Abstract 5326: COSMIC: Enhancing the world's knowledge of somatic mutations in human cancer

COSMIC, the Catalogue Of Somatic Mutations In Cancer (http://cancer.sanger.ac.uk) is the world's largest and most comprehensive online resource for exploring the impact of somatic mutations in human cancer. Now running for over 10 years, the 67th release (Oct 2013) describes 1592109 mutations in 947213 tumour samples across 25606 genes. This information is curated manually from the scientific literature, and automatically from genome resequencing consortium data portals. Full curation of the scientific literature provides in-depth understanding of the impact that each gene has in human cancer, and this has been achieved for 127 point-mutated cancer genes, and 185 fusion gene pairs. Curated genes are selected from the Cancer Gene Census (http://cancer.sanger.ac.uk/census), a listing of all genes with substantial evidence implicating them in cancer promotion, currently numbering 513 and updated frequently.

The mutations discovered in the re-sequencing of over 8000 tumour genomes are now present in COSMIC (viewable in isolation from the genic curations, http://cancer.sanger.ac.uk/wgs). In addition, the Sanger has now fully exome sequenced 1015 common cancer cell lines, identifying 1146874 coding mutations annotated for functional significance, and this is available exclusively in COSMIC at (http://cancer.sanger.ac.uk/cell_lines). While COSMIC has focused on point mutations and gene fusions, many other mutation mechanisms cause oncogenesis and these are now being integrated. The 67th COSMIC release includes copy number mutations integrated into the database and major web page views. To allow easy graphical examination of this data, copy number information was reduced to ‘gain’ and ‘loss’ annotations for inclusion in histograms and tables, with much more precise detail available with a further click. Copy number data is available in detail for every gene in COSMIC, and also for every tissue. Exploring cancer via COSMIC’s Cancer Browser (http://cancer.sanger.ac.uk/cosmic/browse/tissue), results not just in a plot of the most mutated genes, but now also a circular genome plot summarizing the copy number gains and losses across all the samples from that tumour type, all explorable in more detail via clicks on the pictures.

As the genomic data increases in COSMIC, it is becoming more important to qualitatively annotate the information, indicating which is more important or significant to oncogenesis. We are now building systems to better highlight known or putative functional mutations, improving the signal-to-noise ratio of cancer genome resequencing.

Citation Format: C Boutselakis, S A. Forbes, P Gunasekaran, M Jia, D Beare, N Bindal, C Y. Kok, K Leung, D Minjie, R Shepherd, S Bamford, S Ward, C Cole, J W. Teague, M Stratton, P Campbell, U McDermott. COSMIC: Enhancing the world's knowledge of somatic mutations in human cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5326. doi:10.1158/1538-7445.AM2014-5326

Relationships between the racemic structures of substituted mandelic acids containing 8- and 10-membered hydrogen bonded dimer rings

The structures of 27 monosubstituted mandelic acids, including several of their polymorphs, plus unsubstituted mandelic acid itself (two polymorphs) are investigated for structural similarity.

A pilot external quality assurance programme for line-probe assay detection of anti-tuberculosis drug resistance

BACKGROUND

Multidrug-resistant tuberculosis (MDR-TB; resistance to isoniazid and rifampicin) is difficult to detect and control. Line-probe assays (LiPA) are widely used for the rapid detection of MDR-TB.

OBJECTIVE

To ensure the quality of the test, a pilot external quality assurance (EQA) programme was initiated to assess the feasibility of running such a programme and the possibility of improving the proficiency of TB laboratories in performing the test.

DESIGN

Prepared filter-paper-based Mycobacterium tuberculosis DNA samples were shipped to participant laboratories for LiPA EQA. The tests were performed blind, and the results were returned to the organising laboratory for comparison and analysis.

RESULTS

A total of four rounds of EQA samples were dispatched to five laboratories in four countries. Overall inter- and intra-laboratory reproducibility was respectively 97% and 96%. The strengths and weaknesses of the participant laboratories in performing the test were discussed.

CONCLUSION

A LiPA EQA programme can ensure quality and improve the performance of TB laboratories. This is a critical step during the initial stages at the time of setting up this method of testing.

Involvement of interleukin-1 in the differentiation-inducing activity of tumor necrosis factor-alpha on a murine myeloid leukemia (WEHI-3B JCS)

We have shown previously that tumor necrosis factor-alpha (TNF-alpha) inhibits the growth and induces the differentiation of a murine myelomonocytic leukemia (WEHI-3B JCS cells) into macrophage-like cells. In this study, using reverse transcription polymerase chain reaction, we found that both endogenous interleukin-1 alpha and beta (IL-1 alpha, IL-1 beta) mRNA were up-regulated upon TNF-alpha induction. Exogenous IL-1 alpha and IL-1 beta also inhibited the growth as well as induced the differentiation of JCS cells, with IL-1 beta exerting a greater growth-inhibitory effect. Neutralizing anti-IL-1 alpha, anti-IL-1 beta and anti-TNF-alpha antibodies were further used to elucidate the role of IL-1 alpha, IL-1 beta and TNF-alpha in JCS cell differentiation. The results show that the IL-1 alpha-induced monocytic differentiation of JCS cells was effectively blocked by anti-IL-1 beta as well as anti-IL-1 beta antibodies and to a lesser extent by anti-TNF-alpha antibody. In contrast, the differentiation-inducing effect of IL-1 beta on JCS cells was only blocked by anti-IL-1 beta antibody but not by anti-IL-1 alpha or anti-TNF-alpha antibody. Finally, the TNF-alpha-induced monocytic differentiation of JCS cells was significantly blocked by anti-TNF-alpha and to a lesser extent by anti-IL-1 alpha and anti-IL-1 beta antibodies. Collectively, our results suggest that IL-1 beta alone may directly trigger JCS cell differentiation whereas the differentiation-inducing effect of IL-1 alpha may be via the endogenous production of IL-1 beta and/or TNF-alpha. In addition, IL-1 alpha and IL-1 beta may be involved, at least in part, in TNF-alpha-induced monocytic differentiation of the JCS leukemia cells.

Endoscopic submucosal dissection versus local excision for early rectal neoplasms: a comparative study

BACKGROUND

Transanal local excision (LE) is a well-established treatment option for early rectal neoplasms not amenable to complete colonoscopic removal. Endoscopic submucosal dissection (ESD) has been introduced recently as a novel procedure that enables en bloc resection of large rectal neoplasms. To date, no report comparing the two approaches can be found in the literature. This study aimed to compare the short-term clinical outcomes between ESD and LE for early rectal neoplasms.

METHODS

Between 2007 and 2010, 14 patients with early rectal neoplasms deemed not feasible for en bloc endoscopic resection using conventional techniques underwent ESD. They were compared with a matched cohort of 30 patients who had early rectal neoplasms and underwent LE between 2000 and 2009. Short-term clinical outcomes including postprocedure recovery and morbidity were compared between the two groups.

RESULTS

The mean lesion size was comparable between the ESD and LE groups (2.9 vs 2.6 cm; P = 0.423), but the mean distance of the lesions from the anal verge was greater in the ESD group (8.6 vs 5.0 cm; P = 0.001). En bloc resection was achieved for 12 patients (85.7%) in the ESD group and for all the patients in the LE group. The ESD group exhibited a trend toward a longer operative time (77.5 vs 50.0 min; P = 0.081) but lower morbidity (7.1 vs 33.3%; P = 0.076). The time to full ambulation was shorter in the ESD group (0 vs 1 day; P = 0.005), but the hospital stay was similar in the two groups (2.5 vs 4.0 days; P = 0.129).

CONCLUSION

For the treatment of early rectal neoplasms, ESD offers better short-term clinical outcomes in terms of faster recovery and possibly lower morbidity than LE. Further prospective studies with a larger sample are needed to validate the benefits of rectal ESD.

Effects of spectral manipulation on nonindividualized head-related transfer functions (HRTFs)

BACKGROUND

Directional sounds simulated using nonindividualized head-related transfer functions (HRTFs) often result in front-back confusion.

OBJECTIVE

This study was designed to examine how manipulating these nonindividualized HRTF spectra can reduce front-back confusion in headphone-simulated directional sounds.

METHOD

HRTFs of six ear-level directions were studied (angles of 0 degrees, 45 degrees, 135 degrees, 180 degrees, 225 degrees, and 315 degrees). The HRTF gains in each of six frequency bands (200 to 690 Hz, 690 to 2400 Hz, 2400 to 6500 Hz, 6500 to 10000 Hz, 10000 to 14000 Hz, and 14000 to 22000 Hz) were amplified or attenuated by 0, 12, or 18 dB. Each manipulated HRTF generated a directional sound stimulus. For this study, 32 participants were invited to localize the randomly ordered stimuli.

RESULTS

The results indicate that a 12- or 18-dB manipulation of five of the six frequency bands produced significantly better directional accuracy, with significantly less front-back confusion. A reduction of up to 70% in localization error was obtained, along with 66% less front-back confusion. Significant interactions were found between the manipulation level and frequency.

CONCLUSION

A 12-dB spectral manipulation of selected HRTF frequency bands produces better directional accuracy.

APPLICATION

The results of this research could be applied to the development of tunable nonindividualized HRTFs for audio products.