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Katayama Y, Yokota R, Akiyama T, Kobayashi TJ. Machine Learning Approaches to TCR Repertoire Analysis. Front Immunol 2022; 13:858057. [PMID: 35911778 PMCID: PMC9334875 DOI: 10.3389/fimmu.2022.858057] [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: 01/19/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Sparked by the development of genome sequencing technology, the quantity and quality of data handled in immunological research have been changing dramatically. Various data and database platforms are now driving the rapid progress of machine learning for immunological data analysis. Of various topics in immunology, T cell receptor repertoire analysis is one of the most important targets of machine learning for assessing the state and abnormalities of immune systems. In this paper, we review recent repertoire analysis methods based on machine learning and deep learning and discuss their prospects.
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Affiliation(s)
- Yotaro Katayama
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Ryo Yokota
- National Research Institute of Police Science, Kashiwa, Chiba, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Tetsuya J. Kobayashi
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
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2
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Tian G, Li M, Lv G. Analysis of T-Cell Receptor Repertoire in Transplantation: Fingerprint of T Cell-mediated Alloresponse. Front Immunol 2022; 12:778559. [PMID: 35095851 PMCID: PMC8790170 DOI: 10.3389/fimmu.2021.778559] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
T cells play a key role in determining allograft function by mediating allogeneic immune responses to cause rejection, and recent work pointed their role in mediating tolerance in transplantation. The unique T-cell receptor (TCR) expressed on the surface of each T cell determines the antigen specificity of the cell and can be the specific fingerprint for identifying and monitoring. Next-generation sequencing (NGS) techniques provide powerful tools for deep and high-throughput TCR profiling, and facilitate to depict the entire T cell repertoire profile and trace antigen-specific T cells in circulation and local tissues. Tailing T cell transcriptomes and TCR sequences at the single cell level provides a full landscape of alloreactive T-cell clones development and biofunction in alloresponse. Here, we review the recent advances in TCR sequencing techniques and computational tools, as well as the recent discovery in overall TCR profile and antigen-specific T cells tracking in transplantation. We further discuss the challenges and potential of using TCR sequencing-based assays to profile alloreactive TCR repertoire as the fingerprint for immune monitoring and prediction of rejection and tolerance.
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Affiliation(s)
| | - Mingqian Li
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Guoyue Lv
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
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3
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Pai JA, Satpathy AT. High-throughput and single-cell T cell receptor sequencing technologies. Nat Methods 2021; 18:881-892. [PMID: 34282327 PMCID: PMC9345561 DOI: 10.1038/s41592-021-01201-8] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
T cells express T cell receptors (TCRs) composed of somatically recombined TCRα and TCRβ chains, which mediate recognition of major histocompatibility complex (MHC)-antigen complexes and drive the antigen-specific adaptive immune response to pathogens and cancer. The TCR repertoire in each individual is highly diverse, which allows for recognition of a wide array of foreign antigens, but also presents a challenge in analyzing this response using conventional methods. Recent studies have developed high-throughput sequencing technologies to identify TCR sequences, analyze their antigen specificities using experimental and computational tools, and pair TCRs with transcriptional and epigenetic cell state phenotypes in single cells. In this Review, we highlight these technological advances and describe how they have been applied to discover fundamental insights into T cell-mediated immunity.
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Affiliation(s)
- Joy A Pai
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ansuman T Satpathy
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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4
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Granadier D, Iovino L, Kinsella S, Dudakov JA. Dynamics of thymus function and T cell receptor repertoire breadth in health and disease. Semin Immunopathol 2021; 43:119-134. [PMID: 33608819 PMCID: PMC7894242 DOI: 10.1007/s00281-021-00840-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/12/2021] [Indexed: 12/26/2022]
Abstract
T cell recognition of unknown antigens relies on the tremendous diversity of the T cell receptor (TCR) repertoire; generation of which can only occur in the thymus. TCR repertoire breadth is thus critical for not only coordinating the adaptive response against pathogens but also for mounting a response against malignancies. However, thymic function is exquisitely sensitive to negative stimuli, which can come in the form of acute insult, such as that caused by stress, infection, or common cancer therapies; or chronic damage such as the progressive decline in thymic function with age. Whether it be prolonged T cell deficiency after hematopoietic cell transplantation (HCT) or constriction in the breadth of the peripheral TCR repertoire with age; these insults result in poor adaptive immune responses. In this review, we will discuss the importance of thymic function for generation of the TCR repertoire and how acute and chronic thymic damage influences immune health. We will also discuss methods that are used to measure thymic function in patients and strategies that have been developed to boost thymic function.
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Affiliation(s)
- David Granadier
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
- Department of Molecular and Cellular Biology, University of Washington, Seattle, WA, USA
| | - Lorenzo Iovino
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sinéad Kinsella
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jarrod A Dudakov
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Immunology, University of Washington, Seattle, WA, USA.
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5
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The Identity Card of T Cells-Clinical Utility of T-cell Receptor Repertoire Analysis in Transplantation. Transplantation 2020; 103:1544-1555. [PMID: 31033649 DOI: 10.1097/tp.0000000000002776] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is a clear medical need to change the current strategy of "one-size-fits-all" immunosuppression for controlling transplant rejection to precision medicine and targeted immune intervention. As T cells play a key role in both undesired graft rejection and protection, a better understanding of the fate and function of both alloreactive graft-deteriorating T cells and those protecting to infections is required. The T-cell receptor (TCR) is the individual identity card of each T cell clone and can help to follow single specificities. In this context, tracking of lymphocytes with certain specificity in blood and tissue in clinical follow up is of especial importance. After overcoming technical limitations of the past, novel molecular technologies opened new avenues of diagnostics. Using advantages of next generation sequencing, a method was established for T-cell tracing by detection of variable TCR region as identifiers of individual lymphocyte clones. The current review describes principles of laboratory and computational methods of TCR repertoire analysis, and gives an overview on applications for the basic understanding of transplant biology and immune monitoring. The review also delineates methodological pitfalls and challenges. With the outlook on prediction of antigens in immune-mediated processes including those of unknown causative pathogens, monitoring the fate and function of individual T cell clones, and the adoptive transfer of protective effector or regulatory T cells, this review highlights the current and future capability of TCR repertoire analysis.
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6
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Sequencing barcode construction and identification methods based on block error-correction codes. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1580-1592. [PMID: 32303959 DOI: 10.1007/s11427-019-1651-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 02/11/2020] [Indexed: 02/07/2023]
Abstract
Multiplexed sequencing relies on specific sample labels, the barcodes, to tag DNA fragments belonging to different samples and to separate the output of the sequencers. However, the barcodes are often corrupted by insertion, deletion and substitution errors introduced during sequencing, which may lead to sample misassignment. In this paper, we propose a barcode construction method, which combines a block error-correction code with a predetermined pseudorandom sequence to generate a base sequence for labeling different samples. Furthermore, to identify the corrupted barcodes for assigning reads to their respective samples, we present a soft decision identification method that consists of inner decoding and outer decoding. The inner decoder establishes the hidden Markov model (HMM) for base insertion/deletion estimation with the pseudorandom sequence, and adapts the forward-backward (FB) algorithm to output the soft information of each bit in the block code. The outer decoder performs soft decision decoding using the soft information to effectively correct multiple errors in the barcodes. Simulation results show that the proposed methods are highly robust to high error rates of insertions, deletions and substitutions in the barcodes. In addition, compared with the inner decoding algorithm of the barcodes based on watermarks, the proposed inner decoding algorithm can greatly reduce the decoding complexity.
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Mallampati S, Duose DY, Harmon MA, Mehrotra M, Kanagal-Shamanna R, Zalles S, Wistuba II, Sun X, Luthra R. Rational "Error Elimination" Approach to Evaluating Molecular Barcoded Next-Generation Sequencing Data Identifies Low-Frequency Mutations in Hematologic Malignancies. J Mol Diagn 2019; 21:471-482. [PMID: 30794984 PMCID: PMC6521894 DOI: 10.1016/j.jmoldx.2019.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/31/2018] [Accepted: 01/18/2019] [Indexed: 12/18/2022] Open
Abstract
The emergence of highly sensitive molecular diagnostic approaches, such as droplet digital PCR, has allowed the accurate identification of low-frequency variant alleles in clinical specimens; however, the multiplex capabilities of droplet digital PCR for variant detection are inadequate. The incorporation of molecular barcodes or unique IDs into next-generation sequencing libraries through PCR has enabled the detection of low-frequency variant alleles across multiple genomic regions. However, rational library preparation and sequencing data analytic strategies that integrate molecular barcodes have rarely been applied to clinical settings. In this study, we evaluated the parameters that are crucial in the use of molecular barcodes in next-generation sequencing for genotyping clinical specimens from patients with hematologic malignancies. The uniform incorporation of molecular barcodes into DNA templates through PCR was found to be crucial, and the extent of uniformity was governed by multiple interdependent variables. An error elimination strategy was developed for removing sequencing background errors by using molecular barcode sequence information as an alternative to the conventional error correction approach. This approach was successfully used to identify mutations with frequencies as low as 0.15%, and the clonal heterogeneity of hematologic malignancies was revealed. These findings have implications for elucidating heterogeneity and temporal and spatial clonal evolution, evaluating response to therapy, and monitoring relapse in patients with hematologic malignancies.
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Affiliation(s)
- Saradhi Mallampati
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dzifa Y Duose
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Meenakshi Mehrotra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephanie Zalles
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaoping Sun
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Rajyalakshmi Luthra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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8
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Heather JM, Ismail M, Oakes T, Chain B. High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities. Brief Bioinform 2018; 19:554-565. [PMID: 28077404 PMCID: PMC6054146 DOI: 10.1093/bib/bbw138] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
T-cell specificity is determined by the T-cell receptor, a heterodimeric protein coded for by an extremely diverse set of genes produced by imprecise somatic gene recombination. Massively parallel high-throughput sequencing allows millions of different T-cell receptor genes to be characterized from a single sample of blood or tissue. However, the extraordinary heterogeneity of the immune repertoire poses significant challenges for subsequent analysis of the data. We outline the major steps in processing of repertoire data, considering low-level processing of raw sequence files and high-level algorithms, which seek to extract biological or pathological information. The latest generation of bioinformatics tools allows millions of DNA sequences to be accurately and rapidly assigned to their respective variable V and J gene segments, and to reconstruct an almost error-free representation of the non-templated additions and deletions that occur. High-level processing can measure the diversity of the repertoire in different samples, quantify V and J usage and identify private and public T-cell receptors. Finally, we discuss the major challenge of linking T-cell receptor sequence to function, and specifically to antigen recognition. Sophisticated machine learning algorithms are being developed that can combine the paradoxical degeneracy and cross-reactivity of individual T-cell receptors with the specificity of the overall T-cell immune response. Computational analysis will provide the key to unlock the potential of the T-cell receptor repertoire to give insight into the fundamental biology of the adaptive immune system and to provide powerful biomarkers of disease.
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Affiliation(s)
| | | | | | - Benny Chain
- Division of Infection and Immunity, University College of London, Bloomsbury, UK
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9
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Bürckert JP, Faison WJ, Mustin DE, Dubois ARSX, Sinner R, Hunewald O, Wienecke-Baldacchino A, Brieger A, Muller CP. High-throughput sequencing of murine immunoglobulin heavy chain repertoires using single side unique molecular identifiers on an Ion Torrent PGM. Oncotarget 2018; 9:30225-30239. [PMID: 30100985 PMCID: PMC6084394 DOI: 10.18632/oncotarget.25493] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 05/07/2018] [Indexed: 11/25/2022] Open
Abstract
With the advent of high-throughput sequencing (HTS), profiling immunoglobulin (IG) repertoires has become an essential part of immunological research. Advances in sequencing technology enable the IonTorrent Personal Genome Machine (PGM) to cover the full-length of IG mRNA transcripts. Nucleotide insertions and deletions (indels) are the dominant errors of the PGM sequencing platform and can critically influence IG repertoire assessments. Here, we present a PGM-tailored IG repertoire sequencing approach combining error correction through unique molecular identifier (UID) barcoding and indel detection through ImMunoGeneTics (IMGT), the most commonly used sequence alignment database for IG sequences. Using artificially falsified sequences for benchmarking, we found that IMGT's underlying algorithms efficiently detect 98% of the introduced indels. Undetected indels are either located at the end of the sequences or produce masked frameshifts with an insertion and deletion in close proximity. The complementary determining regions 3 (CDR3s) are returned correct for up to 3 insertions or 3 deletions through conservative culling. We further show, that our PGM-tailored unique molecular identifiers result in highly accurate HTS data if combined with the presented processing strategy. In this regard, considering sequences with at least two copies from datasets with UID families of minimum 3 reads result in correct sequences with over 99% confidence. Finally, we show that the protocol can readily be used to generate homogenous datasets for bulk sequencing of murine bone marrow samples. Taken together, this approach will help to establish benchtop-scale sequencing of IG heavy chain transcripts in the field of IG repertoire research.
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Affiliation(s)
- Jean-Philippe Bürckert
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - William J Faison
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Danielle E Mustin
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Axel R S X Dubois
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Regina Sinner
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Oliver Hunewald
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | | | - Anne Brieger
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Claude P Muller
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
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10
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Liu X, Wu J. History, applications, and challenges of immune repertoire research. Cell Biol Toxicol 2018; 34:441-457. [PMID: 29484527 DOI: 10.1007/s10565-018-9426-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 02/14/2018] [Indexed: 12/19/2022]
Abstract
The diversity of T and B cells in terms of their receptor sequences is huge in the vertebrate's immune system and provides broad protection against the vast diversity of pathogens. Immune repertoire is defined as the sum of T cell receptors and B cell receptors (also named immunoglobulin) that makes the organism's adaptive immune system. Before the emergence of high-throughput sequencing, the studies on immune repertoire were limited by the underdeveloped methodologies, since it was impossible to capture the whole picture by the low-throughput tools. The massive paralleled sequencing technology suits perfectly the researches on immune repertoire. In this article, we review the history of immune repertoire studies, in terms of technologies and research applications. Particularly, we discuss several aspects of challenges in this field and highlight the efforts to develop potential solutions, in the era of high-throughput sequencing of the immune repertoire.
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Affiliation(s)
- Xiao Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
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11
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Ahmed AA, Abedalthagafi M. Cancer diagnostics: The journey from histomorphology to molecular profiling. Oncotarget 2018; 7:58696-58708. [PMID: 27509178 PMCID: PMC5295463 DOI: 10.18632/oncotarget.11061] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/19/2016] [Indexed: 12/15/2022] Open
Abstract
Although histomorphology has made significant advances into the understanding of cancer etiology, classification and pathogenesis, it is sometimes complicated by morphologic ambiguities, and other shortcomings that necessitate the development of ancillary tests to complement its diagnostic value. A new approach to cancer patient management consists of targeting specific molecules or gene mutations in the cancer genome by inhibitory therapy. Molecular diagnostic tests and genomic profiling methods are increasingly being developed to identify tumor targeted molecular profile that is the basis of targeted therapy. Novel targeted therapy has revolutionized the treatment of gastrointestinal stromal tumor, renal cell carcinoma and other cancers that were previously difficult to treat with standard chemotherapy. In this review, we discuss the role of histomorphology in cancer diagnosis and management and the rising role of molecular profiling in targeted therapy. Molecular profiling in certain diagnostic and therapeutic difficulties may provide a practical and useful complement to histomorphology and opens new avenues for targeted therapy and alternative methods of cancer patient management.
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Affiliation(s)
- Atif A Ahmed
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Malak Abedalthagafi
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,The Saudi Human Genome Laboratory, Department of Pathology, King Fahad Medical City, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
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12
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Vasar M, Andreson R, Davison J, Jairus T, Moora M, Remm M, Young JPW, Zobel M, Öpik M. Increased sequencing depth does not increase captured diversity of arbuscular mycorrhizal fungi. MYCORRHIZA 2017; 27:761-773. [PMID: 28730541 DOI: 10.1007/s00572-017-0791-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/12/2017] [Indexed: 05/26/2023]
Abstract
The arrival of 454 sequencing represented a major breakthrough by allowing deeper sequencing of environmental samples than was possible with existing Sanger approaches. Illumina MiSeq provides a further increase in sequencing depth but shorter read length compared with 454 sequencing. We explored whether Illumina sequencing improves estimates of arbuscular mycorrhizal (AM) fungal richness in plant root samples, compared with 454 sequencing. We identified AM fungi in root samples by sequencing amplicons of the SSU rRNA gene with 454 and Illumina MiSeq paired-end sequencing. In addition, we sequenced metagenomic DNA without prior PCR amplification. Amplicon-based Illumina sequencing yielded two orders of magnitude higher sequencing depth per sample than 454 sequencing. Initial analysis with minimal quality control recorded five times higher AM fungal richness per sample with Illumina sequencing. Additional quality control of Illumina samples, including restriction of the marker region to the most variable amplicon fragment, revealed AM fungal richness values close to those produced by 454 sequencing. Furthermore, AM fungal richness estimates were not correlated with sequencing depth between 300 and 30,000 reads per sample, suggesting that the lower end of this range is sufficient for adequate description of AM fungal communities. By contrast, metagenomic Illumina sequencing yielded very few AM fungal reads and taxa and was dominated by plant DNA, suggesting that AM fungal DNA is present at prohibitively low abundance in colonised root samples. In conclusion, Illumina MiSeq sequencing yielded higher sequencing depth, but similar richness of AM fungi in root samples, compared with 454 sequencing.
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Affiliation(s)
- Martti Vasar
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai Str, 51005, Tartu, Estonia.
| | - Reidar Andreson
- Institute of Molecular and Cell Biology, University of Tartu, 23b Riia Str, 51010, Tartu, Estonia
- Estonian Biocentre, 23b Riia Str, 51010, Tartu, Estonia
| | - John Davison
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai Str, 51005, Tartu, Estonia
| | - Teele Jairus
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai Str, 51005, Tartu, Estonia
| | - Mari Moora
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai Str, 51005, Tartu, Estonia
| | - Maido Remm
- Institute of Molecular and Cell Biology, University of Tartu, 23b Riia Str, 51010, Tartu, Estonia
| | - J P W Young
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Martin Zobel
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai Str, 51005, Tartu, Estonia
| | - Maarja Öpik
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai Str, 51005, Tartu, Estonia
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13
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Langerak AW, Brüggemann M, Davi F, Darzentas N, van Dongen JJM, Gonzalez D, Cazzaniga G, Giudicelli V, Lefranc MP, Giraud M, Macintyre EA, Hummel M, Pott C, Groenen PJTA, Stamatopoulos K. High-Throughput Immunogenetics for Clinical and Research Applications in Immunohematology: Potential and Challenges. THE JOURNAL OF IMMUNOLOGY 2017; 198:3765-3774. [PMID: 28416603 DOI: 10.4049/jimmunol.1602050] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/09/2017] [Indexed: 11/19/2022]
Abstract
Analysis and interpretation of Ig and TCR gene rearrangements in the conventional, low-throughput way have their limitations in terms of resolution, coverage, and biases. With the advent of high-throughput, next-generation sequencing (NGS) technologies, a deeper analysis of Ig and/or TCR (IG/TR) gene rearrangements is now within reach, which impacts on all main applications of IG/TR immunogenetic analysis. To bridge the generation gap from low- to high-throughput analysis, the EuroClonality-NGS Consortium has been formed, with the main objectives to develop, standardize, and validate the entire workflow of IG/TR NGS assays for 1) clonality assessment, 2) minimal residual disease detection, and 3) repertoire analysis. This concerns the preanalytical (sample preparation, target choice), analytical (amplification, NGS), and postanalytical (immunoinformatics) phases. Here we critically discuss pitfalls and challenges of IG/TR NGS methodology and its applications in hemato-oncology and immunology.
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Affiliation(s)
- Anton W Langerak
- Department of Immunology, Laboratory for Medical Immunology, Erasmus MC, University Medical Center, 3015 CN Rotterdam, the Netherlands;
| | - Monika Brüggemann
- Second Medical Department, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Frédéric Davi
- Département d'Hématologie, Assistance Publique - Hôpitaux de Paris Hopital Pitié-Salpêtrière and Université Pierre et Marie Curie - Université Paris IV, 75005 Paris, France
| | - Nikos Darzentas
- Molecular Medicine Program, Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Jacques J M van Dongen
- Department of Immunology, Laboratory for Medical Immunology, Erasmus MC, University Medical Center, 3015 CN Rotterdam, the Netherlands;
| | - David Gonzalez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7AE, United Kingdom
| | - Gianni Cazzaniga
- Centro Ricerca Tettamanti, Clinica Pediatrica Università Milano-Bicocca, 20900 Monza, Italy
| | | | | | - Mathieu Giraud
- Centre de Recherche en Informatique Signal et Automatique de Lille, CNRS, Université de Lille, 59000 Lille, France
| | - Elizabeth A Macintyre
- Département d'Hématologie, Assistance Publique - Hôpitaux de Paris Necker-Enfants Malades and Paris Descartes, 75015 Paris, France
| | - Michael Hummel
- Institut für Pathologie, Charité - Universitätsmedizin Berlin, D-10117 Berlin, Germany
| | - Christiane Pott
- Second Medical Department, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Patricia J T A Groenen
- Department of Pathology, Radboud University Nijmegen Medical Center, 6525 GA Nijmegen, the Netherlands; and
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology Hellas, GR-57001 Thessaloniki, Greece
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14
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Gonçalves P, Ferrarini M, Molina-Paris C, Lythe G, Vasseur F, Lim A, Rocha B, Azogui O. A new mechanism shapes the naïve CD8 + T cell repertoire: the selection for full diversity. Mol Immunol 2017; 85:66-80. [PMID: 28212502 DOI: 10.1016/j.molimm.2017.01.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 01/16/2017] [Accepted: 01/28/2017] [Indexed: 12/17/2022]
Abstract
During thymic T cell differentiation, TCR repertoires are shaped by negative, positive and agonist selection. In the thymus and in the periphery, repertoires are also shaped by strong inter-clonal and intra-clonal competition to survive death by neglect. Understanding the impact of these events on the T cell repertoire requires direct evaluation of TCR expression in peripheral naïve T cells. Several studies have evaluated TCR diversity, with contradictory results. Some of these studies had intrinsic technical limitations since they used material obtained from T cell pools, preventing the direct evaluation of clonal sizes. Indeed with these approaches, identical TCRs may correspond to different cells expressing the same receptor, or to several amplicons from the same T cell. We here overcame this limitation by evaluating TCRB expression in individual naïve CD8+ T cells. Of the 2269 Tcrb sequences we obtained from 13 mice, 99% were unique. Mathematical analysis of the data showed that the average number of naïve peripheral CD8+ T cells expressing the same TCRB is 1.1 cell. Since TCRA co-expression studies could only increase repertoire diversity, these results reveal that the number of naïve T cells with unique TCRs approaches the number of naïve cells. Since thymocytes undergo multiple rounds of divisions after TCRB rearrangement and 3-5% of thymocytes survive thymic selection events the number of cells expressing the same TCRB was expected to be much higher. Thus, these results suggest a new repertoire selection mechanism, which strongly selects for full TCRB diversity.
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Affiliation(s)
- Pedro Gonçalves
- Lymphocyte Population Biology Unit, CNRS URA 196, Institut Pasteur, Paris, France; INSERM, U1151, CNRS, UMR8253, Faculté de Médecine Paris Descartes, Paris, France.
| | - Marco Ferrarini
- Department of Applied Mathematics, University of Leeds, Leeds LS29JT, UK
| | | | - Grant Lythe
- Department of Applied Mathematics, University of Leeds, Leeds LS29JT, UK
| | - Florence Vasseur
- Lymphocyte Population Biology Unit, CNRS URA 196, Institut Pasteur, Paris, France; INSERM, U1151, CNRS, UMR8253, Faculté de Médecine Paris Descartes, Paris, France
| | - Annik Lim
- Lymphocyte Population Biology Unit, CNRS URA 196, Institut Pasteur, Paris, France
| | - Benedita Rocha
- Lymphocyte Population Biology Unit, CNRS URA 196, Institut Pasteur, Paris, France; INSERM, U1151, CNRS, UMR8253, Faculté de Médecine Paris Descartes, Paris, France.
| | - Orly Azogui
- INSERM, U1151, CNRS, UMR8253, Faculté de Médecine Paris Descartes, Paris, France
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15
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Marusina AI, Ono Y, Merleev AA, Shimoda M, Ogawa H, Wang EA, Kondo K, Olney L, Luxardi G, Miyamura Y, Yilma TD, Villalobos IB, Bergstrom JW, Kronenberg DG, Soulika AM, Adamopoulos IE, Maverakis E. CD4 + virtual memory: Antigen-inexperienced T cells reside in the naïve, regulatory, and memory T cell compartments at similar frequencies, implications for autoimmunity. J Autoimmun 2016; 77:76-88. [PMID: 27894837 DOI: 10.1016/j.jaut.2016.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 11/08/2016] [Indexed: 12/22/2022]
Abstract
It is widely accepted that central and effector memory CD4+ T cells originate from naïve T cells after they have encountered their cognate antigen in the setting of appropriate co-stimulation. However, if this were true the diversity of T cell receptor (TCR) sequences within the naïve T cell compartment should be far greater than that of the memory T cell compartment, which is not supported by TCR sequencing data. Here we demonstrate that aged mice with far fewer naïve T cells, respond to the model antigen, hen eggwhite lysozyme (HEL), by utilizing the same TCR sequence as their younger counterparts. CD4+ T cell repertoire analysis of highly purified T cell populations from naive animals revealed that the HEL-specific clones displayed effector and central "memory" cell surface phenotypes even prior to having encountered their cognate antigen. Furthermore, HEL-inexperienced CD4+ T cells were found to reside within the naïve, regulatory, central memory, and effector memory T cell populations at similar frequencies and the majority of the CD4+ T cells within the regulatory and memory populations were unexpanded. These findings support a new paradigm for CD4+ T cell maturation in which a specific clone can undergo a differentiation process to exhibit a "memory" or regulatory phenotype without having undergone a clonal expansion event. It also demonstrates that a foreign-specific T cell is just as likely to reside within the regulatory T cell compartment as it would the naïve compartment, arguing against the specificity of the regulatory T cell compartment being skewed towards self-reactive T cell clones. Finally, we demonstrate that the same set of foreign and autoreactive CD4+ T cell clones are repetitively generated throughout adulthood. The latter observation argues against T cell-depleting strategies or autologous stem cell transplantation as therapies for autoimmunity-as the immune system has the ability to regenerate pathogenic clones.
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Affiliation(s)
- Alina I Marusina
- Department of Dermatology, School of Medicine, University of California, Sacramento, Davis, CA 95817, United States
| | - Yoko Ono
- Department of Dermatology, School of Medicine, University of California, Sacramento, Davis, CA 95817, United States
| | - Alexander A Merleev
- Department of Dermatology, School of Medicine, University of California, Sacramento, Davis, CA 95817, United States
| | - Michiko Shimoda
- Department of Dermatology, School of Medicine, University of California, Sacramento, Davis, CA 95817, United States
| | - Hiromi Ogawa
- Department of Dermatology, School of Medicine, University of California, Sacramento, Davis, CA 95817, United States
| | - Elizabeth A Wang
- Department of Dermatology, School of Medicine, University of California, Sacramento, Davis, CA 95817, United States
| | - Kayo Kondo
- Department of Dermatology, School of Medicine, University of California, Sacramento, Davis, CA 95817, United States
| | - Laura Olney
- Department of Dermatology, School of Medicine, University of California, Sacramento, Davis, CA 95817, United States
| | - Guillaume Luxardi
- Department of Dermatology, School of Medicine, University of California, Sacramento, Davis, CA 95817, United States
| | - Yoshinori Miyamura
- Department of Dermatology, School of Medicine, University of California, Sacramento, Davis, CA 95817, United States
| | - Tilahun D Yilma
- International Laboratory of Molecular Biology for Tropical Disease Agents, School of Veterinary Medicine, University of California, Davis, CA 95616, United States; Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, United States
| | - Itzel Bustos Villalobos
- Department of Dermatology, School of Medicine, University of California, Sacramento, Davis, CA 95817, United States
| | - Jennifer W Bergstrom
- Department of Dermatology, School of Medicine, University of California, Sacramento, Davis, CA 95817, United States
| | - Daniel G Kronenberg
- Department of Dermatology, School of Medicine, University of California, Sacramento, Davis, CA 95817, United States
| | - Athena M Soulika
- Department of Dermatology, School of Medicine, University of California, Sacramento, Davis, CA 95817, United States
| | - Iannis E Adamopoulos
- Department of Internal Medicine, School of Medicine, University of California, Sacramento, Davis, CA 95817, United States
| | - Emanual Maverakis
- Department of Dermatology, School of Medicine, University of California, Sacramento, Davis, CA 95817, United States.
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16
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Autoimmune susceptibility imposed by public TCRβ chains. Sci Rep 2016; 6:37543. [PMID: 27869234 PMCID: PMC5116635 DOI: 10.1038/srep37543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/01/2016] [Indexed: 11/21/2022] Open
Abstract
Although the TCR repertoire is highly diverse, a small fraction of TCR chains, referred to as public, preferentially form and are shared by most individuals. Prior studies indicated that public TCRβ may be preferentially deployed in autoimmunity. We hypothesized that if these TCRβ modulate the likelihood of a TCRαβ heterodimer productively engaging autoantigen, because they are widely present in the population and often high frequency within individual repertoires, they could also broadly influence repertoire responsiveness to specific autoantigens. We assess this here using a series of public and private TCRβ derived from autoimmune encephalomyelitis-associated TCR. Transgenic expression of public, but not private, disease-associated TCRβ paired with endogenously rearranged TCRα endowed unprimed T cells with autoantigen reactivity. Further, two of six public, but none of five private TCRβ provoked spontaneous early-onset autoimmunity in mice. Our findings indicate that single TCRβ are sufficient to confer on TCRαβ chains reactivity toward disease-associated autoantigens in the context of diverse TCRα. They further suggest that public TCR can skew autoimmune susceptibility, and that subsets of public TCR sequences may serve as disease- specific biomarkers or therapeutic targets.
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17
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Han Y, Li H, Guan Y, Huang J. Immune repertoire: A potential biomarker and therapeutic for hepatocellular carcinoma. Cancer Lett 2016; 379:206-12. [DOI: 10.1016/j.canlet.2015.06.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 12/27/2022]
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18
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Hou D, Chen C, Seely EJ, Chen S, Song Y. High-Throughput Sequencing-Based Immune Repertoire Study during Infectious Disease. Front Immunol 2016; 7:336. [PMID: 27630639 PMCID: PMC5005336 DOI: 10.3389/fimmu.2016.00336] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 08/19/2016] [Indexed: 11/13/2022] Open
Abstract
The selectivity of the adaptive immune response is based on the enormous diversity of T and B cell antigen-specific receptors. The immune repertoire, the collection of T and B cells with functional diversity in the circulatory system at any given time, is dynamic and reflects the essence of immune selectivity. In this article, we review the recent advances in immune repertoire study of infectious diseases, which were achieved by traditional techniques and high-throughput sequencing (HTS) techniques. HTS techniques enable the determination of complementary regions of lymphocyte receptors with unprecedented efficiency and scale. This progress in methodology enhances the understanding of immunologic changes during pathogen challenge and also provides a basis for further development of novel diagnostic markers, immunotherapies, and vaccines.
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Affiliation(s)
- Dongni Hou
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University , Shanghai , China
| | - Cuicui Chen
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University , Shanghai , China
| | - Eric John Seely
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of California San Francisco , San Francisco, CA , USA
| | - Shujing Chen
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University , Shanghai , China
| | - Yuanlin Song
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University , Shanghai , China
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19
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Turchaninova MA, Davydov A, Britanova OV, Shugay M, Bikos V, Egorov ES, Kirgizova VI, Merzlyak EM, Staroverov DB, Bolotin DA, Mamedov IZ, Izraelson M, Logacheva MD, Kladova O, Plevova K, Pospisilova S, Chudakov DM. High-quality full-length immunoglobulin profiling with unique molecular barcoding. Nat Protoc 2016; 11:1599-616. [DOI: 10.1038/nprot.2016.093] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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20
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Nakanishi K, Kukita Y, Segawa H, Inoue N, Ohue M, Kato K. Characterization of the T-cell receptor beta chain repertoire in tumor-infiltrating lymphocytes. Cancer Med 2016; 5:2513-21. [PMID: 27465739 PMCID: PMC5055180 DOI: 10.1002/cam4.828] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 04/22/2016] [Accepted: 04/22/2016] [Indexed: 11/11/2022] Open
Abstract
Tumor‐infiltrating lymphocytes (TILs) are direct effectors of tumor immunity, and their characterization is important for further development of immunotherapy. Recent advances in high‐throughput sequencing technologies have enabled a comprehensive analysis of T‐cell receptor (TCR) complementarity‐determining region 3 (CDR3) sequences, which may provide information of therapeutic importance. We developed a high‐fidelity target sequencing method with the ability for absolute quantitation, and performed large‐scale sequencing of TCR beta chain (TCRB) CDR3 regions in TILs and peripheral blood lymphocytes (PBLs). The estimated TCRB repertoire sizes of PBLs from four healthy individuals and TILs from four colorectal cancer tissue samples were 608,664–1,003,098 and 90,228–223,757, respectively. The usage of J‐ and V‐regions was similar in PBLs and TILs. Proportions of CDR3 amino acid (aa) sequences occupying more than 0.01% of the total molecular population were 0.33–0.43% in PBLs and 1.3–3.6% in TILs. Additional low coverage sequencing of 15 samples identified five CDR3 aa sequences that were shared by nine patients, one sequence shared by 10 patients, and one sequence shared by 12 patients. The estimated size of the TCRB repertoire in TILs was significantly smaller than that in PBLs. The proportion of abundant species (>0.01%) in TILs was larger than that in PBLs. Shared CDR3 aa sequences represent a response to common antigens, and the identification of such CDR3 sequences may be beneficial in developing clinical biomarkers.
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Affiliation(s)
- Katsumi Nakanishi
- Department of Molecular and Medical Genetics, Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Yoji Kukita
- Department of Molecular and Medical Genetics, Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Hidenobu Segawa
- Department of Molecular and Medical Genetics, Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Norimitsu Inoue
- Department of Tumor Immunology, Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Masayuki Ohue
- Department of Surgery, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Kikuya Kato
- Department of Molecular and Medical Genetics, Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan.
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21
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Gerritsen B, Pandit A, Andeweg AC, de Boer RJ. RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data. Bioinformatics 2016; 32:3098-3106. [PMID: 27324198 PMCID: PMC5048062 DOI: 10.1093/bioinformatics/btw339] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 05/26/2016] [Indexed: 12/11/2022] Open
Abstract
Motivation: High Throughput Sequencing (HTS) has enabled researchers to probe the human T cell receptor (TCR) repertoire, which consists of many rare sequences. Distinguishing between true but rare TCR sequences and variants generated by polymerase chain reaction (PCR) and sequencing errors remains a formidable challenge. The conventional approach to handle errors is to remove low quality reads, and/or rare TCR sequences. Such filtering discards a large number of true and often rare TCR sequences. However, accurate identification and quantification of rare TCR sequences is essential for repertoire diversity estimation. Results: We devised a pipeline, called Recover TCR (RTCR), that accurately recovers TCR sequences, including rare TCR sequences, from HTS data (including barcoded data) even at low coverage. RTCR employs a data-driven statistical model to rectify PCR and sequencing errors in an adaptive manner. Using simulations, we demonstrate that RTCR can easily adapt to the error profiles of different types of sequencers and exhibits consistently high recall and high precision even at low coverages where other pipelines perform poorly. Using published real data, we show that RTCR accurately resolves sequencing errors and outperforms all other pipelines. Availability and Implementation: The RTCR pipeline is implemented in Python (v2.7) and C and is freely available at http://uubram.github.io/RTCR/along with documentation and examples of typical usage. Contact:b.gerritsen@uu.nl
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Affiliation(s)
- Bram Gerritsen
- Theoretical Biology and Bioinformatics, Utrecht University, 3584CH the Netherlands
| | - Aridaman Pandit
- Theoretical Biology and Bioinformatics, Utrecht University, 3584CH the Netherlands
| | - Arno C Andeweg
- Department of Viroscience, Rotterdam, Erasmus MC, 3000CA, the Netherlands
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, 3584CH the Netherlands
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22
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Britanova OV, Shugay M, Merzlyak EM, Staroverov DB, Putintseva EV, Turchaninova MA, Mamedov IZ, Pogorelyy MV, Bolotin DA, Izraelson M, Davydov AN, Egorov ES, Kasatskaya SA, Rebrikov DV, Lukyanov S, Chudakov DM. Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians. THE JOURNAL OF IMMUNOLOGY 2016; 196:5005-13. [PMID: 27183615 DOI: 10.4049/jimmunol.1600005] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/16/2016] [Indexed: 01/29/2023]
Abstract
The diversity, architecture, and dynamics of the TCR repertoire largely determine our ability to effectively withstand infections and malignancies with minimal mistargeting of immune responses. In this study, we have employed deep TCRβ repertoire sequencing with normalization based on unique molecular identifiers to explore the long-term dynamics of T cell immunity. We demonstrate remarkable stability of repertoire, where approximately half of all T cells in peripheral blood are represented by clones that persist and generally preserve their frequencies for 3 y. We further characterize the extremes of lifelong TCR repertoire evolution, analyzing samples ranging from umbilical cord blood to centenarian peripheral blood. We show that the fetal TCR repertoire, albeit structurally maintained within regulated borders due to the lower numbers of randomly added nucleotides, is not limited with respect to observed functional diversity. We reveal decreased efficiency of nonsense-mediated mRNA decay in umbilical cord blood, which may reflect specific regulatory mechanisms in development. Furthermore, we demonstrate that human TCR repertoires are functionally more similar at birth but diverge during life, and we track the lifelong behavior of CMV- and EBV-specific T cell clonotypes. Finally, we reveal gender differences in dynamics of TCR diversity constriction, which come to naught in the oldest age. Based on our data, we propose a more general explanation for the previous observations on the relationships between longevity and immunity.
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Affiliation(s)
- Olga V Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Ekaterina M Merzlyak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Dmitriy B Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Ekaterina V Putintseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Maria A Turchaninova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Dmitriy A Bolotin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Mark Izraelson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Alexey N Davydov
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Evgeny S Egorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Sofya A Kasatskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Denis V Rebrikov
- Pirogov Russian National Research Medical University, Moscow 117997, Russia; Vavilov Institute of General Genetics of the Russian Academy of Sciences, Moscow 119991, Russia
| | - Sergey Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
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23
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Zhao Y, Nguyen P, Ma J, Wu T, Jones LL, Pei D, Cheng C, Geiger TL. Preferential Use of Public TCR during Autoimmune Encephalomyelitis. THE JOURNAL OF IMMUNOLOGY 2016; 196:4905-14. [PMID: 27183575 DOI: 10.4049/jimmunol.1501029] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 04/04/2016] [Indexed: 12/21/2022]
Abstract
How the TCR repertoire, in concert with risk-associated MHC, imposes susceptibility for autoimmune diseases is incompletely resolved. Due largely to recombinatorial biases, a small fraction of TCRα or β-chains are shared by most individuals, or public. If public TCR chains modulate a TCRαβ heterodimer's likelihood of productively engaging autoantigen, because they are pervasive and often high frequency, they could also broadly influence disease risk and progression. Prior data, using low-resolution techniques, have identified the heavy use of select public TCR in some autoimmune models. In this study, we assess public repertoire representation in mice with experimental autoimmune encephalomyelitis at high resolution. Saturation sequencing was used to identify >18 × 10(6) TCRβ sequences from the CNSs, periphery, and thymi of mice at different stages of autoimmune encephalomyelitis and healthy controls. Analyses indicated the prominent representation of a highly diverse public TCRβ repertoire in the disease response. Preferential formation of public TCR implicated in autoimmunity was identified in preselection thymocytes, and, consistently, public, disease-associated TCRβ were observed to be commonly oligoclonal. Increased TCR sharing and a focusing of the public TCR response was seen with disease progression. Critically, comparisons of peripheral and CNS repertoires and repertoires from preimmune and diseased mice demonstrated that public TCR were preferentially deployed relative to nonshared, or private, sequences. Our findings implicate public TCR in skewing repertoire response during autoimmunity and suggest that subsets of public TCR sequences may serve as disease-specific biomarkers or influence disease susceptibility or progression.
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Affiliation(s)
- Yunqian Zhao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105; and
| | - Phuong Nguyen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105; and
| | - Jing Ma
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105; and
| | - Tianhua Wu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105; and
| | - Lindsay L Jones
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105; and
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Terrence L Geiger
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105; and
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24
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Beltman JB, Urbanus J, Velds A, van Rooij N, Rohr JC, Naik SH, Schumacher TN. Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells. BMC Bioinformatics 2016; 17:151. [PMID: 27038897 PMCID: PMC4818877 DOI: 10.1186/s12859-016-0999-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 03/23/2016] [Indexed: 12/31/2022] Open
Abstract
Background Next generation sequencing (NGS) of amplified DNA is a powerful tool to describe genetic heterogeneity within cell populations that can both be used to investigate the clonal structure of cell populations and to perform genetic lineage tracing. For applications in which both abundant and rare sequences are biologically relevant, the relatively high error rate of NGS techniques complicates data analysis, as it is difficult to distinguish rare true sequences from spurious sequences that are generated by PCR or sequencing errors. This issue, for instance, applies to cellular barcoding strategies that aim to follow the amount and type of offspring of single cells, by supplying these with unique heritable DNA tags. Results Here, we use genetic barcoding data from the Illumina HiSeq platform to show that straightforward read threshold-based filtering of data is typically insufficient to filter out spurious barcodes. Importantly, we demonstrate that specific sequencing errors occur at an approximately constant rate across different samples that are sequenced in parallel. We exploit this observation by developing a novel approach to filter out spurious sequences. Conclusions Application of our new method demonstrates its value in the identification of true sequences amongst spurious sequences in biological data sets. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0999-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joost B Beltman
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. .,Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC, Leiden, The Netherlands.
| | - Jos Urbanus
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Arno Velds
- Genomics Core Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Nienke van Rooij
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Jan C Rohr
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg and University of Freiburg, Freiburg, Germany
| | - Shalin H Naik
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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25
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Hou XL, Wang L, Ding YL, Xie Q, Diao HY. Current status and recent advances of next generation sequencing techniques in immunological repertoire. Genes Immun 2016; 17:153-64. [PMID: 26963138 DOI: 10.1038/gene.2016.9] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 01/20/2016] [Accepted: 01/20/2016] [Indexed: 01/26/2023]
Abstract
To ward off a wide variety of pathogens, the human adaptive immune system harbors a vast array of T-cell receptors (TCRs) and B-cell receptors (BCRs), collectively referred to as the immune repertoire. High-throughput sequencing (HTS) of TCR/BCR genes allows in-depth molecular analysis of T/B-cell clones, providing an unprecedented level of detail when examining the T/B-cell repertoire of individuals. It can evaluate TCR/BCR complementarity-determining region 3 (CDR3) diversity and assess the clonal composition, including the size of the repertoire; similarities between repertoires; V(D)J segment use; nucleotide insertions and deletions; CDR3 lengths; and amino acid distributions along the CDR3s at sequence-level resolution. Deep sequencing of B-cell and T-cell repertoires offers the potential for a quantitative understanding of the adaptive immune system in healthy and disease states. Recently, paired sequencing strategies have also been developed, which can provide information about the identity of immune receptor pairs encoded by individual T or B lymphocytes. HTS technology provides a previously unimaginable amount of sequence data, accompanied, however, by numerous challenges associated with error correction and interpretation that remain to be solved. The review details some of the technologies and some of the recent achievements in this field.
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Affiliation(s)
- X-L Hou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - L Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Y-L Ding
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Q Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - H-Y Diao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Perales C, Quer J, Gregori J, Esteban JI, Domingo E. Resistance of Hepatitis C Virus to Inhibitors: Complexity and Clinical Implications. Viruses 2015; 7:5746-66. [PMID: 26561827 PMCID: PMC4664975 DOI: 10.3390/v7112902] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 10/23/2015] [Accepted: 10/26/2015] [Indexed: 12/20/2022] Open
Abstract
Selection of inhibitor-resistant viral mutants is universal for viruses that display quasi-species dynamics, and hepatitis C virus (HCV) is no exception. Here we review recent results on drug resistance in HCV, with emphasis on resistance to the newly-developed, directly-acting antiviral agents, as they are increasingly employed in the clinic. We put the experimental observations in the context of quasi-species dynamics, in particular what the genetic and phenotypic barriers to resistance mean in terms of exploration of sequence space while HCV replicates in the liver of infected patients or in cell culture. Strategies to diminish the probability of viral breakthrough during treatment are briefly outlined.
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Affiliation(s)
- Celia Perales
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain.
- Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
| | - Josep Quer
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
- Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
| | - Josep Gregori
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
- Roche Diagnostics SL, 08174 Sant Cugat del Vallès, Spain.
| | - Juan Ignacio Esteban
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
- Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
| | - Esteban Domingo
- Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
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IMonitor: A Robust Pipeline for TCR and BCR Repertoire Analysis. Genetics 2015; 201:459-72. [PMID: 26297338 DOI: 10.1534/genetics.115.176735] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 08/16/2015] [Indexed: 12/21/2022] Open
Abstract
The advance of next generation sequencing (NGS) techniques provides an unprecedented opportunity to probe the enormous diversity of the immune repertoire by deep sequencing T-cell receptors (TCRs) and B-cell receptors (BCRs). However, an efficient and accurate analytical tool is still on demand to process the huge amount of data. We have developed a high-resolution analytical pipeline, Immune Monitor ("IMonitor") to tackle this task. This method utilizes realignment to identify V(D)J genes and alleles after common local alignment. We compare IMonitor with other published tools by simulated and public rearranged sequences, and it demonstrates its superior performance in most aspects. Together with this, a methodology is developed to correct the PCR and sequencing errors and to minimize the PCR bias among various rearranged sequences with different V and J gene families. IMonitor provides general adaptation for sequences from all receptor chains of different species and outputs useful statistics and visualizations. In the final part of this article, we demonstrate its application on minimal residual disease detection in patients with B-cell acute lymphoblastic leukemia. In summary, this package would be of widespread usage for immune repertoire analysis.
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Nazarov VI, Pogorelyy MV, Komech EA, Zvyagin IV, Bolotin DA, Shugay M, Chudakov DM, Lebedev YB, Mamedov IZ. tcR: an R package for T cell receptor repertoire advanced data analysis. BMC Bioinformatics 2015; 16:175. [PMID: 26017500 PMCID: PMC4445501 DOI: 10.1186/s12859-015-0613-1] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/13/2015] [Indexed: 11/18/2022] Open
Abstract
Background The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is required for the rational analysis of massive data generated by next-generation sequencing. Results Here we introduce tcR, a new R package, representing a platform for the advanced analysis of T cell receptor repertoires, which includes diversity measures, shared T cell receptor sequences identification, gene usage statistics computation and other widely used methods. The tool has proven its utility in recent research studies. Conclusions tcR is an R package for the advanced analysis of T cell receptor repertoires after primary TR sequences extraction from raw sequencing reads. The stable version can be directly installed from The Comprehensive R Archive Network (http://cran.r-project.org/mirrors.html). The source code and development version are available at tcR GitHub (http://imminfo.github.io/tcr/) along with the full documentation and typical usage examples.
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Affiliation(s)
- Vadim I Nazarov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. .,National Research University Higher School of Economics, 20 Myasnitskaya Ulitsa, Moscow, 101000, Russia.
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia.
| | - Ekaterina A Komech
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia.
| | - Ivan V Zvyagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Dmitry A Bolotin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia.
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia.
| | - Dmitry M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Yury B Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia.
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya, Moscow, 117997, Russia.
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Egorov ES, Merzlyak EM, Shelenkov AA, Britanova OV, Sharonov GV, Staroverov DB, Bolotin DA, Davydov AN, Barsova E, Lebedev YB, Shugay M, Chudakov DM. Quantitative Profiling of Immune Repertoires for Minor Lymphocyte Counts Using Unique Molecular Identifiers. THE JOURNAL OF IMMUNOLOGY 2015; 194:6155-63. [DOI: 10.4049/jimmunol.1500215] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/08/2015] [Indexed: 12/11/2022]
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Thys K, Verhasselt P, Reumers J, Verbist BMP, Maes B, Aerssens J. Performance assessment of the Illumina massively parallel sequencing platform for deep sequencing analysis of viral minority variants. J Virol Methods 2015; 221:29-38. [PMID: 25917877 DOI: 10.1016/j.jviromet.2015.04.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 03/21/2015] [Accepted: 04/16/2015] [Indexed: 11/26/2022]
Abstract
Massively parallel sequencing (MPS) technology has opened new avenues to study viral dynamics and treatment-induced resistance mechanisms of infections such as human immunodeficiency virus (HIV) and hepatitis C virus (HCV). Whereas the Roche/454 platform has been used widely for the detection of low-frequent drug resistant variants, more recently developed short-read MPS technologies have the advantage of delivering a higher sequencing depth at a lower cost per sequenced base. This study assesses the performance characteristics of Illumina MPS technology for the characterization of genetic variability in viral populations by deep sequencing. The reported results from MPS experiments comprising HIV and HCV plasmids demonstrate that a 0.5-1% lower limit of detection can be achieved readily with Illumina MPS while retaining good accuracy also at low frequencies. Deep sequencing of a set of clinical samples (12 HIV and 9 HCV patients), designed at a similar budget for both MPS platforms, reveals a comparable lower limit of detection for Illumina and Roche/454. Finally, this study shows the possibility to apply Illumina's paired-end sequencing as a strategy to assess linkage between different mutations identified in individual viral subspecies. These results support the use of Illumina as another MPS platform of choice for deep sequencing of viral minority species.
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Affiliation(s)
- Kim Thys
- Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium.
| | - Peter Verhasselt
- Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium.
| | - Joke Reumers
- Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium.
| | - Bie M P Verbist
- Department of Mathematical Modeling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000 Gent, Belgium.
| | - Bart Maes
- Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium.
| | - Jeroen Aerssens
- Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium.
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Heydt C, Kumm N, Fassunke J, Künstlinger H, Ihle MA, Scheel A, Schildhaus HU, Haller F, Büttner R, Odenthal M, Wardelmann E, Merkelbach-Bruse S. Massively parallel sequencing fails to detect minor resistant subclones in tissue samples prior to tyrosine kinase inhibitor therapy. BMC Cancer 2015; 15:291. [PMID: 25886408 PMCID: PMC4404105 DOI: 10.1186/s12885-015-1311-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 04/01/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Personalised medicine and targeted therapy have revolutionised cancer treatment. However, most patients develop drug resistance and relapse after showing an initial treatment response. Two theories have been postulated; either secondary resistance mutations develop de novo during therapy by mutagenesis or they are present in minor subclones prior to therapy. In this study, these two theories were evaluated in gastrointestinal stromal tumours (GISTs) where most patients develop secondary resistance mutations in the KIT gene during therapy with tyrosine kinase inhibitors. METHODS We used a cohort of 33 formalin-fixed, paraffin embedded (FFPE) primary GISTs and their corresponding recurrent tumours with known mutational status. The primary tumours were analysed for the secondary mutations of the recurrences, which had been identified previously. The primary tumours were resected prior to tyrosine kinase inhibitor therapy. Three ultrasensitive, massively parallel sequencing approaches on the GS Junior (Roche, Mannheim, Germany) and the MiSeq(TM) (Illumina, San Diego, CA, USA) were applied. Additionally, nine fresh-frozen samples resected prior to therapy were analysed for the most common secondary resistance mutations. RESULTS With a sensitivity level of down to 0.02%, no pre-existing resistant subclones with secondary KIT mutations were detected in primary GISTs. The sensitivity level varied for individual secondary mutations and was limited by sequencing artefacts on both systems. Artificial T > C substitutions at the position of the exon 13 p.V654A mutation, in particular, led to a lower sensitivity, independent from the source of the material. Fresh-frozen samples showed the same range of artificially mutated allele frequencies as the FFPE material. CONCLUSIONS Although we achieved a sufficiently high level of sensitivity, neither in the primary FFPE nor in the fresh-frozen GISTs we were able to detect pre-existing resistant subclones of the corresponding known secondary resistance mutations of the recurrent tumours. This supports the theory that secondary KIT resistance mutations develop under treatment by "de novo" mutagenesis. Alternatively, the detection limit of two mutated clones in 10,000 wild-type clones might not have been high enough or heterogeneous tissue samples, per se, might not be suitable for the detection of very small subpopulations of mutated cells.
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Affiliation(s)
- Carina Heydt
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Niklas Kumm
- Institute of Pathology, University Hospital Erlangen, Krankenhausstraße 8-10, 91054, Erlangen, Germany.
| | - Jana Fassunke
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Helen Künstlinger
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Michaela Angelika Ihle
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Andreas Scheel
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Hans-Ulrich Schildhaus
- Institute of Pathology, University Hospital Göttingen, Robert-Koch-Strasse 40, 37075, Göttingen, Germany.
| | - Florian Haller
- Institute of Pathology, University Hospital Erlangen, Krankenhausstraße 8-10, 91054, Erlangen, Germany.
| | - Reinhard Büttner
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Margarete Odenthal
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Eva Wardelmann
- Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Albert-Schweitzer-Campus 1, Gebäude D17, 48149, Münster, Germany.
| | - Sabine Merkelbach-Bruse
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
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Abstract
The development of high-throughput DNA sequencing technologies has enabled large-scale characterization of functional antibody repertoires, a new method of understanding protective and pathogenic immune responses. Important parameters to consider when sequencing antibody repertoires include the methodology, the B-cell population and clinical characteristics of the individuals analysed, and the bioinformatic analysis. Although focused sequencing of immunoglobulin heavy chains or complement determining regions can be utilized to monitor particular immune responses and B-cell malignancies, high-fidelity analysis of the full-length paired heavy and light chains expressed by individual B cells is critical for characterizing functional antibody repertoires. Bioinformatic identification of clonal antibody families and recombinant expression of representative members produces recombinant antibodies that can be used to identify the antigen targets of functional immune responses and to investigate the mechanisms of their protective or pathogenic functions. Integrated analysis of coexpressed functional genes provides the potential to further pinpoint the most important antibodies and clonal families generated during an immune response. Sequencing antibody repertoires is transforming our understanding of immune responses to autoimmunity, vaccination, infection and cancer. We anticipate that antibody repertoire sequencing will provide next-generation biomarkers, diagnostic tools and therapeutic antibodies for a spectrum of diseases, including rheumatic diseases.
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Affiliation(s)
- William H. Robinson
- Division of Immunology and Rheumatology, CCSR 4135, 269 Campus Drive, Stanford, CA 94305, USA.
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Podgorny OV, Polina NF, Babenko VV, Karpova IY, Kostryukova ES, Govorun VM, Lazarev VN. Isolation of single Chlamydia-infected cells using laser microdissection. J Microbiol Methods 2015; 109:123-8. [DOI: 10.1016/j.mimet.2014.12.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 12/12/2014] [Accepted: 12/23/2014] [Indexed: 11/15/2022]
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Weitemier K, Straub SCK, Fishbein M, Liston A. Intragenomic polymorphisms among high-copy loci: a genus-wide study of nuclear ribosomal DNA in Asclepias (Apocynaceae). PeerJ 2015; 3:e718. [PMID: 25653903 PMCID: PMC4304868 DOI: 10.7717/peerj.718] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 12/11/2014] [Indexed: 11/20/2022] Open
Abstract
Despite knowledge that concerted evolution of high-copy loci is often imperfect, studies that investigate the extent of intragenomic polymorphisms and comparisons across a large number of species are rarely made. We present a bioinformatic pipeline for characterizing polymorphisms within an individual among copies of a high-copy locus. Results are presented for nuclear ribosomal DNA (nrDNA) across the milkweed genus, Asclepias. The 18S-26S portion of the nrDNA cistron of Asclepias syriaca served as a reference for assembly of the region from 124 samples representing 90 species of Asclepias. Reads were mapped back to each individual’s consensus and at each position reads differing from the consensus were tallied using a custom perl script. Low frequency polymorphisms existed in all individuals (mean = 5.8%). Most nrDNA positions (91%) were polymorphic in at least one individual, with polymorphic sites being less frequent in subunit regions and loops. Highly polymorphic sites existed in each individual, with highest abundance in the “noncoding” ITS regions. Phylogenetic signal was present in the distribution of intragenomic polymorphisms across the genus. Intragenomic polymorphisms in nrDNA are common in Asclepias, being found at higher frequency than any other study to date. The high and variable frequency of polymorphisms across species highlights concerns that phylogenetic applications of nrDNA may be error-prone. The new analytical approach provided here is applicable to other taxa and other high-copy regions characterized by low coverage genome sequencing (genome skimming).
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Affiliation(s)
- Kevin Weitemier
- Department of Botany and Plant Pathology, Oregon State University , Corvallis, OR , USA
| | - Shannon C K Straub
- Department of Biology, Hobart and William Smith Colleges , Geneva, NY , USA
| | - Mark Fishbein
- Department of Botany, Oklahoma State University , Stillwater, OK , USA
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University , Corvallis, OR , USA
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Deakin CT, Deakin JJ, Ginn SL, Young P, Humphreys D, Suter CM, Alexander IE, Hallwirth CV. Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence. Nucleic Acids Res 2014; 42:e129. [PMID: 25013183 PMCID: PMC4176369 DOI: 10.1093/nar/gku607] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Barcoded vectors are promising tools for investigating clonal diversity and dynamics in hematopoietic gene therapy. Analysis of clones marked with barcoded vectors requires accurate identification of potentially large numbers of individually rare barcodes, when the exact number, sequence identity and abundance are unknown. This is an inherently challenging application, and the feasibility of using contemporary next-generation sequencing technologies is unresolved. To explore this potential application empirically, without prior assumptions, we sequenced barcode libraries of known complexity. Libraries containing 1, 10 and 100 Sanger-sequenced barcodes were sequenced using an Illumina platform, with a 100-barcode library also sequenced using a SOLiD platform. Libraries containing 1 and 10 barcodes were distinguished from false barcodes generated by sequencing error by a several log-fold difference in abundance. In 100-barcode libraries, however, expected and false barcodes overlapped and could not be resolved by bioinformatic filtering and clustering strategies. In independent sequencing runs multiple false-positive barcodes appeared to be represented at higher abundance than known barcodes, despite their confirmed absence from the original library. Such errors, which potentially impact barcoding studies in an application-dependent manner, are consistent with the existence of both stochastic and systematic error, the mechanism of which is yet to be fully resolved.
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Affiliation(s)
- Claire T Deakin
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Jeffrey J Deakin
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Samantha L Ginn
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Paul Young
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, Darlinghurst, New South Wales 2010, Australia
| | - David Humphreys
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, Darlinghurst, New South Wales 2010, Australia
| | - Catherine M Suter
- Molecular Genetics Division, Victor Chang Cardiac Research Institute, Sydney, Darlinghurst, New South Wales 2010, Australia Faculty of Medicine, University of New South Wales, Kensington, New South Wales 2052, Australia
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia Discipline of Paediatrics and Child Health, The Children's Hospital at Westmead Clinical School, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
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Development and performance of a targeted whole exome sequencing enrichment kit for the dog (Canis Familiaris Build 3.1). Sci Rep 2014; 4:5597. [PMID: 24998260 PMCID: PMC4083258 DOI: 10.1038/srep05597] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/18/2014] [Indexed: 11/29/2022] Open
Abstract
Whole exome sequencing is a technique that aims to selectively sequence all exons of protein-coding genes. A canine whole exome sequencing enrichment kit was designed based on the latest canine reference genome (build 3.1.72). Its performance was tested by sequencing 2 exome captures, each consisting of 4 pre-capture pooled, barcoded Illumina libraries on an Illumina HiSeq 2500. At an average sequencing depth of 102x, 83 to 86% of the target regions were completely sequenced with a minimum coverage of five and 90% of the reads mapped on the target regions. Additionally, it is shown that the reproducibility within and between captures is high and that pooling four samples per capture is a valid option. Overall, we have demonstrated the strong performance of this WES enrichment kit and are confident it will be a valuable tool in future disease association studies.
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Knief C. Analysis of plant microbe interactions in the era of next generation sequencing technologies. FRONTIERS IN PLANT SCIENCE 2014; 5:216. [PMID: 24904612 PMCID: PMC4033234 DOI: 10.3389/fpls.2014.00216] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 04/30/2014] [Indexed: 05/18/2023]
Abstract
Next generation sequencing (NGS) technologies have impressively accelerated research in biological science during the last years by enabling the production of large volumes of sequence data to a drastically lower price per base, compared to traditional sequencing methods. The recent and ongoing developments in the field allow addressing research questions in plant-microbe biology that were not conceivable just a few years ago. The present review provides an overview of NGS technologies and their usefulness for the analysis of microorganisms that live in association with plants. Possible limitations of the different sequencing systems, in particular sources of errors and bias, are critically discussed and methods are disclosed that help to overcome these shortcomings. A focus will be on the application of NGS methods in metagenomic studies, including the analysis of microbial communities by amplicon sequencing, which can be considered as a targeted metagenomic approach. Different applications of NGS technologies are exemplified by selected research articles that address the biology of the plant associated microbiota to demonstrate the worth of the new methods.
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Affiliation(s)
- Claudia Knief
- Institute of Crop Science and Resource Conservation—Molecular Biology of the Rhizosphere, Faculty of Agriculture, University of BonnBonn, Germany
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Towards error-free profiling of immune repertoires. Nat Methods 2014; 11:653-5. [DOI: 10.1038/nmeth.2960] [Citation(s) in RCA: 317] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 04/09/2014] [Indexed: 01/17/2023]
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Distinctive properties of identical twins' TCR repertoires revealed by high-throughput sequencing. Proc Natl Acad Sci U S A 2014; 111:5980-5. [PMID: 24711416 DOI: 10.1073/pnas.1319389111] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Adaptive immunity in humans is provided by hypervariable Ig-like molecules on the surface of B and T cells. The final set of these molecules in each organism is formed under the influence of two forces: individual genetic traits and the environment, which includes the diverse spectra of alien and self-antigens. Here we assess the impact of individual genetic factors on the formation of the adaptive immunity by analyzing the T-cell receptor (TCR) repertoires of three pairs of monozygous twins by next-generation sequencing. Surprisingly, we found that an overlap between the TCR repertoires of monozygous twins is similar to an overlap between the TCR repertoires of nonrelated individuals. However, the number of identical complementary determining region 3 sequences in two individuals is significantly increased for twin pairs in the fraction of highly abundant TCR molecules, which is enriched by the antigen-experienced T cells. We found that the initial recruitment of particular TCR V genes for recombination and subsequent selection in the thymus is strictly determined by individual genetic factors. J genes of TCRs are selected randomly for recombination; however, the subsequent selection in the thymus gives preference to some α but not β J segments. These findings provide a deeper insight into the mechanism of TCR repertoire generation.
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Li S, Lefranc MP, Miles JJ, Alamyar E, Giudicelli V, Duroux P, Freeman JD, Corbin VDA, Scheerlinck JP, Frohman MA, Cameron PU, Plebanski M, Loveland B, Burrows SR, Papenfuss AT, Gowans EJ. IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling. Nat Commun 2014; 4:2333. [PMID: 23995877 PMCID: PMC3778833 DOI: 10.1038/ncomms3333] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/23/2013] [Indexed: 02/08/2023] Open
Abstract
T cell repertoire diversity and clonotype follow-up in vaccination, cancer, infectious and immune diseases represent a major challenge owing to the enormous complexity of the data generated. Here we describe a next generation methodology, which combines 5'RACE PCR, 454 sequencing and, for analysis, IMGT, the international ImMunoGeneTics information system (IMGT), IMGT/HighV-QUEST web portal and IMGT-ONTOLOGY concepts. The approach is validated in a human case study of T cell receptor beta (TRB) repertoire, by chronologically tracking the effects of influenza vaccination on conventional and regulatory T cell subpopulations. The IMGT/HighV-QUEST paradigm defines standards for genotype/haplotype analysis and characterization of IMGT clonotypes for clonal diversity and expression and achieves a degree of resolution for next generation sequencing verifiable by the user at the sequence level, while providing a normalized reference immunoprofile for human TRB.
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Affiliation(s)
- Shuo Li
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria 3052, Australia
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41
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Greiner TC. Clinical use of next-generation sequencing of TRG gene rearrangements has arrived. Am J Clin Pathol 2014; 141:302-4. [PMID: 24515756 DOI: 10.1309/ajcp5ym3aalkqbii] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Timothy C. Greiner
- Department of Pathology & Microbiology, University of Nebraska Medical Center, Omaha
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Niklas N, Pröll J, Weinberger J, Zopf A, Wiesinger K, Krismer K, Bettelheim P, Gabriel C. Qualifying high-throughput immune repertoire sequencing. Cell Immunol 2014; 288:31-8. [PMID: 24607567 DOI: 10.1016/j.cellimm.2014.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 11/06/2013] [Accepted: 02/12/2014] [Indexed: 10/25/2022]
Abstract
Diversity of B and T cell receptors, achieved by gene recombination and somatic hypermutation, allows the immune system for recognition and targeted reaction against various threats. Next-generation sequencing for assessment of a cell's gene composition and variation makes deep analysis of one individual's immune spectrum feasible. An easy to apply but detailed analysis and visualization strategy is necessary to process all sequences generated. We performed sequencing utilizing the 454 system for CLL and control samples, utilized the IMGT database and applied the presented analysis tools. With the applied protocol, malignant clones are found and characterized, mutational status compared to germline identity is elaborated in detail showing that the CLL mutation status is not as monoclonal as generally thought. On the other hand, this strategy is not solely applicable to the 454 sequencing system but can easily be transferred to any other next-generation sequencing platform.
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Affiliation(s)
- Norbert Niklas
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Johannes Pröll
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Johannes Weinberger
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Agnes Zopf
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Karin Wiesinger
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Konstantin Krismer
- University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria.
| | - Peter Bettelheim
- Division of Hematology/Oncology, Elisabethinen Hospital Linz, Fadingerstraße 1, 4020 Linz, Austria.
| | - Christian Gabriel
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
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43
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The promise and challenge of high-throughput sequencing of the antibody repertoire. Nat Biotechnol 2014; 32:158-68. [PMID: 24441474 PMCID: PMC4113560 DOI: 10.1038/nbt.2782] [Citation(s) in RCA: 471] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 12/04/2013] [Indexed: 12/16/2022]
Abstract
Georgiou and colleagues discuss rapidly evolving methods for high-throughput sequencing of the antibody repertoire, and how the resulting data may be applied to answer basic and translational research questions. Efforts to determine the antibody repertoire encoded by B cells in the blood or lymphoid organs using high-throughput DNA sequencing technologies have been advancing at an extremely rapid pace and are transforming our understanding of humoral immune responses. Information gained from high-throughput DNA sequencing of immunoglobulin genes (Ig-seq) can be applied to detect B-cell malignancies with high sensitivity, to discover antibodies specific for antigens of interest, to guide vaccine development and to understand autoimmunity. Rapid progress in the development of experimental protocols and informatics analysis tools is helping to reduce sequencing artifacts, to achieve more precise quantification of clonal diversity and to extract the most pertinent biological information. That said, broader application of Ig-seq, especially in clinical settings, will require the development of a standardized experimental design framework that will enable the sharing and meta-analysis of sequencing data generated by different laboratories.
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Putintseva EV, Britanova OV, Staroverov DB, Merzlyak EM, Turchaninova MA, Shugay M, Bolotin DA, Pogorelyy MV, Mamedov IZ, Bobrynina V, Maschan M, Lebedev YB, Chudakov DM. Mother and child T cell receptor repertoires: deep profiling study. Front Immunol 2013; 4:463. [PMID: 24400004 PMCID: PMC3872299 DOI: 10.3389/fimmu.2013.00463] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 12/03/2013] [Indexed: 12/03/2022] Open
Abstract
The relationship between maternal and child immunity has been actively studied in the context of complications during pregnancy, autoimmune diseases, and haploidentical transplantation of hematopoietic stem cells and solid organs. Here, we have for the first time used high-throughput Illumina HiSeq sequencing to perform deep quantitative profiling of T cell receptor (TCR) repertoires for peripheral blood samples of three mothers and their six children. Advanced technology allowed accurate identification of 5 × 105 to 2 × 106 TCR beta clonotypes per individual. We performed comparative analysis of these TCR repertoires with the aim of revealing characteristic features that distinguish related mother-child pairs, such as relative TCR beta variable segment usage frequency and relative overlap of TCR beta complementarity-determining region 3 (CDR3) repertoires. We show that thymic selection essentially and similarly shapes the initial output of the TCR recombination machinery in both related and unrelated pairs, with minor effect from inherited differences. The achieved depth of TCR profiling also allowed us to test the hypothesis that mature T cells transferred across the placenta during pregnancy can expand and persist as functional microchimeric clones in their new host, using characteristic TCR beta CDR3 variants as clonal identifiers.
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Affiliation(s)
- Ekaterina V Putintseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Olga V Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Dmitriy B Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Ekaterina M Merzlyak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Maria A Turchaninova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Dmitriy A Bolotin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Vlasta Bobrynina
- Federal Scientific Clinical Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia
| | - Mikhail Maschan
- Federal Scientific Clinical Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia
| | - Yuri B Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia ; Central European Institute of Technology (CEITEC), Masaryk University , Brno , Czech Republic
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Mori A, Deola S, Xumerle L, Mijatovic V, Malerba G, Monsurrò V. Next generation sequencing: new tools in immunology and hematology. Blood Res 2013; 48:242-9. [PMID: 24466547 PMCID: PMC3894381 DOI: 10.5045/br.2013.48.4.242] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 11/21/2013] [Accepted: 12/11/2013] [Indexed: 11/17/2022] Open
Abstract
One of the hallmarks of the adaptive immune system is the specificity of B and T cell receptors. Thanks to somatic recombination, a large repertoire of receptors can be generated within an individual that guarantee the recognition of a vast number of antigens. Monoclonal antibodies have limited applicability, given the high degree of diversity among these receptors, in BCR and TCR monitoring. Furthermore, with regard to cancer, better characterization of complex genomes and the ability to monitor tumor-specific cryptic mutations or translocations are needed to develop better tailored therapies. Novel technologies, by enhancing the ability of BCR and TCR monitoring, can help in the search for minimal residual disease during hematological malignancy diagnosis and follow-up, and can aid in improving bone marrow transplantation techniques. Recently, a novel technology known as next generation sequencing has been developed; this allows the recognition of unique sequences and provides depth of coverage, heterogeneity, and accuracy of sequencing. This provides a powerful tool that, along with microarray analysis for gene expression, may become integral in resolving the remaining key problems in hematology. This review describes the state of the art of this novel technology, its application in the immunological and hematological fields, and the possible benefits it will provide for the hematology and immunology community.
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Affiliation(s)
- Antonio Mori
- Department of Life and Reproduction Science, University of Verona, Verona, Italy
| | - Sara Deola
- Hematology Unit, Bolzano Central Hospital, Bolzano, Italy
| | - Luciano Xumerle
- Department of Life and Reproduction Science, University of Verona, Verona, Italy
| | - Vladan Mijatovic
- Department of Life and Reproduction Science, University of Verona, Verona, Italy
| | - Giovanni Malerba
- Department of Life and Reproduction Science, University of Verona, Verona, Italy
| | - Vladia Monsurrò
- Department of Pathology and Diagnostics, University of Verona, Verona, Italy
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Mamedov IZ, Britanova OV, Zvyagin IV, Turchaninova MA, Bolotin DA, Putintseva EV, Lebedev YB, Chudakov DM. Preparing unbiased T-cell receptor and antibody cDNA libraries for the deep next generation sequencing profiling. Front Immunol 2013; 4:456. [PMID: 24391640 PMCID: PMC3870325 DOI: 10.3389/fimmu.2013.00456] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 11/30/2013] [Indexed: 11/25/2022] Open
Abstract
High-throughput sequencing has the power to reveal the nature of adaptive immunity as represented by the full complexity of T-cell receptor (TCR) and antibody (IG) repertoires, but is at present severely compromised by the quantitative bias, bottlenecks, and accumulated errors that inevitably occur in the course of library preparation and sequencing. Here we report an optimized protocol for the unbiased preparation of TCR and IG cDNA libraries for high-throughput sequencing, starting from thousands or millions of live cells in an investigated sample. Critical points to control are revealed, along with tips that allow researchers to minimize quantitative bias, accumulated errors, and cross-sample contamination at each stage, and to enhance the subsequent bioinformatic analysis. The protocol is simple, reliable, and can be performed in 1–2 days.
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Affiliation(s)
- Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia ; CEITEC, Masaryk University , Brno , Czech Republic
| | - Olga V Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Ivan V Zvyagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia ; CEITEC, Masaryk University , Brno , Czech Republic
| | - Maria A Turchaninova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Dmitriy A Bolotin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Ekaterina V Putintseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Yuriy B Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia ; CEITEC, Masaryk University , Brno , Czech Republic
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47
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Woodsworth DJ, Castellarin M, Holt RA. Sequence analysis of T-cell repertoires in health and disease. Genome Med 2013; 5:98. [PMID: 24172704 PMCID: PMC3979016 DOI: 10.1186/gm502] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
T-cell antigen receptor (TCR) variability enables the cellular immune system to discriminate between self and non-self. High-throughput TCR sequencing (TCR-seq) involves the use of next generation sequencing platforms to generate large numbers of short DNA sequences covering key regions of the TCR coding sequence, which enables quantification of T-cell diversity at unprecedented resolution. TCR-seq studies have provided new insights into the healthy human T-cell repertoire, such as revised estimates of repertoire size and the understanding that TCR specificities are shared among individuals more frequently than previously anticipated. In the context of disease, TCR-seq has been instrumental in characterizing the recovery of the immune repertoire after hematopoietic stem cell transplantation, and the method has been used to develop biomarkers and diagnostics for various infectious and neoplastic diseases. However, T-cell repertoire sequencing is still in its infancy. It is expected that maturation of the field will involve the introduction of improved, standardized tools for data handling, deposition and statistical analysis, as well as the emergence of new and equivalently large-scale technologies for T-cell functional analysis and antigen discovery. In this review, we introduce this nascent field and TCR-seq methodology, we discuss recent insights into healthy and diseased TCR repertoires, and we examine the applications and challenges for TCR-seq in the clinic.
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Affiliation(s)
- Daniel J Woodsworth
- BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada
- Genome Sciences & Technology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Mauro Castellarin
- BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Robert A Holt
- BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 1L3, Canada
- Genome Sciences & Technology Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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48
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Buschmann T, Bystrykh LV. Levenshtein error-correcting barcodes for multiplexed DNA sequencing. BMC Bioinformatics 2013; 14:272. [PMID: 24021088 PMCID: PMC3853030 DOI: 10.1186/1471-2105-14-272] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 08/30/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND High-throughput sequencing technologies are improving in quality, capacity and costs, providing versatile applications in DNA and RNA research. For small genomes or fraction of larger genomes, DNA samples can be mixed and loaded together on the same sequencing track. This so-called multiplexing approach relies on a specific DNA tag or barcode that is attached to the sequencing or amplification primer and hence appears at the beginning of the sequence in every read. After sequencing, each sample read is identified on the basis of the respective barcode sequence.Alterations of DNA barcodes during synthesis, primer ligation, DNA amplification, or sequencing may lead to incorrect sample identification unless the error is revealed and corrected. This can be accomplished by implementing error correcting algorithms and codes. This barcoding strategy increases the total number of correctly identified samples, thus improving overall sequencing efficiency. Two popular sets of error-correcting codes are Hamming codes and Levenshtein codes. RESULT Levenshtein codes operate only on words of known length. Since a DNA sequence with an embedded barcode is essentially one continuous long word, application of the classical Levenshtein algorithm is problematic. In this paper we demonstrate the decreased error correction capability of Levenshtein codes in a DNA context and suggest an adaptation of Levenshtein codes that is proven of efficiently correcting nucleotide errors in DNA sequences. In our adaption we take the DNA context into account and redefine the word length whenever an insertion or deletion is revealed. In simulations we show the superior error correction capability of the new method compared to traditional Levenshtein and Hamming based codes in the presence of multiple errors. CONCLUSION We present an adaptation of Levenshtein codes to DNA contexts capable of correction of a pre-defined number of insertion, deletion, and substitution mutations. Our improved method is additionally capable of recovering the new length of the corrupted codeword and of correcting on average more random mutations than traditional Levenshtein or Hamming codes.As part of this work we prepared software for the flexible generation of DNA codes based on our new approach. To adapt codes to specific experimental conditions, the user can customize sequence filtering, the number of correctable mutations and barcode length for highest performance.
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Affiliation(s)
- Tilo Buschmann
- Institute for Medical Informatics and Biometry (IMB), Faculty of Medicine Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Leonid V Bystrykh
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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Bolotin DA, Shugay M, Mamedov IZ, Putintseva EV, Turchaninova MA, Zvyagin IV, Britanova OV, Chudakov DM. MiTCR: software for T-cell receptor sequencing data analysis. Nat Methods 2013; 10:813-4. [DOI: 10.1038/nmeth.2555] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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50
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Baum PD, Venturi V, Price DA. Wrestling with the repertoire: the promise and perils of next generation sequencing for antigen receptors. Eur J Immunol 2013; 42:2834-9. [PMID: 23108932 DOI: 10.1002/eji.201242999] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Next generation sequencing technologies are revolutionizing the study of immune repertoires. These methods provide a previously unimaginable amount of sequence data, unfortunately accompanied by numerous challenges associated with error correction and interpretation that remain to be solved. For antigen receptors, these challenges will require dedicated solutions beyond those developed for genome sequencing, which may differ depending on the sequencing technology used and the purpose of the experiment. Many investigators are developing such methods, based on different sequencing platforms, but critical details of protocol and performance are proprietary. The field will move forward when these methods are shared and standardized, and when the accuracy, sensitivity and reproducibility of various sequencing, and analytic methods are evaluated using standardized samples in comparative experiments.
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Affiliation(s)
- Paul D Baum
- Department of Medicine, University of California, San Francisco, CA 94114, USA.
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