUDY DESIGN AND METHODS: By using the Danish personal identification number as key, we obtained information on donation intensity before pregnancy, school grade, year of graduation, age of the students, students' sex, and parental length of education and income from various nationwide registers. Linear regression analyses were performed, with grade average as outcome and maternal donation status as explanatory variable (nondonor, n = 177,078; low-frequency donor, n = 4995 [one to five donations in the 3 years before pregnancy]; high-frequency donor, n = 414 [six or more donations in the 3 years before pregnancy), and further adjusted for the covariates listed above. RESULTS: Adjusted normalized (mean, 0; standard deviation [SD], 1) test scores were statistically significantly higher for children of active female donors compared with children of nondonors (SD, 0.104; 95% confidence interval, 0.079-0.129). We observed no differences in scholastic attainment between children of low-frequency donors and high-frequency donors. CONCLUSION: Prepregnancy donation intensity, as a proxy of iron stores, is not associated with subsequent offspring scholastic attainment.

Blood use in hematologic malignancies: a nationwide overview in Sweden between 2000 and 2010.

BACKGROUND: Patients with hematologic malignancies receive large numbers of blood transfusions, and transfusion practices for this patient group are increasingly being scrutinized by randomized controlled trials. However, no studies so far have presented current transfusion statistics on a population level for this patient group. STUDY DESIGN AND METHODS: A retrospective descriptive study was conducted that was based on the Scandinavian Donations and Transfusions Database (SCANDAT2), which includes data on all blood donations and transfusions in Sweden and Denmark since the 1960s. Incident cases of hematologic malignancies were identified in the Swedish Cancer Register between 2000 and 2010. Cases were divided into nine patient groups based on diagnosis. RESULTS: A total of 28,693 patients were included in the cohort. Overall, the transfusion pattern varied depending on diagnosis and age. Patients with aggressive and acute diagnoses generally received more transfusions with immediate decline in transfusion incidence after diagnosis, whereas chronic diagnoses generally maintained more stable, but lower, transfusion incidence. In general, patients with leukemia received more transfusions than patients with lymphoma, and patients with acute leukemia as well as patients that had undergone allogeneic stem cell transplantations received the most transfusions. Within 2 years after diagnosis, patients with acute myeloid leukemia diagnosed at ages 0 to 65 years received on average between 30 to 40 red blood cell transfusions and platelet transfusions, respectively, corresponding to direct material costs close to 200,000 SEK (23,809 USD). CONCLUSION: Results from this population-based overview of blood use in hematologic malignancies showed high variability depending on diagnosis and age.

Socio-demographic characteristics of Danish blood donors.

BACKGROUND: Blood transfusion is an essential component of a modern healthcare system. Because knowledge about blood donor demography may inform the design of strategies for donor recruitment and retention, we used nationwide registers to characterize the entire population of blood donors in Denmark in 2010. METHODS: The study population comprised all Danes in the age range eligible for blood donation (N = 3,236,753) at the end of 2010. From the Scandinavian Donations and Transfusions (SCANDAT) register, we identified 174,523 persons who donated blood in Danish blood banks at least once in 2010. The association between sociodemographic characteristics and blood donor prevalence was examined using regression models. RESULTS: The overall prevalence of blood donation was 5.4% among both women and men. The age-specific prevalence of blood donation peaked at 25 years of age (6.8%) for women and 30 years of age (5.7%) for men. Children of any age were associated with lower prevalence of blood donation among women, while the opposite was seen for men. Middle to high income groups, but not the highest income group, had fourfold higher donor prevalence than the lowest income group (6.7% compared to 1.7%). The prevalence of blood donation was considerably lower among men living with their parents (2.9%) or alone (3.9%) than among men cohabitating with a woman (6.2%). SUMMARY: Social marginalization, as indicated by low income and being a male living without a woman, was associated with lower prevalence of blood donation. However, individuals with very high incomes and women with children were underrepresented in the Danish blood donor population.

Expensive blood safety initiatives may offer less benefit than we think.

BACKGROUND: Various blood safety initiatives have ensured a historically low risk of infection transmission through blood transfusion. Although further prevention of infection transmission is possible through, for example, nucleic acid testing and future introduction of pathogen inactivation, such initiatives are very costly in relation to the benefit they offer. Although estimation of the cost-effectiveness requires detailed information about the survival of transfusion recipients, previous cost-effectiveness analyses have relied on incorrect survival assumptions. STUDY DESIGN AND METHODS: Based on empirical data of more than 1 million Scandinavian transfusion recipients followed for up to 20 years, we present two new survival functions. In a fictitious example we assessed the impact of survival assumptions on the estimated costs per quality-adjusted life-year (QALY) gained, by using the survival functions of three previous cost-effectiveness analyses along with the two new survival functions. CONCLUSIONS: We conclude that despite considerable costs, previous cost-effectiveness studies may have underestimated the costs per QALY gained by as much as 44%.

Infectious mononucleosis, childhood social environment, and risk of Hodgkin lymphoma.

Infectious mononucleosis (IM) has been associated with an increased risk of Hodgkin lymphoma (HL), implicating a role for Epstein-Barr virus (EBV) in HL development. Although essential to the understanding of the association, it has remained uncertain if the relationship is restricted to the EBV-positive subset of HL. We collected information on mononucleosis history and childhood socioenvironmental characteristics in a population-based study of 586 patients with classic HL and 3,187 controls in Denmark and Sweden. Tumor EBV status was established for 499 cases by immunohistochemistry and in situ hybridization techniques. Odds ratios (OR) for the relationship between HL risk and mononucleosis and other risk factors were estimated by logistic regression for HL in younger (18-44 years) and older (45-74 years) adults, overall and by tumor EBV status. All analyses were adjusted for country-specific measures of maternal education and mononucleosis history. IM was associated with an increased risk of EBV-positive [OR, 3.23; 95% confidence interval (95% CI) 1.89-5.55] but not EBV-negative HL (OR, 1.35; 95% CI, 0.86-2.14). Risk of EBV-positive HL varied with time since IM and was particularly pronounced in younger adults (OR, 3.96; 95% CI, 2.19-7.18). IM-associated lymphomas occurred with a median of 2.9 years (1.8-4.9 years) after infection. The EBV specificity of the IM association was corroborated by a case-case comparison of IM history between younger adult EBV-positive and EBV-negative HL patients (OR(IM EBV+ HL versus EBV- HL), 2.68; 95% CI, 1.40-5.12). We found further evidence that IM is associated only with EBV-positive HL. This finding is compatible with the notion that EBV-positive and EBV-negative HL may have different etiologies.