Improving risk models for patients having emergency bowel cancer surgery using linked electronic health records: a national cohort study

BACKGROUND

Life-saving emergency major resection of colorectal cancer (CRC) is a high-risk procedure. Accurate prediction of postoperative mortality for patients undergoing this procedure is essential for both healthcare performance monitoring and preoperative risk assessment. Risk-adjustment models for CRC patients often include patient and tumour characteristics, widely available in cancer registries and audits. The authors investigated to what extent inclusion of additional physiological and surgical measures, available through linkage or additional data collection, improves accuracy of risk models.

METHODS

Linked, routinely-collected data on patients undergoing emergency CRC surgery in England between December 2016 and November 2019 were used to develop a risk model for 90-day mortality. Backwards selection identified a 'selected model' of physiological and surgical measures in addition to patient and tumour characteristics. Model performance was assessed compared to a 'basic model' including only patient and tumour characteristics. Missing data was multiply imputed.

RESULTS

Eight hundred forty-six of 10 578 (8.0%) patients died within 90 days of surgery. The selected model included seven preoperative physiological and surgical measures (pulse rate, systolic blood pressure, breathlessness, sodium, urea, albumin, and predicted peritoneal soiling), in addition to the 10 patient and tumour characteristics in the basic model (calendar year of surgery, age, sex, ASA grade, TNM T stage, TNM N stage, TNM M stage, cancer site, number of comorbidities, and emergency admission). The selected model had considerably better discrimination compared to the basic model (C-statistic: 0.824 versus 0.783, respectively).

CONCLUSION

Linkage of disease-specific and treatment-specific datasets allowed the inclusion of physiological and surgical measures in a risk model alongside patient and tumour characteristics, which improves the accuracy of the prediction of the mortality risk for CRC patients having emergency surgery. This improvement will allow more accurate performance monitoring of healthcare providers and enhance clinical care planning.

Inequalities in the recovery of colorectal cancer services during the COVID-19 pandemic: a national population-based study

AIM

Evidence is lacking on whether there were inequalities in the recovery of colorectal cancer (CRC) services within the English National Health Service (NHS) following the COVID-19 pandemic. The aim of this study was to evaluate recovery according to patient age and socioeconomic status.

METHOD

Using routinely collected data, CRC patients diagnosed and treated in the English NHS were identified for two timeframes: the 'initial pandemic period' (April-June 2020) and the 'pandemic period' (April 2020-March 2022). Poisson models evaluated changes in numbers of diagnoses, major resections, adjuvant chemotherapy and neoadjuvant radiotherapy use for each timeframe, relative to the equivalent pre-pandemic timeframe (April-June 2019 and April 2018-March 2020, respectively), stratified by age and socioeconomic status. Tumour stage at presentation was evaluated over time.

RESULTS

Substantial deficits in diagnoses, major resections and adjuvant chemotherapy were identified in the initial pandemic period, whilst the use of neoadjuvant radiotherapy increased. Overall, these deficits recovered. Patients outside screening age, and in the most deprived group, had greater deficits in diagnoses and major resections. There was no evidence of stage migration by June 2021.

CONCLUSIONS

CRC services showed recovery to baseline during the pandemic. However, evident inequalities must be addressed in ongoing recovery efforts. Long-term outcomes will fully establish the impact of the pandemic on CRC patients.

What is the impact of hospital and surgeon volumes on outcomes in rectal cancer surgery?

AIM

Evidence for a positive volume-outcome relationship for rectal cancer surgery is unclear. This study aims to evaluate the volume-outcome relationship for rectal cancer surgery at hospital and surgeon level in the English National Health Service (NHS).

METHOD

All patients undergoing a rectal cancer resection in the English NHS between 2015 and 2019 were included. Multilevel multivariable logistic regression was used to model relationships between outcomes and mean annual hospital and surgeon volumes (using a linear plus a quadratic term for volume) with adjustment for patient characteristics.

RESULTS

A total of 13 858 patients treated in 166 hospitals were included. Six hospitals (3.6%) performed fewer than 10 rectal cancer resections per year, and 381 surgeons (45.0%) performed fewer than five such resections per year. Patients treated by high-volume surgeons had a reduced length of stay (p = 0.016). No statistically significant volume-outcome relationships were demonstrated for 90-day mortality, 30-day unplanned readmission, unplanned return to theatre, stoma at 18 months following anterior resection, positive circumferential resection margin and 2-year all-cause mortality at either hospital or surgeon level (p values > 0.05).

CONCLUSION

Almost half of colorectal surgeons in England do not meet national guidelines for rectal cancer surgeons to perform a minimum of five major resections annually. However, our results suggest that centralizing rectal cancer surgery with the main focus of increasing operative volume may have limited impact on NHS surgical outcomes. Therefore, quality improvement initiatives should address a wider range of evidence-based process measures, across the multidisciplinary care pathway, to enhance outcomes for patients with rectal cancer.

Severity of Dementia and Survival in Patients Diagnosed with Colorectal Cancer: A National Cohort Study in England and Wales

AIMS

There is little evidence about the survival of patients with colorectal cancer (CRC) also diagnosed with dementia. We quantified dementia severity and estimated how it is associated with 2-year overall survival.

MATERIALS AND METHODS

Records of patients aged 65 years or older diagnosed with CRC in England and Wales were identified. A novel proxy for dementia severity combined dementia diagnosis in administrative hospital data with Eastern Cooperative Oncology Group performance status. Cox regression was used to estimate hazard ratios with and without risk adjustment.

RESULTS

In total, 4033 of 105 250 CRC patients (3.8%) had dementia recorded. Two-year survival decreased with increasing dementia severity from 65.4% without dementia, 53.5% with mild dementia, 33.0% with moderate dementia to 16.5% with severe dementia (hazard ratio comparing severe with no dementia: 2.97; 95% confidence interval 2.79, 3.16). Risk adjustment for comorbidity and cancer stage reduced this association slightly (hazard ratio 2.52; 95% confidence interval 2.37, 2.68) and additional adjustment for treatment factors reduced it further (hazard ratio 1.60; 95% confidence interval 1.50, 1.70).

CONCLUSIONS

Survival of CRC patients varied strongly according to dementia severity, suggesting that a 'one-size-fits-all' policy for the care of CRC patients with dementia is not appropriate. Comprehensive assessment of cancer patients with dementia that considers dementia severity is essential in a shared decision-making process that ensures patients receive the most appropriate treatment for their individual needs and preferences.

Measuring variation in the quality of systemic anti-cancer therapy delivery across hospitals: A national population-based evaluation

AIM

To date, there has been little systematic assessment of the quality of care associated with systemic anti-cancer therapy (SACT) delivery across national healthcare systems. We evaluated hospital-level toxicity rates during SACT treatment as a means of identifying variation in care quality.

METHODS

All colorectal cancer (CRC) patients receiving SACT within 106 English National Health Service (NHS) hospitals between 2016 and 2019 were included. Severe acute toxicity rates were derived from hospital administrative data using a validated coding framework. Variation in hospital-level toxicity rates was assessed separately in the adjuvant and metastatic settings. Toxicity rates were adjusted for age, sex, comorbidity, performance status, tumour site, and TNM staging.

RESULTS

Eight thousand one hundred and seventy three patients received SACT in the adjuvant setting, and 7,683 patients in the metastatic setting. Adjusted severe acute toxicity rates varied between hospitals from 11% to 49% for the adjuvant cohort, and from 25% to 67% for the metastatic cohort. Compared to the national mean toxicity rate in the adjuvant cohort, six hospitals were more than two standard deviations (2SD) above, and four hospitals were more than 2SD below. In the metastatic cohort, six hospitals were more than 2SD above, and seven hospitals were more than 2SD below the national mean toxicity rate. Overall, 12 hospitals (12%) had toxicity rates more than 2SD above the national mean, and 11 (10%) had rates more than 2SD below.

CONCLUSION

There is substantial variation in hospital-level severe acute toxicity rates in both the adjuvant and metastatic settings, despite risk-adjustment. Ongoing reporting of this performance indicator can be used to focus further investigation of toxicity rates and stimulate quality improvement initiatives to improve care.

Impact of patient choice and hospital competition on patient outcomes after rectal cancer surgery: A national population-based study

BACKGROUND

The objective of the current national cohort study was to analyze the correlation between choice and competition on outcomes after cancer surgery in rectal cancer.

METHODS

The analysis included all men who underwent rectal cancer surgery in the English National Health Service between March 2015 and April 2019 (n = 13,996). Multilevel logistic regression was used to assess the effect of a rectal cancer surgery center being located in a competitive environment (based on the number of centers within a threshold distance) and being a successful competitor (based on the ability to attract patients from other hospitals) on eight patient-level outcomes: 30- and 90-day emergency readmissions, 30-day re-operation rates, 90-day postoperative mortality, length of stay >14 days, circumferential resection margin status, rates of primary procedure with a permanent stoma, and rates of persistent stoma 18 months after anterior resection.

RESULTS

With adjustment for patient characteristics, patients who underwent surgery in centers located in a stronger competitive environment were less likely to have an abdominoperineal excision or a Hartman's procedure (odds ratio [OR], 0.73; 95% confidence interval [CI], 0.55-0.97, p = .04). Additionally, individuals who received treatment at hospitals that were successful competitors had a lower risk of a 90-day readmission following rectal cancer surgery (OR, 0.86; 95% CI, 0.76-0.97, p = .03) and were less likely to have a persistent stoma at 18 months after anterior resection (OR, 0.75; 95% CI, 0.61-0.93, p = .02).

CONCLUSIONS

Hospitals located in areas of high competition are associated with better patient outcomes and improved processes of care for rectal cancer surgery.

Outcomes of colorectal cancer resection in patients with inflammatory bowel disease: a national population-based analysis in England and Wales

AIM

The aim was to compare early postoperative outcomes and 2-year cancer-specific mortality following colorectal cancer (CRC) resection in patients with and without inflammatory bowel disease (IBD) in England and Wales.

METHOD

Records for patients in the National Bowel Cancer Audit who had major CRC resection between April 2014 and December 2017 were linked to routinely collected hospital level administrative datasets and chemotherapy and radiotherapy datasets. Multivariable regression models were used to compare outcomes with adjustment for patient and tumour characteristics.

RESULTS

In all, 63 365 patients were included. 1285 (2.0%) had an IBD diagnosis: 839 (65.3%) ulcerative colitis, 435 (33.9%) Crohn's disease and 11 (0.9%) were indeterminate. IBD patients were younger, had more advanced cancer staging and a higher proportion of right-sided tumours. They also had a higher proportion of emergency resection, total/subtotal colectomy, open surgery and stoma formation at resection, with longer hospital admissions and higher rates of unplanned readmission and reoperation. Fewer rectal cancer patients with IBD received neoadjuvant radiotherapy (24.8% vs. 36.0%, P = 0.005) whilst similar proportions of Stage III colon cancer patients received adjuvant chemotherapy. Ninety-day postoperative mortality was similar, but unadjusted 2-year cancer-specific mortality was significantly higher in patients with IBD (subdistribution hazard ratio 1.35, 95% CI 1.18-1.55). Risk adjustment for patient and tumour factors reduced this association (adjusted subdistribution hazard ratio 1.22, 95% CI 1.05-1.43).

CONCLUSION

Patients with IBD and CRC are a distinct patient group who develop CRC at a younger age and undergo more radical surgery. They have worse cancer survival, with the difference in prognosis appearing after the early postoperative period.

Survival outcomes associated with completion of adjuvant oxaliplatin-based chemotherapy for stage III colon cancer: A national population-based study

The impact of cycle completion rates of oxaliplatin-based adjuvant chemotherapy for stage III colon cancer in real-world practice is unknown. We assessed its impact, and that of treatment modification, on 3-year cancer-specific mortality. Four thousand one hundred and forty-seven patients with pathological stage III colon cancer undergoing major resection from 2014 to 2017 in the English National Health Service were included. Chemotherapy data came from linked national administrative datasets. Competing risk regression analysis for 3-year cancer-specific mortality was performed according to completion of <6, 6-11, or 12 5-fluoropyrimidine and oxaliplatin (FOLFOX) cycles, or <4, 4-7, or 8 capecitabine and oxaliplatin (CAPOX) cycles, adjusted for patient, tumour and hospital-level characteristics. Median age was 64 years. Thirty-two per cent of patients had at least one comorbidity. Forty-two per cent of patients had T4 disease, and 40% had N2 disease. Compared to completion of 12 FOLFOX cycles, cancer-specific mortality was higher in patients completing <6 cycles [subdistribution hazard ratios (sHR) 2.17; 95% CI 1.56-3.03] or 6-11 cycles (sHR 1.40; 95% CI 1.09-1.78) (P < .001). Compared to completion of 8 CAPOX cycles, cancer-specific mortality was higher in patients completing <4 cycles (sHR 2.02; 95% CI 1.53-2.67) or 4-7 cycles (sHR 1.63; 95% CI 1.27-2.10) (P < .001). Dose reduction and early oxaliplatin discontinuation did not impact mortality in patients completing all cycles. Completion of all cycles of chemotherapy was associated with improved cancer-specific survival in real-world practice. Poor prognostic factors may have affected findings, however, patients completing <50% of cycles had poor outcomes. Clinicians may wish to facilitate completion with treatment modification in those able to tolerate it.

Determinants of variation in radical local treatment for men with high-risk localised or locally advanced prostate cancer in England

BACKGROUND

Many factors are implicated in the potential 'under-treatment' of prostate cancer but little is known about the between-hospital variation.

METHODS

The National Prostate Cancer Audit (NPCA) database was used to identify high-risk localised or locally advanced prostate cancer patients in England, between January 2014 and December 2017, and the treatments received. Hospital-level variation in radical local treatment was explored visually using funnel plots. The intra-class correlation coefficient (ICC) quantified the between-hospital variation in a random-intercept multivariable logistic regression model.

RESULTS

53,888 men, from 128 hospitals, were included and 35,034 (65.0%) received radical local treatment. The likelihood of receiving radical local treatment was increased in men who were younger (the strongest predictor), more affluent, those with fewer comorbidities, and in those with a non-Black ethnic background. There was more between-hospital variation (P < 0.001) for patients aged ≥80 years (ICC: 0.235) compared to patients aged 75-79 years (ICC: 0.070), 70-74 years (ICC: 0.041), and <70 years (ICC: 0.048). Comorbidity and socioeconomic deprivation did not influence the between-hospital variation.

CONCLUSIONS

Radical local treatment of high-risk localised or locally advanced prostate cancer depended strongly on age and comorbidity, but also on socioeconomic deprivation and ethnicity, with the between-hospital variation being highest in older patients.

Real-world outcomes associated with new cancer medicines approved by the Food and Drug Administration and European Medicines Agency: A retrospective cohort study

Purpose

Real-World Data (RWD) studies are increasingly used to support regulatory approvals, reimbursement decisions, and changes in clinical practice for novel cancer drugs. However, few studies have systematically appraised their quality or compared outcomes to pivotal trials.

Methods

All RWD studies (2010–2019) for drugs approved by the Food and Drug Administration (FDA) and European Medicines Agency (EMA) from 2010 to 2015 for solid organ tumours in the non-curative setting were identified. Quality assessment was undertaken using the Newcastle Ottawa Scale. Survival differences between each RWD study and the pivotal trial were determined using a related sample Wilcoxon signed-rank test.

Results

293 RWD studies for 45 of the 57 drug indications approved by the FDA/EMA were identified. The most common tumour types were prostate cancer (29%, n = 86) and melanoma (15%, n = 43). A quarter of the studies had industry funding. No high-quality studies were identified, and 78% were low quality. Comparative survival analysis between RWD and pivotal trials was possible for 224 studies (37 drug indications). Differences in median survival between the RWD studies and their corresponding trial ranged from −32 months to 21 months (IQR –4·2 months to 1·6 months). Low-quality studies were more likely to report superior survival outcomes (23%) compared to higher quality studies (8%) (p = 0.02).

Conclusion

RWD study quality for novel cancer drugs is low and of insufficient rigour to inform reimbursement decisions and clinical practice. RWD studies seeking publication should provide a completed quality assessment tool on submission. Greater investment in properly designed RWD studies is required.

•

Study provides a systematic appraisal of FDA/EMA approved drugs in real-world practice.

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Most novel FDA/EMA cancer drugs have real-world data (RWD) studies, but the quality is low.

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Variability in survival outcomes exists, and findings should be applied cautiously.

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Most RWD studies reported inferior survival outcomes compared to the pivotal trial.

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Pre-publication critical appraisal checklists should be used for RWD studies.

Validity of chemotherapy information derived from routinely collected healthcare data: A national cohort study of colon cancer patients

BACKGROUND

We used a structured approach to validate chemotherapy information derived from a national routinely collected chemotherapy dataset and from national administrative hospital data.

METHODS

10,280 patients who had surgical resection with stage III colon cancer were included. First, we compared information derived from the national chemotherapy dataset (SACT) and from the administrative hospital dataset (HES) in the English NHS with respect to receipt of adjuvant chemotherapy (ACT). Second, we compared regimen and number of cycles in linked patient-level records. Third, we carried out a sensitivity analysis to establish to what extent the impact of ACT receipt differed according to data source.

RESULTS

6,012 patients (58 %) received ACT according to either dataset. Of these patients, 3,460 (58 %) had ACT records in both datasets, 1,649 (27 %) in SACT alone, and 903 (15 %) in HES alone. Of the 3,460 patients with records in both datasets, 3,320 (96 %) had matching regimens. There was good agreement on cycle number with similar proportions of patients recorded with a single cycle (6 % in SACT vs. 7 % in HES) and slightly fewer patients recorded with more than 8 cycles in SACT (32 % in SACT vs. 35 % in HES). 3-year cancer-specific mortality was similar for patients receiving ACT, regardless of whether a patient received ACT according to SACT alone (16.6 %), according to HES alone (16.8 %), or according to either SACT or HES (17.1 %).

CONCLUSION

Routinely collected national chemotherapy data and administrative hospital data are highly accurate in recording regimen and number of chemotherapy cycles. However, chemotherapy information should ideally be captured from both datasets to avoid under-capture, particularly of oral chemotherapy from administrative hospital data, and to minimise bias.

The impact of the first peak of the COVID-19 pandemic on colorectal cancer services in England and Wales: A national survey

AIM

The object of this work was to study how National Health Service hospitals in England and Wales aimed to maintain effective and safe colorectal cancer (CRC) services during the first peak of the COVID-19 pandemic (April 2020).

METHOD

A national survey was performed among all 148 hospitals providing CRC services. Information was collected about changes in referrals, diagnostic, staging and therapeutic procedures, as well as whether there was access to a 'cold site' (a hospital facility free of COVID-19). Clinicians in each hospital were also asked to give the 'single most important lesson learned' about keeping services safe and effective.

RESULTS

Full responses were received from 123 (83%) hospitals, and information about 'cold sites' was available for 146 (99%). Eighty hospitals (54%) had access to a 'cold site' and this was increased in regions with higher COVID-19 infection rates (p <0.001). Of the 123 responding hospitals, 105 (85%) indicated that referrals of patients with suspected CRC had dropped by at least 30%, and 69 (56%) indicated that treatment plans were altered in at least 50% of CRC patients. However, 'cold site' availability protected the capacity for diagnostic colonoscopy (p = 0.013) and CRC resection (p = 0.010). Many 'lessons learned' highlighted the importance of adequate structural service organization, often mentioning 'cold sites' and regional coordination as examples, good communication and triage of patients based on clinical urgency.

CONCLUSION

Access to 'cold sites', as well as regional coordination, clear communication and strong leadership, were found to be pivotal in maintaining capacity for diagnosis and treatment of CRC during the COVID-19 surge.

Surgical Treatment and Outcomes of Colorectal Cancer Patients During the COVID-19 Pandemic: A National Population-based Study in England

To compare the management and outcomes of colorectal cancer (CRC) patients during the first 2 months of the COVID-19 pandemic with the preceding 6 months.

BACKGROUND

The pandemic has affected the diagnosis and treatment of CRC patients worldwide. Little is known about the safety of major resection and whether creating "cold" sites (COVID-free hospitals) is effective.

METHODS

A national study in England used administrative hospital data for 14,930 CRC patients undergoing surgery between October 1, 2019, and May 31, 2020. Mortality of CRC resection was compared before and after March 23, 2020 ("lockdown" start).

RESULTS

The number of elective CRC procedures dropped sharply during the pandemic (from average 386 to 214 per week), whereas emergency procedures were hardly affected (from 88 to 84 per week). There was little change in characteristics of surgical patients during the pandemic. Laparoscopic surgery decreased from 62.5% to 35.9% for elective and from 17.7% to 9.7% for emergency resections. Surgical mortality increased slightly (from 0.9% to 1.2%, P = 0.06) after elective and markedly (from 5.6% to 8.9%, P = 0.003) after emergency resections. The observed increase in mortality during the first phase of the pandemic was similar in "cold" and "hot" sites (P > 0.5 elective and emergency procedures).

CONCLUSIONS

The pandemic resulted in a 50% reduction in elective CRC procedures during the initial surge and a substantial increase in mortality after emergency resection. There was no evidence that surgery in COVID-free "cold" sites led to better outcomes in the first 2 months.

Frailty in Older Patients Undergoing Emergency Laparotomy: Results From the UK Observational Emergency Laparotomy and Frailty (ELF) Study

OBJECTIVE

This study aimed to document the prevalence of frailty in older adults undergoing emergency laparotomy and to explore relationships between frailty and postoperative morbidity and mortality.

SUMMARY BACKGROUND DATA

The majority of adults undergoing emergency laparotomy are older adults (≥65 y) that carry the highest mortality. Improved understanding is urgently needed to allow development of targeted interventions.

METHODS

An observational multicenter (n=49) UK study was performed (March-June 2017). All older adults undergoing emergency laparotomy were included. Preoperative frailty score was calculated using the progressive Clinical Frailty Score (CFS): 1 (very fit) to 7 (severely frail). Primary outcome measures were the prevalence of frailty (CFS 5-7) and its association to mortality at 90 days postoperative. Secondary outcomes included 30-day mortality and morbidity, length of critical care, and overall hospital stay.

RESULTS

A total of 937 older adults underwent emergency laparotomy: frailty was present in 20%. Ninety-day mortality was 19.5%. After age and sex adjustment, the risk of 90-day mortality was directly associated with frailty: CFS 5 adjusted odds ratio (aOR) 3.18 [95% confidence interval (CI), 1.24-8.14] and CFS 6/7 aOR 6·10 (95% CI, 2.26-16.45) compared with CFS 1. Similar associations were found for 30-day mortality. Increasing frailty was also associated with increased risk of complications, length of Intensive Care Unit, and overall hospital stay.

CONCLUSIONS

A fifth of older adults undergoing emergency laparotomy are frail. The presence of frailty is associated with greater risks of postoperative mortality and morbidity and is independent of age. Frailty scoring should be integrated into acute surgical assessment practice to aid decision-making and development of novel postoperative strategies.

Association between preadmission frailty and care level at discharge in older adults undergoing emergency laparotomy

Background

Older adults undergoing emergency abdominal surgery have significantly poorer outcomes than younger adults. For those who survive, the level of care required on discharge from hospital is unknown and such information could guide decision-making. The ELF (Emergency Laparotomy and Frailty) study aimed to determine whether preoperative frailty in older adults was associated with increased dependence at the time of discharge.

Methods

The ELF study was a UK-wide multicentre prospective cohort study of older patients (65 years or more) undergoing emergency laparotomy during March and June 2017. The objective was to establish whether preoperative frailty was associated with increased care level at discharge compared with preoperative care level. The analysis used a multilevel logistic regression adjusted for preadmission frailty, patient age, sex and care level.

Results

A total of 934 patients were included from 49 hospitals. Mean(s.d.) age was 76·2(6·8) years, with 57·6 per cent women; 20·2 per cent were frail. Some 37·4 per cent of older adults had an increased care level at discharge. Increasing frailty was associated with increased discharge care level, with greater predictive power than age. The adjusted odds ratio for an increase in care level was 4·48 (95 per cent c.i. 2·03 to 9·91) for apparently vulnerable patients (Clinical Frailty Score (CFS) 4), 5·94 (2·54 to 13·90) for those mildly frail (CFS 5) and 7·88 (2·97 to 20·79) for those moderately or severely frail (CFS 6 or 7), compared with patients who were fit.

Conclusion

Over 37 per cent of older adults undergoing emergency laparotomy required increased care at discharge. Frailty scoring was a significant predictor, and should be integrated into all acute surgical units to aid shared decision-making and discharge planning.

‘Blu-Tack’ as an intravesical foreign body: Overcoming a sticky situation

Intravesical foreign bodies can pose a significant urological challenge. An unusual intravesical foreign body described within the literature is ‘Blu-Tack’. This unique material with its distinct physical properties presents a particular challenge in its management. We describe our novel endoscopic approach to the removal of an intravesical ‘Blu-Tack’ mass and suggest this method as a means of facilitating successful extraction of this particular foreign body.

Machine learning classification of OARSI-scored human articular cartilage using magnetic resonance imaging

OBJECTIVE

The purpose of this study is to evaluate the ability of machine learning to discriminate between magnetic resonance images (MRI) of normal and pathological human articular cartilage obtained under standard clinical conditions.

METHOD

An approach to MRI classification of cartilage degradation is proposed using pattern recognition and multivariable regression in which image features from MRIs of histologically scored human articular cartilage plugs were computed using weighted neighbor distance using compound hierarchy of algorithms representing morphology (WND-CHRM). The WND-CHRM method was first applied to several clinically available MRI scan types to perform binary classification of normal and osteoarthritic osteochondral plugs based on the Osteoarthritis Research Society International (OARSI) histological system. In addition, the image features computed from WND-CHRM were used to develop a multiple linear least-squares regression model for classification and prediction of an OARSI score for each cartilage plug.

RESULTS

The binary classification of normal and osteoarthritic plugs yielded results of limited quality with accuracies between 36% and 70%. However, multiple linear least-squares regression successfully predicted OARSI scores and classified plugs with accuracies as high as 86%. The present results improve upon the previously-reported accuracy of classification using average MRI signal intensities and parameter values.

CONCLUSION

MRI features detected by WND-CHRM reflect cartilage degradation status as assessed by OARSI histologic grading. WND-CHRM is therefore of potential use in the clinical detection and grading of osteoarthritis.

Associations between objectively measured physical activity and academic attainment in adolescents from a UK cohort

BACKGROUND

To test for cross-sectional (at age 11) and longitudinal associations between objectively measured free-living physical activity (PA) and academic attainment in adolescents.Method Data from 4755 participants (45% male) with valid measurement of PA (total volume and intensity) by accelerometry at age 11 from the Avon Longitudinal Study of Parents and Children (ALSPAC) was examined. Data linkage was performed with nationally administered school assessments in English, Maths and Science at ages 11, 13 and 16.

RESULTS

In unadjusted models, total volume of PA predicted decreased academic attainment. After controlling for total volume of PA, percentage of time spent in moderate-vigorous intensity PA (MVPA) predicted increased performance in English assessments in both sexes, taking into account confounding variables. In Maths at 16 years, percentage of time in MVPA predicted increased performance for males (standardised β=0.11, 95% CI 0.00 to 0.22) and females (β=0.08, 95% CI 0.00 to 0.16). For females the percentage of time spent in MVPA at 11 years predicted increased Science scores at 11 and 16 years (β=0.14 (95% CI 0.03 to 0.25) and 0.14 (0.07 to 0.21), respectively). The correction for regression dilution approximately doubled the standardised β coefficients.

CONCLUSIONS

Findings suggest a long-term positive impact of MVPA on academic attainment in adolescence.

SnapShot: Visualization to Propel Ice Hockey Analytics

Sports analysts live in a world of dynamic games flattened into tables of numbers, divorced from the rinks, pitches, and courts where they were generated. Currently, these professional analysts use R, Stata, SAS, and other statistical software packages for uncovering insights from game data. Quantitative sports consultants seek a competitive advantage both for their clients and for themselves as analytics becomes increasingly valued by teams, clubs, and squads. In order for the information visualization community to support the members of this blossoming industry, it must recognize where and how visualization can enhance the existing analytical workflow. In this paper, we identify three primary stages of today's sports analyst's routine where visualization can be beneficially integrated: 1) exploring a dataspace; 2) sharing hypotheses with internal colleagues; and 3) communicating findings to stakeholders.Working closely with professional ice hockey analysts, we designed and built SnapShot, a system to integrate visualization into the hockey intelligence gathering process. SnapShot employs a variety of information visualization techniques to display shot data, yet given the importance of a specific hockey statistic, shot length, we introduce a technique, the radial heat map. Through a user study, we received encouraging feedback from several professional analysts, both independent consultants and professional team personnel.

Comparison of American and European practices in the management of patients with primary immunodeficiencies

Primary immunodeficiency diseases (PIDs) comprise a heterogeneous group of rare disorders. This study was devised in order to compare management of these diseases in the northern hemisphere, given the variability of practice among clinicians in North America. The members of two international societies for clinical immunologists were asked about their management protocols in relation to their PID practice. An anonymous internet questionnaire, used previously for a survey of the American Academy of Allergy, Asthma and Immunology (AAAAI), was offered to all full members of the European Society for Immunodeficiency (ESID). The replies were analysed in three groups, according to the proportion of PID patients in the practice of each respondent; this resulted in two groups from North America and one from Europe. The 123 responses from ESID members (23·7%) were, in the majority, very similar to those of AAAAI respondents, with > 10% of their practice devoted to primary immunodeficiency. There were major differences between the responses of these two groups and those of the general AAAAI respondents whose clinical practice was composed of < 10% of PID patients. These differences included the routine use of intravenous immunoglobulin therapy (IVIg) for particular types of PIDs, initial levels of IVIg doses, dosing intervals, routine use of prophylactic antibiotics, perceptions of the usefulness of subcutaneous immunoglobulin therapy (SCIg) and of the risk to patients' health of policies adopted by health-care funders. Differences in practice were identified and are discussed in terms of methods of health-care provision, which suggest future studies for ensuring continuation of appropriate levels of immunoglobulin replacement therapies.

Population prevalence of diagnosed primary immunodeficiency diseases in the United States

RATIONALE

Although health surveys are routinely used to estimate the population incidence and prevalence of many chronic and acute conditions in the U.S. population, they have infrequently been used for "rare" conditions such as primary immunodeficiency diseases (PID). Accurate prevalence measures are needed to separate the truly rare condition from those that primary care doctors are likely to see in their practices today, if early diagnosis and treatment are to be achieved.

METHODS

A national probability sample of 10,000 households was sampled by random digit dialing and screened by telephone to identify how many of the nearly 27,000 household members had been diagnosed with a PID.

RESULTS

A total of 23 household members in 18 households were reported with a specific diagnosis for PID (CVID, IgA, IgG, XLA, SCID, CGD), whereas additional cases were reported as a PID without a confirmatory diagnosis. These findings suggest a population prevalence of diagnosed PID in the United States at approximately 1 in 1,200 persons.

CONCLUSIONS

Diagnoses of PID in the United States are far more common than suggested in the literature.

Delayed chromosome changes in gamma-irradiated normal and Li-Fraumeni fibroblasts

Knockout mice with only one Trp53 allele (+/- genotype) are highly susceptible to radiation-induced cancers, possibly through numerical chromosome changes. Patients with the Li-Fraumeni syndrome, having heterozygous TP53 germline mutations (+/mut genotype), are also susceptible to spontaneous and radiogenic cancers. We have investigated the susceptibility of six Li-Fraumeni syndrome +/mut and six normal fibroblast strains to induced numerical and unstable structural aberrations at six population doublings after exposure to 3 or 6 Gy gamma rays. Four of the irradiated Li-Fraumeni syndrome strains showed small increases in both aberration types, similar to those seen in the normal strains. In two irradiated Li-Fraumeni syndrome strains, there were high levels of induced structural changes, and one of these showed a modest increase in hyperploidy. We suggest that enhanced sensitivity to delayed radiation-induced chromosome changes in Li-Fraumeni syndrome cells requires other genetic alterations in addition to TP53 heterozygosity, apparently in contrast to the situation in Trp53 heterozygous null mice. If such additional alterations occur in vivo in Li-Fraumeni syndrome patients, they may predispose them to radiogenic cancers, mainly through enhanced structural rather than numerical chromosome changes. Our findings raise questions about the validity of quantitative extrapolation of cytogenetic data from Trp53-defective mice to radiogenic cancer risk in humans.

The relationship between radiation-induced G(1)arrest and chromosome aberrations in Li-Fraumeni fibroblasts with or without germline TP53 mutations

We previously showed that cultured fibroblasts from patients with the cancer-prone Li-Fraumeni (LF) syndrome, having heterozygous germline TP53 mutations, sustain less ionizing radiation-induced permanent G(1)arrest than normal fibroblasts. In contrast, fibroblast strains from LF patients without TP53 mutations showed normal G(1)arrest. We have now investigated the relationship between the extent of G(1)arrest and the level of structural chromosome damage (mainly dicentrics, rings and acentric fragments) in cells at their first mitosis after G(1)irradiation, in 9 LF strains with TP53 mutations, 6 without TP53 mutations and 7 normal strains. Average levels of damage in the mutant strains were 50% higher than in normals, whereas in non-mutant LF strains they were 100% higher. DNA double strand breaks (dsb) are known to act as a signal for p53-dependent G(1)arrest and to be the lesions from which chromosome aberrations arise. These results suggest that a minimal level of dsb is required before the signal for arrest is activated and that p53-defective cells have a higher signal threshold than p53-proficient cells. Dsb that do not cause G(1)blockage can progress to mitosis and appear as simple deletions or interact to form exchange aberrations. The elevated levels in the non-mutant strains may arise from defects in the extent or accuracy of dsb repair. In LF cells with or without TP53 mutations, the reduced capacity to eliminate or repair chromosomal damage of the type induced by ionising radiation, may contribute to cancer predisposition in this syndrome.

Chromosome instability in fibroblasts derived from Li-Fraumeni syndrome families without TP53 mutations

The mean in vitro lifespan of dermal fibroblast strains derived from cancer-affected individuals belonging to families conforming to the classical Li-Fraumeni-syndrome or the Li-Fraumeni-like syndrome (LF strains), but in whom no TP53 mutation has been found, was not significantly different to that of normal strains. This was in contrast to LF strains that carry TP53 mutations. Cytogenetic observations of numerical and structural chromosome abnormalities were made on Giemsa stained metaphases prepared at different times during the lifespan of strains. Five strains from different LF families showed significantly increased frequencies of abnormal cells during the last 10% of their lifetime compared with seven normal strains and three other LF strains fell outside the normal range but did not reach significance. Two LF strains fell within the normal range indicating heterogeneity of the phenotype in this subset of LF fibroblasts. Numerical aberrations were the major aberration type observed. These observations of genetic instability are similar, but generally less strongly expressed, to those seen in LF strains with TP53 mutations. The basis for genetic instability in LF strains without TP53 mutations is not known, but appears not to involve defects in either the G(1)checkpoint or the checkpoint kinase hChk2.

Association of Zollinger-Ellison syndrome with pancreatitis: report of five cases

In a retrospective analysis, five cases of Zollinger-Ellison syndrome were found in a typical urban inner-city teaching hospital. Chronic alcohol abuse and heavy smoking characterized these patients, and four of them also had pancreatitis, suggesting an association of gastrin-producing tumors and pancreatic inflammation. Ductal obstruction by neuroendocrine tumors has been reported to cause pancreatitis in a few cases. In this analysis, however, a nonobstructive gastrinoma was the surgical diagnosis in three patients, and it was suggested by imaging studies in the two other cases. The potential other pathomechanisms for a dual cause-effect relationship of gastrinoma and pancreatitis are discussed.

Genomic alterations associated with loss of heterozygosity for TP53 in Li-Fraumeni syndrome fibroblasts

Studies of Li-Fraumeni syndrome fibroblasts heterozygous for germline TP53 mutations have shown that loss of heterozygosity (LOH) occurs during passaging and is associated with genomic instability, such as chromosomal aberrations and aneuploidy to investigate the genomic changes associated with LOH in Li-Fraumeni (LF) fibroblasts, we have analysed cell strains at increasing population doublings (PD) using Comparative Genomic Hybridization (CGH). We have looked at three groups of cell strains: LF mutation-carrying strains which showed LOH for TP53, LF mutation-carrying strains which did not show LOH, and strains from normal individuals. Using CGH, we have detected loss of distinct chromosomal regions associated with LOH in 4 out of 5 mutation-carrying strains. In particular we have found loss of chromosomal regions containing genes involved in cell cycle control or senescence, including loss of 9p and 17p in these strains. Other recurrent changes included loss of chromosomes 4q and 6q, regions shown to contain one or more tumour suppressor genes. No genomic alterations were detected at cumulative PD in the normal strains or in the LF mutation-carrying strains which did not show LOH for TP53. We have also analysed the three groups of strains for microsatellite instability and somatic TP53 mutations, and have found genetic alterations in only one strain.

Radiation-induced G1 arrest is not defective in fibroblasts from Li-Fraumeni families without TP53 mutations

Radiation-induced G1 arrest was studied in four classes of early passage skin fibroblasts comprising 12 normals, 12 heterozygous (mut/wt) TP53 mutation-carriers, two homozygous (mut/-) TP53 mutation-carriers and 16 strains from nine Li-Fraumeni syndrome or Li-Fraumeni-like families in which no TP53 mutation has been found, despite sequencing of all exons, exon-intron boundaries, 3' and 5' untranslated regions and promoter regions. In an assay of p53 allelic expression in yeast, cDNAs from these non-mutation strains behaved as wild-type p53. Using two different assays, we found G1 arrest was reduced in heterozygous strains with mis-sense mutations and one truncation mutation, when compared to the range established for the normal cells. Heterozygous strains with mutations at splice sites behaved like normal cells, whilst homozygous (mut/-) strains showed either extremely reduced, or no, arrest. Strains from all nine non-mutation families gave responses within the normal range. Exceptions to the previously reported inverse correlation between G1 arrest and clonogenic radiation resistance were observed, indicating that these phenotypes are not strictly interdependent.

Lower extremity preference during gross and fine motor skills performed in sitting and standing postures

The evaluation of lower limb preference in physical therapy practice is critical in order for the clinician to assist patients with functional retraining tasks. No studies in the physical therapy literature present a systematic approach to determine the criteria needed to identify the preferred limb. This research was designed to present a series of tests for effectiveness in determining limb preference. The purpose of this study was to determine whether lower limb preference existed in a group of recreationally athletic women when performing either stability or dynamic skills with the lower extremities while sitting or standing. The relationship of such a preference to handedness was also determined. Forty female recreational athletes, 20 right-handed subjects and 20 left-handed subjects, who ranged in age from 21 to 35 years, participated in this study. Subjects performed three repetitions of the following tests in both sitting and standing: kick a ball, swing a leg over a box, pick up a marble with the toes, and trace a triangle with the toes. The subjects were also asked to stand on one leg. The order of performing the tests was randomized. The results indicated that right-handed subjects performed activities more consistently with one lower extremity when compared with left-handed subjects, regardless of posture (sitting or standing). The difference in limb choice between right- and left-handed subjects was significant for all activities (p < .05). The considerable sensitivity of foot and leg performance following neurological insult renders the assessment of foot and leg preference very important for purposes of clinical rehabilitation.

Genetic and functional studies of a germline TP53 splicing mutation in a Li-Fraumeni-like family

We report an extensive Li-Fraumeni-like family in which there is an unusual spectrum of tumours at relatively late onset. A germline TP53 splice donor mutation in exon 4 is present in all affected family members available for testing. The mutation abolishes correct splicing of intron 4 and techniques of RT-PCR have identified three different aberrant transcripts from the mutant TP53 allele. Using the yeast functional assay to analyse transcripts in cells from a number of family members with the mutant allele, TP53 appears wild-type. Functional studies have been carried out on cells from patients with and without cancer who carry the germline mutation, and on cells from unaffected individuals from the same family who do not carry the mutation. Using a number of functional endpoints known to distinguish between cells carrying mutant or wild-type TP53 alleles, we were unable to discriminate normal (wt/wt) from heterozygous (wt/mut) cells by lymphocyte apoptosis and fibroblast survival following low dose rate ionising radiation exposure. However germline mutation carriers show increased sensitivity to radiation-induced chromosome damage in the G2 phase of the cell cycle, and decreased transient and permanent G1 arrest. These studies demonstrate the importance of fully characterising the effects of TP53 germline mutations, and may explain some of the phenotypic features of this family.

Chromosome instability is a predominant trait of fibroblasts from Li-Fraumeni families

Previous work has indicated a role for p53 in cell cycle control, genomic stability and cellular responses to DNA-damaging agents. However, few data are available for human fibroblasts heterozygous for defined germline mutations in TP53. We report studies on 25 strains derived from 12 families with Li-Fraumeni syndrome (LFS) and 18 strains from normal volunteers. The families include three that are classical LFS families, but in whom no TP53 mutation has been found. In the families with mutations, increased longevity and resistance to low-dose-rate ionizing radiation showed a statistically significant association with the presence of TP53 mutations. However, not all heterozygotes had increased longevity or were radioresistant, and fibroblasts from cancer-affected members of LFS families without TP53 mutations showed no significant increase in either of these end points. In contrast, all mutation-carrying strains showed evidence of genomic instability, expressed as aneuploidy, and accumulated structural chromosome aberrations in up to 100% of cells, usually accompanied by loss of the wild-type TP53 allele, immediately before senescence. Levels of aneuploidy higher than in normal cells were also observed in fibroblasts from families without TP53 mutations, suggesting that chromosome instability is a major factor in determining the cancer proneness of these families.

Mapping of 22 new ESTs around a tumor suppressor gene and a senescence gene at 6q16-->q21

Twenty two expressed sequence tags (ESTs) have been mapped at the border of 6q16-->q21 and at the proximal end of 6q21, a candidate for two tumor suppressor genes and a senescence gene. Use of a translocation and deletion hybrid panel together with a 4-Mb YAC contig allowed us to precisely define the position of the ESTs. Thirteen ESTs were placed within the 4-Mb interval at the proximal portion of 6q21 using a restriction map of the YAC contig, seven ESTs span a 2-Mb region on the 6q16-->q21 border, and two are distal to the contig. Refinement of the localization of these ESTs will provide substantial assistance in identifying new genes within the region 6q16-->q21.

Characterization of a 4-Mb region at chromosome 6q21 harboring a replicative senescence gene

A 4-Mb region containing a senescence gene was defined at 6q21 by fluorescence in situ hybridization and deletion mapping after transfer of a normal human chromosome 6 to a BK virus-transformed mouse cell line. By screening three different yeast artificial chromosome (YAC) libraries, a YAC contig was constructed that covers the deleted region at 6q21. The contig is composed of 18 overlapping YACs with a size of 250-1800 kb and contains 3 CpG islands and 10 expressed sequence tags. By sequencing YACs and P1 artificial chromosomes, nine new sequence tagged sites and three new expressed sequence tags were detected that enrich the genetic resources of the region. The contig may also contain a fragile site, FRA6F, located close to a CpG island, which could be a landmark to localize the senescence gene. This YAC contig will be used to detect expressed sequences to clone and characterize the senescence gene at 6q21.

Bioethics for clinicians: 11. Euthanasia and assisted suicide

Euthanasia and assisted suicide involve taking deliberate action to end or assist in ending the life of another person on compassionate grounds. There is considerable disagreement about the acceptability of these acts and about whether they are ethically distinct from decisions to forgo life-sustaining treatment. Euthanasia and assisted suicide are punishable offences under Canadian criminal law, despite increasing public pressure for a more permissive policy. Some Canadian physicians would be willing to practise euthanasia and assisted suicide if these acts were legal. In practice, physicians must differentiate between respecting competent decisions to forgo treatment, providing appropriate palliative care, and acceeding to a request for euthanasia or assisted suicide. Physicians who believe that euthanasia and assisted suicide should be legally accepted in Canada should pursue their convictions only through legal and democratic means.

Analysis of chromosome 6 deletions in lymphoid malignancies provides evidence for a region of minimal deletion within a 2-megabase segment of 6q21

Fluorescence in situ hybridization has been used to define deletion breakpoints within chromosome bands 6q16-21 in cases of lymphoid malignancy. Previous evidence suggested that the region might contain a tumour-suppressor gene. Six yeast artificial chromosome probes, each selected using a single marker, were localized to 6q16-21 and the following order was confirmed; D6S330-D6S283-D6S301-D6S447-D6S246-FYN+ ++. Of 32 cases of lymphoid malignancy, 30 showed deletion of D6S246 and, in the two cases in which D6S246 was retained, the adjacent marker, D6S447, was deleted. These observations imply that a region of minimal deletion is located within a 2-megabase segment of 6q21, between D6S447 and D6S246, providing a candidate region for the location of a tumour-suppressor gene.

Cell cycle arrest defect in Li-Fraumeni Syndrome: a mechanism of cancer predisposition?

Cancer predisposition in approximately 60% of Li-Fraumeni Syndrome (LFS) families is associated with germline mutation of the TP53 gene. The p53 protein has been shown to mediate G1 arrest following DNA damage. We have investigated gamma-irradiation-induced transient and permanent G1 arrest in normal and LFS fibroblasts. The duration of transient G1 arrest varied between strains, but there was no difference in the range between normal (2-12 h) and LFS (1-13 h) cells. However, the extent of permanent G1 arrest was greatly reduced in LFS fibroblasts (mean 33+/-8% of the cell population) compared with normals (mean 67+/-9%) and correlated with their increased radiation survival (r=0.97, P<0.001). This phenotype was observed in LFS fibroblasts both with (seven cases) and without (two cases) TP53 mutation. Parallel studies with fibroblasts derived from cancer-prone, p53-deficient mice revealed no radiation-induced G1 cell cycle arrest in p53 null (-/-) cells. The p53 +/- cells were comparable to the wt p53 cells in transient G1 arrest capacity, but showed a diminished permanent G1 arrest. These data clearly implicate p53 function in permanent G1 arrest. The reduced capacity for DNA damage-induced, permanent G1 arrest in LFS may contribute significantly to cancer predisposition in this familial syndrome.

Fibroblasts from Li-Fraumeni patients are resistant to low dose-rate irradiation

A group of adult skin fibroblast cultures from four individuals representing Li-Fraumeni families with different mutations in the p53 gene were found to be resistant to low dose-rate (0.011 Gy per min) 60Co radiation when compared with a control group of four cultures from normal individuals. The Li-Fraumeni fibroblasts, which could not be distinguished from controls after high dose rate (1.07 Gy per min) irradiation, were shown to be heterozygous (+/mut) at the p53 locus at the time of irradiation.

NMR studies of substrate binding to cytochrome P450 BM3: comparisons to cytochrome P450 cam

The binding of the substrates sodium laurate and sodium 12-bromolaurate to the heme-containing domain of Bacillus megaterium cytochrome P450 BM3 (CYP102) has been studied by measurement of the relaxation effects of the unpaired electrons of the heme iron on the protons of water and of the bound substrates. Substrate binding leads to a conversion of the heme iron from a low-spin to a high-spin state, as shown by changes in the optical spectrum. The relaxation measurements show that this is accompanied by expulsion of water from the sixth coordination position of the iron, the distance between the iron and the water protons increasing from 2.6 to 5.2 A. Corresponding relaxation measurements on the substrate protons lead to the determination of a number of distances between the iron and protons of the bound substrate and, hence, to information on the position and orientation of the substrate in the binding site. Laurate and 12-bromolaurate are found to bind in a very similar way, in an extended conformation with the carboxylate probably close to Arg47 and the other end of the chain 7.6-7.8 A from the heme iron. It is shown that laurate and pyridine can bind simultaneously to the P450 domain and that the iron-laurate distances in this ternary complex are not significantly different from those in the binary complex. These observations are compared with those on the substrate complex of cytochrome P450 cam, and their implications for structural changes involved in the catalytic cycle are discussed.

A radiation hybrid panel for human chromosome 6q

A panel of 63 radiation-reduced hybrids has been derived from a mouse cell line containing a neo-marked human Chromosome (Chr) 6, primarily to provide a resource for higher resolution localization of new markers. Hybrids were generated with radiation doses of 40-400 Gy, selected in G418, and were shown by PCR to contain the neo gene. PCR was also used to score the retention of 15 loci that map from 6q13 to q25.2 of the current consensus map, plus six other loci assigned to 6q26-q27. An average retention frequency of 27.8% was observed, with the highest frequencies at D6S313 and D6S280 (63.5%) located near the centromere at 6q13, and at D6S283 (68.5%) at 6q16.3-q21, presumably close to the neo integration site. Lowest frequencies (4.8%) were observed for telomeric markers. All markers segregated independently except D6S297 and D6S193. Agreement and some improvement to the current consensus map of 6q was made by mapping 12 loci by the non-parametric statistical method of Falk. In addition, deletion mapping with informative hybrids allowed the ordering of six loci from 6q26 to q27 and permitted some integration of maps of this region.

Allelic imbalance of chromosome 6q in ovarian tumours

Previous work has implicated putative tumour-suppressor (ts) genes at 6q27 and a broad region at 6p12-q23. Here we report the results of a coded, randomised study of allelic imbalance at 12 loci on 6q on 40 pairs of coded tumour-blood pairs from patients with ovarian tumours. Our results provide clear evidence for the involvement of different regions of 6q in tumours of different histological subtypes. The involvement in serous tumours of a ts gene at the distal site is confirmed. However, proximal 6q presents a complex picture, with possibly three further ts genes: one at 6q21-23.3 involved at high frequency in benign and endometrioid tumours, another at 6q14-q15, also involved in endometrioid tumours, and a third suggested by a smallest region of deletion at 6q16.3-q21, between D6S275 and D6S300, that appears to be involved in early stage tumours. These observations point the way to a statistical study of the involvement of 6q in tumours of different histological type and staging performed on larger cohorts of samples.

Proximal 6q, a region showing allele loss in primary breast cancer

To define regions of deletion of chromosome 6q in breast cancer, we scored 18 (CA)n microsatellites for allelic imbalance (AI) in 42 paired blood/tumour samples. Heterozygosity frequencies of the markers in the sample population ranged from 31% to 92% (mean 68%). Two regions of the chromosome arm showed AI values greater than the background range of 10-22% (mean 17%) of informative cases that was observed with five markers spanning 6q21-q25.2. Firstly, seven markers gave AI values that averaged 35% in a region flanked by D6S313 (AI = 10%) at 6q13 and D6S283 (AI = 17%) at 6q16.3-21. The second region showed marginally increased AI at 6q25.2-q27 and included D6S193, previously shown to be close to a tumour-suppressor gene involved in ovarian carcinoma. Since AI of 6q in breast cancer was shown previously to be due predominantly to loss of heterozygosity, our results suggest the presence of at least two tumour-suppressor genes on 6q that are involved in breast cancer. The proximal region has not been recognised in breast cancer before and is involved in a higher frequency of tumours than the distal region.

Localization of an epithelial-specific receptor kinase (EDDR1) to chromosome 6q16

A protein receptor tyrosine kinase (EDDR1) has been isolated from a complementary DNA library of SKOV-3, an epithelial ovarian cancer cell line. The primary structure of the predicted amino acid sequence of the protein shows a novel N-terminal region that has homology to a factor VIII-like domain. The C-terminal catalytic domain has all of the canonical sequence motifs of a receptor tyrosine kinase with homology to the TRK-2H protein (49%), which suggests that it is a type II receptor. It is expressed in epithelial cells of several tissues. To determine the chromosomal localization of the gene, somatic cell hybrids were analyzed by PCR amplification using oligonucleotide primers specific for EDDR1. Segregation was observed to a hybrid containing human chromosome 6. Cosmids for EDDR1 were isolated from a human chromosome 6 cosmid library and were shown by fluorescence in situ hybridization to map to 6q16.

Regional assignment by hybrid mapping of 36 expressed sequence tags (ESTs) on human chromosome 6

We have determined the regional chromosome assignment of 36 cDNAs from infant brain libraries by assessing the concordant segregation of PCR products using a human-rodent hybrid mapping panel that subdivides chromosome 6 into 15 regions. These mapped sequences serve as markers for the physical and expression maps of chromosome 6, as well as candidate genes for various disease loci. Sequence analysis has identified putative functions and motifs for some of these genes.

Common region of deletion on the long arm of chromosome 6 in non-Hodgkin's lymphoma and acute lymphoblastic leukaemia

We have used fluorescence in situ hybridisation (FISH) with a series of yeast artificial chromosome (YAC) clones that map to the long arm of chromosome 6 (6q) to define the region(s) of deletion in seven cases of non-Hodgkin's lymphoma (NHL), in which a deletion of 6q had been detected by conventional cytogenetics. The FISH analysis detected two regions of deletion: (i) A proximal region flanked by M6P1 (6q14-15) and FYN (6q21), containing D6S246, which was missing in all seven cases. This locus was also found to be deleted in all six cases of acute lymphoblastic leukaemia (ALL) studied previously. (ii) A second region of 6q, which was distal to 6q23.1 (D6S238) and included ESR (6q25.1) and D6S281 (6q27), which was shown to be present in all our cases of ALL, was found to be deleted in 4 of the 7 cases of NHL. Our results support the suggestion that tumour suppressor genes, involved in the pathogenesis of lymphoid malignancies, may be present within these regions.