Offit, Kenneth

Abstract Introduction Multiple myeloma (MM) is a result of a malignant transformation of plasma cells that is preceded by the presence of an asymptomatic clonal plasma cell expansion, a condition referred to as monoclonal gammopathy of undetermined significance (MGUS). We and others have shown familial aggregation of MM and MGUS. Evidence from epidemiologic, family and genome-wide association studies (GWAS) suggests a genetic component underlying MM etiology. GWAS have successfully established 17 common genetic risk loci for MM to date and recently, rare inherited susceptibility variants in the LSD1 / KDM1A and USP45 genes were identified in familial MM / MGUS kindreds. Family-based approaches may be used to elucidate genetic variation contributing to familial MM. Genetic linkage analysis has historically been used to detect the chromosomal location of disease genes. The objective of this study was to conduct a linkage analysis of MM / MGUS families to identify genomic regions for MM / MGUS. Methods Linkage analysis was performed on whole exome sequencing (WES) data generated from germline DNA extracted from peripheral blood from MM / MGUS families ascertained at four sites, of which 79 were selected with 2 or more affected members with any combination of MM or MGUS. Whole exome capture was performed using Agilent SureSelect 38 Mb paired end sequencing and ran on Illumina HiSeq 2000s/2500s; standard analyses for alignment (GRCh37) and quality control were conducted. The Genome Analysis Toolkit's (GATK) HaplotypeCaller in per-sample mode was used to jointly call all the samples together. Quality control included removing variants that had <75% call rate, <8x coverage, or minor allele frequency <0.01 (1KGenomes). The jointly called WES data from the 79 families consisted of 230 individuals, including 119 MM, 93 MGUS and 18 unaffected relatives. Additional early onset (defined as age <60) MM cases (n=400), sporadic MM cases (n=879) and controls (n=2389) were also included in the joint calling to be used for follow-up of linkage regions. We included independent variants defined as linkage disequilibrium (LD) r2 <0.05 using both PLINK 1.07's LD based variant pruner and also MERLIN's pairwise r2 cluster marker-marker modeling to ensure variant independence. After quality control and LD filtering: 12,946 variants remained. We conducted multipoint linkage analysis using MERLIN (Multipoint Engine for Rapid Likelihood Inference using the Lander-Green approach) and considered both non-parametric and parametric (dominant and recessive) models to test for co-segregation of chromosomal regions with MM / MGUS. A logarithm of the odds (LOD) score greater than 3.3 was significant evidence for linkage. Within the same families, we interrogated any suggestive regions by performing gene-level association tests using the PEDGENE R package to calculate burden and kernel statistics, accounting for family relationships. Follow-up of these genes in the early onset and sporadic MM cases and controls and interrogation of single variants driving the associations of these genes is ongoing. Results Among the 79 families, 28 consisted of two or more MM, 41 had two or more MM and MGUS cases and 10 had two or more MGUS. Analyses of the 79 MM / MGUS families identified chromosome 6 at 123420001-149070000 BP region, with evidence for linkage by the non-parametric model (LOD score=3.3) and supportive evidence for linkage by the dominant parametric model (LOD=2.5) (Figure). The chromosome 6 region, which is outside the HLA-region, contains a total of 72 genes. Using gene-level association tests, we identified four genes within the region (MOXD1, TRDN, ADAT2, LTV1) that were associated within MM / MGUS in the family cases (p<0.05). Discussion We found evidence for a locus on chromosome 6 linked to MM / MGUS. Four genes in this region may be associated with MM / MGUS in these families. Follow-up of these genes/variants in high-risk individuals (early-onset / age <60), sporadic cases and controls will help elucidate genetic mechanisms contributing to familial MM / MGUS. In addition, we demonstrate the benefit of applying a linkage analysis framework to familial WES data for discovery of genomic regions influencing MM / MGUS. Disclosures Dumontet: Roche: Research Funding; Merck: Consultancy, Membership on an entity's Board of Directors or advisory committees; Janssen: Honoraria; Sanofi: Honoraria. Kumar:AbbVie: Membership on an entity's Board of Directors or advisory committees, Research Funding; Janssen: Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; AbbVie: Membership on an entity's Board of Directors or advisory committees, Research Funding; Oncopeptides: Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees; Merck: Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; KITE: Membership on an entity's Board of Directors or advisory committees, Research Funding; Novartis: Research Funding; Roche: Research Funding; Janssen: Membership on an entity's Board of Directors or advisory committees, Research Funding; KITE: Membership on an entity's Board of Directors or advisory committees, Research Funding.

Abstract We previously identified five single nucleotide polymorphisms (SNPs) at four susceptibility loci for diffuse large B-cell lymphoma (DLBCL) in individuals of European ancestry through a large genome-wide association study (GWAS). To further elucidate genetic susceptibility to DLBCL, we sought to validate two loci at 3q13.33 and 3p24.1 that were suggestive in the original GWAS with additional genotyping. In the meta-analysis (5662 cases and 9237 controls) of the four original GWAS discovery scans and three replication studies, the 3q13.33 locus (rs9831894; minor allele frequency [MAF] = 0.40) was associated with DLBCL risk [odds ratio (OR) = 0.83, P = 3.62 × 10−13]. rs9831894 is in linkage disequilibrium (LD) with additional variants that are part of a super-enhancer that physically interacts with promoters of CD86 and ILDR1. In the meta-analysis (5510 cases and 12 817 controls) of the four GWAS discovery scans and four replication studies, the 3p24.1 locus (rs6773363; MAF = 0.45) was also associated with DLBCL risk (OR = 1.20, P = 2.31 × 10−12). This SNP is 29 426-bp upstream of the nearest gene EOMES and in LD with additional SNPs that are part of a highly lineage-specific and tumor-acquired super-enhancer that shows long-range interaction with AZI2 promoter. These loci provide additional evidence for the role of immune function in the etiology of DLBCL, the most common lymphoma subtype.

AbstractEpidemiologic studies show an increased risk of non‐Hodgkin lymphoma (NHL) in patients with autoimmune disease (AD), due to a combination of shared environmental factors and/or genetic factors, or a causative cascade: chronic inflammation/antigen‐stimulation in one disease leads to another. Here we assess shared genetic risk in genome‐wide‐association‐studies (GWAS).Secondary analysis of GWAS of NHL subtypes (chronic lymphocytic leukemia, diffuse large B‐cell lymphoma, follicular lymphoma, and marginal zone lymphoma) and ADs (rheumatoid arthritis, systemic lupus erythematosus, and multiple sclerosis). Shared genetic risk was assessed by (a) description of regional genetic of overlap, (b) polygenic risk score (PRS), (c)"diseasome", (d)meta‐analysis.Descriptive analysis revealed few shared genetic factors between each AD and each NHL subtype. The PRS of ADs were not increased in NHL patients (nor vice versa). In the diseasome, NHLs shared more genetic etiology with ADs than solid cancers (p = .0041). A meta‐analysis (combing AD with NHL) implicated genes of apoptosis and telomere length.This GWAS‐based analysis four NHL subtypes and three ADs revealed few weakly‐associated shared loci, explaining little total risk. This suggests common genetic variation, as assessed by GWAS in these sample sizes, may not be the primary explanation for the link between these ADs and NHLs.

1527 Background: Prospective Registry of Multiplex Testing (PROMPT) is an online registry for individuals who have had multiplex panel testing for cancer susceptibility. The main objective of this registry is to ascertain families to allow penetrance calculations for mutations in less well characterized genes. Methods: Since September 2014, health care providers and commercial laboratories have given PROMPT information with the test results to eligible individuals. Participants with pathogenic mutations or variants of unknown significance in cancer susceptibility genes have self-enrolled in PROMPT. We have sent annual follow-up surveys to participants to capture updated personal and family histories, additional genetic testing in the family, and changes in cancer screening patterns. Results: To date, 5800 participants have enrolled in PROMPT and 2321 follow-up surveys are completed. Of those eligible for follow-up, 1980 (44%) have completed at least one survey. 134 (5.8%) reported a new cancer diagnosis since baseline. Breast cancer (37, 27.6%) and non-Melanoma skin cancer (35, 26.2%) were the most commonly reported new diagnoses. 5.7% of participants with an ATM variant, 5.2% of those with a BRCA2 variant, and 4.3% of those with a CHEK2 variant and at least one follow-up survey have reported a new primary cancer diagnosis (excluding non-Melanoma skin cancer). In addition, 70 (3%) participants reported a cancer recurrence since time of last follow-up. Bone (9, 12.9%) and liver (8, 11.4%) were the most common recurrence sites. 12.7% of those with a TP53 variant, 7.1% of those with a BARD1 variant, and 3.3% of those with an ATM variant and at least one follow-up survey have reported a recurrence. 59 (2.5%) participants had additional clinical genetic testing, and 555 (24%) participants reported clinical genetic testing of family members. Conclusions: PROMPT collects updated health information from participants to achieve the primary goal of determining cancer incidence among carriers of different mutations. Moreover, PROMPT has increased participant contacts through use of annual follow-up surveys and gene-specific surveys with subsets of participants. Ongoing efforts include obtaining pathology reports of new and recurrent cancer diagnoses on study.

PURPOSE Germline CDH1 pathogenic variants (PV) are associated with hereditary diffuse gastric cancer and lobular breast cancer. Although prevalence of CDH1 PV is low in the general population, detection of these variants is increasing with the growing use of multigene panel testing. Little is known about the experiences of individuals tested for CDH1 variants in the multigene panel testing era. METHODS Participants recruited from the Prospective Registry of Multiplex Testing completed a cross-sectional self-report survey regarding CDH1 genetic testing experiences, medical management, and psychosocial adaptation. RESULTS Discordance existed in interpretations of CDH1 results; 13.3% of cases had disagreements in variant classifications among commercial laboratories, and 21.4% had disagreements between participant self-report and ClinVar classification. Survey data were available from 57 individuals reporting either PV (n = 16) or variants of uncertain significance (VUS; n = 41). Those with PV were more likely than those with VUS to report receiving a recommendation for prophylactic gastrectomy, although only 40.0% of those with PV received this recommendation. Participants with VUS were less satisfied with their health care providers’ knowledge and reported less CDH1 knowledge, distress, and worry about discrimination. Participants with PV perceived greater breast cancer risks, but similar gastric cancer risks, as those with VUS. CONCLUSION Few individuals with CDH1 PV report receiving recommendations for prophylactic gastrectomy, and no differences in perceived gastric cancer risk were observed based on participants’ CDH1 results, suggesting serious unmet informational needs.