In this study the investigators looked at adaptive reprogramming impact on the kinome when a MEK inhibitor called GSK1120212 (trametinib) was administered in a "window of opportunity" trial. GSK1120212 is not yet approved by the FDA for use in breast cancer patients. The investigators gave GSK1120212 for a short period of time (one week) to examine MEK and the other kinase expression in cancer cells both before and after the study drug is given. The investigators gave this drug for research purposes only. The length of time it was given is not intended to treat cancer. Recently researchers at UNC developed a process that can comprehensively profile the majority of the individual kinases in the kinome and examine the impact on kinase expression of kinase inhibitors (Duncan et al, Cell 2012, PMID: 22500798). This can tell us which kinases need to be concurrently blocked to augment responsiveness and prevent acquired resistance so that the investigators can design the best combinations of kinase blocking drugs for triple negative breast cancer. This is especially important for individuals with triple negative breast cancer (TNBC) because there are no targeted drugs available that can block molecules that affect tumor growth. The investigators believe that kinase-blocking drugs have the potential to be a more effective treatment for people with TNBC. In this recently published study (Zawistowski et al, Cancer Discovery 2017, PMID: 28108460), TNBC patients treated with trametinib for 7 days resulted in a transcriptional response characterized by significant reprogramming of the tyrosine kinome, and this adaptive bypass response in human tumors was found to be similar to that seen in preclinical models including TNBC cell lines and mouse xenografts. In this study we also examined whether reprogramming differed between TNBC molecular subtypes, finding that basal-like and claudin-low human TNBC cells and mouse tumor subtypes had different adaptive transcriptional responses to MEK-ERK inhibition. Mechanistically we found that genome-wide enhancer remodeling drove the adaptive transcriptional response, suggesting that epigenetic approaches to reprogramming may be more durable than kinase inhibitor polypharmacology.
The Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) is a collaborative effort comprised of a coordinating center and scientific researchers from well-characterized cohort and case-control studies conducted in North America and Europe. This international consortium aims to accelerate the discovery of common and rare genetic risk variants for colorectal cancer by conducting large-scale meta-analyses of existing and newly generated genome-wide association study (GWAS) data, replicating and fine-mapping of GWAS discoveries, and investigating how genetic risk variants are modified by environmental risk factors. To expand these efforts, we assembled case-control sets or nested case-control sets from 20 different North American or European studies. Summary descriptions and study participant inclusions/exclusion criteria for each of these studies are detailed below. The Black Women's Health Study (BWHS): Is the largest follow-up study of the health of African-American women (Cozier et al., 2004; Rosenberg et al., 1995) [PMID: 15018884; PMID: 7722208]. The purpose is to identify and evaluate causes and preventives of cancers and other serious illnesses in African-American women. Among the diseases being studied are breast cancer, colorectal cancer, type 2 diabetes, uterine fibroids, systemic lupus erythematosus, and cardiovascular disease. The study began in 1995, when 59,000 black women from all parts of the United States enrolled through postal questionnaires. The women provided demographic and health data on the 1995 baseline questionnaire, including information on weight, height, smoking, drinking, contraceptive use, use of other selected medications, illnesses, reproductive history, physical activity, diet, use of health care, and other factors. The participants are followed through biennial questionnaires to determine the occurrence of cancers and other illnesses and to update information on risk factors. Self-reports of cancer are confirmed through medical records and state cancer registry records. Mouthwash-swish samples, as a source of DNA, were obtained from ~26,000 BWHS participants in 2002-2007. DNA was isolated from the mouthwash-swish samples at the Boston University Molecular Core Genetics Laboratory using the QIAAMP DNA Mini Kit (Qiagen). All incident colorectal cancer cases with a DNA sample were included in the present analysis. Two controls per case, selected from among BWHS participants free of colorectal cancer at end of follow-up, were matched to cases on year of birth (+/- 2 years) and geographical region of residence (Northeast, South, Midwest, and West). A total 209 colorectal cancer cases and 423 controls were sent for genotyping. Campaign Against Cancer and Heart Disease (CLUE II): The Campaign Against Cancer and Heart Disease, is a prospective cohort designed to identify biomarkers and other factors associated with risk of cancer, heart disease, and other conditions (Kakourou et al., 2015) [PMID: 26220152]. 32,894 participants were recruited from May through October 1989 from Washington County, Maryland and surrounding communities. Colorectal cancer cases (n = 297) and matched controls (n = 296) were identified between 1989 and 2000 among participants in the CLUE II cohort of Washington County, Maryland. Colorectal Cancer Study of Austria (CORSA): In the ongoing colorectal cancer study of Austria (CORSA), more than 13,000 Caucasian participants have been recruited within the province-wide screening project "Burgenland Prevention Trial of Colorectal Disease with Immunological Testing" (B-PREDICT) since 2003 (Hofer et al., 2011) [PMID: 21422235]. All inhabitants of the Austrian province Burgenland aged between 40 and 80 years are annually invited to participate in fecal immunochemical testing and haemoccult positive screening participants are invited for colonoscopy. CORSA includes genomic DNA and plasma of colorectal cancer cases, low-risk and high-risk adenomas, and colonoscopy-negative controls. Controls received a complete colonoscopy and were free of colorectal cancer or polyps. CORSA participants have been recruited in the four KRAGES hospitals in Burgenland, Austria, and additionally, at the Medical University of Vienna (Department of Surgery), the Viennese hospitals "Rudolfstiftung" and the "Sozialmedizinisches Zentrum Sud", and at the Medical University of Graz (Department of Internal Medicine). 1403 colorectal cancer and advanced colorectal adenoma cases, and 1404 matched controls were selected for the study. Distribution of factors sex and age (5 year strata) were evenly matched between cases and controls. Cancer Prevention Study II (CPS II): The CPS II Nutrition cohort is a prospective study of cancer incidence and mortality in the United States, established in 1992 and described in detail elsewhere (Calle et al., 2002; Campbell et al., 2014) [PMID: 12015775; PMID: 25472679]. At enrollment, participants completed a mailed self-administered questionnaire including information on demographic, medical, diet, and lifestyle factors. Follow-up questionnaires to update exposure information and to ascertain newly diagnosed cancers were sent biennially starting in 1997. Reported cancers were verified through medical records, state cancer registry linkage, or death certificates. The Emory University Institutional Review Board approves all aspects of the CPS II Nutrition Cohort. A total of 360 cases and 359 controls were selected for this study. Czech Republic Colorectal Cancer Study (Czech Republic CCS): Cases with positive colonoscopy results for malignancy, confirmed by histology as colon or rectal carcinomas, were recruited between September 2003 and May 2012 in several oncological departments in the Czech Republic (Prague, Pilsen, Benesov, Brno, Liberec, Ples, Pribram, Usti and Labem, and Zlin). Two control groups, sampled at the same time of cases recruitment, were included in the study. The first group consisted of hospital-based individuals with a negative colonoscopy result for malignancy or idiopathic bowel diseases. The reasons for the colonoscopy were: i) positive fecal occult blood test, ii) hemorrhoids, iii) abdominal pain of unknown origin, and iv) macroscopic bleeding. The second control group consisted of healthy blood donor volunteers from a blood donor center in Prague. All individuals were subjected to standard examinations to verify the health status for blood donation and were cancer-free at the time of the sampling. Details of CRC cases and controls have been reported previously (Vymetalkova et al., 2014; Naccarati et al., 2016; Vymetalkova et al., 2016) [PMID: 24755277; PMID: 26735576; PMID: 27803053]. All subjects were informed and provided written consent to participate in the study. They approved the use of their biological samples for genetic analyses, according to the Declaration of Helsinki. The design of the study was approved by the Ethics Committee of the Institute of Experimental Medicine, Prague, Czech Republic. All subjects included in the study were Caucasians and comprised 1792 cases and 1764 matched controls. Controls were matched to CRC cases as 1:1 ratio. Matching was done on age and sex. Age was matched on +-5 years, whereas sex was matched exactly. For the cases without matched controls, matching was done only on sex. Early Detection Research Network (EDRN): The aim of the EDRN initiative is to develop and sustain a biorepository for support of translational research (Amin et al., 2010) [PMID: 21031013]. High-quality biospecimens were accrued and annotated with pertinent clinical, epidemiologic, molecular and genomic information. A user-friendly annotation tool and query tool was developed for this purpose. The various components of this annotation tool include: CDEs are developed from the College of American Pathologists (CAP) Cancer Checklists and North American Association of Central Cancer Registries (NAACR) standards. The CDEs provides semantic and syntactic interoperability of the data sets by describing them in the form of metadata or data descriptor. A total of 352 colorectal case samples and 399 controls were selected for this study. Controls were matched to CRC cases based on age and sex. The EPICOLON Consortium (EPICOLON): The EPICOLON Consortium comprises a prospective, multicentre and population-based epidemiology survey of the incidence and features of CRC in the Spanish population (Fernandez-Rozadilla et al., 2013) [PMID: 23350875]. Cases were selected as patients with de novo histologically confirmed diagnosis of colorectal adenocarcinoma. Patients with familial adenomatous polyposis, Lynch syndrome or inflammatory bowel disease-related CRC, and cases where patients or family refused to participate in the study were excluded. Hospital-based controls were recruited through the blood collection unit of each hospital, together with cases. All of the controls were confirmed to have no history of cancer or other neoplasm and no reported family history of CRC. Controls were randomly selected and matched with cases for hospital, sex and age (+- 5 years). A total of 370 cases and 370 controls were selected for genotyping. Hawaii Adenoma Study: For this adenoma study, two flexible-sigmoidoscopy screening clinics were first used to recruit participants on Oahu, Hawaii. Adenoma cases were identified either from the baseline examination at the Hawaii site of the Prostate Lung Colorectal and Ovarian cancer screening trial during 1996-2000 or at the Kaiser Permanente Hawaii's Gastroenterology Screening Clinic during 1995-2007. In addition, starting in 2002 and up to 2007, we also approached for recruitment all eligible patients who underwent a colonoscopy in the Kaiser Permanente Hawaii Gastroenterology Department. Cases were patients with histologically confirmed first-time adenoma(s) of the colorectum and were of Japanese, Caucasian or Hawaiian race/ethnicity. Controls were selected among patients with a normal colorectum and were individually matched to the cases on age at exam, sex, race/ethnicity, screening date (+-3 months) and clinic and type of examination (colonoscopy or flexible sigmoidoscopy). We recruited 1016 adenoma cases (67.8% of all eligible) and 1355 controls (69.2% of all eligible); 889 cases and 1169 controls agreed to give a blood and 29 cases and 34 controls, a mouthwash sample. A total of 989 cases and 1185 controls were genotyped for this study. Columbus-area HNPCC Study (HNPCC, OSUMC): Patients with colorectal adenocarcinoma diagnosed at six participating hospitals were eligible for this study, regardless of age at diagnosis or family history of cancer. Patients with a clinical diagnosis of familial adenomatous polyposis were not eligible for this study. These six hospitals perform the vast majority of all operations for CRC in the Columbus metropolitan area (population 1.7 million). The institutional review board at all participating hospitals approved the research protocol and consent form in accordance with assurances filed with and approved by the United States Department of Health and Human Services. Briefly, during the period of January 1999 through August 2004, 1,566 eligible patients with CRC were accrued to the study (Hampel et al., 2008) [PMID 18809606]. A total of 1472 colorectal cancer samples had enough blood DNA remaining to be sent for genotyping. Control samples were provided by the Ohio State University Medical Center%#39;s (OSUMC) Human Genetics Sample Bank. The Columbus Area Controls Sample Bank is a collection of control samples for use in human genetics research that includes both donors' anonymized biological specimens and linked phenotypic data. The data and samples are collected under the protocol "Collection and Storage of Controls for Genetics Research Studies", which is approved by the Biomedical Sciences Institutional Review Board at OSUMC. Recruitment takes place in OSUMC primary care and internal medicine clinics. If individuals agree to participate, they provide written informed consent, complete a questionnaire that includes demographic, medical and family history information, and donate a blood sample. 4-7 ml of blood is drawn into each of 3 ACD Solution A tubes and is used for genomic DNA extraction and the establishment of an EBV-transformed lymphoblastoid cell culture, cell pellet in Trizol, and plasma. Controls were matched to CRC cases as 1:1. Matching was done on age at reference time (age_ref), race, and sex. Age_ref was matched on +-5 years. Sex and race were matched exactly. For the cases without matched controls, matching was done only on sex and race with 1:1 ratio. Since controls are fewer than cases, one control is matched on 2 cases at most. Health Professionals Follow-up Study (HPFS): A parallel prospective study to the NHS (Nurses' Health Study). The HPFS cohort comprised 51,529 men aged 40-75 who, in 1986, responded to a mailed questionnaire (Rimm et al., 1990) [PMID: 2090285]. Participants provided information on health related exposures, including current and past smoking history, age, weight, height, diet, physical activity, aspirin use, and family history of colorectal cancer. Colorectal cancer and other outcomes were reported by participants or next-of-kin and were followed up through review of the medical and pathology record by physicians. Overall, more than 97% of self-reported colorectal cancers were confirmed by medical record review. Information was abstracted on histology and primary location. Incident cases were defined as those occurring after the subject provided the blood sample. Prevalent cases were defined as those occurring after enrollment in the study but before the subject provided the blood sample. Follow-up evaluation has been excellent, with 94% of the men responding to date. Colorectal cancer cases were ascertained through January 1, 2008. In 1993-1995, 18,825 men in the HPFS mailed blood samples by overnight courier, which were aliquoted into buffy coat and stored in liquid nitrogen. In 2001-2004, 13,956 men in the HPFS who had not provided a blood sample previously mailed in a swish-and-spit sample of buccal cells. Incident cases were defined as those occurring after the subject provided a blood or buccal sample. Prevalent cases were defined as those occurring after enrollment in the study in 1986, but before the subject provided either a blood or buccal sample. After excluding participants with histories of cancer (except nonmelanoma skin cancer), ulcerative colitis, or familial polyposis, case-control sets were previously constructed. In addition to colorectal cancer cases and controls, a set of adenoma cases and matched controls with available DNA from buffy coat were selected for genotyping. Over the follow-up period, data were collected on endoscopic screening practices and, if individuals had been diagnosed with a polyp, the polyps were confirmed to be adenomatous by medical record review. Adenoma cases were ascertained through January 1, 2008. A separate case-control set was constructed of participants diagnosed with advanced adenoma matched to control participants who underwent a lower endoscopy in the same time period and did not have an adenoma. Advanced adenoma was defined as an adenoma 1 cm or larger in diameter and/or with tubulovillous, villous, or highgrade dysplasia/carcinoma-in-situ histology. Matching criteria included year of birth (within 1 year) and month/ year of blood sampling (within 6 months), the reason for their lower endoscopy (screening, family history, or symptoms), and the time period of any prior endoscopy (within 2 years). Controls matched to cases with a distal adenoma either had a negative sigmoidoscopy or colonoscopy examination, and controls matched to cases with proximal adenoma all had a negative colonoscopy. In total, 159 advanced adenoma cases and 109 controls were selected for genotyping. Leeds Colorectal Cancer Study (LCCS): Following local ethical approval, colorectal cancer cases were recruited from 1997 until 2012 in Leeds, UK through surgical clinics. Initially, funding was provided by the UK Ministry of Agriculture, Farming and Fisheries (subsequently the Food Standards Agency) and Imperial Cancer Research Fund (subsequently Cancer Research UK). Recruitment also occurred similarly in Dundee, Perth and York between the periods of 1997 and 2001 using the same protocol and the data and samples were combined. Pathologically confirmed cases were consented at outpatient clinics, providing information on known and postulated risk factors for colorectal cancer (diet, lifestyle and family history) as well as providing a blood sample for DNA. Exclusion criteria included pre-existing diverticular disease and an inability to complete the questionnaire. The General Practitioners of cases (all UK residents have a nominated General Practitioner to whom to refer initial medical queries) and these GPs were asked to send letters to other persons on their patient list of the same gender and born within 5 years of the case. Subsequently to enhance the number of controls, we systematically invited patients from selected GP practices. Diet was assessed in cases and controls using an extensive dietary and lifestyle questionnaire modified by that produced by the European Prospective Investigation in Cancer (EPIC). The frequency that each specific food items were eaten was recorded and we also obtained average fruit and vegetable consumption as a cross-check. In total, 1591 cases and 739 controls provided a DNA sample. The North Carolina Colon Cancer Studies (NCCCS I/II): The North Carolina Colon Cancer Studies (NCCCS I- colon and NCCCS II-rectal) were population-based case-control studies conducted in 33 counties of North Carolina. Cases were identified using the rapid case ascertainment system of the North Carolina Central Cancer Registry. Patients with a first diagnosis of histologically confirmed invasive adenocarcinoma of the colon (cecum through sigmoid colon) between October 1996 and September 2000 were classified as potential cases in the NCCCS I. The NCCCS II included patients with a first diagnosis of histologically confirmed invasive adenocarcinoma of the sigmoid colon, rectosigmoid, or rectum (hereafter collectively referred to as rectal cancer) between May 2001 and September 2006. Additional eligibility requirements were: aged 40-80 years, residence in one of the 33 counties, ability to give informed consent and complete an interview, had a driver's license or identification card issued by the North Carolina Department of Motor Vehicles (if under the age of 65), and had no objections from the primary physician in regards to contacting the individual. Controls, identified and sampled during the respective study dates, were selected from two sources. Potential controls under the age of 65 were identified using the North Carolina Department of Motor Vehicles records. For those 65 years and older, records from the Center for Medicare and Medicaid Services were used. Controls were matched to cases using randomized recruitment strategies. Recruitment probabilities were done using strata of 5-year age, sex, and race groups. Dietary information was collected using a modified version of the semiquantitative food frequency questionnaire developed at the National Cancer Institute. In addition, participants were asked about vitamin and mineral supplementation, special diets, restaurant eating, sodium use, and fats used in cooking. In NCCCS I, 515 colorectal cases and 687 matched controls were sent for genotyping. In NCCCS II, 796 colorectal cases and 823 controls were sent from the NCCCS II for genotyping. Controls were matched to CRC cases as 1:1 ratio. Matching was done on age, race, and sex. Age was matched on +-5 years. Race and sex was matched exactly. For the cases without matched controls, matching was done only on sex and race. Nurses Health Study (NHS): The NHS cohort began in 1976 when 121,700 married female registered nurses age 30-55 years returned the initial questionnaire that ascertained a variety of important health-related exposures (Belanger et al., 1978) [PMID: 248266]. Since 1976, follow-up questionnaires have been mailed every 2 years. Colorectal cancer and other outcomes were reported by participants or next-of-kin and followed up through review of the medical and pathology record by physicians. Overall, more than 97% of self-reported colorectal cancers were confirmed by medical-record review. Information was abstracted on histology and primary location. The rate of follow-up evaluation has been high: as a proportion of the total possible follow-up time, follow-up evaluation has been more than 92%. Colorectal cancer cases were ascertained through June 1, 2008. In 1989 -1990, 32,826 women in NHS I mailed blood samples by overnight courier, which were aliquoted into buffy coat and stored in liquid nitrogen. In 2001-2004, 29,684 women in NHS I who did not previously provide a blood sample mailed a swish-and-spit sample of buccal cells. Incident cases were defined as those occurring after the subject provided a blood or buccal sample. Prevalent cases were defined as those occurring after enrollment in the study in 1976 but before the subject provided either a blood or buccal sample. After excluding participants with histories of cancer (except nonmelanoma skin cancer), ulcerative colitis, or familial polyposis, case-control sets were previously constructed from which DNA was isolated from either buffy coat or buccal cells for genotyping. In addition to colorectal cancer cases and controls, a set of advanced adenoma cases and matched controls with available DNA from buffy coat were selected for genotyping. Over the follow-up period, data were collected on endoscopic screening practices and, if individuals had been diagnosed with a polyp, the polyps were confirmed to be adenomatous by medical record review. Adenoma cases were ascertained through June 1, 2011. A separate case-control set was constructed of participants diagnosed with advanced adenoma matched to control participants who underwent a lower endoscopy in the same time period and did not have an adenoma. Advanced adenoma was defined as an adenoma more than 1 cm in diameter and/or with tubulovillous, villous, or high-grade dysplasia/carcinoma-in-situ histology. Matching criteria included year of birth (within 1 year) and month/year of blood sampling (within 6 months), the reason for their lower endoscopy (screening, family history, or symptoms), and the time period of any prior endoscopy (within 2 years). Controls matched to cases with a distal adenoma either had a negative sigmoidoscopy or colonoscopy examination, and controls matched to cases with proximal adenoma all had a negative colonoscopy. A total of 272 cases and 236 matched controls were sent to CIDR for the advanced adenoma case-control set. Northern Swedish Health and Disease Study (NSHDS): Comprises over 110,000 participants, including approximately one third with repeated sampling occasions, from three population-based cohorts (Dahlin et al., 2010; Myte et al., 2016) [PMID: 20197478; PMID: 27367522]. The largest is the ongoing Vasterbotten Intervention Programme, in which all residents of Vasterbotten County are invited to a health examination upon turning 30 (some years), 40, 50 and 60 years of age. Extensive measured and self-reported health and lifestyle data, as well as blood samples for central biobanking in Umea, Sweden, are collected at the health exam. Leucocyte DNA samples for 1:1-matched CRC case-control sets from the NSHDS, of which 878 samples are included in this study, have been selected for genotyping. This is in addition to 354 samples from the NSHDS previously analyzed as part of the multicenter EPIC cohort. Cancer-specific and overall survival data are available for all patients. For at least 425 patients, archival tumor tissue has been analyzed for the BRAF V600E mutation and by sequencing codon 12 and 13 for KRAS mutations, as well as for MSI screening status by immunohistochemistry and for an eight-gene CIMP panel using quantitative real-time PCR (MethyLight). Ohio Colorectal Cancer Prevention Initiative (OCCPI, OSUMC): OCCPI (ClinicalTrials.gov identifier: NCT01850654) is a population-based study of colorectal cancer patients diagnosed in one of 51 hospitals throughout the state of Ohio from January 1, 2013 through December 31, 2016. The OCCPI was created to decrease CRC incidence in Ohio by identifying patients with hereditary predisposition (statewide universal tumor screening for newly diagnosed CRC patients), increase colonoscopy compliance for first-degree relatives of CRC patients, and encourage future research through the creation of a biorepository. The 51 Ohio hospitals participating in the OCCPI were selected to represent a cross-section of clinical centers in the state based on high reported volume of CRC patients, affiliation with a high volume hospital, or interest in participation. Institutional Review Board (IRB) approval was obtained by the individual hospitals, Community Oncology Programs, or by ceding review to the OSU IRB. Written informed consent was obtained. A total of 2139 colorectal cases were genotyped. Patients were considered eligible for this study if they were age 18 or older at the time of enrollment, if they had a surgical resection (or biopsy if unresectable) in the state of Ohio demonstrating an adenocarcinoma of the colorectum from 1/1/13 - 12/31/16. Matched control samples were selected from the Ohio State University Medical Center's (OSUMC) Human Genetics Sample Bank in an identical way to the selection for the Columbus-area HNPCC Study (please refer to the description for the Columbus-area HNPCC Study). Prostate, Lung, Colorectal and Ovarian Cancer Screening Trail (PLCO): PLCO enrolled 154,934 participants (men and women, aged between 55 and 74 years) at ten centers into a large, randomized, two-arm trial to determine the effectiveness of screening to reduce cancer mortality. Sequential blood samples were collected from participants assigned to the screening arm. Participation was 93% at the baseline blood draw. In the observational (control) arm, buccal cells were collected via mail using the "swish-and-spit" protocol and participation rate was 65%. Details of this study have been previously described (Huang et al., 2016) [PMID: 27673363] and are available online (http://dcp.cancer.gov/plco). For this study 1651 advanced adenoma cases and 1392 controls were selected for genotyping. Selenium and Vitamin E Prevention Trial (SELECT): The Selenium and Vitamin E Cancer Prevention Trial (SELECT) was a double-blind, placebo controlled clinical trial which explored using selenium and vitamin E alone and in combination to prevent prostate cancer in healthy men (Lippman et al., 2009) [PMID: 19066370]. Secondary endpoints included the prevention of colorectal and lung cancers. SELECT was conducted at 427 sites and centers in the United States, Canada and Puerto Rico; 35,533 men 55 years and older (50 or older if African American) were randomized beginning August 22, 2001. Supplementation was discontinued on October 23, 2008 due to futility. 308 colorectal cancer cases and 308 matched controls were selected from the SELECT population and sent for genotyping. Screening Markers For Colorectal Disease Study and Colonoscopy and Health Study (SMS-REACH): Details on this study population were previously reported (Burnett-Hartman et al., 2014) [PMID: 24875374]. Participants were enrollees in an integrated health-care delivery system in western Washington State (Group Health Cooperative, Seattle, Washington) aged 24-79 years who underwent an index colonoscopy for any indication between 1998 and 2007 and donated a buccal-cell or blood sample for genotyping analysis. Study recruitment took place in 2 phases, with phase 1 occurring in 1998-2003 and phase 2 occurring in 2004-2007. Persons who had undergone a colonoscopy less than 1 year prior to the index colonoscopy, persons with inadequate bowel preparation for the index colonoscopy, and persons with a prior or new diagnosis of colorectal cancer, a familial colorectal cancer syndrome (such as familial adenomatous polyposis), or another colorectal disease were ineligible. Patients diagnosed with adenomas or serrated polyps and persons who were polyp-free at the index colonoscopy (controls) were systematically recruited during both phases of recruitment. Approximately 75% agreed to participate and provided written informed consent. Based on medical records, persons who agreed to participate and those who refused study participation were similar with respect to age, sex, and colorectal polyp status. Study protocols were approved by the institutional review boards of the Group Health Cooperative and the Fred Hutchinson Cancer Research Center (Seattle, Washington). A total of 575 cases and 508 matched were selected for the study. Controls were matched to CRC cases as 1:1 ratio. Matching was done on age_ref, race, and sex. Age_ref was matched on +-5 years. The Women's Health Initiative (WHI): WHI is a long-term national health study that has focused on strategies for preventing heart disease, breast and colorectal cancer, and osteoporotic fractures in postmenopausal women. The original WHI study included 161,808 postmenopausal women enrolled between 1993 and 1998. The Fred Hutchinson Cancer Research Center in Seattle, WA serves as the WHI Clinical Coordinating Center for data collection, management, and analysis of the WHI. The WHI has two major parts: a partial factorial randomized Clinical Trial (CT) and an Observational Study (OS); both were conducted at 40 Clinical Centers nationwide. The CT enrolled 68,132 postmenopausal women between the ages of 50-79 into trials testing three prevention strategies. If eligible, women could choose to enroll in one, two, or all three of the trial components. The components are: Hormone Therapy Trials (HT): This double-blind component examined the effects of combined hormones or estrogen alone on the prevention of coronary heart disease and osteoporotic fractures, and associated risk for breast cancer. Women participating in this component with an intact uterus were randomized to estrogen plus progestin (conjugated equine estrogens [CEE], 0.625 mg/d plus medroxyprogesterone acetate [MPA] 2.5 mg/d] or a matching placebo. Women with prior hysterectomy were randomized to CEE or placebo. Both trials were stopped early, in July 2002 and March 2004, respectively, based on adverse effects. All HT participants continued to be followed without intervention until close-out. Dietary Modification Trial (DM): The Dietary Modification component evaluated the effect of a low-fat and high fruit, vegetable and grain diet on the prevention of breast and colorectal cancers and coronary heart disease. Study participants were randomized to either their usual eating pattern or a low-fat dietary pattern. Calcium/Vitamin D Trial (CaD): This double-blind component began 1 to 2 years after a woman joined one or both of the other clinical trial components. It evaluated the effect of calcium and vitamin D supplementation on the prevention of osteoporotic fractures and colorectal cancer. Women in this component were randomized to calcium (1000 mg/d) and vitamin D (400 IU/d) supplements or a matching placebo. The Observational Study (OS)examines the relationship between lifestyle, environmental, medical and molecular risk factors and specific measures of health or disease outcomes. This component involves tracking the medical history and health habits of 93,676 women not participating in the CT. Recruitment for the observational study was completed in 1998 and participants were followed annually for 8 to 12 years. All centrally confirmed cases of invasive colorectal cancers, or deaths from colorectal cancer were selected as potential cases from September 30, 2015 database. Controls were participants free of colorectal cancer (invasive or in situ) as of September 30, 2015. Potential cases and controls were excluded if they (1) were non-White; (2) had history of colorectal cancers at baseline; (3) lost to follow-up after enrollment; (4) DbGAP ineligible; (5) had <1.25ug of DNA; (6) selected for WHI study M26 Phase I or II; (7) selected for WHI study AS224 and also included in the imputation project. A total of 578 cases and 104,429 controls met the eligibility criteria. Each case was matched with 1 control (1:1) that exactly met the following matching criteria: age (+-5 years), 40 randomization centers (exact), WHI date (+-3 years), CaD date (+-3 years), OS flag (exact), HRT assignments (exact), DM assignments (exact), and CaD assignments (exact). Control selection was done in a time-forward manner, selecting one control for each case from the risk set at the time of the case's event. The matching algorithm was allowed to select the closest match based on a criteria to minimize an overall distance measure (Bergstralh EJ, Kosanke JL. Computerized matching of cases to controls. Technical Report #56, Department of Health Sciences Research, Mayo Clinic, Rochester MN. April 1995). Each matching factor was given the same weight. When exact matches could not be found, the matching criteria were gradually relaxed among unmatched cases and controls until all cases had found matched controls. Using the matching criteria specified above, 559 of the 578 eligible cases found exact matches. The matching criteria was then relaxed to : Age+-5, randomization centers, WHI date +- 3 years, CaD date +- 3 years, OS flag, HRT flag, DM flag, CaD flag. 17 of the remaining 19 unmatched cases found matched controls. By matching on Age+-5, randomization centers, WHI date +- 3 years, CaD date +- 3 years, OS flag, HRT flag, the remaining 2 unmatched cases found their matches.
Lynch Syndrome (LS) tumors are characterized by constitutional mutations in DNA mismatch-repair genes. Colorectal cancers (CRCs) are the predominant tumor type in patients with LS. Here, we have used whole-genome and transcriptome sequencing of LS- CRC to find similarities and differences of mutation and gene expression characteristics between LS-CRC and sporadic CRC (data provided by TCGA via dbGaP). Furthermore, we were interested in the molecular heterogeneity of LS-CRC. We have performed a molecular characterization of LS-tumors and of matched tumor-distant reference colonic mucosa based on whole-genome DNA- and RNA-sequencing analyses. Our data indicates the existence of two subgroups of LS-CRCs, G1 and G2, where G1 tumors show a higher number of somatic mutations, higher microsatellite slippage and a different mutation spectrum.
Both childhood cancers and structural birth defects are critical and costly conditions associated with substantial morbidity and mortality. Elucidating the underlying genetic etiology of these diseases has the potential to profoundly improve preventative measures, diagnostics, and therapeutic interventions. For the current study, families with inherited adolescent idiopathic scoliosis were included. Both affected and unaffected family members were included.
We performed whole genome sequencing and whole-exome sequencing of cell-free DNA (cfDNA) and whole-exome sequencing of matched tumor biopsies and germline DNA from patients with metastatic cancer. Using ichorCNA, a software tool that quantifies tumor content in ultra-low pass whole genome sequencing (~0.1x) of cfDNA without prior genomic characterization of the tumor, we show genome-wide concordance between cfDNA and tumor biopsies and detectability of high tumor fractions (>0.1) in the cfDNA of many patients with metastatic cancer. We then established that whole-exome sequencing of cfDNA can enable comprehensive profiling of tumors from blood, with high tumor-content cfDNA samples demonstrating concordance of clonal somatic mutations, copy number alterations, mutational signatures, and neoantigens with matched tumor biopsies. This study introduces a new method to identify patients that could be eligible for tumor profiling from cfDNA and sheds light on the concordance between metastatic tissue and blood biopsies.
The Gabriella Miller Kids First Pediatric Research Program) (Kids First) is a trans-NIH effort initiated in response to the 2014 Gabriella Miller Kids First Research Act and supported by the NIH Common Fund. This program focuses on gene discovery in pediatric cancers and structural birth defects and the development of the Gabriella Miller Kids First Pediatric Data Resource (Kids First Data Resource). Both childhood cancers and structural birth defects are critical and costly conditions associated with substantial morbidity and mortality. Elucidating the underlying genetic etiology of these diseases has the potential to profoundly improve preventative measures, diagnostics, and therapeutic interventions. All of the WGS and phenotypic data from this study are accessible through dbGaP and https://kidsfirstdrc.org, where other Kids First datasets can also be accessed. The Kids First study of nonsyndromic orofacial cleft (OFC) birth defects in Latin American families is a whole genome sequencing study of 283 Latin-American parent-case trios drawn from ongoing collaborations led by Dr. Mary L. Marazita of the University of Pittsburgh Center for Craniofacial and Dental Genetics, and including a collaboration with Dr. Lina Moreno Uribe and Dr. Andrew Lidral of the University of Iowa. All families were ascertained through the Clinica Noel where patients with OFCs receive care from the Antioquia University School of Dentistry in Medellin, Colombia (key on-site colleagues included Dr. Luz Consuelo Valencia-Ramirez and Dr. Mauricio Arcos-Burgos). Genetic studies have shown that this population is comprised of an admixture of immigrant male Caucasians (mainly Spaniards and Basques) and native Amerindian females. Every subject has had a genetic evaluation, including a pedigree analysis for a family history of clefting and other birth defects, a pregnancy history for environmental exposures, and a complete physical exam to rule out suspected or known syndromes or environmental phenocopies. Sequencing was done by the Broad Institute sequencing center funded by the Kids First program (grant number U24-HD090743). The case in each of the Kids First OFC trios has cleft lip (CL, Figure A below), cleft palate (CP, Figure B), or both (CL+CP, Figure C): OFCs are genetically complex structural birth defects caused by genetic factors, environmental exposures, and their interactions. OFCs are the most common craniofacial anomalies in humans, affecting approximately 1 in 700 newborns, and are one of the most common structural birth defects worldwide. On average a child with an OFC initially faces feeding difficulties, undergoes 6 surgeries, spends 30 days in hospital, receives 5 years of orthodontic treatment, and participates in ongoing speech therapy, leading to an estimated total lifetime treatment cost of about $200,000. Further, individuals born with an OFC have higher infant mortality, higher mortality rates at all other stages of life, increased incidence of mental health problems, and higher risk for other disorders (notably including breast, brain, and colon cancers). Prior genome-wide linkage and association studies have now identified at least 18 genomic regions likely to contribute to the risk for nonsyndromic OFCs. Despite this substantial progress, the functional/pathogenic variants at OFC-associated regions are mostly still unknown. Because previous OFC genomic studies (genome-wide linkage, genome-wide association studies (GWAS), and targeted sequencing) are based on relatively sparse genotyping data, they cannot distinguish between causal variants and variants in linkage disequilibrium with unobserved causal variants. Moreover, it is unknown whether the association or linkage signals are due to single common variants, haplotypes of multiple common variants, clusters of multiple rare variants, or some combination. Finally, we cannot yet attribute specific genetic risk to individual cases and case families. Therefore, the goal of the current study is identify specific OFC risk variants in Latin American families by performing whole genome sequencing of parent-case trios.
Uveal melanoma (UM) is the most common primary cancer of the eye and frequently leads to metastatic death. Metastatic risk can be stratified into low, intermediate and high based on the presence of mutually exclusive mutations in EIF1AX, SF3B1 and BAP1, respectively. The purpose of this study was to comprehensively profile the genetic aberrations in a set of primary uveal melanomas using whole exome sequencing, as well as DNA methylation profiling of selected samples, to improve understanding of its pathogenesis.
The Gabriella Miller Kids First Pediatric Research Program (Kids First) is a trans-NIH effort initiated in response to the 2014 Gabriella Miller Kids First Research Act and supported by the NIH Common Fund. This program focuses on gene discovery in pediatric cancers and structural birth defects and the development of the Gabriella Miller Kids First Pediatric Data Resource (Kids First Data Resource). All of the WGS and phenotypic data from this study are accessible through dbGaP and kidsfirstdrc.org, where other Kids First datasets can also be accessed. Children with disseminated neuroblastoma have a very high risk of treatment failure and death despite receiving intensified chemotherapy, radiation therapy and immunotherapy. The long-term goal of our research program is to ultimately improve neuroblastoma cure rates by first comprehensively defining the genetic basis of the disease. The central hypothesis to be tested here is that neuroblastoma arises largely due to the epistatic interaction of common and rare heritable DNA variation. Here we will perform a comprehensive whole genome sequencing of 563 quartets of neuroblastoma patient germline and diagnostic tumor DNAs and germline DNAs from both parents. The case series was recently collected through a Children's Oncology Group epidemiology clinical trial and is robustly annotated with complete demographic (age, sex, race, ethnicity), clinical (e.g. age at diagnosis, stage, risk group), epidemiologic (parental dietary and exposure questionnaire) and biological (e.g. tumor MYCN status and multiple other tumor genomic measures) co-variates. Subjects were consented for genetic research and DNA is immediately available for shipment for sequencing. We propose Illumina-based whole genome sequencing in the 593 "trio" germline samples (Aim 1; due to missing parent: 487 full neuroblastoma triads, 106 child-single parent dyads = 1673 whole genome sequences) and matched diagnostic tumor DNA (Aim 2; N=366) at 30x sequencing depth (N=2039 whole genome sequences). Also in Aim 2 we will perform whole exome (100x) and RNA sequencing on the 366 tumor DNA and 228 tumor RNA samples from this cohort. Finally, we propose a pilot study of structural variation using long-range sequencing in 10 non-overlapping tumor samples chosen based on potentially relevant chromosomal alterations discovered with conventional NGS. Thus, a total of 2277 individual samples and 2655 sequences will be generated. We will use our established analytic pipeline that is currently being used to study the germline genomes of all cases sequenced through the NCI supported Therapeutically Applicable Research to Generate Effective Treatments program. We plan a three-stage analytic approach, first focusing on classic de novo and inherited Mendelian damaging alterations. We will next integrate our extensive epigenomic data from human neuroblastoma cell lines and genome-wide association study data (N=5,703 neuroblastoma cases to date) to guide a comprehensive assessment of noncoding variants that influence tumor initiation with a recently established analytic pipeline. Finally, we will utilize the tumor DNA analyses to inform relevance via somatic gain or loss of function effects at the sequence and/or copy number levels. All data generated in this project will be immediately placed into the Genomic Data Commons (GDC) and we will compute within this environment by importing our analytic pipelines into the GDC. These data will be fully integrated into the Kids First Data Resource and freely shared with all academically qualified petitioners. This comprehensive data set derived from a large and richly phenotyped series of neuroblastoma DNA quartets will be integrated with existing germline and/or tumor genomic data from over 6,000 neuroblastoma subjects (but none with matched patient-parent germline sequencing data) to provide an unparalleled opportunity to comprehensively discover the genetic basis of neuroblastoma.
When undergoing treatment for breast cancer, many women experience severe side effects, some of which result in treatment-related death and some that can persist for years. Little is understood regarding factors that may predict drug toxicities. Pharmacogenetics, the investigation of variants in candidate genes in drug metabolism pathways, has been used to determine susceptibility to treatment-related toxicities, as well as to cancer recurrence. Although there have been some strong and important findings using this approach, such as identification of single nucleotide polymorphisms (SNPs) that predispose to side effects associated with thiopurines and irinotecan, there has been less progress in assessment of genetic variants that predispose to toxicities resulting from the multi-drug regimen commonly used to treat breast cancer, anthracyclines (A), cyclophosphamide (C), and taxanes (T). These difficulties in identification of key gene variants may be due to the complex metabolic pathways of these drugs, the lack of rate limiting enzymes in the processes, or the limitations of single SNP analysis, rather than capturing all of the variability across the genes. In addition to drug metabolism pathways, however, there may be a number of constitutional factors or other processes that affect damage to normal tissues in the course of chemotherapy, some known or hypothesized, such as DNA repair and oxidative stress pathways, and others not yet discovered. However, there have been no clear candidate genes that account for a large part of the variation in drug or treatment response, and there are likely important genes that influence sensitivity of cells to chemotherapy through unknown pathways which have not yet been identified or hypothesized. The present technological capabilities to screen the entire genome for variants that discriminate populations allows the opportunity to identify these as yet unknown pathways, and open the doors to exciting new avenues of research into mechanisms that had not been previously considered. We conducted a genome-wide scan (GWAS) in a clinical trial (S0221), in which women with high risk breast cancer were treated with different dosing schedules of C, A and T. Blood specimens were collected and banked, and DNA extracted for genotyping on the Illumina OMNI 1M platform. The GWAS data were used to examine genetic variants significantly associated with grades 3 and 4 toxicities, including peripheral neuropathy recorded during the T segment. In S0221, toxicities were graded according to the NCI Common Toxicity Criteria for Adverse Events (CTCAE). The neurotoxicity is predominantly a distal sensory neuropathy, which is characterized by pain, numbness, tingling, and reduced functional capacity in the extremities. Other symptoms include parasthesias, ataxia, impaired vibration and joint position sense, and loss of tendon reflexes. By using a GWAS approach, it is likely that important pathways not previously considered can be revealed as important in susceptibility to treatment-related toxicities, identifying those at greatest risk for alternate drugs or dose reduction, and opening new areas of research for prevention of taxanes-related neuropathy among patients receiving chemotherapy for breast cancer.
The Pediatric Preclinical Testing Consortium (PPTC) is addressing the unmet need of streamlining the development of new therapies for childhood cancers. The PPTC seeks to develop robust biomarkers of anticancer drug activity, and the majority of these are predicted to be genetic mutations that can be detected in tumor DNA and/or RNA. In order to design the most impactful experiments that can be rapidly translated to the clinic, PPTC investigators require a complete genomic characterization of the patient-derived xenograft tumor models that are utilized across the consortium. This will not only allow for the most robust experimental design, but also will increase the engagement of industry partners who seek collaborators poised to provide the proof-of-concept necessary for drugs in their development pipelines. All data and models will be made available to academically qualified investigators.
