Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936.

In a European BIOMED-2 collaborative study, multiplex PCR assays have successfully been developed and standardized for the detection of clonally rearranged immunoglobulin (Ig) and T-cell receptor (TCR) genes and the chromosome aberrations t(11;14) and t(14;18). This has resulted in 107 different primers in only 18 multiplex PCR tubes: three VH-JH, two DH-JH, two Ig kappa (IGK), one Ig lambda (IGL), three TCR beta (TCRB), two TCR gamma (TCRG), one TCR delta (TCRD), three BCL1-Ig heavy chain (IGH), and one BCL2-IGH. The PCR products of Ig/TCR genes can be analyzed for clonality assessment by heteroduplex analysis or GeneScanning. The detection rate of clonal rearrangements using the BIOMED-2 primer sets is unprecedentedly high. This is mainly based on the complementarity of the various BIOMED-2 tubes. In particular, combined application of IGH (VH-JH and DH-JH) and IGK tubes can detect virtually all clonal B-cell proliferations, even in B-cell malignancies with high levels of somatic mutations. The contribution of IGL gene rearrangements seems limited. Combined usage of the TCRB and TCRG tubes detects virtually all clonal T-cell populations, whereas the TCRD tube has added value in case of TCRgammadelta(+) T-cell proliferations. The BIOMED-2 multiplex tubes can now be used for diagnostic clonality studies as well as for the identification of PCR targets suitable for the detection of minimal residual disease.

Addressing the theory practice gap in nurse education: evaluating teaching through audit against NMC standards and final management placement

Introduction
This paper outlines an innovative approach to auditing and evaluating the content of a management and leadership module for undergraduate nursing students after their final management clinical placement. Normally evaluations of teaching in a module take place at the end of a teaching module and therefore do not properly reflect the value of the teaching in relation to practical clinical experience.
Aim
This audit and evaluation sought to explore both the practical value of the teaching and learning, and also the degree to which it the teaching reflected against the NMC Standards of Education and Learning (2010 domain 3).
Methods
Having piloted the evaluative tool with an earlier cohort of nursing students, this evaluation explored both a quantitative assessment employing a Personal Response System (n =172), together with a qualitative dimension (n=116), thus delivering paper-based comments and reflections from students on the value and practicality of the module teaching theory to their final clinical management experience. The quantitative audit data were analysed for frequencies and cross tabulation and the qualitative audit data were thematically analysed.
Results
Results suggest a significant proportion of the students, appreciated the quality of the standard of teaching, but more importantly, ‘valued or highly valued’ the teaching and learning in relation to how it helped to significantly inform their management placement experience. A smaller proportion of the students underlined limitations and areas in which further improvement can be made in teaching and learning to the module.
Conclusion
Significantly positive evaluation by the students of the practical value of teaching and learning, to the theoretical management module. This has proved a useful auditing approach in assessing the theoretical teaching to student’s Level 3 clinical experience, and facilitated significant recommendations as far as developing the teaching and learning to better reflect the practice needs of nursing students

Prior knowledge transfer across transcriptional data sets and technologies using compositional statistics yields new mislabelled ovarian cell line

Here, we describe gene expression compositional assignment (GECA), a powerful, yet simple method based on compositional statistics that can validate the transfer of prior knowledge, such as gene lists, into independent data sets, platforms and technologies. Transcriptional profiling has been used to derive gene lists that stratify patients into prognostic molecular subgroups and assess biomarker performance in the pre-clinical setting. Archived public data sets are an invaluable resource for subsequent in silico validation, though their use can lead to data integration issues. We show that GECA can be used without the need for normalising expression levels between data sets and can outperform rank-based correlation methods. To validate GECA, we demonstrate its success in the cross-platform transfer of gene lists in different domains including: bladder cancer staging, tumour site of origin and mislabelled cell lines. We also show its effectiveness in transferring an epithelial ovarian cancer prognostic gene signature across technologies, from a microarray to a next-generation sequencing setting. In a final case study, we predict the tumour site of origin and histopathology of epithelial ovarian cancer cell lines. In particular, we identify and validate the commonly-used cell line OVCAR-5 as non-ovarian, being gastrointestinal in origin. GECA is available as an open-source R package.