Analysis of rare disruptive germline mutations in 2,135 enriched BRCA-negative breast cancers excludes additional high-impact susceptibility genes

BACKGROUND

Breast cancer has a significant heritable basis, of which approximately 60% remains unexplained. Testing for BRCA1/BRCA2 offers useful discrimination of breast cancer risk within families, and identification of additional breast cancer susceptibility genes could offer clinical utility.

PATIENTS AND METHODS

We included 2,135 invasive breast cancer cases recruited via the BOCS study, a retrospective UK study of familial breast cancer.

ELIGIBILITY CRITERIA

female, BRCA-negative, white European ethnicity, and one of: i) breast cancer family history, ii) bilateral disease, iii) young age of onset (<30 years), iv) concomitant ovarian cancer. We undertook exome sequencing of cases and performed gene-level burden testing of rare damaging variants against those from 51,377 ethnicity-matched population controls from gnomAD.

RESULTS

159/2135 (7.4%) cases had a qualifying variant in an established breast cancer susceptibility gene, with minimal evidence of signal in other cancer susceptibility genes. Known breast cancer susceptibility genes PALB2, CHEK2 and ATM were the only genes to retain statistical significance after correcting for multiple testing. Due to the enrichment of hereditary cases in the series, we had good power (>80%) to detect a gene of BRCA1-like risk (odds ratio = 10.6) down to a population minor allele frequency of 4.6 x 10^-5 (1 in 10,799, less than one tenth that of BRCA1)and of PALB2-like risk (odds ratio = 5.0) down to a population minor allele frequency of 2.8 x 10^-4 (1 in 1,779, less than half that of PALB2). Power was lower for identification of novel moderate penetrance genes (odds ratio = 2-3) like CHEK2 and ATM.

CONCLUSIONS

This is the largest case-control whole-exome analysis of enriched breast cancer published to date. Whilst additional breast cancer susceptibility genes likely exist, those of high penetrance are likely to be of very low mutational frequency. Contention exists regarding the clinical utility of such genes.

What is the value of simulated patient assessment in structured clinical examinations of undergraduate students, and how should it be used?

INTRODUCTION

The aim of this study was to explore correlations between clinical assessor and simulated patient (SP) scores drawn from summative Integrated Structured Clinical Examination (ISCE) and inform the best use of SP scores in future assessments.

MATERIALS AND METHODS

This retrospective study explores summative clinical assessor and formative SP numeric scores drawn from summative ISCE assessments spanning three academic years (2017-18 to 2019-20). Analyses were carried out using R 3.5.1 (R Core Team, 2018), with the stats package.

RESULTS

The sample consisted of 169 final-year BDS students across the three cohorts and included 95 females (56.2%) and 74 males (43.8%). Data from eight substations where SPs were included, were explored. Kendall's Tau, a non-parametric correlation, was used to investigate the relationships between the assessor and SP scores. Clinical assessor scores were out of a total of 20 points across various assessed domains within each substation. The formative SP assessment was out of 10 points with the same five affective domains related to communication included in each substation. Overall, the assessor and patient substation scores were not correlated (τ = 0.04, p = .272) indicating that communication skills alone, as assessed by patients, do not correlate with more holistic performance across other domains. There was significant positive correlation for two of the eight substations with the other substations showing very little correlation.

CONCLUSION

This study shows that assessment of student performance by SPs does not show a correlation with examiner scores and may provide additional information relating to affective skills of students. Notwithstanding the limitations of this study, the findings underscore the need to investigate further the value of involvement of SPs in clinical assessments to explore if scores by SPs can be used to enhance the validity of assessments if used summatively.

Impaired PBPC collection in patients with myeloma after high-dose melphalan

BACKGROUND

Tandem stem cell transplantation is an important treatment option for patients with myeloma and some additional tumors. In an attempt to reduce the contamination of the stem cell graft with tumor cells, patients with myeloma who entered complete remission after the first transplant underwent a second episode of mobilization to obtain progenitor cells for the second transplant.

METHODS

Twenty-two patients with myeloma participated in the study. The first mobilization utilized CY, etoposide and filgrastim. The second mobilization used the same regimen, but seven patients received only filgrastim. The interval between the two collection periods was 6 months (median; range 4-9 months). The preparative regimen for the first transplant consisted of melphalan 200 mg/m(2).

RESULTS

The number of total white cells collected during the two collection episodes was similar: 10.8+/-1.6 x 10(8)/kg white cells vs. 11.8+/-1.7 x 10(8)/kg white cells (P=0.63). The collected CD34(+) cell dose was much larger during the first collection: 45.2+/-8.4 x 10(6)/kg vs. 6.9+/-2.7 x 10(6)/kg (P<0.001). Similarly, the collected colony-forming unit (CFU)-GM dose was much larger during the first collection: 295.4+/-59.3 x 10(4)/kg vs. 67.3+/-21.6x10(4)/kg (P<0.001). While the CD34(+) cells collected during the two collection episodes correlated significantly (r=0.55, P<0.01); the first dose was a median of 14.9-fold larger.

DISCUSSION

No laboratory parameter was able reliably to predict the results of the second collection. A second mobilization/collection episode as part of a tandem transplant approach carries a considerable risk of failing to obtain sufficient progenitor cells.

Matched-pair analysis of hematopoietic progenitor cell mobilization using G-CSF vs. cyclophosphamide, etoposide, and G-CSF: enhanced CD34+ cell collections are not necessarily cost-effective

Using matched-pair analysis, we compared two popular methods of stem cell mobilization in 24 advanced-stage breast cancer patients who underwent two consecutive mobilizing procedures as part of a tandem transplant protocol. For the first cycle, 10 microg/kg/day granulocyte colony-stimulating factor (G-CSF) was given and apheresis commenced on day 4 and continued for < or =5 days (median 3 days). One week after the first cycle of apheresis, 4000 mg/m2 cyclophosphamide, 400 mg/m2 etoposide, and 10 microg/kg G-CSF were administered for < or =16 days (cycle 2). Apheresis was initiated when the white blood cell (WBC) count exceeded 5000 cells/microL and continued for < or =5 days (median 3 days). Mean values of peripheral blood WBC (31,700+/-3200 vs. 30,700+/-3300/microL) were not significantly different between cycles 1 and 2. Mean number of mononuclear cells (MNC) collected per day was slightly greater with G-CSF mobilization than with the combination of chemotherapy and G-CSF (2.5+/-0.21x10(8) vs. 1.8+/-0.19x10(8) cells/kg). Mean daily CD34+ cell yield, however, was nearly six times higher (12.9+/-4.4 vs. 2.2+/-0.5x10(6)/kg; p = 0.01) with chemotherapy plus G-CSF. With G-CSF alone, 13% of aphereses reached the target dose of 5x10(6) CD34+ cells/kg in one collection vs. 57% with chemotherapy plus G-CSF. Transfusions of red blood cells or platelets were necessary in 18 of 24 patients in cycle 2. Three patients were hospitalized with fever for a median of 3 days after cycle 2. No patients received transfusions or required hospitalization during mobilization with G-CSF alone. Resource utilization (cost of drugs, aphereses, cryopreservation, transfusions, hospitalization) was calculated comparing the median number of collections to obtain a target CD34+ cell dose of 5x10(6) cells/kg: four using G-CSF vs. one using the combination in this data set. Resources for G-CSF mobilization cost $7326 vs. $8693 for the combination, even though more apheresis procedures were performed using G-CSF mobilization. The cost of chemotherapy administration, more doses of G-CSF, transfusions, and hospitalizations caused cyclophosphamide, etoposide, and G-CSF to be more expensive than G-CSF alone. A less toxic and less expensive treatment than cyclophosphamide, etoposide, and G-CSF is needed to be more cost-effective than G-CSF alone for peripheral blood progenitor cell mobilization.

Comparison of the distribution of progenitor cells in G-CSF-mobilized peripheral blood and steady-state bone marrow after counterflow centrifugal elutriation

Blood-derived progenitor cells obtained following mobilization with granulocyte colony-stimulating factor (MoPBSC) are increasingly being used as an alternative to bone marrow (BM) in allogeneic stem cell transplantation. The higher numbers of mature T lymphocytes in MoPBSC grafts may increase the risk of (chronic) graft-vs.-host disease. Counterflow centrifugal elutriation (CCE) is an effective method for T-cell depletion of BM grafts. The elutriation characteristics of steady-state BM and MoPBSC were compared using a CCE procedure in which fractions were obtained after small incremental increases in flow rate with constant centrifugal force. Counterflow centrifugal elutriation experiments with MoPBSC from six healthy volunteers showed that 54% of all cells collected were recovered in the < or = 15 mL/minute fractions, whereas experiments with mononuclear BM cells from five healthy volunteers resulted in recovery of 52% of collected cells from the > or = 19 mL/minute fractions. The peak concentrations of CD34+ cells were found in the same fraction (18 mL/minute), but more CD34+ cells from MoPBSC were recovered from the small (< or = 16 mL/minute) fractions (54% for MoPBSC, 26% for BM; p = 0.08). The small CD34+ cells from BM were more frequently lacking CD38 and human leucocyte antigen-DR expression than the small CD34+ cells from MoPBSC. Mature T-cells (CD3+) in BM and MoPBSC samples had similar CCE features, as did early (long-term culture initiating cells, high-proliferative potential colony-forming cells) and more mature (colony-forming units granulocyte/macrophage, BFU-e) hematopoietic progenitor cells. The results of this study suggest that T-cell depletion by CCE of MoPBSC as compared to BM products, may lead to a greater loss of CD34+ cells, but not of immature hematopoietic progenitor cells.

Decision-Theoretic Planning: Structural Assumptions and Computational Leverage

Planning under uncertainty is a central problem in the study of automated sequential decision making, and has been addressed by researchers in many different fields, including AI planning, decision analysis, operations research, control theory and economics. While the assumptions and perspectives adopted in these areas often differ in substantial ways, many planning problems of interest to researchers in these fields can be modeled as Markov decision processes (MDPs) and analyzed using the techniques of decision theory. This paper presents an overview and synthesis of MDP-related methods, showing how they provide a unifying framework for modeling many classes of planning problems studied in AI. It also describes structural properties of MDPs that, when exhibited by particular classes of problems, can be exploited in the construction of optimal or approximately optimal policies or plans. Planning problems commonly possess structure in the reward and value functions used to describe performance criteria, in the functions used to describe state transitions and observations, and in the relationships among features used to describe states, actions, rewards, and observations. Specialized representations, and algorithms employing these representations, can achieve computational leverage by exploiting these various forms of structure. Certain AI techniques -- in particular those based on the use of structured, intensional representations -- can be viewed in this way. This paper surveys several types of representations for both classical and decision-theoretic planning problems, and planning algorithms that exploit these representations in a number of different ways to ease the computational burden of constructing policies or plans. It focuses primarily on abstraction, aggregation and decomposition techniques based on AI-style representations.

Hematopoietic growth factor after autologous peripheral blood transplantation: comparison of G-CSF and GM-CSF

Autologous peripheral blood stem cell (PBSC) transplantation results in rapid hematologic recovery when sufficient numbers of CD34+ cells/kg are infused. Recent studies suggest that filgrastim (G-CSF) administration following transplantation leads to more rapid neutrophil recovery and lower total transplant costs. This study compares the use of G-CSF (5 microg/kg/day) with sargramostim (GM-CSF) 500 microg/day from day 0 until neutrophil recovery (ANC >1500/mm3) in patients with breast cancer or myeloma who had PBSC mobilized with the combination of cyclophosphamide, etoposide, and G-CSF. Twenty patients (13 breast cancer and seven myeloma) received GM-CSF and 26 patients (14 breast cancer and 12 myeloma) received G-CSF. The patients were comparable for age and stage of disease, and received stem cell grafts that were not significantly different (CD34+ x 10(6)/kg was 12.5 +/- 11.1 (mean +/- s.d.) for GM-CSF and 19.8 +/- 18.5 for G-CSF; P = 0.10). The use of red cells (2.8 vs 2.3 units), and platelet transfusions (2.5 vs 3.1) was similar for the two groups, as was the use of intravenous antibiotics (4.3 vs 4.6 days) and the number of days with temperature >38.3 degrees C (2.3 vs 1.8). Platelet recovery was also similar in both groups (platelets >50,000/mm3 reached after 11.8 vs 14.9 days). The recovery of neutrophils, however, was faster using G-CSF. ANC >500/mm3 and >1000/mm3 were reached in the GM-CSF group at 10.5 +/- 1.5 and 11.0 +/- 1.7 days, respectively, whereas with G-CSF only 8.8 +/- 1.2 and 8.9 +/- 2.2 days were required (P < 0.001). As a result, patients given G-CSF received fewer injections than the GM-CSF patients (10.9 vs 12.3). Resource utilization immediately attributable to the use of growth factors and the duration of pancytopenia, excluding hospitalization, were similar for the two groups. This study suggests that neutrophil recovery occurs more quickly following autologous PBSC transplant using G-CSF in comparison to GM-CSF, but the difference is not extensive enough to result in lower total cost.

Optimised separation of E- and Z- isomers of tamoxifen, and its principal metabolites using reversed-phase high performance liquid chromatography

A reversed phase isocratic high-performance liquid chromatographic method is reported in which a formal structured procedure, the solvent selectivity triangle, was applied to predict the mobile phase composition giving baseline resolution of the clinically important triphenylethylene antioestrogenic agent (Z)-tamoxifen, its principal (Z)-metabolites, and also the clinically relevant (E)-geometric isomers of tamoxifen and 4-hydroxytamoxifen. The technique of solvent selectivity triangle was used to select the optimal organic modifier parameter for use with a Hichrom ODS 1 column, to achieve baseline separation of six triphenylethylene solutes. The detection system utilised post-column ultraviolet irradiation to convert solutes into their respective photocyclisation products, followed by fluorescence detection (lambda[ex] = 254 nm, lambda[em] = 360 nm), and the low detection limit for tamoxifen in serum of 0.1 microM. The optimal mobile phase composition was determined to be methanol-acetonitrile-water-trichloroacetic acid (50:31:18.9:0.1, v/v, pH 2.9). A single stage liquid-liquid extraction method for determination of triphenylethylene drugs in serum was developed. Reproducible recoveries for the (Z)-geometric isomers of tamoxifen (84 +/- 3%) and its principal metabolites including Metabolite Y (94 +/- 3%), N-desmethyltamoxifen (94 +/- 3%) and 4-hydroxytamoxifen (92 +/- 3%) were achieved, though more variable results were obtained for their corresponding (E)-geometric isomers (71 +/- 7% and 70 +/- 10%, respectively).

Impaired stem cell collection by consecutive courses of high-dose mobilizing chemotherapy using cyclophosphamide, etoposide, and G-CSF

Tandem cycles of myeloablative chemotherapy can increase dose intensity and total dose of chemotherapy, but sufficient numbers of progenitor cells must be collected to ensure hematologic recovery after each treatment. This study was undertaken to determine if two courses of mobilizing chemotherapy given 4 weeks apart using cyclophosphamide 4000 mg/m2 and etoposide 400 mg/m2, combined with G-CSF 5-10 mg/kg on days 3-16 could each provide sufficient numbers of peripheral blood progenitor cells to support tandem cycles of myeloablative chemotherapy in 20 patients with stage IV breast cancer. Leukapheresis of blood with WBC > 1000/mm3 was performed daily for up to five collections (days 12-16), and mononuclear cells, CFU-GM, and CD34+ cells were compared between the first and second collections. The second course of mobilizing treatment resulted in similar numbers of mononuclear cells collected but far fewer CFU-GM and CD34+ progenitor cells. This prevented using the second collection of progenitor cells as the sole source for the second transplant. The data suggest that a second course of cyclophosphamide, etoposide, and G-CSF given 4 weeks after the first leads to progenitor cell depletion, and efforts to increase the yield of blood-derived progenitors should focus on the initial mobilizing procedure.

Immunomagnetic CD4+ and CD8+ cell depletion for patients at high risk for severe acute GVHD

Acute GVHD remains a major problem in allogeneic BMT, in particular when donors other than HLA-identical siblings are used. To determine the efficacy of an immunomagnetic method for depletion of CD4+ and CD8+ lymphocytes from the marrow graft, a series of 15 patients was studied. Thirteen patients had matched unrelated donors, and two patients had related donors. Cyclosporine was used as GVHD prophylaxis in combination with CD4+ and CD8+ depletion, which removed 94.1 +/- 3.2%, 97.0 +/- 5.1%, and 96.7 +/- 3.1% of CD3+, CD4+ and CD8+ cells, respectively. All patients engrafted promptly with AGC > 500/mm3 after a median of 16 days post-BMT. Acute GVHD grade II-IV developed in 0/2 related transplants and 4/13 MUD transplants; only one patient had grade III-IV acute GVHD. No late graft failure was observed. Three patients relapsed; two had advanced disease at the time of BMT. Seven patients are alive and in CCR after a median of 497 days; actuarial survival is 39% at 24 months. The fever syndrome observed with selective CD8+ cell depletion was not seen with the combined CD4+ and CD8+ cell depletion. Immunomagnetic CD4+ and CD8+ cell depletion of marrow grafts, in combination with in vivo cyclosporine, is a simple, reproducible and effective method to decrease the incidence and severity of acute GVHD in patients at high risk for this complication after allogeneic BMT.

A marrow harvest procedure under local anesthesia

This report details a bone marrow harvest procedure performed outside the hospital setting under local anesthesia, thereby avoiding many of the risks associated with the traditional surgical procedure. In approximately 30 minutes, 450 milliliters of marrow can be collected from eight bone punctures, containing a median of 4.18 x 10(9) cells and 33 x 10(6) progenitor cells as defined by CD34 expression. Reinfusion of a median 1.2 x 10(6) CD34+ cells/kg in 10 breast cancer and lung cancer patients after dose-intensive chemotherapy resulted in the recovery of granulocytes > 100/mm3 by day 14 and platelets > 20,000 by day 21. Without progenitor cell support, such recoveries could take 30 and 40 days, respectively. Collection of marrow using this protocol does not compromise the engraftment capability of the progenitor cells, seldom necessitates blood product support, is safer for the patient, and reduces the cost of harvesting by 75% compared to inpatient or day surgery procedures.

Maturation of mobilized peripheral blood progenitor cells: preclinical and phase I clinical studies

The use of mobilized peripheral blood progenitor cells (PBPC) after high-dose chemotherapy has markedly decreased the period of severe neutropenia. In an attempt to further decrease the duration of neutropenia, the potential of PBPC to mature during in vitro culture was assessed, with special attention being paid to culture medium, growth factors, and cell concentration. Concentrations of 10(6) PBPC/mL resulted in better recovery than 10(7)/mL as far as total cells, CFU-GM, and granulocytes were concerned. The combination of IL-3 + GM-CSF+G-CSF appeared to be better than any of these growth factors alone. Simple media, such as Medium 199, gave poorer cell recovery than more complex media, such as IMDM. With 10(6)/mL nonenriched PBPC in IMDM with IL-3/GM-CSF/G-CSF, on day 15 CFU-GM reached 450% of the initial level. At that point, granulocytes had increased 15-fold. A small phase I study was performed to assess the toxicity of infusing 1000-2000 mL of PBPC cultured for 3 days at 3-10 x 10(6)/mL with IL-3/GM-CSF/G-CSF in LifeCell bags. Although no clear decrease in the duration of neutropenia was observed, the infusions were uncomplicated in 5 of the 6 patients and had minor side effects in the sixth patient. These data suggest that in vitro differentiation of nonenriched PBPC is possible. However, to develop a clinically applicable method, several logistical problems will have to be overcome.

Selective T cell depletion with CD8-conjugated magnetic beads in the prevention of graft-versus-host disease after allogeneic bone marrow transplantation

The effects of a new immunomagnetic method of selectively depleting CD8+ lymphocytes from donor bone marrow were studied in 29 patients undergoing transplantation from HLA-identical sibling (n = 20) or alternative (n = 9) donors. The direct immunomagnetic depletion method consistently removed > 95% of CD8+ cells and the non-specific loss of other cell subsets was only about 15%. Recovery of CFU-GM and BFU-e was on average > 100%. The final graft contained 0.9 +/- 0.6 x 10(8)/kg nucleated cells and 1.4 +/- 2.7 x 10(5)/kg CD8+ cells. Patients also received cyclosporine starting day -1. Engraftment occurred in 28 patients (97%), including three patients who received a non-TBI conditioning regimen. One patient receiving an unrelated transplant failed to engraft. Median time to ANC > 500 x 10(6)/L was 17 (12-23) days. Four of 20 patients receiving grafts from HLA-identical siblings (20%) developed acute GVHD grade > or = II. However, five of eight patients with grafts from alternative donors (63%) had grade > or = II GVHD. Nearly all patients developed fever around day 7, accompanied by fluid overload, mild skin rash and shortness of breath. This syndrome necessitated treatment with steroids. Immunomagnetic CD8 depletion is a simple and reproducible method of selective T cell depletion. In combination with cyclosporine it appears to be effective in the prevention of severe acute GVHD in HLA-identical sibling transplants, but not in transplants from less perfectly matched donors.

A Domain-Independent Algorithm for Plan Adaptation

The paradigms of transformational planning, case-based planning, and plan debugging all involve a process known as plan adaptation - modifying or repairing an old plan so it solves a new problem. In this paper we provide a domain-independent algorithm for plan adaptation, demonstrate that it is sound, complete, and systematic, and compare it to other adaptation algorithms in the literature. Our approach is based on a view of planning as searching a graph of partial plans. Generative planning starts at the graph's root and moves from node to node using plan-refinement operators. In planning by adaptation, a library plan - an arbitrary node in the plan graph - is the starting point for the search, and the plan-adaptation algorithm can apply both the same refinement operators available to a generative planner and can also retract constraints and steps from the plan. Our algorithm's completeness ensures that the adaptation algorithm will eventually search the entire graph and its systematicity ensures that it will do so without redundantly searching any parts of the graph.

Peripheral blood stem cell collection after mobilization with intensive chemotherapy and growth factors

Peripheral blood has become an alternative to bone marrow as a source of stem cells for transplantation. One of the major disadvantages of peripheral blood as a source is the low concentration of stem cells. For successful engraftment, the infusion of at least 6 x 10(8) nucleated cells per kg is required, a cell number obtained by 6-8 cell pheresis sessions. This cell number contains approximately 0.1% CD34 cells equivalent to 600,000 CD34 cells. It is known that chemotherapy and hematopoietic growth factors increase the concentration and total number of progenitor cells in the peripheral blood. In breast and lung cancer patients we are using two cytoreductive regimens: cytoxan 2 g/m2 + platinol 90 mg/m2, and VP-16 600-900 mg/m2+ platinol 90 mg/m2, respectively, in conjunction with G-CSF for stem cell mobilization. At the time of hematopoietic recovery, between day 13 and 16, the absolute number of CD34+ cells increases in 75% of the patients more than 20-fold, from 5,000 to at least 100,000/ml blood, and to more than 40-fold, to 200,000/ml, in 54% of the patients. Therefore, 3.4-7.5 ml blood contains up to 750,000 CD34+ cells, the minimum number of CD34 cells/kg body weight infused when steady-state collected peripheral blood cells are used. Since we use a minimum of 3 x 10(6) CD34+ cells/kg body weight, 15,000 ml of mobilized blood are required. This amount can often be obtained by collecting 500 ml blood by phlebotomy in 2-3 separate sessions, which is an easy and cost-effective method for the patient.

Portal venous branch targeting with a platinum-tipped wire to facilitate transjugular intrahepatic portosystemic shunt (TIPS) procedures

We describe a technique to aid in technically difficult transjugular intrahepatic portosystemic shunt (TIPS) procedures by sonographically guided transabdominal fine-needle portal vein puncture for placement of a 0.018-inch platinum-tipped target guidewire within an appropriate portal venous branch.

A modular seating system for cerebral-palsied children

A seating system for physically handicapped children has been devised in which a series of standard components (neck supports, rolled seats, pommels) can be incorporated to make a seating system appropriate for the individual child.