Accuracy of patient race and ethnicity data in a central cancer registry.

PURPOSE: Race and Hispanic ethnicity data can be challenging for central cancer registries to collect. We evaluated the accuracy of the race and Hispanic ethnicity variables collected by the Utah Cancer Registry compared to self-report. METHODS: Participants were 3,162 cancer survivors who completed questionnaires administered in 2015-2022 by the Utah Cancer Registry. Each survey included separate questions collecting race and Hispanic ethnicity, respectively. Registry-collected race and Hispanic ethnicity were compared to self-reported values for the same individuals. We calculated sensitivity and specificity for each race category and Hispanic ethnicity separately. RESULTS: Survey participants included 323 (10.2%) survivors identifying as Hispanic, a lower proportion Hispanic than the 12.1% in the registry Hispanic variable (sensitivity 88.2%, specificity 96.5%). For race, 43 participants (1.4%) self-identified as American Indian or Alaska Native (AIAN), 32 (1.0%) as Asian, 23 (0.7%) as Black or African American, 16 (0.5%) Pacific Islander (PI), and 2994 (94.7%) as White. The registry race variable classified a smaller proportion of survivors as members of each of these race groups except White. Sensitivity for classification of race as AIAN was 9.3%, Asian 40.6%, Black 60.9%, PI 25.0%, and specificity for each of these groups was > 99%. Sensitivity and specificity for White were 98.8% and 47.4%. CONCLUSION: Cancer registry race and Hispanic ethnicity data often did not match the individual's self-identification. Of particular concern is the high proportion of AIAN individuals whose race is misclassified. Continued attention should be directed to the accurate capture of race and ethnicity data by hospitals.

Cancer survivorship experiences in Utah: an evaluation assessing indicators of survivors' quality of life, health behaviors, and access to health services.

PURPOSE: The 2016-2020 Utah Comprehensive Cancer Prevention and Control Plan prioritized strategies to address cancer survivorship experiences. In this paper we present estimates for nine indicators evaluating these priorities, trends over time, and assess disparities in survivorship experiences across demographic subgroups. METHODS: We surveyed a representative sample of Utah cancer survivors diagnosed between 2012 and 2019 with any reportable cancer diagnosis. We calculated weighted percentages and 95% confidence intervals (CI) for each indicator. We assessed change over time using a test for trend across survey years in a logistic regression model and used Rao-Scott F-adjusted chi-square tests to test the association between demographic characteristics and each survivorship indicator. RESULTS: Most of the 1,793 respondents (93.5%) reported their pain was under control, 85.7% rated their overall health as good, very good, or excellent, but 46.5% experienced physical, mental, or emotional limitations. Only 1.7% of survivors aged 75 or older were current smokers, compared to 5.8% of 65-74-year-olds and 7.9% of survivors aged 55-74 (p < 0.006). No regular physical activity was reported by 20.6% and varied by survivor age and education level. The proportion who received a survivorship care plan increased from 34.6% in 2018 to 43.0% in 2021 (p = 0.025). However, survivors under age 55 were significantly less likely to receive a care plan than older survivors. CONCLUSION: This representative survey of cancer survivors fills a gap in understanding of the cancer survivorship experience in Utah. Results can be used to evaluate and plan additional interventions to improve survivorship quality of life.

Evaluation of direct and maternal responses in reproduction traits based on different selection strategies for postnatal piglet survival in a selection experiment.

BACKGROUND: Postnatal piglet survival is important both in economic and animal welfare terms. It is influenced by the piglet's own direct genetic effects and by maternal genetic effects of the dam, associated with milk production and mothering abilities. These genetic effects might be correlated, affected by other non-genetic factors and unfavourably associated with other reproduction traits such as litter size, which makes the development of optimal breeding strategies a challenge. To identify the optimum selection strategy for piglet survival, a selection experiment was carried out to compare responses in survival and reproduction traits to selection on only direct, only maternal, or both genetic effects of postnatal survival. The data of the experiment were recorded from outdoor reared pigs, with first- and second-generation sires selected based on their estimated breeding values for maternal and direct effects of postnatal survival of indoor reared offspring, respectively, with the opportunity to identify potential genotype-by-environment interaction. RESULTS: A Bayesian multivariate threshold-linear model that was fitted to data on 22,483 piglets resulted in significant (Pr(h2 > 0) = 1.00) estimates of maternal and direct heritabilities between 0.12 and 0.18 for survival traits and between 0.29 and 0.36 for birth weight, respectively. Selection for direct genetic effects resulted in direct and maternal responses in postnatal survival of 1.11% ± 0.17 and - 0.49% ± 0.10, respectively, while selection for maternal genetic effects led to greater direct and maternal responses, of 5.20% ± 0.34 and 1.29% ± 0.20, respectively, in part due to unintentional within-litter selection. Selection for both direct and maternal effects revealed a significant lower direct response (- 1.04% ± 0.12) in comparison to its expected response from single-effect selection, caused by interactions between direct and maternal effects. CONCLUSIONS: Selection successfully improved post- and perinatal survival and birth weight, which indicates that they are genetically determined and that genotype-by-environment interactions between outdoor (experimental data) and indoor (selection data) housed pigs were not important for these traits. A substantially increased overall (direct plus maternal) response was obtained using selection for maternal versus direct or both direct and maternal effects, suggesting that the maternal genetic effects are the main limiting factor for improving piglet survival on which selection pressure should be emphasized.

Prenatal exome sequencing analysis in fetal structural anomalies detected by ultrasonography (PAGE): a cohort study.

BACKGROUND: Fetal structural anomalies, which are detected by ultrasonography, have a range of genetic causes, including chromosomal aneuploidy, copy number variations (CNVs; which are detectable by chromosomal microarrays), and pathogenic sequence variants in developmental genes. Testing for aneuploidy and CNVs is routine during the investigation of fetal structural anomalies, but there is little information on the clinical usefulness of genome-wide next-generation sequencing in the prenatal setting. We therefore aimed to evaluate the proportion of fetuses with structural abnormalities that had identifiable variants in genes associated with developmental disorders when assessed with whole-exome sequencing (WES). METHODS: In this prospective cohort study, two groups in Birmingham and London recruited patients from 34 fetal medicine units in England and Scotland. We used whole-exome sequencing (WES) to evaluate the presence of genetic variants in developmental disorder genes (diagnostic genetic variants) in a cohort of fetuses with structural anomalies and samples from their parents, after exclusion of aneuploidy and large CNVs. Women were eligible for inclusion if they were undergoing invasive testing for identified nuchal translucency or structural anomalies in their fetus, as detected by ultrasound after 11 weeks of gestation. The partners of these women also had to consent to participate. Sequencing results were interpreted with a targeted virtual gene panel for developmental disorders that comprised 1628 genes. Genetic results related to fetal structural anomaly phenotypes were then validated and reported postnatally. The primary endpoint, which was assessed in all fetuses, was the detection of diagnostic genetic variants considered to have caused the fetal developmental anomaly. FINDINGS: The cohort was recruited between Oct 22, 2014, and June 29, 2017, and clinical data were collected until March 31, 2018. After exclusion of fetuses with aneuploidy and CNVs, 610 fetuses with structural anomalies and 1202 matched parental samples (analysed as 596 fetus-parental trios, including two sets of twins, and 14 fetus-parent dyads) were analysed by WES. After bioinformatic filtering and prioritisation according to allele frequency and effect on protein and inheritance pattern, 321 genetic variants (representing 255 potential diagnoses) were selected as potentially pathogenic genetic variants (diagnostic genetic variants), and these variants were reviewed by a multidisciplinary clinical review panel. A diagnostic genetic variant was identified in 52 (8·5%; 95% CI 6·4-11·0) of 610 fetuses assessed and an additional 24 (3·9%) fetuses had a variant of uncertain significance that had potential clinical usefulness. Detection of diagnostic genetic variants enabled us to distinguish between syndromic and non-syndromic fetal anomalies (eg, congenital heart disease only vs a syndrome with congenital heart disease and learning disability). Diagnostic genetic variants were present in 22 (15·4%) of 143 fetuses with multisystem anomalies (ie, more than one fetal structural anomaly), nine (11·1%) of 81 fetuses with cardiac anomalies, and ten (15·4%) of 65 fetuses with skeletal anomalies; these phenotypes were most commonly associated with diagnostic variants. However, diagnostic genetic variants were least common in fetuses with isolated increased nuchal translucency (≥4·0 mm) in the first trimester (in three [3·2%] of 93 fetuses). INTERPRETATION: WES facilitates genetic diagnosis of fetal structural anomalies, which enables more accurate predictions of fetal prognosis and risk of recurrence in future pregnancies. However, the overall detection of diagnostic genetic variants in a prospectively ascertained cohort with a broad range of fetal structural anomalies is lower than that suggested by previous smaller-scale studies of fewer phenotypes. WES improved the identification of genetic disorders in fetuses with structural abnormalities; however, before clinical implementation, careful consideration should be given to case selection to maximise clinical usefulness. FUNDING: UK Department of Health and Social Care and The Wellcome Trust.

Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data.

A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer. Our study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively assess the role of the Knudson two hit genetic model in SCNA generation in prostate cancer. 64 recurrent regions of loss and gain were detected, of which 28 were novel, including regions of loss with more than 15% frequency at Chr4p15.2-p15.1 (15.53%), Chr6q27 (16.50%) and Chr18q12.3 (17.48%). Comprehensive mutation screens of genes, lincRNA encoding sequences, control regions and conserved domains within SCNAs demonstrated that a two-hit genetic model was supported in only a minor proportion of recurrent SCNA losses examined (15/40). We found that recurrent breakpoints and regions of inversion often occur within Knudson model SCNAs, leading to the identification of ZNF292 as a target gene for the deletion at 6q14.3-q15 and NKX3.1 as a two-hit target at 8p21.3-p21.2. The importance of alterations of lincRNA sequences was illustrated by the identification of a novel mutational hotspot at the KCCAT42, FENDRR, CAT1886 and STCAT2 loci at the 16q23.1-q24.3 loss. Our data confirm that the burden of SCNAs is predictive of biochemical recurrence, define nine individual regions that are associated with relapse, and highlight the possible importance of ion channel and G-protein coupled-receptor (GPCR) pathways in cancer development. We concluded that a two-hit genetic model accounts for about one third of SCNA indicating that mechanisms, such haploinsufficiency and epigenetic inactivation, account for the remaining SCNA losses.

Predictors of Response Outcomes for Research Recruitment Through a Central Cancer Registry: Evidence From 17 Recruitment Efforts for Population-Based Studies.

When recruiting research participants through central cancer registries, high response fractions help ensure population-based representation. We conducted multivariable mixed-effects logistic regression to identify case and study characteristics associated with making contact with and obtaining cooperation of Utah cancer cases using data from 17 unique recruitment efforts undertaken by the Utah Cancer Registry (2007-2016) on behalf of the following studies: A Population-Based Childhood Cancer Survivors Cohort Study in Utah, Comparative Effectiveness Analysis of Surgery and Radiation for Prostate Cancer (CEASAR Study), Costs and Benefits of Follow-up Care for Adolescent and Young Adult Cancers, Study of Exome Sequencing for Head and Neck Cancer Susceptibility Genes, Genetic Epidemiology of Chronic Lymphocytic Leukemia, Impact of Remote Familial Colorectal Cancer Risk Assessment and Counseling (Family CARE Project), Massively Parallel Sequencing for Familial Colon Cancer Genes, Medullary Thyroid Carcinoma (MTC) Surveillance Study, Osteosarcoma Surveillance Study, Prostate Cancer Outcomes Study, Risk Education and Assessment for Cancer Heredity Project (REACH Project), Study of Shared Genomic Segment Analysis and Tumor Subtyping in High-Risk Breast-Cancer Gene Pedigrees, Study of Shared Genomic Segment Analysis for Localizing Multiple Myeloma Genes. Characteristics associated with lower odds of contact included Hispanic ethnicity (odds ratio (OR) = 0.34, 95% confidence interval (CI): 0.27, 0.41), nonwhite race (OR = 0.46, 95% CI: 0.35, 0.60), and younger age at contact. Years since diagnosis was inversely associated with making contact. Nonwhite race and age ≥60 years had lower odds of cooperation. Study features with lower odds of cooperation included longitudinal design (OR = 0.50, 95% CI: 0.41, 0.61) and study brochures (OR = 0.70, 95% CI: 0.54, 0.90). Increased odds of cooperation were associated with including a questionnaire (OR = 3.19, 95% CI: 1.54, 6.59), postage stamps (OR = 1.60, 95% CI: 1.21, 2.12), and incentives (OR = 1.62, 95% CI: 1.02, 2.57). Among cases not responding after the first contact, odds of eventual response were lower when >10 days elapsed before subsequent contact (OR = 0.71, 95% CI: 0.59, 0.85). Obtaining high response is challenging, but study features identified in this analysis support better results when recruiting through central cancer registries.

The feasibility of web surveys for obtaining patient-reported outcomes from cancer survivors: a randomized experiment comparing survey modes and brochure enclosures.

BACKGROUND: Central cancer registries are often used to survey population-based samples of cancer survivors. These surveys are typically administered via paper or telephone. In most populations, web surveys obtain much lower response rates than paper surveys. This study assessed the feasibility of web surveys for collecting patient-reported outcomes via a central cancer registry. METHODS: Potential participants were sampled from Utah Cancer Registry records. Sample members were randomly assigned to receive a web or paper survey, and then randomized to either receive or not receive an informative brochure describing the cancer registry. We calculated adjusted risk ratios with 95% confidence intervals to compare response likelihood and the demographic profile of respondents across study arms. RESULTS: The web survey response rate (43.2%) was lower than the paper survey (50.4%), but this difference was not statistically significant (adjusted risk ratio = 0.88, 95% confidence interval = 0.72, 1.07). The brochure also did not significantly influence the proportion responding (adjusted risk ratio = 1.03, 95% confidence interval = 0.85, 1.25). There were few differences in the demographic profiles of respondents across the survey modes. Older age increased likelihood of response to a paper questionnaire but not a web questionnaire. CONCLUSIONS: Web surveys of cancer survivors are feasible without significantly influencing response rates, but providing a paper response option may be advisable particularly when surveying older individuals. Further examination of the varying effects of brochure enclosures across different survey modes is warranted.

Deep Learning and Machine Vision Approaches for Posture Detection of Individual Pigs.

Posture detection targeted towards providing assessments for the monitoring of health and welfare of pigs has been of great interest to researchers from different disciplines. Existing studies applying machine vision techniques are mostly based on methods using three-dimensional imaging systems, or two-dimensional systems with the limitation of monitoring under controlled conditions. Thus, the main goal of this study was to determine whether a two-dimensional imaging system, along with deep learning approaches, could be utilized to detect the standing and lying (belly and side) postures of pigs under commercial farm conditions. Three deep learning-based detector methods, including faster regions with convolutional neural network features (Faster R-CNN), single shot multibox detector (SSD) and region-based fully convolutional network (R-FCN), combined with Inception V2, Residual Network (ResNet) and Inception ResNet V2 feature extractions of RGB images were proposed. Data from different commercial farms were used for training and validation of the proposed models. The experimental results demonstrated that the R-FCN ResNet101 method was able to detect lying and standing postures with higher average precision (AP) of 0.93, 0.95 and 0.92 for standing, lying on side and lying on belly postures, respectively and mean average precision (mAP) of more than 0.93.

Prostate cancer risk regions at 8q24 and 17q24 are differentially associated with somatic TMPRSS2:ERG fusion status.

Molecular and epidemiological differences have been described between TMPRSS2:ERG fusion-positive and fusion-negative prostate cancer (PrCa). Assuming two molecularly distinct subtypes, we have examined 27 common PrCa risk variants, previously identified in genome-wide association studies, for subtype specific associations in a total of 1221 TMPRSS2:ERG phenotyped PrCa cases. In meta-analyses of a discovery set of 552 cases with TMPRSS2:ERG data and 7650 unaffected men from five centers we have found support for the hypothesis that several common risk variants are associated with one particular subtype rather than with PrCa in general. Risk variants were analyzed in case-case comparisons (296 TMPRSS2:ERG fusion-positive versus 256 fusion-negative cases) and an independent set of 669 cases with TMPRSS2:ERG data was established to replicate the top five candidates. Significant differences (P < 0.00185) between the two subtypes were observed for rs16901979 (8q24) and rs1859962 (17q24), which were enriched in TMPRSS2:ERG fusion-negative (OR = 0.53, P = 0.0007) and TMPRSS2:ERG fusion-positive PrCa (OR = 1.30, P = 0.0016), respectively. Expression quantitative trait locus analysis was performed to investigate mechanistic links between risk variants, fusion status and target gene mRNA levels. For rs1859962 at 17q24, genotype dependent expression was observed for the candidate target gene SOX9 in TMPRSS2:ERG fusion-positive PrCa, which was not evident in TMPRSS2:ERG negative tumors. The present study established evidence for the first two common PrCa risk variants differentially associated with TMPRSS2:ERG fusion status. TMPRSS2:ERG phenotyping of larger studies is required to determine comprehensive sets of variants with subtype-specific roles in PrCa.

Genetic selection against intrauterine growth retardation in piglets: a problem at the piglet level with a solution at the sow level.

BACKGROUND: In polytocous livestock species, litter size and offspring weight act antagonistically; in modern pig breeds, selection for increased litter size has resulted in lower mean birth weights, an increased number of small piglets and an increased number of those affected by varying degrees of intrauterine growth retardation (IUGR). IUGR poses life-long challenges, both mental, with morphological brain changes and altered cognition, and physical, such as immaturity of organs, reduced colostrum intake and weight gain. In pigs, head morphology of newborn piglets is a good phenotypic marker for identifying such compromised piglets. Growth retardation could be considered as a property of the dam, in part due to either uterine capacity or insufficiency. A novel approach to this issue is to consider the proportion of IUGR-affected piglets in a litter as an indirect measure of uterine capacity. However, uterine capacity or sufficiency cannot be equated solely to litter size and thus is a trait difficult to measure on farm. RESULTS: A total of 21,159 Landrace × Large White or Landrace × White Duroc piglets (born over 52 weeks) with recorded head morphology and birth weights were followed from birth until death or weaning. At the piglet level, the estimated heritability for IUGR (as defined by head morphology) was low at 0.01 ± 0.01. Piglet direct genetic effects of birth weight (h2 = 0.07 ± 0.02) were strongly negatively correlated with head morphology (- 0.93), in that IUGR-affected piglets tended to have lower birth weights. At the sow level, analysis of the proportion of IUGR-affected piglets in a litter gave a heritability of 0.20 ± 0.06, with high and negative genetic correlations of the proportion of IUGR-affected piglets with average offspring birth weight (- 0.90) and with the proportion of piglets surviving until 24 h (- 0.80). CONCLUSIONS: This suggests that the proportion of IUGR-affected piglets in a litter is a suitable indirect measure of uterine capacity for inclusion in breeding programmes that aim at reducing IUGR in piglets and improving piglet survival.