Routes to diagnosis for cancer - determining the patient journey using multiple routine data sets.
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ABSTRACT:
SUBMITTER: Elliss-Brookes L
PROVIDER: S-EPMC3494426 | biostudies-other | 2012 Oct
REPOSITORIES: biostudies-other
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Project description:ObjectiveThis research describes the clinical pathway and characteristics of two cohorts of patients. The first cohort consists of patients with a confirmed diagnosis of lung cancer while the second consists of patients with a solitary pulmonary nodule (SPN) and no evidence of lung cancer. Linked data from an electronic medical record and the Louisiana Tumor Registry were used in this investigation.Materials and methodsREACHnet is one of 9 clinical research networks (CRNs) in PCORnet®, the National Patient-Centered Clinical Research Network and includes electronic health records for over 8 million patients from multiple partner health systems. Data from Ochsner Health System and Tulane Medical Center were linked to Louisiana Tumor Registry (LTR), a statewide population-based cancer registry, for analysis of patient's clinical pathways between July 2013 and 2017. Patient characteristics and health services utilization rates by cancer stage were reported as frequency distributions. The Kaplan-Meier product limit method was used to estimate the time from index date to diagnosis by stage in lung cancer cohort.ResultsA total of 30,559 potentially eligible patients were identified and 2929 (9.58%) had primary lung cancer. Of these, 1496 (51.1%) were documented in LTR and their clinical pathway to diagnosis was further studied. Time to diagnosis varied significantly by cancer stage. A total of 24,140 patients with an SPN were identified in REACHnet and 15,978 (66.6%) had documented follow up care for 1 year. 1612 (10%) had no evidence of any work up for their SPN. The remaining 14,366 had some evidence of follow up, primarily office visits and additional chest imaging.ConclusionIn both cohorts multiple biopsies were evident in the clinical pathway. Despite clinical workup, 70% of patients in the lung cancer cohort had stage III or IV disease. In the SPN cohort, only 66% were identified as receiving a diagnostic work-up.
| S-EPMC8045203 | biostudies-literature
Project description:Devising computational methods to accurately reconstruct gene regulatory networks given gene expression data is key to systems biology applications. Here we propose a method for reconstructing gene regulatory networks by simultaneous consideration of data sets from different perturbation experiments and corresponding controls. The method imposes three biologically meaningful constraints: (1) expression levels of each gene should be explained by the expression levels of a small number of transcription factor coding genes, (2) networks inferred from different data sets should be similar with respect to the type and number of regulatory interactions, and (3) relationships between genes which exhibit similar differential behavior over the considered perturbations should be favored. We demonstrate that these constraints can be transformed in a fused LASSO formulation for the proposed method. The comparative analysis on transcriptomics time-series data from prokaryotic species, Escherichia coli and Mycobacterium tuberculosis, as well as a eukaryotic species, mouse, demonstrated that the proposed method has the advantages of the most recent approaches for regulatory network inference, while obtaining better performance and assigning higher scores to the true regulatory links. The study indicates that the combination of sparse regression techniques with other biologically meaningful constraints is a promising framework for gene regulatory network reconstructions.
| S-EPMC4750075 | biostudies-literature
Project description:BackgroundLimited data are available on the experiences of patients with autoinflammatory diseases (AIDs) and their families along the path to diagnosis and treatment. We sought to describe these experiences in patients with AIDs including tumor necrosis factor receptor-associated periodic syndrome (TRAPS), mevalonate kinase deficiency/hyperimmunoglobulin D syndrome (MKD/HIDS), and familial Mediterranean fever (FMF).MethodsNinety-minute, semi-structured qualitative interviews and 5-day written/video diaries were used to gather information on the experiences of patients with AIDs and their families.ResultsTwelve families of patients from the US (TRAPS [n = 4], MKD/HIDS [n = 5], FMF [n = 5]) participated in this study from August to November 2015. The study included two families with multiple afflicted siblings. Patients' ages ranged from 1 to 28 years. Most parents reported realizing that something was seriously wrong with their child after medical emergencies and/or hospitalizations, which initiated the difficult path to diagnosis. For most, the process included multiple specialist visits, extensive and repeated testing, and many misdiagnoses. Over time, 92% of parents reported losing confidence in the healthcare system's ability to find an answer to their child's symptoms, while they also struggled with unsupportive school personnel and dismissive friends and relatives. Patients and their parents reported holding on to memories of "what life was like" before the onset of symptoms and mourning their subsequent loss of "normalcy." Even after diagnosis, patients and parents continued to feel uncertain about what to expect in the future.ConclusionsAll families emphasized the need for efficient early diagnosis of AIDs. Initiatives that improve the speed and accuracy of diagnosis, provide more comprehensive patient education, and support patients and families through the illness have the potential to significantly improve the quality of life of patients with AIDs and their families. Healthcare providers should be aware of the impact of the long diagnostic journey on families and work to create an environment of trust and collaboration in the face of a difficult and prolonged diagnostic process.
| S-EPMC6127942 | biostudies-literature
Project description:Models of marine mammal population dynamics have been used extensively to predict abundance. A less common application of these models is to reconstruct historical population dynamics, filling in gaps in observation data by integrating information from multiple sources. We developed an integrated population model for the Florida manatee (Trichechus manatus latirostris) to reconstruct its population dynamics in the southwest region of the state over the past 20 years. Our model improved precision of key parameter estimates and permitted inference on poorly known parameters. Population growth was slow (averaging 1.02; 95% credible interval 1.01-1.03) but not steady, and an unusual mortality event in 2013 led to an estimated net loss of 332 (217-466) manatees. Our analyses showed that precise estimates of abundance could be derived from estimates of vital rates and a few input estimates of abundance, which may mean costly surveys to estimate abundance don't need to be conducted as frequently. Our study also shows that retrospective analyses can be useful to: (1) model the transient dynamics of age distribution; (2) assess and communicate the conservation status of wild populations; and (3) improve our understanding of environmental effects on population dynamics and thus enhance our ability to forecast.
| S-EPMC7846604 | biostudies-literature
Project description:Advances in primary prophylaxis have resulted in improved outcomes for patients with sickle cell anemia (SCA; i.e., hemoglobin SS- and Sβ(0)-thalassemia). Standard prophylactic measures include a first pneumococcal polysaccharide vaccine (PPV) and transcranial Doppler ultrasound (TCD) at age 2 years. Though efficacious, evidence suggests that delivery of these interventions is suboptimal. This study reports adherence to these measures and examines concordance across various data sources, using Registry and Surveillance for Hemoglobinopathies project data.Retrospective database and SCA center chart review identified children with SCA aged 24-36 months between January 1, 2004, and December 31, 2008. PPV and TCD administration were determined through Medicaid and Children's Health Insurance Program administrative claims data, medical record review, and Georgia Registry of Immunization Transaction and Services. Analysis was conducted in 2015.A total of 125 children met inclusion criteria. Forty-five (36.0%) children had documentation of both interventions, whereas 19 (15.2%) had no documentation of either intervention. Sixty-one (48.8%) children obtained only one intervention. Of these, more were likely to have had PPV than TCD (77.0% vs 23.0%, respectively, p<0.001). Agreement between claims data and medical record review was moderate for PPV (κ=0.55) and substantial for TCD (κ=0.74).No single, reliable data source for tracking standard of care for children with SCA statewide was found. According to study data, prophylaxis measures were not universally implemented during the surveillance period. Further research is needed to adequately track changes over time, determine risk groups, and develop methods of evaluating important metrics.
| S-EPMC4918094 | biostudies-other
Project description:BACKGROUND: Fibromyalgia is a painful, debilitating illness with a prevalence of 0.5-5.0% that affects women more than men. It has been shown that the diagnosis of fibromyalgia is associated with improved patient satisfaction and reduced healthcare utilization. This survey examined the patient journey to having their condition diagnosed and studied the impact of the condition on their life. METHODS: A questionnaire survey of 800 patients with fibromyalgia and 1622 physicians in 6 European countries, Mexico and South Korea. Patients were recruited via their physician. RESULTS: Over half the patients (61%) were aged 36-59 years, 84% were women, and the mean time since experiencing fibromyalgia symptoms was 6.5 years. Patients had experienced multiple fibromyalgia symptoms (mean of 7.3 out of 14), with pain, fatigue, sleeping problems and concentration difficulties being the most commonly reported. Most patients rated their chronic widespread pain as moderate or severe and fibromyalgia symptoms were on average "fairly" to "very" disruptive, and had a "moderate" to "strong" impact on patients' lives. 22% were unable to work and 25% were not able to work all the time because of their fibromyalgia. Patients waited on average almost a year after experiencing symptoms before presenting to a physician, and it took an average of 2.3 years and presenting to 3.7 different physicians before receiving a diagnosis of fibromyalgia. Patients rated receiving a diagnosis as somewhat difficult on average and had difficulties communicating their symptoms to the physician. Over one third (35%) felt their chronic widespread pain was not well managed by their current treatment. CONCLUSIONS: This survey provides further evidence that fibromyalgia is characterized by multiple symptoms and has a notable impact on quality of life and function. The diagnosis of fibromyalgia is delayed. Patients wait a significant period of time before presenting to a physician, adding to the prolonged time to diagnosis. Patients typically present with a multitude of symptoms, all resulting in a delay in diagnosis and eventual management. Helping clinicians to diagnose and manage patients with fibromyalgia should benefit both patients and funders of healthcare.
| S-EPMC2874550 | biostudies-literature
Project description:Single-wavelength anomalous dispersion (SAD) utilizing anomalous signal from native S atoms, or other atoms with Z ? 20, generally requires highly redundant data collected using relatively long-wavelength X-rays. Here, the results from two proteins are presented where the anomalous signal from serendipitously acquired surface-bound Ca atoms with an anomalous data multiplicity of around 10 was utilized to drive de novo structure determination. In both cases, the Ca atoms were acquired from the crystallization solution, and the data-collection strategy was not optimized to exploit the anomalous signal from these scatterers. The X-ray data were collected at 0.98?Å wavelength in one case and at 1.74?Å in the other (the wavelength was optimized for sulfur, but the anomalous signal from calcium was exploited for structure solution). Similarly, using a test case, it is shown that data collected at ?1.0?Å wavelength, where the f'' value for sulfur is 0.28?e, are sufficient for structure determination using intrinsic S atoms from a strongly diffracting crystal. Interestingly, it was also observed that SHELXD was capable of generating a substructure solution from high-exposure data with a completeness of 70% for low-resolution reflections extending to 3.5?Å resolution with relatively low anomalous multiplicity. Considering the fact that many crystallization conditions contain anomalous scatterers such as Cl, Ca, Mn etc., checking for the presence of fortuitous anomalous signal in data from well diffracting crystals could prove useful in either determining the structure de novo or in accurately assigning surface-bound atoms.
| S-EPMC5379167 | biostudies-literature
Project description:This paper presents the R/Bioconductor package stepwiseCM, which classifies cancer samples using two heterogeneous data sets in an efficient way. The algorithm is able to capture the distinct classification power of two given data types without actually combining them. This package suits for classification problems where two different types of data sets on the same samples are available. One of these data types has measurements on all samples and the other one has measurements on some samples. One is easy to collect and/or relatively cheap (eg, clinical covariates) compared to the latter (high-dimensional data, eg, gene expression). One additional application for which stepwiseCM is proven to be useful as well is the combination of two high-dimensional data types, eg, DNA copy number and mRNA expression. The package includes functions to project the neighborhood information in one data space to the other to determine a potential group of samples that are likely to benefit most by measuring the second type of covariates. The two heterogeneous data spaces are connected by indirect mapping. The crucial difference between the stepwise classification strategy implemented in this package and the existing packages is that our approach aims to be cost-efficient by avoiding measuring additional covariates, which might be expensive or patient-unfriendly, for a potentially large subgroup of individuals. Moreover, in diagnosis for these individuals test, results would be quickly available, which may lead to reduced waiting times and hence lower the patients' distress. The improvement described remedies the key limitations of existing packages, and facilitates the use of the stepwiseCM package in diverse applications.
| S-EPMC3885337 | biostudies-literature
Project description:As opposed to genome-wide testing of several hundreds of thousands of genes on very few samples, gene panels target as few as tens of genes and enable the simultaneous testing of many samples. For example, some cancer gene panels test for 50 genes that can affect tumor growth and potentially identify treatment options directed against the genetic mutation. The increasing popularity of gene panel testing has spurred the technological development of panels that test for diverse data types such as expression and mutation. Once samples are tested, there is the desire to examine clinical associations based on the panel and for this purpose, one would like to identify, among the samples tested, which show support for a molecular profile (e.g., presence of mutation with increased expression) versus those samples that do not among the genes tested. With user-specified molecular profile of interest, and gene panel data matrices (e.g., gene expression, variants, etc.) that define the profile, shinySISPA (Sample Integrated Set Profile Analysis) is a web-based shiny tool to define two sample groups with and without profile support based on our previously published method from which clinical associations may be readily examined. The shinySISPA can be accessed from http://shinygispa.winship.emory.edu/shinySISPA/.
| S-EPMC6097349 | biostudies-literature
Project description:BackgroundThe promise of precision cancer medicine presently centers around the genomic sequence of a patient's tumor being translated into timely, actionable information to inform clinical care. The analysis of cell-free DNA from liquid biopsy, which contains circulating tumor DNA (ctDNA) in patients with cancer, has proven to be amenable to various settings in oncology. However, open questions surrounding the clinical validity and utility of plasma-based analyses have hindered widespread clinical adoption.Main bodyOwing to the rapid evolution of the field, studies supporting the use of ctDNA as a biomarker throughout a patient's journey with cancer have accumulated in the last few years, warranting a review of the latest status for clinicians who may employ ctDNA in their precision oncology programs. In this work, we take a step back from the intricate coverage of detection approaches described extensively elsewhere and cover basic concepts around the practical implementation of next generation sequencing (NGS)-guided liquid biopsy. We compare relevant targeted and untargeted approaches to plasma DNA analysis, describe the latest evidence for clinical validity and utility, and highlight the value of genome-wide ctDNA analysis, particularly as it relates to early detection strategies and discovery applications harnessing the non-coding genome.ConclusionsThe maturation of liquid biopsy for clinical application will require interdisciplinary efforts to address current challenges. However, patients and clinicians alike may greatly benefit in the future from its incorporation into routine oncology care.
| S-EPMC8935823 | biostudies-literature