Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications

The epitranscriptome embodies many new and largely unexplored functions of RNA. A significant roadblock hindering progress in epitranscriptomics is the identification of more than one modification in individual transcript molecules. We address this with CHEUI (CH3 (methylation) Estimation Using Ionic current). CHEUI predicts N6-methyladenosine (m6A) and 5-methylcytosine (m5C) in individual molecules from the same sample, the stoichiometry at transcript reference sites, and differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals to achieve high single-molecule, transcript-site, and stoichiometry accuracies in multiple tests using synthetic RNA standards and cell line data. CHEUI's capability to identify two modification types in the same sample reveals a co-occurrence of m6A and m5C in individual mRNAs in cell line and tissue transcriptomes. CHEUI provides new avenues to discover and study the function of the epitranscriptome.

Determinants and extent of weight recording in UK primary care: an analysis of 5 million adults' electronic health records from 2000 to 2017

BACKGROUND

Excess weight and unexpected weight loss are associated with multiple disease states and increased morbidity and mortality, but weight measurement is not routine in many primary care settings. The aim of this study was to characterise who has had their weight recorded in UK primary care, how frequently, by whom and in relation to which clinical events, symptoms and diagnoses.

METHODS

A longitudinal analysis of UK primary care electronic health records (EHR) data from 2000 to 2017. Descriptive statistics were used to summarise weight recording in terms of patient sociodemographic characteristics, health professional encounters, clinical events, symptoms and diagnoses. Negative binomial regression was used to model the likelihood of having a weight record each year, and Cox regression to the likelihood of repeated weight recording.

RESULTS

A total of 14,049,871 weight records were identified in the EHR of 4,918,746 patients during the study period, representing 26,998,591 person-years of observation. Around a third of patients had a weight record each year. Forty-nine percent of weight records were repeated within a year with an average time to a repeat weight record of 1.92 years. Weight records were most often taken by nursing staff (38-42%) and GPs (37-39%) as part of a routine clinical care, such as chronic disease reviews (16%), medication reviews (6-8%) and health checks (6-7%), or were associated with consultations for contraception (5-8%), respiratory disease (5%) and obesity (1%). Patient characteristics independently associated with an increased likelihood of weight recording were as follows: female sex, younger and older adults, non-drinkers, ex-smokers, low or high BMI, being more deprived, diagnosed with a greater number of comorbidities and consulting more frequently. The effect of policy-level incentives to record weight did not appear to be sustained after they were removed.

CONCLUSION

Weight recording is not a routine activity in UK primary care. It is recorded for around a third of patients each year and is repeated on average every 2 years for these patients. It is more common in females with higher BMI and in those with comorbidity. Incentive payments and their removal appear to be associated with increases and decreases in weight recording.

Defining, Measuring and Preventing the Diagnosis of Cancer as an Emergency: A Critical Review of Current Evidence

Background: Many patients with cancer are diagnosed through an emergency presentation, which is associated with inferior clinical and patient-reported outcomes compared with those of patients who are diagnosed electively or through screening. Reducing the proportion of patients with cancer who are diagnosed as emergencies is, therefore, desirable; however, the optimal means of achieving this aim are uncertain owing to the involvement of different tumor, patient and health-care factors, often in combination. Methods: We searched the literature to identify all population-based studies that examined emergency presentation as a diagnosis or independent variable. Results: Most relevant evidence relates to patients with colorectal or lung cancer in a few economically developed countries, and defines emergency presentations contextually (that is, whether patients presented to emergency health-care services and/or received emergency treatment shortly before their diagnosis) as opposed to clinically (whether patients presented with life-threatening manifestations of their cancer). Consistent inequalities in the risk of emergency presentations by patient characteristics and cancer type have been described, but limited evidence is available on whether, and how, such presentations can be prevented. Evidence on patients' symptoms and health-care use before presentation as an emergency is sparse. Conclusion: In this review, we describe the extent, causes and implications of a diagnosis of cancer following an emergency presentation, and provide recommendations for public health and health-care interventions, and research efforts aimed at addressing this underresearched aspect of cancer diagnosis.

Variation in 'Fast-Track' Referrals for Suspected Cancer by Patient Characteristic and Cancer Diagnosis: Evidence From 670,000 Patients With Cancers of 35 Different Sites

Background: In England, 'fast-track' (also known as 'two-week wait') general practitioner referrals for suspected cancer in symptomatic patients are used to shorten diagnostic intervals and are supported by clinical guidelines. However, the use of the fast-track pathway may vary for different patient groups. Methods:  We examined data from 669,220 patients with 35 cancers diagnosed 2006-2010 following either fast-track or nonfast track primary-to-secondary care referrals using a bespoke English dataset, the 'Routes to Diagnosis' data. We estimated the proportion of fast-track referrals by sociodemographic characteristics and cancer diagnosis and used logistic regression to estimate respective crude and adjusted odds ratios. We additionally explored whether sociodemographic associations varied by cancer. Results:  There were large variations in the odds of fast-track referral by cancer ( P < 0.001). Patients with testicular and breast cancer were most likely to have been diagnosed after a fast-track referral (adjusted odds ratios 2.73 and 2.35 respectively, using rectal cancer as reference); while patients with brain cancer and leukemias least likely (adjusted odds ratios 0.05 and 0.09 respectively for brain cancer and acute myeloid leukemia). There were sex, age and deprivation differences in the odds of fast-track referral ( P < 0.013), which varied in their size and direction for patients with different cancers ( P < 0.001). For example, fast-track referrals were least likely in younger women with endometrial cancer and in older men with testicular cancer. Conclusion: Fast-track referrals are less likely for cancers characterized by nonspecific presenting symptoms and patients belonging to low incidence demographic strata. Interventions beyond clinical guidelines for “alarm” symptoms are needed to improve diagnostic timeliness.

Timeliness of Presentation and Referral Among Cancer Patients Who Presented With Abdominal Symptoms: Evidence to Inform Symptom Awareness Campaigns

Background: Abdominal symptoms at presentation are common among patients subsequently diagnosed with cancer. While public health education campaigns in England and other countries have traditionally focused on 'red flag' symptoms associated with a single common cancer (e.g., 'blood in poo' and colorectal cancer), there is increasing interest in raising awareness of symptoms grouped by body area or system (eg 'abdominal symptoms'). Evidence regarding the frequency and nature of abdominal symptoms at presentation among a representative cancer patient cohort could inform the design and evaluation of community based cancer symptom awareness campaigns. Aim: To describe the frequency of abdominal symptoms at presentation among an incident cohort of cancer patients, examine variation in diagnostic timeliness and subsequently diagnosed cancer sites by abdominal symptom. Methods: The presenting symptom(s) of 15,956 cancer patients from a national audit of primary care records in England was coded into symptom categories. Eight abdominal symptoms with a range of predictive values and specificity for cancer were studied: abdominal pain, change in bowel habit, bloating/distension, dyspepsia, rectal bleeding, dysphagia, reflux, and nausea/vomiting. We investigated the prevalence of abdominal symptoms among the cancer patient population, examined variation in the length of the patient interval (time from symptom onset to presentation to primary care) and primary care interval (time from presentation to specialist referral) by symptom, and described the associated spectrum of diagnosed cancer sites for each individual symptom. Results: Almost a quarter (23%) of the incident cancer patient population had abdominal symptom(s) at presentation (n=3,661/15,956). The relative lengths of the patient and primary care intervals varied greatly by abdominal symptom. One in two cancer patients who had dysphagia before diagnosis presented 30 days after symptom onset (median (IQR) patient interval: 30 (10-61) days), but were referred immediately (median (IQR) primary care interval: 0 (0-14) days). In comparison, cancer patients who presented with abdominal pain had longer intervals postpresentation (median (IQR) patient interval: 7 (0-28) days, median (IQR) primary care interval: 16 (2-43) days). The majority (88.6%) of cancer patients who presented with an abdominal symptom were diagnosed with an abdominal or adjacent cancer, including colorectal, esophageal, ovarian, and pancreatic cancers. However, the remainder of patients were diagnosed with solid tumors of nonabdominal organ origin (7.6%) or a hematologic cancer (3.8%). Conclusion: Cancer symptom awareness campaigns focusing on abdominal symptoms could contribute to the earlier diagnosis of numerous common and rarer cancers. Evidence regarding the relative lengths of the patient and primary care intervals could be used as a measure of relative need for raising awareness.

Weight loss as a predictor of cancer and serious disease in primary care: an ISAC-approved CPRD protocol for a retrospective cohort study using routinely collected primary care data from the UK

BACKGROUND

Unexpected weight loss is a symptom of serious disease in primary care, for example between 1 in 200 and 1 in 30 patients with unexpected weight loss go on to develop cancer. However, it remains unclear how and when general practitioners (GPs) should investigate unexpected weight loss. Without clarification, GPs may wait too long before referring (choosing to watch and wait and potentially missing a diagnosis) or not long enough (overburdening hospital services and exposing patients to the risks of investigation). The overall aim of this study is to provide the evidence necessary to allow GPs to more effectively manage patients with unexpected weight loss.

METHODS

A retrospective cohort analysis of UK Clinical Practice Research Datalink (CPRD) data to: (1) describe how often in UK primary care the symptom of reported weight loss is coded, when weight is measured, and how GPs respond to a patient attending with unexpected weight loss; (2) identify the predictive value of recorded weight loss for cancer and serious disease in primary care, using cumulative incidence plots to compare outcomes between subgroups and Cox regression to explore and adjust for covariates. Preliminary work in CPRD estimates that weight loss as a symptom is recorded for approximately 148,000 eligible patients > 18 years and is distributed evenly across decades of age, providing adequate statistical power and precision in relation to cancer overall and common cancers individually. Further stratification by cancer stage will be attempted but may not be possible as not all practices within CPRD are eligible for cancer registry linkage, and staging information is often incomplete. The feasibility of using multiple imputation to address missing covariate values will be explored.

DISCUSSION

This will be the largest reported retrospective cohort of primary care patients with weight measurements and unexpected weight loss codes used to understand the association between weight measurement, unexpected weight loss, and serious disease including cancer. Our findings will directly inform international guidelines for the management of unexpected weight loss in primary care populations.

Variation in 'fast-track' referrals for suspected cancer by patient characteristic and cancer diagnosis: evidence from 670 000 patients with cancers of 35 different sites

BACKGROUND

In England, 'fast-track' (also known as 'two-week wait') general practitioner referrals for suspected cancer in symptomatic patients are used to shorten diagnostic intervals and are supported by clinical guidelines. However, the use of the fast-track pathway may vary for different patient groups.

METHODS

We examined data from 669 220 patients with 35 cancers diagnosed in 2006-2010 following either fast-track or 'routine' primary-to-secondary care referrals using 'Routes to Diagnosis' data. We estimated the proportion of fast-track referrals by sociodemographic characteristic and cancer site and used logistic regression to estimate respective crude and adjusted odds ratios. We additionally explored whether sociodemographic associations varied by cancer.

RESULTS

There were large variations in the odds of fast-track referral by cancer (P<0.001). Patients with testicular and breast cancer were most likely to have been diagnosed after a fast-track referral (adjusted odds ratios 2.73 and 2.35, respectively, using rectal cancer as reference); whereas patients with brain cancer and leukaemias least likely (adjusted odds ratios 0.05 and 0.09, respectively, for brain cancer and acute myeloid leukaemia). There were sex, age and deprivation differences in the odds of fast-track referral (P<0.013) that varied in their size and direction for patients with different cancers (P<0.001). For example, fast-track referrals were least likely in younger women with endometrial cancer and in older men with testicular cancer.

CONCLUSIONS

Fast-track referrals are less likely for cancers characterised by nonspecific presenting symptoms and patients belonging to low cancer incidence demographic groups. Interventions beyond clinical guidelines for 'alarm' symptoms are needed to improve diagnostic timeliness.

Evidence of advanced stage colorectal cancer with longer diagnostic intervals: a pooled analysis of seven primary care cohorts comprising 11 720 patients in five countries

Background:

The benefits from expedited diagnosis of symptomatic cancer are uncertain. We aimed to analyse the relationship between stage of colorectal cancer (CRC) and the primary and specialist care components of the diagnostic interval.

Methods:

We identified seven independent data sets from population-based studies in Scotland, England, Canada, Denmark and Spain during 1997–2010 with a total of 11 720 newly diagnosed CRC patients, who had initially presented with symptoms to a primary care physician. Data were extracted from patient records, registries, audits and questionnaires, respectively. Data sets were required to hold information on dates in the diagnostic interval (defined as the time from the first presentation of symptoms in primary care until the date of diagnosis), symptoms at first presentation in primary care, route of referral, gender, age and histologically confirmed stage. We carried out reanalysis of all individual data sets and, using the same method, analysed a pooled individual patient data set.

Results:

The association between intervals and stage was similar in the individual and combined data set. There was a statistically significant convex (∩-shaped) association between primary care interval and diagnosis of advanced (i.e., distant or regional) rather than localised CRC (P=0.004), with odds beginning to increase from the first day on and peaking at 90 days. For specialist care, we saw an opposite and statistically significant concave (∪-shaped) association, with a trough at 60 days, between the interval and diagnosis of advanced CRC (P<0.001).

Conclusions:

This study provides evidence that longer diagnostic intervals are associated with more advanced CRC. Furthermore, the study cannot define a specific ‘safe’ waiting time as the length of the primary care interval appears to have negative impact from day one.

Risk of cervical cancer in symptomatic women aged ≥40 in primary care: A case-control study using electronic records

There are approximately 3,000 new UK diagnoses of cervical cancer annually, with many women presenting symptomatically. We aimed to identify and quantify features of cervical cancer in primary care in a case-control study in the UK. Putative features of cervical cancer were identified, and odd ratios and positive predictive values (PPVs) were calculated. About 1,006 women aged ≥40 years diagnosed with cervical cancer and 4,992 age-, sex- and practice-matched controls were selected from the Clinical Practice Research Datalink. Median age at diagnosis was 61 years (interquartile range 51-75). Seven symptoms and two abnormal investigations were associated with cervical cancer: post-menopausal bleeding, odds ratio 43 (95% confidence interval 25, 75); vaginal discharge or vaginitis 8.8 (5.2, 15), intermenstrual bleeding 4.7 (1.6, 14); haematuria 4.6 (2.1, 10); irregular menstruation 3.8 (1.6, 9.0); urinary tract infection 1.9 (1.3, 2.8); abdominal pain 1.8 (1.4, 2.5); high white cell count 5.1 (2.9, 8.8) and low haemoglobin 2.6 (1.8, 3.8): all p < .005. The PPV of cervical cancer in women aged ≥55 with post-menopausal bleeding was 4.6% (2.5, 8.3). Other than for post-menopausal bleeding no symptom is high risk. Some symptoms, particularly haematuria, may be helpful. The primary care clinician must consider the unlikely diagnosis when the likely diagnosis does not settle with treatment.

Evaluating cytology for the detection of invasive cervical cancer

OBJECTIVE

To assess the sensitivity, the number needed to screen (NNS) and the positive predictive value (PPV) of cervical cytology for the diagnosis of cancer by age in a screening population.

METHODS

A retrospective cohort of women with invasive cervical cancer nested within a census of cervical cytology. All (c. 8 million) women aged 20-64 years with cervical cytology (excluding tests after an earlier abnormality). From April 2007 to March 2010, 3372 women had cervical cancer diagnosed within 12 months of such cytology in England. The sensitivity of cervical cytology to cancer, NNS to detect one cancer and predictive values of cytology were calculated for various 'referral' thresholds. These were calculated for ages 20-24, 25-34, 35-49 and 50-64 years.

RESULTS

The sensitivity of at least moderate dyskaryosis [equivalent to a high-grade squamous intraepithelial lesion (HSIL) or worse] for cancer of 89.4% [95% confidence interval (CI) 88.3-90.4%] in women offered screening was independent of age. At all ages, women with borderline-early recall or mild dyskaryosis on cytology (equivalent to ASC-US and LSIL, respectively, in the Bethesda system) had a similar risk of cervical cancer to the risk in all women tested. The PPV of severe dyskaryosis/?invasive and ?glandular neoplasia cytology (equivalent to squamous cell carcinoma and adenocarcinoma/adenocarcinoma in situ, respectively, in the Bethesda System) were 34% and 12%, respectively; the PPV of severe dyskaryosis (HSIL: severe dysplasia) was 4%. The NNS was lowest when the incidence of cervical cancer was highest, at ages 25-39 years, but the proportion of those with abnormal cytology who have cancer was also lowest in younger women.

CONCLUSIONS

The PPV of at least severe dyskaryosis (HSIL: severe dysplasia) for cancer was 4-10% of women aged 25-64 years, justifying a 2-week referral to colposcopy and demonstrating the importance of failsafe monitoring for such patients. The sensitivity of cytology for cervical cancer was excellent across all age groups.

Symptom appraisal and healthcare-seeking for symptoms suggestive of colorectal cancer: a qualitative study

OBJECTIVES

Timely diagnosis of colorectal cancer is important to improve survival. This study explored symptom appraisal and help-seeking among patients referred to specialist services with symptoms of colorectal cancer.

DESIGN

Qualitative in-depth interview study.

SETTING AND PARTICIPANTS

Participants were recruited on referral to gastroenterology clinics (North East and East of England); interviews were conducted soon after referral. We purposively sampled participants to ensure a range of accounts in terms of age, sex, diagnosis and geographical location.

METHODS

Data collection and analysis were underpinned by the Model of Pathways to Treatment. Framework analysis was used to explore the data within and across cases, focusing on patient beliefs and experiences, disease factors and healthcare influences.

RESULTS

40 participants were interviewed (aged 43-87 years, 17 women, 18 diagnosed with colorectal cancer). Patients diagnosed with and without colorectal cancer had similar symptom pathways. We found a range of interacting and often competing biopsychosocial, contextual and cultural influences on the way in which people recognised, interpreted and acted on their symptoms. People attempted to 'maintain normality' through finding benign explanations for their symptoms. Bodily changes were appraised within the context of usual bowel patterns, comorbidities and life events, and decisions to seek help were made in relation to expectations about the course of symptoms. The 'private nature' of colorectal cancer symptoms could affect both their identification and discussions with others including healthcare professionals. Within the context of the National Health Service, people needed to legitimise appropriate use of healthcare services and avoid being thought of as wasting doctors' time.

CONCLUSIONS

Findings provide guidance for awareness campaigns on reducing stigma around appraising and discussing bowel movements, and the importance of intermittent and non-specific symptoms. Altering perceptions about the appropriate use of health services could have a beneficial effect on time to presentation.

Symptoms and other factors associated with time to diagnosis and stage of lung cancer: a prospective cohort study

BACKGROUND

This prospective cohort study aimed to identify symptom and patient factors that influence time to lung cancer diagnosis and stage at diagnosis.

METHODS

Data relating to symptoms were collected from patients upon referral with symptoms suspicious of lung cancer in two English regions; we also examined primary care and hospital records for diagnostic routes and diagnoses. Descriptive and regression analyses were used to investigate associations between symptoms and patient factors with diagnostic intervals and stage.

RESULTS

Among 963 participants, 15.9% were diagnosed with primary lung cancer, 5.9% with other thoracic malignancies and 78.2% with non-malignant conditions. Only half the cohort had an isolated first symptom (475, 49.3%); synchronous first symptoms were common. Haemoptysis, reported by 21.6% of cases, was the only initial symptom associated with cancer. Diagnostic intervals were shorter for cancer than non-cancer diagnoses (91 vs 124 days, P=0.037) and for late-stage than early-stage cancer (106 vs 168 days, P=0.02). Chest/shoulder pain was the only first symptom with a shorter diagnostic interval for cancer compared with non-cancer diagnoses (P=0.003).

CONCLUSIONS

Haemoptysis is the strongest symptom predictor of lung cancer but occurs in only a fifth of patients. Programmes for expediting earlier diagnosis need to focus on multiple symptoms and their evolution.

Is increased time to diagnosis and treatment in symptomatic cancer associated with poorer outcomes? Systematic review

BACKGROUND

It is unclear whether more timely cancer diagnosis brings favourable outcomes, with much of the previous evidence, in some cancers, being equivocal. We set out to determine whether there is an association between time to diagnosis, treatment and clinical outcomes, across all cancers for symptomatic presentations.

METHODS

Systematic review of the literature and narrative synthesis.

RESULTS

We included 177 articles reporting 209 studies. These studies varied in study design, the time intervals assessed and the outcomes reported. Study quality was variable, with a small number of higher-quality studies. Heterogeneity precluded definitive findings. The cancers with more reports of an association between shorter times to diagnosis and more favourable outcomes were breast, colorectal, head and neck, testicular and melanoma.

CONCLUSIONS

This is the first review encompassing many cancer types, and we have demonstrated those cancers in which more evidence of an association between shorter times to diagnosis and more favourable outcomes exists, and where it is lacking. We believe that it is reasonable to assume that efforts to expedite the diagnosis of symptomatic cancer are likely to have benefits for patients in terms of improved survival, earlier-stage diagnosis and improved quality of life, although these benefits vary between cancers.

Search for gravitational waves associated with γ-ray bursts detected by the interplanetary network

We present the results of a search for gravitational waves associated with 223 γ-ray bursts (GRBs) detected by the InterPlanetary Network (IPN) in 2005-2010 during LIGO's fifth and sixth science runs and Virgo's first, second, and third science runs. The IPN satellites provide accurate times of the bursts and sky localizations that vary significantly from degree scale to hundreds of square degrees. We search for both a well-modeled binary coalescence signal, the favored progenitor model for short GRBs, and for generic, unmodeled gravitational wave bursts. Both searches use the event time and sky localization to improve the gravitational wave search sensitivity as compared to corresponding all-time, all-sky searches. We find no evidence of a gravitational wave signal associated with any of the IPN GRBs in the sample, nor do we find evidence for a population of weak gravitational wave signals associated with the GRBs. For all IPN-detected GRBs, for which a sufficient duration of quality gravitational wave data are available, we place lower bounds on the distance to the source in accordance with an optimistic assumption of gravitational wave emission energy of 10(-2)M⊙c(2) at 150 Hz, and find a median of 13 Mpc. For the 27 short-hard GRBs we place 90% confidence exclusion distances to two source models: a binary neutron star coalescence, with a median distance of 12 Mpc, or the coalescence of a neutron star and black hole, with a median distance of 22 Mpc. Finally, we combine this search with previously published results to provide a population statement for GRB searches in first-generation LIGO and Virgo gravitational wave detectors and a resulting examination of prospects for the advanced gravitational wave detectors.

Search for gravitational waves associated with γ-ray bursts detected by the interplanetary network

We present the results of a search for gravitational waves associated with 223 γ-ray bursts (GRBs) detected by the InterPlanetary Network (IPN) in 2005-2010 during LIGO's fifth and sixth science runs and Virgo's first, second, and third science runs. The IPN satellites provide accurate times of the bursts and sky localizations that vary significantly from degree scale to hundreds of square degrees. We search for both a well-modeled binary coalescence signal, the favored progenitor model for short GRBs, and for generic, unmodeled gravitational wave bursts. Both searches use the event time and sky localization to improve the gravitational wave search sensitivity as compared to corresponding all-time, all-sky searches. We find no evidence of a gravitational wave signal associated with any of the IPN GRBs in the sample, nor do we find evidence for a population of weak gravitational wave signals associated with the GRBs. For all IPN-detected GRBs, for which a sufficient duration of quality gravitational wave data are available, we place lower bounds on the distance to the source in accordance with an optimistic assumption of gravitational wave emission energy of 10(-2)M⊙c(2) at 150 Hz, and find a median of 13 Mpc. For the 27 short-hard GRBs we place 90% confidence exclusion distances to two source models: a binary neutron star coalescence, with a median distance of 12 Mpc, or the coalescence of a neutron star and black hole, with a median distance of 22 Mpc. Finally, we combine this search with previously published results to provide a population statement for GRB searches in first-generation LIGO and Virgo gravitational wave detectors and a resulting examination of prospects for the advanced gravitational wave detectors.

Features of cancer in teenagers and young adults in primary care: a population-based nested case-control study

BACKGROUND

Teenagers and young adults (TYA, 15-24 years) diagnosed with cancer report repeated visits to primary care before referral. We investigated associations of symptoms and consultation frequency in primary care with TYA cancers.

METHODS

Population-based, case-control study was carried out using data from the Clinical Practice Research Datalink (CPRD). A total of 1064 TYA diagnosed with cancer were matched to 13,206 controls. Symptoms independently associated with specific cancers were identified. Likelihood ratios (LRs) and positive predictive values (PPVs) were calculated.

RESULTS

In the 3 months before diagnosis, 397 (42.9%) cases consulted > or =4 times vs 593(11.5%) controls (odds ratio (OR): 12.1; 95% CI: 9.7, 15.1), yielding a PPV for any cancer of 0.018%. The LR of lymphoma with a head/neck mass was 434 (95% CI: 60, 3158), with a PPV of 0.5%. Corresponding figures in other cancers included - LR of leukaemia with lymphadenopathy (any site): 29 (95% CI: 8, 112), PPV 0.015%; LR of CNS tumour with seizure: 56 (95% CI: 19, 163), PPV 0.024%; and LR of sarcoma with lump/mass/swelling: 79 (95% CI: 24, 264), PPV 0.042%.

CONCLUSION

Teenagers and young adults with cancer consulted more frequently than controls in the 3 months before diagnosis. Primary care features of cancer match secondary care reports, but were of very low risk; nonetheless, some features increased the likelihood of cancer substantially and should be taken seriously when assessing TYA.

The risk of oesophago-gastric cancer in symptomatic patients in primary care: a large case-control study using electronic records

Background:

Over 15 000 new oesophago-gastric cancers are diagnosed annually in the United Kingdom, with most being advanced disease. We identified and quantified features of this cancer in primary care.

Methods:

Case–control study using electronic primary-care records of the UK patients aged ⩾40 years was performed. Cases with primary oesophago-gastric cancer were matched to controls on age, sex and practice. Putative features of cancer were identified in the year before diagnosis. Odds ratios (ORs) were calculated for these features using conditional logistic regression, and positive predictive values (PPVs) were calculated.

Results:

A total of 7471 cases and 32 877 controls were studied. Sixteen features were independently associated with oesophago-gastric cancer (all P<0.001): dysphagia, OR 139 (95% confidence interval 112–173); reflux, 5.7 (4.8–6.8); abdominal pain, 2.6 (2.3–3.0); epigastric pain, 8.8 (7.0–11.0); dyspepsia, 6 (5.1–7.1); nausea and/or vomiting, 4.9 (4.0–6.0); constipation, 1.5 (1.2–1.7); chest pain, 1.6 (1.4–1.9); weight loss, 8.9 (7.1–11.2); thrombocytosis, 2.4 (2.0–2.9); low haemoglobin, 2.4 (2.1–2.7); low MCV, 5.2 (4.2–6.4); high inflammatory markers, 1.7 (1.4–2.0); raised hepatic enzymes, 1.3 (1.2–1.5); high white cell count, 1.4 (1.2–1.7); and high cholesterol, 0.8 (0.7–0.8). The only PPV >5% in patients ⩾55 years was for dysphagia. In patients <55 years, all PPVs were <1%.

Conclusion:

Symptoms of oesophago-gastric cancer reported in secondary care were also important in primary care. The results should inform guidance and commissioning policy for upper GI endoscopy.

The Aarhus statement: improving design and reporting of studies on early cancer diagnosis

Early diagnosis is a key factor in improving the outcomes of cancer patients. A greater understanding of the pre-diagnostic patient pathways is vital yet, at present, research in this field lacks consistent definitions and methods. As a consequence much early diagnosis research is difficult to interpret. A consensus group was formed with the aim of producing guidance and a checklist for early cancer-diagnosis researchers. A consensus conference approach combined with nominal group techniques was used. The work was supported by a systematic review of early diagnosis literature, focussing on existing instruments used to measure time points and intervals in early cancer-diagnosis research. A series of recommendations for definitions and methodological approaches is presented. This is complemented by a checklist that early diagnosis researchers can use when designing and conducting studies in this field. The Aarhus checklist is a resource for early cancer-diagnosis research that should promote greater precision and transparency in both definitions and methods. Further work will examine whether the checklist can be readily adopted by researchers, and feedback on the guidance will be used in future updates.

Features of childhood cancer in primary care: a population-based nested case-control study

BACKGROUND

This study investigated the risk of cancer in children with alert symptoms identified in current UK guidance, or with increased consultation frequency in primary care.

METHODS

A population-based, nested case-control study used data from the General Practice Research Database. In all, 1267 children age 0-14 years diagnosed with childhood cancer were matched to 15,318 controls. Likelihood ratios and positive predictive values (PPVs) were calculated to assess risk.

RESULTS

Alert symptoms recorded in the 12 and 3 months before diagnosis were present in 33.7% and 27.0% of cases vs 5.4% and 1.4% of controls, respectively. The PPV of having cancer for any alert symptom in the 3 months before diagnosis was 0.55 per 1000 children. Cases consulted more frequently particularly in the 3 months before diagnosis (86% cases vs 41% controls). Of these, 36% of cases and 9% of controls had consulted 4 times or more. The PPV for cancer in a child consulting 4 times or more in 3 months was 0.13 per 1000 children.

CONCLUSION

Alert symptoms and frequent consultations are associated with childhood cancer. However, individual symptoms and consultation patterns have very low PPVs for cancer in primary care (e.g., of 10,000 children with a recorded alert symptom, approximately 6 would be diagnosed with cancer within 3 months).

An estimation of the worldwide economic and health burden of visual impairment

This study aims to provide a rigorous estimate of the worldwide costs of visual impairment (VI), and the associated health burden. The study used a prevalence-based model. Prevalence rates for mild VI (visual acuity (VA) worse than 6/12 but not worse than 6/18), moderate VI (VA worse than 6/18 but not worse than 6/60) and blindness (VA worse than 6/60) were applied to population forecasts for each World Health Organisation (WHO) subregion. The limited available country cost data were extrapolated between subregions using economic and population health indicators. Age and gender subgroup population numbers were derived from United Nations' data. Costs and the health burden of VI were estimated for each world subregion using published disease prevalence rates, health care expenditures and other economic data. The study includes direct health care costs, indirect costs and the health burden of VI. The total cost of VI globally was estimated at $3 trillion in 2010, of which $2.3 trillion was direct health costs. This burden is projected to increase by approximately 20% by 2020. VI is associated with a considerable disease burden. Unless steps are taken to reduce prevalence through prevention and treatment, this burden will increase alongside global population growth.

Time to diagnosis and mortality in colorectal cancer: a cohort study in primary care

Background:

The relationship between the diagnostic interval and mortality from colorectal cancer (CRC) is unclear. This association was examined by taking account of important confounding factors at the time of first presentation of symptoms in primary care.

Methods:

A total of 268 patients with CRC were included in a prospective, population-based study in a Danish county. The diagnostic interval was defined as the time from first presentation of symptoms until diagnosis. We analysed patients separately according to the general practitioner's interpretation of symptoms. Logistic regression was used to estimate 3-year mortality odds ratios as a function of the diagnostic interval using restricted cubic splines and adjusting for tumour site, comorbidity, age, and sex.

Results:

In patients presenting with symptoms suggestive of cancer or any other serious illness, the risk of dying within 3 years decreased with diagnostic intervals up to 5 weeks and then increased (P=0.002). In patients presenting with vague symptoms, the association was reverse, although not statistically significant.

Conclusion:

Detecting cancer in primary care is two sided: aimed at expediting ill patients while preventing healthy people from going to hospital. This likely explains the counterintuitive findings; but it does not explain the increasing mortality with longer diagnostic intervals. Thus, this study provides evidence for the hypothesis that the length of the diagnostic interval affects mortality in CRC patients.

Pathways to the diagnosis of ovarian cancer in the UK: a cohort study in primary care

OBJECTIVE

To identify the routes patients with ovarian cancer take between first symptom presentation and diagnosis.

DESIGN

Cohort study.

SETTING

The study took place in 39 general practices in Devon, UK.

POPULATION

All ovarian cancer patients identified in the practices, with a diagnosis between 2000 and 2007 inclusive.

METHODS

All patients had their cancer symptoms, referrals, and diagnoses identified and dated using their doctors' records.

MAIN OUTCOME MEASURES

Numbers of patients taking specific routes to diagnosis, together with the time taken to diagnosis.

RESULTS

Three main routes to diagnosis emerged. The first was the expected route of outpatient referral: 195 (92% of the total) had at least one of the seven ovarian cancer symptoms or an abdominal mass. A total of 123 (58%) were referred to a specialist, although only 65 (31%) were referred to a gynaecologist. Thirty-five (17%) were initially investigated within primary care by ultrasound scanning, and a further 35 (17%) were admitted as emergencies. The interval from first symptom to referral was similar across the different pathways, with a median (interquartile range) time between the first symptom presenting to primary care and first investigation or referral being 2.5 (0, 27.5) days. The median interval from first symptom reported in primary care to diagnosis was 74.5 (32, 159) days.

CONCLUSIONS

Only a minority of ovarian cancer patients follow the expected route to diagnosis, of urgent referral to a gynaecologist. In most women, GPs rapidly identified the need to investigate. Avoidable delays generally occurred after the decision to investigate was made.

What happens to new-onset headache in children that present to primary care? A case-cohort study using electronic primary care records

The aim was to describe the consulting behaviour and clinical outcomes of children presenting with headache in primary care. This was a historical cohort study using data from the UK General Practitioner Research Database. Cases were children aged 5-17 years who presented to primary care with primary headache (migraine, tension-type headache, cluster headache) or undifferentiated headache (no further descriptor). Controls were age, sex and practice matched. Their records were examined for consultations, referrals, relevant treatments and specific diseases in the subsequent year. Children with headache (n = 48 575) were identified and matched to controls. At presentation, 9321 (19.2%) of headaches were labelled primary, 549 (1.1%) secondary and 38 705 (79.7%) received no formal diagnosis. Of the latter group, 2084 (5.4%) received a primary headache diagnosis in the subsequent year. Following a diagnosis of migraine, 258 (3.5%) had received a triptan and 1598 (21%) were using propranolol or pizotifen. Total consultations were higher in cases than in controls in the year before the headache: cases ages 5-8 years, mean (s.d.) 5.0 (4.0) consultations; controls 4.0 (3.5) consultations. In 1 year controls had 43 430 consultations, of which 256 (0.6%) were for headache, of whom 64 (25%) were referred to secondary care. Headache was a risk factor for benign and malignant tumours, cerebrovascular disease, primary disorders of raised intracranial pressure and depression. This risk was reduced if a diagnosis of a primary headache disorder could be made. Although there is an increased likelihood of a serious pathology with headache presentations, the risk is small particularly if a diagnosis of a primary headache is made. General practitioners are likely to be underdiagnosing migraine. This study can inform management guidelines for new presentations of headache in primary care, particularly when a secondary pathology is suspected.

The CAPER studies: five case-control studies aimed at identifying and quantifying the risk of cancer in symptomatic primary care patients

Background:

This paper reviews the background to five primary care case-control studies, collectively known as the CAPER studies (Cancer Prediction in Exeter). These studies, on colorectal, lung, prostate and brain tumours, sought to identify the particular features of cancer as reported to primary care. They also sought to quantify the risk of cancer for symptoms and primary care investigations, both individually and paired together.

Methods:

Two studies were on colorectal cancer: the former with 349 cases used hand searching and coding of entries, while the latter obtained 6442 cases from a national electronic database. The lung and prostate studies had 247 and 217 cases, respectively, and used manual methods. The brain study also used a national electronic database, which provided 3505 cases.

Results:

Generally, the symptoms matched previous series from secondary care, though the risks of cancer, expressed as positive predictive values, were lower. Rectal bleeding in colorectal cancer, and haemoptysis in lung cancer both had positive predictive values of 2.4%. The risk of a brain tumour with headache was one in a thousand.

Interpretation:

The results identify areas where current guidance on urgent referral for investigation of suspected cancer could be improved.

What happens to new-onset headache presented to primary care? A case-cohort study using electronic primary care records

In the UK, 4% of general practitioner consultations are for headache, yet the natural history of these presentations is unknown. The objective of this study was to describe the outcome of new headache presentations to the general practitioner. This was a prospective case-control study in adults over a period of 1 year using data from the General Practitioner Research Database, UK. Records of patients who presented with primary headache (migraine, tension-type headache, cluster headache) or undifferentiated headache (no further descriptor) were examined for the subsequent year for subarachnoid haemorrhage, primary brain tumour, benign space-occupying lesion, temporal arteritis, stroke and transient ischaemic attack. We identified 21,758 primary headaches and 63,921 undifferentiated headaches. The likelihood ratio was 29 (9.9, 92) for a subarachnoid haemorrhage after an undifferentiated headache and increased with age. The 1-year risk of a malignant brain tumour with new undifferentiated headache was 0.15%, rising to 0.28% above the age of 50 years. For primary headache the risk was 0.045%. The risk for a benign space-occupying lesion was 0.05% for an undifferentiated and 0.009% for a primary headache. The risk of temporal arteritis was the highest of the conditions studied, 0.66% in the undifferentiated and 0.18% in the primary headache group. Accepting the limitations of this approach, our data can inform management guidelines for new presentations of headache in primary care and confirm the need for follow-up, even if a primary headache diagnosis is made.

The risk of gallbladder cancer from polyps in a large multiethnic series

BACKGROUND

The aim of this study is assess whether patients with Indian ethnic background are at an increased risk of developing gallbladder cancer (GBC) if they have been diagnosed with ultrasonic abnormalities of the gallbladder.

METHODS

Between January 1998 and July 2006, 137,655 abdominal ultrasound examinations were performed in Leeds Teaching Hospitals NHS Trust. After the exclusion of repeat scans and those performed for renal or pelvic disease, 71,431 reports were included in this analysis. Patients in whom the diagnosis of GBC has been made without histology have been identified from the database of Northern and Yorkshire Cancer Registry and the presence of GBC was correlated with ultrasonic gallbladder abnormalities.

RESULTS

Gallbladder polyps (GBP) were detected in 3.3% of patients and these were larger than 10 mm in 0.1% of the cases. Age above 60 years, Indian ethnic background, single GBP larger than 10mm, the presence of gallstones, severe gallbladder wall thickening and irregular thickening were independently associated with the higher odds of developing GBC. The prevalence of malignancy in those with GBP was significantly higher among patients with Indian ethnic background compared to Caucasian patients, 5.5% versus 0.08%, p<0.001.

CONCLUSIONS

The presence of GBP, irrelevant of size, amongst patients of Indian ethnic decent, is an indication for further investigation and/or cholecystectomy.

The importance of anaemia in diagnosing colorectal cancer: a case-control study using electronic primary care records

Although anaemia is recognised as a feature of colorectal cancer, the precise risk is unknown. We performed a case–control study using electronic primary care records from the Health Improvement Network database, UK. A total of 6442 patients had a diagnosis of colorectal cancer, and were matched to 45 066 controls on age, sex, and practice. We calculated likelihood ratios and positive predictive values for colorectal cancer in both sexes across 1 g dl⁻¹ haemoglobin and 10-year age bands, and examined the features of iron deficiency.In men, 178 (5.2%) of 3421 cases and 47 (0.2%) of 23 928 controls had a haemoglobin <9.0 g dl⁻¹, giving a likelihood ratio (95% confidence interval) of 27 (19, 36). In women, the corresponding figures were 227 (7.5%) of 3021 cases and 58 (0.3%) of 21 138 controls, a likelihood ratio of 41 (30, 61). Positive predictive values increased with age and for each 1 g dl⁻¹ reduction in haemoglobin. The risk of cancer for current referral guidance was quantified. For men over 60 years with a haemoglobin <11 g dl⁻¹ and features of iron deficiency, the positive predictive value was 13.3% (9.7, 18) and for women with a haemoglobin <10 g dl⁻¹ and iron deficiency, the positive predictive value was 7.7% (5.7, 11). Current guidance for urgent investigation of anaemia misses some patients with a moderate risk of cancer, particularly men.

Offspring birthweight is not associated with paternal insulin resistance

AIMS/HYPOTHESIS

Low birthweight is associated with insulin resistance and other insulin resistance-related phenotypes: diabetes, hypertension, and vascular disease in later life. The underlying mechanism is unclear. The foetal insulin hypothesis proposes that a single genetic predisposition to beta cell dysfunction/insulin resistance results in both reduced insulin-dependent foetal growth in utero, hence low birthweight, and predisposition to type 2 diabetes. The aim of this study was to test whether, as predicted by the foetal insulin hypothesis, there is an association between measures of paternal insulin resistance and offspring birthweight.

SUBJECTS AND METHODS

The Exeter Family Study of Childhood Health (EFSOCH) is a community-based study within central Exeter (UK), established to test the foetal insulin hypothesis prospectively. Associations were tested between offspring birthweight and paternal insulin resistance, calculated by homeostasis model assessment analysis in 986 families using data relating to singleton, non-diabetic, UK white pregnancies. Ethics approval was given by the North and East Devon local ethics committee.

RESULTS

Offspring birthweight was not significantly correlated with log paternal insulin resistance (r=0, p=0.91), log HDL cholesterol concentration (r=-0.02, p=0.47) or log triglyceride concentration (r=0, p=0.99) when corrected for paternal BMI and common confounders. Multiple linear regression analysis confirmed that paternal insulin resistance was not an independent predictor of offspring birthweight.

CONCLUSIONS/INTERPRETATION

Results from a young, adult, non-diabetic population do not support the foetal insulin hypothesis as an explanation for the association of low birthweight with insulin resistance.

The mortality of colorectal cancer in relation to the initial symptom at presentation to primary care and to the duration of symptoms: a cohort study using medical records

The association between the staging of colorectal cancer and mortality is well known. Much less researched is the relationship between the duration of symptoms and outcome, and whether particular initial symptoms carry a different prognosis. We performed a cohort study of 349 patients with primary colorectal cancer in whom all their prediagnostic symptoms and investigation results were known. Survival data for 3–8 years after diagnosis were taken from the cancer registry. Six features were studied: rectal bleeding, abdominal pain, diarrhoea, constipation, weight loss, and anaemia. Two of these were significantly associated with different staging and mortality. Rectal bleeding as an initial symptom was associated with less advanced staging (odds ratio from one Duke's stage to the next 0.50, 95% confidence interval 0.31, 0.79; P=0.003) and with reduced mortality (Cox's proportional hazard ratio (HR) 0.56 (0.41, 0.79); P=0.001. Mild anaemia, with a haemoglobin of 10.0–12.9 g dl⁻¹, was associated with more advanced staging (odds ratio 2.2 (1.2, 4.3); P=0.021) and worse mortality (HR 1.5 (0.98, 2.3): P=0.064). When corrected for emergency admission, sex, and the site of the tumour, the HR for mild anaemia was 1.7 (1.1, 2.6); P=0.015. No relationship was found between the duration of symptoms and staging or mortality.

What are the clinical features of lung cancer before the diagnosis is made? A population based case-control study

BACKGROUND

Over 38,000 new cases of lung cancer occur each year in the UK. Most are diagnosed after initial presentation to primary care, but the relative importance of the various clinical features is largely unknown.

METHODS

A population based case-control study was undertaken in all 21 general practices in Exeter, Devon, UK (population 128 700). 247 primary lung cancers were studied in subjects aged over 40 years diagnosed between 1998 and 2002 and 1235 controls matched by age, sex and general practice. The entire primary care record for 2 years before diagnosis was coded using the International Classification of Primary Care-2. Univariable and multivariable conditional logistic regression analyses were used to identify and quantify clinical features independently associated with lung cancer. The main outcome measures were odds ratios and positive predictive values for these variables.

RESULTS

Seven symptoms (haemoptysis, loss of weight, loss of appetite, dyspnoea, thoracic pain, fatigue and cough), one physical sign (finger clubbing), and two abnormal investigation results (thrombocytosis and abnormal spirometry) were associated with lung cancer in multivariable analyses, as was cigarette smoking. After excluding variables reported in the final 180 days before diagnosis, haemoptysis, dyspnoea and abnormal spirometry remained independently associated with cancer.

CONCLUSIONS

This study provides an evidence base for selection of patients for investigation of possible lung cancer, both for clinicians and for developers of guidelines.

Clinical features of colorectal cancer before diagnosis: a population-based case-control study

Most colorectal cancers are diagnosed after the onset of symptoms. However, the risk of colorectal cancer posed by particular symptoms is largely unknown, especially in unselected populations like primary care. This was a population-based case–control study in all 21 general practices in Exeter, Devon, UK, aiming to identify and quantify the prediagnostic features of colorectal cancer. In total, 349 patients with colorectal cancer, aged 40 years or more, and 1744 controls, matched by age, sex and general practice, were studied. The full medical record for 2 years before diagnosis was coded using the International Classification of Primary Care-2. We calculated odds ratios for variables independently associated with cancer, using multivariable conditional logistic regressions, and then calculated the positive predictive values of these variables, both individually and in combination. In total, 10 features were associated with colorectal cancer before diagnosis. The positive predictive values (95% confidence interval) of these were rectal bleeding 2.4% (1.9, 3.2); weight loss 1.2% (0.91, 1.6); abdominal pain 1.1% (0.86, 1.3); diarrhoea 0.94% (0.73, 1.1); constipation 0.42% (0.34, 0.52); abnormal rectal examination 4.0% (2.4, 7.4); abdominal tenderness 1.1% (0.77, 1.5); haemoglobin <10.0 g dl⁻¹ 2.3% (1.6, 3.1); positive faecal occult bloods 7.1% (5.1, 10); blood glucose>10 mmol l⁻¹ 0.78% (0.51, 1.1): all P<0.001. Earlier diagnosis of colorectal cancer may be possible using the predictive values for single or multiple symptoms, physical signs or test results.