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Keywords = BioNano optical genome mapping

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18 pages, 2061 KiB  
Article
Toward a Kinh Vietnamese Reference Genome: Constructing a De Novo Genome Assembly Using Long-Read Sequencing and Optical Mapping
by Le Thi Dung, Le Tung Lam, Nguyen Hong Trang, Nguyen Vu Hung Anh, Nguyen Ngoc Nam, Doan Thi Nhung, Tran Huyen Linh, Le Ngoc Giang, Hoang Ha, Nguyen Quang Huy and Truong Nam Hai
Genes 2025, 16(5), 536; https://doi.org/10.3390/genes16050536 - 29 Apr 2025
Viewed by 1023
Abstract
Background: Population-specific reference genomes are essential for improving the accuracy and reliability of genomic analyses across diverse human populations. Although Vietnam ranks as the 16th most populous country in the world, with more than 86% of its population identifying as Kinh, studies specifically [...] Read more.
Background: Population-specific reference genomes are essential for improving the accuracy and reliability of genomic analyses across diverse human populations. Although Vietnam ranks as the 16th most populous country in the world, with more than 86% of its population identifying as Kinh, studies specifically focusing on the Kinh Vietnamese reference genome remain scarce. Therefore, constructing a Kinh Vietnamese reference genome is valuable in the genetic research of Vietnamese. Methods: In this study, we combined PacBio long-read sequencing and Bionano optical mapping data to generate a de novo assembly of a Kinh Vietnamese genome (VHG), which was subsequently polished using multiple Kinh Vietnamese short-read whole-genome sequences (WGSs). Results: The final assembly, named VHG1.2, comprised 3.22 gigabase pairs of high-quality sequence data, demonstrating high accuracy (QV: 48), completeness (BUSCO: 92%), and continuity (295 super scaffolds, super scaffold N50: 50 Kbp). Using multiple bioinformatic tools for variant calling, we observed significant variants when the population-specific reference VHG1.2 was used compared to the standard reference genome hg38. Conclusions: Overall, our genome assembly demonstrates the advantages of a long-read hybrid sequencing approach for de novo assembly and highlights the benefit of using population-specific reference genomes in population genomic analysis. Full article
(This article belongs to the Section Technologies and Resources for Genetics)
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16 pages, 1844 KiB  
Article
Exploring the Potential of Optical Genome Mapping in the Diagnosis and Prognosis of Soft Tissue and Bone Tumors
by Alejandro Berenguer-Rubio, Esperanza Such, Neus Torres Hernández, Paula González-Rojo, Álvaro Díaz-González, Gayane Avetisyan, Carolina Gil-Aparicio, Judith González-López, Nicolay Pantoja-Borja, Luis Alberto Rubio-Martínez, Soraya Hernández-Girón, María Soledad Valera-Cuesta, Cristina Ramírez-Fuentes, María Simonet-Redondo, Roberto Díaz-Beveridge, Carolina de la Calva, José Vicente Amaya-Valero, Cristina Ballester-Ibáñez, Alessandro Liquori, Francisco Giner and Empar Mayordomo-Arandaadd Show full author list remove Hide full author list
Int. J. Mol. Sci. 2025, 26(6), 2820; https://doi.org/10.3390/ijms26062820 - 20 Mar 2025
Viewed by 1115
Abstract
Sarcomas are rare malignant tumors of mesenchymal origin with a high misdiagnosis rate due to their heterogeneity and low incidence. Conventional diagnostic techniques, such as Fluorescence In Situ Hybridization (FISH) and Next-Generation Sequencing (NGS), have limitations in detecting structural variations (SVs), copy number [...] Read more.
Sarcomas are rare malignant tumors of mesenchymal origin with a high misdiagnosis rate due to their heterogeneity and low incidence. Conventional diagnostic techniques, such as Fluorescence In Situ Hybridization (FISH) and Next-Generation Sequencing (NGS), have limitations in detecting structural variations (SVs), copy number variations (CNVs), and predicting clinical behavior. Optical genome mapping (OGM) provides high-resolution genome-wide analysis, improving sarcoma diagnosis and prognosis assessment. This study analyzed 53 sarcoma samples using OGM. Ultra-high molecular weight (UHMW) DNA was extracted from core and resection biopsies, and data acquisition was performed with the Bionano Saphyr platform. Bioinformatic pipelines identified structural variations, comparing them with known alterations for each sarcoma subtype. OGM successfully analyzed 62.3% of samples. Diagnostic-defining alterations were found in 95.2% of cases, refining diagnoses and revealing novel oncogenic and tumor suppressor gene alterations. The challenges included DNA extraction and quality issues from some tissue samples. Despite these limitations, OGM proved to be a powerful diagnostic and predictive tool for bone and soft tissue sarcomas, surpassing conventional methods in resolution and scope, enhancing the understanding of sarcoma genetics, and enabling better patient stratification and personalized therapies. Full article
(This article belongs to the Special Issue Cancer Diagnosis and Treatment: Exploring Molecular Research)
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16 pages, 1382 KiB  
Article
A Comparison of Structural Variant Calling from Short-Read and Nanopore-Based Whole-Genome Sequencing Using Optical Genome Mapping as a Benchmark
by Yang Pei, Melanie Tanguy, Adam Giess, Abhijit Dixit, Louise C. Wilson, Richard J. Gibbons, Stephen R. F. Twigg, Greg Elgar and Andrew O. M. Wilkie
Genes 2024, 15(7), 925; https://doi.org/10.3390/genes15070925 - 16 Jul 2024
Cited by 5 | Viewed by 3815
Abstract
The identification of structural variants (SVs) in genomic data represents an ongoing challenge because of difficulties in reliable SV calling leading to reduced sensitivity and specificity. We prepared high-quality DNA from 9 parent–child trios, who had previously undergone short-read whole-genome sequencing (Illumina platform) [...] Read more.
The identification of structural variants (SVs) in genomic data represents an ongoing challenge because of difficulties in reliable SV calling leading to reduced sensitivity and specificity. We prepared high-quality DNA from 9 parent–child trios, who had previously undergone short-read whole-genome sequencing (Illumina platform) as part of the Genomics England 100,000 Genomes Project. We reanalysed the genomes using both Bionano optical genome mapping (OGM; 8 probands and one trio) and Nanopore long-read sequencing (Oxford Nanopore Technologies [ONT] platform; all samples). To establish a “truth” dataset, we asked whether rare proband SV calls (n = 234) made by the Bionano Access (version 1.6.1)/Solve software (version 3.6.1_11162020) could be verified by individual visualisation using the Integrative Genomics Viewer with either or both of the Illumina and ONT raw sequence. Of these, 222 calls were verified, indicating that Bionano OGM calls have high precision (positive predictive value 95%). We then asked what proportion of the 222 true Bionano SVs had been identified by SV callers in the other two datasets. In the Illumina dataset, sensitivity varied according to variant type, being high for deletions (115/134; 86%) but poor for insertions (13/58; 22%). In the ONT dataset, sensitivity was generally poor using the original Sniffles variant caller (48% overall) but improved substantially with use of Sniffles2 (36/40; 90% and 17/23; 74% for deletions and insertions, respectively). In summary, we show that the precision of OGM is very high. In addition, when applying the Sniffles2 caller, the sensitivity of SV calling using ONT long-read sequence data outperforms Illumina sequencing for most SV types. Full article
(This article belongs to the Special Issue Advances of Optical Genome Mapping in Human Genetics)
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20 pages, 5039 KiB  
Article
Integrating Optical Genome Mapping and Whole Genome Sequencing in Somatic Structural Variant Detection
by Laura Budurlean, Diwakar Bastihalli Tukaramrao, Lijun Zhang, Sinisa Dovat and James Broach
J. Pers. Med. 2024, 14(3), 291; https://doi.org/10.3390/jpm14030291 - 9 Mar 2024
Cited by 1 | Viewed by 4406
Abstract
Structural variants drive tumorigenesis by disrupting normal gene function through insertions, inversions, translocations, and copy number changes, including deletions and duplications. Detecting structural variants is crucial for revealing their roles in tumor development, clinical outcomes, and personalized therapy. Presently, most studies rely on [...] Read more.
Structural variants drive tumorigenesis by disrupting normal gene function through insertions, inversions, translocations, and copy number changes, including deletions and duplications. Detecting structural variants is crucial for revealing their roles in tumor development, clinical outcomes, and personalized therapy. Presently, most studies rely on short-read data from next-generation sequencing that aligns back to a reference genome to determine if and, if so, where a structural variant occurs. However, structural variant discovery by short-read sequencing is challenging, primarily because of the difficulty in mapping regions of repetitive sequences. Optical genome mapping (OGM) is a recent technology used for imaging and assembling long DNA strands to detect structural variations. To capture the structural variant landscape more thoroughly in the human genome, we developed an integrated pipeline that combines Bionano OGM and Illumina whole-genome sequencing and applied it to samples from 29 pediatric B-ALL patients. The addition of OGM allowed us to identify 511 deletions, 506 insertions, 93 duplications/gains, and 145 translocations that were otherwise missed in the short-read data. Moreover, we identified several novel gene fusions, the expression of which was confirmed by RNA sequencing. Our results highlight the benefit of integrating OGM and short-read detection methods to obtain a comprehensive analysis of genetic variation that can aid in clinical diagnosis, provide new therapeutic targets, and improve personalized medicine in cancers driven by structural variation. Full article
(This article belongs to the Special Issue Bioinformatics and Medicine)
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15 pages, 6968 KiB  
Article
Analytic Validation of Optical Genome Mapping in Hematological Malignancies
by Andy W. C. Pang, Karena Kosco, Nikhil S. Sahajpal, Arthi Sridhar, Jen Hauenstein, Benjamin Clifford, Joey Estabrook, Alex D. Chitsazan, Trilochan Sahoo, Anwar Iqbal, Ravindra Kolhe, Gordana Raca, Alex R. Hastie and Alka Chaubey
Biomedicines 2023, 11(12), 3263; https://doi.org/10.3390/biomedicines11123263 - 9 Dec 2023
Cited by 7 | Viewed by 3478
Abstract
Structural variations (SVs) play a key role in the pathogenicity of hematological malignancies. Standard-of-care (SOC) methods such as karyotyping and fluorescence in situ hybridization (FISH), which have been employed globally for the past three decades, have significant limitations in terms of resolution and [...] Read more.
Structural variations (SVs) play a key role in the pathogenicity of hematological malignancies. Standard-of-care (SOC) methods such as karyotyping and fluorescence in situ hybridization (FISH), which have been employed globally for the past three decades, have significant limitations in terms of resolution and the number of recurrent aberrations that can be simultaneously assessed, respectively. Next-generation sequencing (NGS)-based technologies are now widely used to detect clinically significant sequence variants but are limited in their ability to accurately detect SVs. Optical genome mapping (OGM) is an emerging technology enabling the genome-wide detection of all classes of SVs at a significantly higher resolution than karyotyping and FISH. OGM requires neither cultured cells nor amplification of DNA, addressing the limitations of culture and amplification biases. This study reports the clinical validation of OGM as a laboratory-developed test (LDT) according to stringent regulatory (CAP/CLIA) guidelines for genome-wide SV detection in different hematological malignancies. In total, 60 cases with hematological malignancies (of various subtypes), 18 controls, and 2 cancer cell lines were used for this study. Ultra-high-molecular-weight DNA was extracted from the samples, fluorescently labeled, and run on the Bionano Saphyr system. A total of 215 datasets, Inc.luding replicates, were generated, and analyzed successfully. Sample data were then analyzed using either disease-specific or pan-cancer-specific BED files to prioritize calls that are known to be diagnostically or prognostically relevant. Sensitivity, specificity, and reproducibility were 100%, 100%, and 96%, respectively. Following the validation, 14 cases and 10 controls were run and analyzed using OGM at three outside laboratories showing reproducibility of 96.4%. OGM found more clinically relevant SVs compared to SOC testing due to its ability to detect all classes of SVs at higher resolution. The results of this validation study demonstrate the superiority of OGM over traditional SOC methods for the detection of SVs for the accurate diagnosis of various hematological malignancies. Full article
(This article belongs to the Special Issue Advances in Molecular Cytogenetics Volume II)
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11 pages, 1015 KiB  
Article
Feasibility of Optical Genome Mapping from Placental and Umbilical Cord Sampled after Spontaneous or Therapeutic Pregnancy Termination
by Carole Goumy, Zangbéwendé Guy Ouedraogo, Elodie Bellemonte, Eleonore Eymard-Pierre, Gwendoline Soler, Isabelle Perthus, Céline Pebrel-Richard, Laetitia Gouas, Gaëlle Salaun, Lauren Véronèse, Hélène Laurichesse, Claude Darcha and Andrei Tchirkov
Diagnostics 2023, 13(23), 3576; https://doi.org/10.3390/diagnostics13233576 - 30 Nov 2023
Cited by 1 | Viewed by 1694
Abstract
Optical genome mapping (OGM) is an alternative to classical cytogenetic techniques to improve the detection rate of clinically significant genomic abnormalities. The isolation of high-molecular-weight (HMW) DNA is critical for a successful OGM analysis. HMW DNA quality depends on tissue type, sample size, [...] Read more.
Optical genome mapping (OGM) is an alternative to classical cytogenetic techniques to improve the detection rate of clinically significant genomic abnormalities. The isolation of high-molecular-weight (HMW) DNA is critical for a successful OGM analysis. HMW DNA quality depends on tissue type, sample size, and storage conditions. We assessed the feasibility of OGM analysis of DNA from nine umbilical cord (UC) and six chorionic villus (CV) samples collected after the spontaneous or therapeutic termination of pregnancy. We analyzed quality control metrics provided by the Saphyr system (Bionano Genomics) and assessed the length of extracted DNA molecules using pulsed-field capillary electrophoresis. OMG data were successfully analyzed for all six CV samples. Five of the UC samples did not meet the Saphyr quality criteria, mainly due to poor DNA quality. In this regard, we found that DNA quality assessment with pulsed-field capillary electrophoresis can predict a successful OGM analysis. OGM data were fully concordant with the results of standard cytogenetic methods. Moreover, OGM detected an average of 14 additional structural variants involving OMIM genes per sample. On the basis of our results, we established the optimal conditions for sample storage and preparation required for a successful OGM analysis. We recommend checking DNA quality before analysis with pulsed-field capillary electrophoresis if the storage conditions were not ideal or if the quality of the sample is poor. OGM can therefore be performed on fetal tissue harvested after the termination of pregnancy, which opens up the perspective for improved diagnostic yield. Full article
(This article belongs to the Special Issue Fetal Medicine: From Basic Science to Prenatal Diagnosis and Therapy)
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24 pages, 6496 KiB  
Article
Use of Optical Genome Mapping to Detect Structural Variants in Neuroblastoma
by Ruby G. Barford, Emily Whittle, Laura Weir, Fang Chyi Fong, Angharad Goodman, Hannah E. Hartley, Lisa M. Allinson and Deborah A. Tweddle
Cancers 2023, 15(21), 5233; https://doi.org/10.3390/cancers15215233 - 31 Oct 2023
Cited by 2 | Viewed by 4110
Abstract
Background: Neuroblastoma is the most common extracranial solid tumour in children, accounting for 15% of paediatric cancer deaths. Multiple genetic abnormalities have been identified as prognostically significant in neuroblastoma patients. Optical genome mapping (OGM) is a novel cytogenetic technique used to detect structural [...] Read more.
Background: Neuroblastoma is the most common extracranial solid tumour in children, accounting for 15% of paediatric cancer deaths. Multiple genetic abnormalities have been identified as prognostically significant in neuroblastoma patients. Optical genome mapping (OGM) is a novel cytogenetic technique used to detect structural variants, which has not previously been tested in neuroblastoma. We used OGM to identify copy number and structural variants (SVs) in neuroblastoma which may have been missed by standard cytogenetic techniques. Methods: Five neuroblastoma cell lines (SH-SY5Y, NBLW, GI-ME-N, NB1691 and SK-N-BE2(C)) and two neuroblastoma tumours were analysed using OGM with the Bionano Saphyr® instrument. The results were analysed using Bionano Access software and compared to previous genetic analyses including G-band karyotyping, FISH (fluorescent in situ hybridisation), single-nucleotide polymorphism (SNP) array and RNA fusion panels for cell lines, and SNP arrays and whole genome sequencing (WGS) for tumours. Results: OGM detected copy number abnormalities found using previous methods and provided estimates for absolute copy numbers of amplified genes. OGM identified novel SVs, including fusion genes in two cell lines of potential clinical significance. Conclusions: OGM can reliably detect clinically significant structural and copy number variations in a single test. OGM may prove to be more time- and cost-effective than current standard cytogenetic techniques for neuroblastoma. Full article
(This article belongs to the Section Cancer Biomarkers)
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14 pages, 2706 KiB  
Article
Optical Genome Mapping for the Molecular Diagnosis of Facioscapulohumeral Muscular Dystrophy: Advancement and Challenges
by Stephanie Efthymiou, Richard J. L. F. Lemmers, Venugopalan Y. Vishnu, Natalia Dominik, Benedetta Perrone, Stefano Facchini, Elisa Vegezzi, Sabrina Ravaglia, Lindsay Wilson, Patrick J. van der Vliet, Rinkle Mishra, Alisha Reyaz, Tanveer Ahmad, Rohit Bhatia, James M. Polke, Mv Padma Srivastava, Andrea Cortese, Henry Houlden, Silvère M. van der Maarel, Michael G. Hanna and Enrico Bugiardiniadd Show full author list remove Hide full author list
Biomolecules 2023, 13(11), 1567; https://doi.org/10.3390/biom13111567 - 24 Oct 2023
Cited by 11 | Viewed by 3268
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is the second most common muscular dystrophy in adults, and it is associated with local D4Z4 chromatin relaxation, mostly via the contraction of the D4Z4 macrosatellite repeat array on chromosome 4q35. In this study, we aimed to investigate the [...] Read more.
Facioscapulohumeral muscular dystrophy (FSHD) is the second most common muscular dystrophy in adults, and it is associated with local D4Z4 chromatin relaxation, mostly via the contraction of the D4Z4 macrosatellite repeat array on chromosome 4q35. In this study, we aimed to investigate the use of Optical Genome Mapping (OGM) as a diagnostic tool for testing FSHD cases from the UK and India and to compare OGM performance with that of traditional techniques such as linear gel (LGE) and Pulsed-field gel electrophoresis (PFGE) Southern blotting (SB). A total of 6 confirmed and 19 suspected FSHD samples were processed with LGE and PFGE, respectively. The same samples were run using a Saphyr Genome-Imaging Instrument (1-color), and the data were analysed using custom EnFocus FSHD analysis. OGM was able to confirm the diagnosis of FSHD1 in all FSHD1 cases positive for SB (n = 17), and D4Z4 sizing highly correlated with PFGE-SB (p < 0.001). OGM correctly identified cases with mosaicism for the repeat array contraction (n = 2) and with a duplication of the D4Z4 repeat array. OGM is a promising new technology able to unravel structural variants in the genome and seems to be a valid tool for diagnosing FSHD1. Full article
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11 pages, 2105 KiB  
Article
Optical Genome Mapping Enables Detection and Accurate Sizing of RFC1 Repeat Expansions
by Stefano Facchini, Natalia Dominik, Arianna Manini, Stephanie Efthymiou, Riccardo Currò, Bianca Rugginini, Elisa Vegezzi, Ilaria Quartesan, Benedetta Perrone, Shahedah Koya Kutty, Valentina Galassi Deforie, Ricardo P. Schnekenberg, Elena Abati, Anna Pichiecchio, Enza Maria Valente, Cristina Tassorelli, Mary M. Reilly, Henry Houlden, Enrico Bugiardini and Andrea Cortese
Biomolecules 2023, 13(10), 1546; https://doi.org/10.3390/biom13101546 - 19 Oct 2023
Cited by 12 | Viewed by 3060
Abstract
A recessive Short Tandem Repeat expansion in RFC1 has been found to be associated with cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS), and to be a frequent cause of late onset ataxia and sensory neuropathy. The usual procedure for sizing these expansions [...] Read more.
A recessive Short Tandem Repeat expansion in RFC1 has been found to be associated with cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS), and to be a frequent cause of late onset ataxia and sensory neuropathy. The usual procedure for sizing these expansions is based on Southern Blotting (SB), a time-consuming and a relatively imprecise technique. In this paper, we compare SB with Optical Genome Mapping (OGM), a method for detecting Structural Variants (SVs) based on the measurement of distances between fluorescently labelled probes, for the diagnosis of RFC1 CANVAS and disease spectrum. The two methods are applied to 17 CANVAS patients’ blood samples and resulting sizes compared, showing a good agreement. Further, long-read sequencing is used for two patients to investigate the agreement of sizes with either SB or OGM. Our study concludes that OGM represents a viable alternative to SB, allowing for a simpler technique, a more precise sizing of the expansion and ability to expand analysis of SV in the entire genome as opposed to SB which is a locus specific method. Full article
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17 pages, 5703 KiB  
Article
Novel NUP98::ASH1L Gene Fusion in Acute Myeloid Leukemia Detected by Optical Genome Mapping
by Marco Tembrink, Wanda Maria Gerding, Stefan Wieczorek, Thomas Mika, Roland Schroers, Huu Phuc Nguyen, Deepak Ben Vangala and Verena Nilius-Eliliwi
Cancers 2023, 15(11), 2942; https://doi.org/10.3390/cancers15112942 - 27 May 2023
Cited by 11 | Viewed by 3518
Abstract
Optical genome mapping (OGM) recently has demonstrated the potential to improve genetic diagnostics in acute myeloid leukemia (AML). In this study, OGM was utilized as a tool for the detection of genome-wide structural variants and disease monitoring. A previously unrecognized NUP98::ASH1L fusion was [...] Read more.
Optical genome mapping (OGM) recently has demonstrated the potential to improve genetic diagnostics in acute myeloid leukemia (AML). In this study, OGM was utilized as a tool for the detection of genome-wide structural variants and disease monitoring. A previously unrecognized NUP98::ASH1L fusion was detected in an adult patient with secondary AML. OGM identified the fusion of NUP98 to Absent, Small, or Homeotic-Like Histone Lysine Methyltransferase (ASH1L) as result of a complex structural rearrangement between chromosomes 1 and 11. A pipeline for the measurement of rare structural variants (Rare Variant Pipeline, Bionano Genomics, San Diego, CA, USA) was used for detection. As NUP98 and other fusions are relevant for disease classification, this demonstrates the necessity for methods such as OGM for cytogenetic diagnostics in AML. Furthermore, other structural variants showed discordant variant allele frequencies at different time points over the course of the disease and treatment pressure, indicating clonal evolution. These results support OGM to be a valuable tool for primary diagnostics in AML as well as longitudinal testing for disease monitoring and deepening our understanding of genetically heterogenous diseases. Full article
(This article belongs to the Special Issue Optical Genome Mapping in Hematological Malignancies)
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12 pages, 1772 KiB  
Article
Structural Refinement by Direct Mapping Reveals Assembly Inconsistencies near Hi-C Junctions
by Luca Marcolungo, Leonardo Vincenzi, Matteo Ballottari, Michela Cecchin, Emanuela Cosentino, Thomas Mignani, Antonina Limongi, Irene Ferraris, Matteo Orlandi, Marzia Rossato and Massimo Delledonne
Plants 2023, 12(2), 320; https://doi.org/10.3390/plants12020320 - 10 Jan 2023
Viewed by 2863
Abstract
High-throughput chromosome conformation capture (Hi-C) is widely used for scaffolding in de novo assembly because it produces highly contiguous genomes, but its indirect statistical approach can introduce connection errors. We employed optical mapping (Bionano Genomics) as an orthogonal scaffolding technology to assess the [...] Read more.
High-throughput chromosome conformation capture (Hi-C) is widely used for scaffolding in de novo assembly because it produces highly contiguous genomes, but its indirect statistical approach can introduce connection errors. We employed optical mapping (Bionano Genomics) as an orthogonal scaffolding technology to assess the structural solidity of Hi-C reconstructed scaffolds. Optical maps were used to assess the correctness of five de novo genome assemblies based on long-read sequencing for contig generation and Hi-C for scaffolding. Hundreds of inconsistencies were found between the reconstructions generated using the Hi-C and optical mapping approaches. Manual inspection, exploiting raw long-read sequencing data and optical maps, confirmed that several of these conflicts were derived from Hi-C joining errors. Such misjoins were widespread, involved the connection of both small and large contigs, and even overlapped annotated genes. We conclude that the integration of optical mapping data after, not before, Hi-C-based scaffolding, improves the quality of the assembly and limits reconstruction errors by highlighting misjoins that can then be subjected to further investigation. Full article
(This article belongs to the Special Issue Assembly and Phasing of Complex Genomes in Plant)
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15 pages, 3072 KiB  
Article
Optical Genome Mapping in Routine Human Genetic Diagnostics—Its Advantages and Limitations
by Paul Dremsek, Thomas Schwarz, Beatrix Weil, Alina Malashka, Franco Laccone and Jürgen Neesen
Genes 2021, 12(12), 1958; https://doi.org/10.3390/genes12121958 - 8 Dec 2021
Cited by 77 | Viewed by 8491
Abstract
In recent years, optical genome mapping (OGM) has developed into a highly promising method of detecting large-scale structural variants in human genomes. It is capable of detecting structural variants considered difficult to detect by other current methods. Hence, it promises to be feasible [...] Read more.
In recent years, optical genome mapping (OGM) has developed into a highly promising method of detecting large-scale structural variants in human genomes. It is capable of detecting structural variants considered difficult to detect by other current methods. Hence, it promises to be feasible as a first-line diagnostic tool, permitting insight into a new realm of previously unknown variants. However, due to its novelty, little experience with OGM is available to infer best practices for its application or to clarify which features cannot be detected. In this study, we used the Saphyr system (Bionano Genomics, San Diego, CA, USA), to explore its capabilities in human genetic diagnostics. To this end, we tested 14 DNA samples to confirm a total of 14 different structural or numerical chromosomal variants originally detected by other means, namely, deletions, duplications, inversions, trisomies, and a translocation. Overall, 12 variants could be confirmed; one deletion and one inversion could not. The prerequisites for detection of similar variants were explored by reviewing the OGM data of 54 samples analyzed in our laboratory. Limitations, some owing to the novelty of the method and some inherent to it, were described. Finally, we tested the successful application of OGM in routine diagnostics and described some of the challenges that merit consideration when utilizing OGM as a diagnostic tool. Full article
(This article belongs to the Section Genetic Diagnosis)
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17 pages, 1245 KiB  
Article
Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case
by Benjamin Istace, Caroline Belser, Cyril Falentin, Karine Labadie, Franz Boideau, Gwenaëlle Deniot, Loeiz Maillet, Corinne Cruaud, Laurie Bertrand, Anne-Marie Chèvre, Patrick Wincker, Mathieu Rousseau-Gueutin and Jean-Marc Aury
Biology 2021, 10(8), 732; https://doi.org/10.3390/biology10080732 - 30 Jul 2021
Cited by 15 | Viewed by 6530
Abstract
With the rise of long-read sequencers and long-range technologies, delivering high-quality plant genome assemblies is no longer reserved to large consortia. Not only sequencing techniques, but also computer algorithms have reached a point where the reconstruction of assemblies at the chromosome scale is [...] Read more.
With the rise of long-read sequencers and long-range technologies, delivering high-quality plant genome assemblies is no longer reserved to large consortia. Not only sequencing techniques, but also computer algorithms have reached a point where the reconstruction of assemblies at the chromosome scale is now feasible at the laboratory scale. Current technologies, in particular long-range technologies, are numerous, and selecting the most promising one for the genome of interest is crucial to obtain optimal results. In this study, we resequenced the genome of the yellow sarson, Brassica rapa cv. Z1, using the Oxford Nanopore PromethION sequencer and assembled the sequenced data using current assemblers. To reconstruct complete chromosomes, we used and compared three long-range scaffolding techniques, optical mapping, Omni-C, and Pore-C sequencing libraries, commercialized by Bionano Genomics, Dovetail Genomics, and Oxford Nanopore Technologies, respectively, or a combination of the three, in order to evaluate the capability of each technology. Full article
(This article belongs to the Special Issue Crop Improvement Now and Beyond)
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20 pages, 2167 KiB  
Article
Karyotypic Evolution of Sauropsid Vertebrates Illuminated by Optical and Physical Mapping of the Painted Turtle and Slider Turtle Genomes
by Ling Sze Lee, Beatriz M. Navarro-Domínguez, Zhiqiang Wu, Eugenia E. Montiel, Daleen Badenhorst, Basanta Bista, Thea B. Gessler and Nicole Valenzuela
Genes 2020, 11(8), 928; https://doi.org/10.3390/genes11080928 - 12 Aug 2020
Cited by 6 | Viewed by 4918
Abstract
Recent sequencing and software enhancements have advanced our understanding of the evolution of genomic structure and function, especially addressing novel evolutionary biology questions. Yet fragmentary turtle genome assemblies remain a challenge to fully decipher the genetic architecture of adaptive evolution. Here, we use [...] Read more.
Recent sequencing and software enhancements have advanced our understanding of the evolution of genomic structure and function, especially addressing novel evolutionary biology questions. Yet fragmentary turtle genome assemblies remain a challenge to fully decipher the genetic architecture of adaptive evolution. Here, we use optical mapping to improve the contiguity of the painted turtle (Chrysemys picta) genome assembly and use de novo fluorescent in situ hybridization (FISH) of bacterial artificial chromosome (BAC) clones, BAC-FISH, to physically map the genomes of the painted and slider turtles (Trachemys scripta elegans). Optical mapping increased C. picta’s N50 by ~242% compared to the previous assembly. Physical mapping permitted anchoring ~45% of the genome assembly, spanning 5544 genes (including 20 genes related to the sex determination network of turtles and vertebrates). BAC-FISH data revealed assembly errors in C. picta and T. s. elegans assemblies, highlighting the importance of molecular cytogenetic data to complement bioinformatic approaches. We also compared C. picta’s anchored scaffolds to the genomes of other chelonians, chicken, lizards, and snake. Results revealed a mostly one-to-one correspondence between chromosomes of painted and slider turtles, and high homology among large syntenic blocks shared with other turtles and sauropsids. Yet, numerous chromosomal rearrangements were also evident across chelonians, between turtles and squamates, and between avian and non-avian reptiles. Full article
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18 pages, 1699 KiB  
Article
Genome Assembly and Annotation of the Trichoplusia ni Tni-FNL Insect Cell Line Enabled by Long-Read Technologies
by Keyur Talsania, Monika Mehta, Castle Raley, Yuliya Kriga, Sujatha Gowda, Carissa Grose, Matthew Drew, Veronica Roberts, Kwong Tai Cheng, Sandra Burkett, Steffen Oeser, Robert Stephens, Daniel Soppet, Xiongfeng Chen, Parimal Kumar, Oksana German, Tatyana Smirnova, Christopher Hautman, Jyoti Shetty, Bao Tran, Yongmei Zhao and Dominic Espositoadd Show full author list remove Hide full author list
Genes 2019, 10(2), 79; https://doi.org/10.3390/genes10020079 - 23 Jan 2019
Cited by 14 | Viewed by 8266
Abstract
Background: Trichoplusia ni derived cell lines are commonly used to enable recombinant protein expression via baculovirus infection to generate materials approved for clinical use and in clinical trials. In order to develop systems biology and genome engineering tools to improve protein expression in [...] Read more.
Background: Trichoplusia ni derived cell lines are commonly used to enable recombinant protein expression via baculovirus infection to generate materials approved for clinical use and in clinical trials. In order to develop systems biology and genome engineering tools to improve protein expression in this host, we performed de novo genome assembly of the Trichoplusia ni-derived cell line Tni-FNL. Methods: By integration of PacBio single-molecule sequencing, Bionano optical mapping, and 10X Genomics linked-reads data, we have produced a draft genome assembly of Tni-FNL. Results: Our assembly contains 280 scaffolds, with a N50 scaffold size of 2.3 Mb and a total length of 359 Mb. Annotation of the Tni-FNL genome resulted in 14,101 predicted genes and 93.2% of the predicted proteome contained recognizable protein domains. Ortholog searches within the superorder Holometabola provided further evidence of high accuracy and completeness of the Tni-FNL genome assembly. Conclusions: This first draft Tni-FNL genome assembly was enabled by complementary long-read technologies and represents a high-quality, well-annotated genome that provides novel insight into the complexity of this insect cell line and can serve as a reference for future large-scale genome engineering work in this and other similar recombinant protein production hosts. Full article
(This article belongs to the Special Issue Advances in Single Molecule, Real-Time (SMRT) Sequencing)
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