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

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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Artificial intelligence for modelling infectious disease epidemics

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Nature 2025年第8051期638卷 623-635页

作者： Kraemer, Moritz U. G. Tsui, Joseph L.-H. Chang, Serina Y. Lytras, Spyros Khurana, Mark P. Vanderslott, Samantha Bajaj, Sumali Scheidwasser, Neil Curran-Sebastian, Jacob Liam Semenova, Elizaveta Zhang, Mengyan Unwin, H. Juliette T. Watson, Oliver J. Mills, Cathal Dasgupta, Abhishek Ferretti, Luca Scarpino, Samuel V. Koua, Etien Morgan, Oliver Tegally, Houriiyah Paquet, Ulrich Moutsianas, Loukas Fraser, Christophe Ferguson, Neil M. Topol, Eric J. Duchêne, David A. Stadler, Tanja Kingori, Patricia Parker, Michael J. Dominici, Francesca Shadbolt, Nigel Suchard, Marc A. Ratmann, Oliver Flaxman, Seth Holmes, Edward C. Gomez-Rodriguez, Manuel Schölkopf, Bernhard Donnelly, Christl A. Pybus, Oliver G. Cauchemez, Simon Bhatt, Samir Pandemic Sciences Institute University of Oxford Oxford United Kingdom Department of Biology University of Oxford Oxford United Kingdom Department of Electrical Engineering and Computer Science University of California Berkeley Berkeley CA United States UCSF UC Berkeley Joint Program in Computational Precision Health Berkeley CA United States Division of Systems Virology Department of Microbiology and Immunology The Institute of Medical Science The University of Tokyo Tokyo Japan Section of Epidemiology Department of Public Health University of Copenhagen Copenhagen Denmark Oxford Vaccine Group University of Oxford and NIHR Oxford Biomedical Research Centre Oxford United Kingdom Department of Epidemiology and Biostatistics Imperial College London London United Kingdom Department of Computer Science University of Oxford Oxford United Kingdom School of Mathematics University of Bristol Bristol United Kingdom MRC Centre for Global Infectious Disease Analysis School of Public Health Imperial College London London United Kingdom Department of Statistics University of Oxford Oxford United Kingdom Doctoral Training Centre University of Oxford Oxford United Kingdom Institute for Experiential AI Northeastern University MA Boston Thailand Santa Fe Institute Santa Fe NM United States World Health Organization Regional Office for Africa Brazzaville Congo WHO Hub for Pandemic and Epidemic Intelligence Health Emergencies Programme World Health Organization Berlin Germany Centre for Epidemic Response and Innovation (CERI) School for Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa African Institute for Mathematical Sciences (AIMS) South Africa Muizenberg Cape Town South Africa Genomics England London United Kingdom Scripps Research La Jolla CA United States Department of Biosystems Science and Engineering ETH Zürich Basel Switzerland Swiss Institute of Bioinformatics Lausanne Switzerland The Ethox Centre Nuffield

Infectious disease threats to individual and public health are numerous, varied and frequently unexpected. Artificial intelligence (AI) and related technologies, which are already supporting human decision making in economics, medicine and social science, have the potential to transform the scope and power of infectious disease epidemiology. Here we consider the application to infectious disease modelling of AI systems that combine machine learning, computational statistics, information retrieval and data science. We first outline how recent advances in AI can accelerate breakthroughs in answering key epidemiological questions and we discuss specific AI methods that can be applied to routinely collected infectious disease surveillance data. Second, we elaborate on the social context of AI for infectious disease epidemiology, including issues such as explainability, safety, accountability and ethics. Finally, we summarize some limitations of AI applications in this field and provide recommendations for how infectious disease epidemiology can harness most effectively current and future developments in AI. © Springer Nature Limited 2025.

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Effects of triggers of senescence and senolysis in murine pancreatic cancer cells

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Hepatobiliary & Pancreatic Diseases International 2024年第6期23卷 628-637页

作者： Denis Revskij Aline Woitas Bianca Kölle Camilla Umstätter Dietmar Zechner Faiz M Khan Georg Fuellen Robert Jaster Department of MedicineⅡ Division of GastroenterologyRostock University Medical CenterRostockGermany Rudolf-Zenker-Institute of Experimental Surgery Rostock University Medical CenterRostockGermany Department of Systems Biology and Bioinformatics Institute of Computer ScienceUniversity of RostockRostockGermany Institute for Biostatistics and Informatics in Medicine and Ageing Research Rostock University Medical CenterRostockGermany

Background:The combination of senescence triggers with senolytic drugs is considered a promising new approach to cancer ***,we studied the efficacy of the genotoxic agent etoposide(Eto)and irradiation in inducing senescence of Panc02 pancreatic cancer cells,and the capability of the Bcl-2 inhibitor navitoclax(ABT-263;Nav)to trigger ***:Panc02 cells were treated with Eto or irradiated with 5–20 Gy before exposure to *** survival,proliferation,and senescence were assessed by trypan blue staining,quantification of DNA synthesis,and staining of senescence-associatedβ-galactosidase(SA-β-Gal)-positive cells,*** of mRNA were determined by real-time polymerase chain reaction,and protein expression was analyzed by ***02 cells were also grown as pancreatic tumors in mice,which were subsequently treated with Eto and ***:Eto and irradiation had an antiproliferative effect on Panc02 cells that was significantly or tendentially enhanced by *** vivo,Eto and Nav together,but not Eto alone,significantly reduced the proportion of proliferating *** expression of the senescence markerγH2AX and tumor infiltration with T-cells were not affected by the *** vitro,almost all Eto-exposed cells and a significant proportion of cells irradiated with 20 Gy were SA-β-*** of Nav reduced the percentage of SA-β-Gal-positive cells after irradiation but not after pretreatment with *** response to triggers of senescence,cultured Panc02 cells showed increased protein levels ofγH2AX and the autophagy marker LC3B-II,and higher mRNA levels of Cdkn1a,Mdm2,and PAI-1,while the effects of Nav were ***:In vitro and in vivo,the combination of senescence triggers with Nav inhibited tumor cell growth more effectively than the triggers *** data also provide some evidence for senolytic effects of Nav in vitro.

关键词： Pancreatic cancer Panc02 cells Etoposide Irradiation Navitoclax

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Anatomic evaluation of radiographic landmarks for accurate straight antegrade intramedullary nail placement in the humerus

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JSES International 2020年第4期4卷 745-752页

作者： Johnston, Peter S. Hatzidakis, Armodios M. Tagouri, Yahia M. Curran-Everett, Douglas Sears, Benjamin W. Centers for Advanced Orthopaedics Leonardtown MD United States Western Orthopaedics Denver CO United States Medstar St. Marys Hospital Leonardtown MD United States Division of Biostatistics and Bioinformatics National Jewish Health Denver CO United States

Background: Neurovascular insult, nonunion, and iatrogenic rotator cuff injury are concerns when using an intramedullary nail (IMN) for proximal humerus fracture. The purpose of this study was to identify a reproducible starting point and intraoperative imaging for nail insertion optimizing nail depth, tuberosity screw position, and protecting the axillary nerve and rotator cuff insertion. Our hypothesis was that a more medialized starting point would protect soft tissue structures and improve locking screw positioning. Methods: Ten fresh-frozen cadavers underwent antegrade IMN with Grashey and modified lateral “precipice” view imaging. A guidewire was positioned medial to the coracoacromial ligament (CAL) in 5 cadavers and lateral to the CAL in 5. Distances from the nail entry point to anatomic landmarks were measured. Anatomic and histologic evaluations were performed, characterizing the nail perforation zone. Radiographs were compared between groups. Results: The medial CAL group had a greater distance of screw fixation to the axillary nerve, a shorter distance of greater tuberosity (GT) screw fixation at the rotator cuff insertion on the infraspinatus and teres minor tubercles, and greater screw spread with improved lesser tuberosity capture. Two laterally placed implants violated the rotator cuff tendon. Imaging demonstrated that the ideal starting pin position was medial to the articular margin at a distance equal to the width of the rotator cuff insertion footprint. Conclusions: Medial placement optimized fixation of the GT, avoided violation of the rotator cuff tendon and footprint, and was associated with an increased distance of proximal locking screw to the axillary nerve. © 2020 The Authors

关键词： Anatomy Study antegrade humeral nail Cadaver Dissection fragility fracture intramedullary nail fixation Proximal humerus fracture straight intramedullary nail tuberosity fixation

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On testing proportional odds assumptions for proportional odds models

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General Psychiatry 2023年第3期36卷 214-219页

作者： Anqi Liu Hua He Xin M Tu Wan Tang Department of Bostaistis and Data Science Tulane UniversityNew OrleansLouisianaUSA Department of Epidemiology Tulane UniversityNew OrleansLouisianaUSA Division of Biostatistics and Bioinformatics Herbert Wertheim School of Public Health and Human Longevity ScienceUC San DiegoLa JollaCaliforniaUSA

Proportional odds models are commonly used to model ordinal responses,but the proportional odds assumption may not hold in practice,leading to biased *** such as score,Wald and likelihood ratio(LR)have been proposed to evaluate the proportional odds assumption based on models without the *** has proposed an independent binary model-based Wald-type test,and Wolfe and Gould have extended the idea to propose an LR-type *** paper provides a brief review of the Brant and Wolfe-Gould tests for evaluating the proportional odds assumption and evaluates their performance through simulation studies and a real data *** programs are provided in SAS,SPSS and Stata to facilitate the implementation of these tests using standard statistical software *** study highlights the importance of evaluating the proportional odds assumption when using proportional odds models for ordinal *** sample programs provided in this paper make it easy for researchers to apply these tests in their own analyses using standard statistical software packages.

关键词： Gould testing apply

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Multiple imputation using dimension reduction techniques for high-dimensional data

arXiv

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arXiv 2019年

作者： Hodge, Domonique W. Safo, Sandra E. Long, Qi Department of Biostatistics and Bioinformatics Emory University United States Division of Biostatistics University of Minnesota United States Department of Biostatistics Epidemiology and Informatics University of Pennsylvania United States

Missing data present challenges in data analysis. Naive analyses such as complete-case and available-case analysis may introduce bias and loss of efficiency, and produce unreliable results. Multiple imputation (MI) is one of the most widely used methods for handling missing data which can be partly attributed to its ease of use. However, existing MI methods implemented in most statistical software are not applicable to or do not perform well in high-dimensional settings where the number of predictors is large relative to the sample size. To remedy this issue, we develop an MI approach that uses dimension reduction techniques. Specifically, in constructing imputation models in the presence of high-dimensional data our approach uses sure independent screening followed by either sparse principal component analysis (sPCA) or sufficient dimension reduction (SDR) techniques. Our simulation studies, conducted for high-dimensional data, demonstrate that using SIS followed by sPCAto perform MI achieves better performance than the other imputation methods including several existing imputation approaches. We apply our approach to analysis of gene expression data from a prostate cancer study. Copyright © 2019, The Authors. All rights reserved.

关键词： Clustering algorithms

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Idelalisib (Zydelig) Maintenance in B-Cell Non-Hodgkin's Lymphoma after Autologous Stem Cell Transplantation (HDT/ASCT)

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Transplantation and Cellular Therapy 2025年第2期31卷 S396-S396页

作者： Yared, Jean A., MD Singh, Tanmay, MD Beitinjaneh, Prof. Amer M., MD Rapoport, Aaron P., MD Dahiya, Saurabh, MD Atanackovic, Djordje, MD Hardy, Dr. Nancy Maureen, MD Kocoglu, Mehmet H., MD Toth, Tara, PA-C Pineiro, Deanna Goloubeva, Olga G., PhD Transplantation & Cellular Therapy Program Division of Hematology/Oncology Department of Internal Medicine Greenebaum Comprehensive Cancer Center University of Maryland School of Medicine Baltimore MD MedStar Health Baltimore MD University of Miami Miami FL Division of Blood and Marrow Transplantation & Cellular Therapy Stanford University Stanford CA University of Maryland School of Medicine Baltimore MD Transplantation & Cellular Therapy Program Division of Hematology/Oncology Department of Internal Medicine Greenebaum Comprehensive Cancer Center University of Maryland Medical Center Baltimore MD University of Maryland Baltimore MD Division of Biostatistics and Bioinformatics Department of Epidemiology and Public Health University of Maryland School of Medicine Baltimore MD

IntroductionHDT/ACST in patients (pts) with relapsed and/or refractory (r/r) indolent (i) or transformed indolent (ti) B-cell NHL prolongs PFS. Unfortunately, the majority of pts will relapse/die from NHL within 1-3 years (yr) post ASCT. Idelalisib (Zydelig®), the 1 st marketed PI3Kδ inhibitor, has been effective against iNHL (FL) with favorable activity in treated pts, with an ORR of 54%, median PFS of 11 months (m), and a median duration of response of 12.4 m. [DELTA trial (NCT1282424)]. In the post marketing period, we proposed to incorporate maintenance (Mx) with Id post ASCT for pts with iNHL/tiNHL. We studied the safety and efficacy of this strategy. ObjectivesThis is a pilot, prospective, single arm, dual-center (Universities of Maryland and Miami) study of Id Mx in pts with iNHL/tiNHL post HDT/ASCT. Id was given at 150 mg BID (or 100 mg BID in pts with toxicities) for up to 1 yr or 12 cycles (28-day cycle) after ASCT. Id starts between 30 and 120 days after ASCT and continues until disease progression or intolerance. The primary objective was to determine the toxicity and safety. The secondary objective was efficacy with 1-/2- yr PFS and OS. ResultsThe accrual target was 31 pts. The study was closed prematurely for poor accrual due to COVID19 pandemic and emergence of CAR-T therapy. A total of 19 pts [(median age 60); 12 males and 5 females; 11 white non-Hispanic (NH), 2 black NH, 1 Asian NH, and 3 white Hispanic] with r/r iNHL/tiNHL (11 FL Gr 1,2,3a, 1 nodal MZL and 5 Gr3b/tFL) who received a median of 2 prior lines (range: 2-4) of treatment, achieving PR or CR followed by BEAM/ASCT, were consented between Oct 2017 to Sep 2020. 17 pts were enrolled. Dose de-escalation from 150 mg BID to 100 mg BID occurred in 11 (65%) pts. 12 (71%) pts received 12 cycles and 5 pts (29%) received 3 or less cycles due to toxicity (elevated LFTs in 3, rash in 1, and weight loss and dysgeusia in 1 pt). We noted 193 AEs: 29 probably, 98 possibly, 40 unlikely and 26 unrelated to

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Venetoclax and Azacitidine for Newly Diagnosed Non-Elderly Adult Patients with Acute Myeloid Leukemia and Adverse Risk Features

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BLOOD 2020年 136卷 9-9页

作者： Gutman, Jonathan A. Winters, Amanda Amaya, Maria L. McMahon, Christine M. Schowinsky, Jeffrey Abbott, Diana Hammes, Andrew Pei, Shanshan Stevens, Brett M. Jordan, Craig T. Smith, Clayton Pollyea, Daniel A. Division of Hematology University of Colorado Denver CO Department of Pediatrics University of Colorado Denver CO Division of Hematology University of Colorado Aurora CO University of Colorado Aurora CO Department of Biostatistics and Bioinformatics University of Colorado Denver Colorado Springs CO Division of Hematology Department of Medicine University of Colorado Aurora CO Division of Hematology Department of Medicine Univ. of Colorado Denver Aurora CO Division of Hematology University of Colorado Denver Aurora CO

Background: Venetoclax (ven)+azacitidine (aza) is the standard of care for untreated acute myeloid leukemia (AML) patients (pts) ≥75 years or unfit for intensive induction chemotherapy (IC) due to comorbidities. While the standard of care for younger newly diagnosed pts is IC, long term outcomes for all but favorable risk pts are suboptimal. Specifically, pts with adverse risk disease, per the European Leukemia Network (ELN), are more likely to be refractory to IC and have low rates of long term survival. Ven based regimens have a ~70% response rate in the upfront setting; in contrast to IC, those with adverse risk do not have lower response rates. This study explores the feasibility and outcomes of ven+aza for newly diagnosed younger AML pts who are not necessarily unfit for IC, but carry adverse risk features that make them less likely to respond to this therapy. Methods: This is an interim analysis of an ongoing phase 2 study (NCT03573024) of a planned 36 untreated adverse risk AML pts 18-59. Pts have adequate organ function and white blood cell counts <25x10 9 /L (hydrea permitted); “fitness” for IC is not a consideration. In cycle 1, pts receive aza 75mg/m 2 on days (d)1-7 and ven, escalated from 100 to 200 to 400 to 600mg on d1-4. Ven continues at 600mg d5-28 and bone marrow biopsies (BMBX) occur on d14 and 28. Pts who achieve morphologic remission without count recovery have up to 14 days off therapy before subsequent cycles. Non responders discontinue or receive up to 1 additional cycle. Post response (defined as a morphologic leukemia free state [MLFS], complete remission [CR] with incomplete count recovery [CRi] or CR), pts who are measurable residual disease (MRD) negative by multiparameter flow cytometry (MFC) and/or droplet digital PCR (ddPCR) may proceed to MRD negative maintenance: ven 400mg d1-28 with aza 75mg/m 2 d1-5 of sequential 28-day cycles. Pts who are MRD-positive may receive up to 3 additional cycles of consolidation: ven 600mg/day d1-28 and

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Bayesian multiscale modeling for aggregated disease mapping data 3

Bayesian multiscale modeling for aggregated disease mapping ...

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3rd ACM SIGSPATIAL International Workshop on the Use of GIS in Public Health, HealthGIS 2014 - Held in Conjunction with the 22nd ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems, ACM GIS 2014

作者： Aregay, Mehreteab Lawson, Andrew B. Faes, Christel Kirby, Russell Department of Public Heath Sciences Division of Biostatistics and Bioinformatics MUSC Charleston United States Department of Mathematics and Statistics Hasselt University Hasselt Belgium Department of Community and Family Health University of Southern Florida Lakeland United States

ISBN: (纸本)9781450331364

In spatial epidemiology, a scaling effect due to an aggre- gation of data from a finer to a coarser level is a common phenomenon. This article focuses on addressing this issue using a hierarchical Bayesian modeling framework. We pro- pose three difierent multiscale models. The first two models use a shared random effect that the finer level inherits from the coarser level. The third one assumes two separate convo- lution models at the finer and coarser levels. All these mod- els were compared based on deviance information criterion (DIC), Watanabe-Akaike or widely applicable information criterion (WAIC) and predictive accuracy applied on real and simulated data. The results indicate that the models with a shared random effect outperform the other models. Copyright © 2014 ACM.

关键词： Bayesian networks

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Cardiac Allograft Vasculopathy Mediates the Relationship Between Vitamin D Deficiency and Cardiovascular Mortality Following Heart Transplantation

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American heart journal 2025年

作者： Matthew E Gold Sarah Kulkarni Adithiya Yadalam Krishan J Patel Daniel A Gold Nishant Vatsa Vardhmaan Jain Alexander Razavi Yi-An Ko Chang Liu Divya Gupta Laurence S Sperling Arshed A Quyyumi Emory Clinical Cardiovascular Research Institute Division of Cardiology Department of Medicine Emory University School of Medicine Atlanta Georgia. Department of Biostatistics and Bioinformatics Rollins School of Public Health Emory University Atlanta Georgia. Department of Epidemiology Rollins School of Public Health Emory University Atlanta Georgia. Division of Cardiology Department of Medicine Emory University School of Medicine Atlanta Georgia. Emory Clinical Cardiovascular Research Institute Division of Cardiology Department of Medicine Emory University School of Medicine Atlanta Georgia. Electronic address: aquyyum@emory.edu.

BACKGROUND:Patients undergoing orthotopic heart transplantation (OHT) often have vitamin D deficiency (VDD) and cardiac allograft vasculopathy (CAV). Both VDD and CAV are associated with activation of the renin-angiotensin-aldosterone system. Although VDD is associated with adverse cardiovascular outcomes in multiple cohorts, the impact of VDD in OHT patients remains unknown. We hypothesized that lower VD levels would independently predict the presence of CAV and adverse cardiovascular outcomes. METHODS:In 327 participants with OHT recruited prospectively and followed for outcomes, baseline presence of CAV and all-cause and cardiovascular mortality at 5 years were evaluated. Multivariate logistic, cox, and Fine-Gray regression models were used to explore the associations between VDD and outcomes. RESULTS:VDD, present in 95 (29.1%) participants at enrollment, was associated with double the risk of 5-year mortality (HR: 2.08, 95% CI: 1.20-3.60), which was driven mostly by cardiovascular death (SHR: 2.21, 95% CI: 1.13-4.31), and also associated with a 3-fold higher likelihood of having CAV (OR: 3.08, 95% CI: 1.39-6.80) after adjustment for demographic and clinical covariates. There was a significant interaction between VDD and CAV on cardiovascular death (p=0.042). Mediation analysis showed that CAV grade accounts for 26.5% of the overall association between VD and cardiovascular mortality. CONCLUSION:VDD is an independent predictor of all-cause mortality, cardiovascular mortality, and presence of CAV in patients with OHT. Higher CAV grade appears to mediate, at least in part, the impact of VD levels on cardiovascular mortality, suggesting that VDD may contribute to higher risk of death through development of CAV.

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