Citations

Abstract Abstract 1737 Background: The somatic JAK2 V617F (V617F) mutation is found in approximately 95% of polycythemia vera (PV) and 50–60% of essential thrombocythemia (ET) and primary myelofibrosis (PMF) patients. Detection of this mutation occurs primarily through genomic analysis of peripheral blood samples of myeloproliferative neoplasm (MPN) patients. This study demonstrates a novel broad screening mechanism for detection of V617F from myeloid cells in saliva samples from an online cohort of MPN patients and from a broader database of genotyped individuals. Methods: MPN patients were recruited primarily through social media and patient-mediated outreach efforts. Patients gave IRB-approved consent and completed surveys through an online 23andMe account. Participation in the MPN research initiative was free. In collaboration with an uncompensated panel of academic experts, online surveys were developed to collect patient-reported data on diagnosis and results of genetic testing for the V617F mutation. Participants were genotyped on SNP arrays based on the Illumina Omni Express, with additional custom content, including four probes for the V617F mutation. We estimated V617F mutation burden as the median across the four probes of B/(A+B) where A and B were normalized intensities for the reference and mutated alleles, respectively. We estimated sensitivity and specificity of our estimated V617F allele ratio, using the self-reported V617F-positive individuals to approximate the distribution of true positives, and 23andMe members from the broad database (outside of the MPN research cohort) and younger than 40 as likely true negatives. Results: Web-based recruitment efforts led to the accrual of over 900 MPN patients of different subtypes over 12 months. Of these participants, 745 patients have been genotyped and provided MPN-related health history and outcomes through online surveys. The cohort is disproportionately female (71%), with an average age of 53.1 ± 14.9 years. More than 57% of patients indicated a classic MPN diagnosis (PV, ET, PMF, or post PV/ET MF), 19.2% reported an atypical MPN diagnosis (systemic mastocytosis or hypereosinophilic syndrome), 14.5% indicated chronic myelogenous leukemia, and 9.3% of the cohort reported other diagnoses. From this MPN cohort, a total of 345 participants reported mutation test results. Consistent with expectations, the V617F variant was reported by patients in nearly all PV cases (105 of 110 patients with a self-reported diagnosis of PV), and at a lower rate in ET and MF cases (59 of 95 patients and 48 of 61 patients, respectively). In addition to self-reported data, we were specifically able to detect the V617F mutation using SNP array data. We determined a detection threshold for the V617F variant at which 86% of self-reported V617F carriers were scored as positive (i.e. test sensitivity), and 99.975% of young 23andMe customers were scored as negative (i.e. test specificity). Participants with a classic diagnosis in the MPN cohort who carry the V617F variant tended to be older (mean age=59.5 versus 54.6 years) and were less likely to be female (62.5% versus 72.0%) than non-carriers. At this threshold, we detected 133 individuals who likely carry the V617F mutation among a broader set of 23andMe participants (n= 99,700) who were not specifically recruited for the MPN study, corresponding to a prevalence of 0.14%. We estimated the positive predictive value of the test in this cohort, or the expected proportion of positive test results that are true, as 81%. Within the general 23andMe cohort, the frequency of the V617F variant increases with participant age, from a rate of 0.017% for age 20 to 30, to 1.1% for age 80 to 90. We also observed that patients with a high allele burden of V617F frequently had acquired uniparental disomy of chromosome 9p, as determined from calculated heterozygosity scores and no-call rates for this chromosomal arm. Conclusion: We can detect V617F with high specificity and sensitivity from myeloid cells in saliva. This non-invasive source for DNA extraction offers new possibilities for detecting genomic alterations and for finding novel genetic associations in MPN patients as well as the general population. This study demonstrates the feasibility of online technology to significantly accelerate recruitment and research progress in MPNs and other rare diseases. Disclosures: Barnholt: 23andMe, Inc.: Employment. Hinds:23andMe: Employment, Equity Ownership, Patents & Royalties. Kiefer:23andMe, Inc.: Employment. Do:23andMe, Inc.: Employment, Equity Ownership, Patents & Royalties. Eriksson:23andMe, Inc.: Employment, Equity Ownership, Patents & Royalties. Mountain:23andMe, Inc.: Consultancy, Employment, Honoraria, Patents & Royalties. Francke:23andMe, Inc.: Employment, Honoraria, Research Funding; Locus Development: Consultancy, Membership on an entity's Board of Directors or advisory committees. Tung:23andMe, Inc.: Employment. Mesa:23andMe, Inc.: Unpaid advisor and collaborator Other. Gotlib:23andMe, Inc.: Unpaid advisor and collaborator Other. Zehnder:23andMe, Inc.: Unpaid advisor and collaborator Other.

Abstract Abstract 707 Background: Myeloproliferative neoplasms (MPNs) are disorders that result in unregulated overproduction of one or more myeloid blood cell types by the bone marrow. Polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF) comprise the three classic MPNs. The somatic JAK2 V617F mutation is present in 95% of PV patients, and 50–60% of ET and PMF patients. Past work has identified a germline haplotype in JAK2 associated with risk of developing a V617F-positive MPN (Kilpivaara et al; Olcaydu et al; Jones et al, Nat. Genet., 2009). Methods: We recruited a web-based participatory cohort of individuals with MPNs to better understand the genetic basis of these conditions. Participation in this MPN research initiative included free genotyping, and participants provided informed consent and responses to surveys online, under a protocol approved by the external AAHRPP-accredited IRB, Ethical & Independent Review Services. We enrolled and collected saliva samples from more than 700 participants with the following self-reported diagnoses: systemic mastocytosis (n=142), ET (n=145), PV (n=137), PMF (n=50), chronic myelogenous leukemia (n=108), and 97 with overlapping diagnoses (e.g. ET or PV with PMF). Participants were genotyped using a derivative of the Illumina HumanOmniExpress BeadChip with additional custom content, including probes for the JAK2 V617F variant. We performed a genome-wide association study (GWAS) of classic MPN diagnoses (at least one of ET, PV, or MF), using 407 cases from this MPN research initiative and 94,037 controls drawn from the broader 23andMe research participant community. Association was assessed by logistic regression adjusted for age, gender, and 5 principal components to model ancestry. Results: We replicated the known association between germline variation in JAK2 and classic MPNs (rs12340895: odds ratio=2.5, P=7.4 × 10−35). We also identified a novel genome-wide-significant association in TERT, or telomerase reverse transcriptase (rs2853677: odds ratio=1.6 per G allele, P=6.3 × 10−11). The association is consistent with an additive model on the logistic scale (odds ratio=2.6 for 2 versus 0 G alleles). Another variant in TERT, rs2736100, has previously been associated with several non-hematological cancers and with red blood cell count, and our lead SNP is in linkage disequilibrium with TERT variant rs2736100 (r2=0.54). While no other loci reached the threshold of genome-wide significance (P<5.0 × 10−8), we saw a suggestive association with a germline missense variant (F858L) in ATM, or ataxia telangiectasia mutated gene (rs1800056: odds ratio=2.6 per C allele, P=1.4 × 10−5). This variant has also been reported to be associated with breast cancer and chronic lymphocytic leukemia. The rs2853677 TERT variant was associated with each of ET, PV, and PMF, with similar effect sizes. It was not associated with JAK2 V617F mutation status within the MPN cohort (odds ratio=1.0, P=1.0), while the germline JAK2 variant was preferentially associated with V617F-positive MPNs (odds ratio=2.1, P=3.0 × 10−6). The high-risk allele of rs2853677 was also predictive of V617F status among 23andMe participants who had not been recruited into the MPN community (odds ratio=1.6, P=0.0012). These results suggest that while variation in TERT facilitates either acquisition or proliferation of V617F-positive myeloid cells, it also predisposes to MPNs through a V617F-independent mechanism. Conclusion: We have identified a germline variant in TERT which is a new predisposition allele for classic MPNs. These results demonstrate the potential for web-based recruitment methods to contribute to genetic research for uncommon diseases. Disclosures: Hinds: 23andMe: Employment, Equity Ownership, Patents & Royalties. Barnholt:23andMe, Inc.: Employment. Zehnder:23andMe, Inc.: Unpaid advisor and collaborator Other. Kiefer:23andMe, Inc.: Employment. Do:23andMe, Inc.: Employment, Equity Ownership, Patents & Royalties. Eriksson:23andMe, Inc.: Employment, Equity Ownership, Patents & Royalties. Mountain:23andMe, Inc.: Consultancy, Employment, Honoraria, Patents & Royalties, Research Funding. Francke:23andMe, Inc.: Employment, Honoraria, Research Funding; Locus Development: Consultancy, Membership on an entity's Board of Directors or advisory committees. Tung:23andMe, Inc.: Employment. Mesa:23andMe, Inc: Unpaid advisor and collaborator Other. Gotlib:23andMe, Inc.: Unpaid advisor and collaborator Other.

Abstract Background: Prospective validation of breast cancer risk models integrating classical risk factors and genetic variants is required for risk-stratified prevention and screening strategies. The objective of this study was to validate a breast cancer risk model integrating classical risk factors and a 313-variant polygenic risk score (PRS) in multiple prospective cohort studies, and to project five-year risk of breast cancer in six different countries. Methods: The study population included 7,529 cases and 230,103 controls from 14 prospective cohort studies in Australia, Germany, the Netherlands, Sweden, UK, and USA. We used the Individualized Coherent Absolute Risk Estimator (iCARE) tool for risk model building, validation, and risk projection. Expected five-year risk of invasive or in situ breast cancer was compared to observed risk, overall and within deciles of expected risk using goodness of fit statistics. We evaluated calibration of the relative risk through meta-analysis across cohorts, and of the absolute risk within each cohort. Model discrimination was evaluated using the area under the curve (AUC), and percentages of women crossing risk thresholds. Projections of five-year risk distributions were estimated for women of European ancestry aged 50-70 years in the general populations of these six countries. Results: Analysis showed overall good calibration of the integrated iCARE-based model relative risk for both women younger than 50 years (χ2=14.9, P=0.09) and aged 50 years or older (χ2=14.6, P=0.10), with a small overestimation of risk for women in the highest decile of expected risk (RR = 3.5 expected vs 2.3 (95% CI 1.6 to 3.2) observed for women &lt;50 years; and 2.8 expected vs 2.3 (95% CI 2.0 to 2.7) observed for women 50+ years). The age-adjusted AUCs for the integrated model were 63.1 (95% CI 60.9 to 65.3) and 62.9 (95% CI 61.8 to 64.0), for the two age groups respectively. The calibration of absolute risk showed substantial variation across cohorts, particularly for the older group, but had no systematic bias. Model based projections in the general populations showed that compared to the population average, women in the 1st and 99th percentiles of the integrated risk score had relative risks 0.19 and 3.56 respectively. The proportion of women of European ancestry aged 50-70 years with a five-year risk greater than 3% (threshold for consideration of risk-lowering drugs by U.S. Preventive Services Task Force) ranged from 7.1% in Germany to 18.2% in the US, which corresponds to ~5.5 million women in the US. Conclusions: Five-year risk predictions from a model with classical risk factors and PRS are well calibrated and provide substantial risk stratification across multiple cohorts in six different countries. Further studies are needed to evaluate the clinical utility of the validated model for risk stratified screening and prevention of breast cancer. Citation Format: Parichoy Pal Choudhury, Amber Wilcox, Chi Gao, Brian Carter, Anika Husing, Mark Brook, Mikael Eriksson, Kara Martin, Chris Scott, Min Shi, Thomas Ahearn, Michael Jones, Nick Orr, Minouk Schoemaker, Kamila Czene, Jenny Chang-Claude, Jacques Simard, Doug Easton, Marjanka K. Schmidt, Dale Sandler, Clarice R. Weinberg, Celine Vachon, Roger Milne, Per Hall, Anthony Swerdlow, Rudolph Kaaks, Myrto Barrdahl, Mia Gaudet, Antonis Antoniou, Peter Kraft, Montserrat Garcia-Closas, Nilanjan Chatterjee. Validation of breast cancer risk model incorporating classical risk factors and polygenic risk scores in 14 prospective cohort studies in 6 countries [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 962.

5517 Background: Uterine serous carcinoma is a less common subtype of endometrial cancer that is associated with poorer survival. The optimal post-operative adjuvant treatment strategy for these patients remains uncertain. Methods: This multi-institutional, retrospective cohort study evaluated patients with early stage uterine serous carcinoma. Patients with FIGO Stage IA-II disease after surgery, whose tumors had serous or mixed serous/non-serous histology were included. Patients with carcinosarcoma were excluded. Clinical data were abstracted from local medical records. Summary statistics, Fisher’s exact, and Kruskal-Wallis tests were used to analyze demographic and clinical characteristics. Univariable and multivariable analyses were performed for recurrence-free survival (RFS) and overall survival (OS). Results: 634 patients were included. 77% of patients had Stage IA disease, 42% showed no myometrial invasion. The majority had pure serous histology (72%) and LVSI (76%). Adjuvant treatment varied: 12% received no adjuvant therapy, 7% had chemotherapy alone, 51% had cuff brachytherapy, 12% had cuff brachytherapy with chemotherapy (cuff/chemo), and 19% underwent pelvic radiation (EBRT). Complete RFS and OS data were available for 607 and 609 patients, respectively, and the median follow-up time was 58 months. As compared with patients who received no adjuvant therapy, patients who received cuff or cuff/chemo had improved RFS (cuff: HR 0.70, p = 0.02; cuff/chemo HR 0.53, p = 0.01) and OS (cuff HR 0.56, p = 0.001; cuff/chemo HR 0.48, p = 0.01). In a direct comparison, patients with cuff/chemo had better RFS and OS than those with chemotherapy alone (RFS HR 0.52, p = 0.03; OS HR 0.50, p = 0.05). There were no differences in RFS or OS for women who received chemotherapy alone or EBRT. Improved survival with cuff and cuff/chemo persisted on multivariable analyses (included age, stage, LVSI, adjuvant therapy type); additionally, EBRT was also associated with improved OS. In analyses limited to patients without myometrial invasion, patients with cuff or cuff/chemo had improved RFS and OS compared with observation alone. Conclusions: The use of adjuvant cuff brachytherapy with and without chemotherapy was associated with improved RFS and OS in patients with early stage uterine serous carcinoma.

While elevated blood cholesterol has been associated with an increased risk of colorectal cancer (CRC) in observational studies, causality is uncertain. Here we apply a Mendelian randomisation (MR) analysis to examine the potential causal relationship between lipid traits and CRC risk. We used single nucleotide polymorphisms (SNPs) associated with blood levels of total cholesterol (TC), triglyceride (TG), low‐density lipoprotein (LDL), and high‐density lipoprotein (HDL) as instrumental variables (IV). We calculated MR estimates for each risk factor with CRC using SNP‐CRC associations from 9,254 cases and 18,386 controls. Genetically predicted higher TC was associated with an elevated risk of CRC (odds ratios (OR) per unit SD increase = 1.46, 95% confidence interval [CI]: 1.20–1.79, p = 1.68 × 10−4). The pooled ORs for LDL, HDL, and TG were 1.05 (95% CI: 0.92–1.18, p = 0.49), 0.94 (95% CI: 0.84–1.05, p = 0.27), and 0.98 (95% CI: 0.85–1.12, p = 0.75) respectively. A genetic risk score for 3‐hydoxy‐3‐methylglutaryl‐coenzyme A reductase (HMGCR) to mimic the effects of statin therapy was associated with a reduced CRC risk (OR = 0.69, 95% CI: 0.49–0.99, p = 0.046). This study supports a causal relationship between higher levels of TC with CRC risk, and a further rationale for implementing public health strategies to reduce the prevalence of hyperlipidaemia.

Background The rarity of mutations in PALB2, CHEK2 and ATM make it difficult to estimate precisely associated cancer risks. Population-based family studies have provided evidence that at least some of these mutations are associated with breast cancer risk as high as those associated with rare BRCA2 mutations. We aimed to estimate the relative risks associated with specific rare variants in PALB2, CHEK2 and ATM via a multicentre case-control study. Methods We genotyped 10 rare mutations using the custom iCOGS array: PALB2 c.1592delT, c.2816T>G and c.3113G>A, CHEK2 c.349A>G, c.538C>T, c.715G>A, c.1036C>T, c.1312G>T, and c.1343T>G and ATM c.7271T>G. We assessed associations with breast cancer risk (42 671 cases and 42 164 controls), as well as prostate (22 301 cases and 22 320 controls) and ovarian (14 542 cases and 23 491 controls) cancer risk, for each variant. Results For European women, strong evidence of association with breast cancer risk was observed for PALB2 c.1592delT OR 3.44 (95% CI 1.39 to 8.52, p=7.1×10−5), PALB2 c.3113G>A OR 4.21 (95% CI 1.84 to 9.60, p=6.9×10−8) and ATM c.7271T>G OR 11.0 (95% CI 1.42 to 85.7, p=0.0012). We also found evidence of association with breast cancer risk for three variants in CHEK2, c.349A>G OR 2.26 (95% CI 1.29 to 3.95), c.1036C>T OR 5.06 (95% CI 1.09 to 23.5) and c.538C>T OR 1.33 (95% CI 1.05 to 1.67) (p≤0.017). Evidence for prostate cancer risk was observed for CHEK2 c.1343T>G OR 3.03 (95% CI 1.53 to 6.03, p=0.0006) for African men and CHEK2 c.1312G>T OR 2.21 (95% CI 1.06 to 4.63, p=0.030) for European men. No evidence of association with ovarian cancer was found for any of these variants. Conclusions This report adds to accumulating evidence that at least some variants in these genes are associated with an increased risk of breast cancer that is clinically important.