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Sefik E, Duan K, Li Y, Sholar B, Evans L, Pincus J, Ammar Z, Murphy MM, Klaiman C, Saulnier CA, Pulver SL, Goldman-Yassen AE, Guo Y, Walker EF, Li L, Mulle JG, Shultz S. Structural deviations of the posterior fossa and the cerebellum and their cognitive links in a neurodevelopmental deletion syndrome. Mol Psychiatry 2024:10.1038/s41380-024-02584-8. [PMID: 38744992 DOI: 10.1038/s41380-024-02584-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
High-impact genetic variants associated with neurodevelopmental disorders provide biologically-defined entry points for mechanistic investigation. The 3q29 deletion (3q29Del) is one such variant, conferring a 40-100-fold increased risk for schizophrenia, as well as high risk for autism and intellectual disability. However, the mechanisms leading to neurodevelopmental disability remain largely unknown. Here, we report the first in vivo quantitative neuroimaging study in individuals with 3q29Del (N = 24) and neurotypical controls (N = 1608) using structural MRI. Given prior radiology reports of posterior fossa abnormalities in 3q29Del, we focused our investigation on the cerebellum and its tissue-types and lobules. Additionally, we compared the prevalence of cystic/cyst-like malformations of the posterior fossa between 3q29Del and controls and examined the association between neuroanatomical findings and quantitative traits to probe gene-brain-behavior relationships. 3q29Del participants had smaller cerebellar cortex volumes than controls, before and after correction for intracranial volume (ICV). An anterior-posterior gradient emerged in finer grained lobule-based and voxel-wise analyses. 3q29Del participants also had larger cerebellar white matter volumes than controls following ICV-correction and displayed elevated rates of posterior fossa arachnoid cysts and mega cisterna magna findings independent of cerebellar volume. Cerebellar white matter and subregional gray matter volumes were associated with visual-perception and visual-motor integration skills as well as IQ, while cystic/cyst-like malformations yielded no behavioral link. In summary, we find that abnormal development of cerebellar structures may represent neuroimaging-based biomarkers of cognitive and sensorimotor function in 3q29Del, adding to the growing evidence identifying cerebellar pathology as an intersection point between syndromic and idiopathic forms of neurodevelopmental disabilities.
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Affiliation(s)
- Esra Sefik
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychology, Emory University, Atlanta, GA, USA
| | - Kuaikuai Duan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science, Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, USA
| | - Yiheng Li
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Brittney Sholar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Lindsey Evans
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Jordan Pincus
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Zeena Ammar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Melissa M Murphy
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Cheryl Klaiman
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Celine A Saulnier
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Neurodevelopmental Assessment & Consulting Services, Atlanta, GA, USA
| | - Stormi L Pulver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Adam E Goldman-Yassen
- Department of Radiology, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Ying Guo
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Elaine F Walker
- Department of Psychology, Emory University, Atlanta, GA, USA
| | - Longchuan Li
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Jennifer G Mulle
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA.
| | - Sarah Shultz
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA.
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2
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Schloissnig S, Pani S, Rodriguez-Martin B, Ebler J, Hain C, Tsapalou V, Söylev A, Hüther P, Ashraf H, Prodanov T, Asparuhova M, Hunt S, Rausch T, Marschall T, Korbel JO. Long-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590093. [PMID: 38659906 PMCID: PMC11042266 DOI: 10.1101/2024.04.18.590093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Structural variants (SVs) contribute significantly to human genetic diversity and disease 1-4 . Previously, SVs have remained incompletely resolved by population genomics, with short-read sequencing facing limitations in capturing the whole spectrum of SVs at nucleotide resolution 5-7 . Here we leveraged nanopore sequencing 8 to construct an intermediate coverage resource of 1,019 long-read genomes sampled within 26 human populations from the 1000 Genomes Project. By integrating linear and graph-based approaches for SV analysis via pangenome graph-augmentation, we uncover 167,291 sequence-resolved SVs in these samples, considerably advancing SV characterization compared to population-wide short-read sequencing studies 3,4 . Our analysis details diverse SV classes-deletions, duplications, insertions, and inversions-at population-scale. LINE-1 and SVA retrotransposition activities frequently mediate transductions 9,10 of unique sequences, with both mobile element classes transducing sequences at either the 3'- or 5'-end, depending on the source element locus. Furthermore, analyses of SV breakpoint junctions suggest a continuum of homology-mediated rearrangement processes are integral to SV formation, and highlight evidence for SV recurrence involving repeat sequences. Our open-access dataset underscores the transformative impact of long-read sequencing in advancing the characterisation of polymorphic genomic architectures, and provides a resource for guiding variant prioritisation in future long-read sequencing-based disease studies.
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3
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Alfayyadh MM, Maksemous N, Sutherland HG, Lea RA, Griffiths LR. Unravelling the Genetic Landscape of Hemiplegic Migraine: Exploring Innovative Strategies and Emerging Approaches. Genes (Basel) 2024; 15:443. [PMID: 38674378 PMCID: PMC11049430 DOI: 10.3390/genes15040443] [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: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Migraine is a severe, debilitating neurovascular disorder. Hemiplegic migraine (HM) is a rare and debilitating neurological condition with a strong genetic basis. Sequencing technologies have improved the diagnosis and our understanding of the molecular pathophysiology of HM. Linkage analysis and sequencing studies in HM families have identified pathogenic variants in ion channels and related genes, including CACNA1A, ATP1A2, and SCN1A, that cause HM. However, approximately 75% of HM patients are negative for these mutations, indicating there are other genes involved in disease causation. In this review, we explored our current understanding of the genetics of HM. The evidence presented herein summarises the current knowledge of the genetics of HM, which can be expanded further to explain the remaining heritability of this debilitating condition. Innovative bioinformatics and computational strategies to cover the entire genetic spectrum of HM are also discussed in this review.
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Affiliation(s)
| | | | | | | | - Lyn R. Griffiths
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD 4059, Australia; (M.M.A.); (N.M.); (H.G.S.); (R.A.L.)
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4
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Zhang Y, Liu W, Duan J. On the core segmentation algorithms of copy number variation detection tools. Brief Bioinform 2024; 25:bbae022. [PMID: 38340093 PMCID: PMC10858679 DOI: 10.1093/bib/bbae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/26/2023] [Indexed: 02/12/2024] Open
Abstract
Shotgun sequencing is a high-throughput method used to detect copy number variants (CNVs). Although there are numerous CNV detection tools based on shotgun sequencing, their quality varies significantly, leading to performance discrepancies. Therefore, we conducted a comprehensive analysis of next-generation sequencing-based CNV detection tools over the past decade. Our findings revealed that the majority of mainstream tools employ similar detection rationale: calculates the so-called read depth signal from aligned sequencing reads and then segments the signal by utilizing either circular binary segmentation (CBS) or hidden Markov model (HMM). Hence, we compared the performance of those two core segmentation algorithms in CNV detection, considering varying sequencing depths, segment lengths and complex types of CNVs. To ensure a fair comparison, we designed a parametrical model using mainstream statistical distributions, which allows for pre-excluding bias correction such as guanine-cytosine (GC) content during the preprocessing step. The results indicate the following key points: (1) Under ideal conditions, CBS demonstrates high precision, while HMM exhibits a high recall rate. (2) For practical conditions, HMM is advantageous at lower sequencing depths, while CBS is more competitive in detecting small variant segments compared to HMM. (3) In case involving complex CNVs resembling real sequencing, HMM demonstrates more robustness compared with CBS. (4) When facing large-scale sequencing data, HMM costs less time compared with the CBS, while their memory usage is approximately equal. This can provide an important guidance and reference for researchers to develop new tools for CNV detection.
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Affiliation(s)
- Yibo Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Wenyu Liu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Junbo Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education and Department of Biomedical Engineering, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
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5
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Meng X, Wang M, Luo M, Sun L, Yan Q, Liu Y. Systematic evaluation of multiple NGS platforms for structural variants detection. J Biol Chem 2023; 299:105436. [PMID: 37944616 PMCID: PMC10724692 DOI: 10.1016/j.jbc.2023.105436] [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: 09/28/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Structural variations (SV) are critical genome changes affecting human diseases. Although many hybridization-based methods exist, evaluating SVs through next-generation sequencing (NGS) data is still necessary for broader research exploration. Here, we comprehensively compared the performance of 16 SV callers and multiple NGS platforms using NA12878 whole genome sequencing (WGS) datasets. The results indicated that several SV callers performed well relatively, such as Manta, GRIDSS, LUMPY, TARDIS, FermiKit, and Wham. Meanwhile, all NGS platforms have a similar performance using a single software. Additionally, we found that the source of undetected SVs was mostly from long reads datasets, therefore, the more appropriate strategy for accurate SV detection will be an integration of long and shorter reads in the future. At present, in the period of NGS as a mainstream method in bioinformatics, our study would provide helpful and comprehensive guidelines for specific categories of SV research.
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Affiliation(s)
- Xuan Meng
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Miao Wang
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China
| | - Mingjie Luo
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China
| | - Lei Sun
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China
| | - Qin Yan
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China
| | - Yongfeng Liu
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China.
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6
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Pajuste FD, Remm M. GeneToCN: an alignment-free method for gene copy number estimation directly from next-generation sequencing reads. Sci Rep 2023; 13:17765. [PMID: 37853040 PMCID: PMC10584998 DOI: 10.1038/s41598-023-44636-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
Genomes exhibit large regions with segmental copy number variation, many of which include entire genes and are multiallelic. We have developed a computational method GeneToCN that counts the frequencies of gene-specific k-mers in FASTQ files and uses this information to infer copy number of the gene. We validated the copy number predictions for amylase genes (AMY1, AMY2A, AMY2B) using experimental data from digital droplet PCR (ddPCR) on 39 individuals and observed a strong correlation (R = 0.99) between GeneToCN predictions and experimentally determined copy numbers. An additional validation on FCGR3 genes showed a higher concordance for FCGR3A compared to two other methods, but reduced accuracy for FCGR3B. We further tested the method on three different genomic regions (SMN, NPY4R, and LPA Kringle IV-2 domain). Predicted copy number distributions of these genes in a set of 500 individuals from the Estonian Biobank were in good agreement with the previously published studies. In addition, we investigated the possibility to use GeneToCN on sequencing data generated by different technologies by comparing copy number predictions from Illumina, PacBio, and Oxford Nanopore data of the same sample. Despite the differences in variability of k-mer frequencies, all three sequencing technologies give similar predictions with GeneToCN.
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Affiliation(s)
- Fanny-Dhelia Pajuste
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Str., 51010, Tartu, Estonia.
| | - Maido Remm
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia Str., 51010, Tartu, Estonia
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7
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Peroni E, Randi ML, Rosato A, Cagnin S. Acute myeloid leukemia: from NGS, through scRNA-seq, to CAR-T. dissect cancer heterogeneity and tailor the treatment. J Exp Clin Cancer Res 2023; 42:259. [PMID: 37803464 PMCID: PMC10557350 DOI: 10.1186/s13046-023-02841-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/25/2023] [Indexed: 10/08/2023] Open
Abstract
Acute myeloid leukemia (AML) is a malignant blood cancer with marked cellular heterogeneity due to altered maturation and differentiation of myeloid blasts, the possible causes of which are transcriptional or epigenetic alterations, impaired apoptosis, and excessive cell proliferation. This neoplasm has a high rate of resistance to anticancer therapies and thus a high risk of relapse and mortality because of both the biological diversity of the patient and intratumoral heterogeneity due to the acquisition of new somatic changes. For more than 40 years, the old gold standard "one size fits all" treatment approach included intensive chemotherapy treatment with anthracyclines and cytarabine.The manuscript first traces the evolution of the understanding of the pathology from the 1970s to the present. The enormous strides made in its categorization prove to be crucial for risk stratification, enabling an increasingly personalized diagnosis and treatment approach.Subsequently, we highlight how, over the past 15 years, technological advances enabling single cell RNA sequencing and T-cell modification based on the genomic tools are affecting the classification and treatment of AML. At the dawn of the new millennium, the advent of high-throughput next-generation sequencing technologies has enabled the profiling of patients evidencing different facets of the same disease, stratifying risk, and identifying new possible therapeutic targets that have subsequently been validated. Currently, the possibility of investigating tumor heterogeneity at the single cell level, profiling the tumor at the time of diagnosis or after treatments exist. This would allow the identification of underrepresented cellular subclones or clones resistant to therapeutic approaches and thus responsible for post-treatment relapse that would otherwise be difficult to detect with bulk investigations on the tumor biopsy. Single-cell investigation will then allow even greater personalization of therapy to the genetic and transcriptional profile of the tumor, saving valuable time and dangerous side effects. The era of personalized medicine will take a huge step forward through the disclosure of each individual piece of the complex puzzle that is cancer pathology, to implement a "tailored" therapeutic approach based also on engineered CAR-T cells.
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Affiliation(s)
- Edoardo Peroni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padova, 35128, Italy.
| | - Maria Luigia Randi
- First Medical Clinic, Department of Medicine-DIMED, University of Padua, Padua, Italy
| | - Antonio Rosato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padova, 35128, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, Padova, 35131, Italy
- CIR-Myo Myology Center, University of Padova, Padova, 35131, Italy
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8
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Abstract
DNA sequencing has revolutionized medicine over recent decades. However, analysis of large structural variation and repetitive DNA, a hallmark of human genomes, has been limited by short-read technology, with read lengths of 100-300 bp. Long-read sequencing (LRS) permits routine sequencing of human DNA fragments tens to hundreds of kilobase pairs in size, using both real-time sequencing by synthesis and nanopore-based direct electronic sequencing. LRS permits analysis of large structural variation and haplotypic phasing in human genomes and has enabled the discovery and characterization of rare pathogenic structural variants and repeat expansions. It has also recently enabled the assembly of a complete, gapless human genome that includes previously intractable regions, such as highly repetitive centromeres and homologous acrocentric short arms. With the addition of protocols for targeted enrichment, direct epigenetic DNA modification detection, and long-range chromatin profiling, LRS promises to launch a new era of understanding of genetic diversity and pathogenic mutations in human populations.
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Affiliation(s)
- Peter E Warburton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; ,
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert P Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; ,
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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9
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Chang L, Deng E, Wang J, Zhou W, Ao J, Liu R, Su D, Fan X. Single-cell third-generation sequencing-based multi-omics uncovers gene expression changes governed by ecDNA and structural variants in cancer cells. Clin Transl Med 2023; 13:e1351. [PMID: 37517066 PMCID: PMC10387328 DOI: 10.1002/ctm2.1351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/01/2023] Open
Abstract
BACKGROUND Cancer cells often exhibit large-scale genomic variations, such as circular extrachromosomal DNA (ecDNA) and structural variants (SVs), which have been highly correlated with the initiation and progression of cancer. Currently, no adequate method exists to unveil how these variations regulate gene expression in heterogeneous cancer cell populations at a single-cell resolution. METHODS Here, we developed a single-cell multi-omics sequencing method, scGTP-seq, to analyse ecDNA and SVs using long-read sequencing technologies. RESULTS AND CONCLUSIONS We demonstrated that our method can efficiently detect ecDNA and SVs and illustrated how these variations affect transcriptomic changes in various cell lines. Finally, we applied and validated this method in a clinical sample of hepatocellular carcinoma (HCC), demonstrating a feasible way to monitor the evolution of ecDNA and SVs during cancer progression.
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Affiliation(s)
- Lei Chang
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Innovation centre for Advanced Interdisciplinary MedicineThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
- Present address:
Department of Cellular and Molecular MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Enze Deng
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
| | - Jun Wang
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
| | - Wei Zhou
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
| | - Jian Ao
- Innovation centre for Advanced Interdisciplinary MedicineThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
| | - Rong Liu
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
| | - Dan Su
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
- The Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouGuangdong ProvinceP. R. China
| | - Xiaoying Fan
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Innovation centre for Advanced Interdisciplinary MedicineThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
- The Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouGuangdong ProvinceP. R. China
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10
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Ahsan MU, Liu Q, Perdomo JE, Fang L, Wang K. A survey of algorithms for the detection of genomic structural variants from long-read sequencing data. Nat Methods 2023; 20:1143-1158. [PMID: 37386186 DOI: 10.1038/s41592-023-01932-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 05/31/2023] [Indexed: 07/01/2023]
Abstract
As long-read sequencing technologies are becoming increasingly popular, a number of methods have been developed for the discovery and analysis of structural variants (SVs) from long reads. Long reads enable detection of SVs that could not be previously detected from short-read sequencing, but computational methods must adapt to the unique challenges and opportunities presented by long-read sequencing. Here, we summarize over 50 long-read-based methods for SV detection, genotyping and visualization, and discuss how new telomere-to-telomere genome assemblies and pangenome efforts can improve the accuracy and drive the development of SV callers in the future.
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Affiliation(s)
- Mian Umair Ahsan
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jonathan Elliot Perdomo
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, USA
| | - Li Fang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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11
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Laufer VA, Glover TW, Wilson TE. Applications of advanced technologies for detecting genomic structural variation. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108475. [PMID: 37931775 PMCID: PMC10792551 DOI: 10.1016/j.mrrev.2023.108475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/07/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
Chromosomal structural variation (SV) encompasses a heterogenous class of genetic variants that exerts strong influences on human health and disease. Despite their importance, many structural variants (SVs) have remained poorly characterized at even a basic level, a discrepancy predicated upon the technical limitations of prior genomic assays. However, recent advances in genomic technology can identify and localize SVs accurately, opening new questions regarding SV risk factors and their impacts in humans. Here, we first define and classify human SVs and their generative mechanisms, highlighting characteristics leveraged by various SV assays. We next examine the first-ever gapless assembly of the human genome and the technical process of assembling it, which required third-generation sequencing technologies to resolve structurally complex loci. The new portions of that "telomere-to-telomere" and subsequent pangenome assemblies highlight aspects of SV biology likely to develop in the near-term. We consider the strengths and limitations of the most promising new SV technologies and when they or longstanding approaches are best suited to meeting salient goals in the study of human SV in population-scale genomics research, clinical, and public health contexts. It is a watershed time in our understanding of human SV when new approaches are expected to fundamentally change genomic applications.
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Affiliation(s)
- Vincent A Laufer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas W Glover
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas E Wilson
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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12
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Babu M, Snyder M. Multi-Omics Profiling for Health. Mol Cell Proteomics 2023; 22:100561. [PMID: 37119971 PMCID: PMC10220275 DOI: 10.1016/j.mcpro.2023.100561] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/01/2023] Open
Abstract
The world has witnessed a steady rise in both non-infectious and infectious chronic diseases, prompting a cross-disciplinary approach to understand and treating disease. Current medical care focuses on treating people after they become patients rather than preventing illness, leading to high costs in treating chronic and late-stage diseases. Additionally, a "one-size-fits all" approach to health care does not take into account individual differences in genetics, environment, or lifestyle factors, decreasing the number of people benefiting from interventions. Rapid advances in omics technologies and progress in computational capabilities have led to the development of multi-omics deep phenotyping, which profiles the interaction of multiple levels of biology over time and empowers precision health approaches. This review highlights current and emerging multi-omics modalities for precision health and discusses applications in the following areas: genetic variation, cardio-metabolic diseases, cancer, infectious diseases, organ transplantation, pregnancy, and longevity/aging. We will briefly discuss the potential of multi-omics approaches in disentangling host-microbe and host-environmental interactions. We will touch on emerging areas of electronic health record and clinical imaging integration with muti-omics for precision health. Finally, we will briefly discuss the challenges in the clinical implementation of multi-omics and its future prospects.
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Affiliation(s)
- Mohan Babu
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.
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13
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McClinton B, Crinnion LA, McKibbin M, Mukherjee R, Poulter JA, Smith CEL, Ali M, Watson CM, Inglehearn CF, Toomes C. Targeted nanopore sequencing enables complete characterisation of structural deletions initially identified using exon-based short-read sequencing strategies. Mol Genet Genomic Med 2023:e2164. [PMID: 36934458 DOI: 10.1002/mgg3.2164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/23/2023] [Indexed: 03/20/2023] Open
Abstract
BACKGROUND The widespread adoption of exome sequencing has greatly increased the rate of genetic diagnosis for inherited conditions. However, the detection and validation of large deletions remains challenging. While numerous bioinformatics approaches have been developed to detect deletions from whole - exome sequencing and targeted panels, further work is typically required to define the physical breakpoints or integration sites. Accurate characterisation requires either expensive follow - up whole - genome sequencing or the time - consuming, laborious process of PCR walking, both of which are challenging when dealing with the repeat sequences which frequently intersect deletion breakpoints. The aim of this study was to develop a cost-effective, long-range sequencing method to characterise deletions. METHODS Genomic DNA was amplified with primers spanning the deletion using long-range PCR and the products purified. Sequencing was performed on MinION flongle flowcells. The resulting fast5 files were basecalled using Guppy, trimmed using Porechop and aligned using Minimap2. Filtering was performed using NanoFilt. Nanopore sequencing results were verified by Sanger sequencing. RESULTS Four cases with deletions detected following comparative read-depth analysis of targeted short-read sequencing were analysed. Nanopore sequencing defined breakpoints at the molecular level in all cases including homozygous breakpoints in EYS, CNGA1 and CNGB1 and a heterozygous deletion in PRPF31. All breakpoints were verified by Sanger sequencing. CONCLUSIONS In this study, a quick, accurate and cost - effective method is described to characterise deletions identified from exome, and similar data, using nanopore sequencing.
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Affiliation(s)
- Benjamin McClinton
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Laura A Crinnion
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK.,North East and Yorkshire Genomic Laboratory Hub, Central Lab, St James's University Hospital, Leeds, UK
| | - Martin McKibbin
- Department of Ophthalmology, St James's University Hospital, Leeds, UK
| | | | - James A Poulter
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Claire E L Smith
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Manir Ali
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Christopher M Watson
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK.,North East and Yorkshire Genomic Laboratory Hub, Central Lab, St James's University Hospital, Leeds, UK
| | - Chris F Inglehearn
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Carmel Toomes
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
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14
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Kosuthova K, Solc R. Inversions on human chromosomes. Am J Med Genet A 2023; 191:672-683. [PMID: 36495134 DOI: 10.1002/ajmg.a.63063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
Human chromosome inversions are types of balanced structural variations, making them difficult to analyze. Thanks to PEM (paired-end sequencing and mapping), there has been tremendous progress in studying inversions. Inversions play an important role as an evolutionary factor, contributing to the formation of gonosomes, speciation of chimpanzees and humans, and inv17q21.3 or inv8p23.1 exhibit the features of natural selection. Both inversions have been related to pathogenic phenotype by directly affecting a gene structure (e.g., inv5p15.1q14.1), regulating gene expression (e.g., inv7q21.3q35) and by predisposing to other secondary arrangements (e.g., inv7q11.23). A polymorphism of human inversions is documented by the InvFEST database (a database that stores information about clinical predictions, validations, frequency of inversions, etc.), but only a small fraction of these inversions is validated, and a detailed analysis is complicated by the frequent location of breakpoints within regions of repetitive sequences.
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Affiliation(s)
- Klara Kosuthova
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Roman Solc
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
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15
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Zhang Y, Zhang C, Huo W, Wang X, Zhang M, Palmer K, Chen M. An expectation-maximization algorithm for estimating proportions of deletions among bacterial populations with application to study antibiotic resistance gene transfer in Enterococcus faecalis. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:28-43. [PMID: 36744155 PMCID: PMC9888353 DOI: 10.1007/s42995-022-00144-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 08/25/2022] [Indexed: 06/18/2023]
Abstract
The emergence of antibiotic resistance in bacteria limits the availability of antibiotic choices for treatment and infection control, thereby representing a major threat to human health. The de novo mutation of bacterial genomes is an essential mechanism by which bacteria acquire antibiotic resistance. Previously, deletion mutations within bacterial immune systems, ranging from dozens to thousands of base pairs (bps) in length, have been associated with the spread of antibiotic resistance. Most current methods for evaluating genomic structural variations (SVs) have concentrated on detecting them, rather than estimating the proportions of populations that carry distinct SVs. A better understanding of the distribution of mutations and subpopulations dynamics in bacterial populations is needed to appreciate antibiotic resistance evolution and movement of resistance genes through populations. Here, we propose a statistical model to estimate the proportions of genomic deletions in a mixed population based on Expectation-Maximization (EM) algorithms and next-generation sequencing (NGS) data. The method integrates both insert size and split-read mapping information to iteratively update estimated distributions. The proposed method was evaluated with three simulations that demonstrated the production of accurate estimations. The proposed method was then applied to investigate the horizontal transfers of antibiotic resistance genes in concert with changes in the CRISPR-Cas system of E. faecalis. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00144-z.
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Affiliation(s)
- Yu Zhang
- School of Mathematical Sciences, Ocean University of China, Qingdao, 266000 China
- Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX 75080 USA
| | - Cong Zhang
- Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX 75080 USA
| | - Wenwen Huo
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080 USA
| | - Xinlei Wang
- Department of Statistical Science, Southern Methodist University, Dallas, TX 75205 USA
| | - Michael Zhang
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080 USA
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, 100084 China
| | - Kelli Palmer
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080 USA
| | - Min Chen
- Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX 75080 USA
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX 75390 USA
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16
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Genes that are Used Together are More Likely to be Fused Together in Evolution by Mutational Mechanisms: A Bioinformatic Test of the Used-Fused Hypothesis. Evol Biol 2023; 50:30-55. [PMID: 36816837 PMCID: PMC9925542 DOI: 10.1007/s11692-022-09579-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 09/11/2022] [Indexed: 12/05/2022]
Abstract
Cases of parallel or recurrent gene fusions in evolution as well as in genetic disease and cancer are difficult to explain, because unlike point mutations, they can require the repetition of a similar configuration of multiple breakpoints rather than the repetition of a single point mutation. The used-together-fused-together hypothesis holds that genes that are used together repeatedly and persistently in a specific context are more likely to undergo fusion mutation in the course of evolution for mechanistic reasons. This hypothesis offers to explain gene fusion in both evolution and disease under one umbrella. Using bioinformatic data, we tested this hypothesis against alternatives, including that all gene pairs can fuse by random mutation, but among pairs thus fused, those that had interacted previously are more likely to be favored by selection. Results show that across multiple measures of gene interaction, human genes whose orthologs are fused in one or more species are more likely to interact with each other than random pairs of genes of the same genomic distance between pair members; that an overlap exists between genes that fused in the course of evolution in non-human species and genes that undergo fusion in human cancers; and that across six primate species studied, fusions predominate over fissions and exhibit substantial evolutionary parallelism. Together, these results support the used-together-fused-together hypothesis over its alternatives. Multiple implications are discussed, including the relevance of mutational mechanisms to the evolution of genome organization, to the distribution of fitness effects of mutation, to evolutionary parallelism and more. Supplementary Information The online version contains supplementary material available at 10.1007/s11692-022-09579-9.
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17
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Talsania K, Shen TW, Chen X, Jaeger E, Li Z, Chen Z, Chen W, Tran B, Kusko R, Wang L, Pang AWC, Yang Z, Choudhari S, Colgan M, Fang LT, Carroll A, Shetty J, Kriga Y, German O, Smirnova T, Liu T, Li J, Kellman B, Hong K, Hastie AR, Natarajan A, Moshrefi A, Granat A, Truong T, Bombardi R, Mankinen V, Meerzaman D, Mason CE, Collins J, Stahlberg E, Xiao C, Wang C, Xiao W, Zhao Y. Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies. Genome Biol 2022; 23:255. [PMID: 36514120 PMCID: PMC9746098 DOI: 10.1186/s13059-022-02816-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 11/17/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, structural variant (SV) characterization plays a paramount role in cancer target identification, oncology diagnostics, and personalized medicine. As part of the SEQC2 Consortium effort, the present study established and evaluated a consensus SV call set using a breast cancer reference cell line and matched normal control derived from the same donor, which were used in our companion benchmarking studies as reference samples. RESULTS We systematically investigated somatic SVs in the reference cancer cell line by comparing to a matched normal cell line using multiple NGS platforms including Illumina short-read, 10X Genomics linked reads, PacBio long reads, Oxford Nanopore long reads, and high-throughput chromosome conformation capture (Hi-C). We established a consensus SV call set of a total of 1788 SVs including 717 deletions, 230 duplications, 551 insertions, 133 inversions, 146 translocations, and 11 breakends for the reference cancer cell line. To independently evaluate and cross-validate the accuracy of our consensus SV call set, we used orthogonal methods including PCR-based validation, Affymetrix arrays, Bionano optical mapping, and identification of fusion genes detected from RNA-seq. We evaluated the strengths and weaknesses of each NGS technology for SV determination, and our findings provide an actionable guide to improve cancer genome SV detection sensitivity and accuracy. CONCLUSIONS A high-confidence consensus SV call set was established for the reference cancer cell line. A large subset of the variants identified was validated by multiple orthogonal methods.
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Affiliation(s)
- Keyur Talsania
- grid.418021.e0000 0004 0535 8394Sequencing Facility Bioinformatics Group, Advanced Biomedical and Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD USA ,grid.418021.e0000 0004 0535 8394Bioinformatics and Computational Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Tsai-wei Shen
- grid.418021.e0000 0004 0535 8394Sequencing Facility Bioinformatics Group, Advanced Biomedical and Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD USA ,grid.418021.e0000 0004 0535 8394Bioinformatics and Computational Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Xiongfong Chen
- grid.418021.e0000 0004 0535 8394Sequencing Facility Bioinformatics Group, Advanced Biomedical and Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD USA ,grid.418021.e0000 0004 0535 8394Bioinformatics and Computational Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Erich Jaeger
- grid.185669.50000 0004 0507 3954Illumina Inc, Foster City, CA USA
| | - Zhipan Li
- grid.511732.3Sentieon Inc, Mountain View, CA USA
| | - Zhong Chen
- grid.43582.380000 0000 9852 649XCenter for Genomics, Loma Linda University School of Medicine, Loma Linda, CA USA
| | - Wanqiu Chen
- grid.43582.380000 0000 9852 649XCenter for Genomics, Loma Linda University School of Medicine, Loma Linda, CA USA
| | - Bao Tran
- grid.418021.e0000 0004 0535 8394Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | | | - Limin Wang
- grid.48336.3a0000 0004 1936 8075Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD USA
| | | | - Zhaowei Yang
- grid.470124.4Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - Sulbha Choudhari
- grid.418021.e0000 0004 0535 8394Sequencing Facility Bioinformatics Group, Advanced Biomedical and Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD USA ,grid.418021.e0000 0004 0535 8394Bioinformatics and Computational Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Michael Colgan
- grid.483500.a0000 0001 2154 2448Center for Drug Evaluation and Research, FDA, Silver Spring, MD USA
| | - Li Tai Fang
- grid.418158.10000 0004 0534 4718Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc, 1301 Shoreway Road, Belmont, CA 94002 USA
| | - Andrew Carroll
- grid.511991.40000 0004 4910 5831DNAnexus, Mountain View, CA USA
| | - Jyoti Shetty
- grid.418021.e0000 0004 0535 8394Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Yuliya Kriga
- grid.418021.e0000 0004 0535 8394Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Oksana German
- grid.418021.e0000 0004 0535 8394Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Tatyana Smirnova
- grid.418021.e0000 0004 0535 8394Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Tiantain Liu
- grid.43582.380000 0000 9852 649XCenter for Genomics, Loma Linda University School of Medicine, Loma Linda, CA USA
| | - Jing Li
- grid.470124.4Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong China
| | - Ben Kellman
- grid.470262.50000 0004 0473 1353Bionano Genomics, San Diego, CA92121 USA
| | - Karl Hong
- grid.470262.50000 0004 0473 1353Bionano Genomics, San Diego, CA92121 USA
| | - Alex R. Hastie
- grid.470262.50000 0004 0473 1353Bionano Genomics, San Diego, CA92121 USA
| | - Aparna Natarajan
- grid.185669.50000 0004 0507 3954Illumina Inc, Foster City, CA USA
| | - Ali Moshrefi
- grid.185669.50000 0004 0507 3954Illumina Inc, Foster City, CA USA
| | | | - Tiffany Truong
- grid.185669.50000 0004 0507 3954Illumina Inc, Foster City, CA USA
| | - Robin Bombardi
- grid.185669.50000 0004 0507 3954Illumina Inc, Foster City, CA USA
| | | | - Daoud Meerzaman
- grid.48336.3a0000 0004 1936 8075Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD USA
| | - Christopher E. Mason
- grid.5386.8000000041936877XDepartment of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA
| | - Jack Collins
- grid.418021.e0000 0004 0535 8394Sequencing Facility Bioinformatics Group, Advanced Biomedical and Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD USA ,grid.418021.e0000 0004 0535 8394Bioinformatics and Computational Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Eric Stahlberg
- grid.418021.e0000 0004 0535 8394Bioinformatics and Computational Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Chunlin Xiao
- grid.419234.90000 0004 0604 5429National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD USA
| | - Charles Wang
- grid.43582.380000 0000 9852 649XCenter for Genomics, Loma Linda University School of Medicine, Loma Linda, CA USA
| | - Wenming Xiao
- grid.483500.a0000 0001 2154 2448Center for Drug Evaluation and Research, FDA, Silver Spring, MD USA
| | - Yongmei Zhao
- grid.418021.e0000 0004 0535 8394Sequencing Facility Bioinformatics Group, Advanced Biomedical and Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD USA ,grid.418021.e0000 0004 0535 8394Bioinformatics and Computational Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD USA
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18
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Gui J, Ding J, Yin T, Liu Q, Xie Q, Ming L. Chromosomal analysis of 262 miscarried conceptuses: a retrospective study. BMC Pregnancy Childbirth 2022; 22:906. [PMID: 36471261 PMCID: PMC9721014 DOI: 10.1186/s12884-022-05246-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Embryonic chromosomal abnormality is one of the significant causative factors of pregnancy loss. Our goal was to investigate the differences of chromosomal abnormality between different conception modes in miscarried products of conception (POCs). METHODS A retrospective study included 262 miscarried POCs from 167 women undergoing assisted reproductive treatment (ART) and 95 spontaneous pregnant (SP) women during March 2019 to March 2022 in Renmin Hospital of Wuhan University. Subgroups were divided according to age, fertilization method, types and stages of embryo transfer. The profiles of cytogenetic abnormalities in the miscarried POCs were measured via next-generation sequencing. RESULTS The rate of chromosomal abnormality in the fresh embryo transfer group and the cleavage embryo transfer group was significantly higher than that in the frozen embryo transfer group (79.2% vs. 36%, P = 0.0001) and the blastocyst transfer group (66.7% vs. 32.1%, P = 0.0001) respectively. There was no significant difference in the rate of chromosomal abnormalities when compared by maternal age (49.2% vs. 62%, P = 0.066), types of conception (49.7% vs. 57.9%, P = 0.202), fertilization method (49.6% vs. 48.7%, P = 0.927) and frequency of abortion (56% vs. 47.6%, P = 0.183). However, the women aged ≥ 35 years had more frequent numerical abnormality (P = 0.002); patients using assisted reproductive technology had more rate of chromosomal structural abnormalities (26.5% vs. 7.3%, P = 0.005); the ICSI fertilization group has more frequency of deletion/microdeletion than the IVF fertilization group (80% vs. 31.3%, P = 0.019). CONCLUSION Blastocyst transfer might help to reduce the incidence of miscarriage. In addition, "freezing all" should be considered if encountered hyper ovarian stimulation, to avoid the negative effect of high estrogen environment on embryo development. The higher incidence of structural abnormalities in miscarried POCs from assisted reproductive patients reminds us to pay attention to the safety of the technology for offspring.
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Affiliation(s)
- Juan Gui
- grid.412632.00000 0004 1758 2270Department of Reproductive Center, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060 China ,Assisted Reproduction and Embryogenesis Clinical Research Center of Hubei Province, Wuhan, China
| | - Jinli Ding
- grid.412632.00000 0004 1758 2270Department of Reproductive Center, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060 China ,Assisted Reproduction and Embryogenesis Clinical Research Center of Hubei Province, Wuhan, China
| | - Tailang Yin
- grid.412632.00000 0004 1758 2270Department of Reproductive Center, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060 China ,Assisted Reproduction and Embryogenesis Clinical Research Center of Hubei Province, Wuhan, China
| | - Qian Liu
- grid.412632.00000 0004 1758 2270Department of Reproductive Center, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060 China ,Assisted Reproduction and Embryogenesis Clinical Research Center of Hubei Province, Wuhan, China
| | - Qingzhen Xie
- grid.412632.00000 0004 1758 2270Department of Reproductive Center, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060 China ,Assisted Reproduction and Embryogenesis Clinical Research Center of Hubei Province, Wuhan, China
| | - Lei Ming
- grid.412632.00000 0004 1758 2270Department of Reproductive Center, Renmin Hospital of Wuhan University, 238 Jiefang Road, Wuchang District, Wuhan, 430060 China ,Assisted Reproduction and Embryogenesis Clinical Research Center of Hubei Province, Wuhan, China
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Copy Number Variation of the SOX6 Gene and Its Associations with Growth Traits in Ashidan Yak. Animals (Basel) 2022; 12:ani12223074. [PMID: 36428302 PMCID: PMC9686495 DOI: 10.3390/ani12223074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022] Open
Abstract
Copy number variation (CNV) is a fundamental type of structural variation of the genome affecting the economic traits of livestock. The SOX6 gene (sex-determining region Y-box 6), as a transcription factor, has multiple functions with regard to sex determination, embryonic growth, the nervous system development, as well as bone, and various organ formation. This study employed quantitative real-time fluorescence quota PCR (qPCR) for detecting the SOX6-CNV of the 311 Ashidan yaks and analyzed the correlation of the SOX6-CNV with four phenotypes (including body weight, withers height, body length, and chest girth) of the yaks aged 6, 12, 18, and 30 months using ANOVA and multiple comparisons. Furthermore, the SOX6 gene expression was identified in seven different tissues of the yaks. The experiment results demonstrated the expression of SOX6 in each tissue, and the kidney and muscle tissue were found to have higher relative expression levels. Based on the processing by IBM SPSS software, SOX6-CNV was significantly correlated with the chest girth of the 6-months old yaks (p < 0.05) and 30-months yaks (p < 0.05), and withers height of 6 months yaks (p < 0.05) and 18-months yaks (p < 0.05), as well as the normal type of CNV, was chosen for yak breeding. In conclusion, SOX6 might be prominently involved in promoting growth and development of yaks, suggesting that the SOX6 gene can be used in breeding yaks by molecular marker-assisted selection (MAS). The study also offered some important insights into the references and clues for the genetic breeding of yaks.
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20
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Hanlon VCT, Lansdorp PM, Guryev V. A survey of current methods to detect and genotype inversions. Hum Mutat 2022; 43:1576-1589. [PMID: 36047337 DOI: 10.1002/humu.24458] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/11/2022]
Abstract
Polymorphic inversions are ubiquitous in humans, and they have been linked to both adaptation and disease. Following their discovery in Drosophila more than a century ago, inversions have proved to be more elusive than other structural variants. A wide variety of methods for the detection and genotyping of inversions have recently been developed: multiple techniques based on selective amplification by PCR, short- and long-read sequencing approaches, principal component analysis of small variant haplotypes, template strand sequencing, optical mapping, and various genome assembly methods. Many methods apply complex wet lab protocols or increasingly refined bioinformatic analyses. This review is an attempt to provide a practical summary and comparison of the methods that are in current use, with a focus on metrics such as the maximum size of segmental duplications at inversion breakpoints that each method can tolerate, the size range of inversions that they recover, their throughput, and whether the locations of putative inversions must be known beforehand. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Peter M Lansdorp
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, The Netherlands
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21
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Alhazmi S, Alzahrani M, Farsi R, Alharbi M, Algothmi K, Alburae N, Ganash M, Azhari S, Basingab F, Almuhammadi A, Alqosaibi A, Alkhatabi H, Elaimi A, Jan M, Aldhalaan HM, Alrafiah A, Alrofaidi A. Multiple Recurrent Copy Number Variations (CNVs) in Chromosome 22 Including 22q11.2 Associated with Autism Spectrum Disorder. Pharmgenomics Pers Med 2022; 15:705-720. [PMID: 35898556 PMCID: PMC9309317 DOI: 10.2147/pgpm.s366826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/14/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction Autism spectrum disorder (ASD) is a developmental disorder that can cause substantial social, communication, and behavioral challenges. Genetic factors play a significant role in ASD, where the risk of ASD has been increased for unclear reasons. Twin studies have shown important evidence of both genetic and environmental contributions in ASD, where the level of contribution of these factors has not been proven yet. It has been suggested that copy number variation (CNV) duplication and the deletion of many genes in chromosome 22 (Ch22) may have a strong association with ASD. This study screened the CNVs in Ch22 in autistic Saudi children and assessed the candidate gene in the CNVs region of Ch22 that is most associated with ASD. Methods This study included 15 autistic Saudi children as well as 4 healthy children as controls; DNA was extracted from samples and analyzed using array comparative genomic hybridization (aCGH) and DNA sequencing. Results The aCGH detected (in only 6 autistic samples) deletion and duplication in many regions of Ch22, including some critical genes. Moreover, DNA sequencing determined a genetic mutation in the TBX1 gene sequence in autistic samples. This study, carried out using aCGH, found that six autistic patients had CNVs in Ch22, and DNA sequencing revealed mutations in the TBX1 gene in autistic samples but none in the control. Conclusion CNV deletion and the duplication of the TBX1 gene could be related to ASD; therefore, this gene needs more analysis in terms of expression levels.
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Affiliation(s)
- Safiah Alhazmi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maryam Alzahrani
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem Farsi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mona Alharbi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khloud Algothmi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Najla Alburae
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Magdah Ganash
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sheren Azhari
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fatemah Basingab
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asma Almuhammadi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amany Alqosaibi
- Department of Biology, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Heba Alkhatabi
- Centre of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aisha Elaimi
- Centre of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed Jan
- College of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hesham M Aldhalaan
- Center for Autism Research at King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Aziza Alrafiah
- Department of Medical Laboratory Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Correspondence: Aziza Alrafiah, Department of Medical Laboratory Science, King Abdulaziz University, P.O Box 80200, Jeddah, 21589, Saudi Arabia, Tel +966 126401000 Ext. 23495, Fax +966 126401000 Ext. 21686, Email
| | - Aisha Alrofaidi
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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22
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Cosenza MR, Rodriguez-Martin B, Korbel JO. Structural Variation in Cancer: Role, Prevalence, and Mechanisms. Annu Rev Genomics Hum Genet 2022; 23:123-152. [DOI: 10.1146/annurev-genom-120121-101149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Somatic rearrangements resulting in genomic structural variation drive malignant phenotypes by altering the expression or function of cancer genes. Pan-cancer studies have revealed that structural variants (SVs) are the predominant class of driver mutation in most cancer types, but because they are difficult to discover, they remain understudied when compared with point mutations. This review provides an overview of the current knowledge of somatic SVs, discussing their primary roles, prevalence in different contexts, and mutational mechanisms. SVs arise throughout the life history of cancer, and 55% of driver mutations uncovered by the Pan-Cancer Analysis of Whole Genomes project represent SVs. Leveraging the convergence of cell biology and genomics, we propose a mechanistic classification of somatic SVs, from simple to highly complex DNA rearrangement classes. The actions of DNA repair and DNA replication processes together with mitotic errors result in a rich spectrum of SV formation processes, with cascading effects mediating extensive structural diversity after an initiating DNA lesion has formed. Thanks to new sequencing technologies, including the sequencing of single-cell genomes, open questions about the molecular triggers and the biomolecules involved in SV formation as well as their mutational rates can now be addressed. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | | | - Jan O. Korbel
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
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23
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Wang X, Junqing L, Huang T. CNVABNN: An AdaBoost algorithm and neural networks-based detection of copy number variations from NGS data. Comput Biol Chem 2022; 99:107720. [DOI: 10.1016/j.compbiolchem.2022.107720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/03/2022]
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24
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Damert A. SVA retrotransposons and a low copy repeat in humans and great apes: a mobile connection. Mol Biol Evol 2022; 39:6586216. [PMID: 35574660 PMCID: PMC9132208 DOI: 10.1093/molbev/msac103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Segmental duplications (SDs) constitute a considerable fraction of primate genomes. They contribute to genetic variation and provide raw material for evolution. Groups of SDs are characterized by the presence of shared core duplicons. One of these core duplicons, low copy repeat (lcr)16a, has been shown to be particularly active in the propagation of interspersed SDs in primates. The underlying mechanisms are, however, only partially understood. Alu short interspersed elements (SINEs) are frequently found at breakpoints and have been implicated in the expansion of SDs. Detailed analysis of lcr16a-containing SDs shows that the hominid-specific SVA (SINE-R-VNTR-Alu) retrotransposon is an integral component of the core duplicon in Asian and African great apes. In orang-utan, it provides breakpoints and contributes to both interchromosomal and intrachromosomal lcr16a mobility by inter-element recombination. Furthermore, the data suggest that in hominines (human, chimpanzee, gorilla) SVA recombination-mediated integration of a circular intermediate is the founding event of a lineage-specific lcr16a expansion. One of the hominine lcr16a copies displays large flanking direct repeats, a structural feature shared by other SDs in the human genome. Taken together, the results obtained extend the range of SVAs’ contribution to genome evolution from RNA-mediated transduction to DNA-based recombination. In addition, they provide further support for a role of circular intermediates in SD mobilization.
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Affiliation(s)
- Annette Damert
- Infection Biology Unit and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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25
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Porubsky D, Höps W, Ashraf H, Hsieh P, Rodriguez-Martin B, Yilmaz F, Ebler J, Hallast P, Maria Maggiolini FA, Harvey WT, Henning B, Audano PA, Gordon DS, Ebert P, Hasenfeld P, Benito E, Zhu Q, Lee C, Antonacci F, Steinrücken M, Beck CR, Sanders AD, Marschall T, Eichler EE, Korbel JO. Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Cell 2022; 185:1986-2005.e26. [PMID: 35525246 PMCID: PMC9563103 DOI: 10.1016/j.cell.2022.04.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/14/2022] [Accepted: 04/08/2022] [Indexed: 12/13/2022]
Abstract
Unlike copy number variants (CNVs), inversions remain an underexplored genetic variation class. By integrating multiple genomic technologies, we discover 729 inversions in 41 human genomes. Approximately 85% of inversions <2 kbp form by twin-priming during L1 retrotransposition; 80% of the larger inversions are balanced and affect twice as many nucleotides as CNVs. Balanced inversions show an excess of common variants, and 72% are flanked by segmental duplications (SDs) or retrotransposons. Since flanking repeats promote non-allelic homologous recombination, we developed complementary approaches to identify recurrent inversion formation. We describe 40 recurrent inversions encompassing 0.6% of the genome, showing inversion rates up to 2.7 × 10-4 per locus per generation. Recurrent inversions exhibit a sex-chromosomal bias and co-localize with genomic disorder critical regions. We propose that inversion recurrence results in an elevated number of heterozygous carriers and structural SD diversity, which increases mutability in the population and predisposes specific haplotypes to disease-causing CNVs.
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26
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Zhai F, Wang Y, Li H, Wang Y, Zhu X, Kuo Y, Guan S, Li J, Song S, He Q, An J, Zhi X, Lian Y, Huang J, Li R, Qiao J, Yan L, Yan Z. Low-coverage NGS-based PGT-SR accurately discriminate normal/carrier embryos for patients with translocations in IVF. Reprod Biomed Online 2022; 45:473-480. [DOI: 10.1016/j.rbmo.2022.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/09/2022] [Accepted: 05/17/2022] [Indexed: 11/28/2022]
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27
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Komlósi K, Gyenesei A, Bene J. Editorial: Copy Number Variation in Rare Disorders. Front Genet 2022; 13:898059. [PMID: 35450215 PMCID: PMC9016220 DOI: 10.3389/fgene.2022.898059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 02/06/2023] Open
Affiliation(s)
- Katalin Komlósi
- Institute of Human Genetics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Attila Gyenesei
- Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentagothai Research Center, University of Pécs, Pécs, Hungary
| | - Judit Bene
- Department of Medical Genetics, Clinical Centre, Medical School, University of Pécs, Pécs, Hungary
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28
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Akoniyon OP, Adewumi TS, Maharaj L, Oyegoke OO, Roux A, Adeleke MA, Maharaj R, Okpeku M. Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria. BIOLOGY 2022; 11:587. [PMID: 35453786 PMCID: PMC9027812 DOI: 10.3390/biology11040587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/11/2022]
Abstract
Malaria elimination remains an important goal that requires the adoption of sophisticated science and management strategies in the era of the COVID-19 pandemic. The advent of next generation sequencing (NGS) is making whole genome sequencing (WGS) a standard today in the field of life sciences, as PCR genotyping and targeted sequencing provide insufficient information compared to the whole genome. Thus, adapting WGS approaches to malaria parasites is pertinent to studying the epidemiology of the disease, as different regions are at different phases in their malaria elimination agenda. Therefore, this review highlights the applications of WGS in disease management, challenges of WGS in controlling malaria parasites, and in furtherance, provides the roles of WGS in pursuit of malaria reduction and elimination. WGS has invaluable impacts in malaria research and has helped countries to reach elimination phase rapidly by providing required information needed to thwart transmission, pathology, and drug resistance. However, to eliminate malaria in sub-Saharan Africa (SSA), with high malaria transmission, we recommend that WGS machines should be readily available and affordable in the region.
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Affiliation(s)
- Olusegun Philip Akoniyon
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Taiye Samson Adewumi
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Leah Maharaj
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Olukunle Olugbenle Oyegoke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Alexandra Roux
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Matthew A. Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Rajendra Maharaj
- Office of Malaria Research, South African Medical Research Council, Cape Town 7505, South Africa;
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
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29
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Gordeeva V, Sharova E, Arapidi G. Progress in Methods for Copy Number Variation Profiling. Int J Mol Sci 2022; 23:ijms23042143. [PMID: 35216262 PMCID: PMC8879278 DOI: 10.3390/ijms23042143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
Copy number variations (CNVs) are the predominant class of structural genomic variations involved in the processes of evolutionary adaptation, genomic disorders, and disease progression. Compared with single-nucleotide variants, there have been challenges associated with the detection of CNVs owing to their diverse sizes. However, the field has seen significant progress in the past 20–30 years. This has been made possible due to the rapid development of molecular diagnostic methods which ensure a more detailed view of the genome structure, further complemented by recent advances in computational methods. Here, we review the major approaches that have been used to routinely detect CNVs, ranging from cytogenetics to the latest sequencing technologies, and then cover their specific features.
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Affiliation(s)
- Veronika Gordeeva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.S.); (G.A.)
- Moscow Institute of Physics and Technology, National Research University, Moscow Oblast, 141701 Moscow, Russia
- Correspondence:
| | - Elena Sharova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.S.); (G.A.)
| | - Georgij Arapidi
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.S.); (G.A.)
- Moscow Institute of Physics and Technology, National Research University, Moscow Oblast, 141701 Moscow, Russia
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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30
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Frequency and clinical significance of chromosomal inversions prenatally diagnosed by second trimester amniocentesis. Sci Rep 2022; 12:2215. [PMID: 35140290 PMCID: PMC8828714 DOI: 10.1038/s41598-022-06024-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 01/07/2022] [Indexed: 11/09/2022] Open
Abstract
To compare the frequency and clinical significance of familial and de novo chromosomal inversions during prenatal diagnosis. This was a retrospective study of inversions diagnosed prenatally in an Asian population by applying conventional GTG-banding to amniocyte cultures. Data from 2005 to 2019 were extracted from a single-center laboratory database. The types, frequencies, and inheritance patterns of multiple inversions were analyzed. Pericentric variant inversions of chromosome 9 or Y were excluded. In total, 56 (0.27%) fetuses with inversions were identified in the 15-year database of 21,120 confirmative diagnostic procedures. Pericentric and paracentric inversions accounted for 62.5% (35/56) and 37.5% of the inversions, respectively. Familial inversions accounted for nearly 90% of cases, and de novo mutation was identified in two pericentric and two paracentric cases. Inversions were most frequently identified on chromosomes 1 and 2 (16.1% of all inversions), followed by chromosomes 6, 7, and 10 (8.9% of all cases). The indications for invasive testing were as follows: advanced maternal age (67.3%), abnormal ultrasound findings (2.1%), abnormal serum aneuploidy screening (20.4%), and other indications (10.2%). The mode of inheritance was available for 67.9% of cases (38/56), with 89.5% of inversions being inherited (34/38). A slight preponderance of inheritance in female fetuses was observed. Three patients with inherited inversions opted for termination (two had severe central nervous system lesions and one had thalassemia major). Gestation continued for 53 fetuses, who exhibited no structural defects at birth or significant developmental problems a year after birth. Our study indicates that approximately 90% of prenatally diagnosed inversions involve familial inheritance, are spreading, and behave like founder effect mutations in this isolated population on an island. This finding can help to alleviate anxiety during prenatal counseling, which further underscores the importance of parental chromosomal analysis, further genetic studies, and appropriate counseling in cases where a nonfamilial inversion is diagnosed.
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31
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Wang XQ, Goytain A, Dickson BC, Nielsen TO. Advances in Sarcoma Molecular Diagnostics. Genes Chromosomes Cancer 2022; 61:332-345. [DOI: 10.1002/gcc.23025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Xue Qi Wang
- Faculty of Medicine University of British Columbia Vancouver Canada
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver Canada
| | - Angela Goytain
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver Canada
| | - Brendan C. Dickson
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital; Department of Laboratory Medicine and Pathobiology University of Toronto Toronto ON Canada
| | - Torsten Owen Nielsen
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver Canada
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32
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Zhou S, Wu Y, Xie ZX, Jia B, Yuan YJ. Directed genome evolution driven by structural rearrangement techniques. Chem Soc Rev 2021; 50:12788-12807. [PMID: 34651628 DOI: 10.1039/d1cs00722j] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Directed genome evolution simulates the process of natural evolution at the genomic level in the laboratory to generate desired phenotypes. Here we review the applications of recent technological advances in genome writing and editing to directed genome evolution, with a focus on structural rearrangement techniques. We highlight how these techniques can be used to generate diverse genotypes, and to accelerate the evolution of phenotypic traits. We also discuss the perspectives of directed genome evolution.
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Affiliation(s)
- Sijie Zhou
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yi Wu
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Ze-Xiong Xie
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Bin Jia
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Ying-Jin Yuan
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
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33
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Nam H, Lee IH, Sa JK, Kim SS, Pyeon HJ, Lee KH, Lee K, Lee SH, Joo KM. Effects of Long-Term In Vitro Expansion on Genetic Stability and Tumor Formation Capacity of Stem Cells. Stem Cell Rev Rep 2021; 18:241-257. [PMID: 34738209 DOI: 10.1007/s12015-021-10290-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2021] [Indexed: 12/30/2022]
Abstract
Stem cell therapeutics are emerging as novel alternative treatments for various neurodegenerative diseases based on their regenerative potentials. However, stem cell transplantation might have side effects such as tumor formation that limit their clinical applications. Especially, in vitro expansion of stem cells might provoke genetic instability and tumorigenic potential. To address this issue, we analyzed genomic alterations of adult human multipotent neural cells (ahMNCs), a type of human adult neural stem cells, after a long-term in vitro culture process (passage 15) using sensitive analysis techniques including karyotyping, array comparative genomic hybridization (aCGH), and whole exome sequencing (WES). Although karyotyping did not find any major abnormalities in chromosomal number or structure, diverse copy number variations (CNVs) and genetic mutations were detected by aCGH and WES in all five independent ahMNCs. However, the number of CNVs and genetic mutations did not increase and many of them did not persist as in vitro culture progressed. Although most observed CNVs and genetic mutations were not shared by all five ahMNCs, nonsynonymous missense mutations at MUC4 were found in three out of five long-term cultured ahMNC lines. The genetic instability did not confer in vivo tumorigenic potential to ahMNCs. Collectively, these results indicate that, although genetic instability can be induced by long-term in vitro expansion of stem cells, it is not sufficient to fully exert tumor formation capacity of stem cells. Other functional effects of such genetic instability need to be further elucidated.
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Affiliation(s)
- Hyun Nam
- Department of Anatomy & Cell Biology, Sungkyunkwan University School of Medicine, 2066 Seobu-ro, Suwon, Gyeonggi-do, 16419, South Korea.,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Stem Cell and Regenerative Medicine Center, Research Institute for Future Medicine, Samsung Medical Center, Seoul, 06351, South Korea
| | - In-Hee Lee
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Jason K Sa
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| | - Sung Soo Kim
- Department of Anatomy & Cell Biology, Sungkyunkwan University School of Medicine, 2066 Seobu-ro, Suwon, Gyeonggi-do, 16419, South Korea.,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Stem Cell and Regenerative Medicine Center, Research Institute for Future Medicine, Samsung Medical Center, Seoul, 06351, South Korea
| | - Hee-Jang Pyeon
- Department of Anatomy & Cell Biology, Sungkyunkwan University School of Medicine, 2066 Seobu-ro, Suwon, Gyeonggi-do, 16419, South Korea.,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Stem Cell and Regenerative Medicine Center, Research Institute for Future Medicine, Samsung Medical Center, Seoul, 06351, South Korea
| | - Kee Hang Lee
- Department of Anatomy & Cell Biology, Sungkyunkwan University School of Medicine, 2066 Seobu-ro, Suwon, Gyeonggi-do, 16419, South Korea.,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Stem Cell and Regenerative Medicine Center, Research Institute for Future Medicine, Samsung Medical Center, Seoul, 06351, South Korea
| | - Kyunghoon Lee
- Department of Anatomy & Cell Biology, Sungkyunkwan University School of Medicine, 2066 Seobu-ro, Suwon, Gyeonggi-do, 16419, South Korea.,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea.,Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, 06351, South Korea
| | - Sun-Ho Lee
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea. .,Stem Cell and Regenerative Medicine Center, Research Institute for Future Medicine, Samsung Medical Center, Seoul, 06351, South Korea. .,Biomedical Institute for Convergence at Sungkyunkwan University (BICS), Sungkyunkwan University, Suwon, 16419, South Korea. .,Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, South Korea.
| | - Kyeung Min Joo
- Department of Anatomy & Cell Biology, Sungkyunkwan University School of Medicine, 2066 Seobu-ro, Suwon, Gyeonggi-do, 16419, South Korea. .,Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, 16419, South Korea. .,Stem Cell and Regenerative Medicine Center, Research Institute for Future Medicine, Samsung Medical Center, Seoul, 06351, South Korea. .,Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, 06351, South Korea. .,Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, South Korea.
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Cornforth MN, Bedford JS, Bailey SM. Destabilizing Effects of Ionizing Radiation on Chromosomes: Sizing up the Damage. Cytogenet Genome Res 2021; 161:328-351. [PMID: 34488218 DOI: 10.1159/000516523] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/16/2021] [Indexed: 11/19/2022] Open
Abstract
For long-term survival and evolution, all organisms have depended on a delicate balance between processes involved in maintaining stability of their genomes and opposing processes that lead toward destabilization. At the level of mammalian somatic cells in renewal tissues, events or conditions that can tip this balance toward instability have attracted special interest in connection with carcinogenesis. Mutations affecting DNA (and its subsequent repair) would, of course, be a major consideration here. These may occur spontaneously through endogenous cellular processes or as a result of exposure to mutagenic environmental agents. It is in this context that we discuss the rather unique destabilizing effects of ionizing radiation (IR) in terms of its ability to cause large-scale structural rearrangements to the genome. We present arguments supporting the conclusion that these and other important effects of IR originate largely from microscopically visible chromosome aberrations.
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Affiliation(s)
- Michael N Cornforth
- Department of Radiation Oncology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Joel S Bedford
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Susan M Bailey
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, USA
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Abstract
Long-read sequencing technologies have now reached a level of accuracy and yield that allows their application to variant detection at a scale of tens to thousands of samples. Concomitant with the development of new computational tools, the first population-scale studies involving long-read sequencing have emerged over the past 2 years and, given the continuous advancement of the field, many more are likely to follow. In this Review, we survey recent developments in population-scale long-read sequencing, highlight potential challenges of a scaled-up approach and provide guidance regarding experimental design. We provide an overview of current long-read sequencing platforms, variant calling methodologies and approaches for de novo assemblies and reference-based mapping approaches. Furthermore, we summarize strategies for variant validation, genotyping and predicting functional impact and emphasize challenges remaining in achieving long-read sequencing at a population scale.
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Affiliation(s)
- Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
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36
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Wold J, Koepfli KP, Galla SJ, Eccles D, Hogg CJ, Le Lec MF, Guhlin J, Santure AW, Steeves TE. Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern. Mol Ecol 2021; 30:5949-5965. [PMID: 34424587 PMCID: PMC9290615 DOI: 10.1111/mec.16141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/28/2021] [Accepted: 08/18/2021] [Indexed: 12/28/2022]
Abstract
Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP-based approaches to enhance species recovery. We also leverage the existing literature-predominantly in human health, agriculture and ecoevolutionary biology-to identify approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we manage some of the world's most threatened species.
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Affiliation(s)
- Jana Wold
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, Front Royal, Virginia, USA.,Centre for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA.,Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - David Eccles
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Marissa F Le Lec
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand
| | - Joseph Guhlin
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand.,Genomics Aotearoa, Dunedin, Otago, New Zealand
| | - Anna W Santure
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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Abstract
BACKGROUND New diagnostic tools in the field of oncology that became available with introduction of the next generation sequencing call for adjustments in the current clinical workflow. To ensure correct interpretation, newly collected data need to be processed and categorized properly. Thus, current experts in oncology need to be trained and new experts from other fields need to be recruited. OBJECTIVES The molecular tumor board was introduced to bring experts from various specialties together. The goal is to discuss and assess complex oncological cases in the context of new molecular diagnostics and give recommendations regarding individualized therapy. RESULTS After the introduction of the molecular tumor board 2 years ago, the number of cases processed within the molecular tumor board has increased steadily. Of these patients, 70% exhibit molecular alterations that are relevant to therapy. Preliminary results indicate positive responses to the applied therapies and clear improvements in the progression-free and overall survival of patients who would have been considered "untreatable" in the classical clinical setting. CONCLUSION The introduction of new molecular diagnostics makes the establishment of advanced clinical structures mandatory. In this regard, the molecular tumor board continues to gain in importance. Preliminary results point towards a significant impact on the therapy of advanced malignancies. The advancements in sequencing and newly established insights into the interpretation of sequencing results will lead to new therapeutic routes. Inevitably, this will make the molecular tumor board indispensable in the future.
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38
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Liu G, Zhang J. A Cluster-Based Approach for the Discovery of Copy Number Variations From Next-Generation Sequencing Data. Front Genet 2021; 12:699510. [PMID: 34262604 PMCID: PMC8273656 DOI: 10.3389/fgene.2021.699510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
The next-generation sequencing technology offers a wealth of data resources for the detection of copy number variations (CNVs) at a high resolution. However, it is still challenging to correctly detect CNVs of different lengths. It is necessary to develop new CNV detection tools to meet this demand. In this work, we propose a new CNV detection method, called CBCNV, for the detection of CNVs of different lengths from whole genome sequencing data. CBCNV uses a clustering algorithm to divide the read depth segment profile, and assigns an abnormal score to each read depth segment. Based on the abnormal score profile, Tukey's fences method is adopted in CBCNV to forecast CNVs. The performance of the proposed method is evaluated on simulated data sets, and is compared with those of several existing methods. The experimental results prove that the performance of CBCNV is better than those of several existing methods. The proposed method is further tested and verified on real data sets, and the experimental results are found to be consistent with the simulation results. Therefore, the proposed method can be expected to become a routine tool in the analysis of CNVs from tumor-normal matched samples.
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Affiliation(s)
| | - Junying Zhang
- School of Computer Science and Technology, Xidian University, Xi’an, China
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Guzel F, Romano M, Keles E, Piskin D, Ozen S, Poyrazoglu H, Kasapcopur O, Demirkaya E. Next Generation Sequencing Based Multiplex Long-Range PCR for Routine Genotyping of Autoinflammatory Disorders. Front Immunol 2021; 12:666273. [PMID: 34177904 PMCID: PMC8219981 DOI: 10.3389/fimmu.2021.666273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/14/2021] [Indexed: 01/06/2023] Open
Abstract
Background During the last decade, remarkable progress with massive sequencing has been made in the identification of disease-associated genes for AIDs using next-generation sequencing technologies (NGS). An international group of experts described the ideal genetic screening method which should give information about SNVs, InDels, Copy Number Variations (CNVs), GC rich regions. We aimed to develop and validate a molecular diagnostic method in conjunction with the NGS platform as an inexpensive, extended and uniform coverage and fast screening tool which consists of nine genes known to be associated with various AIDs. Methods For the validation of basic and expanded panels, long-range multiplex models were setup on healthy samples without any known variations for MEFV, MVK, TNFRSF1A, NLRP3, PSTPIP1, IL1RN, NOD2, NLRP12 and LPIN2 genes. Patients with AIDs who had already known causative variants in these genes were sequenced for analytical validation. As a last step, multiplex models were validated on patients with pre-diagnosis of AIDs. All sequencing steps were performed on the Illumina NGS platform. Validity steps included the selection of related candidate genes, primer design, development of screening methods, validation and verification of the product. The GDPE (Gentera) bioinformatics pipeline was followed. Results Although there was no nonsynonymous variation in 21 healthy samples, 107 synonymous variant alleles and some intronic and UTR variants were detected. In 10 patients who underwent analytical validation, besides the 11 known nonsynonymous variant alleles, 11 additional nonsynonymous variant alleles and a total of 81 synonymous variants were found. In the clinical validation phase, 46 patients sequenced with multiplex panels, genetic and clinical findings were combined for diagnosis. Conclusion In this study, we describe the development and validation of an NGS-based multiplex array enabling the "long-amplicon" approach for targeted sequencing of nine genes associated with common AIDs. This screening tool is less expensive and more comprehensive compared to other methods and more informative than traditional sequencing. The proposed panel offers advantages to WES or hybridization probe equivalents in terms of CNV analysis, high sensitivity and uniformity, GC-rich region sequencing, InDel detection and intron covering.
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Affiliation(s)
- Ferhat Guzel
- Department of Research and Development, Gentera Biotechnology, Istanbul, Turkey
| | - Micol Romano
- Department of Paediatrics, Division of Paediatric Rheumatology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - Erdi Keles
- Department of Research and Development, Gentera Biotechnology, Istanbul, Turkey
| | - David Piskin
- Department of Paediatrics, Division of Paediatric Rheumatology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada.,Department of Epidemiology and Biostatistics, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - Seza Ozen
- Department of Paediatrics, Division of Paediatric Rheumatology, Hacettepe University, Ankara, Turkey
| | - Hakan Poyrazoglu
- Department of Paediatrics, Division of Paediatric Rheumatology, Erciyes University, Kayseri, Turkey
| | - Ozgur Kasapcopur
- Department of Paediatrics, Division of Paediatric Rheumatology, Cerrhapasa Medical School, Istanbul University, Istanbul, Turkey
| | - Erkan Demirkaya
- Department of Paediatrics, Division of Paediatric Rheumatology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada.,Department of Epidemiology and Biostatistics, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
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Cheng C, Lu Y, Ma W, Li S, Yan J, Du S. Preparation and characterization of polydopamine/melamine microencapsulated red phosphorus and its flame retardance in epoxy resin. RSC Adv 2021; 11:20391-20402. [PMID: 35479930 PMCID: PMC9034026 DOI: 10.1039/d1ra03164c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/02/2021] [Indexed: 11/21/2022] Open
Abstract
Polydopamine/melamine composite microencapsulated red phosphorus (RP@PDA/MA) was prepared and applied as the flame retardant for epoxy resin (EP) in this work. For comparison, polydopamine (PDA) coated red phosphorus (RP@PDA) was also prepared. The microstructure, chemical composition and thermal decomposition of the as prepared samples were systematically characterized. The results showed that PDA and PDA/MA shell structures were fabricated successfully via convenient water-based processes at room temperature. The flame retardance of red phosphorus (RP), RP@PDA, and RP@PDA/MA on EP was evaluated. The results showed that EP blending with 7 wt% RP@PDA/MA passed V-0 degree in the vertical burning test (UL-94), reached a limited oxygen index (LOI) of 30.9% and decreased the peak heat release rate of EP by 65.1% in the cone calorimeter test. The satisfactory flame retardance can be attributed to the intumescent flame retardant system consisting of RP@PDA/MA. The PDA and PDA/MA shell structures also improved the compatibility between RP and EP, thus RP@PDA and RP@PDA/MA had less significant impact on the tensile-strain properties of EP.
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Affiliation(s)
- Chen Cheng
- Army Engineering University of PLA-Shijiazhuang Campus Shijiazhuang Hebei 050003 P. R. China
| | - Yanling Lu
- Army Engineering University of PLA-Shijiazhuang Campus Shijiazhuang Hebei 050003 P. R. China
| | - Weining Ma
- Army Engineering University of PLA-Shijiazhuang Campus Shijiazhuang Hebei 050003 P. R. China
| | - Shaojie Li
- Army Engineering University of PLA-Shijiazhuang Campus Shijiazhuang Hebei 050003 P. R. China
| | - Jun Yan
- Hebei Jiaotong Vocational and Technical College Shijiazhuang Hebei 050003 P. R. China
| | - Shiguo Du
- Army Engineering University of PLA-Shijiazhuang Campus Shijiazhuang Hebei 050003 P. R. China
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41
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Halliwell JA, Baker D, Judge K, Quail MA, Oliver K, Betteridge E, Skelton J, Andrews PW, Barbaric I. Nanopore Sequencing Indicates That Tandem Amplification of Chromosome 20q11.21 in Human Pluripotent Stem Cells Is Driven by Break-Induced Replication. Stem Cells Dev 2021; 30:578-586. [PMID: 33757297 PMCID: PMC8165465 DOI: 10.1089/scd.2021.0013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Copy number variants (CNVs) are genomic rearrangements implicated in numerous congenital and acquired diseases, including cancer. The appearance of culture-acquired CNVs in human pluripotent stem cells (PSCs) has prompted concerns for their use in regenerative medicine. A particular problem in PSC is the frequent occurrence of CNVs in the q11.21 region of chromosome 20. However, the exact mechanism of origin of this amplicon remains elusive due to the difficulty in delineating its sequence and breakpoints. Here, we have addressed this problem using long-read Nanopore sequencing of two examples of this CNV, present as duplication and as triplication. In both cases, the CNVs were arranged in a head-to-tail orientation, with microhomology sequences flanking or overlapping the proximal and distal breakpoints. These breakpoint signatures point to a mechanism of microhomology-mediated break-induced replication in CNV formation, with surrounding Alu sequences likely contributing to the instability of this genomic region.
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Affiliation(s)
- Jason A Halliwell
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Duncan Baker
- Sheffield Diagnostic Genetic Services, Sheffield Children's Hospital, Sheffield, United Kingdom
| | - Kim Judge
- Department of Sequencing R & D, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Michael A Quail
- Department of Sequencing R & D, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Karen Oliver
- Department of Sequencing R & D, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Emma Betteridge
- Department of Sequencing R & D, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Jason Skelton
- Department of Sequencing R & D, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Peter W Andrews
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Ivana Barbaric
- Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
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Zhang Z, Liu G, Chen Y, Xue W, Ji Q, Xu Q, Zhang H, Fan G, Huang H, Jiang L, Chen J. Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content. iScience 2021; 24:102219. [PMID: 33748707 PMCID: PMC7961107 DOI: 10.1016/j.isci.2021.102219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/20/2021] [Accepted: 02/18/2021] [Indexed: 01/23/2023] Open
Abstract
In this study, six bacterial isolates with variable GC, including Escherichia coli as mesophilic reference strain, were selected to compare hybrid assembly strategies based on next-generation sequencing (NGS) of short reads, single-tube long-fragment reads (stLFR) sequencing, and Oxford Nanopore Technologies (ONT) sequencing platforms. We obtained the complete genomes using the hybrid assembler Unicycler based on the NGS and ONT reads; others were de novo assembled using NGS, stLFR, and ONT reads by using different strategies. The contiguity, accuracy, completeness, sequencing costs, and DNA material requirements of the investigated strategies were compared systematically. Although all sequencing data could be assembled into accurate whole-genome sequences, the stLFR sequencing data yield a scaffold with more contiguity with more completeness of gene function than NGS sequencing assemblies. Our research provides a low-cost chromosome-level genome assembly strategy for large-scale sequencing of extremophile genomes with different GC contents.
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Affiliation(s)
- Zhidong Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
- Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences/Xinjiang Key Laboratory of Special Environmental Microbiology, Urumqi, Xinjiang 830091, China
| | - Guilin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Yao Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Weizhen Xue
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Qianyue Ji
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Qiwu Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
- School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 211816, China
| | - Ling Jiang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Jianwei Chen
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao 266555, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, Copenhagen 2100, Denmark
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Sui Y, Peng S. A Mechanism Leading to Changes in Copy Number Variations Affected by Transcriptional Level Might Be Involved in Evolution, Embryonic Development, Senescence, and Oncogenesis Mediated by Retrotransposons. Front Cell Dev Biol 2021; 9:618113. [PMID: 33644055 PMCID: PMC7905054 DOI: 10.3389/fcell.2021.618113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/11/2021] [Indexed: 01/05/2023] Open
Abstract
In recent years, more and more evidence has emerged showing that changes in copy number variations (CNVs) correlated with the transcriptional level can be found during evolution, embryonic development, and oncogenesis. However, the underlying mechanisms remain largely unknown. The success of the induced pluripotent stem cell suggests that genome changes could bring about transformations in protein expression and cell status; conversely, genome alterations generated during embryonic development and senescence might also be the result of genome changes. With rapid developments in science and technology, evidence of changes in the genome affected by transcriptional level has gradually been revealed, and a rational and concrete explanation is needed. Given the preference of the HIV-1 genome to insert into transposons of genes with high transcriptional levels, we propose a mechanism based on retrotransposons facilitated by specific pre-mRNA splicing style and homologous recombination (HR) to explain changes in CNVs in the genome. This mechanism is similar to that of the group II intron that originated much earlier. Under this proposed mechanism, CNVs on genome are dynamically and spontaneously extended in a manner that is positively correlated with transcriptional level or contract as the cell divides during evolution, embryonic development, senescence, and oncogenesis, propelling alterations in them. Besides, this mechanism explains several critical puzzles in these processes. From evidence collected to date, it can be deduced that the message contained in genome is not just three-dimensional but will become four-dimensional, carrying more genetic information.
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Affiliation(s)
- Yunpeng Sui
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
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Xu P, Chen Y, Gao M, Chong Z. ClipSV: improving structural variation detection by read extension, spliced alignment and tree-based decision rules. NAR Genom Bioinform 2021; 3:lqab003. [PMID: 33554118 PMCID: PMC7850140 DOI: 10.1093/nargab/lqab003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 12/02/2020] [Accepted: 01/05/2021] [Indexed: 11/14/2022] Open
Abstract
Structural variation (SV), which consists of genomic variation from 50 to millions of base pairs, confers considerable impacts on human diseases, complex traits and evolution. Accurately detecting SV is a fundamental step to characterize the features of individual genomes. Currently, several methods have been proposed to detect SVs using the next-generation sequencing (NGS) platform. However, due to the short length of sequencing reads and the complexity of SV content, the SV-detecting tools are still limited by low sensitivity, especially for insertion detection. In this study, we developed a novel tool, ClipSV, to improve SV discovery. ClipSV utilizes a read extension and spliced alignment approach to overcoming the limitation of read length. By reconstructing long sequences from SV-associated short reads, ClipSV discovers deletions and short insertions from the long sequence alignments. To comprehensively characterize insertions, ClipSV implements tree-based decision rules that can efficiently utilize SV-containing reads. Based on the evaluations of both simulated and real sequencing data, ClipSV exhibited an overall better performance compared to currently popular tools, especially for insertion detection. As NGS platform represents the mainstream sequencing capacity for routine genomic applications, we anticipate ClipSV will serve as an important tool for SV characterization in future genomic studies.
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Affiliation(s)
- Peng Xu
- Department of Genetics, the University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Yu Chen
- Department of Genetics, the University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Min Gao
- Informatics Institute, the University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Zechen Chong
- Department of Genetics, the University of Alabama at Birmingham, Birmingham, AL, 35294, USA
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Kanth S, Nagaraja A, Puttaiahgowda YM. Polymeric approach to combat drug-resistant methicillin-resistant Staphylococcus aureus. JOURNAL OF MATERIALS SCIENCE 2021; 56:7265-7285. [PMID: 33518799 PMCID: PMC7831626 DOI: 10.1007/s10853-021-05776-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/03/2021] [Indexed: 05/10/2023]
Abstract
ABSTRACT The current global death rate has threatened humans due to increase in deadly unknown infections caused by pathogenic microorganisms. On the contrary, the emergence of multidrug-resistant bacteria is also increasing which is leading to elevated lethality rate worldwide. Development of drug-resistant bacteria has become one of the daunting global challenges due to failure in approaching to combat against them. Methicillin-resistant Staphylococcus aureus (MRSA) is one of those drug-resistant bacteria which has led to increase in global mortality rate causing various lethal infections. Polymer synthesis can be one of the significant approaches to combat MRSA by fabricating polymeric coatings to prevent the spread of infections. This review provides last decade information in the development of various polymers against MRSA. GRAPHICAL ABSTRACT
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Affiliation(s)
- Shreya Kanth
- Department of Chemistry, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, 576104 India
| | - Akshatha Nagaraja
- Department of Chemistry, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, 576104 India
| | - Yashoda Malgar Puttaiahgowda
- Department of Chemistry, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, 576104 India
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Godoy VCSMD, Bellucco FT, Colovati M, Oliveira-Junior HRD, Moysés-Oliveira M, Melaragno MI. Copy number variation (CNV) identification, interpretation, and database from Brazilian patients. Genet Mol Biol 2020; 43:e20190218. [PMID: 33306777 PMCID: PMC7783508 DOI: 10.1590/1678-4685-gmb-2019-0218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/25/2020] [Indexed: 11/22/2022] Open
Abstract
Copy number variations (CNVs) constitute an important class of variation in the
human genome and the interpretation of their pathogenicity considering different
frequencies across populations is still a challenge for geneticists. Since the
CNV databases are predominantly composed of European and non-admixed
individuals, and Brazilian genetic constitution is admixed and ethnically
diverse, diagnostic screenings on Brazilian variants are greatly difficulted by
the lack of populational references. We analyzed a clinical sample of 268
Brazilian individuals, including patients with neurodevelopment disorders and/or
congenital malformations. The pathogenicity of CNVs was classified according to
their gene content and overlap with known benign and pathogenic variants. A
total of 1,504 autosomal CNVs (1,207 gains and 297 losses) were classified as
benign (92.9%), likely benign (1.6%), VUS (2.6%), likely pathogenic (0.2%) and
pathogenic (2.7%). Some of the CNVs were recurrent and with frequency increased
in our sample, when compared to populational open resources of structural
variants: 14q32.33, 22q11.22, 1q21.1, and 1p36.32 gains. Thus, these highly
recurrent CNVs classified as likely benign or VUS were considered non-pathogenic
in our Brazilian sample. This study shows the relevance of introducing CNV data
from diverse cohorts to improve on the interpretation of clinical impact of
genomic variations.
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Affiliation(s)
| | - Fernanda Teixeira Bellucco
- Universidade Federal de São Paulo, Departamento de Morfologia e Genética, Disciplina de Genética, São Paulo, SP, Brazil
| | - Mileny Colovati
- Universidade Federal de São Paulo, Departamento de Morfologia e Genética, Disciplina de Genética, São Paulo, SP, Brazil
| | | | - Mariana Moysés-Oliveira
- Universidade Federal de São Paulo, Departamento de Morfologia e Genética, Disciplina de Genética, São Paulo, SP, Brazil
| | - Maria Isabel Melaragno
- Universidade Federal de São Paulo, Departamento de Morfologia e Genética, Disciplina de Genética, São Paulo, SP, Brazil
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47
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Wong KHY, Ma W, Wei CY, Yeh EC, Lin WJ, Wang EHF, Su JP, Hsieh FJ, Kao HJ, Chen HH, Chow SK, Young E, Chu C, Poon A, Yang CF, Lin DS, Hu YF, Wu JY, Lee NC, Hwu WL, Boffelli D, Martin D, Xiao M, Kwok PY. Towards a reference genome that captures global genetic diversity. Nat Commun 2020; 11:5482. [PMID: 33127893 PMCID: PMC7599213 DOI: 10.1038/s41467-020-19311-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 10/08/2020] [Indexed: 02/05/2023] Open
Abstract
The current human reference genome is predominantly derived from a single individual and it does not adequately reflect human genetic diversity. Here, we analyze 338 high-quality human assemblies of genetically divergent human populations to identify missing sequences in the human reference genome with breakpoint resolution. We identify 127,727 recurrent non-reference unique insertions spanning 18,048,877 bp, some of which disrupt exons and known regulatory elements. To improve genome annotations, we linearly integrate these sequences into the chromosomal assemblies and construct a Human Diversity Reference. Leveraging this reference, an average of 402,573 previously unmapped reads can be recovered for a given genome sequenced to ~40X coverage. Transcriptomic diversity among these non-reference sequences can also be directly assessed. We successfully map tens of thousands of previously discarded RNA-Seq reads to this reference and identify transcription evidence in 4781 gene loci, underlining the importance of these non-reference sequences in functional genomics. Our extensive datasets are important advances toward a comprehensive reference representation of global human genetic diversity. The human reference genome does not fully reflect human genetic diversity. Here, the authors analyse 338 human genome assemblies from diverse populations to identify missing sequences, define non-reference unique insertions and construct a Human Diversity Reference.
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Affiliation(s)
- Karen H Y Wong
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Walfred Ma
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Chun-Yu Wei
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Erh-Chan Yeh
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wan-Jia Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Elin H F Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jen-Ping Su
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Feng-Jen Hsieh
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hsiao-Jung Kao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hsiao-Huei Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Stephen K Chow
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Eleanor Young
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Catherine Chu
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Annie Poon
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Chi-Fan Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Dar-Shong Lin
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan.,Department of Medicine, Mackay Medical College, New Taipei, Taiwan
| | - Yu-Feng Hu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Department of Internal Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ni-Chung Lee
- Departments of Pediatrics and Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Wuh-Liang Hwu
- Departments of Pediatrics and Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Dario Boffelli
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA
| | - David Martin
- Children's Hospital Oakland Research Institute, Oakland, CA, 94609, USA
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, 19104, USA.,Institute of Molecular Medicine and Infectious Disease in the School of Medicine, Drexel University, Philadelphia, PA, 19102, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, 94158, USA. .,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan. .,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, 94143, USA. .,Department of Dermatology, University of California, San Francisco, San Francisco, CA, 94115, USA.
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48
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Olawoye IB, Frost SDW, Happi CT. The Bacteria Genome Pipeline (BAGEP): an automated, scalable workflow for bacteria genomes with Snakemake. PeerJ 2020; 8:e10121. [PMID: 33194387 PMCID: PMC7597632 DOI: 10.7717/peerj.10121] [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: 04/29/2020] [Accepted: 09/16/2020] [Indexed: 11/20/2022] Open
Abstract
Next generation sequencing technologies are becoming more accessible and affordable over the years, with entire genome sequences of several pathogens being deciphered in few hours. However, there is the need to analyze multiple genomes within a short time, in order to provide critical information about a pathogen of interest such as drug resistance, mutations and genetic relationship of isolates in an outbreak setting. Many pipelines that currently do this are stand-alone workflows and require huge computational requirements to analyze multiple genomes. We present an automated and scalable pipeline called BAGEP for monomorphic bacteria that performs quality control on FASTQ paired end files, scan reads for contaminants using a taxonomic classifier, maps reads to a reference genome of choice for variant detection, detects antimicrobial resistant (AMR) genes, constructs a phylogenetic tree from core genome alignments and provide interactive short nucleotide polymorphism (SNP) visualization across core genomes in the data set. The objective of our research was to create an easy-to-use pipeline from existing bioinformatics tools that can be deployed on a personal computer. The pipeline was built on the Snakemake framework and utilizes existing tools for each processing step: fastp for quality trimming, snippy for variant calling, Centrifuge for taxonomic classification, Abricate for AMR gene detection, snippy-core for generating whole and core genome alignments, IQ-TREE for phylogenetic tree construction and vcfR for an interactive heatmap visualization which shows SNPs at specific locations across the genomes. BAGEP was successfully tested and validated with Mycobacterium tuberculosis (n = 20) and Salmonella enterica serovar Typhi (n = 20) genomes which are about 4.4 million and 4.8 million base pairs, respectively. Running these test data on a 8 GB RAM, 2.5 GHz quad core laptop took 122 and 61 minutes on respective data sets to complete the analysis. BAGEP is a fast, calls accurate SNPs and an easy to run pipeline that can be executed on a mid-range laptop; it is freely available on: https://github.com/idolawoye/BAGEP.
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Affiliation(s)
- Idowu B Olawoye
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Simon D W Frost
- Microsoft Research, Redmond, WA, USA.,London School of Hygiene & Tropical Medicine, University of London, London, United Kingdom
| | - Christian T Happi
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.,African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
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49
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Fan L, Wu J, Wu Y, Shi X, Xin X, Li S, Zeng W, Deng D, Feng L, Chen S, Xiao J. Analysis of Chromosomal Copy Number in First-Trimester Pregnancy Loss Using Next-Generation Sequencing. Front Genet 2020; 11:545856. [PMID: 33193619 PMCID: PMC7606984 DOI: 10.3389/fgene.2020.545856] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 09/22/2020] [Indexed: 01/01/2023] Open
Abstract
Embryonic chromosomal abnormality is one of the significant causative factors of early pregnancy loss. Our goal was to evaluate the clinical utility of next-generation sequencing (NGS) technology in identifying chromosomal anomalies associated with first-trimester pregnancy loss. In addition, we attempted to provide fertility guidance to couples anticipating a successful pregnancy. A total of 1,010 miscarriage specimens were collected between March 2016 and January 2019 from women who suffered first-trimester pregnancy loss. Total DNA was isolated from products of conception, and NGS analysis was carried out. We detected a total of 634 cases of chromosomal variants. Among the 634 cases, 462 (72.9%) displayed numerical variants including 383 (60.4%) aneuploidies, 44 (6.9%) polyploidies, and 34 (5.5%) mosaicisms. The other 172 (27.1%) cases showed structural variants including 19 (3.0%) benign copy number variations (CNVs), 52 (8.2%) pathogenic CNVs, and 101 (16%) variants of unknown significance (VOUS) CNVs. When maternal age was ≥ 35 years, the sporadic abortion (SA) group showed an increased frequency of chromosomal variants in comparison with the recurrent miscarriage (RM) group (90/121 vs. 64/104). It was evident that the groups with advanced maternal age had a sharply increased frequency of aneuploidy, whatever the frequency of pregnancy loss (71/121 vs. 155/432, 49/104 vs. 108/349). Our data suggest that NGS could be used for the successful detection of genetic anomalies in pregnancy loss. We recommend that fetal chromosome analysis be offered routinely for all pregnancy losses, regardless of their frequency.
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Affiliation(s)
- Lei Fan
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianli Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuanyuan Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinwei Shi
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xing Xin
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shufang Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wanjiang Zeng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dongrui Deng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ling Feng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Suhua Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juan Xiao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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50
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Guo J, Cao K, Deng C, Li Y, Zhu G, Fang W, Chen C, Wang X, Wu J, Guan L, Wu S, Guo W, Yao JL, Fei Z, Wang L. An integrated peach genome structural variation map uncovers genes associated with fruit traits. Genome Biol 2020; 21:258. [PMID: 33023652 PMCID: PMC7539501 DOI: 10.1186/s13059-020-02169-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/23/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Genome structural variations (SVs) have been associated with key traits in a wide range of agronomically important species; however, SV profiles of peach and their functional impacts remain largely unexplored. RESULTS Here, we present an integrated map of 202,273 SVs from 336 peach genomes. A substantial number of SVs have been selected during peach domestication and improvement, which together affect 2268 genes. Genome-wide association studies of 26 agronomic traits using these SVs identify a number of candidate causal variants. A 9-bp insertion in Prupe.4G186800, which encodes a NAC transcription factor, is shown to be associated with early fruit maturity, and a 487-bp deletion in the promoter of PpMYB10.1 is associated with flesh color around the stone. In addition, a 1.67 Mb inversion is highly associated with fruit shape, and a gene adjacent to the inversion breakpoint, PpOFP1, regulates flat shape formation. CONCLUSIONS The integrated peach SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in peach.
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Affiliation(s)
- Jian Guo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Ke Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Cecilia Deng
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Yong Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Gengrui Zhu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Weichao Fang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Changwen Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Xinwei Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Jinlong Wu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Liping Guan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Shan Wu
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA
| | - Wenwu Guo
- College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Jia-Long Yao
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand.
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA.
- US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA.
| | - Lirong Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China.
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