For almost two decades, breast cancer clinical genetics has operated in an environment where a heritable cause of breast cancer susceptibility is identified in the vast minority of women seeking advice about their personal and/or family history of breast and/or ovarian cancer. A new wave of genetic information is upon us that promises to provide an explanation for the greater proportion of current missing heritability of breast cancer. Whilst researchers refine bioinformatic and analytic methodology necessary to interpret the new genetic data, attention needs to be paid to defining appropriate and coordinated pathways for the translation of this information so that it can be applied in clinical genetic services for the benefit of the majority of women who currently have no explanation for their breast cancer susceptibility. The search for additional breast cancer susceptibility genes remains a very active area of research. Exhausting the power of linkage studies that identified BRCA1 and BRCA2, the research community moved to candidate gene studies that led to the identification of ATM, BRIP1, CHEK2, and PALB2 as so-called "moderate-risk" breast cancer susceptibility genes. Mutations in these genes are rare and although early reports suggested that, on average, they are associated with moderate risks of breast cancer; population-based studies have demonstrated that at least some mutations in these genes are associated with breast cancer risks that are comparable to the average risk associated with BRCA2 mutations. The search for additional breast cancer susceptibility genes has now moved onto research platforms applying massively parallel sequencing capable of sequencing whole human exomes and genomes in single instrument runs. These programs are identifying a large number of additional putative breast cancer susceptibility genes, many of which are currently undergoing validation. It is highly anticipated that the remaining missing heritability of breast cancer will be due to mutations in many different genes, each explaining a small proportion of the currently unexplained heritable breast cancer susceptibility. The characterization of PALB2 as a breast cancer susceptibility gene and subsequent research that has refined our understanding of the prevalence and penetrance of heritable mutations in PALB2 offers a precious opportunity to use the data as a model and develop modes of translation that would be appropriate for the anticipated volume of imminent new information.

The transformation of follicular lymphoma to an aggressive lymphoma is a well-recognised complication that occurs at a rate of approximately 3 % a year for the first 10 years of observation. Transformation is accompanied by increased risk of refractoriness and a poor expectation of survival. Genetic and epigenetic triggers for transformation have been described. Prior to routine use of rituximab, transformed lymphoma was managed in a fashion similar to that for de novo diffuse large B-cell lymphoma, with generally poor results. Rituximab appears to have improved outcomes. Some centres, including our own, use high-dose chemotherapy with stem cell transplantation as consolidation for those with responsive disease. Here, we focus on transformed follicular lymphoma, and provide an overview of the current literature and our approach to management.

Acquired resistance to PARP inhibitors (PARPi) is a major challenge for the clinical management of high grade serous ovarian cancer (HGSOC). Here, we demonstrate CX-5461, the first-in-class inhibitor of RNA polymerase I transcription of ribosomal RNA genes (rDNA), induces replication stress and activates the DNA damage response. CX-5461 co-operates with PARPi in exacerbating replication stress and enhances therapeutic efficacy against homologous recombination (HR) DNA repair-deficient HGSOC-patient-derived xenograft (PDX) in vivo. We demonstrate CX-5461 has a different sensitivity spectrum to PARPi involving MRE11-dependent degradation of replication forks. Importantly, CX-5461 exhibits in vivo single agent efficacy in a HGSOC-PDX with reduced sensitivity to PARPi by overcoming replication fork protection. Further, we identify CX-5461-sensitivity gene expression signatures in primary and relapsed HGSOC. We propose CX-5461 is a promising therapy in combination with PARPi in HR-deficient HGSOC and also as a single agent for the treatment of relapsed disease.

Cyclin-dependent kinase 4/6 (CDK4/6) inhibitors are an established treatment in estrogen receptor-positive breast cancer and are currently in clinical development in melanoma, a tumor that exhibits high rates of CDK4 activation. We analyzed melanoma cells with acquired resistance to the CDK4/6 inhibitor palbociclib and demonstrate that the activity of PRMT5, a protein arginine methyltransferase and indirect target of CDK4, is essential for CDK4/6 inhibitor sensitivity. By indirectly suppressing PRMT5 activity, palbociclib alters the pre-mRNA splicing of MDM4, a negative regulator of p53, leading to decreased MDM4 protein expression and subsequent p53 activation. In turn, p53 induces p21, leading to inhibition of CDK2, the main kinase substituting for CDK4/6 and a key driver of resistance to palbociclib. Loss of the ability of palbociclib to regulate the PRMT5-MDM4 axis leads to resistance. Importantly, combining palbociclib with the PRMT5 inhibitor GSK3326595 enhances the efficacy of palbociclib in treating naive and resistant models and also delays the emergence of resistance. Our studies have uncovered a mechanism of action of CDK4/6 inhibitors in regulating the MDM4 oncogene and the tumor suppressor, p53. Furthermore, we have established that palbociclib inhibition of the PRMT5-MDM4 axis is essential for robust melanoma cell sensitivity and provide preclinical evidence that coinhibition of CDK4/6 and PRMT5 is an effective and well-tolerated therapeutic strategy. Overall, our data provide a strong rationale for further investigation of novel combinations of CDK4/6 and PRMT5 inhibitors, not only in melanoma but other tumor types, including breast, pancreatic, and esophageal carcinoma.

Expression of hypoxia-inducible factor (HIF)1α increases the risk of castrate-resistant prostate cancer (CRPC) and metastases in patients on androgen deprivation therapy (ADT) for prostate cancer (PC). We aimed to investigate the effects of nonspecific HIF1α inhibitors (Digoxin, metformin, and angiotensin-2 receptor blockers) on development of CRPC and metastases while on ADT. A retrospective review of prospectively collected medical records was conducted of all men who had continuous ADT as first-line therapy for CRPC at the Austin Hospital from 1983 to 2011. Association between HIF1α inhibitor medications and time to develop CRPC was investigated using actuarial statistics. Ninety-eight patients meeting the criteria were identified. Eighteen patients (21.4%) were treated with the nonspecific HIF1α inhibitors. Both groups had similar characteristics, apart from patients on HIF1α inhibitors being older (70 years vs. 63.9 years). The median CRPC-free survival was longer in men using HIF1α inhibitors compared to those not on inhibitors (6.7 years vs. 2.7 years, P = 0.01) and there was a 71% reduction in the risk of developing CRPC (HR 0.29 [95% CI 0.10-0.78] P = 0.02) after adjustment for Gleason score, age, and prostate-specific antigen (PSA). The median metastasis-free survival in men on HIF1α inhibitors was also significantly longer compared to those on no inhibitors (5.1 years vs. 2.6 years, P = 0.01) with an 81% reduction in the risk of developing metastases (HR 0.19 [CI 0.05-0.76] P = 0.02) after adjustment for Gleason score, age, and PSA. Nonspecific HIF1α inhibitors appear to increase the progression-free survival and reduce the risk of developing CRPC and metastases in patients on continuous ADT.

Objective The management of low-risk febrile neutropenia (FN) patients through ambulatory programs has demonstrated comparative safety and effectiveness to in-patient strategies. However, there is limited evidence of benefits of changing practice, particularly on a national scale. The aim of this study was to estimate costs and benefits of the program over a 10-year time horizon. Methods A comparative cost analysis from a health system perspective was performed, comparing costs and length of stay (LOS) of patients enrolled in an ambulatory program to a historical cohort who did not receive the program. Generalised linear models were used for analysis and bootstrapped to account for uncertainty. National data of identified FN admissions were used to inform future projections, with varying proportions of low-risk patients and eligibility for the ambulatory program. Results The overall LOS for patients in ambulatory cohort was 1.9 days shorter (95% confidence interval (CI) 1.0-2.8 days), a 50% reduction in in-patient bed-days. Although patients in the ambulatory cohort incurred additional costs due to care received outside hospital (mean (± s.d.) A$828.03 ± 124.30), the mean total cost incurred remained substantially lower than that of the historical cohort (A$2979 lower; 95% CI A$772-5391). On a national scale, this could translate into A$62.7 million in costs averted and 41347 bed-days saved over 10 years if the low-risk prediction rate and eligibility for ambulatory programs remained at currently observed rates. Conclusions The wider implementation of a safe and effective ambulatory program to manage low-risk FN patients can result in significant return-on-investment for the healthcare system by eliminating avoidable costs due to unnecessary lengthy hospital admissions. What is known about the topic? There is strong evidence demonstrating out-patient treatment of low-risk FN patients to be an effective and cost-effective strategy compared with continued in-patient hospitalisation. What does this paper add? This study demonstrates the sustainability of the ambulatory program in ensuring cost benefits and in-patient beds through real-life implementation data. It also provides evidence of the substantial cost and bed-days potentially averted when the cost savings and difference in LOS are estimated on a national scale over a 10-year time horizon. What are the implications for practitioners? The management of low-risk FN patients through ambulatory or out-patient programs is a safe and effective approach. There is strong evidence demonstrating the likely cost savings and considerable bed-days saved, which can be reallocated to meet other medical demands.

BACKGROUND: Genomes of lower organisms have been observed with a large amount of horizontal gene transfers, which cause difficulties in their evolutionary study. Bacteriophage genomes are a typical example. One recent approach that addresses this problem is the unsupervised clustering of genomes based on gene order and genome position, which helps to reveal species relationships that may not be apparent from traditional phylogenetic methods. RESULTS: We propose the use of an overlapping subspace clustering algorithm for such genome classification problems. The advantage of subspace clustering over traditional clustering is that it can associate clusters with gene arrangement patterns, preserving genomic information in the clusters produced. Additionally, overlapping capability is desirable for the discovery of multiple conserved patterns within a single genome, such as those acquired from different species via horizontal gene transfers. The proposed method involves a novel strategy to vectorize genomes based on their gene distribution. A number of existing subspace clustering and biclustering algorithms were evaluated to identify the best framework upon which to develop our algorithm; we extended a generic subspace clustering algorithm called HARP to incorporate overlapping capability. The proposed algorithm was assessed and applied on bacteriophage genomes. The phage grouping results are consistent overall with the Phage Proteomic Tree and showed common genomic characteristics among the TP901-like, Sfi21-like and sk1-like phage groups. Among 441 phage genomes, we identified four significantly conserved distribution patterns structured by the terminase, portal, integrase, holin and lysin genes. We also observed a subgroup of Sfi21-like phages comprising a distinctive divergent genome organization and identified nine new phage members to the Sfi21-like genus: Staphylococcus 71, phiPVL108, Listeria A118, 2389, Lactobacillus phi AT3, A2, Clostridium phi3626, Geobacillus GBSV1, and Listeria monocytogenes PSA. CONCLUSION: The method described in this paper can assist evolutionary study through objectively classifying genomes based on their resemblance in gene order, gene content and gene positions. The method is suitable for application to genomes with high genetic exchange and various conserved gene arrangement, as demonstrated through our application on phages.

BACKGROUND: One of the main types of genetic variations in cancer is Copy Number Variations (CNV). Whole exome sequencing (WES) is a popular alternative to whole genome sequencing (WGS) to study disease specific genomic variations. However, finding CNV in Cancer samples using WES data has not been fully explored. RESULTS: We present a new method, called CoNVEX, to estimate copy number variation in whole exome sequencing data. It uses ratio of tumour and matched normal average read depths at each exonic region, to predict the copy gain or loss. The useful signal produced by WES data will be hindered by the intrinsic noise present in the data itself. This limits its capacity to be used as a highly reliable CNV detection source. Here, we propose a method that consists of discrete wavelet transform (DWT) to reduce noise. The identification of copy number gains/losses of each targeted region is performed by a Hidden Markov Model (HMM). CONCLUSION: HMM is frequently used to identify CNV in data produced by various technologies including Array Comparative Genomic Hybridization (aCGH) and WGS. Here, we propose an HMM to detect CNV in cancer exome data. We used modified data from 1000 Genomes project to evaluate the performance of the proposed method. Using these data we have shown that CoNVEX outperforms the existing methods significantly in terms of precision. Overall, CoNVEX achieved a sensitivity of more than 92% and a precision of more than 50%.

Targeted resequencing by massively parallel sequencing has become an effective and affordable way to survey small to large portions of the genome for genetic variation. Despite the rapid development in open source software for analysis of such data, the practical implementation of these tools through construction of sequencing analysis pipelines still remains a challenging and laborious activity, and a major hurdle for many small research and clinical laboratories. We developed TREVA (Targeted REsequencing Virtual Appliance), making pre-built pipelines immediately available as a virtual appliance. Based on virtual machine technologies, TREVA is a solution for rapid and efficient deployment of complex bioinformatics pipelines to laboratories of all sizes, enabling reproducible results. The analyses that are supported in TREVA include: somatic and germline single-nucleotide and insertion/deletion variant calling, copy number analysis, and cohort-based analyses such as pathway and significantly mutated genes analyses. TREVA is flexible and easy to use, and can be customised by Linux-based extensions if required. TREVA can also be deployed on the cloud (cloud computing), enabling instant access without investment overheads for additional hardware. TREVA is available at http://bioinformatics.petermac.org/treva/.

The role of cytarabine-based induction and autologous stem cell transplantation (ASCT) in front-line treatment of younger patients with mantle cell lymphoma (MCL) is well established, however the utility of intensive approaches in older patients remains unclear. This retrospective study compared first line treatment outcomes in patients aged 60 years or more, treated at six tertiary centres between 2000-2015. 70 patients included had a median age of 69 (60-91) and most (94%) demonstrated advanced stage disease. Treatment regimens included: R-CHOP-like (n = 39), alternating R-CHOP/R-DHAC (n = 10), R-HyperCVAD/R-MA (n = 7), R-CHOP/Cytarabine (Nordic Protocol) (n = 10) and other (n = 4). 16 patients underwent an ASCT. The median follow-up for surviving patients was 37 months. Compared to R-CHOP-like therapies, cytarabine-based regimens were associated with an improved overall response rate (ORR) of 70% vs 33% (p < 0.001) and overall survival (OS) (HR 0.541, [0.292-1.001], p = 0.05). No difference in efficacy between different cytarabine-based regimens was detected, but R-HyperCVAD/R-MA was associated with increased hospitalisation and transfusion requirements. Patients undergoing ASCT demonstrated an improved median OS (HR 0.108 [0.015-0.796], p = 0.029) but were significantly younger. These results reaffirm the use of cytarabine in MCL for selected patients aged over 60. Such regimens should be strongly considered for this population in frontline therapy.

BACKGROUND: The Vk*MYC transgenic and transplant mouse models of multiple myeloma (MM) are well established as a research tool for anti-myeloma drug discovery. However, little is known of the immune response in these models. Understanding the immunological relevance of these models is of increasing importance as immunotherapeutic drugs are developed against MM. METHODS: We set out to examine how cellular immunity is affected in Vk*MYC mouse models and compare that to the immunology of patients with newly diagnosed and relapsed/refractory MM. RESULTS: We found that there were significant immunological responses in mice developing either spontaneous (transgenic) or transplanted MM as a consequence of the degree of tumor burden. Particularly striking were the profound B cell lymphopenia and the expansion of CD8(+) effector memory T cells within the lymphocyte population that progressively developed with advancing disease burden, mirroring changes seen in human MM. High disease burden was also associated with increased inflammatory cytokine production by T lymphocytes, which is more fitting with relapsed/refractory MM in humans. CONCLUSIONS: These findings have important implications for the application of this mouse model in the development of MM immunotherapies. Trial registration LitVacc ANZCTR trial ID ACTRN12613000344796; RevLite ANZCTR trial ID NCT00482261.

It is widely accepted that complex interactions between cancer cells and their surrounding microenvironment contribute to disease development, chemo-resistance and disease relapse. In light of this observed interdependency, novel therapeutic interventions that target specific cancer stroma cell lineages and their interactions are being sought. Here we studied a mouse model of human T-cell acute lymphoblastic leukaemia (T-ALL) and used intravital microscopy to monitor the progression of disease within the bone marrow at both the tissue-wide and single-cell level over time, from bone marrow seeding to development/selection of chemo-resistance. We observed highly dynamic cellular interactions and promiscuous distribution of leukaemia cells that migrated across the bone marrow, without showing any preferential association with bone marrow sub-compartments. Unexpectedly, this behaviour was maintained throughout disease development, from the earliest bone marrow seeding to response and resistance to chemotherapy. Our results reveal that T-ALL cells do not depend on specific bone marrow microenvironments for propagation of disease, nor for the selection of chemo-resistant clones, suggesting that a stochastic mechanism underlies these processes. Yet, although T-ALL infiltration and progression are independent of the stroma, accumulated disease burden leads to rapid, selective remodelling of the endosteal space, resulting in a complete loss of mature osteoblastic cells while perivascular cells are maintained. This outcome leads to a shift in the balance of endogenous bone marrow stroma, towards a composition associated with less efficient haematopoietic stem cell function. This novel, dynamic analysis of T-ALL interactions with the bone marrow microenvironment in vivo, supported by evidence from human T-ALL samples, highlights that future therapeutic interventions should target the migration and promiscuous interactions of cancer cells with the surrounding microenvironment, rather than specific bone marrow stroma, to combat the invasion by and survival of chemo-resistant T-ALL cells.