Impact of sociodemographic factors on the radiotherapeutic management of lung cancer: Results of a Quality Research in Radiation Oncology survey.

PURPOSE: The objective of this study is to describe the impact of sociodemographic (SOC) factors on the management of lung cancer patients treated at radiation therapy facilities participating in the Quality Research in Radiation Oncology survey. METHODS AND MATERIALS: A 2-stage stratified random sample of lung cancer patients treated in 2006 to 2007 at 45 facilities yielded 340 stage I-III non-small cell lung cancer (NSCLC) and 144 limited-stage small cell lung cancer (LS-SCLC) cases. Five SOC variables based on data from the 2000 US Census were analyzed for association with the following clinical factors: patients living in urban versus rural settings (U/R); median household income (AHI); % below poverty level (PPV); % unemployed (PUE); and % with college education (PCE). RESULTS: The 340 NSCLC patients were stage I, 16%; stage II, 11%; stage III, 62%; stage unknown, 11%. Histologic subtypes were adenocarcinoma, 31.8%; squamous cell carcinoma, 35.3%; large cell carcinoma, 3.2%; and NSCLC NOS, 27.7%. The median age was 66 years. Median Karnofsky performance status (KPS) was 80. The 144 LS-SCLC had a median age of 63; 73 were male (50.7%). Median KPS was 80. Stereotactic body radiation therapy (SBRT) and modern imaging utilization was associated with treatment at facilities located in higher SOC regions. SBRT was employed in 46.8% stage I NSCLC patients treated in centers where %PUE was below median versus 14.8% in centers where %PUE was above median (P = .02). Four-dimensional computed tomography was utilized in 14.2% of patients treated in centers located in regions with %PPV below median versus 3.7% in centers located in regions with %PPV above median (P < .01). SCLC patients were more likely to receive all of their planned RT when treated at centers located in regions with lower PPV (95.0% vs 79.1%; P = .04). CONCLUSIONS: SOC factors may impact use of modern treatment planning and delivery and multidisciplinary management of NSCLC and SCLC. These results may suggest an impact of these SOC factors on access to health care.

Can patient comorbidities be included in clinical performance measures for radiation oncology?

PURPOSE: Patient comorbidities may affect the applicability of performance measures that are inherent in multidisciplinary cancer treatment guidelines. This article describes the distribution of common comorbid conditions by disease site and by patient and facility characteristics in patients who received radiation therapy as part of treatment for cancer of the breast, cervix, lung, prostate, and stomach, and investigates the association of comorbidities with treatment decisions. MATERIALS AND METHODS: Stratified two-stage cluster sampling provided a random sample of radiation oncology facilities. Eligible patients were randomly sampled from each participating facility for each disease site, and data were abstracted from medical records. The Adult Comorbidity Evaluation Index (ACE-27) was used to measure comorbid conditions and their severity. National estimates were calculated using SUDAAN statistical software. RESULTS: Multivariable logistic regression models predicted the dependent variable "treatment changed or contraindicated due to comorbidities." The final model showed that ACE-27 was highly associated with change in treatment for patients with severe or moderate index values compared to those with none or mild (P < .001). Two other covariates, age and medical coverage, had no (age) or little (medical coverage) significant contribution to predicting treatment change in the multivariable model. Disease site was associated with treatment change after adjusting for other covariates in the model. CONCLUSIONS: ACE-27 is highly predictive of treatment modifications for patients treated for these cancers who receive radiation as part of their care. A standardized tool identifying patients who should be excluded from clinical performance measures allows more accurate use of these measures.

Patterns of radiation therapy practice for patients treated for intact cervical cancer in 2005 to 2007: a quality research in radiation oncology study.

PURPOSE: To assess practice patterns and compliance with clinical performance measures for radiation therapy (RT) for patients with intact carcinoma of the cervix. METHODS AND MATERIALS: Trained research associates reviewed the records of 261 randomly selected patients who received RT for cervix carcinoma between 2005 and 2007 from 45 facilities randomly selected after stratification by practice type. National estimates of patient and treatment characteristics were calculated from survey data using SUDAAN statistical software. RESULTS: From the survey data, we estimated that only 8% of US facilities treated on average more than 3 eligible patients per year. No small or medium nonacademic facilities in the survey treated more than 3 eligible patients per year. Approximately 65.5% of patients began treatment in a facility that treated 3 or fewer eligible patients per year. Although 87.5% of patients had brachytherapy as part of their treatment, the proportion treated with external beam RT only was about double that estimated from the 1996 to 1999 survey. The use of high-dose-rate brachytherapy sharply increased, particularly in small nonacademic facilities. Overall, patients treated in nonacademic facilities were more likely to have incomplete or protracted treatment; 43% of patients treated in small nonacademic facilities did not have treatment completed within 10 weeks. Also, patients treated in facilities that treated 3 or fewer eligible patients per year were significantly less likely to receive concurrent chemotherapy than were patients treated in other facilities. CONCLUSION: Survey results indicate a disturbingly high rate of noncompliance with established criteria for high-quality care of patients with cervical cancer. Noncompliance rates are particularly high in nonacademic facilities, especially those that treat relatively few patients with intact cervical cancer.

Evaluation of Adherence to Quality Measures for Prostate Cancer Radiotherapy in the United States: Results from the Quality Research in Radiation Oncology (QRRO) Survey.

PURPOSE: To test the feasibility of using proposed quality indicators to assess radiotherapy quality in prostate cancer management based on a 2007 stratified random survey of treating academic and non-academic US institutions. METHODS AND MATERIALS: 414 patients with clinically localized prostate cancer treated with external beam radiotherapy (EBRT) or brachytherapy were selected from 45 institutions. Indicators used as specific measurable clinical performance measures to represent surrogates for quality of radiotherapy delivery included established measures, such as the use of prescription doses ≥75 Gy for intermediate- and high-risk EBRT patients and androgen-deprivation therapy (ADT) in conjunction with EBRT for patients with high-risk disease, and emerging measures, including daily target localization (image-guidance) to correct for organ motion for EBRT patients. RESULTS: 167 patients (47%) were treated with 6 MV photons, 31 (9%) were treated with 10 MV, 65 (18%) received 15 MV, and the remaining 90 (26%) 16-23 MV. For intermediate- plus high-risk patients (n=181), 78% were treated to ≥75 Gy. Among favorable-risk patients, 72% were treated to ≥75 Gy. Among high-risk EBRT patients, 60 (87%) were treated with ADT in conjunction with EBRT and 13% (n=9) with radiotherapy alone. Among low- and intermediate-risk patients, 10% and 42%, respectively, were treated with ADT plus EBRT. For 24% of EBRT patients (85/354), weekly electronic portal imaging was obtained as verification films without daily target localization and the remaining 76% were treated with daily localization of the target using various methods. CONCLUSIONS: Adherence to defined quality indicators was observed in a majority of patients. ≈90% of high-risk patients are treated with ADT plus EBRT and ≈80% of intermediate- and high-risk patients receive prescription doses >=75 Gy, consistent with the published results of randomized trials.

Penetration of recommended procedures for lung cancer staging and management in the United States over 10 years: a quality research in radiation oncology survey.

PURPOSE: To document the penetration of clinical trial results, practice guidelines, and appropriateness criteria into national practice, we compared the use of components of staging and treatment for lung cancer among patients treated in 2006-2007 with those used in patients treated in 1998-1999. METHODS AND MATERIALS: Patient, staging work-up, and treatment characteristics were extracted from the process survey database of the Quality Research in Radiation Oncology (QRRO), consisting of records of 340 patients with locally advanced non-small cell lung cancer (LA-NSCLC) at 44 institutions and of 144 patients with limited-stage small cell lung cancer (LS-SCLC) at 39 institutions. Data were compared for patients treated in 2006-2007 versus those for patients treated in 1998-1999. RESULTS: Use of all recommended procedures for staging and treatment was more common in 2006-2007. Specifically, disease was staged with brain imaging (magnetic resonance imaging or computed tomography) and whole-body imaging (positron emission tomography or bone scanning) in 66% of patients with LA-NSCLC in 2006-2007 (vs 42% in 1998-1999, P=.0001) and in 84% of patients with LS-SCLC in 2006-2007 (vs 58.3% in 1998-1999, P=.0011). Concurrent chemoradiation was used for 77% of LA-NSCLC patients (vs 45% in 1998-1999, P<.0001) and for 90% of LS-SCLC patients (vs 62.5% in 1998-1999, P<.0001). Use of the recommended radiation dose (59-74 Gy for NSCLC and 60-70 Gy as once-daily therapy for SCLC) did not change appreciably, being 88% for NSCLC in both periods and 51% (2006-2007) versus 43% (1998-1999) for SCLC. Twice-daily radiation for SCLC was used for 21% of patients in 2006-2007 versus 8% in 1998-1999. Finally, 49% of patients with LS-SCLC received prophylactic cranial irradiation (PCI) in 2006-2007 (vs 21% in 1998-1999). CONCLUSIONS: Although adherence to all quality indicators improved over time, brain imaging and recommended radiation doses for stage III NSCLC were used in <90% of cases. Use of full thoracic doses and PCI for LS-SCLC also requires improvement.

Quality Research in Radiation Oncology analysis of clinical performance measures in the management of gastric cancer.

BACKGROUND: The specific aim was to determine national patterns of radiation therapy (RT) practice in patients treated for stage IB-IV (nonmetastatic) gastric cancer (GC). METHODS AND MATERIALS: A national process survey of randomly selected US RT facilities was conducted which retrospectively assessed demographics, staging, geographic region, practice setting, and treatment by using on-site record review of eligible GC cases treated from 2005 to 2007. Three clinical performance measures (CPMs), (1) use of computed tomography (CT)-based treatment planning; (2) use of dose volume histograms (DVHs) to evaluate RT dose to the kidneys and liver; and (3) completion of RT within the prescribed time frame; and emerging quality indicators, (i) use of intensity modulated RT (IMRT); (ii) use of image-guided tools (IGRT) other than CT for RT target delineation; and (iii) use of preoperative RT, were assessed. RESULTS: CPMs were computed for 250 eligible patients at 45 institutions (median age, 62 years; 66% male; 60% Caucasian). Using 2000 American Joint Committee on Cancer criteria, 13% of patients were stage I, 29% were stage II, 32% were stage IIIA, 10% were stage IIIB, and 12% were stage IV. Most patients (43%) were treated at academic centers, 32% were treated at large nonacademic centers, and 25% were treated at small to medium sized facilities. Almost all patients (99.5%) underwent CT-based planning, and 75% had DVHs to evaluate normal tissue doses to the kidneys and liver. Seventy percent of patients completed RT within the prescribed time frame. IMRT and IGRT were used in 22% and 17% of patients, respectively. IGRT techniques included positron emission tomography (n=20), magnetic resonance imaging (n=1), respiratory gating and 4-dimensional CT (n=22), and on-board imaging (n=10). Nineteen percent of patients received preoperative RT. CONCLUSIONS: This analysis of radiation practice patterns for treating nonmetastatic GC indicates widespread adoption of CT-based planning with use of DVH to evaluate normal tissue doses. Most patients completed adjuvant RT in the prescribed time frame. IMRT and IGRT were not routinely incorporated into clinical practice during the 2005-2007 period. These data will be a benchmark for future Quality Research in Radiation Oncology GC surveys.

Results from the Quality Research in Radiation Oncology (QRRO) survey: Evaluation of dosimetric outcomes for low-dose-rate prostate brachytherapy.

PURPOSE: We report on quality of dose delivery to target and normal tissues from low-dose-rate prostate brachytherapy using postimplantation dosimetric evaluations from a random sample of U.S. patients. METHODS AND MATERIALS: Nonmetastatic prostate cancer patients treated with external beam radiotherapy or brachytherapy in 2007 were randomly sampled from radiation oncology facilities nationwide. Of 414 prostate cancer cases from 45 institutions, 86 received low-dose-rate brachytherapy. We collected the 30-day postimplantation CT images of these patients and 10 test cases from two other institutions. Scans were downloaded into a treatment planning system and prostate/rectal contours were redrawn. Dosimetric outcomes were reanalyzed and compared with calculated outcomes from treating institutions. RESULTS: Median prostate volume was 33.4cm(3). Reevaluated median V(100), D(90), and V(150) were 91.1% (range, 45.5-99.8%), 101.7% (range, 59.6-145.9%), and 53.9% (range, 15.7-88.4%), respectively. Low gland coverage included 27 patients (39%) with a D(90) lower than 100% of the prescription dose (PD), 12 of whom (17% of the entire group) had a D(90) lower than 80% of PD. There was no correlation between D(90) coverage and prostate volume, number of seeds, or implanted activity. The median V(100) for the rectum was 0.3cm(3) (range, 0-4.3cm(3)). No outcome differences were observed according to the institutional strata. Concordance between reported and reevaluated D(90) values (defined as within ±10%) was observed in 44 of 69 cases. CONCLUSIONS: Central review of postimplantation CT scans to assess the quality of prostate brachytherapy is feasible. Most patients achieved excellent dosimetric outcomes, yet 17% had less than optimal target coverage by the PD. There was concordance between submitted target-coverage parameters and central dosimetric review in 64% of implants. These findings will require further validation in a larger cohort of patients.

Shifting the focus to practice quality improvement in radiation oncology.

To demonstrate how the American College of Radiology, Quality Research in Radiation Oncology (QRRO) process survey database can serve as an evidence base for assessing quality of care in radiation oncology. QRRO has drawn a stratified random sample of radiation oncology facilities in the USA and invited those facilities to participate in a Process Survey. Information from a prior QRRO Facilities Survey has been used along with data collected under the current National Process Survey to calculate national averages and make statistically valid inferences for national process measures for selected cancers in which radiation therapy plays a major role. These measures affect outcomes important to patients and providers and measure quality of care. QRRO's survey data provides national benchmark data for numerous quality indicators. The Process Survey is "fully qualified" as a Practice Quality Improvement project by the American Board of Radiology under its Maintenance of Certification requirements for radiation oncology and radiation physics.

A statistical method for predicting splice variants between two groups of samples using GeneChip expression array data.

BACKGROUND: Alternative splicing of pre-messenger RNA results in RNA variants with combinations of selected exons. It is one of the essential biological functions and regulatory components in higher eukaryotic cells. Some of these variants are detectable with the Affymetrix GeneChip that uses multiple oligonucleotide probes (i.e. probe set), since the target sequences for the multiple probes are adjacent within each gene. Hybridization intensity from a probe correlates with abundance of the corresponding transcript. Although the multiple-probe feature in the current GeneChip was designed to assess expression values of individual genes, it also measures transcriptional abundance for a sub-region of a gene sequence. This additional capacity motivated us to develop a method to predict alternative splicing, taking advance of extensive repositories of GeneChip gene expression array data. RESULTS: We developed a two-step approach to predict alternative splicing from GeneChip data. First, we clustered the probes from a probe set into pseudo-exons based on similarity of probe intensities and physical adjacency. A pseudo-exon is defined as a sequence in the gene within which multiple probes have comparable probe intensity values. Second, for each pseudo-exon, we assessed the statistical significance of the difference in probe intensity between two groups of samples. Differentially expressed pseudo-exons are predicted to be alternatively spliced. We applied our method to empirical data generated from GeneChip Hu6800 arrays, which include 7129 probe sets and twenty probes per probe set. The dataset consists of sixty-nine medulloblastoma (27 metastatic and 42 non-metastatic) samples and four cerebellum samples as normal controls. We predicted that 577 genes would be alternatively spliced when we compared normal cerebellum samples to medulloblastomas, and predicted that thirteen genes would be alternatively spliced when we compared metastatic medulloblastomas to non-metastatic ones. We checked the consistency of some of our findings with information in UCSC Human Genome Browser. CONCLUSION: The two-step approach described in this paper is capable of predicting some alternative splicing from multiple oligonucleotide-based gene expression array data with GeneChip technology. Our method employs the extensive repositories of gene expression array data available and generates alternative splicing hypotheses, which can be further validated by experimental studies.

A class of models for analyzing GeneChip gene expression analysis array data.

BACKGROUND: Various analytical methods exist that first quantify gene expression and then analyze differentially expressed genes from Affymetrix GeneChip gene expression analysis array data. These methods differ in the choice of probe measure (quantification of probe hybridization), summarizing multiple probe intensities into a gene expression value, and analysis of differential gene expression. Research papers that describe these methods focus on performance, and how their approaches differ from others. To better understand the common features and differences between various methods, and to evaluate their impact on the results of gene expression analysis, we describe a class of models, referred to as generalized probe models (GPMs), which encompass various currently available methods. RESULTS: Using an empirical dataset, we compared different formulations of GPMs, and GPMs with three other commonly used methods, i.e. MAS 5.0, dChip, and RMA. The comparison shows that, on a genome-wide scale , different methods yield similar results if the same probe measures are chosen. CONCLUSION: In this paper we present a general framework, i.e. GPMs, which encompasses various methods. GPMs permit the use of a wide range of probe measures and facilitate appropriate comparison between commonly used methods. We demonstrate that the dissimilar results stem primarily from different choice of probe measures, rather than other factors.

Single-stranded linear amplification protocol results in reproducible and reliable microarray data from nanogram amounts of starting RNA.

The range of scientific questions utilizing DNA microarray techniques is limited by the fact that these methods require 5-40 microg of high-quality total RNA. Thus, methods that reliably amplify the starting RNA amount could expand the applicability of DNA microarray technology. We developed a single-stranded linear amplification protocol (SLAP) that combines the reproducibility of in vitro transcription and the amplification robustness of polymerase chain reactions. We compared SLAP to the NIH-IVT amplification protocol. SLAP displayed excellent conservation of the 5'/3' signal and demonstrated the most robust amplification, producing the recommended amounts of biotin-labeled RNA with as little as 0.002 microg of starting RNA. Both SLAP and NIH-IVT methods demonstrated good reproducibility, but SLAP maintained the highest level of reliability with RNA starting amounts of <0.05 microg. These results suggest that SLAP is an excellent alternative to IVT-based amplification protocols when RNA is limited by small sample size.

Estimating haplotype frequencies and standard errors for multiple single nucleotide polymorphisms.

Estimating haplotype frequencies becomes increasingly important in the mapping of complex disease genes, as millions of single nucleotide polymorphisms (SNPs) are being identified and genotyped. When genotypes at multiple SNP loci are gathered from unrelated individuals, haplotype frequencies can be accurately estimated using expectation-maximization (EM) algorithms (Excoffier and Slatkin, 1995; Hawley and Kidd, 1995; Long et al., 1995), with standard errors estimated using bootstraps. However, because the number of possible haplotypes increases exponentially with the number of SNPs, handling data with a large number of SNPs poses a computational challenge for the EM methods and for other haplotype inference methods. To solve this problem, Niu and colleagues, in their Bayesian haplotype inference paper (Niu et al., 2002), introduced a computational algorithm called progressive ligation (PL). But their Bayesian method has a limitation on the number of subjects (no more than 100 subjects in the current implementation of the method). In this paper, we propose a new method in which we use the same likelihood formulation as in Excoffier and Slatkin's EM algorithm and apply the estimating equation idea and the PL computational algorithm with some modifications. Our proposed method can handle data sets with large number of SNPs as well as large numbers of subjects. Simultaneously, our method estimates standard errors efficiently, using the sandwich-estimate from the estimating equation, rather than the bootstrap method. Additionally, our method admits missing data and produces valid estimates of parameters and their standard errors under the assumption that the missing genotypes are missing at random in the sense defined by Rubin (1976).

A method for the assessment of disease associations with single-nucleotide polymorphism haplotypes and environmental variables in case-control studies.

The rough draft of the human genome map has been used to identify most of the functional genes in the human genome, as well as to identify nucleotide variations, known as "single-nucleotide polymorphisms" (SNPs), in these genes. By use of advanced biotechnologies, researchers are beginning to genotype thousands of SNPs from biological samples. Among the many possible applications, one of them is the study of SNP associations with complex human diseases, such as cancers or coronary heart diseases, by using a case-control study design. Through the gathering of environmental risk factors and other lifestyle factors, such a study can be effectively used to investigate interactions between genes and environmental factors in their associations with disease phenotype. Earlier, we developed a method to statistically construct individuals' haplotypes and to estimate the distribution of haplotypes of multiple SNPs in a defined population, by use of estimating-equation techniques. Extending this idea, we describe here an analytic method for assessing the association between the constructed haplotypes along with environmental factors and the disease phenotype. This method is also robust to the model assumptions and is scalable to a large number of SNPs. Asymptotic properties of estimations in the method are proved theoretically and are tested for finite sample sizes by use of simulations. To demonstrate the use of the method, we applied it to assess the possible association between apolipoprotein CIII (six coding SNPs) and restenosis by using a case-control data set. Our analysis revealed two haplotypes that may reduce the risk of restenosis.