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Qu J, Li S, Yu D. Detection of complex chromosome rearrangements using optical genome mapping. Gene 2023; 884:147688. [PMID: 37543218 DOI: 10.1016/j.gene.2023.147688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/15/2023] [Accepted: 08/02/2023] [Indexed: 08/07/2023]
Abstract
Chromosomal structural variations (SVs) are a main cause of human genetic disease. Currently, karyotype, chromosomal microarray analysis (CMA), and fluorescent in situ hybridization (FISH) form the backbone of current routine diagnostics (CRD). These methods have their own limitations. CRD cannot identify cryptic balanced SVs and complex SVs even if these techniques were performed either simultaneously or in a sequential manner. Optical genome mapping (OGM) is a novel technology that can identify several classes of SVs with higher resolution, but studies on the applicability of OGM and its comparison with CRD are inadequate for difficult and complicated chromosomal SVs are lacking. Herein, seven patients with definite complicated SVs involving at least two breakpoints (BPs) were recruited for this study. The results of BPs and SVs from OGM were compared with those from CRD. The results showed that all BPs of five samples and partial BPs of two samples were detected by OGM. The undetected BPs were all close to the repeat-rich gap region. Besides, OGM also detected additional SVs including a cryptic balanced translocation, two additional complex chromosomal rearrangement (CCR). OGM yielded the additional information, such as the orientation of acentric fragments, BP positions, and genes mapped in the BP region for all the cases. The accuracy of additional SVs and BPs detected by OGM was verified by FISH panel and next-generation sequencing and Sanger sequencing. Taken together, OGM exhibit a better performance in detecting chromosomal SVs compared to the CRD. We suggested that OGM method should be utilized in the clinical examination to improve the efficiency and accuracy of genetic disease diagnosis, supplemented by FISH or karyotyping to compensate for the SVs in the repeat-rich gap region if necessary.
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Affiliation(s)
- Jiangbo Qu
- Center for Medical Genetics and Prenatal Diagnosis, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan 250014, Shandong, China.
| | - Shuo Li
- Genetic Testing Center, Qingdao Women and Children's Hospital, Qingdao 266034, Shandong, China.
| | - Dongyi Yu
- Center for Medical Genetics and Prenatal Diagnosis, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan 250014, Shandong, China.
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Zhang S, Pei Z, Lei C, Zhu S, Deng K, Zhou J, Yang J, Lu D, Sun X, Xu C, Xu C. Detection of cryptic balanced chromosomal rearrangements using high-resolution optical genome mapping. J Med Genet 2023; 60:274-284. [PMID: 35710108 DOI: 10.1136/jmedgenet-2022-108553] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/28/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Chromosomal rearrangements have profound consequences in diverse human genetic diseases. Currently, the detection of balanced chromosomal rearrangements (BCRs) mainly relies on routine cytogenetic G-banded karyotyping. However, cryptic BCRs are hard to detect by karyotyping, and the risk of miscarriage or delivering abnormal offspring with congenital malformations in carrier couples is significantly increased. In the present study, we aimed to investigate the potential of single-molecule optical genome mapping (OGM) in unravelling cryptic chromosomal rearrangements. METHODS Eleven couples with normal karyotypes that had abortions/affected offspring with unbalanced rearrangements were enrolled. Ultra-high-molecular-weight DNA was isolated from peripheral blood cells and processed via OGM. The genome assembly was performed followed by variant calling and annotation. Meanwhile, multiple detection strategies, including FISH, long-range-PCR amplicon-based next-generation sequencing and Sanger sequencing were implemented to confirm the results obtained from OGM. RESULTS High-resolution OGM successfully detected cryptic reciprocal translocation in all recruited couples, which was consistent with the results of FISH and sequencing. All high-confidence cryptic chromosomal translocations detected by OGM were confirmed by sequencing analysis of rearrangement breakpoints. Moreover, OGM revealed additional complex rearrangement events such as inverted aberrations, further refining potential genetic interpretation. CONCLUSION To the best of our knowledge, this is the first study wherein OGM facilitate the rapid and robust detection of cryptic chromosomal reciprocal translocations in clinical practice. With the excellent performance, our findings suggest that OGM is well qualified as an accurate, comprehensive and first-line method for detecting cryptic BCRs in routine clinical testing.
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Affiliation(s)
- Shuo Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Zhenle Pei
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Caixia Lei
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Saijuan Zhu
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Ke Deng
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Jing Zhou
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Jingmin Yang
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China.,NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning, Science and Technology Research Institute, Chongqing, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China.,NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning, Science and Technology Research Institute, Chongqing, China
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chenming Xu
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Congjian Xu
- Shanghai Ji Ai Genetics & IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
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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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Yuan Y, Chung CYL, Chan TF. Advances in optical mapping for genomic research. Comput Struct Biotechnol J 2020; 18:2051-2062. [PMID: 32802277 PMCID: PMC7419273 DOI: 10.1016/j.csbj.2020.07.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/08/2020] [Accepted: 07/24/2020] [Indexed: 12/28/2022] Open
Abstract
Recent advances in optical mapping have allowed the construction of improved genome assemblies with greater contiguity. Optical mapping also enables genome comparison and identification of large-scale structural variations. Association of these large-scale genomic features with biological functions is an important goal in plant and animal breeding and in medical research. Optical mapping has also been used in microbiology and still plays an important role in strain typing and epidemiological studies. Here, we review the development of optical mapping in recent decades to illustrate its importance in genomic research. We detail its applications and algorithms to show its specific advantages. Finally, we discuss the challenges required to facilitate the optimization of optical mapping and improve its future development and application.
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Key Words
- 3D, three-dimensional
- DBG, de Bruijn graph
- DLS, direct label and strain
- DNA, deoxyribonucleic acid
- Genome assembly
- Hi-C, high-throughput chromosome conformation capture
- Mb, million base pair
- Next generation sequencing
- OLC, overlap-layout-consensus
- Optical mapping
- PCR, polymerase chain reaction
- PacBio, Pacific Biosciences
- SRS, short-read sequencing
- SV, structural variation
- Structural variation
- bp, base pair
- kb, kilobase pair
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Affiliation(s)
- Yuxuan Yuan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
- AoE Centre for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Claire Yik-Lok Chung
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
- AoE Centre for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security, The Chinese University of Hong Kong, Hong Kong SAR, China
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Bhandari AB, Reifenberger JG, Chuang HM, Cao H, Dorfman KD. Measuring the wall depletion length of nanoconfined DNA. J Chem Phys 2018; 149:104901. [PMID: 30219022 PMCID: PMC6135644 DOI: 10.1063/1.5040458] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/20/2018] [Indexed: 12/14/2022] Open
Abstract
Efforts to study the polymer physics of DNA confined in nanochannels have been stymied by a lack of consensus regarding its wall depletion length. We have measured this quantity in 38 nm wide, square silicon dioxide nanochannels for five different ionic strengths between 15 mM and 75 mM. Experiments used the Bionano Genomics Irys platform for massively parallel data acquisition, attenuating the effect of the sequence-dependent persistence length and finite-length effects by using nick-labeled E. coli genomic DNA with contour length separations of at least 30 µm (88 325 base pairs) between nick pairs. Over 5 × 106 measurements of the fractional extension were obtained from 39 291 labeled DNA molecules. Analyzing the stretching via Odijk's theory for a strongly confined wormlike chain yielded a linear relationship between the depletion length and the Debye length. This simple linear fit to the experimental data exhibits the same qualitative trend as previously defined analytical models for the depletion length but now quantitatively captures the experimental data.
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Affiliation(s)
- Aditya Bikram Bhandari
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Jeffrey G Reifenberger
- Bionano Genomics, Inc., 9640 Towne Centre Drive, Suite 100, San Diego, California 92121, USA
| | - Hui-Min Chuang
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Han Cao
- Bionano Genomics, Inc., 9640 Towne Centre Drive, Suite 100, San Diego, California 92121, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
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Reifenberger JG, Cao H, Dorfman KD. Odijk excluded volume interactions during the unfolding of DNA confined in a nanochannel. Macromolecules 2018; 51:1172-1180. [PMID: 29479117 PMCID: PMC5823525 DOI: 10.1021/acs.macromol.7b02466] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report experimental data on the unfolding of human and E. coli genomic DNA molecules shortly after injection into a 45 nm nanochannel. The unfolding dynamics are deterministic, consistent with previous experiments and modeling in larger channels, and do not depend on the biological origin of the DNA. The measured entropic unfolding force per friction per unit contour length agrees with that predicted by combining the Odijk excluded volume with numerical calculations of the Kirkwood diffusivity of confined DNA. The time scale emerging from our analysis has implications for genome mapping in nanochannels, especially as the technology moves towards longer DNA, by setting a lower bound for the delay time before making a measurement.
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Affiliation(s)
| | - Han Cao
- BioNano Genomics Inc., 9640 Towne Centre Drive, Suite 100, San Diego, CA 92121
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
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Jain A, Dorfman KD. Simulations of knotting of DNA during genome mapping. BIOMICROFLUIDICS 2017; 11:024117. [PMID: 28798853 PMCID: PMC5533507 DOI: 10.1063/1.4979605] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/21/2017] [Indexed: 05/28/2023]
Abstract
Genome mapping involves the confinement of long DNA molecules, in excess of 150 kilobase pairs, in nanochannels near the circa 50 nm persistence length of DNA. The fidelity of the map relies on the assumption that the DNA is linearized by channel confinement, which assumes the absence of knots. We have computed the probability of forming different knot types and the size of these knots for long chains (approximately 164 kilobase pairs) via pruned-enriched Rosenbluth method simulations of a discrete wormlike chain model of DNA in channel sizes ranging from 35 nm to 60 nm. Compared to prior simulations of short DNA in similar confinement, these long molecules exhibit both complex knots, with up to seven crossings, and multiple knots per chain. The knotting probability is a very strong function of channel size, ranging from 0.3% to 60%, and rationalized in the context of Odijk's theory for confined semiflexible chains. Overall, the knotting probability and knot size obtained from these equilibrium measurements are not consistent with experimental measurements of the properties of anomalously bright regions along the DNA backbone during genome mapping experiments. This result suggests that these events in experiments are either knots formed during the processing of the DNA prior to injection into the nanochannel or regions of locally high DNA concentration without a topological constraint. If so, knots during genome mapping are not an intrinsic problem for genome mapping technology.
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Affiliation(s)
- Aashish Jain
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
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