A5008268293- Cancer Genomics and Diagnostics
- Acute Myeloid Leukemia Research
- Immune cells in cancer
- Ovarian cancer diagnosis and treatment
- Cytokine Signaling Pathways and Interactions
- Plant Virus Research Studies
- Polyomavirus and related diseases
- RNA modifications and cancer
- Bacteriophages and microbial interactions
- Protein Degradation and Inhibitors
- Genomics and Phylogenetic Studies
- DNA Repair Mechanisms
- Chromosomal and Genetic Variations
- CRISPR and Genetic Engineering
- PARP inhibition in cancer therapy
- Genomics and Chromatin Dynamics
- Renal cell carcinoma treatment
- Molecular Biology Techniques and Applications
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Cancer Immunotherapy and Biomarkers
- Bioinformatics and Genomic Networks
- Evolution and Genetic Dynamics
- Full-Duplex Wireless Communications
Peter MacCallum Cancer Centre
2015-2024
The University of Melbourne
2015-2024
Vall d'Hebron Hospital Universitari
2024
Vall d'Hebron Institute of Oncology
2024
Hebron University
2024
Walter and Eliza Hall Institute of Medical Research
2017
Royal Women's Hospital
2015
Universitat Autònoma de Barcelona
2012-2014
Center for Research in Agricultural Genomics
2011-2014
Universitat de Barcelona
2012
We report the genome sequence of melon, an important horticultural crop worldwide. assembled 375 Mb double-haploid line DHL92, representing 83.3% estimated melon genome. predicted 27,427 protein-coding genes, which we analyzed by reconstructing 22,218 phylogenetic trees, allowing mapping orthology and paralogy relationships sequenced plant genomes. observed absence recent whole-genome duplications in lineage since ancient eudicot triplication, our data suggest that transposon amplification...
The quantification of the biological diversity in environmental samples using high-throughput DNA sequencing is hindered by PCR bias caused variable primer-template mismatches individual species. In some dietary studies, there added problem that are enriched with predator DNA, so often a predator-specific blocking oligonucleotide used to alleviate problem. However, specific oligonucleotides could coblock nontarget species degree. Here, we accurately estimate extent biases induced universal...
Abstract Merkel cell carcinoma (MCC) is an uncommon, but highly malignant, cutaneous tumor. polyoma virus (MCV) has been implicated in a majority of MCC tumors; however, viral-negative tumors have reported to be more prevalent some geographic regions subject high sun exposure. While the impact MCV and viral T-antigens on development extensively investigated, little known about etiology tumors. We performed targeted capture massively parallel DNA sequencing 619 cancer genes compare gene...
Expression of plant metallothionein genes has been reported in a variety senescing tissues, such as leaves and stems, ripening fruits, wounded proposed to function both metal chaperoning scavenging reactive oxygen species. In this work, it is shown that MT also associated with suberization, after identifying gene actively transcribed Quercus suber cork cells novel MT. This cDNA, isolated from phellem cDNA library, encodes belongs type 2 MTs (QsMT). the QsMT E. coli grown media supplemented...
Abstract Predicting whether a predator is capable of affecting the dynamics prey species in field implies analysis complete diet predator, not simply rates predation on target taxon. Here, we employed Ion Torrent next‐generation sequencing technology to investigate generalist arthropod predator. A dietary requires use general primers, but these will also amplify unless suppressed using blocking probe. However, probes can potentially block other species, particularly if they are...
Circulating tumor DNA (ctDNA) allows noninvasive disease monitoring across a range of malignancies. In metastatic melanoma, the extent to which ctDNA reflects changes in metabolic burden assessed by 18F-labeled fluorodeoxyglucose positron emission tomography (FDG-PET) is unknown. We role analysis combination with FDG-PET monitor and genomic heterogeneity throughout treatment.We performed comprehensive serial 52 patients who received systemic therapy for melanoma. Next-generation sequencing...
Although melanoma is initiated by acquisition of point mutations and limited focal copy number alterations in melanocytes-of-origin, the nature genetic changes that characterise lethal metastatic disease poorly understood. Here, we analyze evolution human progressing from early to late 13 patients sampling their tumours at multiple sites times. Whole exome genome sequencing data 88 tumour samples reveals only gain generally, with net mutational loss some metastases. In contrast, dominated...
Extracellular vesicles (EVs) secreted by tumors are abundant in plasma, but their potential for interrogating the molecular features of through multi-omic profiling remains widely unexplored. Genomic and transcriptomic circulating EV-DNA EV-RNA isolated from vitro vivo models metastatic prostate cancer (mPC) reveal a high contribution tumor material to EV-loaded DNA/RNA, validating findings two cohorts longitudinal plasma samples collected patients during androgen receptor signaling...
Several novel therapeutics are poised to change the natural history of chronic lymphocytic leukaemia (CLL) and increasing use these therapies has highlighted limitations traditional disease monitoring methods. Here we demonstrate that circulating tumour DNA (ctDNA) is readily detectable in patients with CLL. Importantly, ctDNA does not simply mirror genomic information contained within malignant lymphocytes but instead parallels changes across different compartments following treatment...
Abstract Purpose: Women with epithelial ovarian cancer generally have a poor prognosis; however, subset of patients has an unexpected dramatic and durable response to treatment. We sought identify clinical, pathological, molecular determinants exceptional survival in women high-grade serous (HGSC), disease associated the majority deaths. Experimental Design: evaluated histories 2,283 and, after applying stringent clinical pathological selection criteria, identified 96 HGSC that represented...
Low-grade serous ovarian carcinomas (LGSC) are associated with a poor response to chemotherapy and molecularly characterized by RAS pathway activation. Using exome whole genome sequencing, we identified recurrent mutations in the protein translational regulator EIF1AX NF1, USP9X, KRAS, BRAF, NRAS were mutually exclusive; however, found significant co-occurrence of Missense clustered at N-terminus region its role ensuring initiation fidelity. Coexpression mutant proteins promoted...
Lupin products may be valuable as human foods because of their high protein content and potential anticholesterolemic properties. However, a small percentage the population is allergic to lupin. In this study, we use in vitro IgE binding mass spectrometry identify conglutin β, major storage protein, an allergen seeds Lupinus angustifolius albus. Purification β from L. flour confirmed that serum binds protein. Where sera recognized lupin proteins on Western blots, it suggesting for The has...
The spectrum of genomic alterations in ductal carcinoma situ (DCIS) is relatively unexplored, but likely to provide useful insights into its biology, progression invasive and the risk recurrence. DCIS (n=20) with a range phenotypes was assessed by massively parallel sequencing for mutations copy number variants validated Sanger sequencing. PIK3CA were identified 11/20 (55%), TP53 6/20 (30%), GATA3 9/20 (45%). Screening an additional 91 cases final frequency 27% (30/111), high proportion...
ALK, ROS1 and RET gene fusions are important predictive biomarkers for tyrosine kinase inhibitors in lung cancer. Currently, the gold standard method fusion detection is Fluorescence In Situ Hybridization (FISH) while highly sensitive specific, it also labour intensive, subjective analysis, unable to screen a large numbers of fusions. Recent developments high-throughput transcriptome-based methods may provide suitable alternative FISH as they compatible with multiplexing diagnostic...
Cactophilic Drosophila species provide a valuable model to study gene–environment interactions and ecological adaptation. buzzatii mojavensis are two cactophilic that belong the repleta group, but have very different geographical distributions primary host plants. To investigate genomic basis of adaptation, we sequenced genome developmental transcriptome D. compared its gene content with other noncactophilic in same subgenus. The newly (161.5 Mb) comprises 826 scaffolds (>3 kb) contains...
Pharmacologic inhibition of epigenetic enzymes can have therapeutic benefit against hematologic malignancies. In addition to affecting tumor cell growth and proliferation, these agents may induce antitumor immunity. Here, we discovered a novel immunoregulatory mechanism through histone deacetylases (HDAC). models acute myeloid leukemia (AML), differentiation mediated by the HDAC inhibitor (HDACi) panobinostat required activation type I interferon (IFN) pathway. Plasmacytoid dendritic cells...
Highlights•RAD51-IF is feasible in FFPE clinical biopsies from patients with advanced prostate cancer•Low RAD51 scores associate alterations BRCA1/2•Low improved outcomes PARPi or platinum chemotherapy•RAD51-IF captures HRR restoration of function upon drug resistanceSummaryMetastatic cancer (mPC) enriched for homologous recombination repair (HRR) gene alterations, which have prognostic and predictive value. Routine implementation next-generation sequencing (NGS) still limited. We...
Melon (Cucumis melo L.) ranks among the highest-valued fruit crops worldwide. Some genomic tools are available for this crop, including a Sanger transcriptome. We report generation of 689,054 C. high-quality expressed sequence tags (ESTs) from two 454 sequencing runs, using normalized and nonnormalized complementary DNA (cDNA) libraries prepared four genotypes belonging to subspecies main commercial types. ESTs were combined with de novo assembled into 53,252 unigenes. Over 63% unigenes...
Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived CN profiles 100 or input DNA were highly concordant comparable with molecular inversion probe (MIP) array profiles. LC WGS improved samples that performed poorly...
Abstract Purpose: Although ovarian clear cell carcinomas (OCCC) are commonly resistant to platinum-based chemotherapy, good clinical outcomes observed in a subset of patients. The explanation for this is unknown but may be due misclassification high-grade serous cancer (HGSOC) as OCCC or mixed histology. Experimental Design: To discover potential biomarkers survival benefit following we ascertained cohort 68 Japanese and Australian patients whom progression-free (PFS) overall (OS) could...
Early cellular events during secondary embryogenesis were studied in a cork oak recurrent embryogenic system which embryos arise either multicellular budding pathway from compact mass of proliferation or isolated single cells friable callus. The originated the epidermal at hypocotyl whose growth and convolution was characterized by decrease nucleus/cytoplasm ratio marked increase storage products. transition to meristematic primordia occurred periphery accompanied cell dedifferentiation...