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Background: Known cutaneous malignant melanoma (CMM) genes account for melanoma risk in less than 40% of melanoma-prone families, suggesting the existence of additional risk genes or other modifiers. Whole exome sequencing (WES) of high-risk families usually results in the identification of a large number of potential disease-causing genes. However, prioritizing these genes and finding the true disease-causing ones have been challenging. We hypothesize that physically interacting proteins might have a similar effect on cell function and therefore, might produce a shared phenotype or increase the risk when mutated. To test this hypothesis, we applied a network approach integrating WES and protein-protein interaction (PPI) data to detect and prioritize rare variants in melanoma-prone families. Methods: We conducted WES analysis on germline DNA of 212 patients from 45 CMM families (2-5 affected people in a family) without known mutations. Variants that were rare ( Results: The WES analysis described above identified 546 genes that harbored rare variants, likely affect protein function and co-segregated in affected members in CMM families. After applying DADA across all networks, the rankings of these genes were fairly consistent. Top genes included both known CMM genes (such as MC1R, CDKN2B, KITLG, and TINF2) and genes that have not yet been associated with CMM susceptibility (such as FOXK1, AR, LEF1, RGL4, PABPC1, CHEK2, CTBP2, and BLM). These results highlight the importance of known CMM genes and their networks in CMM susceptibility, and demonstrate the potential value of network approaches in gene prioritization. Further evaluation of novel genes is in progress. Citation Format: Sally Yepes, Margaret Tucker, Hela Koka, Kristine Jones, Aurelie Vogt, Laurie Burdette, Wen Luo, Bin Zhu, Meredith Yeager, Belynda Hicks, Neal D. Freedman, Stephen J. Chanock, Alisa M. Goldstein, Xiaohong R. Yang. Whole-exome sequencing and protein interaction networks to prioritize candidate genes for cutaneous melanoma susceptibility [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 1638.

Ewing sarcoma (EWS), a pediatric tumor predominantly occurring in children of European ancestry, is characterized by the EWSR1-FLI1 fusion oncogene. We performed a genome-wide association study (GWAS) of 749 EWS cases and 1,378 unaffected individuals of European ancestry. Our study replicated previously reported susceptibility loci at 1p36.22, 10q21.3, and 15q15.1 and identified new loci at 6p25.1, 8q24.23, 20p11.22, and 20p11.23 (P-values Citation Format: Mitchell J. Machiela, Thomas G.P. Grünewald, Didier Surdez, Stephanie Reynaud, Olivier Mirabeau, Eric Karlins, Rebeca Alba Rubio, Sakina Zaidi, Sandrine Grossetete-Lalami, Stelly Ballet, Eve Lapouble, Valérie Laurence, Jean Michon, Gaelle Pierron, Heinrich Kovar, Nathalie Gaspar, Udo Kontny, Anna González-Neira, Piero Picci, Javier Alonso, Ana Patino-Garcia, Nadège Corradini, Neal D. Freedman, Nathaniel Rothman, Casey L. Dagnall, Laurie Burdett, Kristine Jones, Michelle Manning, Kathleen Wyatt, Weiyin Zhou, Meredith Yeager, David G. Cox, Robert N. Hoover, Javed Khan, Gregory T. Armstrong, Wendy M. Leisenring, Smita Bhatia, Leslie L. Robison, Uta Dirksen, Markus Metzler, Wolfgang Hartmann, Konstantin Strauch, Thomas Kirchner, Andreas E. Kulozik, Lindsay M. Morton, Lisa Mirabello, Margaret A. Tucker, Franck Tirode, Stephen Chanock, Olivier Delattre. Genome-wide association study identifies multiple new loci associated with Ewing sarcoma susceptibility [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr A13.

Ewing sarcoma (EWS) is a rare pediatric tumor predominantly occurring in children of European ancestry and is characterized by the pathognomonic EWSR1-FLI1 fusion oncogene. To identify germline susceptibility loci associated with EWS risk, we performed a genome-wide association study (GWAS) meta-analysis of 749 EWS cases and 1,378 unaffected individuals of European ancestry from sample collections within the Institut Curie, National Cancer Institute and the Childhood Cancer Survivor Study. Our study replicated previously reported susceptibility loci at 1p36.22, 10q21.3 and 15q15.1 as well as identified novel loci at 6p25.1, 8q24.23, 20p11.22 and 20p11.23 (P-values Citation Format: Mitchell J. Machiela, Thomas G. Grünewald, Didier Surdez, Stephanie Reynaud, Olivier Mirabeau, Eric Karlins, Rebeca Alba Rubio, Sakina Zaidi, Sandrine Grossetete-Lalami, Stelly Ballet, Eve Lapouble, Valérie Laurence, Jean Michon, Gaelle Pierron, Heinrich Kovar, Nathalie Gaspar, Udo Kontny, Anna González-Neira, Piero Picci, Javier Alonso, Ana Patino-Garcia, Nadège Corradini, Neal D. Freedman, Nathaniel Rothman, Casey L. Dagnall, Laurie Burdette, Kristine Jones, Michelle Manning, Kathleen Wyatt, Weiyin Zhou, Meredith Yeager, David G. Cox, Robert N. Hoover, Javed Khan, Gregory T. Armstrong, Wendy M. Leisenring, Smita Bhatia, Leslie L. Robison, Uta Dirksen, Markus Metzler, Wolfgang Hartmann, Konstantin Strauch, Thomas Kirchner, Andreas E. Kulozik, Lindsay M. Morton, Lisa Mirabello, Margaret A. Tucker, Franck Tirode, Stephen J. Chanock, Olivier Delattre. Multiple new susceptibility loci identified in genome-wide association study of Ewing sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2970.

Survival rates for osteosarcoma, the most common primary bone cancer, have changed little over the past three decades and are particularly low for patients with metastatic disease. To date, few prognostic factors have been identified to be associated with survival in patients with osteosarcoma. We conducted an international, multi-institutional genome-wide association study (GWAS) to identify germline genetic variants associated with overall survival in 632 patients with osteosarcoma. Subjects were genotyped as part of our previously published osteosarcoma susceptibility GWAS, including 523 patients of >80% European ancestry and 109 patients from Brazil. We performed a time-to-event analysis and estimated hazard ratios (HR) and 95% confidence intervals (CI) using Cox proportional hazards models, with and without adjustment for metastatic disease. Cox models were adjusted for age at diagnosis, gender, significant principal components, and study/center. SNPs that reached P Citation Format: Roelof Koster, Orestis A. Panagiotou, William A. Wheeler, Eric Karlins, Julie M. Gastier-Foster, Silvia Regina Caminada de Toledo, Antonio S. Petrilli, Adrienne M. Flanagan, Roberto Tirabosco, Irene L. Andrulis, Jay S. Wunder, Nalan Gokgoz, Ana Patiño-Garcia, Fernando Lecanda, Massimo Serra, Claudia Hattinger, Piero Picci, Katia Scotlandi, David M. Thomas, Mandy L. Ballinger, Richard Gorlick, Donald A. Barkauskas, Logan G. Spector, Margaret Tucker, Belynda Hicks, Meredith Yeager, Robert Hoover, Stephen J. Chanock, Sharon A. Savage, Lisa J. Mirabello. Genome-wide association study identifies the GLDC/IL33 locus associated with survival of osteosarcoma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2077.

Background: Currently, women are referred for BRCA1/2 mutation testing if their family history of breast and ovarian cancer indicates they have sufficient probability of carrying mutations. In contrast, calls have intensified for population-wide testing for BRCA1/2 founder mutations among Ashkenazi Jews, due to relatively high mutation prevalence (2.5%) and decreasing genotyping costs. However, population-wide testing would strain genetic counseling resources and incur costs from testing mostly mutation-negative women. We compared the performance of population-wide vs. carrier-probability-based BRCA1/2 testing in the community-based Washington Ashkenazi Study (WAS). Methods: BRCA1/2 carrier-probabilities based on reported family histories were calculated using BRCAPRO for 4589 probands (102 BRCA1/2 mutation-carriers) in WAS. For each carrier-probability threshold, we compared the percent of mutations found (sensitivity) vs. the percent of women requiring mutation testing, overall and by proband age. At example carrier-probability thresholds, undetected and detected carriers’ attributes were compared using nonparametric tests. Results: A 1.2% carrier-probability threshold identified 80% of BRCA1/2 mutations in the 35% of women with highest carrier-probability. For women under age 40, 94% of BRCA1/2 mutations were identified in the 50% of women with highest carrier-probability. Compared to identified mutation-carriers, missed mutation-carriers had no personal cancer history, no affected first- and second-degree relatives (p Conclusion: Carrier-probability-based BRCA1/2 mutation testing identified large majorities of mutation-carriers and would have avoided testing for many mutation-negative women. Missed mutation-carriers were older and cancer-free and would gain minimal benefit from risk-reducing interventions. A cost-effective carrier-probability threshold could acceptably tradeoff identifying BRCA1/2 mutation carriers before they get cancer while testing as few women as possible. Citation Format: Ana F. Best, Margaret A. Tucker, Hormuzd A. Katki. Population-wide vs. carrier-probability-based BRCA1/2 mutation testing in the Washington Ashkenazi Study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4271. doi:10.1158/1538-7445.AM2017-4271

In children and adolescents, osteosarcoma (OS) is the most common malignant bone tumor. OS occurs in certain cancer predisposition syndromes at a higher than expected frequency. However, outside of these rare syndromes, OS is significantly more common and its genetic etiology remains poorly understood. We conducted an evaluation of rare exonic variants in 545 unselected OS cases compared with 1061 cancer-free controls using whole-exome sequencing of blood or buccal cell DNA to estimate the prevalence and burden of rare deleterious germline variants. We assessed potentially pathogenic rare variants in 126 established cancer predisposing genes (CPG) and known somatically mutated genes. We also surveyed the exome for genes with a higher burden of rare variants in 342 EUR cases with 994 EUR controls sequenced at the same time. Rare genetic variants, defined by a MAF A total of 14.5% of cases had a predicted pathogenic or high impact variant in an autosomal dominant CPG. A significantly higher pathogenic rare variant burden was present in EUR cases compared with EUR controls (Pburden=3.7x10-05). TP53 had the highest prevalence of pathogenic mutations (5% of EUR cases; Pburden=1.05x10-09). CDKN2A, MEN1, MLH1, MUTYH, PALB2 and VHL had a significantly higher rare variant burden in the EUR cases. 7.5% of cases had a predicted pathogenic or probably pathogenic variant in an autosomal recessive CPG (Pburden=5.4x10-03). Additionally, two males had a pathogenic variant in the X-linked genes, DKC1 and GPC3. In total, 21% of cases had a predicted pathogenic or high impact variant in a CPG (Pburden=2.4x10-07). Exome-wide analysis identified two novel genes with significantly higher rare variant burdens in the cases compared to controls. In conclusion, several CPGs and two novel genes, not previously associated with OS, had an enrichment of rare variants in OS and warrant further follow-up. Our results indicate that a clinically significant fraction of OS cases may harbor one or more mutations worthy of consideration for further investigation and genetic counseling. Citation Format: Roelof Koster, Bin Zhu, Meredith Yeager, Michael Dean, Matthew Gianferante, Lei Song, Joshua Sampson, NCI DCEG Cancer Genomics Research Laboratory, Julie Gastier-Foster, Richard Gorlick, Silvia Regina Caminada de Toledo, Antonio Petrilli, Ana Patiño-Garcia, Fernando Lecanda, Massimo Serra, Claudia Hattinger, Piero Picci, Katia Scotlandi, Adrienne Flanagan, Roberto Tirabosco, Maria Amary, Nilgün Kurucu, Inci Ergurhan Ilhan, Neriman Sari, Mandy Ballinger, David Thomas, Donald Barkauskas, Belynda Hicks, Margaret Tucker, Neil Caporaso, Robert Hoover, Stephen Chanock, Sharon Savage, Lisa Mirabello. Whole-exome sequencing identifies a high frequency of germline deleterious variants in cancer predisposition genes in individuals with osteosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4871. doi:10.1158/1538-7445.AM2017-4871

Previous studies have demonstrated elevated risks for tMDS/AML after chemotherapy for non-Hodgkin lymphoma, Hodgkin lymphoma, and plasma cell neoplasms, but current treatment practices have changed considerably. We utilized large-scale, population-based cancer registry data from the United States to quantify for the first time tMDS/AML risks after chemotherapy for lymphoid malignancies in the current treatment era, including analysis for specific non-Hodgkin lymphoma subtypes. In 17 registries, we identified 121,840 adults without HIV infection who survived ≥1 year following a first primary lymphoid malignancy diagnosis during 2000-2013 and were initially treated with chemotherapy. tMDS/AML risk was compared with that expected in the general population using SIRs. tMDS/AML risk was significantly increased 5- to 9-fold after chemotherapy for the most common lymphoid malignancies, including DLBCL, plasma cell neoplasms, follicular lymphoma, Hodgkin lymphoma, and CLL/SLL (Table 1). Approximately 5-fold increased risks were observed after chemotherapy for marginal zone lymphoma, LPL/WM, and other/unspecified lymphomas. In contrast, risks were strikingly elevated (>10-fold) after chemotherapy for precursor leukemia/lymphoma, Burkitt lymphoma/leukemia, peripheral T-cell lymphoma, and mantle cell lymphoma. Only chemotherapy for hairy cell leukemia was not associated with increased tMDS/AML risk (SIR=1.4), albeit based on small numbers. tMDS/AML risks were higher By time since lymphoid neoplasm diagnosisOverall1.0-4.9 years≥5 yearsFirst primary lymphoid malignancyTotal (N)Mean age at diagnosis (y)NSIR(95%CI)NSIR(95%CI)NSIR(95%CI)Hodgkin lymphoma16,74840.3659.0(6.9, 11.4)4310.7(7.8, 14.5)226.8(4.3, 10.3)CLL/SLL8,47864.31129.4(7.7, 11.3)729.2(7.2, 11.6)409.8(7.0, 13.3)DLBCL31,69259.72045.6(4.8, 6.4)1265.6(4.7, 6.7)785.5(4.4, 6.9)Follicular lymphoma15,65659.51457.8(6.6, 9.2)867.9(6.3, 9.8)597.7(5.8, 9.9)Marginal zone lymphoma4,22362.8295.5(3.7, 7.8)195.7(3.4, 8.9)105.1(2.4, 9.4)Plasma cell neoplasms22,75363.21176.1(5.0, 7.3)795.4(4.3, 6.8)388.2(5.8, 11.2)Precursor leukemia/lymphoma3,53042.73237.3(25.5, 52.7)2852.6(35.0, 76.1)412.3(3.3, 31.4)Mantle cell lymphoma3,52163.44010.1(7.3, 13.8)279.9(6.5, 14.4)1310.7(5.7, 18.3)LPL/WM1,95466.0134.3(2.3, 7.3)105.0(2.4, 9.2)32.8(0.6, 8.2)Peripheral T-cell lymphoma3,15655.73012.7(8.6, 18.1)2315.5(9.8, 23.2)78.0(3.2, 16.5)Burkitt lymphoma/leukemia1,18048.41924.3(14.6, 37.9)1328.6(15.2, 48.9)618.3(6.7, 39.8)Hairy cell leukemia1,70554.631.4(0.3, 4.2)~~Other, unspecified7,24462.0535.7(4.3, 7.4)386.6(4.7, 9.1)154.2(2.3, 6.9) Abbreviations: chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL); confidence interval (CI); diffuse large B-cell lymphoma (DLBCL); lymphoplasmacytic lymphoma/Waldenström macroglobulinemia (LPL/WM); standardized incidence ratio (SIR); Surveillance, Epidemiology, and End Results (SEER); treatment-related myelodysplastic syndrome/acute myeloid leukemia (tMDS/AML). Citation Format: Lindsay M. Morton, Graca M. Dores, Megan M. Herr, Martha S. Linet, Margaret A. Tucker, Rochelle E. Curtis. Risk of tMDS/AML after chemotherapy for first primary lymphoid malignancy, 2000-2013 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-236. doi:10.1158/1538-7445.AM2017-LB-236

Background: Childhood cancer survivors treated with chest radiotherapy have substantially elevated risk for developing breast cancer. Although numerous breast cancer susceptibility variants have been established, genetic predisposition for breast cancer after childhood cancer remains poorly understood. Methods: We conducted the first genome-wide association study of subsequent breast cancer in female childhood cancer survivors within two large-scale cohorts with detailed treatment data and systematic, long-term follow-up: the Childhood Cancer Survivor Study [CCSS; 178 breast cancer cases, 2200 controls (survivors without subsequent neoplasm) of European descent] and the St. Jude Lifetime Cohort (SJLIFE; 29 cases, 574 controls). Genotyping on the Illumina HumanOmni5MExome (CCSS) or Affymetrix 6.0 (SJLIFE) array and imputation based on the 1000 Genomes Project yielded >16 million high quality genotyped or imputed variants available in both studies. Assuming an additive genetic model, we used multivariate Cox regression to quantify the effect of each variant in the overall population and stratified by receipt of ≥10 Gray (Gy) or Results: We identified two loci associated with breast cancer risk among children who received ≥10 Gy radiation to the chest (131 cases, 493 controls): one at 1q41 [rs4342822, risk allele frequency (RAF) = 0.46 in controls, pooled per allele hazard ratio (HR) = 1.94, 95% confidence interval (CI) = 1.50-2.51, Pexact = 1.20×10−8] and another at 11q23 (rs74949440, RAF = 0.02 in controls, HR = 3.71, 95%CI = 2.18-6.32, Pexact = 2.00×10−9). Neither locus was associated with breast cancer risk among children who received 10% of breast cancers in The Cancer Genome Atlas data. The variant rs74949440 is intronic to TAGLN, whose expression levels have been associated with breast cancer prognosis and altered cell death resistance following irradiation in human carcinoma cell lines. Conclusion: These findings represent the first evidence outside of identified high-risk cancer susceptibility genes that certain individuals are genetically predisposed to developing breast cancer after radiotherapy and suggest that radiation exposure may interact with germline genetics to modify breast cancer risk. Citation Format: Lindsay M. Morton, Joshua N. Sampson, Gregory T. Armstrong, Ting-Huei Chen, Melissa Hudson, Eric Karlins, Casey L. Dagnall, Shenchao Li, Carmen L. Wilson, Kumar Srivastava, Wei Liu, Guolian Kang, Kevin Oeffinger, Tara O. Henderson, Chaya S. Moskowitz, Todd M. Gibson, Diana M. Merino, Jeannette R. Wong, Sue Hammond, Joseph P. Neglia, Lucie M. Turcotte, Jeremy Miller, Laura Bowen, William A. Wheeler, Wendy M. Leisenring, John A. Whitton, Laurie Burdette, Belynda D. Hicks, Mitchell J. Machiela, Aurelie Vogt, Zhaoming Wang, Meredith Yeager, Geoffrey Neale, Matthew Lear, Louise C. Strong, Yutaka Yasui, Marilyn Stovall, Rita E. Weathers, Susan A. Smith, Rebecca Howell, Stella M. Davies, Gretchen A. Radloff, Amy Berrington de González, Peter D. Inskip, Preetha Rajaraman, Joseph F. Fraumeni, Smita Bhatia, Stephen J. Chanock, Margaret A. Tucker, Leslie L. Robison. Genome-wide association study identifies two susceptibility loci that modify radiation-related risk for breast cancer after childhood cancer: A report from the Childhood Cancer Survivor Study and St. Jude Lifetime Cohort. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2691.

Cutaneous malignant melanoma (CMM) is an etiologically heterogeneous disease with genetic, host, environmental factors, and their interactions contributing to its development. CDKN2A and CDK4 are the two established major susceptibility genes for melanoma identified so far. Recent evidence suggests that copy number variations (CNVs) may contribute to disease susceptibility in several inherited diseases including cancer. The goals of this study were 1) to assess whether the frequency of CNVs varied by CMM or CDKN2A/CDK4 mutation status; and 2) to identify rare CNVs that were related to melanoma predisposition in these high-risk families. We used genome-wide tiling CGH arrays (Nimblegen 720K exon-focused) to investigate characteristics of CNVs in 174 CMM cases, 44 high-risk unaffected family members (with dysplastic nevi/large number of moles or germline CDKN2A mutations), and 48 unrelated spouses from 50 American melanoma-prone families (21 CDKN2A+, 2 CDK4+, 27 mutation negative). We used the Nexus Copy Number™ built-in FASST2 algorithm to identify significant CNVs (significant threshold = 0.000001; minimal number of probes per segment = 5; log2 ratio>0.3 for gains and -0.3 for losses). We found that the median number of total CNVs, or gains or losses separately, did not show significant differences in CMM cases, high-risk unaffected family members, and unrelated controls. Among CMM cases, CNV frequencies were not significantly associated with germline CDKN2A/CDK4 mutation status, age at melanoma diagnosis, or number of melanomas. Similar results were obtained when number of genes and lengths of DNA segments affected by CNVs were analyzed. Restriction to large CNVs (>10 kb or >100 kb) or rare CNVs (not reported in the Toronto CNV database) did not change results significantly. On the other hand, we identified several rare large CNVs (>10 kb, not reported in unrelated controls) that either involved known melanoma genes or co-segregated with melanoma (observed in multiple CMM cases) within families. These included a 1.3Mb deletion in PARP1 in a single CMM case, a 10 kb deletion in CDKN2A in 4 of 5 CMM cases and two obligate gene carriers in a large family that was negative for CDKN2A mutations by sequencing, a 175 kb deletion in LINGO2 in 2 of 3 CMM cases in one family, a 10 kb deletion in 8q24 in 3 of 4 CMM cases in one family, a 110 kb deletion in 2q22.1 in all three cases in a family, and a 57 kb duplication in 4q32.2 in all five cases in a CDKN2A mutation positive family. The role of these CNVs, particularly those involving genes that have unknown function related to CMM development, in CMM susceptibility remain to be investigated. Citation Format: Xiaohong (Rose) Yang, Jianxin Shi, Hunter Bennett, Laura Burke, Casey Dagnall, Laurie Burdette, Belynda Hicks, Margaret Tucker, Alisa Goldstein. Germline copy number variations in melanoma families with/without CDKN2A/CDK4 mutations. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2755. doi:10.1158/1538-7445.AM2015-2755

Background: Previous studies have reported that non-Hodgkin lymphoma (NHL) survivors have increased risk of developing lung cancer; however, risks associated with specific treatments and immune-related risk factors have not been quantified. Methods: We assessed second lung cancer risk among 44,870 1-year survivors of first primary NHL diagnosed at ages 66-84 years during 1992-2009 from the Surveillance, Epidemiology, and End Results (SEER)-Medicare data linkage. Information on potential risk factors, including NHL treatments, infections, and immune-related medical conditions, was derived from Medicare claims. Results: A total of 700 second lung cancers were diagnosed among NHL survivors, including 259 after chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), 127 after follicular lymphoma (FL), 116 after diffuse large B-cell lymphoma (DLBCL), and 137 after other NHL subtypes. Lung cancer risks were significantly increased among CLL/SLL survivors who received fludarabine-containing chemotherapy without rituximab (Cox regression hazard ratio [HR] = 2.28, 95% confidence interval [CI] = 1.48-3.52). Elevated risks were also seen among DLBCL survivors who received cyclophosphamide-containing chemotherapy (without rituximab HR = 2.13, 95%CI = 1.01-4.47; with rituximab HR = 1.82, 95%CI = 0.87-3.80). After adjusting for history of smoking, lower airway respiratory infections, particularly pneumonia, were associated with increased risks of second lung cancer after CLL/SLL (HR = 2.21, 95%CI = 1.65-2.96), DLBCL (HR = 1.90, 95%CI = 1.26-2.87), and FL (HR = 1.98, 95%CI = 1.31-3.00). The pattern of lung cancer risks associated with autoimmune conditions was complex, with increased risks seen for B-cell activating autoimmune conditions among DLBCL survivors (HR = 1.63, 95%CI = 1.00-2.66) and T-cell activating autoimmune conditions among survivors of other NHL subtypes (HR = 1.56, 95%CI = 1.07-2.27). In contrast, T-cell activating autoimmune conditions were significantly inversely associated with lung cancer among FL survivors (HR = 0.57, 95%CI = 0.34-0.96), and no associations with autoimmune disease were identified among CLL/SLL survivors. Conclusion: We report for the first time that chemotherapy used in treatment of NHL, infections, and autoimmune diseases are associated with the risk of developing lung cancer after NHL. Further research is needed to confirm the observed associations and understand the underlying carcinogenic mechanisms. Citation Format: Clara Lam, Rochelle Curtis, Graca Dores, Eric Engels, Neil Caporaso, Aaron Polliack, Joan Warren, Heather Young, Paul Levine, Angelo Elmi, Joseph Fraumeni, Margaret Tucker, Lindsay Morton. Risk factors for lung cancer among survivors of non-Hodgkin lymphoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-184. doi:10.1158/1538-7445.AM2015-LB-184

Melanoma (CM) incidence continues to increase in the US, Europe, and Australia. A concern has been raised whether this is a true increase of CM or a major increase in over diagnosis of CM. Data cited in support of over diagnosis are that mortality rates have not increased proportionately. Another explanation of disproportionate incidence and mortality is that as CM has become more common and both care providers and the general population are more aware of CM, lesions are identified and removed much earlier, leading to better long-term prognosis. In the US, the 5-year relative survival has increased from 81.8% in 1975 to 92.8% in 2006. The distribution of CM differs between men and women; recent data in the U.S. have shown a distinct increase in CM on the trunk of young women, consistent with tanning (Bradford PT et al., CEBP 2010; 19:2410-6). In 2011, there were 960,231 individuals with CM in the US who are at 8.8-fold increased risk of a second primary CM. The major risk factors for CM include genetic susceptibility (covered in detail by Nick Hayward in this session) and ultraviolet exposure. The major high risk susceptibility genes, CDKN2A and CDK4, were identified in the mid-nineties; mutations in either confer similar risks for CM and similar clinical features. More recently, mutations in POT1 were identified in melanoma-prone families using exome sequencing (Robles-Espinoza CD et al., Nat Genet 2014; 46:478-81; Shi J, et al., Nat Genet 2014; 46:482-6). Other rare high risk susceptibility genes will likely be identified. Genome-wide association studies have identified a number of common variants associated with CM; the causal variants marked by the association signals are in large part still being identified. Nevi, particularly dysplastic nevi, are major host susceptibility factors, but nevus genes have been quite challenging to identify. Using a candidate gene approach, Liang et al. identified variants in CDK6 and XRCC1 that were associated with dysplastic nevi, but not CM (J Invest Derm 2014;134:481-7). Ultraviolet radiation exposure is causal for CM, whether from the sun or artificial lights. Tanning is a complex behavior, and it is difficult to separate the risks associated with outdoor and indoor tanning since most who tan use both sources. Wehner et al. conducted a systematic review and metaanalysis of the prevalence of indoor tanning and found that 35.7% (95% CI 27.5%-44.0%) of adults, 55.0% (33.0%-77.1%) of university students and 19.3% (14.7%-24.0%) of adolescents had ever used indoor tanning (JAMA Dermatol 2014;150:390-400). The prevalences varied also by geographic area and sex. Due to the high exposure rates, particularly in adolescents, parts of Europe, Australia, and North America have passed legislation limiting access by adolescents to indoor tanning. There is also a growing body of evidence that UV exposure may be addictive (Heckman CJ et al., Am J Health Promo 2014;28:168-174). The role of screening for CM has been controversial. In 2009, the USPSTF guidelines did not recommend population-based screening for CM. This year, they are reconsidering the issue, in part because of a public health effort in Germany, where screening for skin cancer was made available for adults over 20 (Katalinic A et al., Cancer, 2012; 118:5395-402). In an observational study, melanoma mortality declined by 47% for men and 49% for women in the screened population. Screening may yield higher benefits in recognized at risk groups (Moloney FJ et al. JAMA Dermatol 2014.514). A number of melanoma risk assessment tools could be useful in prioritizing screening, but have not been fully validated (Vuong K et al; JAMA Dermatol 2014;150:434-444). Citation Format: Margaret A. Tucker. What's new in melanoma etiology? [abstract]. In: Proceedings of the AACR Special Conference on Advances in Melanoma: From Biology to Therapy; Sep 20-23, 2014; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(14 Suppl):Abstract nr IA09.

GenoMEL, comprising major familial melanoma research groups from North America, Europe, Asia, and Australia has created the largest familial melanoma sample yet available to characterize mutations in the high-risk melanoma susceptibility genes CDKN2A/alternate reading frames (ARF), which encodes p16 and p14ARF, and CDK4 and to evaluate their relationship with pancreatic cancer (PC), neural system tumors (NST), and uveal melanoma (UM). This study included 466 families (2,137 patients) with at least three melanoma patients from 17 GenoMEL centers. Overall, 41% (n = 190) of families had mutations; most involved p16 (n = 178). Mutations in CDK4 (n = 5) and ARF (n = 7) occurred at similar frequencies (2-3%). There were striking differences in mutations across geographic locales. The proportion of families with the most frequent founder mutation(s) of each locale differed significantly across the seven regions (P = 0.0009). Single founder CDKN2A mutations were predominant in Sweden (p.R112_L113insR, 92% of family's mutations) and the Netherlands (c.225_243del19, 90% of family's mutations). France, Spain, and Italy had the same most frequent mutation (p.G101W). Similarly, Australia and United Kingdom had the same most common mutations (p.M53I, c.IVS2-105A>G, p.R24P, and p.L32P). As reported previously, there was a strong association between PC and CDKN2A mutations (P < 0.0001). This relationship differed by mutation. In contrast, there was little evidence for an association between CDKN2A mutations and NST (P = 0.52) or UM (P = 0.25). There was a marginally significant association between NST and ARF (P = 0.05). However, this particular evaluation had low power and requires confirmation. This GenoMEL study provides the most extensive characterization of mutations in high-risk melanoma susceptibility genes in families with three or more melanoma patients yet available. (Cancer Res 2006; 66(20): 9818-28)

Sunlight is the major environmental risk factor for melanoma. Descriptive studies have shown latitudinal variation in population incidence and mortality rates [D. C. Whiteman and A. C. Green, Int. J. Dermatol., 38: 481-489, 1999, and B. K. Armstrong, Australian J. Dermatol., 38 (Suppl. 1): 51-56, 1997]. In analytic studies, individual exposure has been particularly difficult to quantify. Lifetime residential history was coupled with levels of midrange UV radiation (UVB flux) to provide a measure of individual exposure to sunlight thought to be less subject to misclassification and recall bias. Data were analyzed from 718 non-Hispanic white patients with invasive cutaneous melanoma from melanoma clinics in Philadelphia and San Francisco. Matched controls were 945 patients from outpatient clinics with similar catchment areas. The association of melanoma risk and history of UVB flux along with the usual outdoor exposure risk factors were studied. A 10% increase in the average annual UVB flux was associated with a 19% [95% confidence interval (CI), 5-35%] increase in individual odds for melanoma for men and 16% (95% CI, 2-32%) for women. In men, a 10% increase in hours outdoors was associated with a 2.8% (95% CI, 1.2-4.5%) increase in odds. Even in women who could develop a deep tan, a 10% increase in hours outdoors was associated with a 5.8% increase in odds (95% CI, 1.4-10.4%). The association between melanoma risk and average annual UVB flux was strong and consistent for men and for women. The association with total adult hours outdoors was notable for men of all skin types and women who develop a suntan.

In spite of progress in the identification of the somatic events associated with Waldenström macroglobulinemia (WM), the genetic determinants of WM susceptibility have not been identified. We have conducted exome sequencing in 32 individuals from 9 well-characterized families at high risk for WM. We sequenced 3 or more patients or obligate carriers from each family. We used Nimblegen v2.0 and v3.0 for exome capture followed by sequencing on the Illumina HiSeq2000. Among quality control measures, we required 80% of coding sequences to achieve 15x coverage. To eliminate other possible sequencing artifacts, variants found in more than 1% of samples sequenced in our laboratory from other studies were excluded. Novoalign v.2.07.14 was used for alignment and GATK was used for local re-alignment and variant calling. A large number of rare ( Citation Format: Mary L. McMaster, Lynn R. Goldin, Melissa Rotunno, Ji He, Laurie Burdette, Amy Hutchinson, Joseph Boland, Meredith Yeager, Margaret A. Tucker, Stephen J. Chanock, Neil E. Caporaso. Exploration of rare variants from exome sequencing in families with Waldenstrom macroglobulinemia (WM). [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1300. doi:10.1158/1538-7445.AM2014-1300

The genetic regulation of the human epigenome is not fully appreciated. Here we describe the effects of genetic variants on the DNA methylome in human lung based on methylation-quantitative trait loci (meQTL) analyses. We report 34,304 cis- and 585 trans-meQTLs, a genetic-epigenetic interaction of surprising magnitude, including a regulatory hotspot. These findings are replicated in both breast and kidney tissues and show distinct patterns: cis-meQTLs mostly localize to CpG sites outside of genes, promoters, and CpG islands (CGIs) while trans-meQTLs are over-represented in promoter CGIs. meQTL SNPs are enriched in CTCF binding sites, DNaseI hypersensitivity regions and histone marks. Importantly, 4 of the 5 established lung cancer risk loci in European ancestry are cis-meQTLs and, in aggregate, cis-meQTLs are enriched for lung cancer risk in a genome-wide analysis of 11,587 subjects. Thus, inherited genetic variation may affect lung carcinogenesis by regulating the human methylome. Citation Format: Jianxin Shi, Crystal Marconett, Jubao Duan, Paula Hyland, Peng Li, Zhaoming Wang, William Wheeler, Mihaela Campan, Jing Huang, Weiyin Zhou, Tim Triche, Laufey Amundadottir, Amy Hutchinson, Po-Han Chen, Beiyun Zhou, Brian Chung, Pier Alberto Bertazzi, Andrew W. Bergen, Mathew Freedman, Diane Lee, Kim Siegmund, Andrew Clay Warner, Ben Berman, Angela C. Pesatori, Zea Borok, Dario Consonni, Nilanjan Chatterjee, Margaret Tucker, Neil Caporaso, Stephen J. Chanock, Ite A. Laird-Offringa, Maria Teresa Landi. Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 287. doi:10.1158/1538-7445.AM2014-287

Approximately 10% of cutaneous malignant melanoma (CMM) cases occur in a familial setting and known high-penetrance melanoma susceptibility genes (CDKN2A, CDK4, BAP1, and TERT) account for melanoma susceptibility in a small proportion of melanoma-prone families. To identify additional high-penetrance susceptibility genes for familial CMM, we performed whole exome sequencing in 101 CMM cases/obligate carriers in 56 unrelated melanoma-prone families recruited from the Romagna area in Italy. We identified a germline founder mutation in Protection Of Telomeres 1(POT1) (g.7:124493086 C>T, p.S270N) in five unrelated melanoma-prone families. The mutation was also found in a single sporadic CMM case from Romagna out of 1,824 Italian cases examined, but it was not seen in public databases, our internal exome databases of over 1000 subjects, and 878 Spanish CMM cases and 3,489 controls (2,038 Italian and 1,451Spanish) genotyped. POT1 is a component of the telomeric shelterin complex that plays a critical role in maintaining telomere integrity and regulating telomere length. The p.S270N mutation is highly conserved among vertebrates and predicted to be deleterious by most computational programs we evaluated. Carriers of the p.S270N mutation had increased length and heterogeneity as well as increased average number of fragile telomeres in peripheral blood mononuclear cell (PBMC) DNA compared to age-matched CMM cases (controls) without the mutation. Exome sequencing analysis of Italian families also identified two other rare missense substitutions in POT1 (g.7:124464052 C>G [p.Q623H] and g.7:124503540 C>T [p.R137H]) that were found in all cases sequenced in two families. Both missense mutations are absent from public databases and 3,489 genotyped controls, and are predicted to be deleterious by most algorithms. The carriers of these two mutations showed slightly but significantly increased telomere intensity signals and telomere fragility in PBMCs compared to age-matched controls. We further sequenced POT1 exons in 768 CMM cases and 768 controls collected from Italy and we found that CMM cases showed a significant increase in the burden of rare exonic variants compared to controls (OR=5.4, 95% CI=1.5-29.2, P=0.0021). Subsequently, we identified two novel recurrent germline missense mutations in POT1 (g.7:124499043 C>T, p.D224N and g.7:124469308 C>G, p.A532P) in American and French familial melanoma cases. Our findings suggest that POT1 is a major susceptibility gene for familial melanoma in several populations and that genes involved in telomere maintenance may play important roles in melanoma development. Citation Format: Jianxin Shi, Xiaohong R. Yang, Bari Ballew, Melissa Rotunno, Donato Calista, Maria C. Fargnoli, Paola Ghiorzo, Brigitte Bressac-de Paillerets, Eduardo Nagore, NCI DCEG Cancer Sequencing Working Group, Xing Hua, Paula Hyland, Jinhu Yin, Haritha Vallabhaneni, Weihang Chai, Sarangan Ravichandran, Alexander Eggermont, Mark Lathrop, Ketty Peris, Giovanna Bianchi-Scarra, Giorgio Landi, Sharon Savage, Joshua Sampson, Ji He, Meredith Yeager, Lynn Goldin, Florence Demenais, Stephen Chanock, Margaret Tucker, Alisa Goldstein, Yie Liu, Maria T. Landi. Exome sequencing identified POT1, a telomere shelterin gene, as a major susceptibility gene for familial cutaneous malignant melanoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 941. doi:10.1158/1538-7445.AM2014-941

The retinoblastoma tumor suppressor gene (RB1) is a key regulator of cell cycle control, most notably through E2F transcription factor binding. Deregulation of RB1 is important in many cancers. Survivors of hereditary retinoblastoma, caused by a germline mutation in RB1, experience substantially elevated risks for subsequent neoplasms, particularly bone and soft tissue sarcomas and melanomas. Oncogenic RB1 mutations arise from a range of DNA alterations and occur throughout the gene. No previous study has evaluated how the specific location and functional consequences of these RB1 mutations may differentially confer risk for specific subsequent neoplasms. As part of a biomarker study nested within a long-term follow-up study of the risk of subsequent cancers in retinoblastoma survivors, we identified germline RB1 mutations in 76/80 (95%) survivors of hereditary retinoblastoma who developed at least one subsequent neoplasm and had sufficient DNA for mutation testing (median follow-up time=47 years, range 7-71 years). Survivors were classified into four groups according to whether they ever developed a soft tissue sarcoma (STS, N=47), melanoma (without STS, N=10), bone tumor (without STS, N=5), or another type of subsequent malignant neoplasm (N=14). The identified mutations were distributed throughout RB1, from the promoter through exon 25. Nonsense, frameshift, or splice mutations that resulted in premature termination of the RB1 residue sequence were identified in 51 (67%) survivors, with the remaining classified as having loss of multiple exons (N=6), loss or rearrangement of a single exon (N=5), a splice mutation (N=7), a missense mutation (N=4), or an intronic substitution with unknown consequence (N=3). Preliminary analyses indicated that RB1 mutations resulting in loss of >2 exons were more common in survivors with a subsequent STS (40/47, 85%) than those with a subsequent melanoma (6/10, 60%) or bone tumor (2/5, 40%; Fisher's exact P Citation Format: Lindsay M. Morton, Jeannette R. Wong, Brenda L. Gallie, David H. Abramson, Johanna M. Seddon, Michael Dean, Bert Gold, Alisa M. Goldstein, Ruth A. Kleinerman, Margaret A. Tucker. Specific RB1 mutations and risk of subsequent neoplasms among survivors of hereditary retinoblastoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1333. doi:10.1158/1538-7445.AM2013-1333

Recent evidence indicates human mosaic abnormalities may be more common than previously expected. We performed an analysis on blood and buccal DNA of 30,918 individuals from a collection of 54 cancer-related studies using a modified mosaic alteration detection algorithm on renormalized B-allele frequencies and log2 relative probe intensity ratios from commercially available Illumina SNP microarray chips. 391 autosomal abnormalities >2Mb in size were detected in 232 (0.75%) individuals. The distribution includes copy-neutral loss of heterozygosity constituting 192 (49%) events, copy gains 85 (22%) events, and copy losses 102 (26%) events. There was no difference between blood and buccal sources of DNA. An overall analysis by age confirmed our earlier finding (p=8.93e-07), which was also observed in controls (p=0.0086). Similarly, an overall analysis by sex confirmed mosaic abnormalities are more frequent in males than females (p=0.0016); and this association was also observed in a control-only analysis (p=0.0019). Two or more distinct autosomal events were observed in 43 individuals. Comparable to earlier studies, the most common events were 4q copy neutral loss of heterozygosity, 9q copy neutral loss of heterozygosity, 13q14 deletion and 20q deletion. 13q14 deletion was observed in cancer-free controls and individuals with epithelial cancers. Cancer specific analyses for bladder, endometrium, stomach, lung (in nonsmoking women from Asia), osteosarcoma, and prostate cancer revealed no significant association with risk for cancer. These results replicate the prevalence and age/sex relationships from our previous findings in an analysis of 57,853 individuals and further suggest the importance of studying mosaic abnormalities in the general human population. The findings underscore the importance of thorough characterization of germline DNA in parallel with somatic characterization. Our results provide further support for age-related genomic senescence and could represent the tip of the iceberg for smaller somatic events. Citation Format: Mitchell J. Machiela, Weiyin Zhou, Meredith Yeager, Kevin Jacobs, Sonja Berndt, Qing Lan, Nathaniel Rothman, Sharon Savage, Phil R. Taylor, Immaculata deVivo, National Cancer Institute Detectable Clonal Mosaicism Consortium, Robert N. Hoover, Margaret A. Tucker, Stephen J. Chanock. Evidence for large somatic structural events detected as autosomal genetic mosaicism in GWAS data. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2542. doi:10.1158/1538-7445.AM2013-2542

CDKN2A and CDK4 are the two major susceptibility genes for melanoma identified so far. However, these two genes only account for melanoma susceptibility in a small proportion of melanoma-prone families, suggesting the existence of other susceptibility genes. In addition, melanoma is among the tumors with the highest mutation rate and a large number of mutated genes have been identified that affect multiple key biological pathways. The goal of this study is to examine whether rare germline sequence variants and/or copy number variations (CNVs) in these genes may influence melanoma risk in melanoma-prone families without known CDKN2A/CDK4 mutations. Methods: We conducted exome sequencing in blood-derived DNA in 75 melanoma cases from 23 American melanoma families with ≥3 affected members. We evaluated rare non-synonymous variants, defined as allele frequency less than 0.1% reported in public databases (dbSNP, 1000 Genomes, or NHLBI's Exome Variant Server), in 37 genes (including BRAF, NRAS, KIT,PTEN, CDKN2A, GRIN2A, etc.) that are frequently mutated in melanoma. We also screened CNVs in these genes using data from the Nimblegen 3x720k exon-focused CGH tiling arrays, in which blood-derived DNA from 79 melanoma cases and 25 spouses were analyzed in the same mutation-negative families. We used the Nexus Copy Number™ built-in FASST2 algorithm to identify significant CNVs (significant threshold=0.000001; minimal number of probes per segment=5; log2 ratio>0.3 for gains and -0.3 for losses). Results: We identified 10 rare variants in 10 genes that showed partial/complete co-segregation with disease and were absent in our internal controls (N∼400). Four of these variants occurred in all cases within their respective families and 3 of them were novel. We did not identify any disease-related CNVs in these genes except for a deletion in exon 1β of CDKN2A/ p14ARF in 6 out of 7 melanoma cases in one big family. Our findings suggest that rare variants in somatically mutated genes may confer susceptibility to melanoma risk in a subset of families. However, these variants need to be validated, checked for functional relevance, and evaluated in a large number of cases and controls to determine their role in disease susceptibility. Citation Format: Xiaohong (Rose) Yang, Laura Burke, Kevin Jacobs, Michael Cullen, Joseph Boland, Laurie Burdett, Michael Malasky, Melissa Rotunno, Meredith Yeager, Stephen Chanock, Margaret Tucker, Alisa Goldstein. Characterization of rare germline variants in somatically mutated melanoma genes in melanoma-prone families. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2553. doi:10.1158/1538-7445.AM2013-2553

Background: Cutaneous malignant melanoma (CMM) is an etiologically heterogeneous disease with genetic, environmental, and host characteristics and their interactions contributing to risk. Recently, gene-specific promoter methylation in blood has been associated with the risk of several cancers including breast, lung and pancreatic. We thus examined whether gene-specific promoter methylation was associated with risk of CMM in individuals from melanoma-prone families. Methods: We measured the promoter methylation status of 15 genes (CDH1, COL1A2, DAPK, DDIT4L, HSPB6, LOX, MT1G, NPM2, p14, p16, PTEN, RASSF1, MAGEA3, TNFRSF10C and TNFRSF10D) previously shown to be aberrantly methylated in melanoma tumors using bisulfite pyrosequencing at 65 CpGs in peripheral blood mononuclear cells (PBMCs) from 236 individuals (114 melanoma cases and 122 unaffected individuals) in 64 melanoma-prone families. For functional validation we obtained gene expression data for 14 out of the 15 genes through independent expression profiling analysis. We also compared the values from each methylated promoter to mRNA expression. We used logistic regression to evaluate the association between CMM status and average promoter methylation controlling for age, sex and adjusting variance for familial correlation. Results: In unaffected individuals, overall promoter methylation levels were low for most of these genes in blood. Only TNFRSF10C (P=0.009) and TNFRSF10D (P=0.010) showed the expected negative correlation between promoter methylation and gene expression. Therefore, we focused on these two genes in subsequent analyses. Compared to controls, CMM cases had significantly lower promoter methylation at TNFRSF10C (P= 0.002) and TNFRSF10D (P=0.045). This difference remained significant after further adjusting for CDKN2A, dysplastic nevi and pigmentation characteristics. Significance: TNFRSF10C and TNFRSF10D encode separate decoy death receptors, whose overexpression in both normal and malignant cells can inhibit apoptosis. Our findings support a potential association between reduced promoter methylation of TNFRSF10C and TNFRSF10D in blood and risk of CMM in our melanoma-prone families. Citation Format: Paula L. Hyland, Laura S. Burke, Ruth M. Pfeiffer, Margaret A. Tucker, Alisa M. Goldstein, Xiaohong R. Yang. Promoter methylation of death receptor decoy genes in blood and risk of melanoma in melanoma-prone families . [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 688. doi:10.1158/1538-7445.AM2013-688

Osteosarcoma (OS), the most common primary malignant bone tumor, has a peak incidence during the pubertal growth spurt. OS occurs at increased frequency in several inherited cancer syndromes (e.g., Li-Fraumeni and Rothmund Thomson syndromes). A limited number of common SNPs associated with OS have been identified in biologically plausible pathways (e.g., growth or DNA repair). We developed an international, multi-institutional study in order to conduct the first genome-wide association study (GWAS) of OS. Participating subjects provided informed consent through local IRBs. Control subjects were cancer free adults derived from large studies in prior GWAS at the NCI. Genotyping of all cases was conducted using the Illumina OmniExpress SNP microarray chip platform in 2 phases. The first phase analyzed 910 osteosarcoma cases. After quality control filtering and assessment of population substructure, 596 cases of European (EUR) ancestry were advanced to the primary GWAS analysis (Phase 1A). We combined data from 2,703 previously genotyped controls drawn from 3 EUR cohorts. There was no evidence for significant population substructure differences between OS cases and controls. The association analysis (1-degree of freedom trend test) was adjusted for study, sex and 4 eigenvectors. The top 30 SNPs (P The fixed-effects meta-analysis of all 941 OS cases and 3,291 controls identified 2 regions that achieved genome-wide significance. The first, rs1906953 on 6p21.3, is associated with susceptibility to OS (P = 8.1x10-9, odds ratio [OR] 1.57, 95% confidence interval [CI] 1.35-1.83). rs1906953 is in intron 7 of GRM4. GRM4 is expressed in osteoblasts and osteoclasts and involved in glutamate signaling, which is suggested to be involved in cell differentiation and regulation of bone formation. The second signal resides in an intergenic region on chromosome 2p25.2; rs7591996 (P = 1.0 x 10-8, OR 0.72, 95% CI 0.65-0.81). Another SNP in this region, rs10208273, is moderately correlated with the first signal (r2= 0.32) and approached genome-wide significance (P = 2.9 x 10-7, OR 1.35, 95% CI 1.21-1.52). A third locus in the ADAMTS6 gene on 5q12.3 is promising but does not yet achieve genome-wide significance: rs17206779 (P = 5.1x10-7, OR 0.75, 95% CI 0.68-0.84). Notably, variants in genes encoding members of the ADAMTS protein family have been associated with height, a known OS risk factor. We have conducted the first GWAS of OS and identified several novel loci associated with OS risk. Further investigation of these loci will advance understanding of OS etiology and biology. Citation Format: Sharon A. Savage, Lisa Mirabello, Zhaoming Wang, Julie Gastier-Foster, Richard Gorlick, Chand Khanna, Adrienne M. Flanagan, Roberto Tirabosco, Irene L. Andrulis, Jay Wunder, Nalan Gokgoz, Ana Patino-Garcia, Luis Sierrasesumaga, Fernando Lecanda, Nilgun Kurucu, Inci Ergurhan Ilhan, Neriman Sari, Massimo Serra, Claudia Hattinger, Piero Picci, Logan Spector, Donald A. Barkauskas, Neyssa Marina, Siliva Caminada de Toledo, Sergio Petrilli, Maria Fernanda Amary, Dina Halai, David Thomas, Chester Douglass, Paul Meltzer, Kevin Jacobs, Charles C. Chung, Sonja I. Berndt, Mark P. Purdue, Neil E. Caporaso, Margaret Tucker, Nathaniel Rothman, Maria Teresa Landi, Debra T. Silverman, Peter Kraft, David J. Hunter, Nuria Malats, Manolis Kogevinas, Sholom Wacholder, Rebecca Troisi, Lee Helman, Joseph F. Fraumeni, Jr., Meredith Yeager, Robert Hoover, Stephen J. Chanock. Genome-wide association study identifies novel loci associated with osteosarcoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4593. doi:10.1158/1538-7445.AM2013-4593

Chromosome 9p21 has been implicated in the pathogenesis of cutaneous malignant melanoma (CMM), glioma, non-small cell lung cancer, and leukemia. This region includes cyclin-dependent kinase inhibitor 2A (CDKN2A), the major known high-risk susceptibility gene for CMM; CDKN2B; antisense noncoding RNA in the INK4 locus (ANRIL), a GWAS hotspot for multiple phenotypes including cancers; methylthioadenosine phosphorylase (MTAP), a gene with tumor suppressor function and a cluster of type I interferon (IFN) genes. The goal of this study was to examine the association between genetic variation in the 9p21 region and multiple cancer outcomes using genotyping data from studies participating in the National Cancer Institute's (NCI) iSelect project. We evaluated up to 202 tagSNPs in 22 genes in the 9p21 region (19.9-32.8 Mb), in case-control studies of thyroid cancer (THC), endometrial cancer (EC), testicular cancer (TC), renal cell carcinoma (RCC), colorectal cancer (CRC), colorectal adenoma (CA), esophageal squamous cell carcinoma (ESCC), gastric cardia cancer (GCC) and osteosarcoma (OS). The number of cases in each of the nine studies ranged from 96 to 1234. We first performed single SNP-based analyses for each study separately, using logistic regression adjusted for age and study-specific covariates. To combine SNP based analyses, we used a newly developed subset-based statistical approach (ASSET), which allow for heterogeneity of SNP effect on different outcomes. This approach exhaustively explores subsets of studies for the presence of association signals, and then evaluates the significance from subsets with the strongest association signal, meanwhile accounting for multiple tests required by the subset search. Gene based P-values were computed using an adaptive rank truncated product (ARTP) statistic and a permutation-based sampling procedure (10,000 permutations) that took into account the numbers of SNPs in each gene and their linkage disequilibrium structure. When analyzing each study separately, we found that a SNP (rs3731257) in CDKN2A was significantly associated with the risk of ESCC after Bonferroni correction for number of SNPs and studies (P=7 x 10-6). Meta-analyses by ASSET found that this SNP was significantly associated with both ESCC and EC (PASSET Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-330. doi:1538-7445.AM2012-LB-330

Genetic mosaicism, the coexistence of cells of distinct genetic composition within an organism, has been associated with developmental and somatic disorders. Recently, we reported on 1,991 individuals from a population-based study of adult bladder cancer where we detected autosomal mosaicism in 1.7% of study subjects, suggesting a higher frequency than previously suspected, but did not reveal a significant association with bladder cancer. We have now extended our analysis to 57,853 subjects, 31,717 cancer cases and 26,136 cancer-free controls, using genome-wide SNP array data generated as part of 13 genome-wide association studies drawn from 48 case-control and case-cohort studies. Detection of autosomal mosaic events was based on assessment of allelic imbalance and copy number changes. We found autosomal mosaicism in blood or buccal mucosa DNA for chromosomal events of size >2 Mb on 641 chromosomes in 517 individuals for an overall frequency of individuals with mosaicism of 0.87%. The most frequent type of event observed was copy-neutral LOH (48.2%), while copy-gains and copy-losses were observed for 15.1% and 34.8% of mosaic events, respectively. The strongest predictor of autosomal mosaicism was age at DNA collection. In cancer-free individuals, the frequency of having a mosaic event was 0.23% for those under 50 and 1.91% between 75 and 79 (p=4.8×10-8). Mosaicism was more frequent in males than females (OR=1.42, 1.14-1.80 95% CI, p=0.002) and in individuals with non-hematologic cancer (0.97% versus 0.74% in cancer-free individuals, OR=1.25, 1.04-1.50 95% CI, p=0.016), with a stronger association in cases who had DNA collected prior to treatment (OR=1.45, 1.18-1.80 95% CI, p=0.0005). Notable associations were observed in stratified analyses of lung (OR=1.56, 1.18-2.08 95% CI, p=0.002) and kidney (OR=1.98, 1.27-3.06 95% CI, p=0.002) cancers, both tobacco-associated malignancies. There was no significant association in non-hematological cancer cases overall between smoking (ever/never) and frequency of mosaicism (OR=1.19, 0.92-1.54 95% CI, p=0.19) or when stratified by cancer site. The frequency of mosaicism was higher in individuals diagnosed with leukemia who had DNA collected at least one year prior to diagnosis (overall OR=35.4, 14.7-76.6 95% CI, p=3.8×10-11); 15.8% had myeloid leukemia and 26.3% had lymphocytic leukemia. We conclude that autosomal mosaicism is present in the population with surprising frequency and particularly in the ageing genome. Further work is required to begin to unravel the underlying mechanisms, particularly as it relates to aging, the timing and expansion of distinct populations of cells bearing markedly different structural events in one or more chromosome. These findings underscore the importance of considering the role and time-dependent nature of somatic events in the etiology of cancer and other late-onset diseases. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3110. doi:1538-7445.AM2012-3110

Background. Exposure to occupational carcinogens is an important preventable cause of lung cancer. Most previous studies were in highly exposed industrial cohorts. Our aim was to quantify lung cancer burden attributable to occupational carcinogens in a general population. Methods. We estimated lung cancer risk associated with occupational carcinogens using a new validated job-exposure matrix (JEM), in the Environment And Genetics in Lung cancer Etiology (EAGLE) study, a large (2100 cases and 2120 controls) population-based case-control study conducted in Lombardy, Italy, between 2002-2005. The JEM translated lifetime work-histories coded into standard job-titles into never, low, and high exposure levels for six known/suspected occupational lung carcinogens. We calculated odds ratios (OR) and 95% confidence intervals (CI) in men (1537 cases and 1617 controls), by multiple logistic regression, adjusted for potential confounders, e.g., tobacco smoking and co-exposure to JEM carcinogens. We estimated the Population Attributable Fraction (PAF) as impact measure. Results. Exposure to asbestos (OR=1.76, 95%CI=1.42 to 2.18), crystalline silica (OR=1.31, 95%CI=1.00 to 1.71), or nickel-chromium (OR=1.18, 95%CI=0.90 to 1.53) was associated with increased risk even at low exposures, with positive trends for intensity and duration. We found an excess risk for exposure to polycyclic aromatic hydrocarbons only among highly exposed workers (OR=1.64, 95%CI=0.99 to 2.70). The PAFs for any exposure to asbestos, crystalline silica and nickel-chromium were 18.1%, 5.7%, and 7.0%, respectively, corresponding to ≈300-800 lung cancer cases/year. Conclusion. These findings support the substantial role of selected occupational carcinogens on lung cancer burden, even in a low exposed general population. Health policy interventions are warranted. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1874. doi:10.1158/1538-7445.AM2011-1874

Cutaneous malignant melanoma incidence rates have been increasing among young women in the United States. Given that tan-seeking behaviors have increased ultraviolet radiation exposures in anatomic sites usually covered by clothing, i.e., trunk among women, we further assessed melanoma incidence trends by gender and anatomic site. Case and population data among Whites were obtained from the Surveillance, Epidemiology, and End Results Tumor Registries (SEER 9, 1975-2006). Age-period-cohort models were used to assess age, calendar-period, and birth-cohort effects. Net drift, the sum of linear trends in the period and cohort effects, was used to show differential secular trends due to period and/or cohort effects such as screening, case ascertainment, sun exposure, etc. Longitudinal age trend (LAT), the sum of the linear trends in the age and period effects, was used to show differential age-related biological effects. There were 105,829 melanomas diagnosed from 1975 through 2006 in the SEER 9 Registries. The overall age-adjusted incidence rate (IR) was 17.70 per 100,000, with a male to female incidence rate ratio (IRR) of 1.40 (p Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 866.

Two genome-wide association studies of prostate cancer identified single nucleotide polymorphism (SNP) markers in a region of chromosome 11q13. As part of the Cancer Genetic Markers of Susceptibility (CGEMS) Initiative the region flanking the most significant marker, rs10896449, was fine mapped using common single nucleotide polymorphisms (SNPs) selected from a two-staged tagging strategy. Of the 120 SNPs analyzed in 10,272 cases and 9,123 controls of European origin, single locus analysis identified 18 SNPs below genome-wide significance (P < 10−8); rs10896449, initially reported remained most significant (P = 7.94 × 10−19). Multi-locus models that included the 18 significant SNPs sequentially identified a second association at rs12793759 (OR = 1.14 P = 4.76 × 10−5), independent of rs10896449 that remained significant after adjustment for multiple testing within the region. A third signal, rs10896438 (OR = 1.07, P = 5.92 × 10−3), independent of both rs10896449 and rs12793759 was detected. To comprehensively catalog genetic variants in strong LD with the above SNPs as well as to determine the region's LD pattern, next-generation sequence analysis of 123 kb (chr11: 68,642,755 - 68,765,690) was performed in 75 individuals of European origin. 447 SNPs with minor allele frequency (MAF) > 1% were identified, which included 180 novel SNPs. Based on r2 > 0.8, 105 SNPs are needed to monitor SNPs with MAF > 1%, whereas 62 SNPs are required for MAF > 5%. 51 SNPs with MAF > 5% are not monitored with r2 > 0.8; 24 singletons (most of which were monitored with r2 > 0.6) and 27 SNPs in 9 correlation bins (r2 > 0.8). For the strongest hits, rs10896449, rs12793759 and rs10896438, 26, 6 and 18 SNPs are correlated with r2 > 0.8, respectively. Our results illustrate the complex architecture of the common genetic variants conferring prostate cancer risk on chromosome 11q13. The fine mapping and sequence analysis point towards a subset of SNPs worthy of follow-up studies designed to understand the molecular basis of the susceptibility alleles. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3863.

Background. Second cancers are a leading cause of morbidity and mortality among cancer survivors. Previous studies have shown increased second cancer risks after non-Hodgkin lymphoma and chronic lymphocytic leukemia (CLL); however, no earlier investigation has quantified differences in second cancer risk by lymphoma subtype, and little is known about the second cancer etiologies. Methods. We evaluated second cancer risks compared with the general population among 62,841 two-month survivors of the most common lymphoma subtypes [CLL/small lymphocytic lymphoma (SLL), follicular lymphoma (FL), and diffuse large B-cell lymphoma (DLBCL)] diagnosed in 13 SEER registry areas during 1992-2006. To investigate specific risk factors for second cancers following lymphoma, we then identified 51,909 patients in the SEER-Medicare linked dataset who were diagnosed with lymphoma at age 66 years or older during 1992-2005. Risk factor data were obtained from Medicare claims for treatment and medical conditions. Patients with second primary invasive cancers were ascertained in the corresponding SEER registry files. Risk factors were modeled using multivariate Cox proportional hazards regression for each lymphoma subtype, adjusting for potential confounders. Results. Lung cancer was the most common second malignancy and occurred in excess compared with the general population for survivors of CLL/SLL and FL but not for survivors of DLBCL [CLL/SLL: standardized incidence ratio (SIR)=1.53, 95% confidence interval (CI) 1.39-1.68; FL: SIR=1.34, 95%CI 1.15-1.55; DLBCL: SIR= 1.03, 95%CI 0.89-1.19)]. A similar pattern was observed for cutaneous melanoma (CLL/SLL: SIR=2.08, 95%CI 1.73-2.48; FL: SIR=1.47, 95%CI 1.09-1.94; DLBCL: SIR=1.16, 95%CI 0.85-1.54). Acute non-lymphocytic leukemia risks were significantly elevated after all three major lymphoma subtypes, with higher risks for FL and DLBCL than for CLL/SLL (CLL/SLL: SIR=1.58, 95%CI 1.03-2.32; FL: SIR=5.32, 95%CI 3.85-7.17; DLBCL: SIR=4.63, 95%CI 3.43-6.12). In the SEER-Medicare linked dataset, 5,002 patients with a second primary invasive cancer after lymphoma were identified, including 744 patients with lung cancer, 198 with melanoma, and 88 with acute non-lymphocytic leukemia. Results will be presented for second cancer risk factors of interest obtained from the Medicare database, including radiotherapy, specific chemotherapeutic agents, history of emphysema and chronic obstructive pulmonary disease, and specific infections (e.g., bronchitis, pneumonia, influenza). Discussion. Identification of risk factors for second cancers after lymphoma will provide valuable information for lymphoma survivors and their physicians as well as advancing our understanding of carcinogenesis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5644.