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1. Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA

Author

Binsheng Gong, Samir Lababidi, Rebecca Kusko, Khaled Bouri, Sarah Prezek, Vishal Thovarai, Anish Prasanna, Ezekiel J. Maier, Mahdi Golkaram, Xingqiang Sun, Konstantinos Kyriakidis, João Paulo Kitajima, Sayed Mohammad Ebrahim Sahraeian, Yunfei Guo, Elaine Johanson, Wendell Jones, Weida Tong, and Joshua Xu

Subjects
Indel calling pipeline, Next-generation sequencing, Precision medicine, Personalized medicine, precisionFDA challenge, Medicine, Science
Abstract

Abstract Accurately calling indels with next-generation sequencing (NGS) data is critical for clinical application. The precisionFDA team collaborated with the U.S. Food and Drug Administration’s (FDA’s) National Center for Toxicological Research (NCTR) and successfully completed the NCTR Indel Calling from Oncopanel Sequencing Data Challenge, to evaluate the performance of indel calling pipelines. Top performers were selected based on precision, recall, and F1-score. The performance of many other pipelines was close to the top performers, which produced a top cluster of performers. The performance was significantly higher in high confidence regions and coding regions, and significantly lower in low complexity regions. Oncopanel capture and other issues may have occurred that affected the recall rate. Indels with higher variant allele frequency (VAF) may generally be called with higher confidence. Many of the indel calling pipelines had good performance. Some of them performed generally well across all three oncopanels, while others were better for a specific oncopanel. The performance of indel calling can further be improved by restricting the calls within high confidence intervals (HCIs) and coding regions, and by excluding low complexity regions (LCR) regions. Certain VAF cut-offs could be applied according to the applications.

Published
2024
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2. Enabling precision medicine via standard communication of HTS provenance, analysis, and results.

Author

Gil Alterovitz, Dennis Dean, Carole Goble, Michael R Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkayastha, Charles H King, Dan Taylor, Elaine Johanson, Elaine E Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K Vora, Jeremy Goecks, Jianchao Yao, Jonas S Almeida, Jonathon Keeney, KanakaDurga Addepalli, Konstantinos Krampis, Krista M Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, and Raja Mazumder

Subjects
Biology (General), QH301-705.5
Abstract

A personalized approach based on a patient's or pathogen's unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet-lab procedures to computational methods. The BioCompute framework (https://w3id.org/biocompute/1.3.0) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated if needed, and compared by scientists, regulators, test developers, and clinicians. Easing the burden of performing the aforementioned tasks greatly extends the range of practical application. Large clinical trials, precision medicine, and regulatory submissions require a set of agreed upon standards that ensures efficient communication and documentation of genomic analyses. The BioCompute paradigm and the resulting BioCompute Objects (BCOs) offer that standard and are freely accessible as a GitHub organization (https://github.com/biocompute-objects) following the "Open-Stand.org principles for collaborative open standards development." With high-throughput sequencing (HTS) studies communicated using a BCO, regulatory agencies (e.g., Food and Drug Administration [FDA]), diagnostic test developers, researchers, and clinicians can expand collaboration to drive innovation in precision medicine, potentially decreasing the time and cost associated with next-generation sequencing workflow exchange, reporting, and regulatory reviews.

Published
2018
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3. Analysis of the BraTS 2023 Intracranial Meningioma Segmentation Challenge.

Author

Dominic LaBella, Ujjwal Baid, Omaditya Khanna, Shan McBurney-Lin, Ryan McLean, Pierre Nedelec, Arif Rashid, Nourel Hoda Tahon, Talissa Altes, Radhika Bhalerao, Yaseen Dhemesh, Devon Godfrey, Fathi Hilal, Scott Floyd, Anastasia Janas, Anahita Fathi Kazerooni, John Kirkpatrick, Collin Kent, Florian Kofler, Kevin Leu, Nazanin Maleki, Bjoern H. Menze, Maxence Pajot, Zachary J. Reitman, Jeffrey D. Rudie, Rachit Saluja, Yury Velichko, Chunhao Wang, Pranav Warman, Maruf Adewole, Jake Albrecht, Udunna Anazodo, Syed Muhammad Anwar, Timothy Bergquist, Sully F. Chen, Verena Chung, Gian Marco Conte, Farouk Dako, James A. Eddy, Ivan Ezhov, Nastaran Khalili, Juan Eugenio Iglesias, Zhifan Jiang, Elaine Johanson, Koen Van Leemput, Hongwei Bran Li, Marius George Linguraru, Xinyang Liu, Aria Mahtabfar, Zeke Meier, Ahmed W. Moawad, John Mongan, Marie Piraud, Russell Takeshi Shinohara, Walter F. Wiggins, Aly H. Abayazeed, Rachel Akinola, András Jakab, Michel Bilello, Maria Correia de Verdier, Priscila Crivellaro, Christos Davatzikos, Keyvan Farahani, John B. Freymann, Christopher Hess, Raymond Y. Huang, Philipp Lohmann, Mana Moassefi, Matthew W. Pease, Philipp Vollmuth, Nico Sollmann, David Diffley, Khanak K. Nandolia, Daniel I. Warren, Ali Hussain, Pascal Fehringer, Yulia Bronstein, Lisa Deptula, Evan G. Stein, Mahsa Taherzadeh, Eduardo Portela de Oliveira, Aoife Haughey, Marinos Kontzialis, Luca Saba, Benjamin Turner, Melanie M. T. Brüßeler, Shehbaz Ansari, Athanasios Gkampenis, David Maximilian Weiss, Aya Mansour, Islam H. Shawali, Nikolay Yordanov, Joel M. Stein, Roula Hourani, Mohammed Yahya Moshebah, Ahmed Magdy Abouelatta, Tanvir Rizvi, Klara Willms, Dann C. Martin, and Abdullah Okar

Published
2024
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4. The Brain Tumor Segmentation (BraTS) Challenge 2023: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs).

Author

Anahita Fathi Kazerooni, Nastaran Khalili, Xinyang Liu, Debanjan Haldar, Zhifan Jiang, Syed Muhammad Anwar, Jake Albrecht, Maruf Adewole, Udunna Anazodo, Hannah Anderson, Sina Bagheri, Ujjwal Baid, Timothy Bergquist, Evan Calabrese, Verena Chung, Gian Marco Conte, Farouk Dako, James A. Eddy, Ivan Ezhov, Ariana Familiar, Keyvan Farahani, Shuvanjan Haldar, Juan Eugenio Iglesias, Anastasia Janas, Elaine Johanson, Florian Kofler, Dominic LaBella, Koen Van Leemput, Hongwei Bran Li, Nazanin Maleki, Zeke Meier, Bjoern H. Menze, Ahmed W. Moawad, Marie Piraud, Tina Poussaint, Zachary Reitman, Jeffrey D. Rudie, Ibraheem Salman Shaikh, Russell Taki Shinohara, Wenxin Tu, Karthik Viswanathan, Chunhao Wang, Jeffrey B. Ware, Benedikt Wiestler, Walter I. Wiggins, Anna Zapaishchykova, Mariam Aboian, Miriam Bornhorst, Peter de Blank, Michelle Deutsch, Maryam Fouladi, Lindsey Hoffman, Benjamin H. Kann, Margot Lazow, Leonie Mikael, Ali Nabavizadeh, Roger J. Packer, Adam C. Resnick, Brian Rood, Arastoo Vossough, Spyridon Bakas, and Marius George Linguraru

Published
2023
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5. The ASNR-MICCAI Brain Tumor Segmentation (BraTS) Challenge 2023: Intracranial Meningioma.

Author

Dominic LaBella, Maruf Adewole, Michelle Alonso-Basanta, Talissa Altes, Syed Muhammad Anwar, Ujjwal Baid, Timothy Bergquist, Radhika Bhalerao, Sully F. Chen, Verena Chung, Gian Marco Conte, Farouk Dako, James A. Eddy, Ivan Ezhov, Devon Godfrey, Fathi Hilal, Ariana Familiar, Keyvan Farahani, Juan Eugenio Iglesias, Zhifan Jiang, Elaine Johanson, Anahita Fathi Kazerooni, Collin Kent, John Kirkpatrick, Florian Kofler, Koen Van Leemput, Hongwei Bran Li, Xinyang Liu, Aria Mahtabfar, Shan McBurney-Lin, Ryan McLean, Zeke Meier, Ahmed W. Moawad, John Mongan, Pierre Nedelec, Maxence Pajot, Marie Piraud, Arif Rashid, Zachary Reitman, Russell Takeshi Shinohara, Yury Velichko, Chunhao Wang, Pranav I. Warman, Walter I. Wiggins, Mariam Aboian, Jake Albrecht, Udunna Anazodo, Spyridon Bakas, Adam E. Flanders, Anastasia Janas, Goldey Khanna, Marius George Linguraru, Bjoern H. Menze, Ayman Nada, Andreas M. Rauschecker, Jeffrey D. Rudie, Nourel Hoda Tahon, Javier E. Villanueva-Meyer, Benedikt Wiestler, and Evan Calabrese

Published
2023
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6. The Brain Tumor Segmentation (BraTS) Challenge 2023: Brain MR Image Synthesis for Tumor Segmentation (BraSyn).

Author

Hongwei Bran Li, Gian Marco Conte, Syed Muhammad Anwar, Florian Kofler, Koen Van Leemput, Marie Piraud, Ivan Ezhov, Felix Meissen, Maruf Adewole, Anastasia Janas, Anahita Fathi Kazerooni, Dominic LaBella, Ahmed W. Moawad, Keyvan Farahani, James A. Eddy, Timothy Bergquist, Verena Chung, Russell Takeshi Shinohara, Farouk Dako, Walter I. Wiggins, Zachary Reitman, Chunhao Wang, Xinyang Liu, Zhifan Jiang, Ariana Familiar, Elaine Johanson, Zeke Meier, Christos Davatzikos, John B. Freymann, Justin S. Kirby, Michel Bilello, Hassan M. Fathallah-Shaykh, Roland Wiest, Jan Kirschke, Rivka R. Colen, Aikaterini Kotrotsou, Pamela LaMontagne, Daniel S. Marcus, Mikhail Milchenko, Arash Nazeri, Marc-André Weber, Abhishek Mahajan, Suyash Mohan, John Mongan, Christopher Hess, Soonmee Cha, Javier E. Villanueva-Meyer, Errol Colak, Priscila Crivellaro, András Jakab, Jake Albrecht, Udunna Anazodo, Mariam Aboian, Thomas Yu, Ujjwal Baid, Spyridon Bakas, Marius George Linguraru, Bjoern H. Menze, Juan Eugenio Iglesias, and Benedikt Wiestler

Published
2023
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7. The Brain Tumor Segmentation (BraTS) Challenge 2023: Glioma Segmentation in Sub-Saharan Africa Patient Population (BraTS-Africa).

Author

Maruf Adewole, Jeffrey D. Rudie, Anu Gbadamosi, Oluyemisi Toyobo, Raymond Confidence, Dong Zhang 0009, Olubukola Omidiji, Rachel Akinola, Mohammad Abba Suwaid, Adaobi Emegoakor, Nancy Ojo, Kenneth Aguh, Chinasa Kalaiwo, Gabriel Babatunde, Afolabi Ogunleye, Yewande Gbadamosi, Kator Iorpagher, Evan Calabrese, Mariam Aboian, Marius George Linguraru, Jake Albrecht, Benedikt Wiestler, Florian Kofler, Anastasia Janas, Dominic LaBella, Anahita Fathi Kazerooni, Hongwei Bran Li, Juan Eugenio Iglesias, Keyvan Farahani, James A. Eddy, Timothy Bergquist, Verena Chung, Russell Takeshi Shinohara, Walter I. Wiggins, Zachary Reitman, Chunhao Wang, Xinyang Liu, Zhifan Jiang, Ariana Familiar, Koen Van Leemput, Christina Bukas, Marie Piraud, Gian Marco Conte, Elaine Johanson, Zeke Meier, Bjoern H. Menze, Ujjwal Baid, Spyridon Bakas, Farouk Dako, Abiodun Fatade, and Udunna Anazodo

Published
2023
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8. The Brain Tumor Segmentation (BraTS) Challenge 2023: Local Synthesis of Healthy Brain Tissue via Inpainting.

Author

Florian Kofler, Felix Meissen, Felix Steinbauer, Robert Graf, Eva Oswald, Ezequiel de la Rosa, Hongwei Bran Li, Ujjwal Baid, Florian A. Hölzl, özgün Turgut, Izabela Horvath, Diana Waldmannstetter, Christina Bukas, Maruf Adewole, Syed Muhammad Anwar, Anastasia Janas, Anahita Fathi Kazerooni, Dominic LaBella, Ahmed W. Moawad, Keyvan Farahani, James A. Eddy, Timothy Bergquist, Verena Chung, Russell Takeshi Shinohara, Farouk Dako, Walter I. Wiggins, Zachary Reitman, Chunhao Wang, Xinyang Liu, Zhifan Jiang, Ariana Familiar, Gian Marco Conte, Elaine Johanson, Zeke Meier, Christos Davatzikos, John B. Freymann, Justin S. Kirby, Michel Bilello, Hassan M. Fathallah-Shaykh, Roland Wiest, Jan Kirschke, Rivka R. Colen, Aikaterini Kotrotsou, Pamela LaMontagne, Daniel S. Marcus, Mikhail Milchenko, Arash Nazeri, Marc-André Weber, Abhishek Mahajan, Suyash Mohan, John Mongan, Christopher Hess, Soonmee Cha, Javier E. Villanueva-Meyer, Errol Colak, Priscila Crivellaro, András Jakab, Jake Albrecht, Udunna Anazodo, Mariam Aboian, Juan Eugenio Iglesias, Koen Van Leemput, Spyridon Bakas, Daniel Rueckert, Benedikt Wiestler, Ivan Ezhov, Marie Piraud, and Bjoern H. Menze

Published
2023
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13. PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

Author

Nathan D. Olson, Justin Wagner, Jennifer McDaniel, Sarah H. Stephens, Samuel T. Westreich, Anish G. Prasanna, Elaine Johanson, Emily Boja, Ezekiel J. Maier, Omar Serang, David Jáspez, José M. Lorenzo-Salazar, Adrián Muñoz-Barrera, Luis A. Rubio-Rodríguez, Carlos Flores, Konstantinos Kyriakidis, Andigoni Malousi, Kishwar Shafin, Trevor Pesout, Miten Jain, Benedict Paten, Pi-Chuan Chang, Alexey Kolesnikov, Maria Nattestad, Gunjan Baid, Sidharth Goel, Howard Yang, Andrew Carroll, Robert Eveleigh, Mathieu Bourgey, Guillaume Bourque, Gen Li, ChouXian Ma, LinQi Tang, YuanPing Du, ShaoWei Zhang, Jordi Morata, Raúl Tonda, Genís Parra, Jean-Rémi Trotta, Christian Brueffer, Sinem Demirkaya-Budak, Duygu Kabakci-Zorlu, Deniz Turgut, Özem Kalay, Gungor Budak, Kübra Narcı, Elif Arslan, Richard Brown, Ivan J. Johnson, Alexey Dolgoborodov, Vladimir Semenyuk, Amit Jain, H. Serhat Tetikol, Varun Jain, Mike Ruehle, Bryan Lajoie, Cooper Roddey, Severine Catreux, Rami Mehio, Mian Umair Ahsan, Qian Liu, Kai Wang, Sayed Mohammad Ebrahim Sahraeian, Li Tai Fang, Marghoob Mohiyuddin, Calvin Hung, Chirag Jain, Hanying Feng, Zhipan Li, Luoqi Chen, Fritz J. Sedlazeck, and Justin M. Zook

Subjects
Genetics, Biochemistry, Genetics and Molecular Biology (miscellaneous)
Abstract

The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 variant call sets for one or more sequencing technologies (Illumina, PacBio HiFi, and Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with updated Genome in a Bottle benchmark sets and genome stratifications. Challenge submissions included numerous innovative methods, with graph-based and machine learning methods scoring best for short-read and long-read datasets, respectively. With machine learning approaches, combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.

Published
2022

14. Power

Author

Elaine Johanson

Subjects
General Earth and Planetary Sciences, General Environmental Science
Published
2022
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15. precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions

Author

Calvin Hung, Jean-Rémi Trotta, Severine Catreux, LinQi Tang, Kübra Narcı, Alexey Kolesnikov, Qian Liu, Mian Umair Ahsan, Emily Boja, Samuel T. Westreich, Özem Kalay, Andrew Carroll, Sinem Demirkaya-Budak, Ivan E. Johnson, Richard J. C. Brown, Benedict Paten, Howard Yang, Amit Jain, Genís Parra, José M. Lorenzo-Salazar, Ezekiel J. Maier, Mathieu Bourgey, ChouXian Ma, Justin Wagner, Miten Jain, Alexey Dolgoborodov, Mike Ruehle, Konstantinos Kyriakidis, David Jáspez, Omar Serang, Vladimir Semenyuk, Fritz J. Sedlazeck, Jordi Morata, Marghoob Mohiyuddin, Christian Brueffer, Chirag Jain, Li Tai Fang, Robert Eveleigh, Gunjan Baid, Sidharth Goel, Raul Tonda, Gungor Budak, Sarah H. Stephens, Maria Nattestad, ShaoWei Zhang, Deniz Turgut, Hanying Feng, Elaine Johanson, Luoqi Chen, H. Serhat Tetikol, Rami Mehio, Adrián Muñoz-Barrera, Gen Li, Guillaume Bourque, Duygu Kabakci-Zorlu, YuanPing Du, Trevor Pesout, Zhipan Li, Varun Jain, Nathan D. Olson, Sayed Mohammad Ebrahim Sahraeian, Anish G. Prasanna, Kishwar Shafin, Jennifer McDaniel, Bryan R. Lajoie, Pi-Chuan Chang, Justin M. Zook, Kai Wang, Cooper Roddey, Andigoni Malousi, Luis A. Rubio-Rodríguez, Carlos Flores, and Elif Arslan

Subjects
FASTQ format, Identification (information), medicine.medical_specialty, chemistry.chemical_compound, chemistry, Computer science, medicine, Benchmark (computing), Medical genetics, Nanopore sequencing, Computational biology, Genome, DNA
Abstract

SummaryThe precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their variant calling pipelines and submitted 64 variant callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, and ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with the new GIAB benchmark sets and genome stratifications. Challenge submissions included a number of innovative methods for all three technologies, with graph-based and machine-learning methods scoring best for short-read and long-read datasets, respectively. New methods out-performed the 2016 Truth Challenge winners, and new machine-learning approaches combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.

Published
2020
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16. Strengthening the BioCompute Standard by Crowdsourcing on PrecisionFDA

Author

Dennis A. Dean, Elaine Johanson, Janisha A. Patel, Eric F. Donaldson, Soner Koc, Nan Xiao, Purkayastha A, Elaine E. Thompson, Raja Mazumder, Charles Hadley King, Stephens Sh, Sean Watford, and Jonathon Keeney

Subjects
World Wide Web, Class (computer programming), business.industry, Interface (Java), Computer science, Container (abstract data type), Crowdsourcing, business
Abstract

BackgroundThe field of bioinformatics has grown at such a rapid pace that a gap in standardization exists when reporting an analysis. In response, the BioCompute project was created to standardize the type and method of information communicated when describing a bioinformatic analysis. Once the project became established, its goals shifted to broadening awareness and usage of BioCompute, and soliciting feedback from a larger audience. To address these goals, the BioCompute project collaborated with precisionFDA on a crowdsourced challenge that ran from May 2019 to October 2019. This challenge had a beginner track where participants submitted BCOs based on a pipeline of their choosing, and an advanced track where participants submitted applications supporting the creation of a BCO and verification of BCO conformance to specifications.ResultsIn total, there were 28 submissions to the beginner track (including submissions from a bioinformatics master’s class at George Washington University) and three submissions to the advanced track. Three top performers were selected from the beginner track, while a single top performer was selected for the advanced track. In the beginner track, top performers differentiated themselves by submitting BCOs that included more than the minimally compliant content. Advanced track submissions were very impressive. They included a complete web application, a command line tool that produced a static result, and a dockerized container that automatically created the BCO as the tool was run. The ability to harmonize the correct function, a simple user experience, and the aesthetics of the tool interface differentiated the tools.ConclusionsDespite being new to the concept, most beginner track scores were high, indicating that most users understood the fundamental concepts of the BCO specification. Novice bioinformatics students were an ideal cohort for this Challenge because of their lack of familiarity with BioCompute, broad diversity of research interests, and motivation to submit high-quality work. This challenge was successful in introducing the BCO to a wider audience, obtaining feedback from that audience, and resulting in a tool novices may use for BCO creation and conformance. In addition, the BCO specification itself was improved based on feedback illustrating the utility of a “wisdom of the crowd” approach to standards development.

Published
2020
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17. Right data for right patient—a precisionFDA NCI–CPTAC Multi-omics Mislabeling Challenge

Author

Bing Zhang, Denise Hinton, Emily S. Boja, Živana Težak, Henry Rodriguez, Elaine Johanson, and Pei Wang

Subjects
0301 basic medicine, Proteomics, Bioinformatics, MEDLINE, Genomics, Computational biology, General Biochemistry, Genetics and Molecular Biology, Food and drug administration, 03 medical and health sciences, Medicine, Humans, Staining and Labeling, business.industry, United States Food and Drug Administration, Comment, Cancer, General Medicine, medicine.disease, humanities, National Cancer Institute (U.S.), United States, 030104 developmental biology, Multi omics, business, Medical genomics
Abstract

To address a critical roadblock that can occur in translational and clinical research, the National Cancer Institute and the Food and Drug Administration, in coordination with the DREAM Challenges, are launching the first computational challenge using multi-omics datasets to detect and correct specimen mislabeling.

Published
2018

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