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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.
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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
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2
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Su C, Chandradoss KR, Malachowski T, Boya R, Ryu HS, Brennand KJ, Phillips-Cremins JE. MASTR-seq: Multiplexed Analysis of Short Tandem Repeats with sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591790. [PMID: 38746155 PMCID: PMC11092654 DOI: 10.1101/2024.04.29.591790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
More than 60 human disorders have been linked to unstable expansion of short tandem repeat (STR) tracts. STR length and the extent of DNA methylation is linked to disease pathology and can be mosaic in a cell type-specific manner in several repeat expansion disorders. Mosaic phenomenon have been difficult to study to date due to technical bias intrinsic to repeat sequences and the need for multi-modal measurements at single-allele resolution. Nanopore long-read sequencing accurately measures STR length and DNA methylation in the same single molecule but is cost prohibitive for studies assessing a target locus across multiple experimental conditions or patient samples. Here, we describe MASTR-seq, M ultiplexed A nalysis of S hort T andem R epeats, for cost-effective, high-throughput, accurate, multi-modal measurements of DNA methylation and STR genotype at single-allele resolution. MASTR-seq couples long-read sequencing, Cas9-mediated target enrichment, and PCR-free multiplexed barcoding to achieve a >ten-fold increase in on-target read mapping for 8-12 pooled samples in a single MinION flow cell. We provide a detailed experimental protocol and computational tools and present evidence that MASTR-seq quantifies tract length and DNA methylation status for CGG and CAG STR loci in normal-length and mutation-length human cell lines. The MASTR-seq protocol takes approximately eight days for experiments and one additional day for data processing and analyses. Key points We provide a protocol for MASTR-seq: M ultiplexed A nalysis of S hort T andem R epeats using Cas9-mediated target enrichment and PCR-free, multiplexed nanopore sequencing. MASTR-seq achieves a >10-fold increase in on-target read proportion for highly repetitive, technically inaccessible regions of the genome relevant for human health and disease.MASTR-seq allows for high-throughput, efficient, accurate, and cost-effective measurement of STR length and DNA methylation in the same single allele for up to 8-12 samples in parallel in one Nanopore MinION flow cell.
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3
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Hook PW, Timp W. Beyond assembly: the increasing flexibility of single-molecule sequencing technology. Nat Rev Genet 2023; 24:627-641. [PMID: 37161088 PMCID: PMC10169143 DOI: 10.1038/s41576-023-00600-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2023] [Indexed: 05/11/2023]
Abstract
The maturation of high-throughput short-read sequencing technology over the past two decades has shaped the way genomes are studied. Recently, single-molecule, long-read sequencing has emerged as an essential tool in deciphering genome structure and function, including filling gaps in the human reference genome, measuring the epigenome and characterizing splicing variants in the transcriptome. With recent technological developments, these single-molecule technologies have moved beyond genome assembly and are being used in a variety of ways, including to selectively sequence specific loci with long reads, measure chromatin state and protein-DNA binding in order to investigate the dynamics of gene regulation, and rapidly determine copy number variation. These increasingly flexible uses of single-molecule technologies highlight a young and fast-moving part of the field that is leading to a more accessible era of nucleic acid sequencing.
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Affiliation(s)
- Paul W Hook
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Winston Timp
- Department of Biomedical Engineering, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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4
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Chapman R, Jones L, D'Angelo A, Suliman A, Anwar M, Bagby S. Nanopore-Based Metagenomic Sequencing in Respiratory Tract Infection: A Developing Diagnostic Platform. Lung 2023; 201:171-179. [PMID: 37009923 PMCID: PMC10067523 DOI: 10.1007/s00408-023-00612-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/14/2023] [Indexed: 04/04/2023]
Abstract
Respiratory tract infection (RTI) remains a significant cause of morbidity and mortality across the globe. The optimal management of RTI relies upon timely pathogen identification via evaluation of respiratory samples, a process which utilises traditional culture-based methods to identify offending microorganisms. This process can be slow and often prolongs the use of broad-spectrum antimicrobial therapy, whilst also delaying the introduction of targeted therapy as a result. Nanopore sequencing (NPS) of respiratory samples has recently emerged as a potential diagnostic tool in RTI. NPS can identify pathogens and antimicrobial resistance profiles with greater speed and efficiency than traditional sputum culture-based methods. Increased speed to pathogen identification can improve antimicrobial stewardship by reducing the use of broad-spectrum antibiotic therapy, as well as improving overall clinical outcomes. This new technology is becoming more affordable and accessible, with some NPS platforms requiring minimal sample preparation and laboratory infrastructure. However, questions regarding clinical utility and how best to implement NPS technology within RTI diagnostic pathways remain unanswered. In this review, we introduce NPS as a technology and as a diagnostic tool in RTI in various settings, before discussing the advantages and limitations of NPS, and finally what the future might hold for NPS platforms in RTI diagnostics.
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Affiliation(s)
- Robert Chapman
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK.
| | - Luke Jones
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Alberto D'Angelo
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Ahmed Suliman
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK
| | - Muhammad Anwar
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK
| | - Stefan Bagby
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
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5
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Malekshoar M, Azimi SA, Kaki A, Mousazadeh L, Motaei J, Vatankhah M. CRISPR-Cas9 Targeted Enrichment and Next-Generation Sequencing for Mutation Detection. J Mol Diagn 2023; 25:249-262. [PMID: 36841425 DOI: 10.1016/j.jmoldx.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/08/2023] [Accepted: 01/27/2023] [Indexed: 02/27/2023] Open
Abstract
Despite the rapid application of next-generation sequencing (NGS) technologies, target sequencing in regions of the genome is often required to diagnose many genetic diseases. Target enrichment can be an effective factor in reducing the cost of sequencing and the duration of sequencing. Recently, several clustered system regularly interspaced short palindromic repeats (CRISPR)-based methods (amplification-free sequencing) have been developed to target enrichment in combination with one of the NGS platforms. CRISPR-based target enrichment strategies act as an auxiliary tool to improve NGS analytical performance, thereby indirectly facilitating nucleic acid detection. The direct DNA cleavage approach by CRISPR-Cas at genome-specific sites enhances the possibility of separating native large fragments from disease-related genomic regions. The CRISPR-Cas can isolate the target region without any amplification; subsequently, long-read sequencing technologies were also implemented. These methods, as promising tools, have the ability to assess genetic and epigenetic composition for clinical application and treatment responses in cancer precision medicine. By modifying CRISPR-based enrichment protocols, it was possible to identify different types of mutations, including structural variants, short tandem repeats, fusion genes, and mobile elements. The Cas9 can specifically eliminate wild-type sequences, and it also enables the enrichment and detection of small amounts of tumor DNA fragments among the highly heterogeneous fragments of wild-type DNA.
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Affiliation(s)
- Mehrdad Malekshoar
- Anesthesiology, Critical Care and Pain Management Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Sajad Ataei Azimi
- Department of Hematology-Oncology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arastoo Kaki
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Leila Mousazadeh
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jamshid Motaei
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Majid Vatankhah
- Anesthesiology, Critical Care and Pain Management Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
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Mighell TL, Nishida A, O'Connell BL, Miller CV, Grindstaff S, Thornton CA, Adey AC, Doherty D, O'Roak BJ. Cas12a-Capture: A Novel, Low-Cost, and Scalable Method for Targeted Sequencing. CRISPR J 2022; 5:548-557. [PMID: 35833801 PMCID: PMC9419982 DOI: 10.1089/crispr.2021.0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/25/2022] [Indexed: 11/12/2022] Open
Abstract
Targeted sequencing remains a valuable technique for clinical and research applications. However, many existing technologies suffer from pervasive guanine-cytosine (GC) sequence content bias, high input DNA requirements, and high cost for custom panels. We have developed Cas12a-Capture, a low-cost and highly scalable method for targeted sequencing. The method utilizes preprogrammed guide RNAs to direct CRISPR-Cas12a cleavage of double-stranded DNA in vitro and then takes advantage of the resulting four to five nucleotide overhangs for selective ligation with a custom sequencing adapter. Addition of a second sequencing adapter and enrichment for ligation products generates a targeted sequence library. We first performed a pilot experiment with 7176 guides targeting 3.5 Mb of DNA. Using these data, we modeled the sequence determinants of Cas12a-Capture efficiency, then designed an optimized set of 11,438 guides targeting 3.0 Mb. The optimized guide set achieves an average 64-fold enrichment of targeted regions with minimal GC bias. Cas12a-Capture variant calls had strong concordance with Illumina Platinum Genome calls, especially for single nucleotide variants, which could be improved by applying basic variant quality heuristics. We believe Cas12a-Capture has a wide variety of potential clinical and research applications and is amendable for selective enrichment for any double-stranded DNA template or genome.
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Affiliation(s)
- Taylor L. Mighell
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA; Portland, Oregon, USA
| | - Andrew Nishida
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA; Portland, Oregon, USA
| | - Brendan L. O'Connell
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA; Portland, Oregon, USA
| | - Caitlin V. Miller
- Department of Pediatrics, University of Washington, Seattle, Washington, USA; and Portland, Oregon, USA
| | - Sally Grindstaff
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA; Portland, Oregon, USA
| | - Casey A. Thornton
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA; Portland, Oregon, USA
| | - Andrew C. Adey
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA; Portland, Oregon, USA
- Knight Cardiovascular Institute, Portland, Oregon, USA
| | - Daniel Doherty
- Department of Pediatrics, University of Washington, Seattle, Washington, USA; and Portland, Oregon, USA
| | - Brian J. O'Roak
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA; Portland, Oregon, USA
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Lu W, Lan X, Zhang T, Sun H, Ma S, Xia Q. Precise Characterization of Bombyx mori Fibroin Heavy Chain Gene Using Cpf1-Based Enrichment and Oxford Nanopore Technologies. INSECTS 2021; 12:insects12090832. [PMID: 34564273 PMCID: PMC8467315 DOI: 10.3390/insects12090832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Bombyx mori (B. mori), an important economic insect, is famous for its silk. B. mori silk is mainly composed of silk fibroin coated with sericin. Among them, the silk fibroin heavy chain protein has the highest content and the largest molecular weight, which is encoded by the silk fibroin heavy chain (FibH) gene. At present, apart from the complete sequence of the FibH of the B. mori strain p50T, there are no other reports regarding this protein. This is mainly because the special structure formed by the GC-rich repetitive sequence in FibH hinders the amplification of polymerase and the application of Sanger sequencing. Here, the FibH sequence of Dazao, which has 99.98% similarity to that of p50T, was obtained by means of CEO. As far as we know, this is the first complete FibH sequence of the Chinese B. mori strain. Additionally, the methylated CG sites in the FibH repeat unit were identified. Abstract To study the evolution of gene function and a species, it is essential to characterize the tandem repetitive sequences distributed across the genome. Cas9-based enrichment combined with nanopore sequencing is an important technique for targeting repetitive sequences. Cpf1 has low molecular weight, low off-target efficiency, and the same editing efficiency as Cas9. There are numerous studies on enrichment sequencing using Cas9 combined with nanopore, while there are only a few studies on the enrichment sequencing of long and highly repetitive genes using Cpf1. We developed Cpf1-based enrichment combined with ONT sequencing (CEO) to characterize the B. mori FibH gene, which is composed of many repeat units with a long and GC-rich sequence up to 17 kb and is not easily amplified by means of a polymerase chain reaction (PCR). CEO has four steps: the dephosphorylation of genomic DNA, the Cpf1 targeted cleavage of FibH, adapter ligation, and ONT sequencing. Using CEO, we determined the fine structure of B. moriFibH, which is 16,845 bp long and includes 12 repetitive domains separated by amorphous regions. Except for the difference of three bases in the intron from the reference gene, the other sequences are identical. Surprisingly, many methylated CG sites were found and distributed unevenly on the FibH repeat unit. The CEO we established is an available means to depict highly repetitive genes, but also a supplement to the enrichment method based on Cas9.
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Affiliation(s)
- Wei Lu
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing 400715, China
| | - Xinhui Lan
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
| | - Tong Zhang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing 400715, China
| | - Hao Sun
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing 400715, China
| | - Sanyuan Ma
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing 400715, China
- Correspondence: (S.M.); (Q.X.)
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China; (W.L.); (X.L.); (T.Z.); (H.S.)
- Chongqing Key Laboratory of Sericulture Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing 400715, China
- Correspondence: (S.M.); (Q.X.)
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8
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Rehder C, Bean LJH, Bick D, Chao E, Chung W, Das S, O'Daniel J, Rehm H, Shashi V, Vincent LM. Next-generation sequencing for constitutional variants in the clinical laboratory, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1399-1415. [PMID: 33927380 DOI: 10.1038/s41436-021-01139-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technologies are now established in clinical laboratories as a primary testing modality in genomic medicine. These technologies have reduced the cost of large-scale sequencing by several orders of magnitude. It is now cost-effective to analyze an individual with disease-targeted gene panels, exome sequencing, or genome sequencing to assist in the diagnosis of a wide array of clinical scenarios. While clinical validation and use of NGS in many settings is established, there are continuing challenges as technologies and the associated informatics evolve. To assist clinical laboratories with the validation of NGS methods and platforms, the ongoing monitoring of NGS testing to ensure quality results, and the interpretation and reporting of variants found using these technologies, the American College of Medical Genetics and Genomics (ACMG) has developed the following technical standards.
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Affiliation(s)
| | - Lora J H Bean
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Elizabeth Chao
- Division of Genetics and Genomics, Department of Pediatrics, University of California, Irvine, CA, USA
| | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Soma Das
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Julianne O'Daniel
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Heidi Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University, Durham, NC, USA
| | - Lisa M Vincent
- Division of Pathology & Laboratory Medicine, Children's National Health System, Washington, DC, USA.,Departments of Pathology and Pediatrics, George Washington University, Washington, DC, USA
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9
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Wallace AD, Sasani TA, Swanier J, Gates BL, Greenland J, Pedersen BS, Varley KE, Quinlan AR. CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing. PLoS One 2021; 16:e0241253. [PMID: 33830997 PMCID: PMC8031414 DOI: 10.1371/journal.pone.0241253] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/19/2021] [Indexed: 11/29/2022] Open
Abstract
A substantial fraction of the human genome is difficult to interrogate with short-read DNA sequencing technologies due to paralogy, complex haplotype structures, or tandem repeats. Long-read sequencing technologies, such as Oxford Nanopore's MinION, enable direct measurement of complex loci without introducing many of the biases inherent to short-read methods, though they suffer from relatively lower throughput. This limitation has motivated recent efforts to develop amplification-free strategies to target and enrich loci of interest for subsequent sequencing with long reads. Here, we present CaBagE, a method for target enrichment that is efficient and useful for sequencing large, structurally complex targets. The CaBagE method leverages the stable binding of Cas9 to its DNA target to protect desired fragments from digestion with exonuclease. Enriched DNA fragments are then sequenced with Oxford Nanopore's MinION long-read sequencing technology. Enrichment with CaBagE resulted in a median of 116X coverage (range 39-416) of target loci when tested on five genomic targets ranging from 4-20kb in length using healthy donor DNA. Four cancer gene targets were enriched in a single reaction and multiplexed on a single MinION flow cell. We further demonstrate the utility of CaBagE in two ALS patients with C9orf72 short tandem repeat expansions to produce genotype estimates commensurate with genotypes derived from repeat-primed PCR for each individual. With CaBagE there is a physical enrichment of on-target DNA in a given sample prior to sequencing. This feature allows adaptability across sequencing platforms and potential use as an enrichment strategy for applications beyond sequencing. CaBagE is a rapid enrichment method that can illuminate regions of the 'hidden genome' underlying human disease.
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Affiliation(s)
- Amelia D. Wallace
- Department of Human Genetics, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Utah Center for Genetic Discovery, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Thomas A. Sasani
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Jordan Swanier
- Department of Human Genetics, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Brooke L. Gates
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
| | - Jeff Greenland
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
| | - Brent S. Pedersen
- Department of Human Genetics, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Utah Center for Genetic Discovery, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Katherine E. Varley
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
| | - Aaron R. Quinlan
- Department of Human Genetics, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Utah Center for Genetic Discovery, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Department of Biomedical Informatics, School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
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10
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Wang Z, Maluenda J, Giraut L, Vieille T, Lefevre A, Salthouse D, Radou G, Moulinas R, Astete S, D'Avezac P, Smith G, André C, Allemand JF, Bensimon D, Croquette V, Ouellet J, Hamilton G. Detection of genetic variation and base modifications at base-pair resolution on both DNA and RNA. Commun Biol 2021; 4:128. [PMID: 33514840 PMCID: PMC7846774 DOI: 10.1038/s42003-021-01648-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 12/28/2020] [Indexed: 11/14/2022] Open
Abstract
Accurate decoding of nucleic acid variation is critical to understand the complexity and regulation of genome function. Here we use a single-molecule magnetic tweezer (MT) platform to identify sequence variation and map a range of important epigenetic base modifications with high sensitivity, specificity, and precision in the same single molecules of DNA or RNA. We have also developed a highly specific amplification-free CRISPR-Cas enrichment strategy to isolate genomic regions from native DNA. We demonstrate enrichment of DNA from both E. coli and the FMR1 5'UTR coming from cells derived from a Fragile X carrier. From these kilobase-length enriched molecules we could characterize the differential levels of adenine and cytosine base modifications on E. coli, and the repeat expansion length and methylation status of FMR1. Together these results demonstrate that our platform can detect a variety of genetic, epigenetic, and base modification changes concomitantly within the same single molecules.
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Affiliation(s)
- Zhen Wang
- Depixus SAS, 3/5 Impasse Reille, 75014, Paris, France
| | | | | | | | | | | | - Gaël Radou
- Depixus SAS, 3/5 Impasse Reille, 75014, Paris, France
| | - Rémi Moulinas
- Depixus SAS, 3/5 Impasse Reille, 75014, Paris, France
| | - Sandra Astete
- Depixus SAS, 3/5 Impasse Reille, 75014, Paris, France
| | - Pol D'Avezac
- Depixus SAS, 3/5 Impasse Reille, 75014, Paris, France
| | - Geoff Smith
- Depixus SAS, 3/5 Impasse Reille, 75014, Paris, France
| | - Charles André
- Depixus SAS, 3/5 Impasse Reille, 75014, Paris, France
| | - Jean-François Allemand
- Laboratoire de physique de L'École normale supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, Paris, 75005, France
- IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005, Paris, France
| | - David Bensimon
- Laboratoire de physique de L'École normale supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, Paris, 75005, France
- IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005, Paris, France
- Department of Chemistry and Biochemistry, UCLA, 607 Charles E Young Drive East, Los Angeles, 90095, USA
| | - Vincent Croquette
- Laboratoire de physique de L'École normale supérieure de Paris, CNRS, ENS, Université PSL, Sorbonne Université, Université de Paris, Paris, 75005, France
- IBENS, Département de biologie, École normale supérieure, CNRS, INSERM, PSL Research University, 75005, Paris, France
- ESPCI Paris, PSL University, 10 rue Vauquelin, 75005, Paris, France
| | - Jimmy Ouellet
- Depixus SAS, 3/5 Impasse Reille, 75014, Paris, France
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11
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Steele JL, Stevens RC, Cabrera OA, Bassill GJ, Cramer SM, Guzman F, Shuber AP. Novel CRISPR-based sequence specific enrichment methods for target loci and single base mutations. PLoS One 2020; 15:e0243781. [PMID: 33362267 PMCID: PMC7757808 DOI: 10.1371/journal.pone.0243781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/25/2020] [Indexed: 01/10/2023] Open
Abstract
The programmable sequence specificity of CRISPR has found uses in gene editing and diagnostics. This manuscript describes an additional application of CRISPR through a family of novel DNA enrichment technologies. CAMP (CRISPR Associated Multiplexed PCR) and cCAMP (chimeric CRISPR Associated Multiplexed PCR) utilize the sequence specificity of the Cas9/sgRNA complex to target loci for the ligation of a universal adapter that is used for subsequent amplification. cTRACE (chimeric Targeting Rare Alleles with CRISPR-based Enrichment) also applies this method to use Cas9/sgRNA to target loci for the addition of universal adapters, however it has an additional selection for specific mutations through the use of an allele-specific primer. These three methods can produce multiplex PCR that significantly reduces the optimization required for every target. The methods are also not specific to any downstream analytical platform. We additionally will present a mutation specific enrichment technology that is non-amplification based and leaves the DNA in its native state: TRACE (Targeting Rare Alleles with CRISPR-based Enrichment). TRACE utilizes the Cas9/sgRNA complex to sterically protect the ends of targeted sequences from exonuclease activity which digests both the normal variant as well as any off-target sequences.
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Affiliation(s)
| | | | - Oscar A. Cabrera
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Gary J. Bassill
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Sabrina M. Cramer
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Felipe Guzman
- Genetics Research LLC, Waltham, Massachusetts, United States of America
| | - Anthony P. Shuber
- Genetics Research LLC, Waltham, Massachusetts, United States of America
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12
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Schultzhaus Z, Wang Z, Stenger D. CRISPR-based enrichment strategies for targeted sequencing. Biotechnol Adv 2020; 46:107672. [PMID: 33253795 DOI: 10.1016/j.biotechadv.2020.107672] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/31/2020] [Accepted: 11/22/2020] [Indexed: 12/26/2022]
Abstract
The ability to easily produce or procure sequencing data has expanded to be within the reach of most clinics and research laboratories, but the complexity of sequence analysis remains a hurdle for many scientists, and a decline in sequencing cost means that the generation of gratuitous information in a given experiment is a challenge that is more and more often being encountered. To address this issue, methods have been present, some dating to the advent of nucleic acid sequencing, for capturing, targeting, or otherwise enriching specific nucleic acids in order to obtain greater depth of reads from a small portion of sequences within a complex sample. However, many of these methods have been complicated and laborious, relying on the design of hundreds to thousands of oligonucleotide probes, fabrication of microarray chips, and long hybridization times. Here, we review these methods, their benefits and uses, and catalog and discuss the implications of a recent development that has enabled a more efficient and expanded set of tools for enriching nucleic acids - the application of CRISPR technology. This introduction and analysis of the capabilities of new CRISPR-based enrichment strategies shows that it has the potential to expand the scope of enrichment to new possibilities, including the coupling of DNA and RNA targeting with long-read, portable sequencing platforms. Moreover, there are several areas where CRISPR-enrichment is a logical next step to more powerful and simplified sequencing for applications such as diagnostics and environmental monitoring.
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Affiliation(s)
- Zachary Schultzhaus
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue, SW, Washington, DC 20375, USA.
| | - Zheng Wang
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue, SW, Washington, DC 20375, USA.
| | - David Stenger
- Center for Biomolecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Avenue, SW, Washington, DC 20375, USA.
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13
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Xu P, Modavi C, Demaree B, Twigg F, Liang B, Sun C, Zhang W, Abate AR. Microfluidic automated plasmid library enrichment for biosynthetic gene cluster discovery. Nucleic Acids Res 2020; 48:e48. [PMID: 32095820 PMCID: PMC7192590 DOI: 10.1093/nar/gkaa131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/22/2020] [Accepted: 02/19/2020] [Indexed: 12/13/2022] Open
Abstract
Microbial biosynthetic gene clusters are a valuable source of bioactive molecules. However, because they typically represent a small fraction of genomic material in most metagenomic samples, it remains challenging to deeply sequence them. We present an approach to isolate and sequence gene clusters in metagenomic samples using microfluidic automated plasmid library enrichment. Our approach provides deep coverage of the target gene cluster, facilitating reassembly. We demonstrate the approach by isolating and sequencing type I polyketide synthase gene clusters from an Antarctic soil metagenome. Our method promotes the discovery of functional-related genes and biosynthetic pathways.
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Affiliation(s)
- Peng Xu
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Cyrus Modavi
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin Demaree
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA, USA
| | - Frederick Twigg
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Benjamin Liang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Chen Sun
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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14
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Minervini CF, Cumbo C, Orsini P, Anelli L, Zagaria A, Specchia G, Albano F. Nanopore Sequencing in Blood Diseases: A Wide Range of Opportunities. Front Genet 2020; 11:76. [PMID: 32140171 PMCID: PMC7043087 DOI: 10.3389/fgene.2020.00076] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/23/2020] [Indexed: 12/20/2022] Open
Abstract
The molecular pathogenesis of hematological diseases is often driven by genetic and epigenetic alterations. Next-generation sequencing has considerably increased our genomic knowledge of these disorders becoming ever more widespread in clinical practice. In 2012 Oxford Nanopore Technologies (ONT) released the MinION, the first long-read nanopore-based sequencer, overcoming the main limits of short-reads sequences generation. In the last years, several nanopore sequencing approaches have been performed in various "-omic" sciences; this review focuses on the challenge to introduce ONT devices in the hematological field, showing advantages, disadvantages and future perspectives of this technology in the precision medicine era.
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Affiliation(s)
| | | | | | | | | | | | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari, Italy
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