bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defining patient-elicited concepts unique to adolescents and young adults with cancer.
Authors: Avutu Viswatej , Lynch Kathleen , Barnett Marie , Vera Jacqueline , Glade Bender Julia Lynne , Tap William D. , Atkinson Thomas Michael 
Published: May 2020

12118 Background: Adolescents and young adults (AYAs) require a multidisciplinary approach to cancer care due to complex biopsychosocial variables and varied developmental maturity. Currently, age and diagnosis determine referral to pediatric or adult oncology with differing care paradigms and service utilization. These issues, in conjunction with differences in tumor biology and lower accrual to clinical trials, have contributed to marginal improvements in outcomes for AYAs. Compounding this dilemma is a lack of validated patient-reported outcome measures (PROs) for AYAs. Tracking standardized PROs longitudinally is a crucial step in understanding psychosocial variables, identifying tailored needs, improving outcomes and standardizing care. However, developing a PRO tool for AYAs first requires identifying AYA-unique domains. Methods: Three, 90-minute focus groups were conducted with AYAs treated at Memorial Sloan Kettering in the context of 1) pediatric oncology, 2) medical oncology, and 3) either service. Topics explored included: experiences of cancer care as an AYA; physical, social and emotional concerns; and information needs, including appropriateness, timing, and depth of information. Thematic content analysis of transcripts was performed by four interdisciplinary coders in weekly iterative consensus rounds. Phase one consisted of identification of key domains to guide line-by-line coding with NVivo software. Phase two consisted of independent review and categorization of codes, followed by three successive consensus meetings to identify distinct themes. Results: A mean of 6 patients (range 5-7) participated in each of the 3 groups; the total sample (n = 17) included 9 males and 8 females, ages 19-35 years (median 26). Four AYA-unique themes were identified: 1. AYAs have an uncertain sense of the future and desire more engagement in conversations pertaining to survivorship, long-term effects and transition to outpatient life. 2. Cancer as an AYA is a socially-isolating experience, prompting a strong desire to connect with peers during and post-treatment. 3. AYAs want control over who can be present during discussions with their care team as the presence of loved ones can impede or facilitate communication. 4. AYAs may be living far away from loved ones during treatment and lack supports needed to help them navigate treatment and daily life. Conclusions: Concept elicitation via focus groups identified novel themes related to survivorship, isolation, communication and social support, which can inform development of AYA-specific PROs.
Performance of the IBIS/Tyrer-Cuzick (TC) Model by race/ethnicity in the Women’s Health Initiative.
Authors: Kurian Allison W. , Hughes Elisha , Bernhisel Ryan , Probst Braden , Lanchbury Jerry , Wagner Susanne , Gutin Alexander , Caswell-Jin Jennifer Lee , Rohan Thomas E , Shadyab Aladdin H. , Manson JoAnn E , Lane Dorothy , Stefanick Marcia L. 
Published: May 2020

1503 Background: The TC model, a breast cancer (BC) risk assessment tool based on family cancer history, reproductive and lifestyle factors is used to guide BC screening and prevention. TC was developed and validated largely in non-Hispanic White (NHW) women. We evaluated the calibration and discrimination of TC version 7.02 among racially/ethnically diverse post-menopausal women enrolled in the Women’s Health Initiative (WHI) clinical trials or observational study. Methods: WHI enrolled post-menopausal women from 1993-1998 and followed them prospectively for BC incidence. We included women aged ≤80 years at enrollment with no prior BC or mastectomy and with data required for TC, including weight, height, ages at menarche, first birth and menopause, menopausal hormone therapy use and family history of breast or ovarian cancer in first or second-degree relatives. Calibration was assessed by the ratio of observed BC cases to the number expected by TC (O/E), with expected cases calculated as the sum of cumulative hazards. We tested for differential discrimination by race/ethnicity (NHW, African American, Hispanic, Asian/Pacific Islander, Native American, other) using Cox regression. Time to BC was modeled using age, race/ethnicity, TC estimate (transformed by log of relative lifetime risk), and a term for interaction between race/ethnicity and TC estimate. Results: During the follow-up period (median 18.9 years, maximum 23.4 years), 6,836 new BC cases were diagnosed among 91,893 women. TC was well-calibrated overall (O/E 0.95) in NHW and African Americans, but over-estimated risk for Hispanics (O/E 0.75, Table). Results suggested good calibration for Asian/Pacific Islanders and Native Americans, but sample sizes were small. Discrimination did not differ significantly by race/ethnicity (two-sided p-value for interaction = 0.33). Conclusions: TC provided similar risk discrimination among post-menopausal women of different racial/ethnic groups over nearly 20 years of follow-up; however, it overestimated risk for Hispanics. Future studies in diverse populations are warranted, with need for a more accurate breast cancer risk assessment tool for Hispanics. [Table: see text]
A randomized controlled trial of video-education or in-person genetic counseling for men with prostate cancer (ProGen).
Authors: Rana Huma Q. , Stopfer Jill E. , Petrucelli Nancie , Koeller Diane R. , Pirzadeh-Miller Sara , Reys Brian , Kipnis Lindsay , Culver Samantha , Vatnick Donna Rachel , Silver Rebecca , Mercado Joanna , Gelman Rebecca Sue , Weitz Michelle , Speare Virginia , Dolinsky Jill S. , Heath Elisabeth I. , Ross Theodora Suzanne , Courtney Kevin Dale , Garber Judy Ellen , Taplin Mary-Ellen ,   ProGen Study Team
Published: May 2020

1507 Background: Approximately 10% of men with advanced prostate cancer (PC) have pathogenic/likely pathogenic variants (PV) in cancer susceptibility genes and their identification may lead to targeted therapy. Genetic testing (GT) can also guide cancer surveillance and prevention for family members. While GT is recommended for men with potentially lethal PC, traditional testing models are strained, and access limited. The ProGen study examined a novel pretest model aimed at providing access to GT while promoting informed consent. Methods: Inclusion criteria were: potentially lethal PC (metastatic, localized with Gleason score ≥8, rising/persistent PSA after local therapy), diagnosis age ≤ 55 years, prior malignancy, family history suggestive of a PV and/or at oncologist’s discretion. Consented subjects from 3 sites were randomized 3:1 to video education (VE) or in-person genetic counseling (GC). Subjects who consented to GT had 67 genes analyzed (Ambry, USA) with results disclosed by telephone by a genetic counselor. Outcomes included GT uptake, PV prevalence, and survey measures of satisfaction, distress, genetics knowledge, family communication, and impact on cancer care (obtained at the time of intervention, and at 1, 4, and 12 months after result disclosure). Two-sided Fischer exact tests were used for between-arm comparisons. Results: Over a 2-year period: 662 subjects were randomized, VE or GC were completed by 604 subjects (VE: 93.1%, GC: 88.8%) of whom 596 subjects (VE:98.9%, GC:97.9%) consented to GT. To date, 591 subjects have completed GT (VE: 99.3%, GC: 98.6%). At the time of intervention, most subjects agreed or strongly agreed that their assigned arm was useful (VE: 95%, GC: 88%). Differences were not statistically significant. Notably, 84 PV were identified in 78 subjects (13.2%), with BRCA1/2 PV accounting for 32% of subjects with a positive result ( BRCA2:21, BRCA1:4). Conclusions: In this randomized trial, both novel VE and traditional GC yielded high GT uptake without significant differences in outcome measures of acceptability and satisfaction. VE enabled access to critical GT results while maintaining the core tenants of informed consent. PV were found in 13.2% of subjects, 32% of whom had BRCA1/2 PV. Analysis of collected survey data to inform strengths and limitations of VE as compared with pretest GC will be presented. Clinical trial information: NCT03328091.
Expanding the diagnostic yield of germline genetic testing in cancer patients using deep learning.
Authors: Aldubayan Saud H , Conway Jake , Witkowski Leora , Kofman Eric , Reardon Brendan , Camp Sabrina , Han Seunghun , Elmarakeby Haitham , Al-Rubaish Abdullah , Al-Sulaiman Abdulsalam , Al-Ali Amein , Taylor-Weiner Amaro , Van Allen Eliezer Mendel 
Published: May 2020

1518 Background: Germline genetic analysis is an essential tool for implementing precision cancer prevention and treatment. However, only a small fraction of cancer patients, even those with features suggestive of a cancer-predisposition syndrome, have detectable pathogenic germline events, which may in part reflect incomplete pathogenic variant detection by current gold-standard methods. Here, we leveraged deep learning approaches to expand the diagnostic utility of genetic analysis in cancer patients. Methods: Systematic analysis of the detection rate of pathogenic cancer-predisposition variants using the standard clinical variant detection method and a deep learning approach in germline whole-exome sequencing data of 2367 cancer patients (n = 1072 prostate cancer, 1295 melanoma). Results: Of 1072 prostate cancer patients, deep learning variant detection identified 16 additional prostate cancer patients with clinically actionable pathogenic cancer-predisposition variants that went undetected by the gold-standard method (198 vs. 182), yielding higher sensitivity (94.7% vs. 87.1%), specificity (64.0% vs. 36.0%), positive predictive value (95.7% vs. 91.9%), and negative predictive value (59.3% vs. 25.0%). Similarly, germline genetic analysis of 1295 melanoma patients showed that, compared with the standard method, deep learning detected 19 additional patients with validated pathogenic variants (93 vs. 74) with fewer false-positive calls (78 vs. 135) leading to a higher diagnostic yield. Collectively, deep learning identified one additional patient with a pathogenic cancer-risk variant, that went undetected by the standard method, for every 52 to 67 cancer patients undergoing germline analysis. Superior performance of deep learning, for detecting putative loss-of-function variants, was also seen across 5197 clinically relevant Mendelian genes in these cohorts. Conclusions: The gold-standard germline variant detection method, universally used in clinical and research settings, has significant limitations for identifying clinically relevant pathogenic disease-causing variants. We determined that deep learning approaches have a clinically significant increase in the diagnostic yield across commonly examined Mendelian gene sets.
Performance of polygenic risk scores for cancer prediction in an academic biobank.
Authors: Desai Heena , Le Anh , Hausler Ryan , Verma Shefali , Verma Anurag , Judy Renae , Doucette Abigail , Gabriel Peter Edward , Damrauer Scott , Ritchie Marilyn , Rader Daniel , Kember Rachel , Maxwell Kara Noelle ,   Regeneron Genetics Center
Published: May 2020

1528 Background: The discovery of rare genetic variants associated with cancer have a tremendous impact on reducing cancer morbidity and mortality when identified; however, rare variants are found in less than 5% of cancer patients. Genome wide association studies (GWAS) have identified hundreds of common genetic variants significantly associated with a number of cancers, but the clinical utility of individual variants or a polygenic risk score (PRS) derived from multiple variants is still unclear. Methods: We tested the ability of polygenic risk score (PRS) models developed from genome-wide significant variants to differentiate cases versus controls in the Penn Medicine Biobank. Cases for 15 different cancers and cancer-free controls were identified using electronic health record billing codes for 11,524 European American and 5,994 African American individuals from the Penn Medicine Biobank. Results: The discriminatory ability of the 15 PRS models to distinguish their respective cancer cases versus controls ranged from 0.68-0.79 in European Americans and 0.74-0.93 in African Americans. Seven of the 15 cancer PRS trended towards an association with their cancer at a p<0.05 (Table), and PRS for prostate, thyroid and melanoma were significantly associated with their cancers at a bonferroni corrected p<0.003 with OR 1.3-1.6 in European Americans. Conclusions: Our data demonstrate that common variants with significant associations from GWAS studies can distinguish cancer cases versus controls for some cancers in an unselected biobank population. Given the small effects, future studies are needed to determine how best to incorporate PRS with other risk factors in the precision prediction of cancer risk. [Table: see text]
Functional analysis of patient-derived PALB2 missense variants of uncertain significance.
Authors: Wu Shijie , Zhou Jiaojiao , Chen Yiding 
Published: May 2020

1531 Background: Inherited PALB2 pathogenic variants are associated with an increased lifetime risk for breast cancer development. However, the interpretation of numerous PALB2 missense variants of uncertain significance (VUS) identified in germline genetic testing remains a challenge. Here, we assessed the impact of breast cancer patient-derived VUS on PALB2 function and identified pathogenic PALB2 missense variants that may increase cancer risk. Methods: A total of seven potentially pathogenic PALB2 VUS identified in 2,279 breast cancer patients were selected for functional analysis. All these selected VUS were assessed by SIFT, Align-GVGD, and PolyPhen2 in silico and were predicted to be deleterious by at least two in silico algorithms. The p.L35P [c.104T > C] variant was also included, for which pathogenicity has been recently confirmed. The effects of the VUS on the homologous recombination (HR) activity of PALB2 were tested by U2OS/DR-GFP reporting system. Functional characterization was further validated by protein co-immunoprecipitation and RAD51 recruitment assay. Results: PALB2 variants p.L24F [c.72G > C] and p.L35P [c.104T > C] showed the most significant disruption to the HR activity of PALB2 relative to the wild-type condition, retaining only 52.2% ( p = 0.0013) and 8.5% ( p < 0.0001) of HR activity respectively. Moderate but statistically significant HR deficiency was observed for four other variants (p.P405A [c.1213C > G], p.T1012I [c.3035C > T], p.E1018D [c.3054G > C], and p.T1099M [c.3296C > T]). We found no statistical differences for the p.K628N [c.1884G > T] and p.R663C [c.1987C > T] in the HR activity compared to wild-type PALB2. The p.L24F and p.L35P variants compromised the BRCA1-PALB2 interaction and reduced RAD51 foci formation in response to DNA damage. Conclusions: We have identified a novel patient-derived pathogenic PALB2 missense variant, p.L24F [c.72G > C], that compromises PALB2-mediated HR activity. We suggest the integration of the identified pathogenic variants into breast cancer genetic counseling and individualized treatment regimens for better clinical outcomes.
Five year letrozole versus placebo in BRCA1/2 germline mutations carriers: Final results of LIBER, a double-blind randomized phase III breast cancer prevention trial.
Authors: Pujol Pascal , Roca Lise , Lortholary Alain , Lasset Christine , Dugast Catherine , Berthet Pascaline , Tennevet Isabelle , Fricker Jean-Pierre , Nathalie Chabbert-Buffet , Gesta Paul , This Pascale , Chiesa Jean , N'Guyen TD , Mailliez Audrey , Venat-Bouvet Laurence , Dreyfus Hélène , Delnatte Capucine , Galibert Virginie , Lemonnier Jerome , Delaloge Suzette 
Published: May 2020

1534 Background: Women with germline BRCA1/2 (gBRCA1/2) mutations have a 70% lifetime risk of breast cancer (BC). Medical prevention by aromatase inhibitors is effective in high-risk patients (pts), including those with familial risk. However, hormone prevention has not been specifically addressed in women (wn) carrying gBRCA1/2 mutations. Methods: LIBER is a randomized, double-blind, placebo-controlled phase III trial evaluating 5-year treatment with letrozole 2.5 mg/day (L) versus placebo (P) on decreasing BC incidence in post-menopausal women with gBRCA1/2 mutations ( NCT00673335 ). Eligible wn were aged 40-70 and could have had unilateral BC > 5 years ago. Randomization was stratified on mutation ( BRCA1/BRCA2), bilateral oophorectomy and history of prior BC. Primary endpoint was 5-year invasive BC-free survival (BC-FS) in wn with or without previous BC. Main secondary endpoints were safety and quality of life (menopause rating scale, SF36). 270 pts were required to observe 37 events to show a gain in 5-year invasive BC-FS from 80% to 92% (HR=0.35) with 1-sided α=0.05 and 90% power. Results: 170 wn were randomized from 02/2008 to 02/2013; 86 and 84 were assigned to the P and L arm. Median age was 55 years (range 40-70). Pt characteristics were well balanced; 59% and 41% carried gBRCA1 and gBRCA2 mutations. In P and L arms, 47% and 43% had prior BC, 43% and 42% stopped treatment prematurely, 37 and 23 serious adverse events occurred, and during active treatment, 8 and 10 wn had grade 3/4 toxicity. Median follow-up was 72.7 months. Five-year BC-FS did not significantly differ between the P and L arms (92% vs 91%, HR 0.83; 95%CI: 0.3-2.3, p=0.73) in the overall population, nor in the subgroups of wn with and without previous BC (74% vs 91%; HR 0.43; 95% CI: 0.1-1.3; 90% vs 86%; HR 1.29; 95% CI 0.4-3.9), gBRCA1 versus gBRCA2 or hormone receptor-positive BC. Letrozole had no effect on quality of life. The two groups did not significantly differ in bone density, which decreased over time in the overall population. Conclusions: In this prospective preventive trial, BC-FS was not significantly decreased by letrozole versus placebo in women with BRCA1/2 mutations. However, the study was underpowered (170 of 270 pts expected). Despite no differences in safety and quality of life, drop-out rate was high in both P and L arms. Clinical trial information: NCT00673335.
Return of results after somatic tumor mutation profiling in advanced cancer: Psychological impacts.
Authors: Butow Phyllis , Davies Grace , Napier Christine , Thomas David Morgan , Bartley Nicole , Goldstein David , Ballinger Mandy L. , Juraskova Ilona , Schlub Timothy E , Tucker Kathy , Meiser Bettina , Young Mary-Anne 
Published: May 2020

1541 Background: Somatic tumor mutation profiling (STMP) is entering clinical practice. We aimed to investigate psychological impacts of receiving results. Methods: Eligible participants had: advanced solid cancers of any histological type; accessible tissue for STMP; and enrolled in the Molecular Screening and Therapeutics (MoST) Program. 1074 participants (91%) completed a baseline assessment prior to STMP (T0), of whom 570 (47%) received results and completed a post-result assessment (T1) of impact of genetic results (MICRA), anxiety and depression (HADS), cancer-specific anxiety (IES), and satisfaction with decision to have STMP. Linear regression models controlling for age, gender, parental status, cultural diversity, education and ECOG status explored associations between result received and psychological outcomes. Results: 360 participants received an actionable result and were recommended personalised treatment: 152 via a MoST sub-study (G1) and 208 via their treating oncologist (G2). 210 received a non-actionable result (G3). At T1, G3 were significantly more distressed and less positive about their result (MICRA subscales) and less satisfied with their decision to have STMP than both G1 and G2; G2 was less positive than G1. IES and HADs were not impacted by type of result. Interactions between gender and age, and result were non-significant for all psychological outcomes. Perceived self-efficacy in coping with results (p=0.015) and knowledge (p=0.04) at T0 was significantly correlated with satisfaction with decision at T1; self efficacy (T0) was also correlated with MICRA total (T1) (p=0.006). Conclusions: Pathway to treatment receipt is less important to advanced cancer patients than actionability. Patients’ self-efficacy to cope with results prior to testing can identify patients vulnerable to distress post-receipt of STMP results who should be offered psychological counseling. Ensuring good knowledge of STMP at consent may avoid decisional regret. [Table: see text]
Ancestry-specific gene expression profiles in TNBC tumors.
Authors: Dean-Colomb Windy Marie , Martini Rachel , Verma Akanksha , White Jason , Elemento Olivier , Davis Melissa , Newman Lisa , Manne Upender , Yates Clayton 
Published: May 2020

1547 Background: Due to persistent disparities in breast cancer mortality, there has been a renewed focus on investigating tumor biology. Deeper exploration has exposed distinctions in tumor biology based upon self-reported race and ancestry. The disparities associated with Triple Negative Breast Cancer (TNBC) across the modern African Diaspora suggests that there is a genetic ancestry connection between its aggressive tumor biology and clinical outcomes. Understanding this connection could hold the key to improving clinical outcomes in this group. Methods: We investigated 75 TNBC primary tumors using Self-Reported Race (SRR) groups: African American (AA, n = 42) and European American (EA, n = 33). Using best practices established by TCGA, we analyzed bulk RNA sequencing to measure changes in genome-wide expression levels. We next quantified global ancestry in a novel manner using RNAseq variants using 1000 Genomes as the reference data. We then identified African and European ancestry-associated genes using a logistic regression (adjusted FDR p < 0.05) between quantified ancestry and gene expression levels. Results: We identified > 150 genes associated with quantified African ancestry. We also found using quantified ancestry was a more robust method to screen for differentially expressed genes than SRR. Using an updated TNBC subtyping method, we noted higher incidences of Basal-like 2 tumors in AAs. Pathway analyses indicated several canonical cancer pathways; including, TP53, NFKB1 and AKT, have altered functionality in patients of African descent. For example, TP53-associated genes were activated in TNBC tumors of AA versus EA. This upregulation, rather than loss of function, is suggestive of polymorphic and/or ancestry-specific expression regulation, likely driven by population-private genetic variants. Lastly, we used TCGA data to validate a subset of African ancestry-specific genes that were upregulated in AA patients in our cohort. Specifically, PIM3, ZBTB22 and PPP2R4 each retained significant upregulation, in our cohort, but also TNBC tumors from TCGA (p = 0.0018, 0.023 and 0.022, respectively). Conclusions: Our study has uncovered ancestry-specific gene expression profiles in TNBC tumors. The distinct distribution of TNBC subtypes and altered functional oncologic pathways are evidence that biological underpinnings in TNBC can be driven by shared genetic ancestry. These findings emphasize the need to investigate patient populations of various ancestral origins in order to fully appreciate the molecular diversity in tumor biology for precision of disease management.