Sinnwell, Jason P.

Introduction Monoclonal gammopathy of undetermined significant (MGUS) is a premalignant plasma cell disorder that is common in individuals over age 50. MGUS prevalence estimates to date have generally been based on results of serum electrophoresis and immunofixation (for heavy chain [HC] MGUS) and additionally, free light chain (for light chain [LC] MGUS). Mass-spectrometry assays, however, can detect lower levels of monoclonal (M) proteins, identify the isotype and provide accurate quantification of the M-protein. Given the evidence that MGUS is likely present at least 10 years prior to its detection, mass spectrometry may provide more accurate estimates of underlying MGUS. We examined the prevalence of HC-MGUS using matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry among three risk groups: European Americans (EA), African Americans (AA) and first-degree relatives (FDR) of patients with multiple myeloma (MM), MGUS, chronic lymphocytic leukemia (CLL) or non-Hodgkin's lymphoma (NHL). Methods We sampled all AA and a random sample of EA participants ages 50 and older enrolled in the Mayo Clinic Biobank. We also selected unaffected first-degree relatives (limiting to ages 50 and older) from our ongoing family study of hematological malignancies. We screened serum samples by the MALDI-TOF mass spectrometry assay, which is clinically used at Mayo Clinic (known as MASS-FIX) for detection and isotypes of M-proteins. The assay uses isotype-specific nanobody enrichment coupled to MALDI-TOF mass spectrometry. For each of the risk groups, HC- MGUS prevalence was estimated by age (50-59, 60-69, 70+). Age- and sex-adjusted prevalence rates were calculated by direct standardization to the 2010 US population. Ninety-five percent confidence intervals (95% CI) for the prevalence rates and comparisons across the three groups were based on the Poisson distribution. Because free LC information was unavailable, LC-MGUS was not estimated. Results A total 327 AA, 854 EA and 792 FDR were screened for M-proteins using the MASS-FIX assay. All three groups had similar sex (42-44% male) and age distributions (mean[SD] age was 64.5[9.5] yrs., 64.4[8.8] yrs. and 64.9[10.5] yrs. for AA, EA and FDR, respectively). As previously noted using conventional detection methods, the overall prevalence of HC-MGUS was higher in the AA population (16.5% [95%CI: 12.2%, 20.8%]) and FDR (21.5% [95%CI: 18.3%, 24.7%]) than in EA (11.2% [95%CI: 8.8%, 13.5%]), both p-values <0.0001. This pattern was generally seen across age groups (Table 1), with increasing prevalence with age. FDR of MM or MGUS cases had a higher prevalence (22.2% [95%CI: 18.4%, 26.0%]) than FDR of CLL or NHL cases (18.8% [95%CI: 13.3%, 24.4%]), although the difference was not statistically significant (p-value=0.82). Overall prevalence estimates of HC-MGUS using MASS-FIX were at least three-fold higher than estimates using conventional methods alone (i.e. age- and sex-adjusted prevalence in Olmsted County, MN, was 3.1% [95% CI: 2.9%-3.4%]). Conclusion We provided some of the first data on prevalence of HC-MGUS across three risk groups, using a sensitive method for detecting monoclonal proteins. The MASS-FIX assay resulted in substantially higher absolute rates of HC-MGUS (at least 3-fold higher) relative to conventional methods. Further, the prevalence of HC-MGUS among the AA and FDR was significantly higher than the EA population. Thus, the more sensitive assay identified greater absolute numbers of individuals with MGUS, but resulted in similar relationships as seen in prior studies across these risk groups. Our results have implications for future studies of the etiology of MGUS and its progression. Disclosures Dispenzieri: Janssen: Research Funding; Pfizer: Research Funding; Alnylam: Research Funding; Intellia: Research Funding; Celgene: Research Funding; Takeda: Research Funding. Kumar:Amgen: Consultancy, Other: Research funding for clinical trials to the institution, Consulting/Advisory Board participation with no personal payments, Research Funding; Janssen Oncology: Other: Research funding for clinical trials to the institution, Consulting/Advisory Board participation with no personal payments; Takeda: Other: Research funding for clinical trials to the institution, Consulting/Advisory Board participation with no personal payments; AbbVie: Other: Research funding for clinical trials to the institution, Consulting/Advisory Board participation with no personal payments; Karyopharm: Consultancy; Genecentrix: Consultancy; Cellectar: Other; Carsgen: Other, Research Funding; Merck: Consultancy, Research Funding; Dr. Reddy's Laboratories: Honoraria; Adaptive Biotechnologies: Consultancy; Celgene/BMS: Other: Research funding for clinical trials to the institution, Consulting/Advisory Board participation with no personal payments; Genentech/Roche: Other: Research funding for clinical trials to the institution, Consulting/Advisory Board participation with no personal payments; Oncopeptides: Consultancy, Other: Independent Review Committee; IRC member; Kite Pharma: Consultancy, Research Funding; BMS: Consultancy, Research Funding; Tenebio: Other, Research Funding; Sanofi: Research Funding; MedImmune: Research Funding; Novartis: Research Funding. Murray:The Binding Site: Patents & Royalties: Patent Use of Mass Spec to identify monoclonal proteins licensed to The Binding Site.

Introduction Monoclonal gammopathy of undetermined significance (MGUS) is a premalignant clonal disorder, which progresses at a rate of 1% per year to multiple myeloma (MM), or other plasma-cell or lymphoid disorders. MGUS is common and occurs in approximately 3% and 5% of persons 50 and 70 years of age or older, respectively. Clinical factors reported to be associated with MGUS progression include MGUS isotype, abnormal serum free light-chain ratio (FLCr), and high serum monoclonal protein (M protein) level (>=1.5 g per deciliter). Body mass index (BMI) has also been seen associated with MGUS progression, but has not been evaluated in context of established clinical prognostic factors. Here, we evaluate the contribution of BMI to MGUS progression beyond clinical prognostic factors in a population-based study and examine differential associations by sex. Methods We studied 594 patients residing in Olmsted County Minnesota, who were identified with MGUS in a screening study conducted between1995 through 2003. Patients with light-chain MGUS were not included. Patients were screened for M-protein [normal (<1.5 g/dl) or high (≥1.5 g/dl)], FLCr [normal (0.26-1.65) or abnormal (<0.26 and/or >1.65)], and isotype (IgG, IgM, IgA, bi-clonal). Follow-up time was calculated from date of MGUS screening to date of last follow-up, death, or progression to MM or another plasma-cell or lymphoid disorder. BMI (kg/m2) was calculated using height and weight values reported close to sample date (80% of patients within 2 years), and then categorized into BMI<25 and BMI≥25. We used Cox regression to estimate the association of BMI with risk of MGUS progression to MM or another plasma-cell or lymphoid disorder, univariately, and accounting for clinical factors. Analyses were also stratified by sex. We report hazard ratios (HR) and 95% confidence intervals (CI). Results Of the 594 patients, 51% were male, and the median age at screening date was 73 (range:50-98 years). The immunoglobulin type was IgG in 71% of patients, IgM in 17%, IgA in 10%, and bi-clonal in 2%. High M protein level was observed in 22% and abnormal FLCr in 28%. BMI≥25 was observed in 67% of patients. The median follow-up time was 10.5 years (range:0-25). Over a median of 6,846 person-years, 465 patients (78%) died and 57 patients progressed and developed MM (N=39), amyloidosis (N=8), lymphoma (N=5), or Waldenstrom macroglobulinemia (N=5). The overall rate of progression was 0.87 events (CI:0.67-1.12) per 100 person-years, and higher among males (1.01, CI:0.73-1.42) than in females (0.72, CI:0.48-1.08), however, the difference was not statistically significant (P=0.24). In univariate analyses, BMI≥25 (HR=2.14, CI:1.05-4.36, P=0.04), non-IgG isotype (HR=2.84, CI:1.68-4.80, P=0.0001), high M protein (HR=2.57, CI: 1.50-4.42, P=0.001), and abnormal FLCr (HR=3.39, CI:1.98-5.82, P<0.0001) were associated with increased risk of progression (Table 1.A). These four factors were independently associated with MGUS progression in a multivariable model, with a c-statistic=0.75 (CI:0.68-0.82). When stratifying by sex, associations of BMI with progression were stronger among females than males (Table 1.B) [c-statistic=0.81 (CI:0.72-0.90) vs 0.71 (CI:0.60-0.82) for females vs. males respectively], however, a test for interaction between BMI and sex was not statistically significant (P=0.15). Conclusions In this study we found evidence that high BMI is a prognostic factor independent of isotype, M protein, and FLC ratio in the full cohort, however, this was mainly driven by the effect in females rather than males. Future studies should further investigate sex differences in evaluating prognostic factors among MGUS patients. Disclosures Dispenzieri: Intellia: Research Funding; Pfizer: Research Funding; Alnylam: Research Funding; Takeda: Research Funding; Celgene: Research Funding; Janssen: Research Funding. Kumar:Genentech/Roche: Other: Research funding for clinical trials to the institution, Consulting/Advisory Board participation with no personal payments; Cellectar: Other; Kite Pharma: Consultancy, Research Funding; Tenebio: Other, Research Funding; BMS: Consultancy, Research Funding; Karyopharm: Consultancy; MedImmune: Research Funding; Sanofi: Research Funding; Celgene/BMS: Other: Research funding for clinical trials to the institution, Consulting/Advisory Board participation with no personal payments; Janssen Oncology: Other: Research funding for clinical trials to the institution, Consulting/Advisory Board participation with no personal payments; Amgen: Consultancy, Other: Research funding for clinical trials to the institution, Consulting/Advisory Board participation with no personal payments, Research Funding; Merck: Consultancy, Research Funding; Adaptive Biotechnologies: Consultancy; Genecentrix: Consultancy; Takeda: Other: Research funding for clinical trials to the institution, Consulting/Advisory Board participation with no personal payments; Dr. Reddy's Laboratories: Honoraria; AbbVie: Other: Research funding for clinical trials to the institution, Consulting/Advisory Board participation with no personal payments; Novartis: Research Funding; Carsgen: Other, Research Funding; Oncopeptides: Consultancy, Other: Independent Review Committee; IRC member.

Abstract Endocrine therapy is underutilized to reduce breast cancer incidence among women at increased risk. Polygenic risk scores (PRSs) assessing 77 breast cancer genetic susceptibility loci personalizes risk estimates. We examined effect of personalized PRS breast cancer risk prediction on intention to take and endocrine therapy uptake among women at increased risk. Eligible participants had a 10-year breast cancer risk ≥5% by Tyrer–Cuzick model [International Breast Cancer Intervention Study (IBIS)] or ≥3.0 % 5-year Gail Model risk with no breast cancer history or hereditary breast cancer syndrome. Breast cancer risk was estimated, endocrine therapy options were discussed, and endocrine therapy intent was assessed at baseline. After genotyping, PRS-updated breast cancer risk estimates, endocrine therapy options, and intent to take endocrine therapy were reassessed; endocrine therapy uptake was assessed during follow-up. From March 2016 to October 2017, 151 patients were enrolled [median (range) age, 56.1 (36.0–76.4 years)]. Median 10-year and lifetime IBIS risks were 7.9% and 25.3%. Inclusion of PRS increased lifetime IBIS breast cancer risk estimates for 81 patients (53.6%) and reduced risk for 70 (46.4%). Of participants with increased breast cancer risk by PRS, 39 (41.9%) had greater intent to take endocrine therapy; of those with decreased breast cancer risk by PRS, 28 (46.7%) had less intent to take endocrine therapy (P < 0.001). On multivariable regression, increased breast cancer risk by PRS was associated with greater intent to take endocrine therapy (P < 0.001). Endocrine therapy uptake was greater among participants with increased breast cancer risk by PRS (53.4%) than with decreased risk (20.9%; P < 0.001). PRS testing influenced intent to take and endocrine therapy uptake. Assessing PRS effect on endocrine therapy adherence is needed. Prevention Relevance: Counseling women at increased breast cancer risk using polygenic risk score (PRS) risk estimates can significantly impact preventive endocrine therapy uptake. Further development of PRS testing to personalize breast cancer risk assessments and endocrine therapy counselling may serve to potentially reduce the incidence of breast cancer in the future.

Abstract Background: Genetic studies have shifted to sequencing-based rare variants discovery after decades of success in identifying common disease variants by Genome-Wide Association Studies using Single Nucleotide Polymorphism chips. Sequencing-based studies require large sample sizes for statistical power but often inadvertently introduce batch effects because samples are typically collected, processed, and sequenced at multiple centers. Conventionally, batch effects are first detected and visualized using Principal Components Analysis and then controlled by including batch covariates in the disease association models. For sequencing-based genetic studies, because all variants included in the association analyses have passed quality control measures, this conventional approach treats every variant as equal and ignores the substantial differences still remaining in variant qualities and characteristics such as genotype quality scores, alternative allele fractions (fraction of reads supporting alternative allele at a variant position) and sequencing depths. Results: In the Alzheimer’s Disease Sequencing Project (ADSP) exome dataset of 9,904 cases and controls, we discovered hidden variant-level differences between sample batches of three sequencing centers and two exome capture kits. Although sequencing centers were included as a covariate in our association models, we observed differences at the variant level in genotype quality and alternative allele fraction between samples processed by different exome capture kits that significantly impacted both the confidence of variant detection and the identification of disease-associated variants. Furthermore, we found that the association signals of a subset of top disease risk variants came exclusively from samples processed by one exome capture kit that was more effective at capturing the alternative alleles compared to the other kit. Conclusions: Our findings highlight the importance of additional variant-level quality control for large sequencing-based genetic studies. More importantly, we demonstrate that automatically filtering out variants with batch differences may lead to false negatives if the batch discordance came largely from quality differences and if the variants from one batch had better quality scores.

AbstractVariance component models have gained popularity for genetic analyses, driven by their flexibility to simultaneously analyze multiple genetic variants in a gene by kernel statistics, and their ability to account for population stratification via genomic relationship matrices. For exploratory analyses with modest sample sizes and a potentially large number of variance components, it can be challenging to use standard maximum‐likelihood or restricted maximum‐likelihood methods to estimate variance components, because these iterative methods often fail to converge when likelihood surfaces are fairly flat, and standard‐likelihood ratio statistical tests are not adequate. To overcome these limitations, we developed a penalized‐likelihood model, whereby the penalty function follows the popular elastic‐net approach, applying both L1 and L2 penalties to the variance components. By simulations, we demonstrate the potential gain in power by using both L1 and L2 penalties, and results from our simulations suggest that assigning 80% of the penalty parameter to the L1 penalty and 20% to the L2 penalty provides a reasonable balance between false‐positive and false‐negative results. Larger sample size improves the properties of our methods, at the cost of longer computation time. Application of our methods to a study of the influence of DNA methylation on levels of cortisol in reaction to stress testing shows how our method can be used to prioritize findings for further functional studies.

Abstract So far, 23 germline susceptibility loci have been associated with multiple myeloma (MM) risk. It is unclear whether the genetic variation associated with MM susceptibility also predisposes to its precursor, monoclonal gammopathy of undetermined significance (MGUS). Leveraging 2434 MM cases, 754 MGUS cases, and 2 independent sets of controls (2567/879), we investigated potential shared genetic susceptibility of MM and MGUS by (1) performing MM and MGUS genome-wide association studies (GWAS); (2) validating the association of a polygenic risk score (PRS) based on 23 established MM loci (MM-PRS) with risk of MM, and for the first time with MGUS; and (3) examining genetic correlation of MM and MGUS. Heritability and genetic estimates yielded 17% (standard error [SE] ±0.04) and 15% (SE ±0.11) for MM and MGUS risk, respectively, and a 55% (SE ±0.30) genetic correlation. The MM-PRS was associated with risk of MM when assessed continuously (odds ratio [OR], 1.17 per SD; 95% confidence interval [CI], 1.13-1.21) or categorically (OR, 1.70; 95% CI, 1.38-2.09 for highest; OR, 0.71; 95% CI, 0.55-0.90 for lowest compared with middle quintile). The MM-PRS was similarly associated with MGUS (OR, 1.19 per SD; 95% CI, 1.14-1.26 as a continuous measure, OR, 1.77, 95%CI: 1.29-2.43 for highest and OR, 0.70, 95%CI: 0.50-0.98 for lowest compared with middle quintile). MM and MGUS associations did not differ by age, sex, or MM immunoglobulin isotype. We validated a 23-SNP MM-PRS in an independent series of MM cases and provide evidence for its association with MGUS. Our results suggest shared common genetic susceptibility to MM and MGUS.

Abstract Mediation analysis attempts to determine whether the relationship between an independent variable (e.g., exposure) and an outcome variable can be explained, at least partially, by an intermediate variable, called a mediator. Most methods for mediation analysis focus on one mediator at a time, although multiple mediators can be jointly analyzed by structural equation models (SEMs) that account for correlations among the mediators. We extend the use of SEMs for the analysis of multiple mediators by creating a sparse group lasso penalized model such that the penalty considers the natural groupings of parameters that determine mediation, as well as encourages sparseness of the model parameters. This provides a way to simultaneously evaluate many mediators and select those that have the most impact, a feature of modern penalized models. Simulations are used to illustrate the benefits and limitations of our approach, and application to a study of DNA methylation and reactive cortisol stress following childhood trauma discovered two novel methylation loci that mediate the association of childhood trauma scores with reactive cortisol stress levels. Our new methods are incorporated into R software called regmed .

Abstract Background: Studies demonstrate breast cancer risk reduction of 50-65% with the use of endocrine therapy (ET) and yet drug uptake and adherence in this setting is suboptimal even among high risk women. A Polygenic Risk Score (PRS) comprised of 77 BC genetic susceptibility loci (Single Nucleotide Polymorphisms (SNP)) can provide a personalized risk assessment and potentially influence ET adherence. We assessed ET adherence at 1 year comparing women whose risk estimate increased due to PRS versus women whose risk estimate decreased due to PRS. The effect of ET use on quality of life (hot flashes, night sweats, vaginal dryness, weight gain, joint pain) was evaluated. Methods: Eligible women required either a 5 year Gail Model risk of ≥3% or 10 year IBIS ( International Breast Intervention Study or Tyrer-Cuzick model) of ≥5%. Women with a history of breast cancer (BC) or hereditary BC syndrome were excluded. High risk women were counseled at baseline using their Gail and IBIS risk scores and ET options were discussed including benefits and risks. Participants completed a self-reported questionnaire at baseline to assess their understanding of breast cancer risk and decision to take preventive ET. Blood samples were obtained and genotyped for 77 SNPs, and the odds ratio from the SNPs were used to modify the IBIS and Gail risk estimates. The BC -PRS risk estimate information was shared with study participants that reflected the IBIS and Gail risk estimates for 5 year, 10 year, & lifetime BC risk with and without the PRS. Follow up questionnaires at year 1 were administered to assess drug adherence and ET usage on quality of life. Results: 151 women were enrolled at Mayo Clinic Rochester and CancerCare Manitoba from 2016 to 2017. The median age was 56.1 (range 36-76.4), 35.6% were premenopausal, 98.7% were Caucasian and 64.7% had>1 family member with BC. Median 5yr, 10yr, & lifetime IBIS- PRS risk estimates were 3.8% (2.0-11.5), 7.9% (5.0-23.1), and 25.3% (5.5 to 92.2). At year 1 (n=112 women) 46 % of those with an increase in risk when considering the BC-PRS score and 16 % with a decrease in risk were taking ET ( p< 0.001). Types of ET taken: tamoxifen-18, raloxifene- 3, exemestane -14 and missing-1. Women taking ET reported weight gain ( 19.4% vs 6.7%, p=0.04) and more joint pain ( 27.8 % vs 12%, p=0.04) when compared to women not taking ET. Conclusion: In high risk women, BC-PRS risk estimates in addition to standard BC risk calculators had a significant impact on preventive ET adherence. ET use was associated with weight gain and joint pain. Citation Format: Sandhya Pruthi, Julian O Kim, Daniel Schaid, Andrew Cooke, Christina Kim, Benjamin Goldenberg, Jason Sinnwell, Debjani Grenier, Fergus Couch, Celine Vachon. Impact of the breast cancer polygenic risk score on preventive endocrine therapy adherence and endocrine therapy usage on quality of life - The Genetic Risk Estimate (GENRE) trial [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr PD3-03.

Abstract Background: TNBC is the most aggressive sub-type of breast cancer and has limited targeted therapies. Atezolizumab was recently FDA-approved for patients with advanced PD-L1+ TNBC. In a well-characterized cohort of patients with early-stage TNBC, we used the FDA-approved PD-L1 SP142 companion assay for atezolizumab to score whole tumor sections for PD-L1 expression. We determined the frequency and scoring distribution of PD-L1 in these tumors and evaluated PD-L1 status for associations with clinicopathologic variables and outcomes. Methods: Whole tumor sections from 498 women with surgically-treated, non-(distant) metastatic TNBC (ER/PR <1% & HER2-negative by central review) were semi-quantitatively scored for % of PD-L1-staining tumor cells (TC) or tumor-associated immune cells (IC) (PD-L1 SP142, Ventana, performed in CAP/CLIA-certified clinical laboratory). Per FDA assay guidelines, PD-L1+ tumors were defined as ≥1% of tumor-associated immune cells (IC) staining per tumor area. Baseline clinical characteristics, histopathologic features, Ki-67 proliferative indices (PI), and stromal tumor infiltrating lymphocytes (TILs) were correlated with PD-L1 status. The impact of tumoral PD-L1 status on invasive disease-free survival (IDFS) and overall survival (OS) was assessed using Cox proportional hazards models. Results: The majority of tumors were pT1-T2 (95%), pN0-1 (85%), and grade 3 (90%) with Ki-67 >15% (80%). 228/498 (46%) tumors were PD-L1+, distributed as IC score 1-5%: 21%, 6-10%: 13%, 11-20%: 5% and >20%: 7%. 270/498 (54%) were PD-L1-. 43 (8.6%) of tumors had PD-L1 staining in TC (all but 1 were also IC+). PD-L1 IC expression was associated with larger tumor size (p = 0.005), higher nodal stage (≥pN1: 43% vs. 31%, p < 0.001), higher grade (grade 3: 95% vs. 86%, p< 0.001), higher Ki-67 PI (>15%: 88% vs. 69%, p <0.001), and stromal TILs (median score: 40% vs. 10%; p < 0.001). PD-L1 IC status was not associated with patient age. Among histologic subtypes, PD-L1+ tumors were more frequently medullary type (31% vs. 6%) and less frequently metaplastic type (4% vs 10%). At time of this analysis, median follow-up for IDFS and OS were 11 years and 7.2 years, respectively. By univariable analysis, absence of PD-L1 IC expression was associated with poorer IDFS (median: 15.5 vs. 20 years, p = 0.04) and OS (9.5 vs. 17.5 years, p < 0.05).By multivariable analysis, tumor size, stromal TILs, nodal status, and adjuvant chemotherapy (CTX) were significantly associated with IDFS. Age, stromal TILs, nodal status, and receipt of adjuvant CTX were associated with OS. PD-L1+ tumors trended toward improved IDFS (statistical significance not reached), HR: 0.68 (95% CI: 0.45-1.03, p= 0.068) but not OS: 0.90 (95% CI: 0.52-1.57, p= 0.32). Conclusion: Using the PD-L1 SP142 companion assay, almost half of early-stage TNBC were PD-L1+ (IC). However, PD-L1 expression correlated with increasing tumor size and nodal burden, as well as histologic grade, Ki-67 PI, stromal TILs and lymphocyte-enriched subtypes. PD-L1 was associated with improved IDFS and OS in univariable analysis but not multivariable analysis. The majority of the PD-L1+ tumors (73%) had IC scores ≤10%, with heterogeneous tumoral staining. Given the low (1%) assay threshold for positivity, these data emphasize the utility of evaluating PD-L1 in whole tumor sections rather than tissue cores. Citation Format: Jodi M Carter, Mei-Yin C Polley, Jason P Sinnwell, Roberto A Leon-Ferre, Fergus J Couch, Krishna R Kalari, Judy C Boughey, Minetta C Liu, Daniel W Visscher, Matthew P Goetz. Frequency, characteristics and prognostic factors of PD-L1+ triple negative breast cancer using the PD-L1 SP142 companion assay [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr PD1-08.

Abstract Background: The combination of cyclin dependent 4/6 kinase inhibitors (CDK4/6i) with endocrine therapy (ET) has resulted in clinically significant improvements in progression-free survival (PFS) and overall survival (OS) in hormone-receptor (HR)-positive metastatic breast cancer (MBC). However, most patients’ disease ultimately progresses on CDK4/6i and ET. Therefore, further research is necessary to understand the mechanisms driving primary and secondary resistance. PROMISE is a multicenter prospective cohort study enrolling women with HR-positive MBC commencing treatment with palbociclib + letrozole (1st line) or palbociclib + fulvestrant (2nd Line). The study provides a comprehensive “omic” assessment of blood, tumor, urine and the fecal microbiome to identify molecular or cellular features associated with primary endocrine resistance (e.g. disease progression ≤ 12 months on treatment) and acquired resistance to CDK 4/6i. Additionally, patient derived xenografts and organoids are created to test new drug strategies designed to overcome resistance to CDK 4/6i and ET. Here, we present initial sequencing results from pretreatment biospecimens collected from PROMISE study participants. Methods: On-study tumor biopsies and blood samples were collected for DNA/RNA sequencing (TempusTM). The analyzed biospecimens were all obtained prior to initiation of palbociclib and ET. We correlated patient clinical characteristics (phenotypes) with molecular data and responses to protocol treatment. The data were analyzed using a series of cutting-edge bioinformatics pipelines for somatic and germline mutations in addition to copy number alterations (CNAs). The study database was locked for analysis on 06/20/2019. Results: We analyzed the somatic single nucleotide variants/INDELs (sSNV/INDEL) profiles across the tumor samples to determine the genes that were least likely to occur as a result of background mutation processes. Twenty-six patients had somatic copy number alterations (sCNA) and/or sSNV/INDEL in at least one of 18 genes with the most significant sSNV/INDEL profiles (p < 0.03) which included clinically and biologically relevant genes. The genes with the most statistically significant sSNV/INDEL mutation profiles were GATA3, PIK3CA, CDH1, and ESR1 (p < 0.0009). We observed a high percentage of tumors with somatic alterations in GATA3 (23% sSNV/INDEL, 15% sCNA), PIK3CA (38%, 12%), CDH1 (19%, 50%) and ESR1 (19%, 58%). ESR1 mutations were more frequent in patients receiving 2nd line treatment. Other frequently altered genes included TP53 (15%, 46%), MAP2K4 (8%, 50%), DNAAF1 (8%, 50%), and CDKN1B (8%, 35%). Further, ZNF317 and F3 were altered in 9 and 7 patients, respectively. Twenty-four samples had alterations in at least one of the CDK4/6 pathway genes (RB1, CCNE2, CCND1, CDK6, ESR1, CDKN2A, CCND3, CDK4, CDK2 and CCNE1). Four patients progressed on therapy; three of the four patients had mutations in PIK3CA, and one had a mutation in ESR1. Results of the RNA sequencing data (N=26) will be presented at the SABCS meeting. Conclusions: This is the first report of a prospective study designed to characterize the genomic landscape of ER+/HER2- MBC prior to palbociclib treatment. We observed high frequencies of known targetable alterations in PIK3CA and ESR1, including in patients that progress, which is consistent with previous reports. RNA sequencing data will be presented at the meeting. Citation Format: Ciara C O Sullivan, Krishna R Kalari, Vera J Suman, Peter T Vedell, Ann Moyer, Erin Carlson, Jason Sinnwell, Tejaswi Alaparthi, Xiaojia Tang, Kevin Thompson, Jaeyun Sung, Alvaro Moreno-Aspitia, Donald Northfelt, Minetta C Liu, Tufia C Haddad, Prema Peethambaram, Saranya Chumsri, Kathryn J Ruddy, Karthik V Giridhar, Roberto A Leon-Ferre, Paula Gill, Mohammad Ranginwala, Asad Javed, Sameer Batoo, Brendan P. McMenomy, Richard Weinshilboum, Liewei Wang, Matthew P Goetz. Comprehensive tumor sequencing to identify biomarkers of palbociclib response: First report of the PROMISE study [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P2-11-07.