Cancer Epidemiology, Biomarkers & Prevention
Authors
Samantha Jean Jones, Sumara Stroshein, Amy M Williams, Dongmeng Liu, John J Spinelli, Joseph M Connors, Angela R Brooks-Wilson
Publication Abstract

Familial aggregation of lymphoid cancers and immune-related disorders suggests a role for genetic susceptibility; however, few studies examine environmental factors. According to the hygiene hypothesis, adult-onset-immune-related diseases may be a consequence of reduced childhood infectious exposures and aberrant immune development. In a cohort of 196 multiple-case lymphoid cancer families, we analyzed environmental factors related to the hygiene hypothesis.

BMC Geriatrics, 2020
Authors
Qianqian Gu, Carly M Sable, Angela Brooks-Wilson, Rachel A Murphy
Publication Abstract

Very few people live to eighty-five years and older (the 'oldest old'), and even fewer live to this age without developing chronic diseases. It is important to understand the relationship, if any, of modifiable factors such as diet on healthy aging. However, there are few studies of diet among healthy oldest old, especially in North American populations. We aimed to characterize dietary patterns among 'super-seniors' (SS) within the Canadian Healthy Aging Study.

Investigational New Drugs, 2020
Authors
Jean-Michel Lavoie, Teresa Mitchell, Sung-Eun Lee, Balvir Deol, Stephen K Chia, Karen A Gelmon, Christian K Kollmannsberger, Anna V Tinker, Steven J M Jones, Marco Marra, Janessa Laskin, Daniel J Renouf
Publication Abstract

Introduction Given the high level of uncertainty surrounding the outcomes of early phase clinical trials, whole genome and transcriptome analysis (WGTA) can be used to optimize patient selection and study assignment. In this retrospective analysis, we reviewed the impact of this approach on one such program. Methods Patients with advanced malignancies underwent fresh tumor biopsies as part of our personalized medicine program (NCT02155621). Tumour molecular data were reviewed for potentially clinically actionable findings and patients were referred to the developmental therapeutics program. Outcomes were reviewed in all patients, including those where trial selection was driven by molecular data (matched) and those where there was no clear molecular rationale (unmatched). Results From January 2014 to January 2018, 28 patients underwent WGTA and enrolled in clinical trials, including 2 patients enrolled in two trials. Fifteen patients were matched to a treatment based on a molecular target. Five patients were matched to a trial based upon single-gene DNA changes, all supported by RNA data. Ten cases were matched on the basis of genome-wide data (n = 4) or RNA gene expression only (n = 6). With a median follow-up of 6.7 months, the median time on treatment was 8.2 weeks. Discussion When compared to single-gene DNA-based data alone, WGTA led to a 3-fold increase in treatment matching. In a setting where there is a high level of uncertainty around both the investigational agents and the biomarkers, more data are needed to fully evaluate the impact of routine use of WGTA.

Nature Genetics, 2020
Authors
Laura Fachal, Hugues Aschard, Jonathan Beesley, Daniel R Barnes, Jamie Allen, Siddhartha Kar, Karen A Pooley, Joe Dennis, Kyriaki Michailidou, Constance Turman, Penny Soucy, Audrey Lemaçon, Michael Lush, Jonathan P Tyrer, Maya Ghoussaini, Mahdi Moradi Marjaneh, Xia Jiang, Simona Agata, Kristiina Aittomäki, M Rosario Alonso, Irene L Andrulis, Hoda Anton-Culver, Natalia N Antonenkova, Adalgeir Arason, Volker Arndt, Kristan J Aronson, Banu K Arun, Bernd Auber, Paul L Auer, Jacopo Azzollini, Judith Balmaña, Rosa B Barkardottir, Daniel Barrowdale, Alicia Beeghly-Fadiel, Javier Benitez, Marina Bermisheva, Katarzyna Białkowska, Amie M Blanco, Carl Blomqvist, William Blot, Natalia V Bogdanova, Stig E Bojesen, Manjeet K Bolla, Bernardo Bonanni, Ake Borg, Kristin Bosse, Hiltrud Brauch, Hermann Brenner, Ignacio Briceno, Ian W Brock, Angela Brooks-Wilson et al.
Publication Abstract

Genome-wide association studies have identified breast cancer risk variants in over 150 genomic regions, but the mechanisms underlying risk remain largely unknown. These regions were explored by combining association analysis with in silico genomic feature annotations. We defined 205 independent risk-associated signals with the set of credible causal variants in each one. In parallel, we used a Bayesian approach (PAINTOR) that combines genetic association, linkage disequilibrium and enriched genomic features to determine variants with high posterior probabilities of being causal. Potentially causal variants were significantly over-represented in active gene regulatory regions and transcription factor binding sites. We applied our INQUSIT pipeline for prioritizing genes as targets of those potentially causal variants, using gene expression (expression quantitative trait loci), chromatin interaction and functional annotations. Known cancer drivers, transcription factors and genes in the developmental, apoptosis, immune system and DNA integrity checkpoint gene ontology pathways were over-represented among the highest-confidence target genes.

Nature Genetics, 2020
Authors
Michelle Chan-Seng-Yue, Jaeseung C Kim, Gavin W Wilson, Karen Ng, Eugenia Flores Figueroa, Grainne M O'Kane, Ashton A Connor, Robert E Denroche, Robert C Grant, Jessica McLeod, Julie M Wilson, Gun Ho Jang, Amy Zhang, Sheng-Ben Liang, Ayelet Borgida, Dianne Chadwick, Sangeetha Kalimuthu, Ilinca Lungu, John M S Bartlett, Paul M Krzyzanowski, Vandana Sandhu, Hervé Tiriac, Fieke E M Froeling, Joanna M Karasinska, James T Topham, Daniel J Renouf, David F Schaeffer, Steven J M Jones, Marco A Marra, Janessa Laskin, Runjan Chetty, Lincoln D Stein, George Zogopoulos, Benjamin Haibe-Kains, Peter J Campbell, David A Tuveson, Jennifer J Knox, Sandra E Fischer, Steven Gallinger, Faiyaz Notta
Publication Abstract

Pancreatic adenocarcinoma presents as a spectrum of a highly aggressive disease in patients. The basis of this disease heterogeneity has proved difficult to resolve due to poor tumor cellularity and extensive genomic instability. To address this, a dataset of whole genomes and transcriptomes was generated from purified epithelium of primary and metastatic tumors. Transcriptome analysis demonstrated that molecular subtypes are a product of a gene expression continuum driven by a mixture of intratumoral subpopulations, which was confirmed by single-cell analysis. Integrated whole-genome analysis uncovered that molecular subtypes are linked to specific copy number aberrations in genes such as mutant KRAS and GATA6. By mapping tumor genetic histories, tetraploidization emerged as a key mutational process behind these events. Taken together, these data support the premise that the constellation of genomic aberrations in the tumor gives rise to the molecular subtype, and that disease heterogeneity is due to ongoing genomic instability during progression.

Leukemia, 2020
Authors
Alexander Pemov, Anand Pathak, Samantha J Jones, Ramita Dewan, Jessica Merberg, Sirisha Karra, Jung Kim, Evgeny Arons, Sarangan Ravichandran, Brian T Luke, Shalabh Suman, Meredith Yeager, Martin J S Dyer, Henry T Lynch, Mark H Greene, Neil E Caporaso, Robert J Kreitman, Lynn R Goldin, John J Spinelli, Angela Brooks-Wilson, Mary L McMaster, Douglas R Stewart
Publication Abstract

Hairy cell leukemia (HCL) is a rare chronic B-cell lymphoproliferative disorder named for its characteristic hair-like cytoplasmic projections from the malignant cells. HCL is classified as an indolent lymphoproliferative neoplasm, representing ~2% of all leukemias with ~1240 new cases diagnosed annually in the US; median age-at-onset is 55 years [1]. It affects males more than females (4:1), and whites more than African-Americans [1]. Although familial and sporadic HCL exhibit similar clinical features, no characteristic germline genetic variation has been found. Familial HCL is rare with fewer than 20 families reported in the literature. Thirteen of the 15 reported pedigrees had two affected individuals; the remaining two pedigrees harbored three, including the family reported here [2,3,4,5]. Investigators have speculated that HCL may be an HLA-linked disorder but, in aggregate, the data are inconclusive [3,4,5]. The discovery that a somatic BRAF mutation (V600E) was nearly universal in HCL (but absent in other B-cell neoplasms) provided major insight into disease biology, identifying a critical therapeutic target [6], but no germline genetic susceptibility variants have been identified. In this study we applied high-throughput sequencing technology to four multiplex HCL pedigrees, seeking to identify shared germline variants conferring HCL susceptibility. In addition, we used CRISPR/Cas9-based genome editing to introduce CASP9 p.H237P, one of the variants shared by all four affected members of the largest pedigree, into a model cell line, followed by measurements of cellular caspase-9 activity and apoptotic response.

Frontiers in oncology, 2020
Authors
Amy Moore, Eleanor Kane, Zhaoming Wang, Orestis A Panagiotou, Lauren R Teras, Alain Monnereau, Nicole Wong Doo, Mitchell J Machiela, Christine F Skibola, Susan L Slager, Gilles Salles, Nicola J Camp, Paige M Bracci, Alexandra Nieters, Roel C H Vermeulen, Joseph Vijai, Karin E Smedby, Yawei Zhang, Claire M Vajdic, Wendy Cozen, John J Spinelli, Henrik Hjalgrim, Graham G Giles, Brian K Link, Jacqueline Clavel, Alan A Arslan, Mark P Purdue, Lesley F Tinker, Demetrius Albanes, Giovanni M Ferri, Thomas M Habermann, Hans-Olov Adami, Nikolaus Becker, Yolanda Benavente, Simonetta Bisanzi, Paolo Boffetta, Paul Brennan, Angela R Brooks-Wilson, Federico Canzian, Lucia Conde, David G Cox, Karen Curtin, Lenka Foretova, Susan M Gapstur, Hervé Ghesquières, Martha Glenn, Bengt Glimelius, Rebecca D Jackson, Qing Lan, Mark Liebow, Marc Maynadie, James McKay, Mads Melbye, Lucia Miligi, Roger L Milne, Thierry J Molina, Lindsay M Morton, Kari E North, Kenneth Offit, Marina Padoan, Alpa V Patel, Sara Piro, Vignesh Ravichandran, Elio Riboli, Silvia de Sanjose, Richard K Severson, Melissa C Southey, Anthony Staines, Carolyn Stewart, Ruth C Travis, Elisabete Weiderpass, Stephanie Weinstein, Tongzhang Zheng, Stephen J Chanock, Nilanjan Chatterjee, Nathaniel Rothman, Brenda M Birmann, James R Cerhan, Sonja I Berndt
Publication Abstract

Although the evidence is not consistent, epidemiologic studies have suggested that taller adult height may be associated with an increased risk of some non-Hodgkin lymphoma (NHL) subtypes. Height is largely determined by genetic factors, but how these genetic factors may contribute to NHL risk is unknown. We investigated the relationship between genetic determinants of height and NHL risk using data from eight genome-wide association studies (GWAS) comprising 10,629 NHL cases, including 3,857 diffuse large B-cell lymphoma (DLBCL), 2,847 follicular lymphoma (FL), 3,100 chronic lymphocytic leukemia (CLL), and 825 marginal zone lymphoma (MZL) cases, and 9,505 controls of European ancestry. We evaluated genetically predicted height by constructing polygenic risk scores using 833 height-associated SNPs. We used logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI) for association between genetically determined height and the risk of four NHL subtypes in each GWAS and then used fixed-effect meta-analysis to combine subtype results across studies. We found suggestive evidence between taller genetically determined height and increased CLL risk (OR = 1.08, 95% CI = 1.00–1.17, p = 0.049), which was slightly stronger among women (OR = 1.15, 95% CI: 1.01–1.31, p = 0.036). No significant associations were observed with DLBCL, FL, or MZL. Our findings suggest that there may be some shared genetic factors between CLL and height, but other endogenous or environmental factors may underlie reported epidemiologic height associations with other subtypes.

Electrophoresis, 2020
Authors
Jianhui Cheng, Gregg B Morin, David D Y Chen
Publication Abstract

A high organic content CE‐MS/MS (HOCE‐MS/MS) method was developed for the proteomic analysis of envelope proteins extracted from spinach leaves. Separation was performed in a 1‐m long hydroxypropyl cellulose coated capillary, using 8% (v/v) formic acid in 70% (v/v) methanol and 22% water as the BGE. A flow‐through microvial interface was used to couple the CE system with an Orbitrap Fusion Lumos mass spectrometer, and field‐amplified sample stacking was used to improve the concentration sensitivity. Using this optimized method, 3579 peptides and 1141 proteins were identified using the Proteome Discoverer software with a 1% false discovery rate at the protein level. Relative to conventional aqueous CE, HOCE‐MS did a better job of discovering hydrophobic peptides and provided more peptide and protein identifications. Relative to nano‐LC‐MS, it achieved comparable peptide and protein identification performance and detected peptides not identified by LC‐MS: of the full set of peptides identified using the two techniques, 19% were identified only using HOCE‐MS. It also outperformed nano‐LC‐MS with respect to the detection of low molecular weight peptides.

Cancers, 2020
Authors
Matthew Richardson, Hae Jung Min, Quan Hong, Katie Compton, Sze Wing Mung, Zoe Lohn, Jennifer Nuk, Mary McCullum, Cheryl Portigal-Todd, Aly Karsan, Dean Regier, Lori A Brotto, Sophie Sun, Kasmintan A Schrader
Publication Abstract

New streamlined models for genetic counseling and genetic testing have recently been developed in response to increasing demand for cancer genetic services. To improve access and decrease wait times, we implemented an oncology clinic-based genetic testing model for breast and ovarian cancer patients in a publicly funded population-based health care setting in British Columbia, Canada. This observational study evaluated the oncology clinic-based model as compared to a traditional one-on-one approach with a genetic counsellor using a multi-gene panel testing approach. The primary objectives were to evaluate wait times and patient reported outcome measures between the oncology clinic-based and traditional genetic counselling models. Secondary objectives were to describe oncologist and genetic counsellor acceptability and experience. Wait times from referral to return of genetic testing results were assessed for 400 patients with breast and/or ovarian cancer undergoing genetic testing for hereditary breast and ovarian cancer from June 2015 to August 2017. Patient wait times from referral to return of results were significantly shorter with the oncology clinic-based model as compared to the traditional model (403 vs. 191 days; p < 0.001). A subset of 148 patients (traditional n = 99; oncology clinic-based n = 49) completed study surveys to assess uncertainty, distress, and patient experience. Responses were similar between both models. Healthcare providers survey responses indicated they believed the oncology clinic-based model was acceptable and a positive experience. Oncology clinic-based genetic testing using a multi-gene panel approach and post-test counselling with a genetic counsellor significantly reduced wait times and is acceptable for patients and health care providers.

Nature, 2020
Authors
The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium
Publication Abstract

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1,2,3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10,11,12,13,14,15,16,17,18.

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