Bias between capnometry and venous carbon dioxide during initial assessment of pediatric emergency department patients: A video-based study

Objective

The bias of capnometry (ETCO2) and venous carbon dioxide (vpCO2) among pediatric emergency department (PED) patients triaged to critical care areas is unknown. We aimed to explore correlations and bias between ETCO2 and vpCO2¸and identify predictors of bias.

Methods

This was an observational, video-based, retrospective study comparing ETCO2 and vpCO2. Pediatric patients with simultaneous ETCO2 and vpCO2 data were included. Our primary aim utilized linear regressions to determine correlations and Bland-Altman analysis to assess bias. Our secondary aim utilized multiple regression to identify clinical covariates contributing to bias. Covariates included age, respiratory rate, heart rate, mean arterial blood pressure, capnometry interface, PED diagnosis, and PED disposition.

Results

A total of 200 PED patients with ETCO2 and vpCO2 data were included. The median (interquartile range [IQR]) ETCO2, vpCO2, and ΔCO2 in mmHg were 38 (32, 46), 49 (41, 61), and 11 (4, 20), respectively. ETCO2 (r = 0.76) and ΔCO2 (r = 0.71) were highly correlated with vpCO2. The mean bias between ETCO2 and vpCO2 was -14.1 mmHg (95% confidence interval [CI], -41.9 -13.7). The bias between ETCO2 and vpCO2 increased at higher values of each measure. ETCO2 sampling interface was the only independent predictor of vpCO2 in our multivariate analysis. Patients requiring bag-valve mask (BVM) ventilation had the highest median bias between ETCO2 and vpCO2 (29 mmHg, IQR 15, 37).

Conclusion

ETCO2 and vpCO2 were highly correlated. However, bias increased at higher levels of both ETCO2 and vpCO2. Among PED patients, ETCO2's ability to approximate vpCO2 diminishes with worsening hypercarbic respiratory failure.

Abstract SP147: Aging

As for most human cancer types we now have substantial understanding of the landscape of somatic mutations in breast cancer. However, there is relatively little knowledge of the somatic mutations present in normal breast epithelium. This may potentially be instructive in identifying the earliest stages of breast neoplasia and in understanding why the risk of breast cancer is high compared to other tissues of the body. By sequencing laser capture microdissected elements of normal breast epithelium from healthy women, women with breast cancer and women with breast cancer predisposition we are able to provide the first comprehensive insights into somatic mutagenesis in normal breast and compare these with other normal human tissues.

Citation Format: M Stratton. Aging [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr SP147.

Abstract B022: Properties of T-cell-recognized neoantigens

Over the past years we have learned that the T-cell-based immune system frequently responds to the neoantigens that arise as a consequence of the accumulated DNA damage causing the malignant transformation. Furthermore, recognition of neoantigens appears an important driver of the clinical activity of both T-cell checkpoint blockade and adoptive T-cell therapy as cancer immunotherapies. From the efforts dissecting the neoantigen-specific T-cell response it has become clear that only a very minor fraction of the accumulated mutations is recognized by the immune system, and the challenge to unravel the neoantigen-specific T-cell response lies in identifying which neoantigens are more likely to be true T-cell epitopes. We have analyzed neoantigen-specific T-cell reactivity in 12 melanoma patients using an in silico epitope prediction pipeline based on RNA expression, predicted HLA binding affinity, proteasomal processing and self-similarity to predict potential neoepitopes. We screened for T-cell recognition of 7000 epitopes from these 12 patients (average ~550 epitopes per patient, range: 96-1902) using our pMHC multimer combinatorial encoding technology and found 19 epitopes to be recognized by T-cells (hits) and 6981 to be “non-hits.” Based on these data we have examined the properties of T-cell recognized neoantigens. An intriguing observation is an enrichment within T-cell recognized epitopes of epitopes with the mutation positioned within the last 4 amino acids (C-terminal end of the peptide) compared to the screened set of epitopes. Fifteen out of 19 hits (approximately 80%) harbored a mutation within the last 4 amino acids of the peptide, whereas within the full set of screen epitopes it is 43%. While it is currently unclear what the reason is for this, this could reflect a biologic importance in T-cell recognition of the C-terminal part of the epitope. Furthermore, RNA expression and predicted binding affinity to HLA are important informative parameters for selecting T-cell recognized epitopes. A striking observation is that predicted binding affinity not only correlates with likelihood of observing a T-cell response but also the magnitude of this T-cell response, suggesting a hierarchy within neoantigens, and that not all neoantigens are of equal immunologic quality. In summary, our findings indicate that T-cell recognized neoantigens may differ from the neoantigen pool not recognized. In particular regarding position of the mutation with the epitope, RNA abundance and predicted HLA binding affinity. Importantly, our data reveal a hierarchy within neoantigens comparable to immunodominance known from viral infections. This hierarchy appears to depend mostly on binding affinity. These observations are likely to be highly relevant when selecting neoantigens for therapeutic manipulation such as vaccines.

Citation Format: Pia Kvistborg, Marit M. van Buuren, Daisy Philips, Nienke van Rooij, Arno Velds, Sam Behjati, Marlous van den Braber, Mireille Toebes, Lorenzo Fanchi, Maarten Slagter, Marie Stentoft Svane, Patrick Hwu, Joost van den Berg, Michael Stratton, Christian Blank, John B.A.G. Haanen, Can Kesmir, Ton N.M. Schumacher. Properties of T-cell-recognized neoantigens [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B022.

The genomic landscape of cutaneous SCC reveals drivers and a novel azathioprine associated mutational signature

Cutaneous squamous cell carcinoma (cSCC) has a high tumour mutational burden (50 mutations per megabase DNA pair). Here, we combine whole-exome analyses from 40 primary cSCC tumours, comprising 20 well-differentiated and 20 moderately/poorly differentiated tumours, with accompanying clinical data from a longitudinal study of immunosuppressed and immunocompetent patients and integrate this analysis with independent gene expression studies. We identify commonly mutated genes, copy number changes and altered pathways and processes. Comparisons with tumour differentiation status suggest events which may drive disease progression. Mutational signature analysis reveals the presence of a novel signature (signature 32), whose incidence correlates with chronic exposure to the immunosuppressive drug azathioprine. Characterisation of a panel of 15 cSCC tumour-derived cell lines reveals that they accurately reflect the mutational signatures and genomic alterations of primary tumours and provide a valuable resource for the validation of tumour drivers and therapeutic targets.

The Human Cell Atlas

The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.

The Human Cell Atlas

The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.

Abstract A009: Benchmarking the foreign antigen space of human malignancies

In a number of studies evaluating checkpoint blockade efficacy in cancer treatment, high mutational load of the tumor has been shown to correlate with clinical response, consistent with the notion that T-cell recognition of mutation derived (neo)-antigens plays a sizable role in immune based tumor eradication. Mutational load varies widely between and within malignancies, and is now frequently used as a proxy for the foreignness of cancers. However, in the absence of any well-defined reference points, it is difficult to understand which human tumors can be considered substantially foreign on the basis of the neo-antigens they carry.

Here we aim to benchmark the foreign antigen space of human cancers against a series of pathogen genomes for which T cell control has been documented. For this purpose, we developed a neo-antigen prediction pipeline that processes single nucleotide variants, indels and structural variants and filters candidate neo-peptides based on i). probability of successful proteasomal processing, ii). HLA-affinity, iii). RNA expression and iv). dissimilarity from self proteins. Having gathered a set of experimentally identified HIV-derived peptides, we determined the precision of our pipeline to be ∼40% for the HLA*A0201 allele of MHC-I, a substantially higher precision than achieved using prior methodologies.

Using this strategy, we aim to answer three classes of questions. First, how do the foreign antigen spaces of different tumors and tumor subtypes compare to the predicted neo-antigen load of human pathogens which are known to be sufficiently foreign to be controlled by T-cells? Second, is the foreignness of virus-induced cancers, such as EBV-positive lymphomas and HPV+ head and neck carcinomas and cervical cancer primarily determined by viral proteins or by DNA damage derived antigens? Third, what are the total neo-antigen yields and yield rates of different types of DNA damage? In this, we contrast variants by transcript effects (e.g. single nucleotide variants vs. indels), their predicted role in oncogenesis (i.e. driver vs. passenger variants) or their likelihood of having been generated by any of the mutational processes operative in the tumor in question. Results of these and other analyses will be presented.

Citation Format: Maarten Slagter, Lorenzo Fanchi, Marit M. van Buuren, Jorg J A Calis, Philip Schouten, Sabine Linn, Marlous Hoogstraat, Arno Velds, Hendrik Veelken, Ron M. Kerkhoven, Andrew Menzies, Ludmil B. Alexandrov, Michael Stratton, Lodewyk Wessels, Ton N. Schumacher. Benchmarking the foreign antigen space of human malignancies [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr A009.

Abstract P6-08-10: Mutational signatures impact the breast cancer transcriptome and distinguish mitotic from immune response pathways

A comprehensive whole genome analysis of a large breast cancer cohort of 560 cases (Nik-Zainal et al, submitted 2015) reports novel and existing DNA substitution and rearrangement signatures next a comprehensive list of events driving the breast cancer cell to its malignant potency. In the current study, we linked the observed genetic diversity to the breast cancer transcriptome for 260 cases for which whole genome and whole transcriptome data were both available.

Cluster analysis of the global gene expression showed the familiar view of a coherent basal-like and a heterogeneous luminal subgroup. New and previously reported1 subtype-specific aberrations with concordant expression changes were found in TP53, PIK3CA, PTEN, CCND1, CDH1 and GATA3, and mutations in PIK3CA, PTEN, AKT1 and AKT2 were mutually exclusive confirming they are active in the same pathway in breast cancer.

Integrating the identified DNA substitutions signatures with the transcriptome, we observed that the total number of substitutions in a cancer, irrespective of substitution type, was positively associated with cell cycle regulated gene expression and with adverse outcome.

In addition and more remarkably, we observed that the number substitution of two substitution signatures2 particularly associated with immune-response specific gene expression, with increased amount of tumor infiltrating lymphocytes and with a better outcome. These two signatures comprised 1) mutations of the APOBEC-type (predominant C>G in a TCN context), and 2) mutations which lacks specific features but which are strongly associated with genetic and epigenetic inactivating aberrations in BRCA1 and BRCA2.

Thus, while earlier reports3-5 imply that the sheer number of driver events triggers an immune-response, we refine this statement by observing that substitutions of a particular type are much very effective in doing so explaining the superior outcome of cancer having these particular types of substitutions. This result also implies that purposefully augmenting T-cell reactivity against amino-acid substitutions resulting from either of these two DNA substitution types could potentially improve immunotherapies in breast cancer.

1. Comprehensive molecular portraits of human breast tumours. Nature 490, 61-70 (2012).

2. Alexandrov, L.B., et al. Signatures of mutational processes in human cancer. Nature 500, 415-421 (2013).

3. Rizvi, N.A., et al. Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science 348, 124-128 (2015).

4. Schumacher, T.N. & Schreiber, R.D. Neoantigens in cancer immunotherapy. Science 348, 69-74 (2015).

5. Snyder, A., et al. Genetic basis for clinical response to CTLA-4 blockade in melanoma. N Engl J Med 371, 2189-2199 (2014).

Citation Format: Martens JWM, Smid M, Rodríguez-González G, Sieuwerts AM, Prager-Van der Smissen WJC, Van Der Vlugt - Daane M, Van Galen A, Nik-Zainal S, Staaf J, Brinkman AB, Van de Vijver MJ, Richardson AL, Berentsen K, Caldas C, Butler A, Martin S, Davies HD, Debets R, Meijer-Van Gelder ME, Van Deurzen CHM, Ramakrishna MR, Ringnér M, Viari A, Birney E, Børresen-Dale A-L, Stunnenberg HG, Stratton M, Foekens JA. Mutational signatures impact the breast cancer transcriptome and distinguish mitotic from immune response pathways. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-08-10.

Abstract LB-161: Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

Mitochondrial genomes are separated from the nuclear genome for most of the cell cycle by the nuclear double membrane, intervening cytoplasm and the mitochondrial double membrane. Despite these physical barriers we show that somatically acquired mitochondrial-nuclear genome fusion sequences are present in cancer cells. Most occur in conjunction with intranuclear genomic rearrangements and the features of the fusion fragments indicate that non-homologous end joining and/or replication-dependent DNA double strand break repair are the dominant mechanism involved. Remarkably, mitochondrial-nuclear genome fusions occur at a similar rate per base pair of DNA as interchromosomal nuclear rearrangements, indicating the presence of a high frequency of contact between mitochondrial and nuclear DNA in some somatic cells. Transmission of mitochondrial DNA to the nuclear genome occurs in neoplastically transformed cells, but we do not exclude the possibility that some mitochondrial-nuclear DNA fusions observed in cancer occurred years earlier in normal somatic cells.

Citation Format: Young Seok Ju, Jose Tubio, William Mifsud, Beiyuan Fu, ICGC Prostate Cancer, Bone Cancer, Breast Cancer Working Groups, Fengtang Yang, Peter Campbell, Michael Stratton. Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-161. doi:10.1158/1538-7445.AM2015-LB-161

Gene electro transfer of plasmid encoding vascular endothelial growth factor for enhanced expression and perfusion in the ischemic swine heart

Myocardial ischemia can damage heart muscle and reduce the heart's pumping efficiency. This study used an ischemic swine heart model to investigate the potential for gene electro transfer of a plasmid encoding vascular endothelial growth factor for improving perfusion and, thus, for reducing cardiomyopathy following acute coronary syndrome. Plasmid expression was significantly greater in gene electro transfer treated tissue compared to injection of plasmid encoding vascular endothelial growth factor alone. Higher gene expression was also seen in ischemic versus non-ischemic groups with parameters 20 Volts (p<0.03), 40 Volts (p<0.05), and 90 Volts (p<0.05), but not with 60 Volts (p<0.09) while maintaining a pulse width of 20 milliseconds. The group with gene electro transfer of plasmid encoding vascular endothelial growth factor had increased perfusion in the area at risk compared to control groups. Troponin and creatine kinase increased across all groups, suggesting equivalent ischemia in all groups prior to treatment. Echocardiography was used to assess ejection fraction, cardiac output, stroke volume, left ventricular end diastolic volume, and left ventricular end systolic volume. No statistically significant differences in these parameters were detected during a 2-week time period. However, directional trends of these variables were interesting and offer valuable information about the feasibility of gene electro transfer of vascular endothelial growth factor in the ischemic heart. The results demonstrate that gene electro transfer can be applied safely and can increase perfusion in an ischemic area. Additional study is needed to evaluate potential efficacy.

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

Abstract 2206: Genomics of Drug Sensitivity in Cancer (GDSC): A resource for therapeutic biomarker discovery in cancer cells

The Genomic of Drug Sensitivity in Cancer (GDSC; www.cancerRxgene.org) resource facilitates development of targeted cancer therapies through pre-clinical identification of therapeutic biomarkers. GDSC is the largest public resource for information on drug sensitivity in cancer cells and links these data to extensive genomic information to identify molecular features that influence anticancer drug response.

There is compelling evidence that alterations in cancer genomes strongly influence clinical responses to anticancer therapies. There are several examples where genomic changes are used as molecular biomarkers to stratify patients most likely to benefit from a treatment (e.g. BRAF in melanoma). Despite these successes, the majority of cancer drugs have not been linked to specific molecular features that could be used to direct their clinical use to maximize patient benefit. We are using pharmacogenomic profiling in cancer cell lines as a biomarker discovery platform by systematically linking pharmacological data with genomic information in cancer cells. The GDSC database contains drug sensitivity data generated from high-throughput screening performed by the Cancer Genome Project at the Wellcome Trust Sanger Institute and the Center for Molecular Therapeutics at Massachusetts General Hospital using a collection of &gt;1,200 cancer cell lines. GDSC release v3 (November 2012) contains drug sensitivity data for almost 80,000 experiments, describing response to 142 anticancer drugs across over 700 cancer cell lines. To identify molecular markers of drug response, cell line drug sensitivity data are integrated with large genomic datasets obtained from COSMIC (Catalogue of Somatic Mutations in Cancer), including information on somatic mutations in cancer genes, gene amplification and deletion, tissue type and transcriptional data. Analysis of GDSC data is through a web portal based on queries of specific anticancer drugs or cancer genes. Interactive graphical representations of the data are used throughout with links to related resources, and all datasets are freely available and downloadable. The GDSC database will undergo significant expansion in coming years as drug sensitivity and genomic datasets increase in size and complexity. GDSC provides a unique public resource incorporating large drug sensitivity and genomic datasets to facilitate discovery of new therapeutic biomarkers for cancer therapies.

Citation Format: Wanjuan Yang, Jorge Soares, Patricia Greninger, Elena Edelman, Howard Lightfoot, Simon Forbes, Ramaswamy Sridhar, P. Andrew Futreal, Daniel Haber, Michael Stratton, Cyril Benes, Ultan McDermott, Mathew Garnett. Genomics of Drug Sensitivity in Cancer (GDSC): A resource for therapeutic biomarker discovery in cancer cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2206. doi:10.1158/1538-7445.AM2013-2206

Recurrent deletion of ZNF630 at Xp11.23 is not associated with mental retardation

ZNF630 is a member of the primate-specific Xp11 zinc finger gene cluster that consists of six closely related genes, of which ZNF41, ZNF81, and ZNF674 have been shown to be involved in mental retardation. This suggests that mutations of ZNF630 might influence cognitive function. Here, we detected 12 ZNF630 deletions in a total of 1,562 male patients with mental retardation from Brazil, USA, Australia, and Europe. The breakpoints were analyzed in 10 families, and in all cases they were located within two segmental duplications that share more than 99% sequence identity, indicating that the deletions resulted from non-allelic homologous recombination. In 2,121 healthy male controls, 10 ZNF630 deletions were identified. In total, there was a 1.6-fold higher frequency of this deletion in males with mental retardation as compared to controls, but this increase was not statistically significant (P-value = 0.174). Conversely, a 1.9-fold lower frequency of ZNF630 duplications was observed in patients, which was not significant either (P-value = 0.163). These data do not show that ZNF630 deletions or duplications are associated with mental retardation.

Use of low-frequency electrical stimulation for the treatment of plantar fasciitis

BACKGROUND

Recent research has discussed the use of low-frequency electrical stimulation to increase blood flow by eliciting muscular contraction in soft tissues. This randomized clinical trial examined the efficacy of low-frequency electrical stimulation combined with stretching exercises and foot orthoses in individuals diagnosed as having plantar fasciitis for less than 6 months.

METHODS

Twenty-six participants aged 18 to 65 years diagnosed as having plantar fasciitis were randomly assigned to two treatment groups: a control group receiving only stretching and orthoses and a treatment group receiving low-frequency electrical stimulation in addition to stretching and orthoses. To assess treatment response, a visual analog scale was used to determine first-step morning pain, and changes in daily activity levels were monitored by using a validated outcome measure. All of the participants were assessed before starting treatment, after 4 weeks of treatment, and 3 months after the conclusion of treatment.

RESULTS

Participants in the control and experimental groups demonstrated pain reduction and improvements in functional activity levels after 4 weeks and 3 months.

CONCLUSIONS

Regardless of whether low-frequency electrical stimulation was used as an intervention, the use of plantar fascia-specific stretching and prefabricated foot orthoses provided short-term (3-month) pain relief and improvement in functional activity levels.

Sequencing of Breast Cancer Genomes

All cancer genomes carry somatic mutations. The recent advent of second generation sequencing technologies has brought closer the prospect of sequencing large numbers of cancer genomes. Early studies in breast cancer have investigated the prevalence and nature of rearrangements. These studies have shown that there are many more rearrangements in breast cancer than have previously been appreciated, some of which have distinctive patterns suggesting underlying DNA repair defects. These studies are now leading into the sequencing of complete breast cancer genomes which aim to generate comprehensive catalogues of somatic mutations. These will include point mutations, rearrangements and copy number changes and most of the driver and passenger mutations operative in individual cancers.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr ES3-2.

Brain sex differences and hormone influences: a moving experience?

Sex differences in the nervous system come in many forms. Although a majority of sexually dimorphic characteristics in the brain have been described in older animals, mechanisms that determine sexually differentiated brain characteristics often operate during critical perinatal periods. Both genetic and hormonal factors likely contribute to physiological mechanisms in development to generate the ontogeny of sexual dimorphisms in brain. Relevant mechanisms may include neurogenesis, cell migration, cell differentiation, cell death, axon guidance and synaptogenesis. On a molecular level, there are several ways to categorize factors that drive brain development. These range from the actions of transcription factors in cell nuclei that regulate the expression of genes that control cell development and differentiation, to effector molecules that directly contribute to signalling from one cell to another. In addition, several peptides or proteins in these and other categories might be referred to as 'biomarkers' of sexual differentiation with undetermined functions in development or adulthood. Although a majority of sex differences are revealed as a direct consequence of hormone actions, some may only be revealed after genetic or environmental disruption. Sex differences in cell positions in the developing hypothalamus, and steroid hormone influences on cell movements in vitro, suggest that cell migration may be one target for early molecular actions that impact brain development and sexual differentiation.

Somatic KIT mutations occur predominantly in seminoma germ cell tumors and are not predictive of bilateral disease: report of 220 tumors and review of literature

Mutations in the KIT gene occur in approximately 8% of all testicular germ cell tumors (TGCT) and KIT is the most frequently mutated known cancer gene. One report has shown that 93% of patients with bilateral disease have a mutation at codon 816 of the KIT gene. Importantly, this suggests that the identification of a mutation in KIT is predictive of the development of a contralateral TGCT. We investigated the frequency and type of mutations in KIT in a series of 220 tumors from 211 patients with TGCTs and extragonadal germ cell tumors. In 170 patients with unilateral TGCT and no additional germ cell tumour, we identified one exon 11 mutation in a patient with unilateral TGCT and eight activating KIT mutations in exon 17 (9/175, 5.1%). In 32 patients with bilateral TGCT, one patient had an activating KIT mutation in exon 17 (3.1%). The incidence of activating KIT mutations in sporadic TGCT vs. familial TGCT was not significantly different. All mutations were identified in seminomas. Three extragonadal primary germ cell tumors were examined and in one tumor an activating KIT mutation was demonstrated in the pineal germinoma. Interestingly, this mutation was also seen in the patient's testicular seminoma. We find no evidence for an increased frequency of KIT mutations in bilateral TGCT.

A multicenter study of cancer incidence in CHEK2 1100delC mutation carriers

The CHEK2 1100delC protein-truncating mutation has a carrier frequency of approximately 0.7% in Northern and Western European populations and confers an approximately 2-fold increased risk of breast cancer. It has also been suggested to increase risks of colorectal and prostate cancer, but its involvement with these or other types of cancer has not been confirmed. The incidence of cancer other than breast cancer in 11,116 individuals from 734 non-BRCA1/2 breast cancer families from the United Kingdom, Germany, Netherlands, and the United States was compared with that predicted by population rates. Relative risks (RR) to carriers and noncarriers were estimated by maximum likelihood, via the expectation-maximization algorithm to allow for unknown genotypes. Sixty-seven families contained at least one tested CHEK2 1100delC mutation carrier. There was evidence of underreporting of cancers in male relatives (422 cancers observed, 860 expected) but not in females (322 observed, 335 expected); hence, we focused on cancer risks in female carriers. The risk of cancers other than breast cancer in female carriers was not significantly elevated, although a modest increase in risk could not be excluded (RR, 1.18; 95% confidence interval, 0.64-2.17). The carrier risk was not significantly raised for any individual cancer site, including colorectal cancer (RR, 1.60; 95% confidence interval, 0.54-4.71). However, between ages 20 to 50 years, the risks of colorectal and lung cancer were both higher in female carriers than noncarriers (P = 0.041 and 0.0001, respectively). There was no evidence of a higher prostate cancer risk in carriers than noncarriers (P = 0.26), although underreporting of male cancers limited our power to detect such a difference. Our results suggest that the risk of cancer associated with CHEK2 1100delC mutations is restricted to breast cancer, although we cannot rule out a small increase in overall cancer risk.

Distinct Genomic Profiles in Hereditary Breast Tumors Identified by Array-Based Comparative Genomic Hybridization

Mutations in BRCA1 and BRCA2 account for a significant proportion of hereditary breast cancers. Earlier studies have shown that inherited and sporadic tumors progress along different somatic genetic pathways and that global gene expression profiles distinguish between these groups. To determine whether genomic profiles similarly discriminate among BRCA1, BRCA2, and sporadic tumors, we established DNA copy number profiles using comparative genomic hybridization to BAC-clone microarrays providing <1 Mb resolution. Tumor DNA was obtained from BRCA1 (n = 14) and BRCA2 (n = 12) mutation carriers, as well as sporadic cases (n = 26). Overall, BRCA1 tumors had a higher frequency of copy number alterations than sporadic breast cancers (P = 0.00078). In particular, frequent losses on 4p, 4q, and 5q in BRCA1 tumors and frequent gains on 7p and 17q24 in BRCA2 tumors distinguish these from sporadic tumors. Distinct amplicons at 3q27.1-q27.3 were identified in BRCA1 tumors and at 17q23.3-q24.2 in BRCA2 tumors. A homozygous deletion on 5q12.1 was found in a BRCA1 tumor. Using a set of 169 BAC clones that detect significantly (P < 0.001) different frequencies of copy number changes in inherited and sporadic tumors, these could be discriminated into separate groups using hierarchical clustering. By comparing DNA copy number and RNA expression for genes in these regions, several candidate genes affected by up- or down-regulation were identified. Moreover, using support vector machines, we correctly classified BRCA1 and BRCA2 tumors (P < 0.0000004 and 0.00005, respectively). Further validation may prove this tumor classifier to be useful for selecting familial breast cancer cases for further mutation screening, particularly, as these data can be obtained using archival tissue.

Screening for BRCA2 mutations in 81 Dutch breast-ovarian cancer families

We have analysed 81 families with a history of breast and/or ovarian cancer for the presence of germline mutations in BRCA2 with a number of different mutation screening techniques. The protein truncation test (PTT) for exons 10 and 11 detected four different frame-shifting mutations in six of these families. Four of the remaining 75 families had given positive linkage evidence for being due to BRCA2. In these families the entire coding region was analysed by single-strand conformational polymorphism, leading to the detection of a non-sense and a splice-site mutation in two of them. While these studies were in progress, Southern analysis of BRCA1 revealed that in our study-population of 81 families, 15 families were segregating either the exon 13 or exon 22 deletion in BRCA1 (Petrij-Bosch et al (1997) Nat Genet 17: 341-345). This prompted us to examine BRCA2 in the remaining 58 families by Southern analysis, using two different restriction enzymes. No aberrations were found in the restriction patterns. Thus, contrary to BRCA1, large genomic rearrangements within the BRCA2 gene do not represent a major mutation mechanism among Dutch breast cancer families.

The out-of-hospital use of a domestic violence screen for assessing patient risk

OBJECTIVES

To determine the following: 1) whether a Domestic Violence Scene Assessment Screen (DVSAS) is accurate at predicting domestic violence (DV) when compared with results on the validated Abuse Assessment Screen (AAS), and 2) whether EMTs can perform accurately on a DVSAS after they have finished a transport so as not to interfere with routine care.

METHODS

All patients transported by ambulance from domestic environments (i.e., home) by an urban EMS system were included in the study. A ten-question screen was developed to assess whether a domestic environment had a high risk of having DV (DVSAS). A positive answer to any of the questions was considered to be a positive result on the screen. A trained observer with no clinical duties rode on the ambulance for randomized shifts during a two-month period. The observer completed the DVSAS while at the scene, then the patient, if able, completed the AAS. After finishing the transport, the EMT completed the DVSAS based on his or her memory of the scene. Results of the observer DVSAS were compared with the results of the EMT DVSAS and with the AAS.

RESULTS

A total of 43 transports from domestic scenes were included in the study. The observer DVSAS alone was positive in five cases (12%), the EMT DVSAS alone was positive in five cases (12%), and both were positive in seven cases (17%). Agreement between the EMT and the observer yielded a kappa of 0.56 adjusted for chance. Of 15 (42%) patients able to complete the AAS, one (7%) was positive on the AAS alone, four (27%) were positive on the observer DVSAS alone, and three (29%) were positive on both. The observer DVSAS agreed with the AAS results in ten of 15 (66%) of cases. When compared with the AAS, the observer DVSAS had a sensitivity of 75%, specificity of 55%, positive predictive value of 38%, and negative predictive value of 86%.

CONCLUSION

Emergency medical technicians can complete the DVSAS at the end of a transport with good agreement with results obtained by an independent observer at the scene. The DVSAS is able to reflect the results of the AAS with moderate to good agreement.

Radiosynthesis and preliminary evaluation of 5-[123/125I]iodo-3-(2(S)-azetidinylmethoxy)pyridine: a radioligand for nicotinic acetylcholine receptors

The radiochemical syntheses of 5-[125I]iodo-3-(2(S)-azetidinylmethoxy)pyridine (5-[125I]-iodo-A-85380, [125I]1) and 5-[123I]-iodo-A-85380, [123I]1, were accomplished by radioiodination of 5-trimethylstannyl-3-((1-tert-butoxycarbonyl-2(S)-azetidinyl)metho xy)pyridine, 2, followed by acidic deprotection. Average radiochemical yields of [125I]1 and [123I]1 were 40-55%; and the average specific radioactivities were 1,700 and 7,000 mCi/mumol, respectively. Binding affinities of [125I]1 and [123I]1 in vitro (rat brain membranes) were each characterized by a Kd value of 11 pM. Preliminary in vivo assay and ex vivo autoradiography of mouse brain indicated that [125I]1 selectively labels nicotinic acetylcholine receptors (nAChRs) with very high affinity and specificity. These studies suggest that [123I]1 may be useful as a radioligand for single photon emission computed tomography (SPECT) imaging of nAChRs.

Understanding the 1996 census migration data

"The Australian Census provides two approaches to measuring migration: indicators which distinguish movers from non-movers, and a geographic classification which identifies each person's usual residence on census night, and their usual address one year and five years previously. Although these data represent a rich source of information, they contain several traps for the unwary. We show that differences in the variables and classifications used can result in marked variations in the apparent intensity and patterns of migration. The questionnaire and processing methodology used in the 1996 Census also resulted in a number of inconsistencies between the migration indicators and the usual address information. We examine the magnitude and source of these anomalies, assess their implications and propose a partial solution."

Haplotype and phenotype analysis of nine recurrent BRCA2 mutations in 111 families: results of an international study

Several BRCA2 mutations are found to occur in geographically diverse breast and ovarian cancer families. To investigate both mutation origin and mutation-specific phenotypes due to BRCA2, we constructed a haplotype of 10 polymorphic short tandem-repeat (STR) markers flanking the BRCA2 locus, in a set of 111 breast or breast/ovarian cancer families selected for having one of nine recurrent BRCA2 mutations. Six of the individual mutations are estimated to have arisen 400-2,000 years ago. In particular, the 6174delT mutation, found in approximately 1% of individuals of Ashkenazi Jewish ancestry, was estimated to have arisen 29 generations ago (1-LOD support interval 22-38). This is substantially more recent than the estimated age of the BRCA1 185delAG mutation (46 generations), derived from our analogous study of BRCA1 mutations. In general, there was no evidence of multiple origins of identical BRCA2 mutations. Our study data were consistent with the previous report of a higher incidence of ovarian cancer in families with mutations in a 3.3-kb region of exon 11 (the ovarian cancer cluster region [OCCR]) (P=.10); but that higher incidence was not statistically significant. There was significant evidence that age at diagnosis of breast cancer varied by mutation (P<.001), although only 8% of the variance in age at diagnosis could be explained by the specific mutation, and there was no evidence of family-specific effects. When the age at diagnosis of the breast cancer cases was examined by OCCR, cases associated with mutations in the OCCR had a significantly older mean age at diagnosis than was seen in those outside this region (48 years vs. 42 years; P=.0005).

Genetic heterogeneity and penetrance analysis of the BRCA1 and BRCA2 genes in breast cancer families. The Breast Cancer Linkage Consortium

The contribution of BRCA1 and BRCA2 to inherited breast cancer was assessed by linkage and mutation analysis in 237 families, each with at least four cases of breast cancer, collected by the Breast Cancer Linkage Consortium. Families were included without regard to the occurrence of ovarian or other cancers. Overall, disease was linked to BRCA1 in an estimated 52% of families, to BRCA2 in 32% of families, and to neither gene in 16% (95% confidence interval [CI] 6%-28%), suggesting other predisposition genes. The majority (81%) of the breast-ovarian cancer families were due to BRCA1, with most others (14%) due to BRCA2. Conversely, the majority of families with male and female breast cancer were due to BRCA2 (76%). The largest proportion (67%) of families due to other genes was found in families with four or five cases of female breast cancer only. These estimates were not substantially affected either by changing the assumed penetrance model for BRCA1 or by including or excluding BRCA1 mutation data. Among those families with disease due to BRCA1 that were tested by one of the standard screening methods, mutations were detected in the coding sequence or splice sites in an estimated 63% (95% CI 51%-77%). The estimated sensitivity was identical for direct sequencing and other techniques. The penetrance of BRCA2 was estimated by maximizing the LOD score in BRCA2-mutation families, over all possible penetrance functions. The estimated cumulative risk of breast cancer reached 28% (95% CI 9%-44%) by age 50 years and 84% (95% CI 43%-95%) by age 70 years. The corresponding ovarian cancer risks were 0.4% (95% CI 0%-1%) by age 50 years and 27% (95% CI 0%-47%) by age 70 years. The lifetime risk of breast cancer appears similar to the risk in BRCA1 carriers, but there was some suggestion of a lower risk in BRCA2 carriers <50 years of age.

Common BRCA1 variants and susceptibility to breast and ovarian cancer in the general population

Most multiple case families of young onset breast cancer and ovarian cancer are thought to be due to highly penetrant mutations in the predisposing genes BRCA1 and BRCA2. However, these mutations are uncommon in the population and they probably account for only a few percent of all breast cancer incidence. A much larger fraction of breast cancer might, in principle, be due to common variants which confer more modest individual risks. There are several common polymorphisms in the BRCA1 gene which generate amino acid substitutions. We have examined the frequency of four of these polymorphisms: Gln356Arg, Pro871Leu, Glu1038Gly and Ser1613Gly in large series of breast and ovarian cancer cases and matched controls. Due to strong linkage disequilibrium, these four sites generate only three haplotypes with a frequency > 1.3%. The most common haplotypes, defined by the alleles Gln356Pro871Glu1038Ser1613 and Gln356Leu871Gly1038Gly1613, have frequencies of 0.57 and 0.32 respectively, and these frequencies do not differ significantly between patient and control groups. Thus the most common polymorphisms of the BRCA1 gene do not make a significant contribution to breast or ovarian cancer risk. However, our data suggest that the Arg356 allele may have a different genotype distribution in breast cancer patients from that in controls (Arg356 homozygotes are more frequent in the control groups, P = 0.01), indicating that it may be protective against breast cancer. If this finding can be confirmed, it may provide an insight into the structural features of the BRCA1 protein that are important for its function.

Cloning, chromosomal mapping and expression pattern of the mouse Brca2 gene

A proportion of human breast cancers result from an inherited predisposition to the disease. Mutations in the BRCA2 gene confer a high risk of breast cancer and are responsible for almost half of these cases. The recent cloning of the human BRCA2 gene has revealed that it encodes a large protein having little significant homology to known proteins. Here we describe the mouse Brca2 gene. The gene maps to mouse chromosome 5, consistent with its location on human chromosome 13q12. We have sequenced cDNA for the entire 3329 amino acid Brca2 protein and this has revealed that, like Brca1, Brca2 is relatively poorly conserved between humans and mice. Brca2 is transcribed in a diverse range of mouse tissues, and the pattern of expression is strikingly similar to that of Brca1. Taken together, our data highlight some intriguing similarities between two genes involved in inherited breast cancer susceptibility.

Haplotype and phenotype analysis of six recurrent BRCA1 mutations in 61 families: results of an international study

Several BRCA1 mutations have now been found to occur in geographically diverse breast and ovarian cancer families. To investigate mutation origin and mutation-specific phenotypes due to BRCA1, we constructed a haplotype of nine polymorphic markers within or immediately flanking the BRCA1 locus in a set of 61 breast/ovarian cancer families selected for having one of six recurrent BRCA1 mutations. Tests of both mutations and family-specific differences in age at diagnosis were not significant. A comparison of the six mutations in the relative proportions of cases of breast and ovarian cancer was suggestive of an effect (P = .069), with 57% of women presumed affected because of the 1294 del 40 BRCA1 mutation having ovarian cancer, compared with 14% of affected women with the splice-site mutation in intron 5 of BRCA1. For the BRCA1 mutations studied here, the individual mutations are estimated to have arisen 9-170 generations ago. In general, a high degree of haplotype conservation across the region was observed, with haplotype differences most often due to mutations in the short-tandem-repeat markers, although some likely instances of recombination also were observed. For several of the instances, there was evidence for multiple, independent, BRCA1 mutational events.

Performance-based and physiological measures of situational awareness

Several situational awareness (SA) and workload measurement techniques were investigated in simulated air-to-ground missions. These techniques included measures of effectiveness, subjective ratings, performance measures, and physiological measures. The results demonstrated strengths and weaknesses in all of these techniques. Measures of effectiveness and subjective ratings suggested that the experimental manipulations were effective in altering SA. The performance measures produced mixed results. Physiological measures detected some intriguing effects in the EEG. Overall, the complexity of the relationship between SA and workload encourages the use of multiple tools in any SA evaluation.

Localisation of the breast-ovarian cancer susceptibility gene (BRCA1) on 17q12-21 to an interval of < or = 1 cM

A breast-ovarian cancer susceptibility gene, BRCA1, which is responsible for disease in approximately 45% of breast cancer families and most families that contain breast and ovarian cancer, has been assigned by genetic linkage to 17q12-21. Here, we report the analysis of three marker-disease recombinants in families that contain breast and ovarian cancer, two of which strongly suggest a location for BRCA1 telomeric to D17S702, a microsatellite polymorphism, and a third which suggests a location centromeric to EDH17B, the gene encoding estradiol-17B dehydrogenase. If the interpretation of these recombinants is correct, the results localise BRCA1 to an interval of < or = 1 cM.