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The epidemiological landscape of lung cancer: current status, temporal trend and future projections based on the latest estimates from GLOBOCAN 2022

Journal of the National Cancer Center

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Journal of the National cancer Center 2025年

作者： Ji, Yuting Zhang, Yunmeng Liu, Siwen Li, Jingjing Jin, Qianyun Wu, Jie Duan, Hongyuan Liu, Xiaomin Yang, Lei Huang, Yubei Department of Epidemiology and Biostatistics Key Laboratory of Molecular Cancer Epidemiology Tianjin National Clinical Research Center for Cancer Tianjin Medical University Cancer Institute and Hospital Tianjin Medical University Tianjin China Peking University Cancer Hospital (Inner Mongolia Campus)/Affiliated Cancer Hospital of Inner Mongolia Medical University Inner Mongolia Cancer Center Hohhot China Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing) Beijing Office for Cancer Prevention and Control Peking University Cancer Hospital & Institute Beijing China

Background: Given the relatively unfavorable prognosis and significant geographic differences in lung cancer burden, it is critical to update the global landscape of lung cancer to inform local strategies. Methods: Based on the GLOBOCAN 2022, the age-standardized incidence rate (ASIR) and mortality rate (ASMR) were compared and linked to the Human Development Index (HDI) across different populations. The temporal trends in ASIR/ASMR were characterized as estimated annual percentage change (EAPC), and demographic projections were performed up to 2050. Results: Globally, an estimated 2,480,675 cases and 1,817,469 deaths from lung cancer occurred in 2022. Both ASIR and ASMR of lung cancer varied widely by world region, with ASIR ranging from 2.06 to 39.38 per 100,000 and ASMR from 1.95 to 31.70 per 100,000. China alone accounted for >40 % of cases and deaths worldwide. Both ASIR and ARMR of lung cancer increased with HDI (R²: 0.54 and 0.47, all P values <0.001), regardless of gender. Based on available data, both ASIR during 2001–2010 and ASMR during 2001–2015 showed decreasing trends in males (EAPC: 1.50 % and −2.22 %) but increasing trends in females (EAPC: 1.08 % and 0.07 %). Similar trends in ASIR and ASMR were observed among the elder population (≥50 years);however, downward trends were observed in the younger population (<50 years). Alongside the aging and growth of the population, estimated cases and deaths from overall lung cancer would increase by 86.2 % and 95.2 % up to 2050 as compared with estimates in 2022, respectively. Notably, increased early-onset lung cancer was only observed in transitioning countries, while decreased early-onset lung cancer was observed in transitioned countries. Conclusion: Lung cancer maintained as the leading cancer burden worldwide. Unless timely preventive interventions in tobacco mitigation, early screening, and precise treatment, the global lung cancer burden is expected to increase in the future, especially for tr

关键词： HDI incidence Lung cancer mortality temporal trend

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Uncovering the Genetics of Poor and Exceptional Survivorship after Unrelated Donor Allogeneic Hematopoietic Cell Transplantation (HCT)

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Blood 2024年 144卷 930-930页

作者： Angel Earle Pankhil Shah Susan E. Steck Jiajia Zhang Nadine El Kalach Lara E. Sucheston-Campbell Stephen R. Spellman Marcelo C. Pasquini Meilun He Qianqian Zhu Theresa E. Hahn Alyssa I Clay-Gilmour Department of Epidemiology and Biostatistics University of South Carolina Winnsboro SC Department of Epidemiology and Biostatistics | Arnold School of Public Health University of South Carolina Lexington SC Department of Epidemiology and Biostatistics University of South Carolina Columbia SC College of Pharmacy The Ohio State University Pleasanton CA Center for International Blood and Marrow Transplant Research Minneapolis MN Center for International Blood and Marrow Transplant Research Medical College of Wisconsin Milwaukee WI CIBMTR® (Center for International Blood and Marrow Transplant Research) NMDP Minneapolis MN Department of Biostatistics and Bioinformatics Roswell Park Comprehensive Cancer Center Buffalo NY Cancer Prevention and Control Roswell Park Comprehensive Cancer Center Buffalo NY

Introduction: A previous genome-wide association study (GWAS) investigated joint and independent genetic factors in recipients and donors contributing to death in the first year after unrelated donor HCT (DISCOVeRY-BMT study, PMID: 34746714). The current study leveraged DISCOVeRY-BMT data to identify non-human leukocyte antigen (HLA) genetic factors related to poor and exceptional survivorship after allogeneic HCT. Methods: DISCOVeRY-BMT, a collaboration with the Center for International Blood and Marrow Transplant Research (CIBMTR) consists of 2 cohorts of acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), and myelodysplastic syndrome (MDS) patients treated 2000-2011 and their ≥8/8 HLA-matched unrelated donors. Standard genotyping using the Illumina OmniExpress BeadChip and quality control were performed. Imputation used the Trans-Omics in Precision Medicine (TOPMed) Imputation Server (GRCh38). Given 80% of patients who survive 24 months post-HCT survive to 10 years (PMID: 28232372), we categorized patients who were alive with <120 but >24 months follow-up as exceptional survivors. Standard and poor survivors are those who died between 24-120 months post-HCT and <24 months post-HCT, respectively. GWAS was performed with additive multivariable logistic-Firth hybrid regression models adjusting for age at HCT, sex, cohort, disease (AML, ALL, MDS), disease status (early or advanced), year of HCT, and principal components. Summary statistics and median survival in months were calculated in R.4.4.1. P < 5 × 10⁻⁸ denoted genome-wide significance. Results: Study sample consisted of 2886 European ancestry recipients, with survivors comprising 32% exceptional (N=937, median survival=142 months), 15% standard (N=441, median survival=47 months), and 53% poor (N=1508, median survival=5 months). Distributions by disease (17-21% ALL, 60-62% AML, 18-21% MDS) were similar in exceptional, standard, and poor survivor cases. Exceptional survivor cases had slightly highe

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Frailty and Other Factors Associated With Early Outcomes in Middle-to Older Age Trauma Patients: A Prospective Cohort Study

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American Journal of Geriatric Psychiatry 2024年第2期32卷 244-255页

作者： Yeh, Tian-Shin Kang, Jiunn-Horng Littlejohns, Thomas J. Wu, Chia-Chieh Chen, Jin-Hua Piravej, Krisna Chiu, Wen-Ta Lam, Carlos Department of Physical Medicine and Rehabilitation School of Medicine College of Medicine Taipei Medical University Taipei Taiwan Department of Physical Medicine and Rehabilitation Wan Fang Hospital Taipei Medical University Taipei Taiwan Department of Epidemiology and Nutrition Harvard T. H. Chan School of Public Health Harvard University Boston MA United States Department of Physical Medicine and Rehabilitation National Taiwan University Hospital Taipei Taiwan Department of Physical Medicine and Rehabilitation College of Medicine National Taiwan University Taipei Taiwan Department of Physical Medicine and Rehabilitation Taipei Medical University Hospital Taipei Taiwan Graduate Institute of Nanomedicine and Medical Engineering College of Biomedical Engineering Taipei Medical University Taipei Taiwan International Ph.D. Program in Medicine College of Medicine Taipei Medical University Taipei Taiwan Professional Master Program in Artificial Intelligence in Medicine College of Medicine Taipei Medical University Taipei Taiwan Nuffield Department of Population Health University of Oxford Oxford United Kingdom Emergency Department Wan Fang Hospital Taipei Medical University Taipei Taiwan Department of Emergency School of Medicine College of Medicine Taipei Medical University Taipei Taiwan Graduate Institute of Data Science College of Management Taipei Medical University Taipei Taiwan Institutional Research Center Office of Data Science Taipei Medical University Taipei Taiwan Biostatistics Center Department of Medical Research Wan Fang Hospital Taipei Medical University Taipei Taiwan Department of Rehabilitation Medicine Faculty of Medicine Chulalongkorn University Bangkok Thailand Department of Chula Neuroscience Center King Chulalongkorn Memorial Hospital Bangkok Thailand Graduate Institute of Injury Prevention and Control College of Public Health Taipei Medical University Taipei Taiwan AHMC Health System Alhambra CA United States

Objectives: To prospectively investigate associations of frailty and other predictor variables with functional recovery and health outcomes in middle-aged and older patients with trauma. Design: Single-center prospective cohort study. Setting: Emergency department of Wan Fang Hospital in Taiwan. Participants: Trauma patients aged 45 and older. Measurements: Frailty was assessed with the Clinical Frailty Scale (CFS). Injury mechanisms, pre-existing diseases, and fracture locations were recorded at baseline. The primary outcome was functional recovery assessed using the Barthel Index (BI). Secondary outcomes were new care needs, unscheduled return visits, and falls 3 months postinjury. Results: A total of 588 participants were included in the final analysis. For every one-point increase in the CFS, the multivariable-adjusted odds ratio (OR, 95% confidence interval [CI]) of failure to retain the preinjury BI was 1.34 (1.16–1.55);associations were consistent across levels of age and injury severities. Significant joint associations of frailty and age with poor functional recovery were observed. CFS was also associated with new care needs (OR for every one-point increase, 1.36, 95% CI, 1.17–1.58), unscheduled return visits (OR 1.26, 95% CI, 1.04–1.51), and falls (OR 1.23, 95% CI, 1.01–1.51). Other variables associated with failure to retain preinjury BI included road traffic accident and presence of hip fracture. Conclusion: Frailty was significantly associated with poor functional and health outcomes regardless of injury severity in middle-aged and older patients with trauma. Injury mechanisms and fracture locations were also significant predictors of functional recovery postinjury. © 2023 American Association for Geriatric Psychiatry

关键词： Clinical Frailty Scale Frailty functional recovery injury middle-to older age

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U.S. Vietnamese parents' trusted sources of information and preferences for intervention messaging about HPV vaccination: A mixed methods study

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PEC Innovation 2023年 3卷 100189-100189页

作者： Vu, Milkie Berg, Carla J. Pham, Nhat-Ha T. Tiro, Jasmin A. Escoffery, Cam Spring, Bonnie Bednarczyk, Robert A. Ta, Danny Kandula, Namratha R. Department of Preventive Medicine Feinberg School of Medicine Northwestern University United States Department of Prevention and Community Health Milken Institute School of Public Health George Washington University United States George Washington Cancer Center George Washington University United States College of Arts and Sciences University of Pennsylvania United States Department of Public Health Sciences University of Chicago United States Cancer Prevention and Population Science Program Comprehensive Cancer Center University of Chicago United States Department of Behavioral Social and Health Education Sciences Rollins School of Public Health Emory University United States Emory Prevention Research Center Emory University United States Cancer Prevention and Control Program Winship Cancer Institute Emory University United States Hubert Department of Global Health Rollins School of Public Health Emory University United States Nell Hodgson Woodruff School of Nursing Rollins School of Public Health Emory University United States Department of Medicine Feinberg School of Medicine Northwestern University United States Department of Epidemiology Rollins School of Public Health Emory University United States Emory Vaccine Center Emory University United States

Objective: Assess trusted sources of information, perceived message effectiveness, and preferred dissemination strategies regarding adolescent HPV vaccination among U.S. Vietnamese parents. Methods: Data came from an observational, explanatory sequential mixed-methods study with U.S. Vietnamese parents of adolescents (408 survey participants;32 interview participants). Surveys and interviews were conducted in both Vietnamese and English. Mixed-methods data were integrated and analyzed for confirmation, expansion, or discordance. Results: Both quantitative and qualitative findings confirm high trust in HPV vaccination information from providers, government agencies, and cancer organizations. Messages perceived as effective emphasize vaccine safety, experts' endorsement, importance of vaccination prior to HPV exposure, and preventable cancers. Qualitative findings expanded quantitative results, demonstrating a desire for evidence-based information in the Vietnamese language and addressing cultural concerns (e.g., effectiveness or potential side effects specific to Vietnamese adolescents, whether parents should delay HPV vaccination for Vietnamese adolescents). Quantitative and qualitative findings were incongruent about whether parents would trust information about HPV vaccination that is disseminated via social media. Conclusion: We identified credible messengers, feasible strategies, and elements of impactful messages for interventions to increase adolescent HPV vaccination for U.S. Vietnamese. Innovation: We focus on a high-risk, underserved population and integrate mixed-methods design and analysis. © 2023 The Authors

关键词： Asian Americans cancer Health education interventions HPV vaccination Immunization Vietnamese

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Polygenic risk score and lung adenocarcinoma risk among never-smokers by EGFR mutation status-a brief report

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Journal of thoracic oncology : official publication of the International Association for the Study of Lung cancer 2024年第4期20卷 521-530页

作者： Batel Blechter Chao Agnes Hsiung Xiaoyu Wang Haoyu Zhang Wei Jie Seow Jianxin Shi Nilanjan Chatterjee Hee Nam Kim Maria Pik Wong Yun-Chul Hong Jason Yy Wong Juncheng Dai H Dean Hosgood Zhaoming Wang I-Shou Chang Jiyeon Choi Jiucun Wang Minsun Song Wei Hu Wei Zheng Jin Hee Kim Baosen Zhou Demetrius Albanes Min-Ho Shin Lap Ping Chung She-Juan An Hong Zheng Yasushi Yatabe Xu-Chao Zhang Young Tae Kim Xiao-Ou Shu Young-Chul Kim Roel C H Vermeulen Bryan A Bassig Jiang Chang James Chung Man Ho Bu-Tian Ji Michiaki Kubo Yataro Daigo Yukihide Momozawa Yoichiro Kamatani Takayuki Honda Hideo Kunitoh Shun-Ichi Watanabe Yohei Miyagi Haruhiko Nakayama Shingo Matsumoto Masahiro Tsuboi Koichi Goto Zhihua Yin Atsushi Takahashi Akiteru Goto Yoshihiro Minamiya Kimihiro Shimizu Kazumi Tanaka Tangchun Wu Fusheng Wei Jian Su Yeul Hong Kim In-Jae Oh Victor Ho Fun Lee Wu-Chou Su Yuh-Min Chen Gee-Chen Chang Kuan-Yu Chen Ming-Shyan Huang Hsien-Chih Lin Adeline Seow Jae Yong Park Sun-Seog Kweon Chien-Jen Chen Yu-Tang Gao Chen Wu Biyun Qian Daru Lu Jianjun Liu Hyo-Sung Jeon Chin-Fu Hsiao Jae Sook Sung Ying-Huang Tsai Yoo Jin Jung Huan Guo Zhibin Hu Tzu-Yu Chen Laurie Burdett Meredith Yeager Amy Hutchinson Sonja I Berndt Wei Wu Junwen Wang Jin Eun Choi Kyong Hwa Park Sook Whan Sung Li Liu Chang Hyun Kang Chung-Hsing Chen Jun Xu Peng Guan Wen Tan Chih-Liang Wang Alan Dart Loon Sihoe Ying Chen Yi Young Choi Jun Suk Kim Ho-Il Yoon Qiuyin Cai In Kyu Park Ping Xu Qincheng He Chih-Yi Chen Junjie Wu Wei-Yen Lim Kun-Chieh Chen John K C Chan Jihua Li Hongyan Chen Chong-Jen Yu Li Jin Joseph F Fraumeni Jie Liu Maria Teresa Landi Taiki Yamaji Yang Yang Belynda Hicks Kathleen Wyatt Shengchao A Li Hongxia Ma Bao Song Zhehai Wang Sensen Cheng Xuelian Li Yangwu Ren Motoki Iwasaki Junjie Zhu Gening Jiang Ke Fei Guoping Wu Li-Hsin Chien Fang-Yu Tsai Jinming Yu Victoria L Stevens Pan-Chyr Yang Dongxin Lin Kexin Chen Yi-Long Wu Keitaro Matsuo Nathaniel Rothman Kouya Shiraishi Hongbing Shen Stephen J Chanock Takashi Kohno Qing Lan Division of Cancer Epidemiology and Genetics National Cancer Institute Rockville MD USA. Institute of Population Health Sciences National Health Research Institutes Zhunan Taiwan. Division of Cancer Epidemiology and Genetics National Cancer Institute Rockville MD USA Saw Swee Hock School of Public Health National University of Singapore and National University Health System Singapore Singapore Department of Medicine Yong Loo Lin School of Medicine National University of Singapore and National University Health System Singapore Singapore. Department of Oncology School of Medicine Johns Hopkins University Baltimore MD USA Department of Biostatistics Johns Hopkins Bloomberg School of Public Health Baltimore MD USA. Department of Preventive Medicine Chonnam National University Medical School Gwangju Republic of Korea. Department of Pathology Queen Mary Hospital Hong Kong Hong Kong. Department of Preventive Medicine Seoul National University College of Medicine Seoul Republic of Korea. Epidemiology and Community Health Branch National Heart Lung and Blood Institute Bethesda MD USA. Department of Epidemiology School of Public Health Nanjing Medical University Nanjing China. Department of Epidemiology and Population Health Albert Einstein College of Medicine New York USA. Department of Computational Biology St. Jude Children's Research Hospital Memphis TN USA. National Institute of Cancer Research National Health Research Institutes Zhunan Taiwan. Ministry of Education Key Laboratory of Contemporary Anthropology School of Life Sciences Fudan University Shanghai China State Key Laboratory of Genetic Engineering School of Life Sciences Fudan University Shanghai China. Department of Statistics & Research Institute of Natural Sciences Sookmyung Women's University Seoul 04310 Korea. Division of Epidemiology Department of Medicine Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center Nashville TN USA. Department of Environmental Health

We assessed the association between a genome-wide polygenic risk score (PRS) developed for lung adenocarcinoma (LUAD) risk and mutation on the epidermal growth factor receptor (EGFR) gene in 998 East Asian never-smoking female LUAD cases (518 EGFR-positive; 480 EGFR-negative) and 4,544 never-smoking controls using case-case and multinomial regression analyses. We found that the PRS was more strongly associated with EGFR-positive LUAD compared to EGFR-negative LUAD, where the association between the fourth quartile of the PRS and EGFR-positive LUAD (OR=8.63, 95% CI:5.67, 13.14) was significantly higher than the association between the fourth quartile of the PRS with EGFR-negative LUAD (OR=3.50, 95% CI: 2.44, 5.00) (p-heterogeneity=3.66x10). Our findings suggest that germline genetic susceptibility may be differentially associated with LUAD in never-smoking female East Asian patients depending on the cancer's mutation status, which may have important public health and clinical implications.

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Ovarian cancer risk and survival according to tumor sex hormone receptor expression: An ovarian cancer association consortium and ovarian tumor tissue analysis consortium pooled analysis

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Gynecologic oncology 2025年 198卷 112-129页

作者： Zhuxuan Fu Lauren Borho Sarah E Taylor Linda E Kelemen Anna DeFazio Penelope M Webb Martin Köbel Nicola S Meagher Renhua Na Antonis C Antoniou Alison H Brand Catherine J Kennedy Nikilyn Nevins Paul D P Pharoah Yurii B Shvetsov Stacey J Winham Jennifer Alsop Matthias W Beckmann Adelyn Bolithon Jessica Boros David D L Bowtell James D Brenton Michael E Carney Anita Chudecka-Głaz Linda S Cook Cezary Cybulski Peter A Fasching Sian Fereday Renée T Fortner María J García Ellen L Goode Marc T Goodman Jacek Gronwald Arndt Hartmann Brenda Y Hernandez Estrid Høgdall David G Huntsman Allan Jensen Mercedes Jimenez-Linan Janine M Joseph Beth Y Karlan Ewa Kaznowska Susanne K Kjaer Tomasz Kluz Jennifer M Koziak Jenny Lester Teri A Longacre Maria Lycke Valerie McGuire Kirsten B Moysich Rachel A Murphy Sandra Orsulic Susan J Ramus Cristina Rodríguez-Antona Joseph H Rothstein Spinder Samra Weiva Sieh Helen Steed Karin Sundfeldt Aline Talhouk Jan Uciński Chen Wang Nicolas Wentzensen Alice S Whittemore Lynne R Wilkens Thomas Songer Maria Mori Brooks Lu Tang Francesmary Modugno Department of Epidemiology University of Pittsburgh School of Public Health Pittsburgh PA 15213 USA St. Luke's Mid America Heart Institute. St Luke's Health System. Kansas City MO USA. Division of Gynecologic Oncology Department of Obstetrics Gynecology and Reproductive Sciences. University of Pittsburgh School of Medicine. Pittsburgh PA 15213 USA. South Carolina Department of Public Health. Columbia SC USA. Centre for Cancer Research. The Westmead Institute for Medical Research. Sydney New South Wales 2145 Australia Faculty of Medicine and Health. The University of Sydney. Sydney New South Wales 2006 Australia. Department of Gynaecological Oncology. Westmead Hospital. Sydney New South Wales 2145 Australia The Daffodil Centre The University of Sydney. A Joint Venture with Cancer Council NSW. Sydney New South Wales 2006 Australia. Population Health Program. QIMR Berghofer. Brisbane Queensland 4006 Australia School of Public Health. The University of Queensland. Brisbane 4006 Australia. Department of Pathology and Laboratory Medicine. University of Calgary Foothills Medical Center. Calgary AB T2N 2T9 Canada. The Daffodil Centre The University of Sydney. A Joint Venture with Cancer Council NSW. Sydney New South Wales 2006 Australia School of Clinical Medicine UNSW Medicine and Health. University of NSW Sydney. Sydney New South Wales 2052 Australia. Centre for Cancer Genetic Epidemiology Department of Public Health and Primary Care. University of Cambridge. Cambridge CB1 8RN UK. Department of Gynaecological Oncology. Westmead Hospital. Sydney New South Wales 2145 Australia. Department of Computational Biomedicine. Cedars-Sinai Medical Center. West Hollywood CA 90069 USA. University of Hawaii Cancer Center. Honolulu HI USA. Department of Quantitative Health Sciences Division of Computational Biology. Mayo Clinic. Rochester MN 55905 USA. Center for Cancer Genetic Epidemiology Department of Oncology University of Cambridge Cambridge CB1 8RN UK. Department of Gynecology and

OBJECTIVE:Many epithelial ovarian cancer (EOC) risk factors relate to sex hormones. The association between these factors and the expression of androgen receptor (AR), estrogen receptor-α (ER), and progesterone receptor (PR) in tumors is unknown. METHOD:We linked epidemiologic, AR/ER/PR tumor expression, and survival data from 19 studies in the Ovarian cancer Association Consortium (OCAC; 4762 cases, 20,888 controls) and the Ovarian Tumor Tissue Analysis (OTTA) consortium (5737 cases). We estimated odds ratios (ORs) and 95 % confidence intervals (CIs) between hormonally-linked factors and tumor AR/ER/PR expression using polytomous logistic regression. We assessed survival by AR/ER/PR tumor expression overall and by histotype using Kaplan-Meier curves and Cox proportional hazards models. RESULTS:Overweight/obesity was associated with higher risk of ER- tumors (OR:1.53, 95 % I:1.18-1.98). Hysterectomy was associated with greater risk of ER+ tumors (OR:4.99, 95 % CI:4.27-5.83), which varied by AR expression (P0.003). Postmenopause was associated with a higher risk of PR- tumors (OR 1.52, 95 % CI 1.26-1.83), which varied based by AR (P < 0.001) and ER (P < 0.001) expression. Gravidity, oral contraception duration, and breastfeeding duration showed differing dose-response relationships according to AR/ER/PR expression. Hormone therapy use, postmenopause, physical inactivity, and being obese/overweight prior to diagnosis were differentially associated with survival based on AR/ER/PR expression and histotype. CONCLUSION:EOC has varying risk and prognostic profiles depending on both histotype and AR/ER/PR expression. Biological mechanisms underlying the association between hormonally-linked factors and EOC need to be studied by both histotypes and by AR, ER, and PR expression.

关键词： Epithelial ovarian cancer Hormonal factors Hormone receptor Risk Survival androgen receptor estrogen receptor progesterone receptor

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SeqSQC: A Bioconductor Package for Evaluating the Sample Quality of Next-generation Sequencing Data

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Genomics, Proteomics & Bioinformatics 2019年第2期17卷 211-218页

作者： Qian Liu Qiang Hu Song Yao Marilyn L. Kwan Janise M. Roh Hua Zhao Christine B. Ambrosone Lawrence H. Kushi Song Liu Qianqian Zhu Department of Biostatistics University at Buffalo SUNY Buffalo NY14260 USA Department of Biostatistics and Bioinformatics Roswell Park Comprehensive Cancer Center Buffalo NY14263 USA Department of Cancer Prevention and Control Roswell Park Comprehensive Cancer Center Buffalo NY14263 USA Division of Research Kaiser Permanente Northern California Oakland CA94612 USA Department of Epidemiology The University of Texas MD Anderson Cancer Center Houston TX77030 USA

As next-generation sequencing (NGS) technology has become widely used to identify genetic causal variants for various diseases and traits,a number of packages for checking NGS data quality have sprung up in public domains. In addition to the quality of sequencing data,sample quality issues,such as gender mismatch,abnormal inbreeding coefficient,cryptic relatedness,and population outliers,can also have fundamental impact on downstream analysis. However,there is a lack of tools specialized in identifying problematic samples from NGS data,often due to the limitation of sample size and variant counts. We developed SeqSQC,a Bioconductor package,to automate and accelerate sample cleaning in NGS data of any scale. SeqSQC is designed for efficient data storage and access,and equipped with interactive plots for intuitive data visualization to expedite the identification of problematic samples. SeqSQC is available at http://bioconductor. org/packages/SeqSQC.

关键词： Next-generation sequencing Quality assessment 1000 Genomes Project Whole-exome sequencing Bioconductor package

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Determining Filipinos’ Preferences for Colorectal cancer Screening Tests: Insights From a Choice-Based Conjoint Analysis

AJPM Focus

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AJPM Focus 2025年第1期4卷 100300-100300页

作者： Crochetiere, Austin Lauzon, Marie Chaplin, Antwon Almario, Christopher V. Department of Medicine Cedars-Sinai Medical Center Los Angeles California United States Biostatistics Shared Resource Cedars-Sinai Cancer Los Angeles California United States Cedars-Sinai Center for Outcomes Research and Education (CS-CORE) Los Angeles California United States Karsh Division of Gastroenterology and Hepatology Cedars-Sinai Medical Center Los Angeles California United States Division of Health Services Research Cedars-Sinai Medical Center Los Angeles California United States Division of Informatics Cedars-Sinai Medical Center Los Angeles California United States Cancer Prevention & Control Program Cedars-Sinai Cancer Los Angeles California United States

Introduction: Filipinos in the U.S. have worse colorectal cancer screening rates and outcomes than non-Hispanic Whites, despite 85% of Filipinos being proficient in English and having insurance rates, education, and incomes that exceed those of the general population. To begin to address this disparity, the authors used conjoint analysis—a method that assesses complex decision making—to better understand Filipinos’ preferences for the different colorectal cancer screening test options. Methods: The authors conducted a conjoint analysis survey among unscreened Filipinos aged ≥40 years at average risk for colorectal cancer to determine the relative importance of screening test attributes in their decision making (e.g., modality, effectiveness at reducing colorectal cancer risk, bowel prep). The authors also performed simulations to estimate the proportion of people who would prefer to do an annual fecal immunochemical test or colonoscopy every 10 years for their screening. Results: Overall, 105 Filipinos completed the survey;most respondents were female (74.3%) and aged 40–49 years (84.8%). The authors observed that test modality was the most important factor in respondents’ decision making. After conducting simulations using the conjoint analysis data, the authors noted that 70 (66.7%) Filipinos preferred to do an annual fecal immunochemical test for their screening, whereas 35 (33.3%) wanted to do a colonoscopy every 10 years. Conclusions: The authors found that 2 in 3 Filipinos prefer fecal immunochemical test to colonoscopy for their colorectal cancer screening. To address colorectal cancer disparities in the Filipino community, investigators, health systems, public health agencies, and community organizations need to develop culturally tailored, sustainable interventions, and such programs may want to focus on improving education on and access to fecal immunochemical test. © 2024 The Author(s)

关键词： colorectal cancer screening disparities Filipino patient preference

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Contribution of Germline Predisposition Gene Mutations to Breast cancer Risk in African American Women (vol 112, pg 1213, 2020)

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JNCI-JOURNAL OF THE NATIONAL cancer INSTITUTE 2020年第10期112卷 1213-1221页

作者： Palmer, Julie R. Department of Medicine Boston University School of Medicine and Slone Epidemiology Center Boston MA 02118 USA Departments of Health Sciences Research Laboratory Medicine and Pathology and Oncology Mayo Clinic Rochester MN 55902 USA Department of Health Research & Policy Stanford University School of Medicine Stanford CA 94305 USA Department of Preventive Medicine University of Southern California Los Angeles CA 90033 USA Epidemiology Research American Cancer Society Atlanta GA 30303 USA Department of Medicine Vanderbilt University Medical Center Nashville TN 37232 USA Department of Medicine UC Irvine Irvine CA 92697 USA Department of Population Health Sciences and Carbone Cancer Center University of Wisconsin-Madison Madison WI 53726 USA Department of Population Sciences City of Hope Duarte CA 91010 USA Department of Cancer Prevention and Control Roswell Park Comprehensive Cancer Center Buffalo NY 14203 USA Cancer Epidemiology and Health Outcomes Rutgers Cancer Institute of New New Brunswick NJ 08903 USA Department of Epidemiology Harvard T. H. Chan School of Public Health Boston MA 02115 USA Population Sciences in the Pacific Program (Cancer Epidemiology) University of Hawaii Cancer Center Honolulu HI 96813 USA Epidemiology Branch National Institute of Environmental Health Sciences Research Triangle Park NC 27709 USA Abramson Cancer Center and Basser Center for BRCA University of Pennsylvania Philadelphia PA 19104 USA and 16Department of Dermatology Huntsman Cancer Institute University of Utah Salt Lake City UT 84112 USA

BACKGROUND:The risks of breast cancer in African American (AA) women associated with inherited mutations in breast cancer predisposition genes are not well defined. Thus, whether multigene germline hereditary cancer testing panels are applicable to this population is unknown. We assessed associations between mutations in panel-based genes and breast cancer risk in 5054 AA women with breast cancer and 4993 unaffected AA women drawn from 10 epidemiologic studies. METHODS:Germline DNA samples were sequenced for mutations in 23 cancer predisposition genes using a QIAseq multiplex amplicon panel. Prevalence of mutations and odds ratios (ORs) for associations with breast cancer risk were estimated with adjustment for study design, age, and family history of breast cancer. RESULTS:Pathogenic mutations were identified in 10.3% of women with estrogen receptor (ER)-negative breast cancer, 5.2% of women with ER-positive breast cancer, and 2.3% of unaffected women. Mutations in BRCA1, BRCA2, and PALB2 were associated with high risks of breast cancer (OR = 47.55, 95% confidence interval [CI] = 10.43 to >100; OR = 7.25, 95% CI = 4.07 to 14.12; OR = 8.54, 95% CI = 3.67 to 24.95, respectively). RAD51D mutations were associated with high risk of ER-negative disease (OR = 7.82, 95% CI = 1.61 to 57.42). Moderate risks were observed for CHEK2, ATM, ERCC3, and FANCC mutations with ER-positive cancer, and RECQL mutations with all breast cancer. CONCLUSIONS:The study identifies genes that predispose to breast cancer in the AA population, demonstrates the validity of current breast cancer testing panels for use in AA women, and provides a basis for increased referral of AA patients for cancer genetic testing.

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Meta-Analysis of Genome-Wide Association Studies of Acute Myeloid Leukemia (AML) Patients Identifies Variants Associated with Risk of 11q23/KMT2A-Translocated and Core-Binding Factor (CBF) AML and Suggests a Role for Transcription Elongation in Leukemogenesis

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BLOOD 2020年 136卷 29-30页

作者： Walker, Christopher J. Wang, Junke Clay-Gilmour, Alyssa I. Mrozek, Krzysztof Nicolet, Deedra Oakes, Christopher C. Kohlschmidt, Jessica Powell, Bayard L. Kolitz, Jonathan E. Carroll, Andrew J. Karaesmen, Ezgi Rizvi, Abbas A. Zhu, Qianqian Yan, Li Preus, Leah Liu, Song Wang, Yiwen Stram, Daniel O. Pooler, Loreall Sheng, Xin Haiman, Christopher Van den Berg, David Webb, Amy Brock, Guy Spellman, Stephen R. Pasquini, Marcelo C. McCarthy, Philip L. Allan, James M. Stolzel, Friedrich Onel, Kenan Stone, Richard M. Garzon, Ramiro Bloomfield, Clara D. Byrd, John C. De la Chapelle, Albert Hahn, Theresa E. Eisfeld, Ann-Kathrin Sucheston-Campbell, Lara E. The Ohio State University Comprehensive Cancer Center Columbus OH College of Pharmacy The Ohio State University Columbus OH Arnold School of Public Health- Department of Epidemiology & Biostatistics University of South Carolina Greenville SC The Ohio State University Comprehensive Cancer Center Columbus OH OSU Columbus OH Alliance Statistics and Data Center The Ohio State University Comprehensive Cancer Center Columbus OH Wake Forest Univ. School of Med. Winston Salem NC Northwell Health Cancer Institute Zucker School of Medicine at Hofstra/Northwell Lake Success NY Department of Genetics University of Alabama at Birmingham Birmingham AL The Ohio State University Columbus OH Department of Biostatistics and Bioinformatics Roswell Park Comprehensive Cancer Center Buffalo NY Department of Biostatistics Roswell Park Comprehensive Cancer Center Buffalo NY University of Southern California Keck School of Medicine of USC Los Angeles CA University of Southern California Los Angeles CA College of Veterinary Medicine Cancer Prevention & Control Columbus OH

The first three authors contributed equally. The last three authors share senior authorship. Background: Although there has been an increased recognition of the contribution of germline variants to development of myeloid neoplasms, only two large-scale case-control genome-wide association studies (GWASs) have been conducted to identify variants that predispose to AML. Importantly, these studies were dedicated to AML predisposition in general, without investigation of molecularly distinct AML subtypes. Thus, we performed the first dedicated meta-analysis combining the two GWASs to investigate predisposing variants to cytogenetic AML subsets characterized by recurrent translocations and inversions. Methods: Two sets of adult de novo AML patients treated on Alliance for Clinical Trials in Oncology (Alliance) protocols, and two sets of adult de novo AML patients reported to CIBMTR (2000-11) from DISCOVeRY-BMT cohorts were compared with four sets of population-matched non-leukemic individuals of European ancestry. Illumina Infinium arrays were used for genotyping. The haplotype reference consortium was used for imputation and comparisons were performed using SNPtest and METAL with fixed-effects, for CBF-AML (n=251, including t(8;21), n=115; inv(16), n=136) and AML with 11q23/ KMT2A translocations (n=177). Blood or bone marrow samples from subsets of these patients and additional AML patients with other cytogenetic abnormalities were used for total transcriptome RNA sequencing with Illumina instruments. Results: Two risk loci reached genome-wide significance in AML patients with 11q23/ KMT2A translocations (Fig 1A). The most significant single nucleotide polymorphism (SNP) in the 4q21.3 risk locus, rs17668899[A] ( P = 2.32 x 10 -8 , odds ratio [OR] = 3.92 [2.43-6.32]) is in intron 6 of the AFF1 gene (also called AF4 ) (Fig 1B), within an enhancer that interacts with the AFF1 transcription start site (Fig 1C, left). KMT2A- translocated AML patients with the risk allele had

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