GLO1-A novel amplified gene in human cancer

To identify a novel amplified cancer gene a systematic screen of 975 human cancer DNA samples, 750 cell lines and 225 primary tumors, using the Affymetrix 10K SNP microarray was undertaken. The screen identified 193 amplicons. A previously uncharacterized amplicon located on 6p21.2 whose 1 Mb minimal common amplified region contained eight genes (GLO1, DNAH8, GLP1R, C6orf64, KCNK5, KCNK17, KCNK16, and C6orf102) was further investigated to determine which gene(s) are the biological targets of this amplicon. Real time quantitative PCR (qPCR) analysis of all amplicon 6p21.2 genes in 618 human cancer cell lines identified GLO1, encoding glyoxalase 1, to be the most frequently amplified gene [twofold or greater amplification in 8.4% (49/536) of cancers]. Also the association between amplification and overexpression was greatest for GLO1. RNAi knockdown of GLO1 had the greatest and most consistent impact on cell accumulation and apoptosis. Cell lines with GLO1 amplification were more sensitive to inhibition of GLO1 by bromobenzylglutathione cyclopentyl diester (BBGC). Subsequent qPCR of 520 primary tumor samples identified twofold and greater amplification of GLO1 in 8/37 (22%) of breast, 12/71 (17%) of sarcomas, 6/53 (11.3%) of nonsmall cell lung, 2/23 (8.7%) of bladder, 6/93 (6.5%) of renal and 5/83 (6%) of gastric cancers. Amplification of GLO1 was rare in colon cancer (1/35) and glioma (1/94). Collectively the results indicate that GLO1 is at least one of the targets of gene amplification on 6p21.2 and may represent a useful target for therapy in cancers with GLO1 amplification.

The genetics of affective disorder and suicide

Suicidal behaviour shows evidence of familial clustering and the twin data on completed suicide suggest moderate heritability. The extent to which the genetics of suicidal behaviour overlaps with the genetics of affective disorders is unclear but there is overwhelming evidence that both bipolar and unipolar disorder are substantially influenced by genes. So far, candidate gene studies of suicidality have provoked much interest, but recently, attention has also turned to candidate gene approaches to suicidal ideation emerging during antidepressant treatment. The advent of genome-wide association studies (GWAS) has had a major impact on studies of affective disorder with some provocative new findings. The GWAS approach is also beginning to be applied in the search for genes that underlie suicidal ideation and behaviour.

Abstract 90: Mining for cancer causing mutations in whole genome sequence data

The Cancer Genome Project at the Wellcome Trust Sanger Institute, UK is using massively parallel sequencing technologies to systematically screen exome and genome sequence for diverse categories of mutations. The rapid developments in new sequencing technologies have allowed many new approaches for the detection and characterisation of a wide range of mutation types. We employ a variety of automated and semi-automated techniques to identify and classify copy number variation, chromosomal rearrangements, small insertion/deletion and substitution mutations in both cell lines and primary tumours.

Large scale, genome wide changes are detected by mapping read-pairs to a reference genome. Copy number is assessed by taking correctly mapping read-pairs, applying a circular binary segmentation algorithm and correcting for regional mapping bias throughout the genome. Using the high quality read mappings where the paired reads are an unexpected distance apart, putative rearrangements can be identified and confirmed either by local de novo sequence assembly where high sequencing coverage is available or by capillary sequencing for low coverage data.

Smaller scale mutations are detected using local read coverage to provide detailed information on the genotype and allelic content of samples. The detection techniques can be used on both whole genome and exome pull-down sequence data. Substitutions are detected using a novel algorithm based on expectation maximisation (Calculate Variants with Expectation Maximisation using New sequencing technology, or CaVEMaN) written in-house and confirmed using capillary sequencing.

Putative mutations of all types are compared to external resources (eg Ensembl, dbSNP) to infer genomic context and possible deleterious consequences. In-house tools have been developed to help automate the curation and annotation of mutations and once confirmed they are submitted to COSMIC as gene associated mutations, small scale intragenic mutations, chromosomal rearrangements or fusion gene products.

Reference URL's

Wellcome Trust Sanger Institute - http://www.sanger.ac.uk

COSMIC - http://www.sanger.ac.uk/genetics/CGP/cosmic

CGP - http://www.sanger.ac.uk/genetics/CGP/

Ensembl - http://www.ensembl.org

dbSNP - http://www.ncbi.nlm.nih.gov/projects/SNP

Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 90.

Novel candidate cancer genes identified by a large-scale cross-species comparative oncogenomics approach

Comparative genomic hybridization (CGH) can reveal important disease genes but the large regions identified could sometimes contain hundreds of genes. Here we combine high-resolution CGH analysis of 598 human cancer cell lines with insertion sites isolated from 1,005 mouse tumors induced with the murine leukemia virus (MuLV). This cross-species oncogenomic analysis revealed candidate tumor suppressor genes and oncogenes mutated in both human and mouse tumors, making them strong candidates for novel cancer genes. A significant number of these genes contained binding sites for the stem cell transcription factors Oct4 and Nanog. Notably, mice carrying tumors with insertions in or near stem cell module genes, which are thought to participate in cell self-renewal, died significantly faster than mice without these insertions. A comparison of the profile we identified to that induced with the Sleeping Beauty (SB) transposon system revealed significant differences in the profile of recurrently mutated genes. Collectively, this work provides a rich catalogue of new candidate cancer genes for functional analysis.

Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes

Clear cell renal cell carcinoma (ccRCC) is the most common form of adult kidney cancer, characterized by the presence of inactivating mutations in the VHL gene in most cases, and by infrequent somatic mutations in known cancer genes. To determine further the genetics of ccRCC, we have sequenced 101 cases through 3,544 protein-coding genes. Here we report the identification of inactivating mutations in two genes encoding enzymes involved in histone modification-SETD2, a histone H3 lysine 36 methyltransferase, and JARID1C (also known as KDM5C), a histone H3 lysine 4 demethylase-as well as mutations in the histone H3 lysine 27 demethylase, UTX (KMD6A), that we recently reported. The results highlight the role of mutations in components of the chromatin modification machinery in human cancer. Furthermore, NF2 mutations were found in non-VHL mutated ccRCC, and several other probable cancer genes were identified. These results indicate that substantial genetic heterogeneity exists in a cancer type dominated by mutations in a single gene, and that systematic screens will be key to fully determining the somatic genetic architecture of cancer.

A comprehensive catalogue of somatic mutations from a human cancer genome

All cancers carry somatic mutations. A subset of these somatic alterations, termed driver mutations, confer selective growth advantage and are implicated in cancer development, whereas the remainder are passengers. Here we have sequenced the genomes of a malignant melanoma and a lymphoblastoid cell line from the same person, providing the first comprehensive catalogue of somatic mutations from an individual cancer. The catalogue provides remarkable insights into the forces that have shaped this cancer genome. The dominant mutational signature reflects DNA damage due to ultraviolet light exposure, a known risk factor for malignant melanoma, whereas the uneven distribution of mutations across the genome, with a lower prevalence in gene footprints, indicates that DNA repair has been preferentially deployed towards transcribed regions. The results illustrate the power of a cancer genome sequence to reveal traces of the DNA damage, repair, mutation and selection processes that were operative years before the cancer became symptomatic.

A small-cell lung cancer genome with complex signatures of tobacco exposure

Cancer is driven by mutation. Worldwide, tobacco smoking is the principal lifestyle exposure that causes cancer, exerting carcinogenicity through >60 chemicals that bind and mutate DNA. Using massively parallel sequencing technology, we sequenced a small-cell lung cancer cell line, NCI-H209, to explore the mutational burden associated with tobacco smoking. A total of 22,910 somatic substitutions were identified, including 134 in coding exons. Multiple mutation signatures testify to the cocktail of carcinogens in tobacco smoke and their proclivities for particular bases and surrounding sequence context. Effects of transcription-coupled repair and a second, more general, expression-linked repair pathway were evident. We identified a tandem duplication that duplicates exons 3-8 of CHD7 in frame, and another two lines carrying PVT1-CHD7 fusion genes, indicating that CHD7 may be recurrently rearranged in this disease. These findings illustrate the potential for next-generation sequencing to provide unprecedented insights into mutational processes, cellular repair pathways and gene networks associated with cancer.

Collaboration across the pond: the multi-school progress testing project

This collaborative project between the National Board of Medical Examiners and four schools in the UK is investigating the feasibility and utility of a cross-school progress testing program drawing on test material recently retired from the United States Medical Licensing Examination (USMLE) Step 2 Clinical Knowledge (CK) examination. This article describes the design of the progress test; the process used to build, translate (localize), review, and finalize test forms; the approach taken to (web-based) test administration; and the procedure used to calculate and report scores. Results to date have demonstrated that it is feasible to use test items written for the US licensing examination as a base for developing progress test forms for use in the UK. Some content areas can be localized more readily than others, and care is clearly needed in review and revision of test materials to ensure that it is clinically appropriate and suitably phrased for use in the UK. Involvement of content experts in review and vetting of the test material is essential, and it is clearly desirable to supplement expert review with the use of quality control procedures based on the item statistics as a final check on the appropriateness of individual test items.

Cumulative achievement testing: progress testing in reverse

This collaborative project between the National Board of Medical Examiners (NBME) and Case Western Reserve University (CWRU) School of Medicine explored the design and use of cumulative achievement tests in basic science education. In cumulative achievement testing, integrative end-of-unit tests are deliberately constructed to systematically retest topics covered in previous units as well as material from the just-completed unit. CWRU faculty developed and administered a series of six web-based cumulative achievement tests using retired United States Medical Licensing Examination (USMLE) step 1 test material and tools provided by NBME's Customized Assessment Services, and trends in student performance were examined as the new CWRU basic science curriculum unfolded. This article provides the background information about test design and administration, as well as samples of score reporting information for students and faculty. While firm conclusions about the effectiveness of cumulative achievement testing are not warranted after a pilot test at a single school, preliminary results suggest that cumulative achievement testing may be an effective complement to progress testing, with the former used to encourage retention of already-covered material and the latter used to assess growth toward the knowledge and skills expected of a graduating student.

PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data

High-throughput oligonucleotide microarrays are commonly employed to investigate genetic disease, including cancer. The algorithms employed to extract genotypes and copy number variation function optimally for diploid genomes usually associated with inherited disease. However, cancer genomes are aneuploid in nature leading to systematic errors when using these techniques. We introduce a preprocessing transformation and hidden Markov model algorithm bespoke to cancer. This produces genotype classification, specification of regions of loss of heterozygosity, and absolute allelic copy number segmentation. Accurate prediction is demonstrated with a combination of independent experimental techniques. These methods are exemplified with affymetrix genome-wide SNP6.0 data from 755 cancer cell lines, enabling inference upon a number of features of biological interest. These data and the coded algorithm are freely available for download.

A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation

Large-scale systematic resequencing has been proposed as the key future strategy for the discovery of rare, disease-causing sequence variants across the spectrum of human complex disease. We have sequenced the coding exons of the X chromosome in 208 families with X-linked mental retardation (XLMR), the largest direct screen for constitutional disease-causing mutations thus far reported. The screen has discovered nine genes implicated in XLMR, including SYP, ZNF711 and CASK reported here, confirming the power of this strategy. The study has, however, also highlighted issues confronting whole-genome sequencing screens, including the observation that loss of function of 1% or more of X-chromosome genes is compatible with apparently normal existence.

Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer

Somatically acquired epigenetic changes are present in many cancers. Epigenetic regulation is maintained via post-translational modifications of core histones. Here, we describe inactivating somatic mutations in the histone lysine demethylase gene UTX, pointing to histone H3 lysine methylation deregulation in multiple tumor types. UTX reintroduction into cancer cells with inactivating UTX mutations resulted in slowing of proliferation and marked transcriptional changes. These data identify UTX as a new human cancer gene.

Development of an in situ methodology for the clinical evaluation of dentine hypersensitivity occlusion ingredients

OBJECTIVE

The aim of these clinical studies was to evaluate an in situ dentine tubule occlusion model, and to determine the occluding effect from novel occluding agents on patent dentine tubules compared to a positive control (8% strontium acetate--Sensodyne Mint) and negative control (a non-occluding agent) after four days of brushing treatment.

METHODS

These two in situ clinical studies were of single-center, randomized, crossover, single-blind design. Healthy participants wore two lower intra-oral appliances retaining four dentine samples for four treatment days for each period of the study. Samples were power-brushed each day with the test product. Assessment utilized surface topological analysis with a replica-based methodology under scanning electron microscopy (SEM).

RESULTS

Both clinical trials demonstrated that the positive control (8% strontium acetate) occluded dentine tubules significantly better (p = 0.0007; p < 0.0009) than the negative controls in the two studies, respectively. The experimental occluding agents demonstrated varying degrees of success for occluding effect compared to the controls.

CONCLUSION

The methodology clearly demonstrates that this in situ clinical model can robustly and reproducibly detect the dentine tubular occlusive effects of positive and negative controls in the treatment of dentine hypersensitivity brushed on the dentine surface. Using this methodology, new occlusion agents for the relief of dentine hypersensitivity can be assessed for occlusive effects on dentine.

X-linked protocadherin 19 mutations cause female-limited epilepsy and cognitive impairment

Epilepsy and mental retardation limited to females (EFMR) is a disorder with an X-linked mode of inheritance and an unusual expression pattern. Disorders arising from mutations on the X chromosome are typically characterized by affected males and unaffected carrier females. In contrast, EFMR spares transmitting males and affects only carrier females. Aided by systematic resequencing of 737 X chromosome genes, we identified different protocadherin 19 (PCDH19) gene mutations in seven families with EFMR. Five mutations resulted in the introduction of a premature termination codon. Study of two of these demonstrated nonsense-mediated decay of PCDH19 mRNA. The two missense mutations were predicted to affect adhesiveness of PCDH19 through impaired calcium binding. PCDH19 is expressed in developing brains of human and mouse and is the first member of the cadherin superfamily to be directly implicated in epilepsy or mental retardation.

Prototype system for enhancement of frontal chest radiographs using eigenimage processing

A prototype system is described for enhancement of radiographic images in the eigen domain. The images chosen to enhance are frontal chest radiographs. This class of images has been chosen because it is both a clinically important examination and an example of the high-resolution images used within radiology. The enhancement method is based on principal components analysis, a multivariate statistical technique first used within image processing for face recognition. The method requires a training set of normal images to identify normal patterns of variance. The enhancement process then removes these normal patterns of variance, often increasing the relative intensity of pathologies. Enhanced images presented in this paper include a range of common pathologies found on chest radiographs. Details of implementation, computing expense and possible applications within radiology are discussed.