Pathogenic Germline Variants in 10,389 Adult Cancers

We conducted the largest investigation of predisposition variants in cancer to date, discovering 853 pathogenic or likely pathogenic variants in 8% of 10,389 cases from 33 cancer types. Twenty-one genes showed single or cross-cancer associations, including novel associations of SDHA in melanoma and PALB2 in stomach adenocarcinoma. The 659 predisposition variants and 18 additional large deletions in tumor suppressors, including ATM, BRCA1, and NF1, showed low gene expression and frequent (43%) loss of heterozygosity or biallelic two-hit events. We also discovered 33 such variants in oncogenes, including missenses in MET, RET, and PTPN11 associated with high gene expression. We nominated 47 additional predisposition variants from prioritized VUSs supported by multiple evidences involving case-control frequency, loss of heterozygosity, expression effect, and co-localization with mutations and modified residues. Our integrative approach links rare predisposition variants to functional consequences, informing future guidelines of variant classification and germline genetic testing in cancer.

Facilitators and Barriers for Advance Care Planning Among Ethnic and Racial Minorities in the U.S.: A Systematic Review of the Current Literature

Growing evidence suggests a low engagement in advance care planning (ACP) among ethnic minorities in the U.S. The purpose of this study was to synthesize findings from prior research about ACP among ethnic minorities. An extensive literature search was conducted using multiple electronic databases. After applying inclusion criteria, 26 studies were included. Four categories of facilitators and barriers to ACP were identified: (1) Socio-demographic factors, (2) health status, literacy and experiences, (3) cultural values, and (4) spirituality. Socio-demographic factors showed inconsistent findings regarding their association with ACP engagement. Worse health status and knowledge about ACP are common facilitators across ethnic minority groups, whereas mistrust toward the health care system was a barrier only for Blacks. Collectivistic cultural values influenced ACP engagement among Latinos and Asian Americans; however, spirituality/religion played an important role among Blacks. The implications for culturally competent approaches to promote ACP and future research directions are discussed.

Productive aging via volunteering: Does social cohesion influence level of engagement?

This study investigated whether neighborhood social cohesion influenced volunteer intensity over two years. The sample was drawn from Health and Retirement Study respondents who completed the 2010 or 2012 Psychosocial and Lifestyle Questionnaire (n = 12,929). Results showed that compared to nonvolunteers, a one-unit increase in neighborhood social cohesion increased the odds of moderate (OR: 1.07, p < .05) and high volunteering (OR: 1.10, p < .001). However, other productive roles, social contact, and education were significant in distinguishing high intensity from moderate volunteering while neighborhood social cohesion was not. Social workers should consider the neighborhood environment when recruiting volunteers.

Rural/urban residence and childhood and adolescent cancer survival in the United States

BACKGROUND

To the authors' knowledge, no previous study has examined the relationship between rural/urban residence and childhood or adolescent cancer survival in the United States. Using the Surveillance, Epidemiology, and End Results 18 registries database, the authors examined childhood and adolescent cancer survival by rural/urban residence as defined by Rural-Urban Continuum Codes (RUCCs).

METHODS

The authors obtained data from Surveillance, Epidemiology, and End Results 18 registries for individuals diagnosed at ages birth to 19 years with a first primary malignant cancer from 2000 through 2010. Rural/urban residence at the time of diagnosis was defined using both metropolitan/nonmetropolitan county classifications and individual RUCC categories. Cox proportional hazards regression was used to compute adjusted hazard ratios (HRs) and 95% confidence intervals (95% CIs) for the association between rural/urban residence and cancer survival. The authors also examined effect modification by age group, sex, race/ethnicity, and cancer type.

RESULTS

Among 41,879 cancer cases, approximately 54.7% were non-Hispanic white, 54.3% were male, and 90.4% lived in a metropolitan county. Individuals living in nonmetropolitan counties versus metropolitan counties had a similar risk of cancer death (HR,  1.03; 95% CI, 0.94-1.13) as did those living in nonmetropolitan rural counties with <2500 individuals nonadjacent to a metropolitan area versus those living in metropolitan counties of ≥1 million individuals (HR,  0.98; 95% CI, 0.71-1.37). Evidence for effect modification largely was absent.

CONCLUSIONS

The results of the current study suggest that childhood and adolescent cancer survival in the United States does not vary by rural/urban residence at the time of diagnosis as defined by RUCCs. The widespread availability of public health insurance for children and adolescents and a nationwide network of pediatric cancer providers may explain this finding.

Volunteering among First-Generation Asian Ethnic Groups Residing in California

This study was a cross-sectional investigation of volunteer activity among four distinct Asian ethnic subgroups-Chinese, Filipino, Korean, and Vietnamese-who have immigrated to the United States. Data from the 2011-2012 California Health Interview Survey (CHIS) were used with an analytic sample of Chinese (n = 547), Filipino (n = 229), Korean (n = 490), and Vietnamese (n = 546) adults 50 and older. A series of logistic regression models were estimated to examine differences and similarities across the four ethnic groups in volunteer activity. Consistent with previous studies, Asian immigrants with more years of education and those who became U.S. citizens were more likely to participate in volunteering. However, the correlates were not consistent within Asian ethnic subgroups. For example, education was not a significant factor for older Korean immigrants while it was a salient factor among other Asian subgroups. Results showed similarities and differences associated with volunteer participation among diverse ethnic subgroups. The findings underscored the importance of culture-specific information in creating inclusive opportunities for volunteering.

Use of reproducible research practices in public health: A survey of public health analysts

Objective

Use of reproducible research practices improves the quality of science and the speed of scientific development. We sought to understand use of reproducible research practices in public health and associated barriers and facilitators.

Methods

In late 2017, we surveyed members of the American Public Health Association Applied Public Health Statistics section and others; 247 of 278 who screened eligible answered the survey, and 209 answered every applicable question. The survey included questions about file management, code annotation and documentation, reproducibility of analyses, and facilitators and barriers of using reproducible practices.

Results

Just 14.4% of participants had shared code, data, or both. Many participants reported their data (33%) and code (43.2%) would be difficult for colleagues to find if they left their institution. Top reported barriers to using reproducible practices were data privacy (49.8%) and lack of time (41.7%). Participants suggested training (50.9%) and requirements by journals (44.4%) and funders (40.2%) to increase use of reproducible research practices.

Conclusions

Increasing use of reproducible research practices is important for public health and requires action from researchers, training programs, funders, and journals.

Characteristics of The Cancer Genome Atlas cases relative to U.S. general population cancer cases

Background

Despite anecdotal reports of differences in clinical and demographic characteristics of The Cancer Genome Atlas (TCGA) relative to general population cancer cases, differences have not been systematically evaluated.

Methods

Data from 11,160 cases with 33 cancer types were ascertained from TCGA data portal. Corresponding data from the Surveillance, Epidemiology, and End Results (SEER) 18 and North American Association of Central Cancer Registries databases were obtained. Differences in characteristics were compared using Student’s t, Chi-square, and Fisher’s exact tests. Differences in mean survival months were assessed using restricted mean survival time analysis and generalised linear model.

Results

TCGA cases were 3.9 years (95% CI 1.7–6.2) younger on average than SEER cases, with a significantly younger mean age for 20/33 cancer types. Although most cancer types had a similar sex distribution, race and stage at diagnosis distributions were disproportional for 13/18 and 25/26 assessed cancer types, respectively. Using 12 months as an end point, the observed mean survival months were longer for 27 of 33 TCGA cancer types.

Conclusions

Differences exist in the characteristics of TCGA vs. general population cancer cases. Our study highlights population subgroups where increased sample collection is warranted to increase the applicability of cancer genomic research results to all individuals.

Integrative omics analyses broaden treatment targets in human cancer

Background

Although large-scale, next-generation sequencing (NGS) studies of cancers hold promise for enabling precision oncology, challenges remain in integrating NGS with clinically validated biomarkers.

Methods

To overcome such challenges, we utilized the Database of Evidence for Precision Oncology (DEPO) to link druggability to genomic, transcriptomic, and proteomic biomarkers. Using a pan-cancer cohort of 6570 tumors, we identified tumors with potentially druggable biomarkers consisting of drug-associated mutations, mRNA expression outliers, and protein/phosphoprotein expression outliers identified by DEPO.

Results

Within the pan-cancer cohort of 6570 tumors, we found that 3% are druggable based on FDA-approved drug-mutation interactions in specific cancer types. However, mRNA/phosphoprotein/protein expression outliers and drug repurposing across cancer types suggest potential druggability in up to 16% of tumors. The percentage of potential drug-associated tumors can increase to 48% if we consider preclinical evidence. Further, our analyses showed co-occurring potentially druggable multi-omics alterations in 32% of tumors, indicating a role for individualized combinational therapy, with evidence supporting mTOR/PI3K/ESR1 co-inhibition and BRAF/AKT co-inhibition in 1.6 and 0.8% of tumors, respectively. We experimentally validated a subset of putative druggable mutations in BRAF identified by a protein structure-based computational tool. Finally, analysis of a large-scale drug screening dataset lent further evidence supporting repurposing of drugs across cancer types and the use of expression outliers for inferring druggability.

Conclusions

Our results suggest that an integrated analysis platform can nominate multi-omics alterations as biomarkers of druggability and aid ongoing efforts to bring precision oncology to patients.

Electronic supplementary material

The online version of this article (10.1186/s13073-018-0564-z) contains supplementary material, which is available to authorized users.

Abstract 1194: U.S. childhood and adolescent cancer survival between 1992 and 2013: An analysis of population-based data

Background

Monitoring cancer survival over time and across different demographic groups is an important part of cancer control. In the current study, our objective was to examine U.S. cancer survival patterns in childhood and adolescent cancer patients between different time periods and demographic groups.

Methods

Survival data for primary cancers diagnosed in individuals ≤ 19 years from 1992 to 2014 were obtained from the Surveillance, Epidemiology, and End Results 13 database. Five-year relative survival rates were estimated according to the cohort method using SEER*Stat software. Survival differences were examined for subgroups defined by diagnosis time period (1992-1994, 1995-1999, 2000-2004, 2005-2009), sex (male and female), age at diagnosis (&lt;1, 1-4, 5-9, 10-14, 15-19 years) and race/ethnicity (Non-Hispanic White, Non-Hispanic-Black, Hispanic, and Non-Hispanic Other). The annual percent change (APC) in 5-year relative survival was estimated using Joinpoint software. Finally, period survival analysis was also conducted using SEER*Stat software to provide the most up-to-date five-year relative survival predictions using data from cases diagnosed between 2007 and 2013.

Results

Five-year relative survival increased significantly for cancers overall (75.9% vs. 82.9 for 1992-1994 and 2005-2009 respectively, p&lt;0.001) and for half of the cancer subtypes. The largest improvements were observed for leukemias, myeloproliferative and myelodysplastic disease (+ 11.6%, p&lt;0.001) and lymphomas and reticuloendothelial neoplasms (+5.8%, p&lt;0.001). Significant improvement in relative survival over time was also observed for both sexes with APCs of 0.67 (males) and 0.51 (females), across all age groups with APCs of 0.68 (infants), 0.63 (1-4 years), 0.68 (10-14 years) and 0.65 (15-19 years) except 5-9 years (APC: 0.32), and all racial/ethnic groups with APCs of 0.61 (non-Hispanic White), 0.64 (Non-Hispanic Black), 0.51 (Hispanic), and 0.75 (Non-Hispanic Other). No statistically significant differences in the APCs were observed between sex, age, and race/ethnicity subgroups. However, survival disparities were apparent across age and race/ethnicity subgroups in period analyses, with infant and Hispanic, non-Hispanic Black and non-Hispanic Other cases having lower survival rates than older and non-Hispanic White cases (infant: 77.2% vs 1-4 years: 85.5%, 5-9 years: 84.1%, 10-14 years: 84.2% and 15-19 years: 84.0%; Non-Hispanic Black: 81.6%, Non-Hispanic Other: 81.2%, and Hispanic: 79.8% vs. Non-Hispanic White: 87.5%).

Conclusion

Our results indicate that childhood and adolescent cancer survival continues to improve for all demographic groups. However, persistent inferior survival rates in infants and in minority race/ethnicity groups reinforces the need for continued research that aims to eliminate childhood and adolescent cancer survival inequities.

Citation Format: Xiaoyan Wang, Kimberly J. Johnson. U.S. childhood and adolescent cancer survival between 1992 and 2013: An analysis of population-based data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1194.

Parental age and risk of genetic syndromes predisposing to nervous system tumors: nested case-control study

Purpose

Phacomatoses are genetic syndromes that are associated with increased risk of developing nervous system tumors. Phacomatoses are usually inherited, but many develop de novo, with unknown etiology. In this population-based study, we investigated the effect of parental age on the risk of phacomatoses in offspring.

Patients and methods

The study was a population-based nested case–control study. All individuals born and residing in Sweden between January 1960 and December 2010 were eligible for inclusion. Using the Patient Register, 4625 phacomatosis cases were identified and further classified as familial or nonfamilial. Ten matched controls per case were randomly selected from the eligible population. Data were analyzed using conditional logistic regression. Analyses were conducted for neurofibromatosis alone (n=2089) and other phacomatoses combined (n=2536).

Results

Compared with offspring of fathers aged 25–29 years, increased risk estimates of nonfamilial neurofibromatosis were found for offspring of fathers aged 35–39 years (odds ratio [OR]=1.43 [95% CI 1.16–1.74]) and ≥40 years (OR =1.74 [95% CI 1.38–2.19]). For other nonfamilial phacomatoses, the risk estimate for offspring of fathers aged ≥40 years was OR =1.23 (95% CI 1.01–1.50). Paternal age was not associated with familial phacomatoses, and no consistent association was observed with maternal age.

Conclusion

The findings show a consistent increase in risk of de novo occurrence of phacomatoses predisposing to nervous system tumors in offspring with increasing paternal age, most pronounced for neurofibromatosis, while maternal age did not seem to influence the risk. These findings suggest an increasing rate of new mutations in the NF1 and NF2 genes in spermatozoa of older fathers.

Male Breast Cancer: An Updated Surveillance, Epidemiology, and End Results Data Analysis

BACKGROUND

Male breast cancer is rare and understudied compared with female breast cancer. A current comparison with female breast cancer could assist in bridging this gap. Although conflicting data have been reported on male and female survival outcomes, data from 1973 through 2005 in the Surveillance, Epidemiology, and End Results (SEER) program have demonstrated that the improvement in breast cancer survival in men has fallen behind that of women. As treatment for breast cancer has improved significantly, an updated analysis using a contemporary population is necessary.

MATERIALS AND METHODS

An analysis of SEER data from patients with a diagnosis of primary breast cancer from 2005 to 2010 were included. A Cox regression model was used to examine the association between sex and breast cancer mortality after controlling for prognostic factors, including age, race, marital status, disease stage, estrogen and progesterone receptor status, lymph node involvement, tumor grade, surgery, and geography. Subgroup analyses were performed by race and stage.

RESULTS

We included a total of 289,673 breast cancer cases (2054 men) with a diagnosis from 2005 to 2010. The 5-year survival rate for male patients was lower than that for female patients (82.8% vs. 88.5%). After controlling for other factors, the risk of death in men was 43% greater than that in women during the follow-up period (hazard ratio, 1.43; 95% confidence interval, 1.26-1.61). Similar results were noted in the race and stage subgroup analyses.

CONCLUSION

In recent years, male breast cancer patients have had worse survival outcomes compared with those of female patients.

Parental Age and Risk of Infant Leukaemia: A Pooled Analysis

BACKGROUND

Infant leukaemia (IL) is extremely rare with fewer than 150 cases occurring each year in the United States. Little is known about its causes. However, recent evidence supports a role of de novo mutations in IL aetiology. Parental age has been associated with several adverse outcomes in offspring, including childhood cancers. Given the role of older parental age in de novo mutations in offspring, we carried out an analysis of parental age and IL.

METHODS

We evaluated the relationship between parental age and IL in a case-control study using registry data from New York, Minnesota, California, Texas, and Washington. Records from 402 cases [219 acute lymphoblastic leukaemia (ALL), 131 acute myeloid leukaemia (AML), and 52 other] and 45 392 controls born during 1981-2004 were analysed. Odds ratios (OR) and 95% confidence intervals (CI) were calculated by logistic regression. Estimates were adjusted for infant sex, birth year category, maternal race, state, and mutually adjusted for paternal or maternal age, respectively.

RESULTS

Infants with mothers' age ≥40 years had an increased risk of developing AML (OR 4.80, 95% CI 1.80, 12.76). In contrast, paternal age <20 was associated with increased risk of ALL (OR 3.69, 95% CI 1.62, 8.41).

CONCLUSION

This study demonstrates increased risk of infant ALL in relation to young paternal age. Given record linkage, there is little concern with recall or selection bias, although data are lacking on MLL gene status and other potentially important variables. Parent of origin effects, de novo mutations, and/or carcinogenic exposures may be involved in IL aetiology.

Congenital neurodevelopmental anomalies in pediatric and young adult cancer

Congenital anomalies that are diagnosed in at least 120,000 US infants every year are the leading cause of infant death and contribute to disability and pediatric hospitalizations. Several large-scale epidemiologic studies have provided substantial evidence of an association between congenital anomalies and cancer risk in children, suggesting potential underlying cancer-predisposing conditions and the involvement of developmental genetic pathways. Electronic medical records from 1,107 pediatric, adolescent, and young adult oncology patients were reviewed. The observed number (O) of congenital anomalies among children with a specific pediatric cancer subtype was compared to the expected number (E) of anomalies based on the frequency of congenital anomalies in the entire study population. The O/E ratios were tested for significance using Fisher's exact test. The Kaplan-Meier method was used to compare overall and neurological malignancy survival rates following tumor diagnosis. Thirteen percent of patients had a congenital anomaly diagnosis prior to their cancer diagnosis. When stratified by congenital anomaly subtype, there was an excess of neurological anomalies among children with central nervous system tumors (O/E = 1.56, 95%CI 1.13-2.09). Male pediatric cancer patients were more likely than females to have a congenital anomaly, particularly those <5 years of age (O/E 1.35, 95%CI 0.97-1.82). Our study provides additional insight into the association between specific congenital anomaly types and pediatric cancer development. Moreover, it may help to inform the development of new screening policies and support hypothesis-driven research investigating mechanisms underlying tumor predisposition in children with congenital anomalies.

Pediatric cancer risk in association with birth defects: A systematic review

BACKGROUND

Many epidemiological studies have examined associations between birth defects (BDs) and pediatric malignancy over the past several decades. Our objective was to conduct a systematic literature review of studies reporting on this association.

METHODS

We used librarian-designed searches of the PubMed Medline and Embase databases to identify primary research articles on pediatric neoplasms and BDs. English language articles from PubMed and Embase up to 10/12/2015, and in PubMed up to 5/12/2017 following an updated search, were eligible for inclusion if they reported primary epidemiological research results on associations between BDs and pediatric malignancies. Two reviewers coded each article based on the title and abstract to identify eligible articles that were abstracted using a structured form. Additional articles were identified through reference lists and other sources. Results were synthesized for pediatric cancers overall and for nine major pediatric cancer subtypes.

RESULTS

A total of 14,778 article citations were identified, of which 80 met inclusion criteria. Pediatric cancer risk was increased in most studies in association with BDs overall with some notable specific findings, including increased risks for CNS tumors in association with CNS abnormalities and positive associations between rib anomalies and several pediatric cancer types.

CONCLUSIONS

Some children born with BDs may be at increased risk for specific pediatric malignancy types. This work provides a foundation for future investigations that are needed to clarify specific BD types predisposing toward malignancy and possible underlying causes of both BDs and malignancy.

Blood biomarker analysis to differentiate between pseudo-progression and true disease progression in post-treatment glioblastoma

e13501

Background: Current standard treatment for patients with glioblastoma (GBM) includes glucocorticoid therapy, temozolomide (TMZ), and radiation (RT) which may result in lymphotoxic and immunosuppressive effects. MRI use is currently unreliable in differentiating true from pseudo-progression pathology. Recent studies have suggested that total lymphocyte count (TLC) and CD4 cell count are associated with clinical outcomes. Our objective was to investigate whether TLC or CD4 may help to differentiate treatment effect (pesudoprogression) from tumor progression. Methods: Patients were eligible for this retrospective study if they had 1) GBM diagnosed between February 2010 and July 2015, 2) series of cell counts and clinical follow-ups monitored at Washington University, and 3) tumor progression documented by MRI and pathology. The data were analyzed using descriptive statistics, chi-square tests, Kaplan-Meier survival curves, and progression-free survival. Results: A total of 728 charts were reviewed, of which 45adults met eligibility criteria. The median age and KPS scores were 58 years and 80, respectively. MGMT was detected in 33% of patients and 69% of patients had undergone a gross total resection. Median TLC at baseline was 1700 cells/mm3 (range 400-3100). After the completion of RT/TMZ, TLC dropped 41% to a median of 1000 cells/mm3 (range 200-2900). Median TLC was 1000 cells/mm3 (range 300-2900) at the first MRI documented progression. Patients underwent surgery for this MRI documented progression. Pathology revealed that 62% of patients had true tumor progression, 33% had mixed treatment effect and residual tumor, and 4% had necrosis. The median time from diagnosis to progression was 15 months. There were no statistically significant differences in overall survival or progression free survival found in patients with higher vs lower TLC at baseline, completion of RT/TMZ, and time of progression. Conclusions: These preliminary results do not indicate that TLC level in GBM patients can differentiate between true disease progression and pseudo-progression. A larger sample size that includes patients with CD4 data is needed to confirm these results.

Neurofibromatosis type 1

Neurofibromatosis type 1 is a complex autosomal dominant disorder caused by germline mutations in the NF1 tumour suppressor gene. Nearly all individuals with neurofibromatosis type 1 develop pigmentary lesions (café-au-lait macules, skinfold freckling and Lisch nodules) and dermal neurofibromas. Some individuals develop skeletal abnormalities (scoliosis, tibial pseudarthrosis and orbital dysplasia), brain tumours (optic pathway gliomas and glioblastoma), peripheral nerve tumours (spinal neurofibromas, plexiform neurofibromas and malignant peripheral nerve sheath tumours), learning disabilities, attention deficits, and social and behavioural problems, which can negatively affect quality of life. With the identification of NF1 and the generation of accurate preclinical mouse strains that model some of these clinical features, therapies that target the underlying molecular and cellular pathophysiology for neurofibromatosis type 1 are becoming available. Although no single treatment exists, current clinical management strategies include early detection of disease phenotypes (risk assessment) and biologically targeted therapies. Similarly, new medical and behavioural interventions are emerging to improve the quality of life of patients. Although considerable progress has been made in understanding this condition, numerous challenges remain; a collaborative and interdisciplinary approach is required to manage individuals with neurofibromatosis type1 and to develop effective treatments.

Integrated analysis of germline and somatic variants in ovarian cancer

We report the first large-scale exome-wide analysis of the combined germline-somatic landscape in ovarian cancer. Here we analyse germline and somatic alterations in 429 ovarian carcinoma cases and 557 controls. We identify 3,635 high confidence, rare truncation and 22,953 missense variants with predicted functional impact. We find germline truncation variants and large deletions across Fanconi pathway genes in 20% of cases. Enrichment of rare truncations is shown in BRCA1, BRCA2 and PALB2. In addition, we observe germline truncation variants in genes not previously associated with ovarian cancer susceptibility (NF1, MAP3K4, CDKN2B and MLL3). Evidence for loss of heterozygosity was found in 100 and 76% of cases with germline BRCA1 and BRCA2 truncations, respectively. Germline-somatic interaction analysis combined with extensive bioinformatics annotation identifies 222 candidate functional germline truncation and missense variants, including two pathogenic BRCA1 and 1 TP53 deleterious variants. Finally, integrated analyses of germline and somatic variants identify significantly altered pathways, including the Fanconi, MAPK and MLL pathways.