RAGs: A novel approach to computerized genetic risk assessment and decision support from pedigrees

OBJECTIVES

To assist general practitioners in evaluating patients' genetic risk of cancer on the basis of family history data.

METHODS

A new computer application, RAGs (Risk Assessment in Genetics), has been developed to help doctors create graphical family trees and assess the genetic risk of breast and colorectal cancer. RAGs possesses two features that distinguish it from similar software: (i) a user-centred design, which takes into account the requirements of the doctor-patient encounter; (ii) effective and accessible risk reporting by employing qualitative evidence for or against increased risk, which is more easily understood than numerical probabilities. The system allows any rule-based genetic risk guideline to be implemented, and may be readily modified to cater for the varying degrees of information required by different specialists.

RESULTS

RAGs permits fast, accurate data entry, and results in more appropriate management decisions than those made via other techniques. In addition, RAGs enables both the clinician and the patient to understand how it arrives at its conclusions, since the use of qualitative evidence allows the program to provide explanations for its reasoning.

CONCLUSIONS

The RAGs system promises to help practitioners be more effective gatekeepers to genetic services. It may empower doctors both to make an informed choice when deciding to refer patients who are at increased genetic risk of breast or colorectal cancer, and to reassure those who are at low risk.

New developments in genetics-knowledge, attitudes and information needs of practice nurses

BACKGROUND

In response to increased referrals to geneticists and the predicted patient demand for genetic counselling, it has been proposed that some genetics services should be provided in primary care. Practice nurses are ideally placed to collect family history information and advise patients accordingly in new patient, family planning, well women/men and chronic disease clinics, but little is known about their knowledge, skills and attitudes towards providing genetic advice.

OBJECTIVES

The survey aimed to measure the current situation with regard to: the prevalence of family history recording by practice nurses; confidence in collecting and acting upon family history; and practice nurses' knowledge about familial disorders and genetics. It also investigated what practice nurses think their role should be in relation to the delivery of genetic services; their educational needs; and the most appropriate ways of delivering training/support.

METHODS

A postal questionnaire survey was carried out of all practices nurses (n = 909) in four Health Authorities in England (Oxfordshire, Northamptonshire, Nottingham and North Nottinghamshire) and one Health Board in Scotland (Lothian). Analyses were primarily descriptive.

RESULTS

A total of 600 nurses (response rate = 66.0%) returned a completed questionnaire. Ninety-six per cent of practice nurses reported that they routinely collect family history information. Over half of the respondents had been consulted in the previous 3 months by patients with a worry about family history of cancer. Approximately 60% of nurses felt confident about collecting the relevant details regarding a family history of breast cancer but felt less confident in collecting the information regarding familial colorectal cancer. Nurses were also unsure how to proceed, with over a third of nurses referring patients to the GP even if they thought the patient was at population risk or, conversely, not referring those that they thought were at considerably higher risk to the GP. There was a reported need for education about familial disease in general and overall agreement that nurses could play a role in genetics in primary care.

CONCLUSION

This study provides evidence of considerable activity from practice nurses regarding routine collection of family history. There is a need for further education for practice nurses regarding family history information and the new genetics so that this information is managed appropriately.

Referral of patients with a family history of breast/ovarian cancer--GPs' knowledge and expectations

BACKGROUND

Primary care is expected to play a significant role in the management of patients with genetic problems. Currently, this particularly involves patients with a family history of cancer. If GPs are to exercise their gatekeeper role efficiently in this area, they must be able to evaluate genetic risk and make appropriate referral decisions.

OBJECTIVES

The aim of this study was to examine GPs' ability to assess risk and to make appropriate referral decisions for women with a family history of breast/ovarian cancer, and to determine their expectations of a referral to secondary care.

METHOD

A questionnaire survey was carried out of the 282 GP principals working within Bedfordshire Health Authority. GPs were asked to make decisions for six simulated cases of women presenting with a family history of breast or ovarian cancer.

RESULTS

A total of 164 (58%) GPs returned completed questionnaires. Across the six family histories, the percentage of GPs making an appropriate risk assessment ranged from 21% [95% confidence interval (CI) 14-27%] to 63% (95% CI 56-71%), and an appropriate referral decision ranged from 40% (95% CI 32-48%) to 80% (95% CI 73-86%). Regardless of their accuracy of risk assessment, most GPs were consistent in deciding not to refer low risk women and to refer moderate and high risk women (range 71-85% of GPs for the six family histories). Only 43 (26%, 95% CI 20-33%) of GPs knew the three most important criteria for risk assessment.

CONCLUSIONS

GPs require more help and education to enable them to perform their gatekeeper role satisfactorily when assessing patients with a family history of breast/ovarian cancer.

Is informed choice in genetic testing a different breed of informed decision-making? A discussion paper

Traditionally genetic counselling has promoted a non-directive approach to patients' decision-making but the feasibility of this has been questioned. Unlike most branches of medicine, which are shifting away from a paternalistic model, genetic counselling is approaching shared decision-making from a different perspective. There are certain features of genetic counselling and genetic testing which may complicate the drive towards shared decision-making and informed choice: 1. Genetic test results can have broader implications than non-genetic test results. 2. Genetic test results may be perceived by the patient differently to non-genetic test results. 3. Carrier status for autosomal recessive conditions may be difficult for patients to conceptualize. 4. Decisions in genetic counselling are often multiple and sequential. 5. Most information in genetic counselling is based on probabilities and uncertainties. Each of these features is discussed in relation to achieving shared decision-making in genetic testing and the implications for genetic counsellors are described. The points raised, however, have broader implications for medicine as several of the features, although central to genetic testing, are not entirely unique. Lessons learnt from genetic testing and genetic counselling in achieving shared decision-making could help develop methods of promoting informed choice in other medical arenas such as cancer screening.

A method for continuous monitoring of the ground reaction force during daily activity

Theoretical models and experimental studies of bone remodeling have identified peak cyclic force levels (or cyclic tissue strain energy density), number of daily loading cycles, and load (strain) rate as possible contributors to the bone modeling and remodeling stimulus. To test our theoretical model and further investigate the influence of mechanical forces on bone density, we have focused on the calcaneus as a model site loaded by calcaneal surface tractions which are predominantly determined by the magnitude of the external ground reaction force (GRF). During daily activity the body is subjected to a random external loading history supplied primarily by the GRF consisting of body weight (BW) plus inertial forces (related to intensity of activity) accelerating the body center of mass. We have hypothesized that monitoring the vertical component of the GRF (GRFz) may provide a useful method of quantifying activity level in order to investigate the influence of mechanical forces on muscle and bone. GRF loading histories among individuals are known to vary greatly in peak force levels and daily cycles and we suggest these differences may be reflected in differences in lower limb musculoskeletal properties. We report here development of instrumentation to monitor the vertical component of the ground reaction force during normal daily activity.

NMR local range investigations in amorphous starchy substrates I. Structural heterogeneity probed by (13)C CP-MAS NMR

The (13)C CP-MAS (Cross Polarization and Magic Angle Spinning) NMR signatures of a series of amorphous and semi-crystalline samples prepared from various starchy substrates (native potato starch, amylopectin, amylose) following different techniques of preparation (casting, freeze drying, solvent exchange) are compared. Decompositions of the C1 resonance spectra reveal the existence of four or five main types of alpha(1-4) linkages, which can be quantified. The influence of the intrinsic primary structure (linear or branched) and of the preparation procedure on conformational changes and resulting crystallinity are interpreted in terms of distributions of average glycosidic linkages dihedral angles (Phi, Psi). The role of hydration is also considered. An improved understanding at different structural levels is obtained in relation to local and intermediate range orders. Such information may be useful for the understanding of the structural evolution of a large variety of starchy substrates before or after treatments widely used in industrial processes.

NMR local range investigations in amorphous starchy substrates: II-Dynamical heterogeneity probed by (1)H/(13)C magnetization transfer and 2D WISE solid state NMR

In the preceding paper, we have investigated the structural heterogeneous character of a series of amorphous samples prepared from various starchy substrates (native potato starch, amylopectin and amylose) following different techniques of preparation (casting, freeze drying and solvent exchange). Spectral decompositions of the C1 resonances of the (13)C CP-MAS (Cross Polarization and Magic Angle Spinning) spectra under (1)H decoupling have shown the existence of five main types of alpha(1-4) linkages. In this part, 2D solid state NMR WISE experiments and the (13)C/(1)H magnetization transfer in CP as a local probe for both structures and dynamics were used. The (13)C CP magnetization curves versus contact time of each C1 component in each recorded spectrum were fitted with an analytic function taking into account two (1)H reservoirs. Interpretation of the characteristic times derived from fitting yields some improvements on the knowledge of the heterogeneity of the samples and on the water molecules distribution.

Common hereditary cancers and implications for primary care

The identification of genes that place individuals at high risk of breast, ovarian, and colorectal cancer has greatly advanced our understanding of cancer predisposition over the past decade. This knowledge has received much attention from the media, and referrals to geneticists and surgeons, and requests for genetic testing, have risen. We review the published evidence for the management of people at increased risk of hereditary cancers, to draw attention to areas of uncertainty and to discuss implications for primary care. We focus on common inherited cancers, since they will have the greatest effect on clinical practice over the next decade. Cancer genetics offers a model of how information on the genetics of other common diseases could affect primary care in the future. Strategies to support the integration of genetic medicine in primary care are needed to enable primary-care practitioners to identify individuals at raised genetic risk and to reassure patients for whom genetic testing and increased surveillance offer little benefit.

Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots

The upper side of the angiosperm leaf is specialized for efficient capture of sunlight whereas the lower side is specialized for gas exchange. In Arabidopsis, the establishment of polarity in the leaf probably requires the generation and perception of positional information along the radial (adaxial versus abaxial or central versus peripheral) dimension of the plant. This is because the future upper (adaxial) side of the leaf develops from cells closer to the centre of the shoot, whereas the future under (abaxial) side develops from cells located more peripherally. Here we implicate the Arabidopsis PHABULOSA and PHAVOLUTA genes in the perception of radial positional information in the leaf primordium. Dominant phabulosa (phb) and phavoluta (phv) mutations cause a dramatic transformation of abaxial leaf fates into adaxial leaf fates. They do so by altering the predicted sterol/lipid-binding domains of ATHB14 and ATHB9, proteins of previously unknown function that also contain DNA-binding motifs. This change probably renders the protein constitutively active, implicating this domain as a central regulator of protein function and the PHB and PHV proteins as receptors for an adaxializing signal.

Unique gene expression patterns in liver and kidney associated with exposure to chemical toxicants

DNA arrays containing 260 unique genes involved in phase I and II metabolism, heat shock, DNA repair, inflammation, transcription, and housekeeping were used to examine gene expression patterns in liver and kidney in response to five classes of chemicals (polyaromatic hydrocarbons: benzo(a)pyrene, 3-methylcholanthrene; DNA alkylators: dimethylnitrosamine, ethylnitrosourea; peroxisome proliferators: diethylhexylphthalate, clofibrate; heavy metals: CdCl(2), HgCl(2); and oxidative stressors: CCl(4), bromobenzene). Time course experiments in mice were carried out in both tissues for each chemical and dose-response studies were used to further evaluate several of these chemicals. Each pair of chemicals yielded a similar pattern of gene expression distinct from the other four classes of chemicals. Both peroxisome proliferators up-regulated Cyp4a10, acyl-CoA thioesterase, and insulin-like growth factor binding protein-1, whereas the DNA alkylators altered the expression of monokine induced by gamma-interferon, the metallothioneins, p21, and several acute phase proteins. For each of the five classes of chemicals tested, several genes that were induced or repressed were common in each chemical exposure, whereas other genes were unique for that specific class of compound. Both time and dose are important factors in differentiating between chemical classes. Likewise, comparison of changes in messenger RNA expression between the kidney and liver of treated animals indicates that gene arrays may be useful in determining the comparative toxicity of chemicals in various tissues but that exposure to uncharacterized chemicals will have to be monitored in several tissues.

Computer support for interpreting family histories of breast and ovarian cancer in primary care: comparative study with simulated cases

OBJECTIVES

To evaluate the potential effect of computer support on general practitioners' management of familial breast and ovarian cancer, and to compare the effectiveness of two different types of computer program.

DESIGN

Crossover experiment with balanced block design.

PARTICIPANTS

Of a random sample of 100 general practitioners from Buckinghamshire who were invited, 41 agreed to participate. From these, 36 were selected for a fully balanced study.

INTERVENTIONS

Doctors managed 18 simulated cases: 6 with computerised decision support system Risk Assessment in Genetics (RAGs), 6 with Cyrillic (an established pedigree drawing program designed for clinical geneticists), and 6 with pen and paper.

MAIN OUTCOME MEASURES

Number of appropriate management decisions made (maximum 6), mean time taken to reach a decision, number of pedigrees accurately drawn (maximum 6). Secondary measures were method of support preferred for particular aspects of managing family histories of cancer; importance of specific information on cancer genetics that might be provided by an "ideal computer program."

RESULTS

RAGs resulted in significantly more appropriate management decisions (median 6) than either Cyrillic (median 3) or pen and paper (median 3); median difference between RAGs and Cyrillic 2.5 (95% confidence interval 2.0 to 3.0; P<0.0001). RAGs also resulted in significantly more accurate pedigrees (median 5) than both Cyrillic (median 3.5) and pen and paper (median 2); median difference between RAGs and Cyrillic 1.5 (1.0 to 2.0; P<0.0001). The time taken to use RAGs (median 178 seconds) was 51 seconds longer per case (95% confidence interval 36 to 65; P<0.0001) than pen and paper (median 124 seconds) but was less than Cyrillic (median 203 seconds; difference 23. (5 to 43; P=0.02)). 33 doctors (92% (78% to 98%)) preferred using RAGs overall. The most important elements of an "ideal computer program" for genetic advice in primary care were referral advice, the capacity to create pedigrees, and provision of evidence and explanations to support advice.

CONCLUSIONS

RAGs could enable general practitioners to be more effective gatekeepers to genetics services, empowering them to reassure the majority of patients with a family history of breast and ovarian cancer who are not at increased genetic risk.

Correlation between 31P chemical shift tensor and local structure in lithium cyclohexaphosphates Li6P6O18 x 3H2O and Li6P6O18

To understand the surprising behavior between the variations of the P'-P-P" angles and the correlated variations of the O'-P-O" ones, two lithium cyclohexaphosphate compounds Li6P6O18 x 3H2O and Li6P6O18 are studied by solid state nuclear magnetic resonance (NMR) spectroscopy. The two compounds exhibit the same [P6O18]6- ring anions but with 3m or 1 internal symmetry, respectively. Such symmetries induce local distortions that are exhibited by NMR spectroscopy. One-dimensional (1D) NMR gives information on structural sites of 7Li and 31P ions and the crystallographic non-equivalencies are observed. Nevertheless, in the anhydrous compound, X-ray diffraction and NMR results do not completely agree and some discrepancy exists between the number of sites observed with the first technique and the number of lines exhibited in the NMR spectra either for 7Li or 31P nuclei. This problem is elucidated by using 2D double quantum NMR spectroscopy coupled with theoretical considerations. We find that the 31P chemical shift tensor is dependent on the deviations of the O-P-O angles from those in the regular tetrahedron. Within the same empirical model, we suggest that the surprising behavior between the variations of the P'-P-P" and the ones of the O'-P-O" is related to the overall charge on the PO4 group. We also find the positions of the isotropic lines for 7Li essentially depend on the site co-ordination of this nuclei.

Stereolithographic models of biopolymers

Stereolithography (STL) has been used to make plastic models of the solvent accessible surfaces of biopolymers. Models have been made of proteins and proteins bound to DNA and RNA. The STL process uses a laser to photopolymerize a liquid resin. Using the ACES (accurate, clear, epoxy, solid) building technique, parts are made with minimum postcure shrinkage. Protein Data Bank files are converted to STL files that represent the surface topology of the biopolymer as a series of triangles and an index that describes their orientation. The models are useful in teaching biomolecular structure and the principle of docking. They are especially useful to the visually impaired.

The 'new genetics' and primary care: GPs' views on their role and their educational needs

BACKGROUND

Given the limited specialist resources available to cope with the rising demand for genetic services, it has been proposed that at least some of these services are provided by primary care in the future.

OBJECTIVE

We aimed to explore GPs' attitudes towards new developments in genetics, to establish the role they envisage for primary care and to clearly define the education, information and training needed to support them in this role.

METHODS

We carried out a qualitative study with GPs using four focus groups (26 GPs) and 15 individual semi-structured interviews.

RESULTS

GPs perceive genetics as an important and increasingly relevant topic for primary care. Views on the appropriate level of involvement for primary care are mixed. GPs currently lack the relevant knowledge and skills to manage patients concerned about their family history. Other potential barriers to increasing primary care involvement included the time and costs involved, and ethical and legal concerns.

CONCLUSION

If primary care is to become more involved in the delivery of genetic services in the future, then a major educational effort is required to raise awareness of the potential scope and limitations of new developments.

A systematic review of the literature exploring the role of primary care in genetic services

BACKGROUND

In response to growing demands on genetics departments and advances in genetic medicine, it has been proposed that primary care should provide a frontline service in clinical genetics. However, there are concerns that primary care may be unwilling or ill prepared to take on this new role.

OBJECTIVES

This study aimed to review systematically the literature exploring the role of primary care in delivering genetic services, and define potential methods of supporting primary care in the provision of genetics services.

METHODS

Seven electronic databases were searched. This was complemented by contacting experts in the field and handsearching reference lists. In total, 230 papers were identified, including traditional reviews, of which 96 were examined in detail. Fifty-one papers are included in this review. On account of the heterogeneity of papers identified, we conducted a qualitative synthesis of the results, focusing on five key questions.

RESULTS

GPs accept that they have an increasing role to play in genetics, but lack confidence in their ability to do so because of limited knowledge of clinical genetics. Evidence from pilot studies of cystic fibrosis screening provides the strongest evidence for the feasibility of providing genetic services in primary care.

CONCLUSIONS

Although genetic issues currently constitute a relatively small part of the overall workload in primary care, this will almost certainly change in the light of new genetic discoveries. Educational programmes and referral guidelines, computer decision support and genetic nurse specialist outreach clinics may provide useful methods of supporting GPs in the new field of primary care genetics.

Computer support for recording and interpreting family histories of breast and ovarian cancer in primary care (RAGs): qualitative evaluation with simulated patients

OBJECTIVES

To explore general practitioners' attitudes towards and use of a computer program for assessing genetic risk of cancer in primary care.

DESIGN

Qualitative analysis of semistructured interviews and video recordings of simulated consultations.

PARTICIPANTS

Purposive sample of 15 general practitioners covering a range of computer literacy, interest in genetics, age, and sex.

INTERVENTIONS

Each doctor used the program in two consultations in which an actor played a woman concerned about her family history of cancer. Consultations were videotaped and followed by interviews with the video as a prompt to questioning. MAIN OUTCOME MESURESs: Use of computer program in the Consultation.

RESULTS

The program was viewed as an appropriate application of information technology because of the complexity of cancer genetics and a sense of "guideline chaos" in primary care. Doctors found the program easy to use, but it often affected their control of the consultation. They needed to balance their desire to share the computer screen with the patient, driven by their concerns about the effect of the computer on doctor-patient communication, against the risk of premature disclosure of bad news.

CONCLUSIONS

This computer program could provide the necessary support to assist assessment of genetic risk of cancer in primary care. The potential impact of computer software on the consultation should not be underestimated. This study highlights the need for careful evaluation when developing medical information systems.