1
|
Chen H, Zhang Y, Wang B, Liao R, Duan X, Yang C, Chen J, Hao Y, Shu Y, Cai L, Leng X, Qian NS, Sun D, Niu B, Zhou Q. Characterization and mitigation of artifacts derived from NGS library preparation due to structure-specific sequences in the human genome. BMC Genomics 2024; 25:227. [PMID: 38429743 PMCID: PMC10908179 DOI: 10.1186/s12864-024-10157-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/23/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND Hybridization capture-based targeted next generation sequencing (NGS) is gaining importance in routine cancer clinical practice. DNA library preparation is a fundamental step to produce high-quality sequencing data. Numerous unexpected, low variant allele frequency calls were observed in libraries using sonication fragmentation and enzymatic fragmentation. In this study, we investigated the characteristics of the artifact reads induced by sonication and enzymatic fragmentation. We also developed a bioinformatic algorithm to filter these sequencing errors. RESULTS We used pairwise comparisons of somatic single nucleotide variants (SNVs) and insertions and deletions (indels) of the same tumor DNA samples prepared using both ultrasonic and enzymatic fragmentation protocols. Our analysis revealed that the number of artifact variants was significantly greater in the samples generated using enzymatic fragmentation than using sonication. Most of the artifacts derived from the sonication-treated libraries were chimeric artifact reads containing both cis- and trans-inverted repeat sequences of the genomic DNA. In contrast, chimeric artifact reads of endonuclease-treated libraries contained palindromic sequences with mismatched bases. Based on these distinctive features, we proposed a mechanistic hypothesis model, PDSM (pairing of partial single strands derived from a similar molecule), by which these sequencing errors derive from ultrasonication and enzymatic fragmentation library preparation. We developed a bioinformatic algorithm to generate a custom mutation "blacklist" in the BED region to reduce errors in downstream analyses. CONCLUSIONS We first proposed a mechanistic hypothesis model (PDSM) of sequencing errors caused by specific structures of inverted repeat sequences and palindromic sequences in the natural genome. This new hypothesis predicts the existence of chimeric reads that could not be explained by previous models, and provides a new direction for further improving NGS analysis accuracy. A bioinformatic algorithm, ArtifactsFinder, was developed and used to reduce the sequencing errors in libraries produced using sonication and enzymatic fragmentation.
Collapse
Affiliation(s)
- HuiJuan Chen
- Beijing ChosenMed Clinical Laboratory Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, 100176, China
- Computer Network Information Center, Chinese Academy of Sciences,, University of Chinese Academy of Sciences, Beijing, 100190, China
- WillingMed Technology Beijing Co., Ltd., Beijing, 100176, China
| | - YiRan Zhang
- Beijing ChosenMed Clinical Laboratory Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, 100176, China
| | - Bing Wang
- Beijing ChosenMed Clinical Laboratory Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, 100176, China
| | - Rui Liao
- Beijing ChosenMed Clinical Laboratory Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, 100176, China
| | - XiaoHong Duan
- Beijing ChosenMed Clinical Laboratory Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, 100176, China
- ChosenMed Technology (Zhejiang) Co. Ltd., Zhejiang, 311103, China
| | - ChunYan Yang
- Beijing ChosenMed Clinical Laboratory Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, 100176, China
| | - Jing Chen
- Beijing ChosenMed Clinical Laboratory Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, 100176, China
| | - YanTong Hao
- Beijing ChosenMed Clinical Laboratory Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, 100176, China
| | - YingShuang Shu
- Beijing ChosenMed Clinical Laboratory Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, 100176, China
| | - LiLi Cai
- Beijing ChosenMed Clinical Laboratory Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, 100176, China
| | - Xue Leng
- Beijing ChosenMed Clinical Laboratory Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, 100176, China
| | - Nian-Song Qian
- Department of Oncology,Senior Department of Respiratory and Critical Care Medicine, The Eighth Medical Center of Chinese, PLA General Hospital, No.17A Heishanhu Road, Haidian District, Beijing, 100853, China.
| | - DaWei Sun
- Beijing ChosenMed Clinical Laboratory Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, 100176, China.
- ChosenMed Technology (Zhejiang) Co. Ltd., Zhejiang, 311103, China.
| | - Beifang Niu
- Beijing ChosenMed Clinical Laboratory Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, 100176, China.
- Computer Network Information Center, Chinese Academy of Sciences,, University of Chinese Academy of Sciences, Beijing, 100190, China.
- ChosenMed Technology (Zhejiang) Co. Ltd., Zhejiang, 311103, China.
| | - Qiming Zhou
- Beijing ChosenMed Clinical Laboratory Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, 100176, China.
- ChosenMed Technology (Zhejiang) Co. Ltd., Zhejiang, 311103, China.
| |
Collapse
|
2
|
Giannakopoulou E, Lehander M, Virding Culleton S, Yang W, Li Y, Karpanen T, Yoshizato T, Rustad EH, Nielsen MM, Bollineni RC, Tran TT, Delic-Sarac M, Gjerdingen TJ, Douvlataniotis K, Laos M, Ali M, Hillen A, Mazzi S, Chin DWL, Mehta A, Holm JS, Bentzen AK, Bill M, Griffioen M, Gedde-Dahl T, Lehmann S, Jacobsen SEW, Woll PS, Olweus J. A T cell receptor targeting a recurrent driver mutation in FLT3 mediates elimination of primary human acute myeloid leukemia in vivo. NATURE CANCER 2023; 4:1474-1490. [PMID: 37783807 PMCID: PMC10597840 DOI: 10.1038/s43018-023-00642-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 08/28/2023] [Indexed: 10/04/2023]
Abstract
Acute myeloid leukemia (AML), the most frequent leukemia in adults, is driven by recurrent somatically acquired genetic lesions in a restricted number of genes. Treatment with tyrosine kinase inhibitors has demonstrated that targeting of prevalent FMS-related receptor tyrosine kinase 3 (FLT3) gain-of-function mutations can provide significant survival benefits for patients, although the efficacy of FLT3 inhibitors in eliminating FLT3-mutated clones is variable. We identified a T cell receptor (TCR) reactive to the recurrent D835Y driver mutation in the FLT3 tyrosine kinase domain (TCRFLT3D/Y). TCRFLT3D/Y-redirected T cells selectively eliminated primary human AML cells harboring the FLT3D835Y mutation in vitro and in vivo. TCRFLT3D/Y cells rejected both CD34+ and CD34- AML in mice engrafted with primary leukemia from patients, reaching minimal residual disease-negative levels, and eliminated primary CD34+ AML leukemia-propagating cells in vivo. Thus, T cells targeting a single shared mutation can provide efficient immunotherapy toward selective elimination of clonally involved primary AML cells in vivo.
Collapse
Grants
- G0801073 Medical Research Council
- MC_UU_00016/5 Medical Research Council
- MC_UU_12009/5 Medical Research Council
- South-Eastern Regional Health Authority Norway, the Research Council of Norway, the Norwegian Cancer Society, the Norwegian Childhood Cancer Foundation, Stiftelsen Kristian Gerhard Jebsen, European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 865805), the University of Oslo and Oslo University Hospital and Novo Nordisk Foundation.
- Knut and Alice Wallenberg Foundation, The Swedish Research Council, Tobias Foundation, Torsten Söderberg Foundation, Center for Innovative Medicine (CIMED) at Karolinska Institutet, and The UK Medical Research Council
- Technical University of Denmark (DTU)
- Aarhus University Hospital
- Leiden University Medical Center
- Oslo University Hospital
- Karolinska University Hospital
- University of Oslo and Oslo University Hospital
Collapse
Affiliation(s)
- Eirini Giannakopoulou
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Madeleine Lehander
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Stina Virding Culleton
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Weiwen Yang
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Yingqian Li
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Terhi Karpanen
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Tetsuichi Yoshizato
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Even H Rustad
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Morten Milek Nielsen
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ravi Chand Bollineni
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Trung T Tran
- Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Marina Delic-Sarac
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Thea Johanne Gjerdingen
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Karolos Douvlataniotis
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Maarja Laos
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Muhammad Ali
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Amy Hillen
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Stefania Mazzi
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Desmond Wai Loon Chin
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Adi Mehta
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Jeppe Sejerø Holm
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Amalie Kai Bentzen
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Marie Bill
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Tobias Gedde-Dahl
- Hematology Department, Section for Stem Cell Transplantation, Oslo University Hospital, Rikshospitalet, Clinic for Cancer Medicine, Oslo, Norway
| | - Sören Lehmann
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Hospital, Stockholm, Sweden
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Sten Eirik W Jacobsen
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Karolinska University Hospital, Stockholm, Sweden.
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | - Petter S Woll
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Johanna Olweus
- Department of Cancer Immunology, Oslo University Hospital Radiumhospitalet, Oslo, Norway.
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| |
Collapse
|
3
|
Wilson TE, Ahmed S, Higgins J, Salk J, Glover T. svCapture: efficient and specific detection of very low frequency structural variant junctions by error-minimized capture sequencing. NAR Genom Bioinform 2023; 5:lqad042. [PMID: 37181851 PMCID: PMC10167630 DOI: 10.1093/nargab/lqad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/15/2023] [Accepted: 04/28/2023] [Indexed: 05/16/2023] Open
Abstract
Error-corrected sequencing of genomic targets enriched by probe-based capture has become a standard approach for detecting single-nucleotide variants (SNVs) and small insertion/deletions (indels) present at very low variant allele frequencies. Less attention has been given to comparable strategies for rare structural variant (SV) junctions, where different error mechanisms must be addressed. Working from samples with known SV properties, we demonstrate that duplex sequencing (DuplexSeq), which demands confirmation of variants on both strands of a source DNA molecule, eliminates false SV junctions arising from chimeric PCR. DuplexSeq could not address frequent intermolecular ligation artifacts that arise during Y-adapter addition prior to strand denaturation without requiring multiple source molecules. In contrast, tagmentation libraries coupled with data filtering based on strand family size greatly reduced both artifact classes and enabled efficient and specific detection of single-molecule SV junctions. The throughput of SV capture sequencing (svCapture) and base-level accuracy of DuplexSeq provided detailed views of the microhomology profile and limited occurrence of de novo SNVs near the junctions of hundreds of newly created SVs, suggesting end joining as a possible formation mechanism. The open source svCapture pipeline enables rare SV detection as a routine addition to SNVs/indels in properly prepared capture sequencing libraries.
Collapse
Affiliation(s)
- Thomas E Wilson
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Samreen Ahmed
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jake Higgins
- TwinStrand Biosciences Inc., Seattle, WA 98121, USA
| | - Jesse J Salk
- TwinStrand Biosciences Inc., Seattle, WA 98121, USA
| | - Thomas W Glover
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
4
|
Tanaka M, Yokoyama K, Hayashi H, Isaki S, Kitatani K, Wang T, Kawata H, Matsuzawa H, Gurumurthy CB, Miura H, Ohtsuka M. CRISPR-KRISPR: a method to identify on-target and random insertion of donor DNAs and their characterization in knock-in mice. Genome Biol 2022; 23:228. [PMID: 36284311 PMCID: PMC9594901 DOI: 10.1186/s13059-022-02779-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/30/2022] [Indexed: 12/26/2022] Open
Abstract
CRISPR tools can generate knockout and knock-in animal models easily, but the models can contain off-target genomic lesions or random insertions of donor DNAs. Simpler methods to identify off-target lesions and random insertions, using tail or earpiece DNA, are unavailable. We develop CRISPR-KRISPR (CRISPR-Knock-ins and Random Inserts Searching PRotocol), a method to identify both off-target lesions and random insertions. CRISPR-KRISPR uses as little as 3.4 μg of genomic DNA; thus, it can be easily incorporated as an additional step to genotype founder animals for further breeding.
Collapse
Affiliation(s)
- Masayuki Tanaka
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Keiko Yokoyama
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Hideki Hayashi
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Sanae Isaki
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Kanae Kitatani
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Ting Wang
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Hisako Kawata
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Hideyuki Matsuzawa
- grid.265061.60000 0001 1516 6626Support Center for Medical Research and Education, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Channabasavaiah B. Gurumurthy
- grid.266813.80000 0001 0666 4105Mouse Genome Engineering Core Facility, University of Nebraska Medical Center, Omaha, NE USA ,grid.266813.80000 0001 0666 4105Genome Editing and Education Center Nebraska (GEEC-Nebraska), College of Medicine, University of Nebraska Medical Center, Omaha, NE USA ,grid.266813.80000 0001 0666 4105Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE USA
| | - Hiromi Miura
- grid.265061.60000 0001 1516 6626Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa 259-1193 Japan
| | - Masato Ohtsuka
- grid.265061.60000 0001 1516 6626Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa 259-1193 Japan ,grid.265061.60000 0001 1516 6626The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa 259-1193 Japan
| |
Collapse
|
5
|
Alekseenko A, Wang J, Barrett D, Pelechano V. OPUSeq simplifies detection of low-frequency DNA variants and uncovers fragmentase-associated artifacts. NAR Genom Bioinform 2022; 4:lqac048. [PMID: 35769342 PMCID: PMC9235115 DOI: 10.1093/nargab/lqac048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Detection of low-frequency DNA variants (below 1%) is becoming increasingly important in biomedical research and clinical practice, but is challenging to do with standard sequencing approaches due to high error rates. The use of double-stranded unique molecular identifiers (dsUMIs) allows correction of errors by comparing reads arising from the same original DNA duplex. However, the implementation of such approaches is still challenging. Here, we present a novel method, one-pot dsUMI sequencing (OPUSeq), which allows incorporation of dsUMIs in the same reaction as the library PCR. This obviates the need for adapter pre-synthesis or additional enzymatic steps. OPUSeq can be incorporated into standard DNA library preparation approaches and coupled with hybridization target capture. We demonstrate successful error correction and detection of variants down to allele frequency of 0.01%. Using OPUSeq, we also show that the use of enzymatic fragmentation can lead to the appearance of spurious double-stranded variants, interfering with detection of variant fractions below 0.1%.
Collapse
Affiliation(s)
- Alisa Alekseenko
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden
| | - Jingwen Wang
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden
| | - Donal Barrett
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 17165, Solna, Sweden
| |
Collapse
|