1
|
Dyshlovoy SA, Paigin S, Afflerbach AK, Lobermeyer A, Werner S, Schüller U, Bokemeyer C, Schuh AH, Bergmann L, von Amsberg G, Joosse SA. Applications of Nanopore sequencing in precision cancer medicine. Int J Cancer 2024. [PMID: 39031959 DOI: 10.1002/ijc.35100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/25/2024] [Accepted: 06/25/2024] [Indexed: 07/22/2024]
Abstract
Oxford Nanopore Technologies sequencing, also referred to as Nanopore sequencing, stands at the forefront of a revolution in clinical genetics, offering the potential for rapid, long read, and real-time DNA and RNA sequencing. This technology is currently making sequencing more accessible and affordable. In this comprehensive review, we explore its potential regarding precision cancer diagnostics and treatment. We encompass a critical analysis of clinical cases where Nanopore sequencing was successfully applied to identify point mutations, splice variants, gene fusions, epigenetic modifications, non-coding RNAs, and other pivotal biomarkers that defined subsequent treatment strategies. Additionally, we address the challenges of clinical applications of Nanopore sequencing and discuss the current efforts to overcome them.
Collapse
Affiliation(s)
- Sergey A Dyshlovoy
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Oxford, UK
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefanie Paigin
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Ann-Kristin Afflerbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Annabelle Lobermeyer
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Werner
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute for Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Paediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carsten Bokemeyer
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna H Schuh
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Oxford, UK
| | - Lina Bergmann
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gunhild von Amsberg
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Martini-Klinik, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon A Joosse
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
2
|
Kolesnikov A, Cook D, Nattestad M, Brambrink L, McNulty B, Gorzynski J, Goenka S, Ashley EA, Jain M, Miga KH, Paten B, Chang PC, Carroll A, Shafin K. Local read haplotagging enables accurate long-read small variant calling. Nat Commun 2024; 15:5907. [PMID: 39003259 PMCID: PMC11246426 DOI: 10.1038/s41467-024-50079-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 06/28/2024] [Indexed: 07/15/2024] Open
Abstract
Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving third-generation sequencing platforms like Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) are introducing newer platforms and data types. It has been demonstrated that variant calling methods based on deep neural networks can use local haplotyping information with long-reads to improve the genotyping accuracy. However, using local haplotype information creates an overhead as variant calling needs to be performed multiple times which ultimately makes it difficult to extend to new data types and platforms as they get introduced. In this work, we have developed a local haplotype approximate method that enables state-of-the-art variant calling performance with multiple sequencing platforms including PacBio Revio system, ONT R10.4 simplex and duplex data. This addition of local haplotype approximation simplifies long-read variant calling with DeepVariant.
Collapse
Affiliation(s)
| | - Daniel Cook
- Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA, USA
| | | | | | - Brandy McNulty
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | - Miten Jain
- Northeastern university, Boston, MA, USA
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Pi-Chuan Chang
- Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA, USA
| | - Andrew Carroll
- Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA, USA.
| | - Kishwar Shafin
- Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA, USA.
| |
Collapse
|
3
|
Dobner J, Nguyen T, Pavez-Giani MG, Cyganek L, Distelmaier F, Krutmann J, Prigione A, Rossi A. mtDNA analysis using Mitopore. Mol Ther Methods Clin Dev 2024; 32:101231. [PMID: 38572068 PMCID: PMC10988129 DOI: 10.1016/j.omtm.2024.101231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/08/2024] [Indexed: 04/05/2024]
Abstract
Mitochondrial DNA (mtDNA) analysis is crucial for the diagnosis of mitochondrial disorders, forensic investigations, and basic research. Existing pipelines are complex, expensive, and require specialized personnel. In many cases, including the diagnosis of detrimental single nucleotide variants (SNVs), mtDNA analysis is still carried out using Sanger sequencing. Here, we developed a simple workflow and a publicly available webserver named Mitopore that allows the detection of mtDNA SNVs, indels, and haplogroups. To simplify mtDNA analysis, we tailored our workflow to process noisy long-read sequencing data for mtDNA analysis, focusing on sequence alignment and parameter optimization. We implemented Mitopore with eliBQ (eliminate bad quality reads), an innovative quality enhancement that permits the increase of per-base quality of over 20% for low-quality data. The whole Mitopore workflow and webserver were validated using patient-derived and induced pluripotent stem cells harboring mtDNA mutations. Mitopore streamlines mtDNA analysis as an easy-to-use fast, reliable, and cost-effective analysis method for both long- and short-read sequencing data. This significantly enhances the accessibility of mtDNA analysis and reduces the cost per sample, contributing to the progress of mtDNA-related research and diagnosis.
Collapse
Affiliation(s)
- Jochen Dobner
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Thach Nguyen
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Mario Gustavo Pavez-Giani
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Lukas Cyganek
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jean Krutmann
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
- Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Alessandro Prigione
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Andrea Rossi
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| |
Collapse
|
4
|
Ermini L, Driguez P. The Application of Long-Read Sequencing to Cancer. Cancers (Basel) 2024; 16:1275. [PMID: 38610953 PMCID: PMC11011098 DOI: 10.3390/cancers16071275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Cancer is a multifaceted disease arising from numerous genomic aberrations that have been identified as a result of advancements in sequencing technologies. While next-generation sequencing (NGS), which uses short reads, has transformed cancer research and diagnostics, it is limited by read length. Third-generation sequencing (TGS), led by the Pacific Biosciences and Oxford Nanopore Technologies platforms, employs long-read sequences, which have marked a paradigm shift in cancer research. Cancer genomes often harbour complex events, and TGS, with its ability to span large genomic regions, has facilitated their characterisation, providing a better understanding of how complex rearrangements affect cancer initiation and progression. TGS has also characterised the entire transcriptome of various cancers, revealing cancer-associated isoforms that could serve as biomarkers or therapeutic targets. Furthermore, TGS has advanced cancer research by improving genome assemblies, detecting complex variants, and providing a more complete picture of transcriptomes and epigenomes. This review focuses on TGS and its growing role in cancer research. We investigate its advantages and limitations, providing a rigorous scientific analysis of its use in detecting previously hidden aberrations missed by NGS. This promising technology holds immense potential for both research and clinical applications, with far-reaching implications for cancer diagnosis and treatment.
Collapse
Affiliation(s)
- Luca Ermini
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health, L-1210 Luxembourg, Luxembourg
| | - Patrick Driguez
- Bioscience Core Lab, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|
5
|
Kingsmore SF, Nofsinger R, Ellsworth K. Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review. NPJ Genom Med 2024; 9:17. [PMID: 38413639 PMCID: PMC10899612 DOI: 10.1038/s41525-024-00404-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES. URGS outperformed RGS and RES with faster time to diagnosis, and higher rate of diagnosis and clinical utility. Diagnostic and clinical outcomes will improve as methods evolve, costs decrease, and testing is implemented within precision medicine delivery systems attuned to ICU needs. URGS, RGS, and RES are currently performed in <5% of the ~200,000 children likely to benefit annually due to lack of payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition of possible genetic diseases, and current formatting as tests rather than as a rapid precision medicine delivery system. The gap between actual and optimal outcomes in children in ICUs is currently increasing since expanded use of URGS, RGS, and RES lags growth in those likely to benefit through new therapies. There is sufficient evidence to conclude that URGS, RGS, or RES should be considered in all children with diseases of uncertain etiology at ICU admission. Minimally, diagnostic URGS, RGS, or RES should be ordered early during admissions of critically ill infants and children with suspected genetic diseases.
Collapse
Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
| | - Russell Nofsinger
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Kasia Ellsworth
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| |
Collapse
|
6
|
Eisenstein M. Super-speedy sequencing puts genomic diagnosis in the fast lane. Nature 2024; 626:915-917. [PMID: 38374432 DOI: 10.1038/d41586-024-00483-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
|
7
|
Mahmoud M, Huang Y, Garimella K, Audano PA, Wan W, Prasad N, Handsaker RE, Hall S, Pionzio A, Schatz MC, Talkowski ME, Eichler EE, Levy SE, Sedlazeck FJ. Utility of long-read sequencing for All of Us. Nat Commun 2024; 15:837. [PMID: 38281971 PMCID: PMC10822842 DOI: 10.1038/s41467-024-44804-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/03/2024] [Indexed: 01/30/2024] Open
Abstract
The All of Us (AoU) initiative aims to sequence the genomes of over one million Americans from diverse ethnic backgrounds to improve personalized medical care. In a recent technical pilot, we compare the performance of traditional short-read sequencing with long-read sequencing in a small cohort of samples from the HapMap project and two AoU control samples representing eight datasets. Our analysis reveals substantial differences in the ability of these technologies to accurately sequence complex medically relevant genes, particularly in terms of gene coverage and pathogenic variant identification. We also consider the advantages and challenges of using low coverage sequencing to increase sample numbers in large cohort analysis. Our results show that HiFi reads produce the most accurate results for both small and large variants. Further, we present a cloud-based pipeline to optimize SNV, indel and SV calling at scale for long-reads analysis. These results lead to widespread improvements across AoU.
Collapse
Affiliation(s)
- M Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Y Huang
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - K Garimella
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - P A Audano
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - W Wan
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - N Prasad
- Discovery Life Sciences, Huntsville, AL, 35806, USA
| | - R E Handsaker
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
| | - S Hall
- Discovery Life Sciences, Huntsville, AL, 35806, USA
| | - A Pionzio
- Discovery Life Sciences, Huntsville, AL, 35806, USA
| | - M C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - M E Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02141, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - E E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - S E Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - F J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
| |
Collapse
|
8
|
Smolka M, Paulin LF, Grochowski CM, Horner DW, Mahmoud M, Behera S, Kalef-Ezra E, Gandhi M, Hong K, Pehlivan D, Scholz SW, Carvalho CMB, Proukakis C, Sedlazeck FJ. Detection of mosaic and population-level structural variants with Sniffles2. Nat Biotechnol 2024:10.1038/s41587-023-02024-y. [PMID: 38168980 PMCID: PMC11217151 DOI: 10.1038/s41587-023-02024-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/11/2023] [Indexed: 01/05/2024]
Abstract
Calling structural variations (SVs) is technically challenging, but using long reads remains the most accurate way to identify complex genomic alterations. Here we present Sniffles2, which improves over current methods by implementing a repeat aware clustering coupled with a fast consensus sequence and coverage-adaptive filtering. Sniffles2 is 11.8 times faster and 29% more accurate than state-of-the-art SV callers across different coverages (5-50×), sequencing technologies (ONT and HiFi) and SV types. Furthermore, Sniffles2 solves the problem of family-level to population-level SV calling to produce fully genotyped VCF files. Across 11 probands, we accurately identified causative SVs around MECP2, including highly complex alleles with three overlapping SVs. Sniffles2 also enables the detection of mosaic SVs in bulk long-read data. As a result, we identified multiple mosaic SVs in brain tissue from a patient with multiple system atrophy. The identified SV showed a remarkable diversity within the cingulate cortex, impacting both genes involved in neuron function and repetitive elements.
Collapse
Affiliation(s)
- Moritz Smolka
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
| | - Luis F Paulin
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
| | | | - Dominic W Horner
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Queen Square Institute of Neurology, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sairam Behera
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA
| | - Ester Kalef-Ezra
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Queen Square Institute of Neurology, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Mira Gandhi
- Pacific Northwest Research Institute (PNRI), Seattle, WA, USA
| | - Karl Hong
- Bionano Genomics, San Diego, CA, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Pacific Northwest Research Institute (PNRI), Seattle, WA, USA
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, Royal Free Campus, Queen Square Institute of Neurology, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
| |
Collapse
|
9
|
Wambach JA, Wegner DJ, Kitzmiller J, White FV, Heins HB, Yang P, Paul AJ, Granadillo JL, Eghtesady P, Kuklinski C, Turner T, Fairman K, Stone K, Wilson T, Breman A, Smith J, Schroeder MC, Neidich JA, Whitsett JA, Cole FS. Homozygous, Intragenic Tandem Duplication of SFTPB Causes Neonatal Respiratory Failure. Am J Respir Cell Mol Biol 2024; 70:78-80. [PMID: 38156804 PMCID: PMC10768837 DOI: 10.1165/rcmb.2023-0156le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024] Open
Affiliation(s)
| | | | | | | | | | - Ping Yang
- Washington University School of MedicineSt. Louis, Missouri
| | | | | | | | | | - Tiffany Turner
- Indiana University School of MedicineIndianapolis, Indiana
| | - Korre Fairman
- Indiana University School of MedicineIndianapolis, Indiana
| | - Kristyne Stone
- Indiana University School of MedicineIndianapolis, Indiana
| | | | - Amy Breman
- Indiana University School of MedicineIndianapolis, Indiana
| | | | | | | | | | | |
Collapse
|
10
|
Zhan L, Jin T, Zhou J, Xu W, Chen Y, Mezzenga R. Fast Probing Amyloid Polymorphism via Nanopore Translocation. NANO LETTERS 2023; 23:9912-9919. [PMID: 37856435 DOI: 10.1021/acs.nanolett.3c02860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Neurodegenerative diseases are characterized by the presence of cross-β-sheet amyloid fibrils and a rich mesoscopic polymorphism, requiring noninvasive detection with high fidelity. Here, we introduce a methodology that can probe via a sensitive synthetic nanopore the complex polymorphism of amyloid fibrils by an automated and fast screening protocol. Statistically analyzing the translocation events on two model amyloid systems derived from β-lactoglobulin and lysozyme allows extracting the cross-sectional configuration of hydrated amyloid fibrils from current block amplitude and correlating dwell time with fibril length. These findings are consistent with the amyloid polymorphs observed in solution by atomic force microscopy. Furthermore, the ionic current signal of a single translocation event can reveal abnormally aggregated conformations of amyloid fibrils without potential artifacts associated with microscopy methods. This study introduces an effective approach to physically discriminating and separating amyloid and may serve in the rapid diagnosis of early aggregating pathological amyloidosis.
Collapse
Affiliation(s)
- Lijian Zhan
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Tonghui Jin
- Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Jiangtao Zhou
- Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Wei Xu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland
- Department of Materials, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| |
Collapse
|
11
|
Zeibich R, Kwan P, J. O’Brien T, Perucca P, Ge Z, Anderson A. Applications for Deep Learning in Epilepsy Genetic Research. Int J Mol Sci 2023; 24:14645. [PMID: 37834093 PMCID: PMC10572791 DOI: 10.3390/ijms241914645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Epilepsy is a group of brain disorders characterised by an enduring predisposition to generate unprovoked seizures. Fuelled by advances in sequencing technologies and computational approaches, more than 900 genes have now been implicated in epilepsy. The development and optimisation of tools and methods for analysing the vast quantity of genomic data is a rapidly evolving area of research. Deep learning (DL) is a subset of machine learning (ML) that brings opportunity for novel investigative strategies that can be harnessed to gain new insights into the genomic risk of people with epilepsy. DL is being harnessed to address limitations in accuracy of long-read sequencing technologies, which improve on short-read methods. Tools that predict the functional consequence of genetic variation can represent breaking ground in addressing critical knowledge gaps, while methods that integrate independent but complimentary data enhance the predictive power of genetic data. We provide an overview of these DL tools and discuss how they may be applied to the analysis of genetic data for epilepsy research.
Collapse
Affiliation(s)
- Robert Zeibich
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia; (R.Z.); (P.K.); (T.J.O.); (P.P.)
| | - Patrick Kwan
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia; (R.Z.); (P.K.); (T.J.O.); (P.P.)
- Department of Neurology, Alfred Health, Melbourne, VIC 3004, Australia
- Department of Neurology, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Terence J. O’Brien
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia; (R.Z.); (P.K.); (T.J.O.); (P.P.)
- Department of Neurology, Alfred Health, Melbourne, VIC 3004, Australia
- Department of Neurology, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Piero Perucca
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia; (R.Z.); (P.K.); (T.J.O.); (P.P.)
- Department of Neurology, Alfred Health, Melbourne, VIC 3004, Australia
- Department of Neurology, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
- Epilepsy Research Centre, Department of Medicine, Austin Health, The University of Melbourne, Melbourne, VIC 3084, Australia
- Bladin-Berkovic Comprehensive Epilepsy Program, Department of Neurology, Austin Health, The University of Melbourne, Melbourne, VIC 3084, Australia
| | - Zongyuan Ge
- Faculty of Engineering, Monash University, Melbourne, VIC 3800, Australia;
- Monash-Airdoc Research, Monash University, Melbourne, VIC 3800, Australia
| | - Alison Anderson
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia; (R.Z.); (P.K.); (T.J.O.); (P.P.)
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
| |
Collapse
|
12
|
Kolesnikov A, Cook D, Nattestad M, McNulty B, Gorzynski J, Goenka S, Ashley EA, Jain M, Miga KH, Paten B, Chang PC, Carroll A, Shafin K. Local read haplotagging enables accurate long-read small variant calling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.07.556731. [PMID: 37745389 PMCID: PMC10515762 DOI: 10.1101/2023.09.07.556731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving third-generation sequencing platforms like Pacific Biosciences (PacBio) and Oxford nanopore technologies (ONT) are introducing newer platforms and data types. It has been demonstrated that variant calling methods based on deep neural networks can use local haplotyping information with long-reads to improve the genotyping accuracy. However, using local haplotype information creates an overhead as variant calling needs to be performed multiple times which ultimately makes it difficult to extend to new data types and platforms as they get introduced. In this work, we have developed a local haplotype approximate method that enables state-of-the-art variant calling performance with multiple sequencing platforms including PacBio Revio system, ONT R10.4 simplex and duplex data. This addition of local haplotype approximation makes DeepVariant a universal variant calling solution for long-read sequencing platforms.
Collapse
Affiliation(s)
| | - Daniel Cook
- Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA
| | | | - Brandy McNulty
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, USA
| | | | | | | | - Miten Jain
- Northeastern university, Boston, MA, USA
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, USA
| | | | | | | |
Collapse
|
13
|
Ahmadi E, Sadeghi A, Chakraborty S. Slip-Coupled Electroosmosis and Electrophoresis Dictate DNA Translocation Speed in Solid-State Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:12292-12301. [PMID: 37603825 DOI: 10.1021/acs.langmuir.3c01230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Controlling the DNA translocation speed is critical in nanopore sequencing, but remains rather challenging in practice, as attributable to a complex coupling between nanoscale fluidics and electrically mediated migration of DNA in a dynamically evolving manner. One important factor influencing the translocation speed is the DNA-liquid slippage stemming from the hydrophobic nature of the oligonucleotide, an aspect that has been widely ignored in the reported literature. In an effort to circumvent this conceptual deficit, here we first develop an analytical model to bring out the slip-mediated coupling between the electroosmosis and DNA-electrophoresis in a solid-state nanopore at low surface charge limits, ignoring the end effects. Subsequently, we compare these results with the numerical simulation data on electrokinetically modulated DNA translocation in such a nanopore, albeit of finite length with due accommodation of the end effects, connecting two end reservoirs by deploying a fully coupled Poisson-Nernst-Plank-Stokes flow model. Both the numerical and analytical results indicate that the DNA translocation speed is a linearly increasing function of the slip length, with more than four-fold increase being observed for a slip length as minimal as 0.5 nm as compared to the no-slip scenario. Considering specific strategies on demand for arresting high translocation speeds for accurate DNA sequencing, the above results establish a theoretical proposition for the same, premised on an analytical expression of the DNA-hydrophobicity modulated enhancement in the translocation speed for designing a nanopore-based sequencing platform─a paradigm that remained to be underemphasized thus far.
Collapse
Affiliation(s)
- Elham Ahmadi
- Department of Mechanical Engineering, University of Kurdistan, Sanandaj 66177-15175, Iran
| | - Arman Sadeghi
- Department of Mechanical Engineering, University of Kurdistan, Sanandaj 66177-15175, Iran
| | - Suman Chakraborty
- Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| |
Collapse
|
14
|
van Dijk EL, Naquin D, Gorrichon K, Jaszczyszyn Y, Ouazahrou R, Thermes C, Hernandez C. Genomics in the long-read sequencing era. Trends Genet 2023; 39:649-671. [PMID: 37230864 DOI: 10.1016/j.tig.2023.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
Long-read sequencing (LRS) technologies have provided extremely powerful tools to explore genomes. While in the early years these methods suffered technical limitations, they have recently made significant progress in terms of read length, throughput, and accuracy and bioinformatics tools have strongly improved. Here, we aim to review the current status of LRS technologies, the development of novel methods, and the impact on genomics research. We will explore the most impactful recent findings made possible by these technologies focusing on high-resolution sequencing of genomes and transcriptomes and the direct detection of DNA and RNA modifications. We will also discuss how LRS methods promise a more comprehensive understanding of human genetic variation, transcriptomics, and epigenetics for the coming years.
Collapse
Affiliation(s)
- Erwin L van Dijk
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Delphine Naquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Kévin Gorrichon
- National Center of Human Genomics Research (CNRGH), 91000 Évry-Courcouronnes, France
| | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Rania Ouazahrou
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Claude Thermes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Céline Hernandez
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| |
Collapse
|
15
|
Wang H, Fu T, Du Y, Gao W, Huang K, Liu Z, Chandak P, Liu S, Van Katwyk P, Deac A, Anandkumar A, Bergen K, Gomes CP, Ho S, Kohli P, Lasenby J, Leskovec J, Liu TY, Manrai A, Marks D, Ramsundar B, Song L, Sun J, Tang J, Veličković P, Welling M, Zhang L, Coley CW, Bengio Y, Zitnik M. Scientific discovery in the age of artificial intelligence. Nature 2023; 620:47-60. [PMID: 37532811 DOI: 10.1038/s41586-023-06221-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/16/2023] [Indexed: 08/04/2023]
Abstract
Artificial intelligence (AI) is being increasingly integrated into scientific discovery to augment and accelerate research, helping scientists to generate hypotheses, design experiments, collect and interpret large datasets, and gain insights that might not have been possible using traditional scientific methods alone. Here we examine breakthroughs over the past decade that include self-supervised learning, which allows models to be trained on vast amounts of unlabelled data, and geometric deep learning, which leverages knowledge about the structure of scientific data to enhance model accuracy and efficiency. Generative AI methods can create designs, such as small-molecule drugs and proteins, by analysing diverse data modalities, including images and sequences. We discuss how these methods can help scientists throughout the scientific process and the central issues that remain despite such advances. Both developers and users of AI toolsneed a better understanding of when such approaches need improvement, and challenges posed by poor data quality and stewardship remain. These issues cut across scientific disciplines and require developing foundational algorithmic approaches that can contribute to scientific understanding or acquire it autonomously, making them critical areas of focus for AI innovation.
Collapse
Affiliation(s)
- Hanchen Wang
- Department of Engineering, University of Cambridge, Cambridge, UK
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
- Department of Research and Early Development, Genentech Inc, South San Francisco, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Tianfan Fu
- Department of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Yuanqi Du
- Department of Computer Science, Cornell University, Ithaca, NY, USA
| | - Wenhao Gao
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kexin Huang
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Ziming Liu
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Payal Chandak
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA
| | - Shengchao Liu
- Mila - Quebec AI Institute, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Peter Van Katwyk
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, USA
- Data Science Institute, Brown University, Providence, RI, USA
| | - Andreea Deac
- Mila - Quebec AI Institute, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Anima Anandkumar
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
- NVIDIA, Santa Clara, CA, USA
| | - Karianne Bergen
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, USA
- Data Science Institute, Brown University, Providence, RI, USA
| | - Carla P Gomes
- Department of Computer Science, Cornell University, Ithaca, NY, USA
| | - Shirley Ho
- Center for Computational Astrophysics, Flatiron Institute, New York, NY, USA
- Department of Astrophysical Sciences, Princeton University, Princeton, NJ, USA
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Physics and Center for Data Science, New York University, New York, NY, USA
| | | | - Joan Lasenby
- Department of Engineering, University of Cambridge, Cambridge, UK
| | - Jure Leskovec
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | - Arjun Manrai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Debora Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Le Song
- BioMap, Beijing, China
- Mohamed bin Zayed University of Artificial Intelligence, Abu Dhabi, United Arab Emirates
| | - Jimeng Sun
- University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Jian Tang
- Mila - Quebec AI Institute, Montreal, Quebec, Canada
- HEC Montréal, Montreal, Quebec, Canada
- CIFAR AI Chair, Toronto, Ontario, Canada
| | - Petar Veličković
- Google DeepMind, London, UK
- Department of Computer Science and Technology, University of Cambridge, Cambridge, UK
| | - Max Welling
- University of Amsterdam, Amsterdam, Netherlands
- Microsoft Research Amsterdam, Amsterdam, Netherlands
| | - Linfeng Zhang
- DP Technology, Beijing, China
- AI for Science Institute, Beijing, China
| | - Connor W Coley
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yoshua Bengio
- Mila - Quebec AI Institute, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Marinka Zitnik
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Data Science Initiative, Cambridge, MA, USA.
- Kempner Institute for the Study of Natural and Artificial Intelligence, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
16
|
Vears DF, Savulescu J, Christodoulou J, Wall M, Newson AJ. Are We Ready for Whole Population Genomic Sequencing of Asymptomatic Newborns? Pharmgenomics Pers Med 2023; 16:681-691. [PMID: 37415831 PMCID: PMC10321326 DOI: 10.2147/pgpm.s376083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023] Open
Abstract
The introduction of genomic sequencing technologies into routine newborn screening programs in some form is not only inevitable but also already occurring in some settings. The question is therefore not "if" but "when and how" genomic newborn screening (GNBS) should be implemented. In April 2022, the Centre for Ethics of Paediatric Genomics held a one-day symposium exploring ethical issues relating to the use of genomic sequencing in a range of clinical settings. This review article synthesises the panel discussion and presents both the potential benefits of wide-scale implementation of genomic newborn screening, as well as its practical and ethical issues, including obtaining appropriate consent, and health system implications. A more in-depth understanding of the barriers associated with implementing genomic newborn screening is critical to the success of GNBS programs, both from a practical perspective and also in order to maintain public trust in an important public health initiative.
Collapse
Affiliation(s)
- Danya F Vears
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, Victoria, Australia
- University of Melbourne, Melbourne, Victoria, 3052, Australia
| | - Julian Savulescu
- Chen Su Lan Centennial Professor in Medical Ethics, Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Visiting Professorial Fellow in Biomedical Ethics, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Distinguished Visiting Professor in Law, Melbourne University, Carlton, Victoria, Australia
- Oxford Uehiro Centre for Practical Ethics, University of Oxford, Oxford, UK
| | - John Christodoulou
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, Victoria, Australia
- University of Melbourne, Melbourne, Victoria, 3052, Australia
| | - Meaghan Wall
- Victorian Clinical Genetics Service, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Ainsley J Newson
- Faculty of Medicine & Health, Sydney School of Public Health, Sydney Health Ethics, The University of Sydney, Sydney, New South Wales, Australia
| |
Collapse
|
17
|
Lunke S, Bouffler SE, Patel CV, Sandaradura SA, Wilson M, Pinner J, Hunter MF, Barnett CP, Wallis M, Kamien B, Tan TY, Freckmann ML, Chong B, Phelan D, Francis D, Kassahn KS, Ha T, Gao S, Arts P, Jackson MR, Scott HS, Eggers S, Rowley S, Boggs K, Rakonjac A, Brett GR, de Silva MG, Springer A, Ward M, Stallard K, Simons C, Conway T, Halman A, Van Bergen NJ, Sikora T, Semcesen LN, Stroud DA, Compton AG, Thorburn DR, Bell KM, Sadedin S, North KN, Christodoulou J, Stark Z. Integrated multi-omics for rapid rare disease diagnosis on a national scale. Nat Med 2023:10.1038/s41591-023-02401-9. [PMID: 37291213 PMCID: PMC10353936 DOI: 10.1038/s41591-023-02401-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/12/2023] [Indexed: 06/10/2023]
Abstract
Critically ill infants and children with rare diseases need equitable access to rapid and accurate diagnosis to direct clinical management. Over 2 years, the Acute Care Genomics program provided whole-genome sequencing to 290 families whose critically ill infants and children were admitted to hospitals throughout Australia with suspected genetic conditions. The average time to result was 2.9 d and diagnostic yield was 47%. We performed additional bioinformatic analyses and transcriptome sequencing in all patients who remained undiagnosed. Long-read sequencing and functional assays, ranging from clinically accredited enzyme analysis to bespoke quantitative proteomics, were deployed in selected cases. This resulted in an additional 19 diagnoses and an overall diagnostic yield of 54%. Diagnostic variants ranged from structural chromosomal abnormalities through to an intronic retrotransposon, disrupting splicing. Critical care management changed in 120 diagnosed patients (77%). This included major impacts, such as informing precision treatments, surgical and transplant decisions and palliation, in 94 patients (60%). Our results provide preliminary evidence of the clinical utility of integrating multi-omic approaches into mainstream diagnostic practice to fully realize the potential of rare disease genomic testing in a timely manner.
Collapse
Affiliation(s)
- Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
| | | | - Chirag V Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Sarah A Sandaradura
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Meredith Wilson
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Jason Pinner
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
- Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Melbourne, Victoria, Australia
- Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Christopher P Barnett
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, South Australia, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Mathew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Hobart, Tasmania, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Benjamin Kamien
- Genetic Services of Western Australia, Perth, Western Australia, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Mary-Louise Freckmann
- Department of Clinical Genetics, The Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Dean Phelan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Karin S Kassahn
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Thuong Ha
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Song Gao
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Peer Arts
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Matilda R Jackson
- Australian Genomics, Melbourne, Victoria, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Hamish S Scott
- Australian Genomics, Melbourne, Victoria, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Stefanie Eggers
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Simone Rowley
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Kirsten Boggs
- Australian Genomics, Melbourne, Victoria, Australia
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
| | - Ana Rakonjac
- Australian Genomics, Melbourne, Victoria, Australia
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
| | - Gemma R Brett
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Michelle G de Silva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Amanda Springer
- Monash Genetics, Monash Health, Melbourne, Victoria, Australia
- Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Michelle Ward
- Genetic Services of Western Australia, Perth, Western Australia, Australia
| | - Kirsty Stallard
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Cas Simons
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Thomas Conway
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Andreas Halman
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Nicole J Van Bergen
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Tim Sikora
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Liana N Semcesen
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - David A Stroud
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Alison G Compton
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David R Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Katrina M Bell
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Simon Sadedin
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Kathryn N North
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - John Christodoulou
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia.
- Australian Genomics, Melbourne, Victoria, Australia.
| |
Collapse
|
18
|
Șoldănescu I, Lobiuc A, Covașă M, Dimian M. Detection of Biological Molecules Using Nanopore Sensing Techniques. Biomedicines 2023; 11:1625. [PMID: 37371721 PMCID: PMC10295350 DOI: 10.3390/biomedicines11061625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Modern biomedical sensing techniques have significantly increased in precision and accuracy due to new technologies that enable speed and that can be tailored to be highly specific for markers of a particular disease. Diagnosing early-stage conditions is paramount to treating serious diseases. Usually, in the early stages of the disease, the number of specific biomarkers is very low and sometimes difficult to detect using classical diagnostic methods. Among detection methods, biosensors are currently attracting significant interest in medicine, for advantages such as easy operation, speed, and portability, with additional benefits of low costs and repeated reliable results. Single-molecule sensors such as nanopores that can detect biomolecules at low concentrations have the potential to become clinically relevant. As such, several applications have been introduced in this field for the detection of blood markers, nucleic acids, or proteins. The use of nanopores has yet to reach maturity for standardization as diagnostic techniques, however, they promise enormous potential, as progress is made into stabilizing nanopore structures, enhancing chemistries, and improving data collection and bioinformatic analysis. This review offers a new perspective on current biomolecule sensing techniques, based on various types of nanopores, challenges, and approaches toward implementation in clinical settings.
Collapse
Affiliation(s)
- Iuliana Șoldănescu
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Stefan cel Mare University of Suceava, 720229 Suceava, Romania; (I.Ș.); (M.D.)
| | - Andrei Lobiuc
- Department of Biomedical Sciences, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
| | - Mihai Covașă
- Department of Biomedical Sciences, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
| | - Mihai Dimian
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Stefan cel Mare University of Suceava, 720229 Suceava, Romania; (I.Ș.); (M.D.)
- Department of Computer, Electronics and Automation, Stefan cel Mare University of Suceava, 720229 Suceava, Romania
| |
Collapse
|
19
|
Samarakoon H, Ferguson JM, Gamaarachchi H, Deveson IW. Accelerated nanopore basecalling with SLOW5 data format. Bioinformatics 2023; 39:btad352. [PMID: 37252813 PMCID: PMC10261880 DOI: 10.1093/bioinformatics/btad352] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/12/2023] [Accepted: 05/29/2023] [Indexed: 06/01/2023] Open
Abstract
MOTIVATION Nanopore sequencing is emerging as a key pillar in the genomic technology landscape but computational constraints limiting its scalability remain to be overcome. The translation of raw current signal data into DNA or RNA sequence reads, known as 'basecalling', is a major friction in any nanopore sequencing workflow. Here, we exploit the advantages of the recently developed signal data format 'SLOW5' to streamline and accelerate nanopore basecalling on high-performance computing (HPC) and cloud environments. RESULTS SLOW5 permits highly efficient sequential data access, eliminating a potential analysis bottleneck. To take advantage of this, we introduce Buttery-eel, an open-source wrapper for Oxford Nanopore's Guppy basecaller that enables SLOW5 data access, resulting in performance improvements that are essential for scalable, affordable basecalling. AVAILABILITY AND IMPLEMENTATION Buttery-eel is available at https://github.com/Psy-Fer/buttery-eel.
Collapse
Affiliation(s)
- Hiruna Samarakoon
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Australia
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - James M Ferguson
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Australia
| | - Hasindu Gamaarachchi
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Australia
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ira W Deveson
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| |
Collapse
|
20
|
Samarakoon H, Ferguson JM, Jenner SP, Amos TG, Parameswaran S, Gamaarachchi H, Deveson IW. Flexible and efficient handling of nanopore sequencing signal data with slow5tools. Genome Biol 2023; 24:69. [PMID: 37024927 PMCID: PMC10080837 DOI: 10.1186/s13059-023-02910-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Nanopore sequencing is being rapidly adopted in genomics. We recently developed SLOW5, a new file format with advantages for storage and analysis of raw signal data from nanopore experiments. Here we introduce slow5tools, an intuitive toolkit for handling nanopore data in SLOW5 format. Slow5tools enables lossless data conversion and a range of tools for interacting with SLOW5 files. Slow5tools uses multi-threading, multi-processing, and other engineering strategies to achieve fast data conversion and manipulation, including live FAST5-to-SLOW5 conversion during sequencing. We provide examples and benchmarking experiments to illustrate slow5tools usage, and describe the engineering principles underpinning its performance.
Collapse
Affiliation(s)
- Hiruna Samarakoon
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW, Australia
| | - James M Ferguson
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia
| | - Sasha P Jenner
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia
| | - Timothy G Amos
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia
| | - Sri Parameswaran
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Hasindu Gamaarachchi
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia.
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia.
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW, Australia.
| | - Ira W Deveson
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW, Australia.
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia.
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
| |
Collapse
|
21
|
Berger B, Yu YW. Navigating bottlenecks and trade-offs in genomic data analysis. Nat Rev Genet 2023; 24:235-250. [PMID: 36476810 DOI: 10.1038/s41576-022-00551-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2022] [Indexed: 12/12/2022]
Abstract
Genome sequencing and analysis allow researchers to decode the functional information hidden in DNA sequences as well as to study cell to cell variation within a cell population. Traditionally, the primary bottleneck in genomic analysis pipelines has been the sequencing itself, which has been much more expensive than the computational analyses that follow. However, an important consequence of the continued drive to expand the throughput of sequencing platforms at lower cost is that often the analytical pipelines are struggling to keep up with the sheer amount of raw data produced. Computational cost and efficiency have thus become of ever increasing importance. Recent methodological advances, such as data sketching, accelerators and domain-specific libraries/languages, promise to address these modern computational challenges. However, despite being more efficient, these innovations come with a new set of trade-offs, both expected, such as accuracy versus memory and expense versus time, and more subtle, including the human expertise needed to use non-standard programming interfaces and set up complex infrastructure. In this Review, we discuss how to navigate these new methodological advances and their trade-offs.
Collapse
Affiliation(s)
- Bonnie Berger
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Yun William Yu
- Department of Computer and Mathematical Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Tri-Campus Department of Mathematics, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
22
|
Lang J, Yang J, Xu M. Editorial: Bioinformatics analysis tools for nanopore sequencing and applications. Front Bioeng Biotechnol 2023; 11:1189769. [PMID: 37057135 PMCID: PMC10086359 DOI: 10.3389/fbioe.2023.1189769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023] Open
Affiliation(s)
- Jidong Lang
- Department of Bioinformatics, Qitan Technology Co., Ltd., Beijing, China
- *Correspondence: Jidong Lang,
| | | | - Miao Xu
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, United States
| |
Collapse
|
23
|
Guan X, Li H, Chen L, Qi G, Jin Y. Glass Capillary-Based Nanopores for Single Molecule/Single Cell Detection. ACS Sens 2023; 8:427-442. [PMID: 36670058 DOI: 10.1021/acssensors.2c02102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A glass capillary-based nanopore (G-nanopore), due to its tapered tip, easy tunability in orifice size, and especially its flexible surface modifications that can be tailored to effectively capture and enhance the ionic current signal of single entities (single molecules, single cells, and single particles), offers a powerful and nanoconfined sensing platform for diverse biological measurements of single cells and single molecules. Compared with other artificial two-dimensional solid-state nanopores, its conical tip and high spatial and temporal resolution characteristics facilitate noninvasive single molecule and selected area (subcellular) single cell detections (e.g., DNA mutations, highly expressed proteins, and small molecule markers that reflect the change characteristics of the tumor), as a small G-nanopore (≤100 nm) does negligible damage to cell functions and cell membrane integrity when inserted through the cell membrane. In this brief review, we summarize the preparation of G-nanopores and discuss the advantages of them as solid-state sensing platforms for single molecule and single cell detection applications as well as for cancer diagnosis and treatment applications. We also describe the current bottlenecks that limit the widespread use of G-nanopores in clinical applications and provide an outlook on future developments. The brief review will provide the reader with a quick survey of this field and facilitate the rapid development of a G-nanopore sensing platform for future tumor diagnosis and personalized medicine based on single-molecule/single-cell bioassay.
Collapse
Affiliation(s)
- Xin Guan
- School of Basic Medical Sciences, Beihua University, Jilin 132013, Jilin, P. R. China
| | - Haijuan Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Limei Chen
- School of Basic Medical Sciences, Beihua University, Jilin 132013, Jilin, P. R. China
| | - Guohua Qi
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Yongdong Jin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China.,University of Science and Technology of China, Hefei 230026, Anhui, P. R. China
| |
Collapse
|
24
|
The Current State of Nanopore Sequencing. Methods Mol Biol 2023; 2632:3-14. [PMID: 36781717 DOI: 10.1007/978-1-0716-2996-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Nanopore sensing is a disruptive, revolutionary way in which to sequence nucleic acids, including both native DNA and RNA molecules. First commercialized with the MinIONTM sequencer from Oxford Nanopore TechnologiesTM in 2015, this review article looks at the current state of nanopore sequencing as of June 2022. Covering the unique characteristics of the technology and how it functions, we then go on to look at the ability of the platform to deliver sequencing at all scales-from personal to high-throughput devices-before looking at how the scientific community is applying the technology around the world to answer their biological questions.
Collapse
|
25
|
Kim DS, Wiel L, Ashley EA. Mind the Gap: The Complete Human Genome Unlocks Benefits for Clinical Genomics. Clin Chem 2023; 69:6-8. [PMID: 36112529 DOI: 10.1093/clinchem/hvac133] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 06/23/2022] [Indexed: 01/11/2023]
Affiliation(s)
- Daniel Seung Kim
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laurens Wiel
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Euan A Ashley
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
26
|
Jezkova J, Shaw S, Taverner NV, Williams HJ. Rapid genome sequencing for pediatrics. Hum Mutat 2022; 43:1507-1518. [PMID: 36086948 PMCID: PMC9826377 DOI: 10.1002/humu.24466] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/30/2022] [Accepted: 09/06/2022] [Indexed: 01/11/2023]
Abstract
The advancements made in next-generation sequencing (NGS) technology over the past two decades have transformed our understanding of genetic variation in humans and had a profound impact on our ability to diagnose patients with rare genetic diseases. In this review, we discuss the recently developed application of rapid NGS techniques, used to diagnose pediatric patients with suspected rare diseases who are critically ill. We highlight the challenges associated with performing such clinical diagnostics tests in terms of the laboratory infrastructure, bioinformatic analysis pipelines, and the ethical considerations that need to be addressed. We end by looking at what future developments in this field may look like and how they can be used to augment the genetic data to further improve the diagnostic rates for these high-priority patients.
Collapse
Affiliation(s)
- Jana Jezkova
- All Wales Medical Genomics Service, Cardiff and Vale NHS TrustHeath HospitalCardiffUK
| | - Sophie Shaw
- All Wales Medical Genomics Service, Cardiff and Vale NHS TrustHeath HospitalCardiffUK
| | - Nicola V. Taverner
- All Wales Medical Genomics Service, Cardiff and Vale NHS TrustHeath HospitalCardiffUK,Centre for Medical Education, School of MedicineCardiff UniversityHeath ParkCardiffUK
| | - Hywel J. Williams
- Division of Cancer and Genetics, Genetic and Genomic Medicine, School of MedicineCardiff UniversityHeath ParkCardiffUK
| |
Collapse
|
27
|
Conlin LK, Aref-Eshghi E, McEldrew DA, Luo M, Rajagopalan R. Long-read sequencing for molecular diagnostics in constitutional genetic disorders. Hum Mutat 2022; 43:1531-1544. [PMID: 36086952 PMCID: PMC9561063 DOI: 10.1002/humu.24465] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/11/2022]
Abstract
Long-read sequencing (LRS) has been around for more than a decade, but widespread adoption of the technology has been slow due to the perceived high error rates and high sequencing cost. This is changing due to the recent advancements to produce highly accurate sequences and the reducing costs. LRS promises significant improvement over short read sequencing in four major areas: (1) better detection of structural variation (2) better resolution of highly repetitive or nonunique regions (3) accurate long-range haplotype phasing and (4) the detection of base modifications natively from the sequencing data. Several successful applications of LRS have demonstrated its ability to resolve molecular diagnoses where short-read sequencing fails to identify a cause. However, the argument for increased diagnostic yield from LRS remains to be validated. Larger cohort studies may be required to establish the realistic boundaries of LRS's clinical utility and analytical validity, as well as the development of standards for clinical applications. We discuss the limitations of the current standard of care, and contrast with the applications and advantages of two major LRS platforms, PacBio and Oxford Nanopore, for molecular diagnostics of constitutional disorders, and present a critical argument about the potential of LRS in diagnostic settings.
Collapse
Affiliation(s)
- Laura K. Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Erfan Aref-Eshghi
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Deborah A. McEldrew
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Minjie Luo
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ramakrishnan Rajagopalan
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| |
Collapse
|
28
|
Sun Z, Liu X, Liu W, Li J, Yang J, Qiao F, Ma J, Sha J, Li J, Xu LQ. AutoNanopore: An Automated Adaptive and Robust Method to Locate Translocation Events in Solid-State Nanopore Current Traces. ACS OMEGA 2022; 7:37103-37111. [PMID: 36312336 PMCID: PMC9608407 DOI: 10.1021/acsomega.2c02927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Solid-state nanopore sequencing has shown impressive performances in several research scenarios but is still challenging, mainly due to the ultrafast speed of DNA translocation and significant noises embedded in raw signals. Hence, event detection, aiming to locate precisely these translocation events, is the fundamental step of data analysis. However, existing event detection methods use either a user-defined global threshold or an adaptive threshold determined by the data, assuming the baseline current to be stable over time. These disadvantages limit their applications in real-world application scenarios, especially considering that the results of different methods are often inconsistent. In this study, we develop an automated adaptive method called AutoNanopore, for fast and accurate event detection in current traces. The method consists of three consecutive steps: current trace segmentation, current amplitude outlier identification by straightforward statistical analyses, and event characterization. Then we propose ideas/metrics on how to quantitatively evaluate the performance of an event detection method, followed by comparing the performance of AutoNanopore against two state-of-the-art methods, OpenNanopore and EventPro. Finally, we examine if one method can detect the overlapping events detected by the other two, demonstrating that AutoNanopore has the highest coverage ratio. Moreover, AutoNanopore also performs well in detecting challenging events: e.g., those with significantly varying baselines.
Collapse
Affiliation(s)
- Zepeng Sun
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
| | - Xinlong Liu
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
| | - Wei Liu
- Jiangsu
Key Laboratory for Design and Manufacture of Micro-Nano Biomedical
Instruments, School of Mechanical Engineering, Southeast University, Nanjing210096, People’s Republic
of China
| | - Jiahui Li
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
| | - Jing Yang
- Key
Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing210096, People’s Republic of China
| | - Feng Qiao
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
| | - Jianjun Ma
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
| | - Jingjie Sha
- Jiangsu
Key Laboratory for Design and Manufacture of Micro-Nano Biomedical
Instruments, School of Mechanical Engineering, Southeast University, Nanjing210096, People’s Republic
of China
| | - Jian Li
- Key
Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing210096, People’s Republic of China
| | - Li-Qun Xu
- China
Mobile (Chengdu) Industrial Research Institute, Chengdu610000, People’s Republic of China
| |
Collapse
|
29
|
Keraite I, Becker P, Canevazzi D, Frias-López C, Dabad M, Tonda-Hernandez R, Paramonov I, Ingham MJ, Brun-Heath I, Leno J, Abulí A, Garcia-Arumí E, Heath SC, Gut M, Gut IG. A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome. Nat Commun 2022; 13:5902. [PMID: 36202811 PMCID: PMC9537161 DOI: 10.1038/s41467-022-33530-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
Methods to reconstruct the mitochondrial DNA (mtDNA) sequence using short-read sequencing come with an inherent bias due to amplification and mapping. They can fail to determine the phase of variants, to capture multiple deletions and to cover the mitochondrial genome evenly. Here we describe a method to target, multiplex and sequence at high coverage full-length human mitochondrial genomes as native single-molecules, utilizing the RNA-guided DNA endonuclease Cas9. Combining Cas9 induced breaks, that define the mtDNA beginning and end of the sequencing reads, as barcodes, we achieve high demultiplexing specificity and delineation of the full-length of the mtDNA, regardless of the structural variant pattern. The long-read sequencing data is analysed with a pipeline where our custom-developed software, baldur, efficiently detects single nucleotide heteroplasmy to below 1%, physically determines phase and can accurately disentangle complex deletions. Our workflow is a tool for studying mtDNA variation and will accelerate mitochondrial research. Accurate analysis of mitochondrial DNA is important for mitochondrial disease clinical research and diagnostics. Here, authors present a method using Cas9 cleavage, nanopore sequencing and a custom pipeline to identify pathogenic variants, deletions and accurately quantify heteroplasmy to below 1%.
Collapse
Affiliation(s)
- Ieva Keraite
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Philipp Becker
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Qiagen, Hilden, Germany
| | - Davide Canevazzi
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Cristina Frias-López
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marc Dabad
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Raúl Tonda-Hernandez
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ida Paramonov
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Matthew John Ingham
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona) - The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Joint IRB-BSC Program in Computational Biology, Barcelona, Spain
| | - Jordi Leno
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, VHIR, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Anna Abulí
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, VHIR, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Elena Garcia-Arumí
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Research Group on Neuromuscular and Mitochondrial Disorders, VHIR, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Simon Charles Heath
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain.
| | - Ivo Glynne Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain.
| |
Collapse
|
30
|
Lang J. NanoCoV19: An analytical pipeline for rapid detection of severe acute respiratory syndrome coronavirus 2. Front Genet 2022; 13:1008792. [PMID: 36186464 PMCID: PMC9520466 DOI: 10.3389/fgene.2022.1008792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/22/2022] [Indexed: 11/28/2022] Open
Abstract
Nanopore sequencing technology (NST) has become a rapid and cost-effective method for the diagnosis and epidemiological surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 2019 (COVID-19) pandemic. Compared with short-read sequencing platforms (e.g., Illumina’s), nanopore long-read sequencing platforms effectively shorten the time required to complete the detection process. However, due to the principles and data characteristics of NST, the accuracy of sequencing data has been reduced, thereby limiting monitoring and lineage analysis of SARS-CoV-2. In this study, we developed an analytical pipeline for SARS-CoV-2 rapid detection and lineage identification that integrates phylogenetic-tree and hotspot mutation analysis, which we have named NanoCoV19. This method not only can distinguish and trace the lineages contained in the alpha, beta, delta, gamma, lambda, and omicron variants of SARS-CoV-2 but is also rapid and efficient, completing overall analysis within 1 h. We hope that NanoCoV19 can be used as an auxiliary tool for rapid subtyping and lineage analysis of SARS-CoV-2 and, more importantly, that it can promote further applications of NST in public-health and -safety plans similar to those formulated to address the COVID-19 outbreak.
Collapse
|
31
|
Lunke S, Stark Z. Can Rapid Nanopore Sequencing Bring Genomic Testing to the Bedside? Clin Chem 2022; 68:1484-1485. [PMID: 35848937 DOI: 10.1093/clinchem/hvac111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022]
Affiliation(s)
- Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,University of Melbourne, Melbourne, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,University of Melbourne, Melbourne, Australia.,Australian Genomics, Melbourne, Australia
| |
Collapse
|
32
|
Kingsmore SF. Dispatches from Biotech beginning BeginNGS: Rapid newborn genome sequencing to end the diagnostic and therapeutic odyssey. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:243-256. [PMID: 36218021 PMCID: PMC9588745 DOI: 10.1002/ajmg.c.32005] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 01/11/2023]
Abstract
In this Dispatch from Biotech, we briefly review the urgent need for extensive expansion of newborn screening (NBS) by genomic sequencing, and the reasons why early attempts had limited success. During the next decade transformative developments will continue in society and in the pharmaceutical, biotechnology, informatics, and medical sectors that enable prompt addition of genetic disorders to NBS by rapid whole genome sequencing (rWGS) upon introduction of new therapies that qualify them according to the Wilson and Jungner criteria (Wilson, J. M. G., & Jungner, G., World Health Organization. (1968). Principles and Practice of Screening for Disease. World Health Organization. Retrieved from https://apps.who.int/iris/handle/10665/37650). Herein we describe plans, progress, and clinical trial designs for BeginNGS (Newborn Genome Sequencing to end the diagnostic and therapeutic odyssey), a new international, pre-competitive, public-private consortium that proposes to implement a self-learning healthcare delivery system for screening all newborns for over 400 hundred genetic diseases, diagnostic confirmation, implementation of effective treatment, and acceleration of orphan drug development. We invite investigators and stakeholders worldwide to join the consortium in a prospective, multi-center, international trial of the clinical utility and cost effectiveness of BeginNGS.
Collapse
Affiliation(s)
- Stephen F. Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's HospitalSan DiegoCaliforniaUSA
| | | |
Collapse
|
33
|
Gorzynski JE, Goenka SD, Shafin K, Jensen TD, Fisk DG, Grove ME, Spiteri E, Pesout T, Monlong J, Bernstein JA, Ceresnak S, Chang PC, Christle JW, Chubb H, Dunn K, Garalde DR, Guillory J, Ruzhnikov MR, Wright C, Wusthoff CJ, Xiong K, Hollander SA, Berry GJ, Jain M, Sedlazeck FJ, Carroll A, Paten B, Ashley EA. Ultra-Rapid Nanopore Whole Genome Genetic Diagnosis of Dilated Cardiomyopathy in an Adolescent With Cardiogenic Shock. Circ Genom Precis Med 2022; 15:e003591. [DOI: 10.1161/circgen.121.003591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- John E. Gorzynski
- Stanford University, CA (J.E.G., S.D.G., T.D.J., E.S., J.A.B., S.C., J.W.C., H.C., M.R.Z.R., C.J.W., K.X., S.A.H., G.J.B., E.A.A.)
| | - Sneha D. Goenka
- Stanford University, CA (J.E.G., S.D.G., T.D.J., E.S., J.A.B., S.C., J.W.C., H.C., M.R.Z.R., C.J.W., K.X., S.A.H., G.J.B., E.A.A.)
| | - Kishwar Shafin
- University of California at Santa Cruz Genomics Institute, Santa Cruz, CA (K.S., T.P., J.M., M.J., B.P.)
| | - Tanner D. Jensen
- Stanford University, CA (J.E.G., S.D.G., T.D.J., E.S., J.A.B., S.C., J.W.C., H.C., M.R.Z.R., C.J.W., K.X., S.A.H., G.J.B., E.A.A.)
| | | | | | - Elizabeth Spiteri
- Stanford University, CA (J.E.G., S.D.G., T.D.J., E.S., J.A.B., S.C., J.W.C., H.C., M.R.Z.R., C.J.W., K.X., S.A.H., G.J.B., E.A.A.)
| | - Trevor Pesout
- University of California at Santa Cruz Genomics Institute, Santa Cruz, CA (K.S., T.P., J.M., M.J., B.P.)
| | - Jean Monlong
- University of California at Santa Cruz Genomics Institute, Santa Cruz, CA (K.S., T.P., J.M., M.J., B.P.)
| | - Jonathan A. Bernstein
- Stanford University, CA (J.E.G., S.D.G., T.D.J., E.S., J.A.B., S.C., J.W.C., H.C., M.R.Z.R., C.J.W., K.X., S.A.H., G.J.B., E.A.A.)
| | - Scott Ceresnak
- Stanford University, CA (J.E.G., S.D.G., T.D.J., E.S., J.A.B., S.C., J.W.C., H.C., M.R.Z.R., C.J.W., K.X., S.A.H., G.J.B., E.A.A.)
| | | | - Jeffrey W. Christle
- Stanford University, CA (J.E.G., S.D.G., T.D.J., E.S., J.A.B., S.C., J.W.C., H.C., M.R.Z.R., C.J.W., K.X., S.A.H., G.J.B., E.A.A.)
| | - Henry Chubb
- Stanford University, CA (J.E.G., S.D.G., T.D.J., E.S., J.A.B., S.C., J.W.C., H.C., M.R.Z.R., C.J.W., K.X., S.A.H., G.J.B., E.A.A.)
| | - Kyla Dunn
- Stanford Children’s Health, Palo Alto, CA (K.D.)
| | | | - Joseph Guillory
- Oxford Nanopore Technologies, United Kingdom (D.R.G., J.G., C.W.)
| | - Maura R.Z. Ruzhnikov
- Stanford University, CA (J.E.G., S.D.G., T.D.J., E.S., J.A.B., S.C., J.W.C., H.C., M.R.Z.R., C.J.W., K.X., S.A.H., G.J.B., E.A.A.)
| | - Chris Wright
- Oxford Nanopore Technologies, United Kingdom (D.R.G., J.G., C.W.)
| | - Courtney J. Wusthoff
- Stanford University, CA (J.E.G., S.D.G., T.D.J., E.S., J.A.B., S.C., J.W.C., H.C., M.R.Z.R., C.J.W., K.X., S.A.H., G.J.B., E.A.A.)
| | - Katherine Xiong
- Stanford University, CA (J.E.G., S.D.G., T.D.J., E.S., J.A.B., S.C., J.W.C., H.C., M.R.Z.R., C.J.W., K.X., S.A.H., G.J.B., E.A.A.)
| | - Seth A. Hollander
- Stanford University, CA (J.E.G., S.D.G., T.D.J., E.S., J.A.B., S.C., J.W.C., H.C., M.R.Z.R., C.J.W., K.X., S.A.H., G.J.B., E.A.A.)
| | - Gerald J. Berry
- Stanford University, CA (J.E.G., S.D.G., T.D.J., E.S., J.A.B., S.C., J.W.C., H.C., M.R.Z.R., C.J.W., K.X., S.A.H., G.J.B., E.A.A.)
| | - Miten Jain
- University of California at Santa Cruz Genomics Institute, Santa Cruz, CA (K.S., T.P., J.M., M.J., B.P.)
| | | | | | - Benedict Paten
- University of California at Santa Cruz Genomics Institute, Santa Cruz, CA (K.S., T.P., J.M., M.J., B.P.)
| | - Euan A. Ashley
- Stanford University, CA (J.E.G., S.D.G., T.D.J., E.S., J.A.B., S.C., J.W.C., H.C., M.R.Z.R., C.J.W., K.X., S.A.H., G.J.B., E.A.A.)
| |
Collapse
|