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Conant D, Hsiau T, Rossi N, Oki J, Maures T, Waite K, Yang J, Joshi S, Kelso R, Holden K, Enzmann BL, Stoner R. Inference of CRISPR Edits from Sanger Trace Data. CRISPR J 2022; 5:123-130. [PMID: 35119294 DOI: 10.1089/crispr.2021.0113] [Citation(s) in RCA: 221] [Impact Index Per Article: 110.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Efficient and precise genome editing requires a fast, quantitative, and inexpensive assay to assess genotype following editing. Here, we present ICE (Inference of CRISPR Edits), which enables robust analysis of CRISPR edits using Sanger data. ICE proposes potential outcomes for editing with guide RNAs, and then determines which are supported by the data via regression. The ICE algorithm is robust and reproducible, and it can be used to analyze CRISPR experiments within days after transfection. We also confirm that ICE produces accurate estimates of editing outcomes across a variety of benchmarks, and within the context of other existing Sanger analysis tools. The ICE tool is free to use and open source, and offers several improvements over current analysis tools, such as batch analysis and support for a variety of editing conditions. It is available online at ice.synthego.com, and the source code is available at github.com/synthego-open/ice.
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Affiliation(s)
| | - Tim Hsiau
- Synthego, Redwood City, California, USA
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2
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Viner I, Kokaeva L, Spirin V, Miettinen O. Significance of incongruent DNA loci in the taxonomy of wood-decaying Basidioradulum radula. Mycologia 2021; 113:995-1008. [PMID: 34236937 DOI: 10.1080/00275514.2021.1930449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Modern taxonomic studies of Agaricomycetes rely on the integrative analyses of morphology, environmental data, geographic distribution, and usually several DNA loci. However, sampling and selection of DNA loci for the analyses are commonly shallow. In this study, we suggest minimal numbers of necessary specimens to sample and DNA loci to analyze in order to prevent inadequate taxonomic decisions in species groups with minor morphological and genealogical differences. We sampled four unlinked nuclear DNA gene regions (nuc rDNA ITS1-5.8S-ITS2, gh63, rpb2, and tef1) to revise the systematics of a common wood-decaying species Basidioradulum radula (Hymenochaetales) on an intercontinental set of specimens collected in the Northern Hemisphere. The DNA loci analyzed violate the genealogical concordance phylogenetic species recognition principles, thus confirming a single-species interpretation. We conclude that Hyphodontia syringae is a younger synonym of B. radula.
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Affiliation(s)
- Ilya Viner
- Botanical Museum, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, 00014, Finland.,Faculty of Biology, Lomonosov State University, Leninskie Gory 1/12, 119234 Moscow, Russia
| | - Lyudmila Kokaeva
- Faculty of Biology, Lomonosov State University, Leninskie Gory 1/12, 119234 Moscow, Russia
| | - Viacheslav Spirin
- Botanical Museum, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, 00014, Finland
| | - Otto Miettinen
- Botanical Museum, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, 00014, Finland
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3
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Seroussi E. Estimating Copy-Number Proportions: The Comeback of Sanger Sequencing. Genes (Basel) 2021; 12:283. [PMID: 33671263 PMCID: PMC7922598 DOI: 10.3390/genes12020283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 12/28/2022] Open
Abstract
Determination of the relative copy numbers of mixed molecular species in nucleic acid samples is often the objective of biological experiments, including Single-Nucleotide Polymorphism (SNP), indel and gene copy-number characterization, and quantification of CRISPR-Cas9 base editing, cytosine methylation, and RNA editing. Standard dye-terminator chromatograms are a widely accessible, cost-effective information source from which copy-number proportions can be inferred. However, the rate of incorporation of dye terminators is dependent on the dye type, the adjacent sequence string, and the secondary structure of the sequenced strand. These variable rates complicate inferences and have driven scientists to resort to complex and costly quantification methods. Because these complex methods introduce their own biases, researchers are rethinking whether rectifying distortions in sequencing trace files and using direct sequencing for quantification will enable comparable accurate assessment. Indeed, recent developments in software tools (e.g., TIDE, ICE, EditR, BEEP and BEAT) indicate that quantification based on direct Sanger sequencing is gaining in scientific acceptance. This commentary reviews the common obstacles in quantification and the latest insights and developments relevant to estimating copy-number proportions based on direct Sanger sequencing, concluding that bidirectional sequencing and sophisticated base calling are the keys to identifying and avoiding sequence distortions.
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Affiliation(s)
- Eyal Seroussi
- Institute of Animal Science, Agricultural Research Organization (ARO), HaMaccabim Road, P.O.B 15159, Rishon LeTsiyon 7528809, Israel
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Biodiversity and apomixis: Insights from the East-Asian holly ferns in Polystichum section Xiphopolystichum. Mol Phylogenet Evol 2018; 127:345-355. [PMID: 29763663 DOI: 10.1016/j.ympev.2018.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 04/30/2018] [Accepted: 05/03/2018] [Indexed: 11/24/2022]
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Vidya NG, Rajkumar S, Vasavada AR. Genetic investigation of ocular developmental genes in 52 patients with anophthalmia/microphthalmia. Ophthalmic Genet 2018; 39:344-352. [DOI: 10.1080/13816810.2018.1436184] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Nair Gopinathan Vidya
- Department of Molecular Genetics & Biochemistry, Iladevi Cataract & IOL Research Centre, Ahmedabad, India
- Research scholar, Manipal University, Karnataka
| | - Sankaranarayanan Rajkumar
- Department of Molecular Genetics & Biochemistry, Iladevi Cataract & IOL Research Centre, Ahmedabad, India
| | - Abhay R. Vasavada
- Department of Cataract and Refractive Surgery, Raghudeep Eye Hospital, Ahmedabad, India
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Veeranagouda Y, Debono-Lagneaux D, Fournet H, Thill G, Didier M. CRISPR-Cas9-Edited Site Sequencing (CRES-Seq): An Efficient and High-Throughput Method for the Selection of CRISPR-Cas9-Edited Clones. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2018; 121:31.14.1-31.14.11. [PMID: 29337372 DOI: 10.1002/cpmb.53] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The emergence of clustered regularly interspaced short palindromic repeats-Cas9 (CRISPR-Cas9) gene editing systems has enabled the creation of specific mutants at low cost, in a short time and with high efficiency, in eukaryotic cells. Since a CRISPR-Cas9 system typically creates an array of mutations in targeted sites, a successful gene editing project requires careful selection of edited clones. This process can be very challenging, especially when working with multiallelic genes and/or polyploid cells (such as cancer and plants cells). Here we described a next-generation sequencing method called CRISPR-Cas9 Edited Site Sequencing (CRES-Seq) for the efficient and high-throughput screening of CRISPR-Cas9-edited clones. CRES-Seq facilitates the precise genotyping up to 96 CRISPR-Cas9-edited sites (CRES) in a single MiniSeq (Illumina) run with an approximate sequencing cost of $6/clone. CRES-Seq is particularly useful when multiple genes are simultaneously targeted by CRISPR-Cas9, and also for screening of clones generated from multiallelic genes/polyploid cells. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Yaligara Veeranagouda
- Molecular Biology and Genomics, Translational Sciences, Sanofi R&D, Chilly-Mazarin, France
| | | | - Hamida Fournet
- Molecular Biology and Genomics, Translational Sciences, Sanofi R&D, Chilly-Mazarin, France
| | - Gilbert Thill
- Molecular Biology and Genomics, Translational Sciences, Sanofi R&D, Chilly-Mazarin, France
| | - Michel Didier
- Molecular Biology and Genomics, Translational Sciences, Sanofi R&D, Chilly-Mazarin, France
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Dehairs J, Talebi A, Cherifi Y, Swinnen JV. CRISP-ID: decoding CRISPR mediated indels by Sanger sequencing. Sci Rep 2016; 6:28973. [PMID: 27363488 PMCID: PMC4929496 DOI: 10.1038/srep28973] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 06/07/2016] [Indexed: 01/01/2023] Open
Abstract
The advent of next generation gene editing technologies has revolutionized the fields of genome engineering in allowing the generation of gene knockout models and functional gene analysis. However, the screening of resultant clones remains challenging due to the simultaneous presence of different indels. Here, we present CRISP-ID, a web application which uses a unique algorithm for genotyping up to three alleles from a single Sanger sequencing trace, providing a robust and readily accessible platform to directly identify indels and significantly speed up the characterization of clones.
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Affiliation(s)
- Jonas Dehairs
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Ali Talebi
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | | | - Johannes V Swinnen
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
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Li K, Wang G, Andersen T, Zhou P, Pu WT. Optimization of genome engineering approaches with the CRISPR/Cas9 system. PLoS One 2014; 9:e105779. [PMID: 25166277 PMCID: PMC4148324 DOI: 10.1371/journal.pone.0105779] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Accepted: 07/25/2014] [Indexed: 01/25/2023] Open
Abstract
Designer nucleases such as TALENS and Cas9 have opened new opportunities to scarlessly edit the mammalian genome. Here we explored several parameters that influence Cas9-mediated scarless genome editing efficiency in murine embryonic stem cells. Optimization of transfection conditions and enriching for transfected cells are critical for efficiently recovering modified clones. Paired gRNAs and wild-type Cas9 efficiently create programmed deletions, which facilitate identification of targeted clones, while paired gRNAs and the Cas9D10A nickase generated smaller targeted indels with lower chance of off-target mutagenesis. Genome editing is also useful for programmed introduction of exogenous DNA sequences at a target locus. Increasing the length of the homology arms of the homology-directed repair template strongly enhanced targeting efficiency, while increasing the length of the DNA insert reduced it. Together our data provide guidance on optimal design of scarless gene knockout, modification, or knock-in experiments using Cas9 nuclease.
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Affiliation(s)
- Kai Li
- Deparment of Cardiology, Boston Children’s Hospital, Boston, MA, United States of America
| | - Gang Wang
- Deparment of Cardiology, Boston Children’s Hospital, Boston, MA, United States of America
| | | | - Pingzhu Zhou
- Deparment of Cardiology, Boston Children’s Hospital, Boston, MA, United States of America
| | - William T. Pu
- Deparment of Cardiology, Boston Children’s Hospital, Boston, MA, United States of America
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, United States of America
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Fantin YS, Neverov AD, Favorov AV, Alvarez-Figueroa MV, Braslavskaya SI, Gordukova MA, Karandashova IV, Kuleshov KV, Myznikova AI, Polishchuk MS, Reshetov DA, Voiciehovskaya YA, Mironov AA, Chulanov VP. Base-calling algorithm with vocabulary (BCV) method for analyzing population sequencing chromatograms. PLoS One 2013; 8:e54835. [PMID: 23382983 PMCID: PMC3557274 DOI: 10.1371/journal.pone.0054835] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 12/19/2012] [Indexed: 02/01/2023] Open
Abstract
Sanger sequencing is a common method of reading DNA sequences. It is less expensive than high-throughput methods, and it is appropriate for numerous applications including molecular diagnostics. However, sequencing mixtures of similar DNA of pathogens with this method is challenging. This is important because most clinical samples contain such mixtures, rather than pure single strains. The traditional solution is to sequence selected clones of PCR products, a complicated, time-consuming, and expensive procedure. Here, we propose the base-calling with vocabulary (BCV) method that computationally deciphers Sanger chromatograms obtained from mixed DNA samples. The inputs to the BCV algorithm are a chromatogram and a dictionary of sequences that are similar to those we expect to obtain. We apply the base-calling function on a test dataset of chromatograms without ambiguous positions, as well as one with 3-14% sequence degeneracy. Furthermore, we use BCV to assemble a consensus sequence for an HIV genome fragment in a sample containing a mixture of viral DNA variants and to determine the positions of the indels. Finally, we detect drug-resistant Mycobacterium tuberculosis strains carrying frameshift mutations mixed with wild-type bacteria in the pncA gene, and roughly characterize bacterial communities in clinical samples by direct 16S rRNA sequencing.
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Affiliation(s)
- Yuri S. Fantin
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Alexey D. Neverov
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander V. Favorov
- Department of Oncology, Division of Biostatistics and Bioinformatics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIGenetika, Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Maria A. Gordukova
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Inga V. Karandashova
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Konstantin V. Kuleshov
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Anna I. Myznikova
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Maya S. Polishchuk
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Moscow, Russia
- Department of Statistics, University of California, Berkeley, California, United States of America
| | - Denis A. Reshetov
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Yana A. Voiciehovskaya
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Andrei A. Mironov
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems (the Kharkevich Institute), Moscow, Russia
| | - Vladimir P. Chulanov
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
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Chang CT, Tsai CN, Tang CY, Chen CH, Lian JH, Hu CY, Tsai CL, Chao A, Lai CH, Wang TH, Lee YS. Mixed sequence reader: a program for analyzing DNA sequences with heterozygous base calling. ScientificWorldJournal 2012; 2012:365104. [PMID: 22778697 PMCID: PMC3385616 DOI: 10.1100/2012/365104] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Accepted: 04/01/2012] [Indexed: 01/21/2023] Open
Abstract
The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3.
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Affiliation(s)
- Chun-Tien Chang
- Department of Computer Science, National Tsing Hua University, Hsin-Chu, Taiwan
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