Genomic characterisation of diffuse large B-cell lymphoma.

Diffuse large B-cell lymphoma (DLBCL) is a genomically heterogenous disease comprised of many subtypes that display significantly different clinical outcomes, in the context of treatment with conventional immunochemotherapy. Poor clinical outcomes in some subtypes, and imperfect identification of high risk individuals in otherwise low risk subgroups, demonstrate there is room for improvement in the subclassification and risk stratification of DLBCL. In addition, more comprehensive profiling may lead to improved molecular testing guided treatment selection.

Laboratory quality assessment of candidate gene panel testing for acute myeloid leukaemia: a joint ALLG / RCPAQAP initiative.

Accurate classification of acute myeloid leukaemia (AML) has become increasingly reliant on molecular characterisation of this blood cancer. Throughout Australia and New Zealand massively parallel sequencing (MPS) is being adopted by diagnostic laboratories for the routine evaluation of patients with AML. This technology enables the surveying of many genes simultaneously, with many technical advantages over single gene testing approaches.

AmpliVar: mutation detection in high-throughput sequence from amplicon-based libraries.

Conventional means of identifying variants in high-throughput sequencing align each read against a reference sequence, and then call variants at each position. Here, we demonstrate an orthogonal means of identifying sequence variation by grouping the reads as amplicons prior to any alignment. We used AmpliVar to make key-value hashes of sequence reads and group reads as individual amplicons using a table of flanking sequences.

Assessing the safety of cytotoxic T lymphocytes transduced with a dominant negative transforming growth factor-beta receptor.

Transforming growth factor (TGF)-beta, a pleiotropic cytokine that regulates cell growth, is secreted by many human tumors and markedly inhibits tumor-specific cellular immunity. It has previously been shown by our group that transduction of cytotoxic T lymphocytes (CTLs) with a retroviral vector expressing the dominant-negative TGFbeta type II receptor (DNR) overcomes this tumor evasion in a model of Epstein-Barr virus (EBV)-positive Hodgkin disease. TGFbeta is an important physiologic regulator of T-cell growth and survival, however, abrogation of this regulatory signal in genetically modified cells is potentially problematic.