Search

The number of clinical laboratories using next-generation sequencing (NGS) methods for the assessment of somatic variants has been growing rapidly. (1,2) This explosion has been driven by the increasing numbers [...], Context.--As laboratories increasingly turn from single-analyte testing in hematologic malignancies to next-generation sequencing-based panel testing, there is a corresponding need for proficiency testing to ensure adequate performance of these next-generation sequencing assays for optimal patient care. Objective.--To report the performance of laboratories on proficiency testing from the first 4 College of American Pathologists Next-Generation Sequencing Hematologic Malignancy surveys. Design.--College of American Pathologists proficiency testing results for 36 different engineered variants and/or allele fractions as well as a sample with no pathogenic variants were analyzed for accuracy and associated assay performance characteristics. Results.--The overall sensitivity observed for all variants was 93.5% (2190 of 2341) with 99.8% specificity (22 800 of 22 840). The false-negative rate was 6.5% (151 of 2341), and the largest single cause of these errors was difficulty in identifying variants in the sequence of CEBPA that is rich in cytosines and guanines. False-positive results (0.18%; 40 of 22 840) were most likely the result of preanalytic or postanalytic errors. Interestingly, the variant allele fractions were almost uniformly lower than the engineered fraction (as measured by digital polymerase chain reaction). Extensive troubleshooting identified a multifactorial cause for the low variant allele fractions, a result of an interaction between the linearized nature of the plasmid and the Illumina TruSeq chemistry. Conclusions.--Laboratories demonstrated an overall accuracy of 99.2% (24 990 of 25 181) with 99.8% specificity and 93.5% sensitivity when examining 36 clinically relevant somatic single-nucleotide variants with a variant allele fraction of 10% or greater. The data also highlight an issue with artificial linearized plasmids as survey material for next-generation sequencing. doi: 10.5858/arpa.2019-0352-CP

Objective: Maori women in New Zealand have higher incidence of and mortality from cervical cancer than non-Maori women, however limited research has examined differences in treatment and survival between these groups. This study aims to determine if ethnic disparities in treatment and survival exist among a cohort of Maori and non-Maori women with cervical cancer. Methods: A retrospective cohort study of 1911 women (344 Maori and 1567 non-Maori) identified from the New Zealand Cancer Register with cervical cancer (adenocarcinoma, adenosquamous or squamous cell carcinoma) between 1 January 1996 and 31 December 2006. Results: Maori women with cervical cancer had a higher receipt of total hysterectomies, and similar receipt of radical hysterectomies and brachytherapy as primary treatment, compared to non-Maori women (age and stage adjusted). Over the cohort period, Maori women had poorer cancer specific survival than non-Maori women (mortality hazard ratio (HR) 2.07, 95% confidence interval (CI): 1.63-2.62). From 1996 to 2005, the survival for Maori improved significantly relative to non-Maori. Conclusion: Maori continue to have higher incidence and mortality than non-Maori from cervical cancer although disparities are improving. Survival disparities are also improving. Treatment (as measured) by ethnicity is similar. Implications: Primary prevention and early detection remain key interventions for addressing Maori needs and reducing inequalities in cervical cancer in New Zealand. Key words: Cervix neoplasms, cervical cancer, survival, survival analyses, ethnicity, treatment. Aust NZ J Public Health. 2010; 34:193-99 doi: 10.1111/j.1753-6405.2010.00506.x

Drawing on in-depth interviews with cancer patients. This article examines patients' perspectives on the nature of evidence and the degree to which different understandings of evidence inform decision-making about complementary and alternative medicine (CAM) and biomedical cancer treatments. Results illustrate the ways in which many cancer patients critically engage with questions about the nature of knowledge and the potential pitfalls of science. Their accounts can largely be characterized by a dialectical tension between individuation (espoused by many CAM therapies) and depersonalization (implicit in biomedical care); a tension mediated by individual cancer patient's prognosis and age. On the basis of the results we argue for a re-focusing of social theory to embrace an understanding of grass-roots ontological tensions seen in the experiences of individual cancer patients. The problematic nature of maintaining a narrowly defined 'evidence-base' policy on CAM and cancer is also discussed in light of the data. KEY WORDS cancer / complementary medicine / evidence-based medicine

Cancer surveillance research requires estimates of the prevalence of cancer risk factors and screening for small areas such as counties. Two popular data sources are the Behavioral Risk Factor Surveillance System (BRFSS), a telephone survey conducted by state agencies, and the National Health Interview Survey (NHIS), an area probability sample survey conducted through face-to-face interviews. Both data sources have advantages and disadvantages. The BRFSS is a larger survey and almost every county is included in the survey, but it has lower response rates as is typical with telephone surveys and it does not include subjects who live in households with no telephones. On the other hand, the NHIS is a smaller survey, with the majority of counties not included; but it includes both telephone and nontelephone households, and has higher response rates. A preliminary analysis shows that the distributions of cancer screening and risk factors are different for telephone and nontelephone households. Thus, information from the two surveys may be combined to address both nonresponse and noncoverage errors. A hierarchical Bayesian approach that combines information from both surveys is used to construct county-level estimates. The proposed model incorporates potential noncoverage and nonresponse biases in the BRFSS as well as complex sample design features of both surveys. A Markov chain Monte Carlo method is used to simulate draws from the joint posterior distribution of unknown quantities in the model that uses design-based direct estimates and county-level covariates. Yearly prevalence estimates at the county level for 49 states, as well as for the entire state of Alaska and the District of Columbia, are developed for six outcomes using BRFSS and NHIS data from the years 1997-2000. The outcomes include smoking and use of common cancer screening procedures. The NHIS/BRFSS combined county-level estimates are substantially different from those based on the BRFSS alone. KEY WORDS: BRFSS; Cancer screening; Complex sample survey; Gibbs sampling; Hierarchical model; Mammography; NHIS; Pap smear; Simulation; Smoking.

OBJECTIVE: To investigate whether removal of the laxative preparation would improve colorectal cancer (CRC) screening rates. RESPONDENTS AND METHODS: Data are from a mixed-mode mail and telephone survey of 1636 [...]