501
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Wang Y, Wang A, Liu Z, Thurman AL, Powers LS, Zou M, Zhao Y, Hefel A, Li Y, Zabner J, Au KF. Single-molecule long-read sequencing reveals the chromatin basis of gene expression. Genome Res 2019; 29:1329-1342. [PMID: 31201211 PMCID: PMC6673713 DOI: 10.1101/gr.251116.119] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/10/2019] [Indexed: 11/25/2022]
Abstract
Genome-wide chromatin accessibility and nucleosome occupancy profiles have been widely investigated, while the long-range dynamics remain poorly studied at the single-cell level. Here, we present a new experimental approach, methyltransferase treatment followed by single-molecule long-read sequencing (MeSMLR-seq), for long-range mapping of nucleosomes and chromatin accessibility at single DNA molecules and thus achieve comprehensive-coverage characterization of the corresponding heterogeneity. MeSMLR-seq offers direct measurements of both nucleosome-occupied and nucleosome-evicted regions on a single DNA molecule, which is challenging for many existing methods. We applied MeSMLR-seq to haploid yeast, where single DNA molecules represent single cells, and thus we could investigate the combinatorics of many (up to 356) nucleosomes at long range in single cells. We illustrated the differential organization principles of nucleosomes surrounding the transcription start site for silent and actively transcribed genes, at the single-cell level and in the long-range scale. The heterogeneous patterns of chromatin status spanning multiple genes were phased. Together with single-cell RNA-seq data, we quantitatively revealed how chromatin accessibility correlated with gene transcription positively in a highly heterogeneous scenario. Moreover, we quantified the openness of promoters and investigated the coupled chromatin changes of adjacent genes at single DNA molecules during transcription reprogramming. In addition, we revealed the coupled changes of chromatin accessibility for two neighboring glucose transporter genes in response to changes in glucose concentration.
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Affiliation(s)
- Yunhao Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA.,Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Anqi Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA.,Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Zujun Liu
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA.,Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Andrew L Thurman
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Linda S Powers
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Meng Zou
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Yue Zhao
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA.,Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Adam Hefel
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Yunyi Li
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Joseph Zabner
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA.,Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA.,Department of Biostatistics, University of Iowa, Iowa City, Iowa 52242, USA
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502
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Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data. Nat Commun 2019; 10:2449. [PMID: 31164644 PMCID: PMC6547721 DOI: 10.1038/s41467-019-10168-2] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/25/2019] [Indexed: 02/06/2023] Open
Abstract
DNA base modifications, such as C5-methylcytosine (5mC) and N6-methyldeoxyadenosine (6mA), are important types of epigenetic regulations. Short-read bisulfite sequencing and long-read PacBio sequencing have inherent limitations to detect DNA modifications. Here, using raw electric signals of Oxford Nanopore long-read sequencing data, we design DeepMod, a bidirectional recurrent neural network (RNN) with long short-term memory (LSTM) to detect DNA modifications. We sequence a human genome HX1 and a Chlamydomonas reinhardtii genome using Nanopore sequencing, and then evaluate DeepMod on three types of genomes (Escherichia coli, Chlamydomonas reinhardtii and human genomes). For 5mC detection, DeepMod achieves average precision up to 0.99 for both synthetically introduced and naturally occurring modifications. For 6mA detection, DeepMod achieves ~0.9 average precision on Escherichia coli data, and have improved performance than existing methods on Chlamydomonas reinhardtii data. In conclusion, DeepMod performs well for genome-scale detection of DNA modifications and will facilitate epigenetic analysis on diverse species. DNA modification generates unique electric signals in Oxford Nanopore sequencing data but the signals can be complicated to decipher. Here, the authors develop a deep learning framework, DeepMod, to detect DNA base modifications including 5mC and 6mA using Nanopore sequencing data
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503
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Hodges E. Sequencing in High Definition Drives a Changing Worldview of the Epigenome. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a033076. [PMID: 30201789 DOI: 10.1101/cshperspect.a033076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Single-molecule sequencing approaches have transformed the study of the human epigenome, accelerating efforts to describe genome function beyond the sequences that encode proteins. The post-genome era has ignited strong interest in the noncoding genome and profiling epigenetic signatures genome-wide have been critical for the identification and characterization of noncoding gene-regulatory sequences in various cellular and developmental contexts. These technologies enable quantification of epigenetic marks through digital assessment of DNA fragments. With the capacity to probe both the DNA sequence and count DNA molecules at once with unparalleled throughput and sensitivity, deep sequencing has been especially transformative to the study of DNA methylation. This review will discuss advances in epigenome profiling with a particular focus on DNA methylation, highlighting how deep sequencing has generated new insights into the role of DNA methylation in gene regulation. Technical aspects of profiling DNA methylation, remaining challenges, and the future of DNA methylation sequencing are also described.
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Affiliation(s)
- Emily Hodges
- Department of Biochemistry and Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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504
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Ebler J, Haukness M, Pesout T, Marschall T, Paten B. Haplotype-aware diplotyping from noisy long reads. Genome Biol 2019; 20:116. [PMID: 31159868 PMCID: PMC6547545 DOI: 10.1186/s13059-019-1709-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 05/06/2019] [Indexed: 12/19/2022] Open
Abstract
Current genotyping approaches for single-nucleotide variations rely on short, accurate reads from second-generation sequencing devices. Presently, third-generation sequencing platforms are rapidly becoming more widespread, yet approaches for leveraging their long but error-prone reads for genotyping are lacking. Here, we introduce a novel statistical framework for the joint inference of haplotypes and genotypes from noisy long reads, which we term diplotyping. Our technique takes full advantage of linkage information provided by long reads. We validate hundreds of thousands of candidate variants that have not yet been included in the high-confidence reference set of the Genome-in-a-Bottle effort.
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Affiliation(s)
- Jana Ebler
- Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, Saarbrücken, 66123, Germany
- Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, Saarbrücken, Germany
- Graduate School of Computer Science, Saarland University, Saarland Informatics Campus E1.3, Saarbrücken, Germany
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, 95064, CA, USA
| | - Trevor Pesout
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, 95064, CA, USA
| | - Tobias Marschall
- Center for Bioinformatics, Saarland University, Saarland Informatics Campus E2.1, Saarbrücken, 66123, Germany.
- Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, Saarbrücken, Germany.
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, 95064, CA, USA.
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505
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Noakes MT, Brinkerhoff H, Laszlo AH, Derrington IM, Langford KW, Mount JW, Bowman JL, Baker KS, Doering KM, Tickman BI, Gundlach JH. Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage. Nat Biotechnol 2019; 37:651-656. [PMID: 31011178 PMCID: PMC6658736 DOI: 10.1038/s41587-019-0096-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 03/11/2019] [Indexed: 12/20/2022]
Abstract
Nanopore DNA sequencing is limited by low base-calling accuracy. Improved base-calling accuracy has so far relied on specialized base-calling algorithms, different nanopores and motor enzymes, or biochemical methods to re-read DNA molecules. Two primary error modes hamper sequencing accuracy: enzyme mis-steps and sequences with indistinguishable signals. We vary the driving voltage from 100 to 200 mV, with a frequency of 200 Hz, across a Mycobacterium smegmatis porin A (MspA) nanopore, thus changing how the DNA strand moves through the nanopore. A DNA helicase moves the DNA through the nanopore in discrete steps, and the variable voltage moves the DNA continuously between these steps. The electronic signal produced with variable voltage is used to overcome the primary error modes in base calling. We found that single-passage de novo base-calling accuracy of 62.7 ± 0.5% with a constant driving voltage improves to 79.3 ± 0.3% with a variable driving voltage. The variable-voltage sequencing mode is complementary to other methods to boost the accuracy of nanopore sequencing and could be incorporated into any enzyme-actuated nanopore sequencing device.
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Affiliation(s)
- Matthew T Noakes
- Department of Physics, University of Washington, Seattle, WA, USA
| | | | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, WA, USA
| | - Ian M Derrington
- Department of Physics, University of Washington, Seattle, WA, USA
| | - Kyle W Langford
- Department of Physics, University of Washington, Seattle, WA, USA
| | - Jonathan W Mount
- Department of Physics, University of Washington, Seattle, WA, USA
| | - Jasmine L Bowman
- Department of Physics, University of Washington, Seattle, WA, USA
| | | | - Kenji M Doering
- Department of Physics, University of Washington, Seattle, WA, USA
| | | | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, WA, USA.
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506
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Vu T, Borgesi J, Soyring J, D'Alia M, Davidson SL, Shim J. Employing LiCl salt gradient in the wild-type α-hemolysin nanopore to slow down DNA translocation and detect methylated cytosine. NANOSCALE 2019; 11:10536-10545. [PMID: 31116213 DOI: 10.1039/c9nr00502a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this research, we demonstrate a label-free detection, biological nanopore-based method to distinguish methylated cytosine (mC) from naked cytosine (C) in sample mixtures containing both C and mC at a prolonged translocation duration. Using a 15-fold increase in LiCl salt concentration going from a cis to trans chamber, we increased the translocation dwell time of ssDNA by over 5-fold and the event capture rate by 6-fold in comparison with the symmetric concentration of 1.0 M KCl (control). This is a consequence of counter-ion binding and effective lowering of the overall charge of DNA, which in turn lessens the electrophoretic drive of the system and slows the translocation velocity. Moreover, salt gradients can create a large electric field that will funnel ions and polymers towards the pore, increasing the capture rate and translocation dwell time of DNA. As a result, in 0.2 M-3.0 M LiCl solution, ssDNA achieved a prolonged dwell time of 52 μs per nucleotide and a capture rate of 60 ssDNA per second. Importantly, lowering the translocation speed of ssDNA enhances the resulting resolution, allowing 5'-mC to be distinguished from C without using methyl-specific labels. We successfully distinguished 5'-mC from C when mixed together at ratios of 1 : 1, 3 : 7 and 7 : 3. The distribution of current blockade amplitudes of all mixtures adopted bimodal shapes, with peak-to-peak ratios coarsely corresponding to the mixture composition (e.g. the density and distribution of events shifted in correspondence with changes in 18b-0mC and 18-2mC concentration ratios in the mixture).
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Affiliation(s)
- Trang Vu
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA.
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507
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Zeng H, He B, Yi C. Compilation of Modern Technologies To Map Genome-Wide Cytosine Modifications in DNA. Chembiochem 2019; 20:1898-1905. [PMID: 30809902 DOI: 10.1002/cbic.201900035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Indexed: 12/19/2022]
Abstract
Over the past few decades, various DNA modification detection methods have been developed; many of the high-resolution methods are based on bisulfite treatment, which leads to DNA degradation, to a degree. Thus, novel bisulfite-free approaches have been developed in recent years and shown to be useful for epigenome analysis in otherwise difficult-to-handle, but important, DNA samples, such as hmC-seal and hmC-CATCH. Herein, an overview of advances in the development of epigenome sequencing methods for these important DNA modifications is provided.
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Affiliation(s)
- Hu Zeng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Department of Chemical Biology and, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering and, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Bo He
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Department of Chemical Biology and, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering and, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Department of Chemical Biology and, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering and, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
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508
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Smith AM, Jain M, Mulroney L, Garalde DR, Akeson M. Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing. PLoS One 2019; 14:e0216709. [PMID: 31095620 PMCID: PMC6522004 DOI: 10.1371/journal.pone.0216709] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/27/2019] [Indexed: 11/19/2022] Open
Abstract
The ribosome small subunit is expressed in all living cells. It performs numerous essential functions during translation, including formation of the initiation complex and proofreading of base-pairs between mRNA codons and tRNA anticodons. The core constituent of the small ribosomal subunit is a ~1.5 kb RNA strand in prokaryotes (16S rRNA) and a homologous ~1.8 kb RNA strand in eukaryotes (18S rRNA). Traditional sequencing-by-synthesis (SBS) of rRNA genes or rRNA cDNA copies has achieved wide use as a 'molecular chronometer' for phylogenetic studies, and as a tool for identifying infectious organisms in the clinic. However, epigenetic modifications on rRNA are erased by SBS methods. Here we describe direct MinION nanopore sequencing of individual, full-length 16S rRNA absent reverse transcription or amplification. As little as 5 picograms (~10 attomole) of purified E. coli 16S rRNA was detected in 4.5 micrograms of total human RNA. Nanopore ionic current traces that deviated from canonical patterns revealed conserved E. coli 16S rRNA 7-methylguanosine and pseudouridine modifications, and a 7-methylguanosine modification that confers aminoglycoside resistance to some pathological E. coli strains.
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Affiliation(s)
- Andrew M. Smith
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Miten Jain
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Logan Mulroney
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | | | - Mark Akeson
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
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509
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Kobow K, Ziemann M, Kaipananickal H, Khurana I, Mühlebner A, Feucht M, Hainfellner JA, Czech T, Aronica E, Pieper T, Holthausen H, Kudernatsch M, Hamer H, Kasper BS, Rössler K, Conti V, Guerrini R, Coras R, Blümcke I, El-Osta A, Kaspi A. Genomic DNA methylation distinguishes subtypes of human focal cortical dysplasia. Epilepsia 2019; 60:1091-1103. [PMID: 31074842 PMCID: PMC6635741 DOI: 10.1111/epi.14934] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 04/09/2019] [Accepted: 04/09/2019] [Indexed: 12/26/2022]
Abstract
Objectives Focal cortical dysplasia (FCD) is a major cause of drug‐resistant focal epilepsy in children, and the clinicopathological classification remains a challenging issue in daily practice. With the recent progress in DNA methylation–based classification of human brain tumors we examined whether genomic DNA methylation and gene expression analysis can be used to also distinguish human FCD subtypes. Methods DNA methylomes and transcriptomes were generated from massive parallel sequencing in 15 surgical FCD specimens, matched with 5 epilepsy and 6 nonepilepsy controls. Results Differential hierarchical cluster analysis of DNA methylation distinguished major FCD subtypes (ie, Ia, IIa, and IIb) from patients with temporal lobe epilepsy patients and nonepileptic controls. Targeted panel sequencing identified a novel likely pathogenic variant in DEPDC5 in a patient with FCD type IIa. However, no enrichment of differential DNA methylation or gene expression was observed in mechanistic target of rapamycin (mTOR) pathway–related genes. Significance Our studies extend the evidence for disease‐specific methylation signatures toward focal epilepsies in favor of an integrated clinicopathologic and molecular classification system of FCD subtypes incorporating genomic methylation.
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Affiliation(s)
- Katja Kobow
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Mark Ziemann
- Epigenetics in Human Health and Disease, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Harikrishnan Kaipananickal
- Epigenetics in Human Health and Disease, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Ishant Khurana
- Epigenetics in Human Health and Disease, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Angelika Mühlebner
- Department of Pediatrics and Adolescent Medicine, Medical University Vienna, Vienna, Austria.,Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Martha Feucht
- Department of Pediatrics and Adolescent Medicine, Medical University Vienna, Vienna, Austria
| | | | - Thomas Czech
- Department of Neurosurgery, Medical University Vienna, Vienna, Austria
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Stichting Epilepsie Instellingen Nederland (SEIN), Zwolle, The Netherlands
| | - Tom Pieper
- Department of Neuropaediatrics and Neurological Rehabilitation, Epilepsy Centre for Children and Adolescents, Schoen Clinic Vogtareuth, Vogtareuth, Germany
| | - Hans Holthausen
- Department of Neuropaediatrics and Neurological Rehabilitation, Epilepsy Centre for Children and Adolescents, Schoen Clinic Vogtareuth, Vogtareuth, Germany
| | - Manfred Kudernatsch
- Department of Neurosurgery and Epilepsy Surgery, Schoen Clinic Vogtareuth, Vogtareuth, Germany
| | - Hajo Hamer
- Department of Neurology, Erlangen Epilepsy Center, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Burkhard S Kasper
- Department of Neurology, Erlangen Epilepsy Center, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Karl Rössler
- Department of Neurosurgery, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Valerio Conti
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Neuroscience Department, A Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Neuroscience Department, A Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Roland Coras
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Ingmar Blümcke
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Assam El-Osta
- Epigenetics in Human Health and Disease, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia.,Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong City, Hong Kong SAR
| | - Antony Kaspi
- Epigenetics in Human Health and Disease, Central Clinical School, Monash University, Melbourne, Victoria, Australia
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510
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Nicholls SM, Quick JC, Tang S, Loman NJ. Ultra-deep, long-read nanopore sequencing of mock microbial community standards. Gigascience 2019; 8:giz043. [PMID: 31089679 PMCID: PMC6520541 DOI: 10.1093/gigascience/giz043] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/22/2019] [Accepted: 03/27/2019] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, and consequently have great potential for the study of microbial communities. However, the best approaches for analysis of long-read metagenomic data are unknown. Additionally, rigorous evaluation of bioinformatics tools is hindered by a lack of long-read data from validated samples with known composition. FINDINGS We sequenced 2 commercially available mock communities containing 10 microbial species (ZymoBIOMICS Microbial Community Standards) with Oxford Nanopore GridION and PromethION. Both communities and the 10 individual species isolates were also sequenced with Illumina technology. We generated 14 and 16 gigabase pairs from 2 GridION flowcells and 150 and 153 gigabase pairs from 2 PromethION flowcells for the evenly distributed and log-distributed communities, respectively. Read length N50 ranged between 5.3 and 5.4 kilobase pairs over the 4 sequencing runs. Basecalls and corresponding signal data are made available (4.2 TB in total). Alignment to Illumina-sequenced isolates demonstrated the expected microbial species at anticipated abundances, with the limit of detection for the lowest abundance species below 50 cells (GridION). De novo assembly of metagenomes recovered long contiguous sequences without the need for pre-processing techniques such as binning. CONCLUSIONS We present ultra-deep, long-read nanopore datasets from a well-defined mock community. These datasets will be useful for those developing bioinformatics methods for long-read metagenomics and for the validation and comparison of current laboratory and software pipelines.
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Affiliation(s)
- Samuel M Nicholls
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Joshua C Quick
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Shuiquan Tang
- Zymo Research Corporation, 17062 Murphy Ave., Irvine, CA 92614, USA
| | - Nicholas J Loman
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
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511
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Kono N, Arakawa K. Nanopore sequencing: Review of potential applications in functional genomics. Dev Growth Differ 2019; 61:316-326. [DOI: 10.1111/dgd.12608] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Nobuaki Kono
- Institute for Advanced Biosciences Keio University Tsuruoka Yamagata Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences Keio University Tsuruoka Yamagata Japan
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512
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Carvalho CMB, Coban-Akdemir Z, Hijazi H, Yuan B, Pendleton M, Harrington E, Beaulaurier J, Juul S, Turner DJ, Kanchi RS, Jhangiani SN, Muzny DM, Gibbs RA, Stankiewicz P, Belmont JW, Shaw CA, Cheung SW, Hanchard NA, Sutton VR, Bader PI, Lupski JR. Interchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome. Genome Med 2019; 11:25. [PMID: 31014393 PMCID: PMC6480824 DOI: 10.1186/s13073-019-0633-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/02/2019] [Indexed: 12/13/2022] Open
Abstract
Background Intrachromosomal triplications (TRP) can contribute to disease etiology via gene dosage effects, gene disruption, position effects, or fusion gene formation. Recently, post-zygotic de novo triplications adjacent to copy-number neutral genomic intervals with runs of homozygosity (ROH) have been shown to result in uniparental isodisomy (UPD). The genomic structure of these complex genomic rearrangements (CGRs) shows a consistent pattern of an inverted triplication flanked by duplications (DUP-TRP/INV-DUP) formed by an iterative DNA replisome template-switching mechanism during replicative repair of a single-ended, double-stranded DNA (seDNA), the ROH results from an interhomolog or nonsister chromatid template switch. It has been postulated that these CGRs may lead to genetic abnormalities in carriers due to dosage-sensitive genes mapping within the copy-number variant regions, homozygosity for alleles at a locus causing an autosomal recessive (AR) disease trait within the ROH region, or imprinting-associated diseases. Methods Here, we report a family wherein the affected subject carries a de novo 2.2-Mb TRP followed by 42.2 Mb of ROH and manifests clinical features overlapping with those observed in association with chromosome 14 maternal UPD (UPD(14)mat). UPD(14)mat can cause clinical phenotypic features enabling a diagnosis of Temple syndrome. This CGR was then molecularly characterized by high-density custom aCGH, genome-wide single-nucleotide polymorphism (SNP) and methylation arrays, exome sequencing (ES), and the Oxford Nanopore long-read sequencing technology. Results We confirmed the postulated DUP-TRP/INV-DUP structure by multiple orthogonal genomic technologies in the proband. The methylation status of known differentially methylated regions (DMRs) on chromosome 14 revealed that the subject shows the typical methylation pattern of UPD(14)mat. Consistent with these molecular findings, the clinical features overlap with those observed in Temple syndrome, including speech delay. Conclusions These data provide experimental evidence that, in humans, triplication can lead to segmental UPD and imprinting disease. Importantly, genotype/phenotype analyses further reveal how a post-zygotically generated complex structural variant, resulting from a replication-based mutational mechanism, contributes to expanding the clinical phenotype of known genetic syndromes. Mechanistically, such events can distort transmission genetics resulting in homozygosity at a locus for which only one parent is a carrier as well as cause imprinting diseases. Electronic supplementary material The online version of this article (10.1186/s13073-019-0633-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA.
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA
| | - Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA
| | | | | | | | - Sissel Juul
- Oxford Nanopore Technologies Inc, New York, NY, USA.,Oxford Nanopore Technologies Inc, San Francisco, CA, USA
| | | | | | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA.,Texas Children's Hospital, Houston, TX, USA
| | | | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, USA
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513
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Deep learning in bioinformatics: Introduction, application, and perspective in the big data era. Methods 2019; 166:4-21. [PMID: 31022451 DOI: 10.1016/j.ymeth.2019.04.008] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 03/23/2019] [Accepted: 04/15/2019] [Indexed: 12/13/2022] Open
Abstract
Deep learning, which is especially formidable in handling big data, has achieved great success in various fields, including bioinformatics. With the advances of the big data era in biology, it is foreseeable that deep learning will become increasingly important in the field and will be incorporated in vast majorities of analysis pipelines. In this review, we provide both the exoteric introduction of deep learning, and concrete examples and implementations of its representative applications in bioinformatics. We start from the recent achievements of deep learning in the bioinformatics field, pointing out the problems which are suitable to use deep learning. After that, we introduce deep learning in an easy-to-understand fashion, from shallow neural networks to legendary convolutional neural networks, legendary recurrent neural networks, graph neural networks, generative adversarial networks, variational autoencoder, and the most recent state-of-the-art architectures. After that, we provide eight examples, covering five bioinformatics research directions and all the four kinds of data type, with the implementation written in Tensorflow and Keras. Finally, we discuss the common issues, such as overfitting and interpretability, that users will encounter when adopting deep learning methods and provide corresponding suggestions. The implementations are freely available at https://github.com/lykaust15/Deep_learning_examples.
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514
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Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads. Nat Methods 2019; 16:429-436. [PMID: 31011185 DOI: 10.1038/s41592-019-0394-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/18/2019] [Indexed: 12/19/2022]
Abstract
Replication of eukaryotic genomes is highly stochastic, making it difficult to determine the replication dynamics of individual molecules with existing methods. We report a sequencing method for the measurement of replication fork movement on single molecules by detecting nucleotide analog signal currents on extremely long nanopore traces (D-NAscent). Using this method, we detect 5-bromodeoxyuridine (BrdU) incorporated by Saccharomyces cerevisiae to reveal, at a genomic scale and on single molecules, the DNA sequences replicated during a pulse-labeling period. Under conditions of limiting BrdU concentration, D-NAscent detects the differences in BrdU incorporation frequency across individual molecules to reveal the location of active replication origins, fork direction, termination sites, and fork pausing/stalling events. We used sequencing reads of 20-160 kilobases to generate a whole-genome single-molecule map of DNA replication dynamics and discover a class of low-frequency stochastic origins in budding yeast. The D-NAscent software is available at https://github.com/MBoemo/DNAscent.git .
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515
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DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning. Bioinformatics 2019; 35:4586-4595. [DOI: 10.1093/bioinformatics/btz276] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 04/06/2019] [Accepted: 04/11/2019] [Indexed: 01/19/2023] Open
Abstract
Abstract
Motivation
The Oxford Nanopore sequencing enables to directly detect methylation states of bases in DNA from reads without extra laboratory techniques. Novel computational methods are required to improve the accuracy and robustness of DNA methylation state prediction using Nanopore reads.
Results
In this study, we develop DeepSignal, a deep learning method to detect DNA methylation states from Nanopore sequencing reads. Testing on Nanopore reads of Homo sapiens (H. sapiens), Escherichia coli (E. coli) and pUC19 shows that DeepSignal can achieve higher performance at both read level and genome level on detecting 6 mA and 5mC methylation states comparing to previous hidden Markov model (HMM) based methods. DeepSignal achieves similar performance cross different DNA methylation bases, different DNA methylation motifs and both singleton and mixed DNA CpG. Moreover, DeepSignal requires much lower coverage than those required by HMM and statistics based methods. DeepSignal can achieve 90% above accuracy for detecting 5mC and 6 mA using only 2× coverage of reads. Furthermore, for DNA CpG methylation state prediction, DeepSignal achieves 90% correlation with bisulfite sequencing using just 20× coverage of reads, which is much better than HMM based methods. Especially, DeepSignal can predict methylation states of 5% more DNA CpGs that previously cannot be predicted by bisulfite sequencing. DeepSignal can be a robust and accurate method for detecting methylation states of DNA bases.
Availability and implementation
DeepSignal is publicly available at https://github.com/bioinfomaticsCSU/deepsignal.
Supplementary information
Supplementary data are available at bioinformatics online.
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516
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Yegnasubramanian S, De Marzo AM, Nelson WG. Prostate Cancer Epigenetics: From Basic Mechanisms to Clinical Implications. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a030445. [PMID: 29959132 DOI: 10.1101/cshperspect.a030445] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A level of epigenetic programming, encoded by complex sets of chemical marks on DNA and histones, and by context-specific DNA, RNA, protein interactions, that all regulate the structure, organization, and function of the genome, is critical to establish both normal and neoplastic cell identities and functions. This structure-function relationship of the genome encoded by the epigenetic programming can be thought of as an epigenetic cityscape that is built on the underlying genetic landscape. Alterations in the epigenetic cityscape of prostate cancer cells compared with normal prostate tissues have a complex interplay with genetic alterations to drive prostate cancer initiation and progression. Indeed, mutations in genes encoding epigenetic enzymes are often observed in human cancers including prostate cancer. Interestingly, alterations in the prostate cancer epigenetic cityscape can be highly recurrent, a facet that can be exploited for development of biomarkers and potentially as therapeutic targets.
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Affiliation(s)
- Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, Maryland 21231
| | - Angelo M De Marzo
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, Maryland 21231
| | - William G Nelson
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, Maryland 21231
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517
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Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540-546. [DOI: 10.1038/s41587-019-0072-8] [Citation(s) in RCA: 1327] [Impact Index Per Article: 265.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 02/06/2019] [Indexed: 01/02/2023]
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518
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Zhao L, Zhang H, Kohnen MV, Prasad KVSK, Gu L, Reddy ASN. Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing. Front Genet 2019; 10:253. [PMID: 30949200 PMCID: PMC6438080 DOI: 10.3389/fgene.2019.00253] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/06/2019] [Indexed: 12/18/2022] Open
Abstract
Nanopore sequencing from Oxford Nanopore Technologies (ONT) and Pacific BioSciences (PacBio) single-molecule real-time (SMRT) long-read isoform sequencing (Iso-Seq) are revolutionizing the way transcriptomes are analyzed. These methods offer many advantages over most widely used high-throughput short-read RNA sequencing (RNA-Seq) approaches and allow a comprehensive analysis of transcriptomes in identifying full-length splice isoforms and several other post-transcriptional events. In addition, direct RNA-Seq provides valuable information about RNA modifications, which are lost during the PCR amplification step in other methods. Here, we present a comprehensive summary of important applications of these technologies in plants, including identification of complex alternative splicing (AS), full-length splice variants, fusion transcripts, and alternative polyadenylation (APA) events. Furthermore, we discuss the impact of the newly developed nanopore direct RNA-Seq in advancing epitranscriptome research in plants. Additionally, we summarize computational tools for identifying and quantifying full-length isoforms and other co/post-transcriptional events and discussed some of the limitations with these methods. Sequencing of transcriptomes using these new single-molecule long-read methods will unravel many aspects of transcriptome complexity in unprecedented ways as compared to previous short-read sequencing approaches. Analysis of plant transcriptomes with these new powerful methods that require minimum sample processing is likely to become the norm and is expected to uncover novel co/post-transcriptional gene regulatory mechanisms that control biological outcomes during plant development and in response to various stresses.
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Affiliation(s)
- Liangzhen Zhao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Markus V. Kohnen
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kasavajhala V. S. K. Prasad
- Program in Cell and Molecular Biology, Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Anireddy S. N. Reddy
- Program in Cell and Molecular Biology, Department of Biology, Colorado State University, Fort Collins, CO, United States
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519
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Wheway G, Mitchison HM. Opportunities and Challenges for Molecular Understanding of Ciliopathies-The 100,000 Genomes Project. Front Genet 2019; 10:127. [PMID: 30915099 PMCID: PMC6421331 DOI: 10.3389/fgene.2019.00127] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/05/2019] [Indexed: 01/11/2023] Open
Abstract
Cilia are highly specialized cellular organelles that serve multiple functions in human development and health. Their central importance in the body is demonstrated by the occurrence of a diverse range of developmental disorders that arise from defects of cilia structure and function, caused by a range of different inherited mutations found in more than 150 different genes. Genetic analysis has rapidly advanced our understanding of the cell biological basis of ciliopathies over the past two decades, with more recent technological advances in genomics rapidly accelerating this progress. The 100,000 Genomes Project was launched in 2012 in the UK to improve diagnosis and future care for individuals affected by rare diseases like ciliopathies, through whole genome sequencing (WGS). In this review we discuss the potential promise and medical impact of WGS for ciliopathies and report on current progress of the 100,000 Genomes Project, reviewing the medical, technical and ethical challenges and opportunities that new, large scale initiatives such as this can offer.
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Affiliation(s)
- Gabrielle Wheway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Hannah M. Mitchison
- Genetics and Genomic Medicine, University College London, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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520
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Kagohara LT, Stein-O’Brien GL, Kelley D, Flam E, Wick HC, Danilova LV, Easwaran H, Favorov AV, Qian J, Gaykalova DA, Fertig EJ. Epigenetic regulation of gene expression in cancer: techniques, resources and analysis. Brief Funct Genomics 2019; 17:49-63. [PMID: 28968850 PMCID: PMC5860551 DOI: 10.1093/bfgp/elx018] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Cancer is a complex disease, driven by aberrant activity in numerous signaling pathways in even individual malignant cells. Epigenetic changes are critical mediators of these functional changes that drive and maintain the malignant phenotype. Changes in DNA methylation, histone acetylation and methylation, noncoding RNAs, posttranslational modifications are all epigenetic drivers in cancer, independent of changes in the DNA sequence. These epigenetic alterations were once thought to be crucial only for the malignant phenotype maintenance. Now, epigenetic alterations are also recognized as critical for disrupting essential pathways that protect the cells from uncontrolled growth, longer survival and establishment in distant sites from the original tissue. In this review, we focus on DNA methylation and chromatin structure in cancer. The precise functional role of these alterations is an area of active research using emerging high-throughput approaches and bioinformatics analysis tools. Therefore, this review also describes these high-throughput measurement technologies, public domain databases for high-throughput epigenetic data in tumors and model systems and bioinformatics algorithms for their analysis. Advances in bioinformatics data that combine these epigenetic data with genomics data are essential to infer the function of specific epigenetic alterations in cancer. These integrative algorithms are also a focus of this review. Future studies using these emerging technologies will elucidate how alterations in the cancer epigenome cooperate with genetic aberrations during tumor initiation and progression. This deeper understanding is essential to future studies with epigenetics biomarkers and precision medicine using emerging epigenetic therapies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Daria A Gaykalova
- Corresponding authors: Daria A. Gaykalova, Otolaryngology - Head and Neck Surgery, The Johns Hopkins University School of Medicine, 1550 Orleans Street, Rm 574, CRBII Baltimore, MD 21231, USA. Tel.: +1 410 614 2745; Fax: +1 410 614 1411; E-mail: ; Elana J. Fertig, Assistant Professor of Oncology, Division of Biostatistics and Bioinformatics, Johns Hopkins University, 550 N Broadway, 1101 E Baltimore, MD 21205, USA. Tel.: +1 410 955 4268; Fax: +1 410 955 0859; E-mail:
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521
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Sharim H, Grunwald A, Gabrieli T, Michaeli Y, Margalit S, Torchinsky D, Arielly R, Nifker G, Juhasz M, Gularek F, Almalvez M, Dufault B, Chandra SS, Liu A, Bhattacharya S, Chen YW, Vilain E, Wagner KR, Pevsner J, Reifenberger J, Lam ET, Hastie AR, Cao H, Barseghyan H, Weinhold E, Ebenstein Y. Long-read single-molecule maps of the functional methylome. Genome Res 2019; 29:646-656. [PMID: 30846530 PMCID: PMC6442387 DOI: 10.1101/gr.240739.118] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 02/25/2019] [Indexed: 01/23/2023]
Abstract
We report on the development of a methylation analysis workflow for optical detection of fluorescent methylation profiles along chromosomal DNA molecules. In combination with Bionano Genomics genome mapping technology, these profiles provide a hybrid genetic/epigenetic genome-wide map composed of DNA molecules spanning hundreds of kilobase pairs. The method provides kilobase pair–scale genomic methylation patterns comparable to whole-genome bisulfite sequencing (WGBS) along genes and regulatory elements. These long single-molecule reads allow for methylation variation calling and analysis of large structural aberrations such as pathogenic macrosatellite arrays not accessible to single-cell second-generation sequencing. The method is applied here to study facioscapulohumeral muscular dystrophy (FSHD), simultaneously recording the haplotype, copy number, and methylation status of the disease-associated, highly repetitive locus on Chromosome 4q.
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Affiliation(s)
- Hila Sharim
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
| | - Assaf Grunwald
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
| | - Tslil Gabrieli
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
| | - Yael Michaeli
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
| | - Sapir Margalit
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
| | - Dmitry Torchinsky
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
| | - Rani Arielly
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
| | - Gil Nifker
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
| | - Matyas Juhasz
- Institute of Organic Chemistry RWTH Aachen University, D-52056 Aachen, Germany
| | - Felix Gularek
- Institute of Organic Chemistry RWTH Aachen University, D-52056 Aachen, Germany
| | - Miguel Almalvez
- Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC 20010, USA
| | - Brandon Dufault
- Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC 20010, USA
| | - Sreetama Sen Chandra
- Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC 20010, USA
| | - Alexander Liu
- Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC 20010, USA
| | - Surajit Bhattacharya
- Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC 20010, USA
| | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC 20010, USA
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC 20010, USA
| | - Kathryn R Wagner
- Kennedy Krieger Institute and Departments of Neurology and Neuroscience, The Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Jonathan Pevsner
- Kennedy Krieger Institute and Departments of Neurology and Neuroscience, The Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | | | - Ernest T Lam
- Bionano Genomics, Incorporated, San Diego, California 92121, USA
| | - Alex R Hastie
- Bionano Genomics, Incorporated, San Diego, California 92121, USA
| | - Han Cao
- Bionano Genomics, Incorporated, San Diego, California 92121, USA
| | - Hayk Barseghyan
- Center for Genetic Medicine Research, Children's National Health System, Children's Research Institute, Washington, DC 20010, USA
| | - Elmar Weinhold
- Institute of Organic Chemistry RWTH Aachen University, D-52056 Aachen, Germany
| | - Yuval Ebenstein
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 6997801, Israel
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522
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Beaulaurier J, Schadt EE, Fang G. Deciphering bacterial epigenomes using modern sequencing technologies. Nat Rev Genet 2019; 20:157-172. [PMID: 30546107 PMCID: PMC6555402 DOI: 10.1038/s41576-018-0081-3] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prokaryotic DNA contains three types of methylation: N6-methyladenine, N4-methylcytosine and 5-methylcytosine. The lack of tools to analyse the frequency and distribution of methylated residues in bacterial genomes has prevented a full understanding of their functions. Now, advances in DNA sequencing technology, including single-molecule, real-time sequencing and nanopore-based sequencing, have provided new opportunities for systematic detection of all three forms of methylated DNA at a genome-wide scale and offer unprecedented opportunities for achieving a more complete understanding of bacterial epigenomes. Indeed, as the number of mapped bacterial methylomes approaches 2,000, increasing evidence supports roles for methylation in regulation of gene expression, virulence and pathogen-host interactions.
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Affiliation(s)
- John Beaulaurier
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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523
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Jadhav V, Hoogerheide DP, Korlach J, Wanunu M. Porous Zero-Mode Waveguides for Picogram-Level DNA Capture. NANO LETTERS 2019; 19:921-929. [PMID: 30484321 PMCID: PMC9701543 DOI: 10.1021/acs.nanolett.8b04170] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We have recently shown that nanopore zero-mode waveguides are effective tools for capturing picogram levels of long DNA fragments for single-molecule DNA sequencing. Despite these key advantages, the manufacturing of large arrays is not practical due to the need for serial nanopore fabrication. To overcome this challenge, we have developed an approach for the wafer-scale fabrication of waveguide arrays on low-cost porous membranes, which are deposited using molecular-layer deposition. The membrane at each waveguide base contains a network of serpentine pores that allows for efficient electrophoretic DNA capture at picogram levels while eliminating the need for prohibitive serial pore milling. Here, we show that the loading efficiency of these porous waveguides is up to 2 orders of magnitude greater than their nanopore predecessors. This new device facilitates the scaling-up of the process, greatly reducing the cost and effort of manufacturing. Furthermore, the porous zero-mode waveguides can be used for applications that benefit from low-input single-molecule real-time sequencing.
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Affiliation(s)
- Vivek Jadhav
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - David P. Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California 94025, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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524
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Liu Q, Georgieva DC, Egli D, Wang K. NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data. BMC Genomics 2019; 20:78. [PMID: 30712508 PMCID: PMC6360650 DOI: 10.1186/s12864-018-5372-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Recent advances in single-molecule sequencing techniques, such as Nanopore sequencing, improved read length, increased sequencing throughput, and enabled direct detection of DNA modifications through the analysis of raw signals. These DNA modifications include naturally occurring modifications such as DNA methylations, as well as modifications that are introduced by DNA damage or through synthetic modifications to one of the four standard nucleotides. METHODS To improve the performance of detecting DNA modifications, especially synthetically introduced modifications, we developed a novel computational tool called NanoMod. NanoMod takes raw signal data on a pair of DNA samples with and without modified bases, extracts signal intensities, performs base error correction based on a reference sequence, and then identifies bases with modifications by comparing the distribution of raw signals between two samples, while taking into account of the effects of neighboring bases on modified bases ("neighborhood effects"). RESULTS We evaluated NanoMod on simulation data sets, based on different types of modifications and different magnitudes of neighborhood effects, and found that NanoMod outperformed other methods in identifying known modified bases. Additionally, we demonstrated superior performance of NanoMod on an E. coli data set with 5mC (5-methylcytosine) modifications. CONCLUSIONS In summary, NanoMod is a flexible tool to detect DNA modifications with single-base resolution from raw signals in Nanopore sequencing, and will facilitate large-scale functional genomics experiments that use modified nucleotides.
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Affiliation(s)
- Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Daniela C. Georgieva
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY 10032 USA
| | - Dieter Egli
- Department of Pediatrics, Columbia University, New York, NY 10032 USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
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525
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McIntyre ABR, Alexander N, Grigorev K, Bezdan D, Sichtig H, Chiu CY, Mason CE. Single-molecule sequencing detection of N6-methyladenine in microbial reference materials. Nat Commun 2019; 10:579. [PMID: 30718479 PMCID: PMC6362088 DOI: 10.1038/s41467-019-08289-9] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 12/19/2018] [Indexed: 11/17/2022] Open
Abstract
The DNA base modification N6-methyladenine (m6A) is involved in many pathways related to the survival of bacteria and their interactions with hosts. Nanopore sequencing offers a new, portable method to detect base modifications. Here, we show that a neural network can improve m6A detection at trained sequence contexts compared to previously published methods using deviations between measured and expected current values as each adenine travels through a pore. The model, implemented as the mCaller software package, can be extended to detect known or confirm suspected methyltransferase target motifs based on predictions of methylation at untrained contexts. We use PacBio, Oxford Nanopore, methylated DNA immunoprecipitation sequencing (MeDIP-seq), and whole-genome bisulfite sequencing data to generate and orthogonally validate methylomes for eight microbial reference species. These well-characterized microbial references can serve as controls in the development and evaluation of future methods for the identification of base modifications from single-molecule sequencing data.
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Affiliation(s)
- Alexa B R McIntyre
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, 10065, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, 10065, NY, USA
| | - Noah Alexander
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, 10065, NY, USA
| | - Kirill Grigorev
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, 10065, NY, USA
| | - Daniela Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, 10065, NY, USA
| | - Heike Sichtig
- US Food and Drug Administration, Silver Spring, 20993, MD, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, 94107, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, 94107, CA, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, 10065, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, 10021, NY, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, 10021, NY, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, 10021, NY, USA.
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526
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Fu S, Wang A, Au KF. A comparative evaluation of hybrid error correction methods for error-prone long reads. Genome Biol 2019; 20:26. [PMID: 30717772 PMCID: PMC6362602 DOI: 10.1186/s13059-018-1605-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 12/05/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Third-generation sequencing technologies have advanced the progress of the biological research by generating reads that are substantially longer than second-generation sequencing technologies. However, their notorious high error rate impedes straightforward data analysis and limits their application. A handful of error correction methods for these error-prone long reads have been developed to date. The output data quality is very important for downstream analysis, whereas computing resources could limit the utility of some computing-intense tools. There is a lack of standardized assessments for these long-read error-correction methods. RESULTS Here, we present a comparative performance assessment of ten state-of-the-art error-correction methods for long reads. We established a common set of benchmarks for performance assessment, including sensitivity, accuracy, output rate, alignment rate, output read length, run time, and memory usage, as well as the effects of error correction on two downstream applications of long reads: de novo assembly and resolving haplotype sequences. CONCLUSIONS Taking into account all of these metrics, we provide a suggestive guideline for method choice based on available data size, computing resources, and individual research goals.
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Affiliation(s)
- Shuhua Fu
- Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Anqi Wang
- Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Kin Fai Au
- Department of Internal Medicine, University of Iowa, Iowa City, IA, 52242, USA.
- Department of Biostatistics, University of Iowa, Iowa City, IA, 52242, USA.
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA.
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527
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Zaikova E, Goerlitz DS, Tighe SW, Wagner NY, Bai Y, Hall BL, Bevilacqua JG, Weng MM, Samuels-Fair MD, Johnson SS. Antarctic Relic Microbial Mat Community Revealed by Metagenomics and Metatranscriptomics. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00001] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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528
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Kuderna LFK, Lizano E, Julià E, Gomez-Garrido J, Serres-Armero A, Kuhlwilm M, Alandes RA, Alvarez-Estape M, Juan D, Simon H, Alioto T, Gut M, Gut I, Schierup MH, Fornas O, Marques-Bonet T. Selective single molecule sequencing and assembly of a human Y chromosome of African origin. Nat Commun 2019; 10:4. [PMID: 30602775 PMCID: PMC6315018 DOI: 10.1038/s41467-018-07885-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 12/02/2018] [Indexed: 12/19/2022] Open
Abstract
Mammalian Y chromosomes are often neglected from genomic analysis. Due to their inherent assembly difficulties, high repeat content, and large ampliconic regions, only a handful of species have their Y chromosome properly characterized. To date, just a single human reference quality Y chromosome, of European ancestry, is available due to a lack of accessible methodology. To facilitate the assembly of such complicated genomic territory, we developed a novel strategy to sequence native, unamplified flow sorted DNA on a MinION nanopore sequencing device. Our approach yields a highly continuous assembly of the first human Y chromosome of African origin. It constitutes a significant improvement over comparable previous methods, increasing continuity by more than 800%. Sequencing native DNA also allows to take advantage of the nanopore signal data to detect epigenetic modifications in situ. This approach is in theory generalizable to any species simplifying the assembly of extremely large and repetitive genomes. Due to various structural and sequence complexities, the human Y chromosome is challenging to sequence and characterize. Here, the authors develop a strategy to sequence native, unamplified flow sorted Y chromosomes with a nanopore sequencing platform, and report the first assembly of a human Y chromosome of African origin.
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Affiliation(s)
- Lukas F K Kuderna
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia, 08003, Spain.
| | - Esther Lizano
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia, 08003, Spain.
| | - Eva Julià
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Carrer del Doctor Aiguader 88, PRBB Building, Barcelona, 08003, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Jessica Gomez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Aitor Serres-Armero
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia, 08003, Spain
| | - Martin Kuhlwilm
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia, 08003, Spain
| | - Regina Antoni Alandes
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain
| | - Marina Alvarez-Estape
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia, 08003, Spain
| | - David Juan
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia, 08003, Spain
| | - Heath Simon
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain.,Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Tyler Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain.,Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain.,Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain.,Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Mikkel Heide Schierup
- Bioinformatics Research Center, Aarhus University, C.F. Moellers Alle 8, DK-8000 Aarhus C, Denmark.,Department of Bioscience, Aarhus University, Ny Munkegade 116, DK-8000 Aarhus C, Denmark
| | - Oscar Fornas
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia, 08003, Spain. .,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain. .,Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, Barcelona, 08003, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, Catalonia, 08010, Spain. .,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, Cerdanyola del Vallès, Barcelona, 08193, Spain.
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529
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Philips JG, Dudley KJ, Waterhouse PM, Hellens RP. The Rapid Methylation of T-DNAs Upon Agrobacterium Inoculation in Plant Leaves. FRONTIERS IN PLANT SCIENCE 2019; 10:312. [PMID: 30930927 PMCID: PMC6428780 DOI: 10.3389/fpls.2019.00312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/26/2019] [Indexed: 05/10/2023]
Abstract
Agrobacterium tumefaciens has been foundational in the development of transgenic plants for both agricultural biotechnology and plant molecular research. However, the transformation efficiency and level of transgene expression obtained for any given construct can be highly variable. These inefficiencies often require screening of many lines to find one with consistent and heritable transgene expression. Transcriptional gene silencing is known to affect transgene expression, and is associated with DNA methylation, especially of cytosines in symmetric CG and CHG contexts. While the specificity, heritability and silencing-associated effects of DNA methylation of transgene sequences have been analyzed in many stably transformed plants, the methylation status of transgene sequences in the T-DNA during the transformation process has not been well-studied. Here we used agro-infiltration of the eGFP reporter gene in Nicotiana benthamiana leaves driven by either an AtEF1α-A4 or a CaMV-35S promoter to study early T-DNA methylation patterns of these promoter sequences. The T-DNA was examined by amplicon sequencing following sodium bisulfite treatment using three different sequencing platforms: Sanger sequencing, Ion Torrent PGM, and the Illumina MiSeq. Rapid DNA methylation was detectable in each promoter region just 2-3 days post-infiltration and the levels continued to rapidly accumulate over the first week, then steadily up to 21 days later. Cytosines in an asymmetric context (CHH) were the most heavily and rapidly methylated. This suggests that early T-DNA methylation may be important in determining the epigenetic and transcriptional fate of integrated transgenes. The Illumina MiSeq platform was the most sensitive and robust way of detecting and following the methylation profiles of the T-DNA promoters. The utility of the methods was then used to show a subtle but significant difference in promoter methylation during intron-mediated enhancement. In addition, the method was able to detect an increase in promoter methylation when the eGFP reporter gene was targeted by siRNAs generated by co-infiltration of a hairpin RNAi construct.
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Affiliation(s)
- Joshua G. Philips
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
- *Correspondence: Joshua G. Philips,
| | - Kevin J. Dudley
- Institute for Future Environments, Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD, Australia
| | - Peter M. Waterhouse
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
- Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
| | - Roger P. Hellens
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
- Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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530
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Schalamun M, Nagar R, Kainer D, Beavan E, Eccles D, Rathjen JP, Lanfear R, Schwessinger B. Harnessing the MinION: An example of how to establish long-read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora. Mol Ecol Resour 2019; 19:77-89. [PMID: 30118581 PMCID: PMC7380007 DOI: 10.1111/1755-0998.12938] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 11/28/2022]
Abstract
Long-read sequencing technologies are transforming our ability to assemble highly complex genomes. Realizing their full potential is critically reliant on extracting high-quality, high-molecular-weight (HMW) DNA from the organisms of interest. This is especially the case for the portable MinION sequencer which enables all laboratories to undertake their own genome sequencing projects, due to its low entry cost and minimal spatial footprint. One challenge of the MinION is that each group has to independently establish effective protocols for using the instrument, which can be time-consuming and costly. Here, we present a workflow and protocols that enabled us to establish MinION sequencing in our own laboratories, based on optimizing DNA extraction from a challenging plant tissue as a case study. Following the workflow illustrated, we were able to reliably and repeatedly obtain >6.5 Gb of long-read sequencing data with a mean read length of 13 kb and an N50 of 26 kb. Our protocols are open source and can be performed in any laboratory without special equipment. We also illustrate some more elaborate workflows which can increase mean and average read lengths if this is desired. We envision that our workflow for establishing MinION sequencing, including the illustration of potential pitfalls and suggestions of how to adapt it to other tissue types, will be useful to others who plan to establish long-read sequencing in their own laboratories.
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Affiliation(s)
- Miriam Schalamun
- Research School of BiologyThe Australian National UniversityActonACTAustralia
- Present address:
University of Natural Resources and Life SciencesViennaAustria
| | - Ramawatar Nagar
- Research School of BiologyThe Australian National UniversityActonACTAustralia
| | - David Kainer
- Research School of BiologyThe Australian National UniversityActonACTAustralia
| | - Eleanor Beavan
- Research School of BiologyThe Australian National UniversityActonACTAustralia
| | - David Eccles
- Malaghan Institute of Medical ResearchWellingtonNew Zealand
- Present address:
Malaghan Institute of Medical ResearchWellingtonNew Zealand
| | - John P. Rathjen
- Research School of BiologyThe Australian National UniversityActonACTAustralia
| | - Robert Lanfear
- Research School of BiologyThe Australian National UniversityActonACTAustralia
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531
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Zascavage RR, Thorson K, Planz JV. Nanopore sequencing: An enrichment-free alternative to mitochondrial DNA sequencing. Electrophoresis 2019; 40:272-280. [PMID: 30511783 PMCID: PMC6590251 DOI: 10.1002/elps.201800083] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 10/25/2018] [Accepted: 11/03/2018] [Indexed: 12/31/2022]
Abstract
Mitochondrial DNA sequence data are often utilized in disease studies, conservation genetics and forensic identification. The current approaches for sequencing the full mtGenome typically require several rounds of PCR enrichment during Sanger or MPS protocols followed by fairly tedious assembly and analysis. Here we describe an efficient approach to sequencing directly from genomic DNA samples without prior enrichment or extensive library preparation steps. A comparison is made between libraries sequenced directly from native DNA and the same samples sequenced from libraries generated with nine overlapping mtDNA amplicons on the Oxford Nanopore MinION™ device. The native and amplicon library preparation methods and alternative base calling strategies were assessed to establish error rates and identify trends of discordance between the two library preparation approaches. For the complete mtGenome, 16 569 nucleotides, an overall error rate of approximately 1.00% was observed. As expected with mtDNA, the majority of error was detected in homopolymeric regions. The use of a modified basecaller that corrects for ambiguous signal in homopolymeric stretches reduced the error rate for both library preparation methods to approximately 0.30%. Our study indicates that direct mtDNA sequencing from native DNA on the MinION™ device provides comparable results to those obtained from common mtDNA sequencing methods and is a reliable alternative to approaches using PCR-enriched libraries.
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Affiliation(s)
- Roxanne R. Zascavage
- Department of MicrobiologyImmunology and GeneticsUniversity of North Texas Health Science CenterFort WorthTXUSA
- Department of Criminology and Criminal JusticeUniversity of Texas at ArlingtonArlingtonTXUSA
| | - Kelcie Thorson
- Department of MicrobiologyImmunology and GeneticsUniversity of North Texas Health Science CenterFort WorthTXUSA
- Zoetis Inc.ParsippanyNJUSA
| | - John V. Planz
- Department of MicrobiologyImmunology and GeneticsUniversity of North Texas Health Science CenterFort WorthTXUSA
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532
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Plesivkova D, Richards R, Harbison S. A review of the potential of the MinION™ single‐molecule sequencing system for forensic applications. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/wfs2.1323] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Diana Plesivkova
- Forensic Science Programme, School of Chemical Sciences University of Auckland Auckland New Zealand
| | - Rebecca Richards
- Forensic Science Programme, School of Chemical Sciences University of Auckland Auckland New Zealand
| | - SallyAnn Harbison
- Institute of Environmental Science and Research Ltd Auckland New Zealand
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533
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Kumar S, Chinnusamy V, Mohapatra T. Epigenetics of Modified DNA Bases: 5-Methylcytosine and Beyond. Front Genet 2018; 9:640. [PMID: 30619465 PMCID: PMC6305559 DOI: 10.3389/fgene.2018.00640] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/27/2018] [Indexed: 12/12/2022] Open
Abstract
Modification of DNA bases plays vital roles in the epigenetic control of gene expression in both animals and plants. Though much attention is given to the conventional epigenetic signature 5-methylcytosine (5-mC), the field of epigenetics is attracting increased scientific interest through the discovery of additional modifications of DNA bases and their roles in controlling gene expression. Theoretically, each of the DNA bases can be modified; however, modifications of cytosine and adenine only are known so far. This review focuses on the recent findings of the well-studied cytosine modifications and yet poorly characterized adenine modification which serve as an additional layer of epigenetic regulation in animals and discuss their potential roles in plants. Cytosine modification at symmetric (CG, CHG) and asymmetric (CHH) contexts is a key epigenetic feature. In addition to the ROS1 family mediated demethylation, Ten-Eleven Translocation family proteins-mediated hydroxylation of 5-mC to 5-hydroxymethylcytosine as additional active demethylation pathway are also discussed. The epigenetic marks are known to be associated with the regulation of several cellular and developmental processes, pluripotency of stem cells, neuron cell development, and tumor development in animals. Therefore, the most recently discovered N6-methyladenine, an additional epigenetic mark with regulatory potential, is also described. Interestingly, these newly discovered modifications are also found in the genomes which lack canonical 5-mC, signifying their independent epigenetic functions. These modified DNA bases are considered to be important players in epigenomics. The potential for combinatorial interaction among the known modified DNA bases suggests that epigenetic codon is likely to be substantially more complicated than it is thought today.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Agricultural Research Institute (ICAR), New Delhi, India
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534
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535
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Abstract
Aside from post-translational histone modifications and small RNA populations, the epigenome of an organism is defined by the level and spectrum of DNA methylation. Methyl groups can be covalently bound to the carbon-5 of cytosines or the carbon-6 of adenine bases. DNA methylation can be found in both prokaryotes and eukaryotes. In the latter, dynamic variation is shown across species, along development, and by cell type. DNA methylation usually leads to a lower binding affinity of DNA-interacting proteins and often results in a lower expression rate of the subsequent genome region, a process also referred to as transcriptional gene silencing. We give an overview of the current state of research facilitating the planning and implementation of whole-genome bisulfite-sequencing (WGBS) experiments. We refrain from discussing alternative methods for DNA methylation analysis, such as reduced representation bisulfite sequencing (rrBS) and methylated DNA immunoprecipitation sequencing (MeDIPSeq), which have value in specific experimental contexts but are generally disadvantageous compared to WGBS.
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536
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Treangen TJ, Pop M. You can't always sequence your way out of a tight spot: Next-generation sequencing holds great promise for pathogen detection, but the devil is in the details. EMBO Rep 2018; 19:embr.201847036. [PMID: 30467235 DOI: 10.15252/embr.201847036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Todd J Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Mihai Pop
- Department of Computer Science and University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA
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537
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Ai Y, Xing J, Zhang A, Zhao C, Liu Y, Xie B, Chen W, Cui G, Lu Z, Wang X. Computational Study on the Excited-State Decay of 5-Methylcytosine and 5-Hydroxymethylcytosine: The Common Form of DNA Methylation and Its Oxidation Product. J Phys Chem B 2018; 122:10424-10434. [DOI: 10.1021/acs.jpcb.8b07830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | | | | | | | | | - Binbin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | | | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | | | - Xiangke Wang
- NAAM Research Group, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, School for Radiological and Interdisciplinary Sciences, Soochow University, Suzhou 215123, P. R. China
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538
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Insights into imprinting from parent-of-origin phased methylomes and transcriptomes. Nat Genet 2018; 50:1542-1552. [PMID: 30349119 DOI: 10.1038/s41588-018-0232-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 08/08/2018] [Indexed: 01/23/2023]
Abstract
Imprinting is the preferential expression of one parental allele over the other. It is controlled primarily through differential methylation of cytosine at CpG dinucleotides. Here we combine 285 methylomes and 11,617 transcriptomes from peripheral blood samples with parent-of-origin phased haplotypes, to produce a new map of imprinted methylation and gene expression patterns across the human genome. We demonstrate how imprinted methylation is a continuous rather than a binary characteristic. We describe at high resolution the parent-of-origin methylation pattern at the 15q11.2 Prader-Willi/Angelman syndrome locus, with nearly confluent stochastic paternal methylation punctuated by 'spikes' of maternal methylation. We find examples of polymorphic imprinted methylation unrelated (at VTRNA2-1 and PARD6G) or related (at CHRNE) to nearby SNP genotypes. We observe RNA isoform-specific imprinted expression patterns suggestive of a methylation-sensitive transcriptional elongation block. Finally, we gain new insights into parent-of-origin-specific effects on phenotypes at the DLK1/MEG3 and GNAS loci.
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539
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540
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Sarathy A, Athreya NB, Varshney LR, Leburton JP. Classification of Epigenetic Biomarkers with Atomically Thin Nanopores. J Phys Chem Lett 2018; 9:5718-5725. [PMID: 30226383 DOI: 10.1021/acs.jpclett.8b02200] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We use the electronic properties of 2D solid-state nanopore materials to propose a versatile and generally applicable biosensor technology by using a combination of molecular dynamics, nanoscale device simulations, and statistical signal processing algorithms. As a case study, we explore the classification of three epigenetic biomarkers, the methyl-CpG binding domain 1 (MBD-1), MeCP2, and γ-cyclodextrin, attached to double-stranded DNA to identify regions of hyper- or hypomethylations by utilizing a matched filter. We assess the sensing ability of the nanopore device to identify the biomarkers based on their characteristic electronic current signatures. Such a matched filter-based classifier enables real-time identification of the biomarkers that can be easily implemented on chip. This integration of a sensor with signal processing architectures could pave the way toward the development of a multipurpose technology for early disease detection.
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541
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Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing. G3-GENES GENOMES GENETICS 2018; 8:3131-3141. [PMID: 30087105 PMCID: PMC6169393 DOI: 10.1534/g3.118.200160] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Drosophila genus is a unique group containing a wide range of species that occupy diverse ecosystems. In addition to the most widely studied species, Drosophila melanogaster, many other members in this genus also possess a well-developed set of genetic tools. Indeed, high-quality genomes exist for several species within the genus, facilitating studies of the function and evolution of cis-regulatory regions and proteins by allowing comparisons across at least 50 million years of evolution. Yet, the available genomes still fail to capture much of the substantial genetic diversity within the Drosophila genus. We have therefore tested protocols to rapidly and inexpensively sequence and assemble the genome from any Drosophila species using single-molecule sequencing technology from Oxford Nanopore. Here, we use this technology to present highly contiguous genome assemblies of 15 Drosophila species: 10 of the 12 originally sequenced Drosophila species (ananassae, erecta, mojavensis, persimilis, pseudoobscura, sechellia, simulans, virilis, willistoni, and yakuba), four additional species that had previously reported assemblies (biarmipes, bipectinata, eugracilis, and mauritiana), and one novel assembly (triauraria). Genomes were generated from an average of 29x depth-of-coverage data that after assembly resulted in an average contig N50 of 4.4 Mb. Subsequent alignment of contigs from the published reference genomes demonstrates that our assemblies could be used to close over 60% of the gaps present in the currently published reference genomes. Importantly, the materials and reagents cost for each genome was approximately $1,000 (USD). This study demonstrates the power and cost-effectiveness of long-read sequencing for genome assembly in Drosophila and provides a framework for the affordable sequencing and assembly of additional Drosophila genomes.
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542
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Han R, Li Y, Gao X, Wang S. An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing. Bioinformatics 2018; 34:i722-i731. [DOI: 10.1093/bioinformatics/bty555] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Renmin Han
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
| | - Yu Li
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
| | - Sheng Wang
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
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543
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Li Y, Han R, Bi C, Li M, Wang S, Gao X. DeepSimulator: a deep simulator for Nanopore sequencing. Bioinformatics 2018; 34:2899-2908. [PMID: 29659695 PMCID: PMC6129308 DOI: 10.1093/bioinformatics/bty223] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/31/2018] [Accepted: 04/04/2018] [Indexed: 12/18/2022] Open
Abstract
Motivation Oxford Nanopore sequencing is a rapidly developed sequencing technology in recent years. To keep pace with the explosion of the downstream data analytical tools, a versatile Nanopore sequencing simulator is needed to complement the experimental data as well as to benchmark those newly developed tools. However, all the currently available simulators are based on simple statistics of the produced reads, which have difficulty in capturing the complex nature of the Nanopore sequencing procedure, the main task of which is the generation of raw electrical current signals. Results Here we propose a deep learning based simulator, DeepSimulator, to mimic the entire pipeline of Nanopore sequencing. Starting from a given reference genome or assembled contigs, we simulate the electrical current signals by a context-dependent deep learning model, followed by a base-calling procedure to yield simulated reads. This workflow mimics the sequencing procedure more naturally. The thorough experiments performed across four species show that the signals generated by our context-dependent model are more similar to the experimentally obtained signals than the ones generated by the official context-independent pore model. In terms of the simulated reads, we provide a parameter interface to users so that they can obtain the reads with different accuracies ranging from 83 to 97%. The reads generated by the default parameter have almost the same properties as the real data. Two case studies demonstrate the application of DeepSimulator to benefit the development of tools in de novo assembly and in low coverage SNP detection. Availability and implementation The software can be accessed freely at: https://github.com/lykaust15/DeepSimulator. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yu Li
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
| | - Renmin Han
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
| | - Chongwei Bi
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mo Li
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sheng Wang
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
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544
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Recent progress, methods and perspectives in forensic epigenetics. Forensic Sci Int Genet 2018; 37:180-195. [PMID: 30176440 DOI: 10.1016/j.fsigen.2018.08.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 08/15/2018] [Indexed: 01/19/2023]
Abstract
Forensic epigenetics, i.e., investigating epigenetics variation to resolve forensically relevant questions unanswerable with standard forensic DNA profiling has been gaining substantial ground over the last few years. Differential DNA methylation among tissues and individuals has been proposed as useful resource for three forensic applications i) determining the tissue type of a human biological trace, ii) estimating the age of an unknown trace donor, and iii) differentiating between monozygotic twins. Thus far, forensic epigenetic investigations have used a wide range of methods for CpG marker discovery, prediction modelling and targeted DNA methylation analysis, all coming with advantages and disadvantages when it comes to forensic trace analysis. In this review, we summarize the most recent literature on these three main topics of current forensic epigenetic investigations and discuss limitations and practical considerations in experimental design and data interpretation, such as technical and biological biases. Moreover, we provide future perspectives with regard to new research questions, new epigenetic markers and recent technological advances that - as we envision - will move the field towards forensic epigenomics in the near future.
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545
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Martín-Del-Campo R, Bárcenas-Ibarra A, Sifuentes-Romero I, Llera-Herrera R, García-Gasca A. Methylation status of the putative Pax6 promoter in olive ridley sea turtle embryos with eye defects: An initial approach. Mech Dev 2018; 154:287-295. [PMID: 30110613 DOI: 10.1016/j.mod.2018.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/05/2018] [Accepted: 08/10/2018] [Indexed: 12/26/2022]
Abstract
Normal development involves the interplay of genetic and epigenetic regulatory mechanisms. Pax6 is an eye-selector factor responsible for initiating the regulatory cascade for the development of the eyes. For the olive ridley sea turtle (Lepidochelys olivacea), a threatened species, eye malformations have been reported. In order to study the DNA methylation status of the putative promoter of the Pax6 gene in embryos with ocular malformations, an exploratory study was carried out in which DNA was isolated from embryos with anophthalmia, microphthalmia, and cyclopia, as well as from their normal counterparts. The 5'-flanking region from the Pax6 gene was isolated, showing two CpG islands (CGIs). The methylation status of CGIs in malformed embryos was compared with that of normal embryos by bisulfite sequencing. Putative transcription factor binding sites and regulatory features were identified. Methylation patterns were observed in both CpG and non-CpG contexts, and were unique for each malformed embryo; in the CpG context, an embryo with cyclopia showed a methylated cytosine upstream the CGI-1 not present in other embryos, an embryo with left anophthalmia presented two methylated cytosines in the CGI-1, whereas an embryo with left anophthalmia and right microphthalmia showed two methylated cytosines in the CGI-2. Normal embryos did not show methylated cytosines in the CGI-1, but one of them showed one methylcytosine in the CGI-2. Methylated transcription factor-binding sites may affect Pax6 expression associated to the cellular response to environmental compounds and hypoxia, signal transduction, cell cycle, lens physiology and development, as well as the transcription rate. Although preliminary, these results suggest that embryos with ocular malformations present unique DNA methylation patterns in the putative promoter of the Pax6 gene in L. olivacea, and probably those subtle, random changes in the methylation status can cause (at least in part) the aberrant phenotypes observed in these embryos.
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Affiliation(s)
- Rodolfo Martín-Del-Campo
- Laboratory of Molecular Biology, Centro de Investigación en Alimentación y Desarrollo (CIAD), Avenida Sábalo Cerritos s/n, Mazatlán, Sinaloa 82110, Mexico.
| | - Annelisse Bárcenas-Ibarra
- Laboratory of Molecular Biology, Centro de Investigación en Alimentación y Desarrollo (CIAD), Avenida Sábalo Cerritos s/n, Mazatlán, Sinaloa 82110, Mexico
| | - Itzel Sifuentes-Romero
- Department of Biological Sciences, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431, USA.
| | - Raúl Llera-Herrera
- Laboratory of Molecular Biology, Centro de Investigación en Alimentación y Desarrollo (CIAD), Avenida Sábalo Cerritos s/n, Mazatlán, Sinaloa 82110, Mexico; Instituto de Ciencias del Mar y Limnología (Unidad Académica Mazatlán), Universidad Nacional Autónoma de México, Avenida Joel Montes Camarena s/n, PO Box 811, Mazatlán, Sinaloa 82040, Mexico
| | - Alejandra García-Gasca
- Laboratory of Molecular Biology, Centro de Investigación en Alimentación y Desarrollo (CIAD), Avenida Sábalo Cerritos s/n, Mazatlán, Sinaloa 82110, Mexico.
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546
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Patel A, Belykh E, Miller EJ, George LL, Martirosyan NL, Byvaltsev VA, Preul MC. MinION rapid sequencing: Review of potential applications in neurosurgery. Surg Neurol Int 2018; 9:157. [PMID: 30159201 PMCID: PMC6094492 DOI: 10.4103/sni.sni_55_18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 05/22/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Gene sequencing has played an integral role in the advancement and understanding of disease pathology and treatment. Although historically expensive and time consuming, new sequencing technologies improve our capability to obtain the genetic information in an accurate and timely manner. Within neurosurgery, gene sequencing is routinely used in the diagnosis and treatment of neurosurgical diseases, primarily for brain tumors. This paper reviews nanopore sequencing, an innovation utilized by MinION and outlines its potential use for neurosurgery. METHODS A literature search was conducted for publications containing the keywords of Oxford MinION, nanopore sequencing, brain tumor, glioma, whole genome sequencing (WGS), epigenomics, molecular neuropathology, and next-generation sequencing (NGS). In total, 64 articles were selected and used for this review. RESULTS The Oxford MinION nanopore sequencing technology has had successful applications within clinical microbiology, human genome sequencing, and cancer genotyping across multiple specialties. Technical details, methodology, and current use of MinION sequencing are discussed through the prism of potential applications to solve neurosurgery-related scientific and diagnostic questions. The MinION device has proven to provide rapid and accurate reads with longer read lengths when compared with NGS. For applications within neurosurgery, the MinION device is capable of providing critical diagnostic information for central nervous system (CNS) tumors within a single day. CONCLUSIONS MinION provides rapid and accurate gene sequencing with better affordability and convenience compared with current NGS methods. Widespread success of the MinION nanopore sequencing technology in providing accurate, rapid, and convenient gene sequencing suggests a promising future within research laboratories and to improve care for neurosurgical patients.
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Affiliation(s)
- Arpan Patel
- Department of Neurosurgery, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona, USA
- College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Evgenii Belykh
- Department of Neurosurgery, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona, USA
- Department of Neurosurgery, Irkutsk State Medical University, Irkutsk, Russia
| | - Eric J. Miller
- Department of Neurosurgery, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona, USA
- College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Laeth L. George
- Department of Neurosurgery, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona, USA
- College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Nikolay L. Martirosyan
- Department of Neurosurgery, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona, USA
| | - Vadim A. Byvaltsev
- Department of Neurosurgery, Irkutsk State Medical University, Irkutsk, Russia
| | - Mark C. Preul
- Department of Neurosurgery, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, Arizona, USA
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547
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Atack JM, Tan A, Bakaletz LO, Jennings MP, Seib KL. Phasevarions of Bacterial Pathogens: Methylomics Sheds New Light on Old Enemies. Trends Microbiol 2018; 26:715-726. [PMID: 29452952 PMCID: PMC6054543 DOI: 10.1016/j.tim.2018.01.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 01/06/2018] [Accepted: 01/26/2018] [Indexed: 01/04/2023]
Abstract
A wide variety of bacterial pathogens express phase-variable DNA methyltransferases that control expression of multiple genes via epigenetic mechanisms. These randomly switching regulons - phasevarions - regulate genes involved in pathogenesis, host adaptation, and antibiotic resistance. Individual phase-variable genes can be identified in silico as they contain easily recognized features such as simple sequence repeats (SSRs) or inverted repeats (IRs) that mediate the random switching of expression. Conversely, phasevarion-controlled genes do not contain any easily identifiable features. The study of DNA methyltransferase specificity using Single-Molecule, Real-Time (SMRT) sequencing and methylome analysis has rapidly advanced the analysis of phasevarions by allowing methylomics to be combined with whole-transcriptome/proteome analysis to comprehensively characterize these systems in a number of important bacterial pathogens.
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Affiliation(s)
- John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4222, Australia.
| | - Aimee Tan
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4222, Australia
| | - Lauren O Bakaletz
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, OH 43205, USA
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4222, Australia
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4222, Australia.
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548
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Arakawa K, Kono N, Ohtoshi R, Nakamura H, Tomita M. The complete mitochondrial genome of Eumeta variegata (Lepidoptera: Psychidae). MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:812-813. [PMID: 33474332 PMCID: PMC7799889 DOI: 10.1080/23802359.2018.1495119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The complete mitochondrial genome of Eumeta variegate, largest bagworm moth in Japan, has been sequenced using a nanopore sequencer as a single long read. The genome has a total length of 16,601 bp, consisting of 13 protein-coding genes, 20 tRNA, 2 rRNA genes, and an AT-rich control region. The nucleotide composition was extremely AT-rich, with 42.4% A, 40.4% T, 6.67% G, and 10.6% C. This is the second report of a complete mitochondrial genome of Psychidae, and the sequence information together with a phylogenetic analysis would provide a reference data in the future studies of Lepidoptera and Psychidae.
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Affiliation(s)
- Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Nobuaki Kono
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | | | | | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
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549
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Nishitani S, Parets SE, Haas BW, Smith AK. DNA methylation analysis from saliva samples for epidemiological studies. Epigenetics 2018; 13:352-362. [PMID: 29912612 DOI: 10.1080/15592294.2018.1461295] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Abstract
Saliva is a non-invasive, easily accessible tissue, which is regularly collected in large epidemiological studies to examine genetic questions. Recently, it is becoming more common to use saliva to assess DNA methylation. However, DNA extracted from saliva is a mixture of both bacterial and human DNA derived from epithelial and immune cells in the mouth. Thus, there are unique challenges to using salivary DNA in methylation studies that can influence data quality. This study assesses: (1) quantification of human DNA after extraction; (2) delineation of human and bacterial DNA; (3) bisulfite conversion (BSC); (4) quantification of BSC DNA; (5) PCR amplification of BSC DNA from saliva and; (6) quantitation of DNA methylation with a targeted assay. The framework proposed will allow saliva samples to be more widely used in targeted epigenetic studies.
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Affiliation(s)
- Shota Nishitani
- a Department of Gynecology and Obstetrics , Emory University School of Medicine , Atlanta , GA , USA.,b Department of Psychiatry and Behavioral Sciences , Emory University School of Medicine , Atlanta , GA , USA
| | - Sasha E Parets
- b Department of Psychiatry and Behavioral Sciences , Emory University School of Medicine , Atlanta , GA , USA
| | - Brian W Haas
- c Department of Psychology , University of Georgia , Athens , GA , USA
| | - Alicia K Smith
- a Department of Gynecology and Obstetrics , Emory University School of Medicine , Atlanta , GA , USA.,b Department of Psychiatry and Behavioral Sciences , Emory University School of Medicine , Atlanta , GA , USA
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550
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Pollard MO, Gurdasani D, Mentzer AJ, Porter T, Sandhu MS. Long reads: their purpose and place. Hum Mol Genet 2018; 27:R234-R241. [PMID: 29767702 PMCID: PMC6061690 DOI: 10.1093/hmg/ddy177] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 05/08/2018] [Indexed: 12/20/2022] Open
Abstract
In recent years long-read technologies have moved from being a niche and specialist field to a point of relative maturity likely to feature frequently in the genomic landscape. Analogous to next generation sequencing, the cost of sequencing using long-read technologies has materially dropped whilst the instrument throughput continues to increase. Together these changes present the prospect of sequencing large numbers of individuals with the aim of fully characterizing genomes at high resolution. In this article, we will endeavour to present an introduction to long-read technologies showing: what long reads are; how they are distinct from short reads; why long reads are useful and how they are being used. We will highlight the recent developments in this field, and the applications and potential of these technologies in medical research, and clinical diagnostics and therapeutics.
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Affiliation(s)
- Martin O Pollard
- Human Genetics - Wellcome Sanger Institute, Hinxton, Cambridge, UK
- University of Cambridge - Department of Medicine, Addenbrookes Hospital, Box 157, Hills Road, Cambridge, UK
| | - Deepti Gurdasani
- Human Genetics - Wellcome Sanger Institute, Hinxton, Cambridge, UK
- University of Cambridge - Department of Medicine, Addenbrookes Hospital, Box 157, Hills Road, Cambridge, UK
| | - Alexander J Mentzer
- Human Genetics - Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford, UK
| | - Tarryn Porter
- Human Genetics - Wellcome Sanger Institute, Hinxton, Cambridge, UK
- University of Cambridge - Department of Medicine, Addenbrookes Hospital, Box 157, Hills Road, Cambridge, UK
| | - Manjinder S Sandhu
- Human Genetics - Wellcome Sanger Institute, Hinxton, Cambridge, UK
- University of Cambridge - Department of Medicine, Addenbrookes Hospital, Box 157, Hills Road, Cambridge, UK
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