2
|
Mathew MT, Babcock M, Hou YCC, Hunter JM, Leung ML, Mei H, Schieffer K, Akkari Y. Clinical Cytogenetics: Current Practices and Beyond. J Appl Lab Med 2024; 9:61-75. [PMID: 38167757 DOI: 10.1093/jalm/jfad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/17/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Throughout history, the field of cytogenetics has witnessed significant changes due to the constant evolution of technologies used to assess chromosome number and structure. Similar to the evolution of single nucleotide variant detection from Sanger sequencing to next-generation sequencing, the identification of chromosome alterations has progressed from banding to fluorescence in situ hybridization (FISH) to chromosomal microarrays. More recently, emerging technologies such as optical genome mapping and genome sequencing have made noteworthy contributions to clinical laboratory testing in the field of cytogenetics. CONTENT In this review, we journey through some of the most pivotal discoveries that have shaped the development of clinical cytogenetics testing. We also explore the current test offerings, their uses and limitations, and future directions in technology advancements. SUMMARY Cytogenetics methods, including banding and targeted assessments like FISH, continue to hold crucial roles in cytogenetic testing. These methods offer a rapid turnaround time, especially for conditions with a known etiology involving recognized cytogenetic aberrations. Additionally, laboratories have the flexibility to now employ higher-throughput methodologies to enhance resolution for cases with greater complexity.
Collapse
Affiliation(s)
- Mariam T Mathew
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States
- Department of Pathology, The Ohio State University, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States
| | - Melanie Babcock
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States
- Department of Pathology, The Ohio State University, Columbus, OH, United States
| | - Ying-Chen Claire Hou
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States
- Department of Pathology, The Ohio State University, Columbus, OH, United States
| | - Jesse M Hunter
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States
- Department of Pathology, The Ohio State University, Columbus, OH, United States
| | - Marco L Leung
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States
- Department of Pathology, The Ohio State University, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States
| | - Hui Mei
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States
- Department of Pathology, The Ohio State University, Columbus, OH, United States
| | - Kathleen Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States
- Department of Pathology, The Ohio State University, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States
| | - Yassmine Akkari
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States
- Department of Pathology, The Ohio State University, Columbus, OH, United States
| |
Collapse
|
5
|
Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, Chen B, Chikhi R, Clausen PTLC, Cristian A, Dabrowski PW, Darling AE, Egan R, Eskin E, Georganas E, Goltsman E, Gray MA, Hansen LH, Hofmeyr S, Huang P, Irber L, Jia H, Jørgensen TS, Kieser SD, Klemetsen T, Kola A, Kolmogorov M, Korobeynikov A, Kwan J, LaPierre N, Lemaitre C, Li C, Limasset A, Malcher-Miranda F, Mangul S, Marcelino VR, Marchet C, Marijon P, Meleshko D, Mende DR, Milanese A, Nagarajan N, Nissen J, Nurk S, Oliker L, Paoli L, Peterlongo P, Piro VC, Porter JS, Rasmussen S, Rees ER, Reinert K, Renard B, Robertsen EM, Rosen GL, Ruscheweyh HJ, Sarwal V, Segata N, Seiler E, Shi L, Sun F, Sunagawa S, Sørensen SJ, Thomas A, Tong C, Trajkovski M, Tremblay J, Uritskiy G, Vicedomini R, Wang Z, Wang Z, Wang Z, Warren A, Willassen NP, Yelick K, You R, Zeller G, Zhao Z, Zhu S, Zhu J, Garrido-Oter R, Gastmeier P, Hacquard S, Häußler S, Khaledi A, Maechler F, Mesny F, Radutoiu S, Schulze-Lefert P, Smit N, Strowig T, Bremges A, Sczyrba A, McHardy AC. Critical Assessment of Metagenome Interpretation: the second round of challenges. Nat Methods 2022; 19:429-440. [PMID: 35396482 PMCID: PMC9007738 DOI: 10.1038/s41592-022-01431-4] [Citation(s) in RCA: 106] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 02/14/2022] [Indexed: 12/20/2022]
Abstract
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses. This study presents the results of the second round of the Critical Assessment of Metagenome Interpretation challenges (CAMI II), which is a community-driven effort for comprehensively benchmarking tools for metagenomics data analysis.
Collapse
Affiliation(s)
- Fernando Meyer
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Adrian Fritz
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany
| | - Zhi-Luo Deng
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | | | - Till Robin Lesker
- German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany.,Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Gary Robertson
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Mohammed Alser
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Dmitry Antipov
- Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | | | | | | | | | - Jan Buchmann
- Institute for Biological Data Science, Heinrich-Heine-University, Düsseldorf, Germany
| | - Aydin Buluç
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,University of California, Berkeley, Berkeley, CA, USA
| | - Bo Chen
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,University of California, Berkeley, Berkeley, CA, USA
| | | | - Philip T L C Clausen
- National Food Institute, Division of Global Surveillance, Technical University of Denmark, Lyngby, Denmark
| | - Alexandru Cristian
- Drexel University, Philadelphia, PA, USA.,Google Inc., Philadelphia, PA, USA
| | - Piotr Wojciech Dabrowski
- Robert Koch-Institut, Berlin, Germany.,Hochschule für Technik und Wirtschaft Berlin, Berlin, Germany
| | | | - Rob Egan
- DOE Joint Genome Institute, Berkeley, CA, USA.,Lawrence Berkeley National Laboratories, Berkeley, CA, USA
| | - Eleazar Eskin
- University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Eugene Goltsman
- DOE Joint Genome Institute, Berkeley, CA, USA.,Lawrence Berkeley National Laboratories, Berkeley, CA, USA
| | - Melissa A Gray
- Drexel University, Philadelphia, PA, USA.,Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Philadelphia, PA, USA
| | - Lars Hestbjerg Hansen
- University of Copenhagen, Department of Plant and Environmental Science, Frederiksberg, Denmark
| | - Steven Hofmeyr
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,University of California, Berkeley, Berkeley, CA, USA
| | - Pingqin Huang
- School of Computer Science, Fudan University, Shanghai, China
| | - Luiz Irber
- University of California, Davis, Davis, CA, USA
| | - Huijue Jia
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, China
| | - Tue Sparholt Jørgensen
- Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Lyngby, Denmark.,Aarhus University, Department of Environmental Science, Roskilde, Denmark
| | - Silas D Kieser
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | | | - Axel Kola
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Mikhail Kolmogorov
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Anton Korobeynikov
- Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia.,Department of Statistical Modelling, Saint Petersburg State University, Saint Petersburg, Russia
| | - Jason Kwan
- University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Chenhao Li
- Genome Institute of Singapore, Singapore, Singapore
| | | | - Fabio Malcher-Miranda
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
| | | | - Vanessa R Marcelino
- Sydney Medical School, The University of Sydney, Sydney, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
| | | | - Pierre Marijon
- Department of Computer Science, Inria, University of Lille, CNRS, Lille, France
| | - Dmitry Meleshko
- Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Daniel R Mende
- Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Alessio Milanese
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland.,Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Niranjan Nagarajan
- Genome Institute of Singapore, A*STAR, Singapore, Singapore.,National University of Singapore, Singapore, Singapore
| | | | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Leonid Oliker
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,University of California, Berkeley, Berkeley, CA, USA
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | | | - Vitor C Piro
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany
| | | | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Evan R Rees
- University of Wisconsin-Madison, Madison, WI, USA
| | - Knut Reinert
- Institute for Bioinformatics, FU Berlin, Berlin, Germany
| | - Bernhard Renard
- Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany.,Bioinformatics Unit (MF1), Robert Koch Institute, Berlin, Germany
| | | | - Gail L Rosen
- Drexel University, Philadelphia, PA, USA.,Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Philadelphia, PA, USA.,Center for Biological Discovery from Big Data, Philadelphia, PA, USA
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | - Varuni Sarwal
- University of California, Los Angeles, Los Angeles, CA, USA
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Enrico Seiler
- Institute for Bioinformatics, FU Berlin, Berlin, Germany
| | - Lizhen Shi
- Florida Polytechnic University, Lakeland, FL, USA
| | - Fengzhu Sun
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland
| | | | - Ashleigh Thomas
- DOE Joint Genome Institute, Berkeley, CA, USA.,University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Mirko Trajkovski
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Julien Tremblay
- Energy, Mining and Environment, National Research Council Canada, Montreal, Quebec, Canada
| | | | | | - Zhengyang Wang
- School of Computer Science, Fudan University, Shanghai, China
| | - Ziye Wang
- School of Mathematical Sciences, Fudan University, Shanghai, China
| | - Zhong Wang
- Department of Energy Joint Genome Institute, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,School of Natural Sciences, University of California at Merced, Merced, CA, USA
| | | | | | - Katherine Yelick
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,University of California, Berkeley, Berkeley, CA, USA
| | - Ronghui You
- School of Computer Science, Fudan University, Shanghai, China
| | - Georg Zeller
- Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | | | - Shanfeng Zhu
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.,Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
| | - Jie Zhu
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Susanne Häußler
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ariane Khaledi
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Fantin Mesny
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | | | | | - Nathiana Smit
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Till Strowig
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Andreas Bremges
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.,German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Alice Carolyn McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany. .,Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany. .,German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany. .,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany.
| |
Collapse
|