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.

Characteristics of white blood cell count in acute lymphoblastic leukemia: A COST LEGEND phenotype-genotype study.

BACKGROUND: White blood cell count (WBC) as a measure of extramedullary leukemic cell survival is a well-known prognostic factor in acute lymphoblastic leukemia (ALL), but its biology, including impact of host genome variants, is poorly understood. METHODS: We included patients treated with the Nordic Society of Paediatric Haematology and Oncology (NOPHO) ALL-2008 protocol (N = 2347, 72% were genotyped by Illumina Omni2.5exome-8-Bead chip) aged 1-45 years, diagnosed with B-cell precursor (BCP-) or T-cell ALL (T-ALL) to investigate the variation in WBC. Spline functions of WBC were fitted correcting for association with age across ALL subgroups of immunophenotypes and karyotypes. The residuals between spline WBC and actual WBC were used to identify WBC-associated germline genetic variants in a genome-wide association study (GWAS) while adjusting for age and ALL subtype associations. RESULTS: We observed an overall inverse correlation between age and WBC, which was stronger for the selected patient subgroups of immunophenotype and karyotypes (ρBCP-ALL  = -.17, ρT-ALL  = -.19; p < 3 × 10-4 ). Spline functions fitted to age, immunophenotype, and karyotype explained WBC variation better than age alone (ρ = .43, p << 2 × 10-6 ). However, when the spline-adjusted WBC residuals were used as phenotype, no GWAS significant associations were found. Based on available annotation, the top 50 genetic variants suggested effects on signal transduction, translation initiation, cell development, and proliferation. CONCLUSION: These results indicate that host genome variants do not strongly influence WBC across ALL subsets, and future studies of why some patients are more prone to hyperleukocytosis should be performed within specific ALL subsets that apply more complex analyses to capture potential germline variant interactions and impact on WBC.

Family Formation and Socio-Economic Status among 35-Year-Old Men Who Have Survived Cancer in Childhood and Early Adulthood: A Register-Based Cohort Study.

INTRODUCTION: The number of children and young adults who survive cancer has steadily increased over the past decades. Consequently, life circumstances after cancer have gained increasing importance. The aim of this study was to explore family formation and socio-economic status among 35-year-old men having survived cancer in childhood or early adulthood compared to an age-matched comparison group. METHODS: This study is a national, register-based cohort study among 35-year-old men. Men diagnosed with cancer in childhood and early adulthood were registered between 1978 and 2016. At the time of diagnosis, each patient was randomly matched with 150 men without cancer from the background population within the same birth year. Those still alive at the age of 35 years were included in the study population. RESULTS: The study population consisted of 4,222 men diagnosed with cancer in childhood or early adulthood and 794,589 men in the age-matched comparison group. Men who have survived cancer during childhood or early adulthood have a reduced probability of having children, and lower probability of getting married or of cohabitation than those from an age-matched comparison group. Men who have survived CNS cancer also have a lower probability of having a higher education than high school and a higher probability of being outside the workforce than those from an age-matched comparison group. DISCUSSION/CONCLUSION: Many men who have survived cancer during childhood or early adulthood are influenced by their cancer later in life, which was apparent in family formation, educational achievements, and labour market attachment. Continued focus on rehabilitation and needs for support among the male survivors of childhood and youth cancer is warranted.

Socioeconomic position and prediagnostic health care contacts in children with cancer in Denmark: a nationwide register study.

BACKGROUND: While underlying mechanisms and pathways of social inequalities in cancer survival have been extensively examined in adults, this is less so for children with cancer. Hypothesized mechanisms include prediagnostic utilization of and navigation through the health care system, which may differ by socioeconomic resources of the families. In this nationwide register-based study we investigated the association between measures of family socioeconomic position in relation to prediagnostic health care contacts and stage of disease at diagnosis in children with cancer in Denmark. METHODS: We identified all children diagnosed with a cancer at ages 0-15 years in 1998-2016 (N = 3043) from the Danish Childhood Cancer Registry. We obtained comprehensive information on measures of socioeconomic position, parental health and prediagnostic contacts to both general practitioners and hospitals 24 months prior to diagnosis from various national registries. We fitted multivariable conditional logistic regression models for the association of family socioeconomic and health-related variables with firstly, frequent health care contacts and secondly, advanced stage. RESULTS: We found higher odds ratios (OR) of frequent both overall and emergency health care contacts in the last 3 months before diagnosis in children from households with short parental education and mixed affiliation to work market, when compared to children with high family socioeconomic position. Further, children of parents with depression or of non-Western origin, respectively, had higher OR for frequent overall and emergency contacts. We found no association between socioeconomic position, parental health and stage of disease. CONCLUSION: Families with socioeconomic disadvantage, non-Western origin or depression more frequently utilize prediagnostic health care services, both generally and in the acute setting, indicating that some disadvantaged families may struggle to navigate the health care system when their child is sick. Reassuringly, this was not reflected in disparities in stage at diagnosis. In order to improve the diagnostic process and potentially reduce health care contacts, attention and support should be given to families with a high number of health care contacts over a short period of time.

Social Inequalities Along the Childhood Cancer Continuum: An Overview of Evidence and a Conceptual Framework to Identify Underlying Mechanisms and Pathways.

Inequalities in health according to social conditions are regarded as unnecessary and unjust. There is a large body of evidence on inequalities in adult cancer, observable throughout the societies on a national level as well as on a global scale. Socioeconomic influences on health matter at all ages including childhood, for which childhood cancer is the leading cause of disease related death in high-income countries (HICs). Substantial differences in the reported incidence of childhood cancers have been observed globally by socioeconomic development of a population. This is reflected in the higher incidence rates reported for HICs, particularly for acute lymphoblastic leukemia, and for cancer in infants (below 1 year), compared to low- and middle-income countries (LMICs). Considerable inequalities between populations and degree of socioeconomic development are also noted for survival from childhood cancer, with substantially lower survival rates seen in most LMICs compared to HICs. With respect to inequalities by socioeconomic position (SEP) within countries, findings of an association between SEP and childhood cancer risk are diverse and limited to studies from HICs. On the contrary, observations on social inequalities in survival within countries are accumulating and indicate that survival inequalities do not only concern resource-poor countries but also high-income populations including European countries. In turn, a childhood cancer diagnosis in itself may have implications on the parents' socioeconomic situation as well as on the later socioeconomic life after having survived the disease. The underlying mechanisms and causal pathways of these empirically demonstrated social inequalities are poorly understood, although it is of significant public health relevance for any actions or strategies to reduce childhood cancer-related inequity. We propose a conceptual framework on potential underlying mechanism and pathways specifically addressing social inequalities in childhood cancer and after childhood cancer to (i) illustrate potential pathways by which social determinants may create health inequities at different points of the childhood cancer continuum; (ii) illustrate potential pathways by which a childhood cancer diagnosis may impact the socioeconomic situation of the concerned family or the later life of a childhood survivor; and (iii) point out how major determinants may relate to each other.

Socioeconomic Factors and Ninth Grade School Performance in Childhood Leukemia and CNS Tumor Survivors.

BACKGROUND: Childhood cancer survivors can experience deficits in school performance in adolescence. Few studies have investigated how social and socioeconomic factors influence and modify school performance. This study investigates the hypothesis that social and parental socioeconomic factors influence ninth grade school performance in childhood leukemia and central nervous system (CNS) tumor survivors and that the effect is different from that in healthy peers. METHODS: We analyzed data from nationwide Danish registers on school grades for children who finished ninth grade during 2002-2015 in Denmark. Using a unique within-school matched design, we compared grades from childhood cancer survivors with grades from healthy peers. Social factors were maternal/paternal civil status, immigrant status, and country of origin. Parental socioeconomic factors were measured by education and income. The study consisted of 36 426 children, of whom 460 and 289 were leukemia and CNS tumor survivors, respectively. RESULTS: School grades varied considerably across social strata. However, the grades among CNS tumor survivors varied notably less in the following effect modifiers: parental educational attainment, income, and immigrant status. On the contrary, no significant effect modifiers were found among leukemia survivors as compared with healthy peers. CONCLUSION: There is a strong effect of social and parental socioeconomic factors on school performance in healthy adolescence in Denmark. The same pattern is seen in survivors of leukemia, but a different pattern is seen in survivors of CNS tumors. This finding suggests that impairment of school-related functions differ between leukemia and CNS tumor survivors. This study contributes to knowledge on learning in adolescence in childhood cancer survivors by investigating several social and socioeconomic effect modifiers with nationwide register data and a unique statistical method particularly suitable for comparing school grades. Improved insight could make it possible to identify high-risk groups that may need different means of help.

Extremely low-frequency magnetic fields and risk of childhood leukemia: A risk assessment by the ARIMMORA consortium.

Exposure to extremely low-frequency magnetic fields (ELF-MF) was evaluated in an International Agency for Research on Cancer (IARC) Monographs as "possibly carcinogenic to humans" in 2001, based on increased childhood leukemia risk observed in epidemiological studies. We conducted a hazard assessment using available scientific evidence published before March 2015, with inclusion of new research findings from the Advanced Research on Interaction Mechanisms of electroMagnetic exposures with Organisms for Risk Assessment (ARIMMORA) project. The IARC Monograph evaluation scheme was applied to hazard identification. In ARIMMORA for the first time, a transgenic mouse model was used to mimic the most common childhood leukemia: new pathogenic mechanisms were indicated, but more data are needed to draw definitive conclusions. Although experiments in different animal strains showed exposure-related decreases of CD8+ T-cells, a role in carcinogenesis must be further established. No direct damage of DNA by exposure was observed. Overall in the literature, there is limited evidence of carcinogenicity in humans and inadequate evidence of carcinogenicity in experimental animals, with only weak supporting evidence from mechanistic studies. New exposure data from ARIMMORA confirmed that if the association is nevertheless causal, up to 2% of childhood leukemias in Europe, as previously estimated, may be attributable to ELF-MF. In summary, ARIMMORA concludes that the relationship between ELF-MF and childhood leukemia remains consistent with possible carcinogenicity in humans. While this scientific uncertainty is dissatisfactory for science and public health, new mechanistic insight from ARIMMORA experiments points to future research that could provide a step-change in future assessments. Bioelectromagnetics. 37:183-189, 2016. © 2016 Wiley Periodicals, Inc.

Effect of socioeconomic position on survival after childhood cancer in Denmark.

Background One fifth of all deaths among children in Europe are accounted for by cancer. If this is to be reduced there is a need for studies on not only biology and treatment approaches but also on how social factors influence cure rates. We investigated how various socioeconomic characteristics were associated with survival after childhood cancer. Material and methods In a nationwide cohort of 3797 children diagnosed with cancer [hematological cancer, central nervous system (CNS) tumors, non-CNS solid tumors] before age 20 between 1990 and 2009 we identified parents and siblings and obtained individual level parental socioeconomic variables and vital status through 2012 by linkage to population-based registries. Hazard ratios (HR) and 95% confidence intervals (CI) for dying were estimated using multivariate Cox proportional hazard models. Results For all children with cancer combined, survival was slightly but not statistically significantly better the higher the education of the mother or the father, and with maternal income. Significantly better survival was observed when parents were living together compared to living alone and worse survival when the child had siblings compared to none. Young (<20) or older (≥40) maternal age showed non-significant associations, but based on small numbers. For hematological cancers, no significant associations were observed. For CNS tumors, better survival was seen with parents living together (HR 0.70, CI 0.51-0.97). For non-CNS solid tumors, survival was better with high education of the mother (HR 0.66, CI 0.44-0.99) compared to basic and worse for children with one (HR 1.45, CI 1.11-1.89) or two or more siblings (HR 1.29, CI 0.93-1.79) (p for trend 0.02) compared to none. Conclusion The impact of socioeconomic characteristics on childhood cancer survival, despite equal access to protocolled and free-of-charge treatment, warrants further and more direct studies of underlying mechanisms in order to target these as a means to improve survival rates.

Classification of treatment-related mortality in children with cancer: a systematic assessment.

Treatment-related mortality is an important outcome in paediatric cancer clinical trials. An international group of experts in supportive care in paediatric cancer developed a consensus-based definition of treatment-related mortality and a cause-of-death attribution system. The reliability and validity of the system was tested in 30 deaths, which were independently assessed by two clinical research associates and two paediatric oncologists. We defined treatment-related mortality as death occurring in the absence of progressive cancer. Of the 30 reviewed deaths, the reliability of classification for treatment-related mortality was noted as excellent by clinical research associates (κ=0·83, 95% CI 0·60-1·00) and paediatric oncologists (0·84, 0·63-1·00). Criterion validity was established because agreement between the consensus classifications by clinical research associates and paediatric oncologists was almost perfect (0·92, 0·78-1·00). Our approach should allow comparison of treatment-related mortality across trials and across time.