Molecular Genetic Characteristics of FANCI, a Proposed New Ovarian Cancer Predisposing Gene

FANCI was recently identified as a new candidate ovarian cancer (OC)-predisposing gene from the genetic analysis of carriers of FANCI c.1813C>T; p.L605F in OC families. Here, we aimed to investigate the molecular genetic characteristics of FANCI, as they have not been described in the context of cancer. We first investigated the germline genetic landscape of two sisters with OC from the discovery FANCI c.1813C>T; p.L605F family (F1528) to re-affirm the plausibility of this candidate. As we did not find other conclusive candidates, we then performed a candidate gene approach to identify other candidate variants in genes involved in the FANCI protein interactome in OC families negative for pathogenic variants in BRCA1, BRCA2, BRIP1, RAD51C, RAD51D, and FANCI, which identified four candidate variants. We then investigated FANCI in high-grade serous ovarian carcinoma (HGSC) from FANCI c.1813C>T carriers and found evidence of loss of the wild-type allele in tumour DNA from some of these cases. The somatic genetic landscape of OC tumours from FANCI c.1813C>T carriers was investigated for mutations in selected genes, copy number alterations, and mutational signatures, which determined that the profiles of tumours from carriers were characteristic of features exhibited by HGSC cases. As other OC-predisposing genes such as BRCA1 and BRCA2 are known to increase the risk of other cancers including breast cancer, we investigated the carrier frequency of germline FANCI c.1813C>T in various cancer types and found overall more carriers among cancer cases compared to cancer-free controls (p = 0.007). In these different tumour types, we also identified a spectrum of somatic variants in FANCI that were not restricted to any specific region within the gene. Collectively, these findings expand on the characteristics described for OC cases carrying FANCI c.1813C>T; p.L605F and suggest the possible involvement of FANCI in other cancer types at the germline and/or somatic level.

Genetic analyses of DNA repair pathway associated genes implicate new candidate cancer predisposing genes in ancestrally defined ovarian cancer cases

Not all familial ovarian cancer (OC) cases are explained by pathogenic germline variants in known risk genes. A candidate gene approach involving DNA repair pathway genes was applied to identify rare recurring pathogenic variants in familial OC cases not associated with known OC risk genes from a population exhibiting genetic drift. Whole exome sequencing (WES) data of 15 OC cases from 13 families tested negative for pathogenic variants in known OC risk genes were investigated for candidate variants in 468 DNA repair pathway genes. Filtering and prioritization criteria were applied to WES data to select top candidates for further analyses. Candidates were genotyped in ancestry defined study groups of 214 familial and 998 sporadic OC or breast cancer (BC) cases and 1025 population-matched controls and screened for additional carriers in 605 population-matched OC cases. The candidate genes were also analyzed in WES data from 937 familial or sporadic OC cases of diverse ancestries. Top candidate variants in ERCC5, EXO1, FANCC, NEIL1 and NTHL1 were identified in 5/13 (39%) OC families. Collectively, candidate variants were identified in 7/435 (1.6%) sporadic OC cases and 1/566 (0.2%) sporadic BC cases versus 1/1025 (0.1%) controls. Additional carriers were identified in 6/605 (0.9%) OC cases. Tumour DNA from ERCC5, NEIL1 and NTHL1 variant carriers exhibited loss of the wild-type allele. Carriers of various candidate variants in these genes were identified in 31/937 (3.3%) OC cases of diverse ancestries versus 0-0.004% in cancer-free controls. The strategy of applying a candidate gene approach in a population exhibiting genetic drift identified new candidate OC predisposition variants in DNA repair pathway genes.

A functionally impaired missense variant identified in French Canadian families implicates FANCI as a candidate ovarian cancer-predisposing gene

Background

Familial ovarian cancer (OC) cases not harbouring pathogenic variants in either of the BRCA1 and BRCA2 OC-predisposing genes, which function in homologous recombination (HR) of DNA, could involve pathogenic variants in other DNA repair pathway genes.

Methods

Whole exome sequencing was used to identify rare variants in HR genes in a BRCA1 and BRCA2 pathogenic variant negative OC family of French Canadian (FC) ancestry, a population exhibiting genetic drift. OC cases and cancer-free individuals from FC and non-FC populations were investigated for carrier frequency of FANCI c.1813C>T; p.L605F, the top-ranking candidate. Gene and protein expression were investigated in cancer cell lines and tissue microarrays, respectively.

Results

In FC subjects, c.1813C>T was more common in familial (7.1%, 3/42) than sporadic (1.6%, 7/439) OC cases (P = 0.048). Carriers were detected in 2.5% (74/2950) of cancer-free females though female/male carriers were more likely to have a first-degree relative with OC (121/5249, 2.3%; Spearman correlation = 0.037; P = 0.011), suggesting a role in risk. Many of the cancer-free females had host factors known to reduce risk to OC which could influence cancer risk in this population. There was an increased carrier frequency of FANCI c.1813C>T in BRCA1 and BRCA2 pathogenic variant negative OC families, when including the discovery family, compared to cancer-free females (3/23, 13%; OR = 5.8; 95%CI = 1.7–19; P = 0.005). In non-FC subjects, 10 candidate FANCI variants were identified in 4.1% (21/516) of Australian OC cases negative for pathogenic variants in BRCA1 and BRCA2, including 10 carriers of FANCI c.1813C>T. Candidate variants were significantly more common in familial OC than in sporadic OC (P = 0.04). Localization of FANCD2, part of the FANCI-FANCD2 (ID2) binding complex in the Fanconi anaemia (FA) pathway, to sites of induced DNA damage was severely impeded in cells expressing the p.L605F isoform. This isoform was expressed at a reduced level, destabilized by DNA damaging agent treatment in both HeLa and OC cell lines, and exhibited sensitivity to cisplatin but not to a poly (ADP-ribose) polymerase inhibitor. By tissue microarray analyses, FANCI protein was consistently expressed in fallopian tube epithelial cells and only expressed at low-to-moderate levels in 88% (83/94) of OC samples.

Conclusions

This is the first study to describe candidate OC variants in FANCI, a member of the ID2 complex of the FA DNA repair pathway. Our data suggest that pathogenic FANCI variants may modify OC risk in cancer families.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13073-021-00998-5.

Exome sequencing of familial high-grade serous ovarian carcinoma reveals heterogeneity for rare candidate susceptibility genes

High-grade serous ovarian carcinoma (HGSOC) has a significant hereditary component, approximately half of which cannot be explained by known genes. To discover genes, we analyse germline exome sequencing data from 516 BRCA1/2-negative women with HGSOC, focusing on genes enriched with rare, protein-coding loss-of-function (LoF) variants. Overall, there is a significant enrichment of rare protein-coding LoF variants in the cases (p < 0.0001, chi-squared test). Only thirty-four (6.6%) have a pathogenic variant in a known or proposed predisposition gene. Few genes have LoF mutations in more than four individuals and the majority are detected in one individual only. Forty-three highly-ranked genes are identified with three or more LoF variants that are enriched by three-fold or more compared to GnomAD. These genes represent diverse functional pathways with relatively few involved in DNA repair, suggesting that much of the remaining heritability is explained by previously under-explored genes and pathways.

Genomics education for medical professionals - the current UK landscape

Genomics education in the UK is at an early stage of development, and its pace of evolution has lagged behind that of the genomics research upon which it is based. As a result, knowledge of genomics and its applications remains limited among non-specialist clinicians. In this review article, we describe the complex landscape for genomics education within the UK, and highlight the large number and variety of organisations that can influence, direct and provide genomics training to medical professionals. Postgraduate genomics education is being shaped by the work of the Health Education England (HEE) Genomics Education Programme, working in conjunction with the Joint Committee on Genomics in Medicine. The success of their work will be greatly enhanced by the full cooperation and engagement of the many groups, societies and organisations involved with medical education and training (such as the royal colleges). Without this cooperation, there is a risk of poor coordination and unnecessary duplication of work. Leadership from an organisation such as the HEE Genomics Education Programme will have a key role in guiding the formulation and delivery of genomics education policy by various stakeholders among the different disciplines in medicine.

Performance of SOAR (systolic blood pressure, oxygenation, age and respiratory rate) scoring criteria in community-acquired pneumonia: a prospective multi-centre study

BACKGROUND

severity assessment in community-acquired pneumonia (CAP) is important as it is associated with significant mortality. In this study, we compared a previously suggested severity assessment rule for CAP- SOAR (systolic blood pressure, oxygenation, age and respiratory rate)- against the CURB-65 criteria.

METHODS

we conducted a prospective study in three hospitals in Norfolk and Suffolk, UK. Consecutive patients with CAP were scored for severity with CURB-65 (n = 190), and SOAR (when there was sufficient information, n = 112). Mortality data was collected at 6 weeks.

RESULTS

there were 100 males (53%). The age range was 18-101 years (mean 72 years, median 76 years). Sixty-five (34%) had severe pneumonia by CURB-65, and 56 patients out of 112 (50%) had severe pneumonia by SOAR. Patients with severe CAP were significantly more likely to be older, female, and to have higher urea levels and a lower PaO(2):FiO(2) ratio on admission. There were a total of 54 deaths during follow-up (33 of these in the SOAR-categorised group). There were 32 deaths (50%) in the severe and 22 deaths (18%) in the non-severe groups by CURB-65. There were 23 deaths (70%) in the severe and 22 deaths (30%) in the non-severe groups by SOAR. For CURB-65, sensitivity, specificity, positive and negative predictive values were 60.6, 72.2, 47.6 and 81.4%. For SOAR, the respective values were 69.7%, 58.2, 41.1 and 82.1%.

CONCLUSION

SOAR had demonstrably better sensitivity, but lower specificity compared with CURB-65 in this patient cohort. SOAR might be more suitable for assessing disease severity as an alternative or adjunct to CURB-65, particularly in the elderly.

Are shock index and adjusted shock index useful in predicting mortality and length of stay in community-acquired pneumonia?

BACKGROUND

Community Acquired Pneumonia (CAP) is a common infection which is associated with a significant mortality. Shock index, heart rate divided by blood pressure, has been shown to predict mortality in several conditions including sepsis, acute myocardial infarction and traumatic injuries. Very little is known about the prognostic value of shock index in community acquired pneumonia (CAP).

OBJECTIVE

To examine the usefulness of shock index (SI) and adjusted shock index (corrected to temperature) (ASI) in predicting mortality and hospital length of stay in patients admitted to hospital with CAP.

METHODS

A prospective study was conducted in three hospitals in Norfolk & Suffolk, UK. We compared risk of mortality and longer length of stay for low (=<1.0, i.e. heart rate =< systolic BP) and high (>1.0, i.e. heart rate > systolic BP) SI and ASI adjusting for age, sex and other parameters which have been shown to be associated with mortality in CAP.

RESULTS

A total of 190 patients were included (males=53%). The age range was 18-101 years (median=76 years). Patients with SI & ASI >1.0 had higher likelihood of dying within 6 weeks from admission. The adjusted odds ratio for 30 days mortality were 2.48 (1.04-5.92; p=0.04) for SI and 3.16 (1.12-8.95; p=0.03) for ASI. There was no evidence to suggest that they predict longer length of stay.

CONCLUSION

Both SI and ASI of >1.0 predict 6 weeks mortality but not longer length of stay in CAP.

Confusion, Urea, Respiratory Rate and Shock Index or Adjusted Shock Index (CURSI or CURASI) criteria predict mortality in community-acquired pneumonia

BACKGROUND

Community-acquired pneumonia (CAP) is common and associated with a significant mortality. Shock index, heart rate divided by systolic blood pressure, has been shown to be associated with outcome in sepsis.

OBJECTIVE

To examine the usefulness of two new criteria CURSI (confusion, urea, respiratory rate and shock index), and CURASI where shock index is replaced by temperature adjusted shock index in mortality assessment of CAP.

METHODS

A prospective study was conducted in Norfolk and Suffolk, UK. We explored the usefulness of CURSI and CURASI which we derived and performed mapping exercise using a different cohort. In this study we compared these new indices with the CURB-65 criteria in correctly predicting mortality in CAP.

RESULTS

A total of 190 patients were included (males=53%). The age range was 18-101 years (median=76 years). There were a total of 54 deaths during a six-week follow-up. All died within 30-days. Sixty-five (34%) had severe pneumonia by CURB-65. Using CURSI and CURASI, 71(37%) and 69(36%) had severe pneumonia, respectively. The sensitivity, specificity, positive and negative predictive values in predicting death during six-week follow-up were comparable among three indices examined. The Receiver Operating Characteristic curve values (95%CI) for the criteria were 0.67(0.60-0.75) for CURB-65, 0.67(0.59-0.74) for CURSI and 0.66(0.58-0.74) for CURASI (p>0.05). There were strong agreements between these three indices (Kappa values > or =0.75 for all). Repeating analyses in those who were aged 65years and over (n=135) did not alter the results.

CONCLUSIONS

Both CURSI and CURASI are similarly useful to CURB-65 in predicting deaths associated with CAP including older patients.

Performance of CURB-65 and CURB-age in community-acquired pneumonia

BACKGROUND

Community-acquired pneumonia (CAP) is common and associated with significant mortality. In this study, we validated a newly proposed severity assessment rule for CAP, CURB-age, and also compared with to the currently recommended criteria in UK, CURB-65.

METHODS

We conducted a prospective study in three hospitals in Norfolk and Suffolk, UK. One hundred and ninety patients were included and followed up for 6 weeks.

RESULTS

Of 190 patients, 100 were men (53%). The age range was 18-101 years (median 76 years). Sixty-five (34%) had severe pneumonia by CURB-65 and 54 (28%) had severe pneumonia by CURB-age. There were 54 deaths during follow-up. There were 32 deaths (50%) in severe and 22 deaths (18%) in non-severe group by CURB-65. There were 27 deaths each in both the groups by CURB-age (50% of severe cases and 20% of non-severe cases). For CURB-65, sensitivity, specificity, and positive and negative predictive values were 59.3% (45.0-72.4), 75.7% (67.6-82.7), 49.2% (36.6-61.9) and 82.4% (74.6-88.6), respectively. For CURB-age, the respective values were 50.0% (31.1-63.9), 80.1% (72.4-86.5), 50.0% (36.1-63.9) and 80.1% (72.4-86.5). Exclusion of patients aged < 65 years did not alter the results.

CONCLUSIONS

Despite better specificity in correctly identifying 6-week mortality for CAP, CURB-age appears to be less sensitive than CURB-65. Our findings further assure the usefulness of CURB-65 for predicting mortality in CAP.

Microcytosis and possible early iron deficiency in paediatric inpatients: a retrospective audit

Background

Iron deficiency anaemia is a common paediatric problem worldwide, with significant neurodevelopmental morbidity if left untreated. A decrease in the mean corpuscular volume (MCV) can be used as a surrogate marker for detecting early iron deficiency prior to definitive investigation and treatment. An audit cycle was therefore undertaken to evaluate and improve the identification, follow-up and treatment of abnormally low MCV results amongst the paediatric inpatients in an English district general hospital.

Methods

The audit cycle was performed retrospectively over two three-month periods (February to April 2006; September to November 2006), amongst patients aged between one month and 16 years that had full blood counts performed whilst admitted on the paediatric ward. Patients with at least one abnormally low MCV result were identified, and their notes reviewed. We looked for any underlying explanation for the result, adequate documentation of the result as abnormal, and instigation of follow-up or treatment. In-between the two audit periods, the results of the first audit period were presented to the medical staff and suggestions were made for improvements in documentation and follow-up of abnormal results. The z-test was used to test for equality of proportions between the two audit samples.

Results

Out of 701 inpatients across both audit periods that had full blood counts, 61 (8.7%) had a low MCV result. Only 15% of patients in each audit period had an identifiable explanation for their low MCV values. Amongst the remaining 85% with either potentially explicable or inexplicable results, there was a significant increase in documentation of results as abnormal from 25% to 91% of cases between the first and second audit periods (p = 0.00 using z-test). However, there was no accompanying increase in the proportion of patients who received follow-up or treatment for their abnormal results.

Conclusion

Abnormal red cell indices that may indicate iron deficiency are frequently missed amongst paediatric inpatients. Medical staff education and the use of appropriate protocols or pathways could further improve detection and treatment rates in this setting.

An audit of the first year of screening for depression in patients with diabetes and ischaemic heart disease under the Quality and Outcomes Framework

BACKGROUND

Depression is more prevalent in those with chronic ill-health. Screening for depression in patients with diabetes and ischaemic heart disease was included in the Quality and Outcomes Framework (QOF) in 2006.

AIM

To investigate if screening in accordance with the QOF leads to improved detection and treatment of depression in the target groups.

METHOD

We conducted an audit of records in a single semi-rural general practice. Records of patients in the target groups for the year ending 31 March 2007 were audited to calculate the proportions of patients who were screened, detected to have depression and received treatment.

RESULTS

Out of 435 eligible patients, 365 (84%) were screened. Of those not currently depressed or under treatment for depression, only three patients (1%) screened positive. None were subsequently diagnosed as having depression.

CONCLUSION

Screening in our practice did not result in any new diagnoses of depression. It remains to be seen whether depression screening in other practices will result in substantial improvement in the identification and treatment of depression in high-risk groups.