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Hansen MH, Cédile O, Kjeldsen MLG, Thomassen M, Preiss B, von Neuhoff N, Abildgaard N, Nyvold CG. Toward Cytogenomics: Technical Assessment of Long-Read Nanopore Whole-Genome Sequencing for Detecting Large Chromosomal Alterations in Mantle Cell Lymphoma. J Mol Diagn 2023; 25:796-805. [PMID: 37683892 DOI: 10.1016/j.jmoldx.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 06/20/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023] Open
Abstract
The current advances and success of next-generation sequencing hold the potential for the transition of cancer cytogenetics toward comprehensive cytogenomics. However, the conventional use of short reads impedes the resolution of chromosomal aberrations. Thus, this study evaluated the detection and reproducibility of extensive copy number alterations and chromosomal translocations using long-read Oxford Nanopore Technologies whole-genome sequencing compared with short-read Illumina sequencing. Using the mantle cell lymphoma cell line Granta-519, almost 99% copy-number reproducibility at the 100-kilobase resolution between replicates was demonstrated, with 98% concordance to Illumina. Collectively, the performance of copy number calling from 1.5 million to 7.5 million long reads was comparable to 1 billion Illumina-based reads (50× coverage). Expectedly, the long-read resolution of canonical translocation t(11;14)(q13;q32) was superior, with a sequence similarity of 89% to the already published CCND1/IGH junction (9× coverage), spanning up to 69 kilobases. The cytogenetic profile of Granta-519 was in general agreement with the literature and karyotype, although several differences remained unresolved. In conclusion, contemporary long-read sequencing is primed for future cytogenomics or sequencing-guided cytogenetics. The combined strength of long- and short-read sequencing is apparent, where the high-precision junctional mapping complements and splits paired-end reads. The potential is emphasized by the flexible single-sample genomic data acquisition of Oxford Nanopore Technologies with the high resolution of allelic imbalances using Illumina short-read sequencing.
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Affiliation(s)
- Marcus H Hansen
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark.
| | - Oriane Cédile
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark; OPEN, Odense Patient Data Explorative Network, Odense University Hospital, Odense, Denmark
| | - Marie L G Kjeldsen
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Birgitte Preiss
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Nils von Neuhoff
- Department of Pediatric Hematology and Oncology, Essen University Hospital and University of Duisburg-Essen, Essen, Germany
| | - Niels Abildgaard
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Charlotte G Nyvold
- Hematology-Pathology Research Laboratory, Research Unit of Hematology and Research Unit of Pathology, University of Southern Denmark and Odense University Hospital, Odense, Denmark; Department of Hematology, Odense University Hospital, Odense, Denmark; OPEN, Odense Patient Data Explorative Network, Odense University Hospital, Odense, Denmark
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2
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Ferraj A, Audano PA, Balachandran P, Czechanski A, Flores JI, Radecki AA, Mosur V, Gordon DS, Walawalkar IA, Eichler EE, Reinholdt LG, Beck CR. Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements. CELL GENOMICS 2023; 3:100291. [PMID: 37228752 PMCID: PMC10203049 DOI: 10.1016/j.xgen.2023.100291] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/03/2023] [Accepted: 03/10/2023] [Indexed: 05/25/2023]
Abstract
Diverse inbred mouse strains are important biomedical research models, yet genome characterization of many strains is fundamentally lacking in comparison with humans. In particular, catalogs of structural variants (SVs) (variants ≥ 50 bp) are incomplete, limiting the discovery of causative alleles for phenotypic variation. Here, we resolve genome-wide SVs in 20 genetically distinct inbred mice with long-read sequencing. We report 413,758 site-specific SVs affecting 13% (356 Mbp) of the mouse reference assembly, including 510 previously unannotated coding variants. We substantially improve the Mus musculus transposable element (TE) callset, and we find that TEs comprise 39% of SVs and account for 75% of altered bases. We further utilize this callset to investigate how TE heterogeneity affects mouse embryonic stem cells and find multiple TE classes that influence chromatin accessibility. Our work provides a comprehensive analysis of SVs found in diverse mouse genomes and illustrates the role of TEs in epigenetic differences.
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Affiliation(s)
- Ardian Ferraj
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06032, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Peter A. Audano
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | | | - Jacob I. Flores
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Alexander A. Radecki
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06032, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Varun Mosur
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - David S. Gordon
- Howard Hughes Medical Institute and Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Isha A. Walawalkar
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06032, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Evan E. Eichler
- Howard Hughes Medical Institute and Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Christine R. Beck
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06032, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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3
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Cook CB, Armstrong L, Boerkoel CF, Clarke LA, du Souich C, Demos MK, Gibson WT, Gill H, Lopez E, Patel MS, Selby K, Abu-Sharar Z, Elliott AM, Friedman JM. Somatic mosaicism detected by genome-wide sequencing in 500 parent-child trios with suspected genetic disease: clinical and genetic counseling implications. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006125. [PMID: 34697084 PMCID: PMC8751411 DOI: 10.1101/mcs.a006125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/13/2021] [Indexed: 01/28/2023] Open
Abstract
Identifying genetic mosaicism is important in establishing a diagnosis, assessing recurrence risk, and providing accurate genetic counseling. Next-generation sequencing has allowed for the identification of mosaicism at levels below those detectable by conventional Sanger sequencing or chromosomal microarray analysis. The CAUSES Clinic was a pediatric translational trio-based genome-wide (exome or genome) sequencing study of 500 families (531 children) with suspected genetic disease at BC Children's and Women's Hospitals. Here we present 12 cases of apparent mosaicism identified in the CAUSES cohort: nine cases of parental mosaicism for a disease-causing variant found in a child and three cases of mosaicism in the proband for a de novo variant. In six of these cases, there was no evidence of mosaicism on Sanger sequencing—the variant was not detected on Sanger sequencing in three cases, and it appeared to be heterozygous in three others. These cases are examples of six clinical manifestations of mosaicism: a proband with classical clinical features of mosaicism (e.g., segmental abnormalities of skin pigmentation or asymmetrical growth of bilateral body parts), a proband with unusually mild manifestations of a disease, a mosaic proband who is clinically indistinguishable from the constitutive phenotype, a mosaic parent with no clinical features of the disease, a mosaic parent with mild manifestations of the disease, and a family in which both parents are unaffected and two siblings have the same disease-causing constitutional mutation. Our data demonstrate the importance of considering the possibility of mosaicism whenever exome or genome sequencing is performed and that its detection via genome-wide sequencing can permit more accurate genetic counseling.
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Affiliation(s)
- Courtney B Cook
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Linlea Armstrong
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
| | - Cornelius F Boerkoel
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Lorne A Clarke
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Christèle du Souich
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
| | - Michelle K Demos
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Vancouver, British Columbia, Canada V6H 0B3
| | - William T Gibson
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
| | - Harinder Gill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Elena Lopez
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Millan S Patel
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1
| | - Kathryn Selby
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Vancouver, British Columbia, Canada V6H 0B3
| | - Ziad Abu-Sharar
- Division of Neurology, Department of Pediatrics, BC Children's Hospital, Vancouver, British Columbia, Canada V6H 0B3
| | | | - Alison M Elliott
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4.,Women's Health Research Institute, Vancouver, British Columbia, Canada V6H 2N9
| | - Jan M Friedman
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada V6H 3N1.,BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada V5Z 4H4
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4
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Fuentes RR, de Ridder D, van Dijk ADJ, Peters SA. Domestication shapes recombination patterns in tomato. Mol Biol Evol 2021; 39:6379725. [PMID: 34597400 PMCID: PMC8763028 DOI: 10.1093/molbev/msab287] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Meiotic recombination is a biological process of key importance in breeding, to generate genetic diversity and develop novel or agronomically relevant haplotypes. In crop tomato, recombination is curtailed as manifested by linkage disequilibrium decay over a longer distance and reduced diversity compared with wild relatives. Here, we compared domesticated and wild populations of tomato and found an overall conserved recombination landscape, with local changes in effective recombination rate in specific genomic regions. We also studied the dynamics of recombination hotspots resulting from domestication and found that loss of such hotspots is associated with selective sweeps, most notably in the pericentromeric heterochromatin. We detected footprints of genetic changes and structural variants, among them associated with transposable elements, linked with hotspot divergence during domestication, likely causing fine-scale alterations to recombination patterns and resulting in linkage drag.
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Affiliation(s)
- Roven Rommel Fuentes
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB The Netherlands
| | - Sander A Peters
- Applied Bioinformatics, Wageningen Plant Research, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
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5
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Jeffet J, Margalit S, Michaeli Y, Ebenstein Y. Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale. Essays Biochem 2021; 65:51-66. [PMID: 33739394 PMCID: PMC8056043 DOI: 10.1042/ebc20200021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022]
Abstract
The human genome contains multiple layers of information that extend beyond the genetic sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident for the case of two different cell types in the human body. The great variation in structure and function displayed by cells with identical genetic background is attributed to additional genomic information content. This includes large-scale genetic aberrations, as well as diverse epigenetic patterns that are crucial for regulating specific cell functions. These genetic and epigenetic patterns operate in concert in order to maintain specific cellular functions in health and disease. Single-molecule optical genome mapping is a high-throughput genome analysis method that is based on imaging long chromosomal fragments stretched in nanochannel arrays. The access to long DNA molecules coupled with fluorescent tagging of various genomic information presents a unique opportunity to study genetic and epigenetic patterns in the genome at a single-molecule level over large genomic distances. Optical mapping entwines synergistically chemical, physical, and computational advancements, to uncover invaluable biological insights, inaccessible by sequencing technologies. Here we describe the method's basic principles of operation, and review the various available mechanisms to fluorescently tag genomic information. We present some of the recent biological and clinical impact enabled by optical mapping and present recent approaches for increasing the method's resolution and accuracy. Finally, we discuss how multiple layers of genomic information may be mapped simultaneously on the same DNA molecule, thus paving the way for characterizing multiple genomic observables on individual DNA molecules.
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Affiliation(s)
- Jonathan Jeffet
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sapir Margalit
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Michaeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
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6
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The Cytogenomic "Theory of Everything": Chromohelkosis May Underlie Chromosomal Instability and Mosaicism in Disease and Aging. Int J Mol Sci 2020; 21:ijms21218328. [PMID: 33171981 PMCID: PMC7664247 DOI: 10.3390/ijms21218328] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 01/28/2023] Open
Abstract
Mechanisms for somatic chromosomal mosaicism (SCM) and chromosomal instability (CIN) are not completely understood. During molecular karyotyping and bioinformatic analyses of children with neurodevelopmental disorders and congenital malformations (n = 612), we observed colocalization of regular chromosomal imbalances or copy number variations (CNV) with mosaic ones (n = 47 or 7.7%). Analyzing molecular karyotyping data and pathways affected by CNV burdens, we proposed a mechanism for SCM/CIN, which had been designated as “chromohelkosis” (from the Greek words chromosome ulceration/open wound). Briefly, structural chromosomal imbalances are likely to cause local instability (“wreckage”) at the breakpoints, which results either in partial/whole chromosome loss (e.g., aneuploidy) or elongation of duplicated regions. Accordingly, a function for classical/alpha satellite DNA (protection from the wreckage towards the centromere) has been hypothesized. Since SCM and CIN are ubiquitously involved in development, homeostasis and disease (e.g., prenatal development, cancer, brain diseases, aging), we have metaphorically (ironically) designate the system explaining chromohelkosis contribution to SCM/CIN as the cytogenomic “theory of everything”, similar to the homonymous theory in physics inasmuch as it might explain numerous phenomena in chromosome biology. Recognizing possible empirical and theoretical weaknesses of this “theory”, we nevertheless believe that studies of chromohelkosis-like processes are required to understand structural variability and flexibility of the genome.
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7
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Brandies PA, Tang S, Johnson RSP, Hogg CJ, Belov K. The first Antechinus reference genome provides a resource for investigating the genetic basis of semelparity and age-related neuropathologies. GIGABYTE 2020; 2020:gigabyte7. [PMID: 36824596 PMCID: PMC9631953 DOI: 10.46471/gigabyte.7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/04/2020] [Indexed: 12/14/2022] Open
Abstract
Antechinus are a genus of mouse-like marsupials that exhibit a rare reproductive strategy known as semelparity and also naturally develop age-related neuropathologies similar to those in humans. We provide the first annotated antechinus reference genome for the brown antechinus (Antechinus stuartii). The reference genome is 3.3 Gb in size with a scaffold N50 of 73Mb and 93.3% complete mammalian BUSCOs. Using bioinformatic methods we assign scaffolds to chromosomes and identify 0.78 Mb of Y-chromosome scaffolds. Comparative genomics revealed interesting expansions in the NMRK2 gene and the protocadherin gamma family, which have previously been associated with aging and age-related dementias respectively. Transcriptome data displayed expression of common Alzheimer's related genes in the antechinus brain and highlight the potential of utilising the antechinus as a future disease model. The valuable genomic resources provided herein will enable future research to explore the genetic basis of semelparity and age-related processes in the antechinus.
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Affiliation(s)
- Parice A. Brandies
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Simon Tang
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Robert S. P. Johnson
- Zoologica: Veterinary and Zoological Consulting, Millthorpe, New South Wales, Australia
| | - Carolyn J. Hogg
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia, Corresponding author. E-mail:
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8
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Dong J, Qi M, Wang S, Yuan X. DINTD: Detection and Inference of Tandem Duplications From Short Sequencing Reads. Front Genet 2020; 11:924. [PMID: 32849857 PMCID: PMC7433346 DOI: 10.3389/fgene.2020.00924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/24/2020] [Indexed: 11/21/2022] Open
Abstract
Tandem duplication (TD) is an important type of structural variation (SV) in the human genome and has biological significance for human cancer evolution and tumor genesis. Accurate and reliable detection of TDs plays an important role in advancing early detection, diagnosis, and treatment of disease. The advent of next-generation sequencing technologies has made it possible for the study of TDs. However, detection is still challenging due to the uneven distribution of reads and the uncertain amplitude of TD regions. In this paper, we present a new method, DINTD (Detection and INference of Tandem Duplications), to detect and infer TDs using short sequencing reads. The major principle of the proposed method is that it first extracts read depth and mapping quality signals, then uses the DBSCAN (Density-Based Spatial Clustering of Applications with Noise) algorithm to find the possible TD regions. The total variation penalized least squares model is fitted with read depth and mapping quality signals to denoise signals. A 2D binary search tree is used to search the neighbor points effectively. To further identify the exact breakpoints of the TD regions, split-read signals are integrated into DINTD. The experimental results of DINTD on simulated data sets showed that DINTD can outperform other methods for sensitivity, precision, F1-score, and boundary bias. DINTD is further validated on real samples, and the experiment results indicate that it is consistent with other methods. This study indicates that DINTD can be used as an effective tool for detecting TDs.
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Affiliation(s)
- Jinxin Dong
- School of Computer Science and Technology, Xidian University, Xi'an, China.,School of Computer Science and Technology, Liaocheng University, Liaocheng, China
| | - Minyong Qi
- School of Computer Science and Technology, Xidian University, Xi'an, China.,School of Computer Science and Technology, Liaocheng University, Liaocheng, China
| | - Shaoqiang Wang
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Xiguo Yuan
- School of Computer Science and Technology, Xidian University, Xi'an, China
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Sullivan BA. A sampling of methods to study chromosome and genome structure and function. Chromosome Res 2020; 28:1-5. [PMID: 32157563 PMCID: PMC7185174 DOI: 10.1007/s10577-020-09629-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 11/29/2022]
Abstract
As a scientist, one’s perspective of the human genome is informed by the way it is studied – at the level of single nucleotides, a single gene, a specific genomic region, an entire chromosome, the complete karyotype, or the nucleus that encompasses both the genome and the nuclear components that support genome structure, function, stability, and inheritance. Experimentally investigating aspects of genome structure and chromosome number and higher order packaging requires different technical approaches that offer varying levels of resolution. This special issue of Chromosome Research provides overviews of a few current methodologies to study chromosome and genome organization and function, with a particular focus on contemporary sequencing-based approaches.
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Affiliation(s)
- Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Division of Human Genetics, Duke University School of Medicine, Durham, NC, 27710, USA.
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