Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer.

Circulating tumour DNA analysis can be used to track tumour burden and analyse cancer genomes non-invasively but the extent to which it represents metastatic heterogeneity is unknown. Here we follow a patient with metastatic ER-positive and HER2-positive breast cancer receiving two lines of targeted therapy over 3 years. We characterize genomic architecture and infer clonal evolution in eight tumour biopsies and nine plasma samples collected over 1,193 days of clinical follow-up using exome and targeted amplicon sequencing. Mutation levels in the plasma samples reflect the clonal hierarchy inferred from sequencing of tumour biopsies. Serial changes in circulating levels of sub-clonal private mutations correlate with different treatment responses between metastatic sites. This comparison of biopsy and plasma samples in a single patient with metastatic breast cancer shows that circulating tumour DNA can allow real-time sampling of multifocal clonal evolution.We thank the Human Research Tissue Bank at Addenbrooke’s Hospital which is supported by the NIHR Cambridge Biomedical Research Centre. We acknowledge the support of Cancer Research UK, the University of Cambridge, National Institute for Health Research Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre. Dr. Dawson was supported by an Australian National Breast Cancer Foundation and Victorian Cancer Agency Early Career Fellowship. Dr. Murtaza was supported by Science Foundation Arizona’s Bisgrove Scholars Early Tenure Track award.This is the final version of the article. It first appeared from Nature Publishing Group via http://dx.doi.org/10.1038/ncomms976

Comparison of statistical methods of haplotype reconstruction and logistic regression for association studies

Investigating association between disease and single nucleotide polymorphisms (SNPs) has been an approach for genetic association studies and more recently investigating association between disease and haplotypes has become another accepted method. Haplotypes are physically linked combinations of alleles from a stretch of DNA and can serve to increase power of finding an association due to interactions between inclusive SNPs and the increased area of chromosome that is taken into consideration. Determining haplotypes experimentally or by family studies is a costly and timeinefficient method, so haplotype reconstruction by statistical methods has become an adopted practice. The problem with computational methods is the extra. source of error from ambiguous haplotypes that has to be included in statistical analysis. This paper investigates methods of error management with three different 1ogistic regression packages, two of which are specific to analysis of genetic data. Methods are applied to simulated data and a data set looking for genetic risk factors for non-Hodgkin Lymphoma

Genomic Landscape of Epithelioid Sarcoma

We carried out whole genome and transcriptome sequencing on four tumor/normal pairs of epithelioid sarcoma. These index cases were supplemented with whole transcriptome sequencing of three additional tumors and three cell lines. Unlike in rhabdoid tumors (the other major group of SMARCB1-negative cancers), epithelioid sarcoma shows a complex genome with a higher mutational rate, comparable to that of ovarian carcinomas. Despite this mutational burden, SMARCB1 mutations remain the most recurrent event and are likely critical drivers of tumor formation. Several cases show SMARCB1 alleles that do not go through biallelic inactivation and we explore this further in vitro. Finding CDKN2A deletions in our discovery cohort, we evaluated CDKN2A protein expression in a tissue microarray. 37% (6/16) of cases had lost CDKN2A in greater than or equal to 90% of cells while the remaining cases had maintained the protein. RNAseq based expression analysis of epithelioid sarcoma cell lines shows a unique profile that does not cluster with any particular tissue type nor with other SWI/SNF aberrant lines. The maintenance of expression of most SWI/SNF members other than SMARCB1 prompted us to evaluate protein level expression of other complex members. In vitro studies show that other SWI/SNF proteins are expressed as part of a residual complex, similar to previous observations in rhabdoid tumor lines. This residual SWI/SNF is susceptible to synthetic lethality and may therefore indicate a therapeutic opportunity.Medicine, Faculty ofNon UBCPathology and Laboratory Medicine, Department ofReviewedFacultyResearcherOthe

Effect of heme oxygenase-1 polymorphisms on lung function and gene expression

Background. Oxidative stress induced by smoking is considered to be important in the pathogenesis of Chronic Obstructive Pulmonary Disease (COPD). Heme oxygenase-1 (HMOX1) is an essential enzyme in heme catabolism that is induced by oxidative stress and may play a protective role as an antioxidant in the lung. We determined whether HMOX1 polymorphisms were associated with lung function in COPD patients and whether the variants had functional effects. Methods We genotyped five single nucleotide polymorphisms (SNPs) in the HMOX1 gene in Caucasians who had the fastest (n = 278) and the slowest (n = 304) decline of FEV1 % predicted, selected from smokers in the NHLBI Lung Health Study. These SNPs were also studied in Caucasians with the lowest (n = 535) or the highest (n = 533) baseline lung function. Reporter genes were constructed containing three HMOX1 promoter polymorphisms and the effect of these polymorphisms on H2O2 and hemin-stimulated gene expression was determined. The effect of the HMOX1 rs2071749 SNP on gene expression in alveolar macrophages was investigated. Results We found a nominal association (p = 0.015) between one intronic HMOX1 SNP (rs2071749) and lung function decline but this did not survive correction for multiple comparisons. This SNP was in perfect linkage disequilibrium with rs3761439, located in the promoter of HMOX1. We tested rs3761439 and two other putatively functional polymorphisms (rs2071746 and the (GT)n polymorphism) in reporter gene assays but no significant effects on gene expression were found. There was also no effect of rs2071749 on HMOX1 gene expression in alveolar macrophages. Conclusions We found no association of the five HMOX1 tag SNPs with lung function decline and no evidence that the three promoter polymorphisms affected the regulation of the HMOX1 gene.Non UBCMedicine, Faculty ofMedicine, Department ofRespiratory Medicine, Division ofExperimental Medicine, Division ofReviewedFacult

Correction: Type-Specific Cell Line Models for Type-Specific Ovarian Cancer Research.

[This corrects the article on p. e72162 in vol. 8.]