Quantification of subclonal distributions of recurrent genomic aberrations in paired pre-treatment and relapse samples from patients with B-cell chronic lymphocytic leukemia

Genome-wide array approaches and sequencing analyses are powerful tools for identifying genetic aberrations in cancers, including leukemias and lymphomas. However, the clinical and biological significance of such aberrations and their subclonal distribution are poorly understood. Here, we present the first genome-wide array based study of pre-treatment and relapse samples from patients with B-cell chronic lymphocytic leukemia (B-CLL) that uses the computational statistical tool OncoSNP. We show that quantification of the proportion of copy number alterations (CNAs) and copy neutral loss of heterozygosity regions (cnLOHs) in each sample is feasible. Furthermore, we (i) reveal complex changes in the subclonal architecture of paired samples at relapse compared with pre-treatment, (ii) provide evidence supporting an association between increased genomic complexity and poor clinical outcome (iii) report previously undefined, recurrent CNA/cnLOH regions that expand or newly occur at relapse and therefore might harbor candidate driver genes of relapse and/or chemotherapy resistance. Our findings are likely to impact on future therapeutic strategies aimed towards selecting effective and individually tailored targeted therapies.

What do patients choose to tell their doctors? Qualitative analysis of potential barriers to reattributing medically unexplained symptoms

BACKGROUND

Despite both parties often expressing dissatisfaction with consultations, patients with medically unexplained symptoms (MUS) prefer to consult their general practitioners (GPs) rather than any other health professional. Training GPs to explain how symptoms can relate to psychosocial problems (reattribution) improves the quality of doctor-patient communication, though not necessarily patient health.

OBJECTIVE

To examine patient experiences of GPs' attempts to reattribute MUS in order to identify potential barriers to primary care management of MUS and improvement in outcome.

DESIGN

Qualitative study.

PARTICIPANTS

Patients consulting with MUS whose GPs had been trained in reattribution. A secondary sample of patients of control GPs was also interviewed to ascertain if barriers identified were specific to reattribution or common to consultations about MUS in general.

APPROACH

Thematic analysis of in-depth interviews.

RESULTS

Potential barriers include the complexity of patients' problems and patients' judgements about how to manage their presentation of this complexity. Many did not trust doctors with discussion of emotional aspects of their problems and chose not to present them. The same barriers were seen amongst patients whose GPs were not trained, suggesting the barriers are not particular to reattribution.

CONCLUSIONS

Improving GP explanation of unexplained symptoms is insufficient to reduce patients' concerns. GPs need to (1) help patients to make sense of the complex nature of their presenting problems, (2) communicate that attention to psychosocial factors will not preclude vigilance to physical disease and (3) ensure a quality of doctor-patient relationship in which patients can perceive psychosocial enquiry as appropriate.

Cluster randomised controlled trial of training practices in reattribution for medically unexplained symptoms

BACKGROUND

Reattribution is frequently taught to general practitioners (GPs) as a structured consultation that provides a psychological explanation for medically unexplained symptoms.

AIMS

To determine if practice-based training of GPs in reattribution changes doctor-patient communication, thereby improving outcomes in patients with medically unexplained symptoms of 3 months' duration.

METHOD

Cluster randomised controlled trial in 16 practices, 74 GPs and 141 patients with medically unexplained symptoms of 6 hours of reattribution training v. treatment as usual.

RESULTS

With training, the proportion of consultations mostly consistent with reattribution increased (31 v. 2%, P=0.002). Training was associated with decreased quality of life (health thermometer difference -0.9, 95% CI -1.6 to -0.1; P=0.027) with no other effects on patient outcome or health contacts.

CONCLUSIONS

Practice-based training in reattribution changed doctor-patient communication without improving outcome of patients with medically unexplained symptoms.

Peering through the barriers in GPs' explanations for declining to participate in research: the role of professional autonomy and the economy of time

BACKGROUND

The level of participation in research by GPs is low internationally. Previous reports of the reasons why practitioners decline opportunities for research participation have tended to recount the barriers that they describe as if they are objective accounts.

OBJECTIVE

By theoretical sampling of practitioners who had declined to participate in a research trial, we sought to interpret the functional significance and interrelationship of the barriers that they reported.

METHODS

Twenty-three GPs who had declined to participate in a trial of training to manage medically unexplained symptoms were interviewed and their accounts analysed interpretatively.

RESULTS

The practitioners described general practice and research as alien fields. Research lacked intrinsic, clinical or professional value and was linked to evidence-based medicine which they rejected as incompatible with person-centered care. Every doctor described a lack of time for research, but time was an elastic resource that payment could release from the reservoir of their 'own time'.

CONCLUSION

The findings should inform the design and interpretation of future quantitative surveys to identify how common the attitudes that we report are. Doctors with the attitudes of those whom we interviewed will not be drawn into research by measures predicated on the assumption that it is intrinsically, clinically or professionally valuable. If they cannot be convinced of its utility, value could be conferred by payment for participation.

Why do general practitioners decline training to improve management of medically unexplained symptoms?

BACKGROUND

General practitioners' (GPs) communication with patients presenting medically unexplained symptoms (MUS) has the potential to somatize patients' problems and intensify dependence on medical care. Several reports indicate that GPs have negative attitudes about patients with MUS. If these attitudes deter participation in training or other methods to improve communication, practitioners who most need help will not receive it.

OBJECTIVE

To identify how GPs' attitudes to patients with MUS might inhibit their participation with training to improve management.

DESIGN

Qualitative study.

PARTICIPANTS

GPs (N = 33) who had declined or accepted training in reattribution techniques in the context of a research trial.

APPROACH

GPs were interviewed and their accounts analysed qualitatively.

RESULTS

Although attitudes that devalued patients with MUS were common in practitioners who had declined training, these coexisted, in the same practitioners, with evidence of intuitive and elaborate psychological work with these patients. However, these practitioners devalued their psychological skills. GPs who had accepted training also described working psychologically with MUS but devalued neither patients with MUS nor their own psychological skills.

CONCLUSIONS

GPs' attitudes that suggested disengagement from patients with MUS belied their pursuit of psychological objectives. We therefore suggest that, whereas negative attitudes to patients have previously been regarded as the main barrier to involvement in measures to improve patient management, GPs devaluing of their own psychological skills with these patients may be more important.

Mercury-reactive lymphocytes in peripheral blood are not a marker for dental amalgam associated disease

OBJECTIVES

The popular press and publications associated with alternative medicine increasingly report that chronic ill health, particularly myalgic encephalitis like conditions, are associated with mercury amalgam fillings. There are no scientifically proven definitive tests to support these claims. One of the more scientific tests in vogue is to assess the level of blood-borne mercury-reactive lymphocytes and to conclude that patients with high levels have developed a hypersensitivity reaction to mercury. The objective of this study was to determine the diagnostic value of this test.

METHODS

This study represents an open comparison of mercury-reactive lymphocyte levels in healthy control individuals with those in patients complaining of symptoms associated with adverse effects of dental metal amalgam fillings. The healthy control group consisted of 51 male and female individuals, aged between 12 and 82 years, with and without dental amalgam fillings. The patient group consisted of 70 male and female individuals, aged between 12 and 87 years, and with the exception of one patient, with three or more mercury amalgam fillings of more than 1 year's duration. In vitro lymphocyte responses to mercury, and to nickel, as an example of a metal commonly associated with hypersensitivity reactions, and to more conventional protein antigens were determined.

RESULTS

In the blood of patients and controls, there were similar levels of specifically reactive lymphocytes to all of the in vitro stimulating agents, but there were significantly higher numbers of sub-normal and non-responders within the patient group.

CONCLUSIONS

The incidence and quantity of mercury-reactive lymphocytes in the blood are not pathogenic markers of illness associated with dental metal amalgams, but may rather reflect exposure to mercury. The clinical relevance of the decreased in vitro lymphocyte responses in the patient group needs further investigation.

High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

We describe here a system for the rapid identification, assay development, and characterization of gene-based single nucleotide polymorphisms (SNPs). This system couples informatics tools that mine candidate SNPs from public expressed sequence tag resources and automatically designs assay reagents with detection by a chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry platform. As a proof of concept of this system, a genomewide collection of reagents for 9,115 gene-based SNP genetic markers was rapidly developed and validated. These data provide preliminary insights into patterns of polymorphism in a genomewide collection of gene-based polymorphisms.

Analysis of Medication Incidents and Development of a Medication Incident Rate Clinical Indicator

Most health service organisations depend solely upon spontaneous voluntary reporting of medication incidents and a wide variety of available denominators are used in order to calculate the Medication Incident Rate (MIR). This paper describes how nursing staff and clinical pharmacists reviewed medication incident data, revised and established new systems of reporting and developed a clinically useful, rate-based MIR Clinical Indicator. In order to make the MIR more meaningful, the frequency of occurrence of incidents was considered within the context of the total number of medications given to patients. This was achieved by undertaking a point prevalence audit of all inpatient medication charts (n=372) to determine the total number of doses of medication given to patients during a 24 hour period (n=3211). This value was then used as the denominator for the MIR indicator. During 1998, a total of 475 medication incidents were reported; the average number of incidents was 1.3 per 24 hours. The MIR per 1000 doses was calculated to be 0.4. In most cases (77%) the incident caused no harm to the patient and no change in treatment was required, and the most 'severe' category for any incident was that active treatment was required (3% of reported incidents). The most common type of incident was the omission of a dose of medication (50%). A wide range of drugs were involved in the incidents, most commonly morphine (3.4%). The authors consider that the development and use of the MIR Clinical Indicator has positively influenced clinical practice in some areas at the authors' hospital.

FOG-2, a novel F-box containing protein, associates with the GLD-1 RNA binding protein and directs male sex determination in the C. elegans hermaphrodite germline

Male sex determination in the Caenorhabditis elegans hermaphrodite germline requires translational repression of tra-2 mRNA by the GLD-1 RNA binding protein. We cloned fog-2 by finding that its gene product physically interacts with GLD-1, forming a FOG-2/GLD-1/tra-2 3′untranslated region ternary complex. FOG-2 has an N-terminal F-box and a novel C-terminal domain called FTH. Canonical F-box proteins act as bridging components of the SCF ubiquitin ligase complex; the N-terminal F-box binds a Skp1 homolog, recruiting ubiquination machinery, while a C-terminal protein-protein interaction domain binds a specific substrate for degradation. However, since both fog-2 and gld-1 are necessary for spermatogenesis, FOG-2 cannot target GLD-1 for ubiquitin-mediated degradation. We propose that FOG-2 also acts as a bridge, bringing GLD-1 bound to tra-2 mRNA into a multiprotein translational repression complex, thus representing a novel function for an F-box protein. fog-2 is a member of a large, apparently rapidly evolving, C. elegans gene family that has expanded, in part, by local duplications; fog-2 related genes have not been found outside nematodes. fog-2 may have arisen during evolution of self-fertile hermaphroditism from an ancestral female/male species.

Expression-based genetic/physical maps of single-nucleotide polymorphisms identified by the cancer genome anatomy project

SNPs (Single-Nucleotide Polymorphisms), the most common DNA variant in humans, represent a valuable resource for the genetic analysis of cancer and other illnesses. These markers may be used in a variety of ways to investigate the genetic underpinnings of disease. In gene-based studies, the correlations between allelic variants of genes of interest and particular disease states are assessed. An extensive collection of SNP markers may enable entire molecular pathways regulating cell metabolism, growth, or differentiation to be analyzed by this approach. In addition, high-resolution genetic maps based on SNPs will greatly facilitate linkage analysis and positional cloning. The National Cancer Institute's CGAP-GAI (Cancer Genome Anatomy Project Genetic Annotation Initiative) group has identified 10,243 SNPs by examining publicly available EST (Expressed Sequence Tag) chromatograms. More than 6800 of these polymorphisms have been placed on expression-based integrated genetic/physical maps. In addition to a set of comprehensive SNP maps, we have produced maps containing single nucleotide polymorphisms in genes expressed in breast, colon, kidney, liver, lung, or prostate tissue. The integrated maps, a SNP search engine, and a Java-based tool for viewing candidate SNPs in the context of EST assemblies can be accessed via the CGAP-GAI web site (http://cgap.nci.nih.gov/GAI/). Our SNP detection tools are available to the public for noncommercial use.

Disperse: a simple and efficient approach to parallel database searching

SUMMARY

A general system for performing multiple independent database searches in parallel is presented. Run-time addition and removal of clients, robust failure and error trapping and near 100% efficiency with very large numbers of clients are achieved by a flexible asynchronous, client-driven approach.

Monitoring for nitrate in UK-grown lettuce and spinach

To comply with European Commission requirements, the UK is carrying out a monitoring programme on nitrate concentrations in lettuce and spinach. This paper reports the results obtained between June 1996 and April 1998. A total of 182 samples of protected lettuce, 131 samples of outdoor-grown lettuce and 34 samples of fresh spinach were taken from the main growing areas of the UK. Nitrate concentrations in protected lettuce were influenced by the season with summer-grown crops (mean of 2382 mg/kg) having lower levels than those grown in the winter (mean of 3124 mg/kg). Weather conditions also affected concentrations in protected lettuces with long hours of sunshine and low rainfall associated with low nitrate levels. Nitrate concentrations in outdoor-grown lettuces were lower (mean of 1085 mg/kg) than those in protected lettuces but there were insufficient data to determine if they were affected by the weather conditions or season. Similarly there were insufficient data to determine if weather conditions or season influenced nitrate concentrations in spinach (mean of 1900 mg/kg) but regional differences were observed.