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Lotfizadeh F, Masoudi AA, Vaez Torshizi R, Emrani H. Genome-wide association study of copy number variations with shank traits in a F 2 crossbred chicken population. Anim Genet 2024; 55:559-574. [PMID: 38764135 DOI: 10.1111/age.13447] [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: 10/02/2023] [Revised: 04/21/2024] [Accepted: 05/02/2024] [Indexed: 05/21/2024]
Abstract
Copy number variations (CNVs) are large-scale changes in the DNA sequence that can affect the genetic structure and phenotype of an organism. The purpose of this study was to investigate the existing CNVs and their associations with the shank diameter (ShD) and shank length (ShL) traits using data from an F2 crossbred chicken population. To carry out the study, 312 chickens were genotyped using the Illumina 60k SNP Beadchip. The shank traits of the birds were measured from day 1 to 12 weeks of age. penncnv and cnvruler tools were used to find copy numbers and regions with copy number changes (CNVR), respectively. The CNVRanger package was used to perform a genome-wide association study between shank traits and CNVs. Gene ontology research in CNVRs was carried out using the david database. In this investigation, 966 CNVs and 606 regions with copy number changes were discovered. The copy number states and variations were randomly distributed along the length of the autosomal chromosomes. Weeks 1-4, 9 and 12 of growth revealed a significant association of copy number variations with shank traits, false discovery rate (FDR-corrected p-value < 0.01), and the majority of CNVs that were statistically significant were found on chromosomes 1-3. These CNV segments are nearby genes such as KCNJ12, FGF6 and MYF5, which are fundamental to growth and development. In addition, gene set analyses revealed terms related to muscle physiology, regulation of cellular processes and potassium channels.
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Affiliation(s)
- Fateme Lotfizadeh
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Ali Akbar Masoudi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Rasoul Vaez Torshizi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Hossein Emrani
- Animal Science Research Institute of Iran, Agricultural Research, Education and Extension Organization, Karaj, Iran
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2
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Rodriguez-Gil JL, Nagy PL, Francke U. Optical genome mapping with genome sequencing identifies subtelomeric Xq28 deletion and inserted 7p22.3 duplication in a male with multisystem developmental disorder. Am J Med Genet A 2024:e63814. [PMID: 39011850 DOI: 10.1002/ajmg.a.63814] [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: 11/01/2023] [Revised: 03/24/2024] [Accepted: 06/27/2024] [Indexed: 07/17/2024]
Abstract
We report a 17-year-old male with supravalvular stenosis, initial failure to thrive and delayed early development, short stature, acromelia, dysmorphic facial features, hypertelorism, macrocephaly, syringomyelia, hypertension, and anxiety disorder. Fluorescent in situ hybridization (FISH), chromosomal microarray analysis (CMA), and exome sequencing (ES) were nondiagnostic. Combined optical genome mapping (OGM) and genome sequencing (GS) showed a complex rearrangement including an X chromosome with a 22.5 kb deletion in band Xq28 replaced by a 61.4 kb insertion of duplicated chromosome 7p22.3 material. The deletion removes the distal 3' untranslated region (UTR) of FUNDC2, the entire CMC4 and MTCP1, and the first five exons of BRCC3. Transcriptome analysis revealed absent expression of CMC4 and MTCP1 and BRCC3 with normal transcript level of FUNDC2. The inserted duplication includes only one known gene: UNCX. Similar overlapping Xq28 deletions have been reported to be associated with Moyamoya disease (MMD), short stature, hypergonadotropic hypogonadism (HH), and facial dysmorphism. Although he has short stature, our patient does not have signs of Moyamoya arteriopathy or hypogonadism. The structurally abnormal X chromosome was present in his mother, but not in his unaffected brother, maternal uncle, or maternal grandparents. We propose that the combination of his absent Xq28 and duplicated 7p22.3 genomic material is responsible for his phenotype. This case highlights the potential of combined OGM and GS for detecting complex structural variants compared with standard of care genetic testing such as CMA and ES.
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Affiliation(s)
- Jorge L Rodriguez-Gil
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, California, USA
- Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University, Stanford, California, USA
| | | | - Uta Francke
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, California, USA
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3
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Ng GYQ, Hande MP. Use of peptide nucleic acid probe to determine telomere dynamics in improving chromosome analysis in genetic toxicology studies. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2024; 897:503773. [PMID: 39054004 DOI: 10.1016/j.mrgentox.2024.503773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/01/2024] [Accepted: 05/22/2024] [Indexed: 07/27/2024]
Abstract
Genetic toxicology, strategically located at the intersection of genetics and toxicology, aims to demystify the complex interplay between exogenous agents and our genetic blueprint. Telomeres, the protective termini of chromosomes, play instrumental roles in cellular longevity and genetic stability. Traditionally karyotyping and fluorescence in situ hybridisation (FISH), have been indispensable tools for chromosomal analysis following exposure to genotoxic agents. However, their scope in discerning nuanced molecular dynamics is limited. Peptide Nucleic Acids (PNAs) are synthetic entities that embody characteristics of both proteins and nucleic acids and have emerged as potential game-changers. This perspective report comprehensively examines the vast potential of PNAs in genetic toxicology, with a specific emphasis on telomere research. PNAs' superior resolution and precision make them a favourable choice for genetic toxicological assessments. The integration of PNAs in contemporary analytical workflows heralds a promising evolution in genetic toxicology, potentially revolutionizing diagnostics, prognostics, and therapeutic avenues. In this timely review, we attempted to assess the limitations of current PNA-FISH methodology and recommend refinements.
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Affiliation(s)
- Gavin Yong Quan Ng
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Manoor Prakash Hande
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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Dakal TC, Dhabhai B, Pant A, Moar K, Chaudhary K, Yadav V, Ranga V, Sharma NK, Kumar A, Maurya PK, Maciaczyk J, Schmidt‐Wolf IGH, Sharma A. Oncogenes and tumor suppressor genes: functions and roles in cancers. MedComm (Beijing) 2024; 5:e582. [PMID: 38827026 PMCID: PMC11141506 DOI: 10.1002/mco2.582] [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: 09/18/2023] [Revised: 04/21/2024] [Accepted: 04/26/2024] [Indexed: 06/04/2024] Open
Abstract
Cancer, being the most formidable ailment, has had a profound impact on the human health. The disease is primarily associated with genetic mutations that impact oncogenes and tumor suppressor genes (TSGs). Recently, growing evidence have shown that X-linked TSGs have specific role in cancer progression and metastasis as well. Interestingly, our genome harbors around substantial portion of genes that function as tumor suppressors, and the X chromosome alone harbors a considerable number of TSGs. The scenario becomes even more compelling as X-linked TSGs are adaptive to key epigenetic processes such as X chromosome inactivation. Therefore, delineating the new paradigm related to X-linked TSGs, for instance, their crosstalk with autosome and involvement in cancer initiation, progression, and metastasis becomes utmost importance. Considering this, herein, we present a comprehensive discussion of X-linked TSG dysregulation in various cancers as a consequence of genetic variations and epigenetic alterations. In addition, the dynamic role of X-linked TSGs in sex chromosome-autosome crosstalk in cancer genome remodeling is being explored thoroughly. Besides, the functional roles of ncRNAs, role of X-linked TSG in immunomodulation and in gender-based cancer disparities has also been highlighted. Overall, the focal idea of the present article is to recapitulate the findings on X-linked TSG regulation in the cancer landscape and to redefine their role toward improving cancer treatment strategies.
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Affiliation(s)
- Tikam Chand Dakal
- Department of BiotechnologyGenome and Computational Biology LabMohanlal Sukhadia UniversityUdaipurRajasthanIndia
| | - Bhanupriya Dhabhai
- Department of BiotechnologyGenome and Computational Biology LabMohanlal Sukhadia UniversityUdaipurRajasthanIndia
| | - Anuja Pant
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Kareena Moar
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Kanika Chaudhary
- School of Life Sciences. Jawaharlal Nehru UniversityNew DelhiIndia
| | - Vikas Yadav
- School of Life Sciences. Jawaharlal Nehru UniversityNew DelhiIndia
| | - Vipin Ranga
- Dearptment of Agricultural BiotechnologyDBT‐NECAB, Assam Agricultural UniversityJorhatAssamIndia
| | | | - Abhishek Kumar
- Manipal Academy of Higher EducationManipalKarnatakaIndia
- Institute of Bioinformatics, International Technology ParkBangaloreIndia
| | - Pawan Kumar Maurya
- Department of BiochemistryCentral University of HaryanaMahendergarhHaryanaIndia
| | - Jarek Maciaczyk
- Department of Stereotactic and Functional NeurosurgeryUniversity Hospital of BonnBonnGermany
| | - Ingo G. H. Schmidt‐Wolf
- Department of Integrated OncologyCenter for Integrated Oncology (CIO)University Hospital BonnBonnGermany
| | - Amit Sharma
- Department of Stereotactic and Functional NeurosurgeryUniversity Hospital of BonnBonnGermany
- Department of Integrated OncologyCenter for Integrated Oncology (CIO)University Hospital BonnBonnGermany
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Porubsky D, Eichler EE. A 25-year odyssey of genomic technology advances and structural variant discovery. Cell 2024; 187:1024-1037. [PMID: 38290514 DOI: 10.1016/j.cell.2024.01.002] [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: 10/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 02/01/2024]
Abstract
This perspective focuses on advances in genome technology over the last 25 years and their impact on germline variant discovery within the field of human genetics. The field has witnessed tremendous technological advances from microarrays to short-read sequencing and now long-read sequencing. Each technology has provided genome-wide access to different classes of human genetic variation. We are now on the verge of comprehensive variant detection of all forms of variation for the first time with a single assay. We predict that this transition will further transform our understanding of human health and biology and, more importantly, provide novel insights into the dynamic mutational processes shaping our genomes.
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Affiliation(s)
- David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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Lynch A, Bradford S, Burkard ME. The reckoning of chromosomal instability: past, present, future. Chromosome Res 2024; 32:2. [PMID: 38367036 DOI: 10.1007/s10577-024-09746-y] [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: 01/11/2024] [Revised: 01/11/2024] [Accepted: 01/27/2024] [Indexed: 02/19/2024]
Abstract
Quantitative measures of CIN are crucial to our understanding of its role in cancer. Technological advances have changed the way CIN is quantified, offering increased accuracy and insight. Here, we review measures of CIN through its rise as a field, discuss considerations for its measurement, and look forward to future quantification of CIN.
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Affiliation(s)
- Andrew Lynch
- UW Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI, USA
- Division of Hematology/Oncology, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Shermineh Bradford
- UW Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI, USA
- Division of Hematology/Oncology, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Mark E Burkard
- UW Carbone Cancer Center, University of Wisconsin, Madison, WI, USA.
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI, USA.
- Division of Hematology/Oncology, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA.
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Yang S, Ning C, Yang C, Li W, Zhang Q, Wang D, Tang H. Identify Candidate Genes Associated with the Weight and Egg Quality Traits in Wenshui Green Shell-Laying Chickens by the Copy Number Variation-Based Genome-Wide Association Study. Vet Sci 2024; 11:76. [PMID: 38393094 PMCID: PMC10892766 DOI: 10.3390/vetsci11020076] [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: 12/18/2023] [Revised: 02/03/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Copy number variation (CNV), as an essential source of genetic variation, can have an impact on gene expression, genetic diversity, disease susceptibility, and species evolution in animals. To better understand the weight and egg quality traits of chickens, this paper aimed to detect CNVs in Wenshui green shell-laying chickens and conduct a copy number variation regions (CNVRs)-based genome-wide association study (GWAS) to identify variants and candidate genes associated with their weight and egg quality traits to support related breeding efforts. In our paper, we identified 11,035 CNVRs in Wenshui green shell-laying chickens, which collectively spanned a length of 13.1 Mb, representing approximately 1.4% of its autosomal genome. Out of these CNVRs, there were 10,446 loss types, 491 gain types, and 98 mixed types. Notably, two CNVRs showed significant correlations with egg quality, while four CNVRs exhibited significant associations with body weight. These significant CNVRs are located on chromosome 4. Further analysis identified potential candidate genes that influence weight and egg quality traits, including FAM184B, MED28, LAP3, ATOH8, ST3GAL5, LDB2, and SORCS2. In this paper, the CNV map of the Wenshui green shell-laying chicken genome was constructed for the first time through population genotyping. Additionally, CNVRs can be employed as molecular markers to genetically improve chickens' weight and egg quality traits.
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Affiliation(s)
- Suozhou Yang
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
| | - Chao Ning
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
| | - Cheng Yang
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
| | - Wenqiang Li
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
- College of Animal Science and Technology, China Agricultural University, Beijing 100083, China
| | - Dan Wang
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
| | - Hui Tang
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China; (S.Y.); (C.N.); (C.Y.); (W.L.)
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai’an 271018, China;
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Ye JC, Tang G. Optical Genome Mapping: A Machine-Based Platform in Cytogenomics. Methods Mol Biol 2024; 2825:113-124. [PMID: 38913305 DOI: 10.1007/978-1-0716-3946-7_5] [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] [Indexed: 06/25/2024]
Abstract
Optical genome mapping (OGM) has generated excitement following decades of research and development. Now, commercially available technical platforms have been used to compare various other cytogenetic and cytogenomic technologies, including karyotype, microarrays, and DNA sequencing, with impressive results. In this chapter, using OGM as a case study, we advocate for a new trend in future cytogenomics, emphasizing the power of machine automation to deliver higher-quality cytogenomic data. By briefly discussing OGM, along with its major advantages and limitations, we underscore the importance of karyotype-based genomic research, from both a theoretical framework and a new technology perspective. We also call for the encouragement of further technological platform development for the future of cytogenetics and cytogenomics.
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Affiliation(s)
- Jing Christine Ye
- Department of Lymphoma/Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Guilin Tang
- Department of Hematopathology, Division of Pathology-Lab Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Feliciello G, Czyz ZT, Polzer BM. Array-Based Comparative Genomic Hybridization for the Detection of Copy Number Alterations in Single Cells. Methods Mol Biol 2024; 2752:167-187. [PMID: 38194034 DOI: 10.1007/978-1-0716-3621-3_11] [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] [Indexed: 01/10/2024]
Abstract
Comprehensive genome-wide analyses of single cells represent an important tool for clinical applications, such as pre-implantation diagnostic and prenatal diagnosis, as well as for cancer research purpose. For the latter, studies of tumor heterogeneity, circulating tumor cells (CTCs), and disseminated cancer cells (DCCs) require the analysis of single-cell genomes. Here we describe a reliable and robust array-based comparative genomic hybridization (aCGH) protocol based on Ampli 1™ whole genome amplification that allows the detection of copy number alterations (CNAs) in single cancer cells as small as 100 kb.
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Affiliation(s)
- Giancarlo Feliciello
- Cellular and Molecular Diagnostics Group, Division of Personalized Cancer Therapy, Fraunhofer Institute of Toxicology and Experimental Medicine ITEM-R, Regensburg, Germany.
| | - Zbigniew Tadeusz Czyz
- Experimental Medicine and Therapy Research, University Regensburg, Regensburg, Germany
| | - Bernhard M Polzer
- Cellular and Molecular Diagnostics Group, Division of Personalized Cancer Therapy, Fraunhofer Institute of Toxicology and Experimental Medicine ITEM-R, Regensburg, Germany
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Wu C, Maegawa GHB, Zhang H. Integrating whole-genome sequencing and transcriptomic findings in the diagnosis and management of Coffin-Siris syndrome. Brain Dev 2023; 45:495-504. [PMID: 37302973 DOI: 10.1016/j.braindev.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/15/2023] [Accepted: 05/28/2023] [Indexed: 06/13/2023]
Abstract
INTRODUCTION Although the whole-exome sequencing (WES) approach has been widely used in clinic, many rare diseases with syndromic and nonsyndromic neurological manifestations remain undiagnosed. Coffin-Siris syndrome (CSS) is a rare autosomal dominant genetic disease characterized by neurodevelopmental delay. A suspected diagnosis can be made based on the typical CSS clinical features; however, molecular genetic testing is necessary for a confirmed diagnosis. OBJECTIVES Three CSS-like patients with negative results in the WES and chromosomal microarray analysis (CMA) were recruited in this study. METHODS We used whole-genome sequencing (WGS) technology to sequence the peripheral blood of the three families. To further explore the possible pathogenesis of CSS, we performed RNA-sequencing (RNA-seq). RESULTS WGS identified the three CSS patients were carrying de novo copy number variants of the ARID1B gene, which have not been reported before. RNA-seq identified 184 differentially expressed genes (DEGs), with 116 up-regulated and 68 down-regulated. Functional annotation of DEGs showed that two biological processes (immune response, chemokine activity) and two signaling pathways (cytokine-cytokine receptor interaction, chemokine activity) were highlighted. We speculated that ARID1B deficiency might trigger abnormal immune responses, which may be involved in the pathophysiologic mechanisms of CSS. CONCLUSION Our research provided further support for WGS application in CSS diagnosis and made an investigational approach for the underlying mechanisms of CSS.
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Affiliation(s)
- Chenchen Wu
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Gustavo H B Maegawa
- Department of Pediatrics Columbia, University Irving Medical Center, New York-Presbyterian Morgan Stanley Children's Hospital, 622 West 168th Street, PH 17W/PH 11W, New York, NY 10032, United States
| | - Huiwen Zhang
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China.
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Tendi EA, Morello G, Guarnaccia M, La Cognata V, Petralia S, Messina MA, Meli C, Fiumara A, Ruggieri M, Cavallaro S. Detection of Single-Nucleotide and Copy Number Defects Underlying Hyperphenylalaninemia by Next-Generation Sequencing. Biomedicines 2023; 11:1899. [PMID: 37509538 PMCID: PMC10377317 DOI: 10.3390/biomedicines11071899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Hyperphenylalaninemia (HPA) is the most common inherited amino acid metabolism disorder characterized by serious clinical manifestations, including irreversible brain damage, intellectual deficiency and epilepsy. Due to its extensive genic and allelic heterogeneity, next-generation sequencing (NGS) technology may help to identify the molecular basis of this genetic disease. Herein, we describe the development and validation of a targeted NGS (tNGS) approach for the simultaneous detection of single-nucleotide changes and copy number variations (CNVs) in genes associated with HPA (PAH, GCH1, PTS, QDPR, PCBD1, DNAJC12) or useful for its differential diagnosis (SPR). Our tNGS approach offers the possibility to detail, with a high accuracy and in a single workflow, the combined effect of a broader spectrum of genomic variants in a comprehensive view, providing a significant step forward in the development of optimized patient care and management.
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Affiliation(s)
- Elisabetta Anna Tendi
- Biomedical Sciences Department, Institute for Biomedical Research and Innovation, National Research Council, Via Paolo Gaifami 18, 95026 Catania, Italy
| | - Giovanna Morello
- Biomedical Sciences Department, Institute for Biomedical Research and Innovation, National Research Council, Via Paolo Gaifami 18, 95026 Catania, Italy
| | - Maria Guarnaccia
- Biomedical Sciences Department, Institute for Biomedical Research and Innovation, National Research Council, Via Paolo Gaifami 18, 95026 Catania, Italy
| | - Valentina La Cognata
- Biomedical Sciences Department, Institute for Biomedical Research and Innovation, National Research Council, Via Paolo Gaifami 18, 95026 Catania, Italy
| | - Salvatore Petralia
- Department of Drug and Health Sciences, University of Catania, 95125 Catania, Italy
| | - Maria Anna Messina
- Regional Reference Center for the Treatment and Control of Congenital Metabolic Diseases of Childhood, Department of Clinical and Experimental Medicine, University Hospital Policlinico "Rodolico-San Marco", 95123 Catania, Italy
| | - Concetta Meli
- Regional Reference Center for the Treatment and Control of Congenital Metabolic Diseases of Childhood, Department of Clinical and Experimental Medicine, University Hospital Policlinico "Rodolico-San Marco", 95123 Catania, Italy
| | - Agata Fiumara
- Regional Reference Center for the Treatment and Control of Congenital Metabolic Diseases of Childhood, Department of Clinical and Experimental Medicine, University Hospital Policlinico "Rodolico-San Marco", 95123 Catania, Italy
| | - Martino Ruggieri
- Unit of Rare Diseases of the Nervous System in Childhood, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University Hospital Policlinico "Rodolico-San Marco", 95123 Catania, Italy
| | - Sebastiano Cavallaro
- Biomedical Sciences Department, Institute for Biomedical Research and Innovation, National Research Council, Via Paolo Gaifami 18, 95026 Catania, Italy
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Dyhr JJ, Linderoth IR, Hansen DN, Frøkjaer JB, Peters DA, Sinding M, Sørensen A. Confined placental mosaicism: placental size and function evaluated on magnetic resonance imaging. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2023; 62:130-136. [PMID: 36730148 DOI: 10.1002/uog.26174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
OBJECTIVES Evidence regarding placental function in pregnancies complicated by confined placental mosaicism (CPM) is conflicting. We aimed to compare placental function between CPM and non-CPM pregnancies prenatally and at birth. A secondary objective was to evaluate the relationship between placental function and chromosomal subtype of CPM. METHODS This was a retrospective study of pregnancies with CPM and control pregnancies delivered at a tertiary hospital in Denmark between 2014 and 2017. Placental volume and placental transverse relaxation time (T2*) were estimated on magnetic resonance imaging (MRI), fetal weight and uterine artery pulsatility index (UtA-PI) were estimated on ultrasound and fetoplacental ratio was assessed on MRI and at birth. These estimates of placental function were adjusted for gestational age and compared between groups using the Wilcoxon rank-sum test. Within the group of CPM pregnancies, measures of placental function were compared between those at high risk (chromosome numbers 2, 3, 7, 13 and 16) and those at low risk (chromosome numbers 5, 18 and 45X). RESULTS A total of 90 pregnancies were included, of which 12 had CPM and 78 were controls. MRI and ultrasound examinations were performed at a median gestational age of 32.6 weeks (interquartile range, 24.7-35.3 weeks). On MRI assessment, CPM placentae were characterized by a lower placental T2* Z-score (P = 0.004), a lower fetoplacental ratio (P = 0.03) and a higher UtA-PI Z-score (P = 0.03), compared with non-CPM placentae. At birth, the fetoplacental ratio was significantly lower (P = 0.02) and placental weight Z-score was higher (P = 0.01) in CPM pregnancies compared with non-CPM pregnancies. High-risk CPM pregnancies showed a reduced placental T2* Z-score (P = 0.003), lower birth-weight Z-score (P = 0.041), earlier gestational age at delivery (P = 0.019) and higher UtA-PI Z-score (P = 0.028) compared with low-risk CPM pregnancies. Low-risk CPM pregnancies did not differ in any of these parameters from non-CPM pregnancies. CONCLUSIONS CPM pregnancies are characterized by an enlarged and dysfunctional placenta. Placental function was highly related to the chromosomal type of CPM; placental dysfunction was seen predominantly in high-risk CPM pregnancies in which chromosomes 2, 3, 7, 13 or 16 were involved. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- J J Dyhr
- Department of Obstetrics and Gynecology, Aalborg University Hospital, Aalborg, Denmark
| | - I R Linderoth
- Department of Obstetrics and Gynecology, Aalborg University Hospital, Aalborg, Denmark
| | - D N Hansen
- Department of Obstetrics and Gynecology, Aalborg University Hospital, Aalborg, Denmark
| | - J B Frøkjaer
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Radiology, Aalborg University Hospital, Aalborg, Denmark
| | - D A Peters
- Department of Clinical Engineering, Central Denmark Region, Aarhus, Denmark
| | - M Sinding
- Department of Obstetrics and Gynecology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - A Sørensen
- Department of Obstetrics and Gynecology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
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13
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Wan Mohamad Zamri WN, Mohd Yunus N, Abdul Aziz AA, Zulkipli NN, Sulong S. Perspectives on the Application of Cytogenomic Approaches in Chronic Lymphocytic Leukaemia. Diagnostics (Basel) 2023; 13:964. [PMID: 36900108 PMCID: PMC10001075 DOI: 10.3390/diagnostics13050964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/12/2023] [Accepted: 02/15/2023] [Indexed: 03/06/2023] Open
Abstract
Chronic lymphocytic leukaemia (CLL) is a haematological malignancy characterised by the accumulation of monoclonal mature B lymphocytes (positive for CD5+ and CD23+) in peripheral blood, bone marrow, and lymph nodes. Although CLL is reported to be rare in Asian countries compared to Western countries, the disease course is more aggressive in Asian countries than in their Western counterparts. It has been postulated that this is due to genetic variants between populations. Various cytogenomic methods, either of the traditional type (conventional cytogenetics or fluorescence in situ hybridisation (FISH)) or using more advanced technology such as DNA microarrays, next generation sequencing (NGS), or genome wide association studies (GWAS), were used to detect chromosomal aberrations in CLL. Up until now, conventional cytogenetic analysis remained the gold standard in diagnosing chromosomal abnormality in haematological malignancy including CLL, even though it is tedious and time-consuming. In concordance with technological advancement, DNA microarrays are gaining popularity among clinicians as they are faster and better able to accurately diagnose the presence of chromosomal abnormalities. However, every technology has challenges to overcome. In this review, CLL and its genetic abnormalities will be discussed, as well as the application of microarray technology as a diagnostic platform.
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Affiliation(s)
| | - Nazihah Mohd Yunus
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Ahmad Aizat Abdul Aziz
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
| | - Ninie Nadia Zulkipli
- School of Biomedicine, Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Kuala Terengganu 21300, Malaysia
| | - Sarina Sulong
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia
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14
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Heng E, Thanedar S, Heng HH. Challenges and Opportunities for Clinical Cytogenetics in the 21st Century. Genes (Basel) 2023; 14:493. [PMID: 36833419 PMCID: PMC9956237 DOI: 10.3390/genes14020493] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
The powerful utilities of current DNA sequencing technology question the value of developing clinical cytogenetics any further. By briefly reviewing the historical and current challenges of cytogenetics, the new conceptual and technological platform of the 21st century clinical cytogenetics is presented. Particularly, the genome architecture theory (GAT) has been used as a new framework to emphasize the importance of clinical cytogenetics in the genomic era, as karyotype dynamics play a central role in information-based genomics and genome-based macroevolution. Furthermore, many diseases can be linked to elevated levels of genomic variations within a given environment. With karyotype coding in mind, new opportunities for clinical cytogenetics are discussed to integrate genomics back into cytogenetics, as karyotypic context represents a new type of genomic information that organizes gene interactions. The proposed research frontiers include: 1. focusing on karyotypic heterogeneity (e.g., classifying non-clonal chromosome aberrations (NCCAs), studying mosaicism, heteromorphism, and nuclear architecture alteration-mediated diseases), 2. monitoring the process of somatic evolution by characterizing genome instability and illustrating the relationship between stress, karyotype dynamics, and diseases, and 3. developing methods to integrate genomic data and cytogenomics. We hope that these perspectives can trigger further discussion beyond traditional chromosomal analyses. Future clinical cytogenetics should profile chromosome instability-mediated somatic evolution, as well as the degree of non-clonal chromosomal aberrations that monitor the genomic system's stress response. Using this platform, many common and complex disease conditions, including the aging process, can be effectively and tangibly monitored for health benefits.
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Affiliation(s)
- Eric Heng
- Stanford University, 450 Jane Stanford Way, Stanford, CA 94305, USA
| | - Sanjana Thanedar
- Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Henry H. Heng
- Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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15
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Abstract
Over the past decade, advances in plant genotyping have been critical in enabling the identification of genetic diversity, in understanding evolution, and in dissecting important traits in both crops and native plants. The widespread popularity of single-nucleotide polymorphisms (SNPs) has prompted significant improvements to SNP-based genotyping, including SNP arrays, genotyping by sequencing, and whole-genome resequencing. More recent approaches, including genotyping structural variants, utilizing pangenomes to capture species-wide genetic diversity and exploiting machine learning to analyze genotypic data sets, are pushing the boundaries of what plant genotyping can offer. In this chapter, we highlight these innovations and discuss how they will accelerate and advance future genotyping efforts.
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16
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Dashnau JL, Xue Q, Nelson M, Law E, Cao L, Hei D. A risk-based approach for cell line development, manufacturing and characterization of genetically engineered, induced pluripotent stem cell-derived allogeneic cell therapies. Cytotherapy 2023; 25:1-13. [PMID: 36109321 DOI: 10.1016/j.jcyt.2022.08.001] [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: 04/04/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 12/27/2022]
Abstract
Advances in cellular reprogramming and gene-editing approaches have opened up the potential for a new class of ex vivo cell therapies based on genetically engineered, induced pluripotent stem cell (iPSC)-derived allogeneic cells. While these new therapies share some similarities with their primary cell-derived autologous and allogeneic cell therapy predecessors, key differences exist in the processes used for generating genetically engineered, iPSC-derived allogeneic therapies. Specifically, in iPSC-derived allogeneic therapies, donor selection and gene-editing are performed once over the lifetime of the product as opposed to as part of the manufacturing of each product batch. The introduction of a well-characterized, fully modified, clonally derived master cell bank reduces risks that have been inherent to primary-cell derived autologous and allogeneic therapies. Current regulatory guidance, which was largely developed based on the learnings gained from earlier generation therapies, leaves open questions around considerations for donor eligibility, starting materials and critical components, cell banking and genetic stability. Here, a risk-based approach is proposed to address these considerations, while regulatory guidance continues to evolve.
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Affiliation(s)
| | - Qiong Xue
- Takeda Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Monica Nelson
- Century Therapeutics, Inc., Philadelphia, Pennsylvania, USA
| | - Eric Law
- Century Therapeutics, Inc., Philadelphia, Pennsylvania, USA
| | - Lan Cao
- Takeda Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Derek Hei
- Clade Therapeutics, One Kendall Square, Cambridge, Massachusetts, USA
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17
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Choosing the Probe for Single-Molecule Fluorescence Microscopy. Int J Mol Sci 2022; 23:ijms232314949. [PMID: 36499276 PMCID: PMC9735909 DOI: 10.3390/ijms232314949] [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: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications.
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18
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Cuenca-Guardiola J, de la Morena-Barrio B, García JL, Sanchis-Juan A, Corral J, Fernández-Breis JT. Improvement of large copy number variant detection by whole genome nanopore sequencing. J Adv Res 2022:S2090-1232(22)00241-7. [PMID: 36323370 PMCID: PMC10403694 DOI: 10.1016/j.jare.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 10/18/2022] [Accepted: 10/22/2022] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION Whole-genome sequencing using nanopore technologies can uncover structural variants, which are DNA rearrangements larger than 50 base pairs. Nanopore technologies can also characterize their boundaries with single-base accuracy, owing to the kilobase-long reads that encompass either full variants or their junctions. Other methods, such as next-generation short read sequencing or PCR assays, are limited in their capabilities to detect or characterize structural variants. However, the existing software for nanopore sequencing data analysis still reports incomplete variant sets, which also contain erroneous calls, a considerable obstacle for the molecular diagnosis or accurate genotyping of populations. METHODS We compared multiple factors affecting variant calling, such as reference genome version, aligner (minimap2, NGMLR, and lra) choice, and variant caller combinations (Sniffles, CuteSV, SVIM, and NanoVar), to find the optimal group of tools for calling large (>50 kb) deletions and duplications, using data from seven patients exhibiting gross gene defects on SERPINC1 and from a reference variant set as the control. The goal was to obtain the most complete, yet reasonably specific group of large variants using a single cell of PromethION sequencing, which yielded lower depth coverage than short-read sequencing. We also used a custom method for the statistical analysis of the coverage value to refine the resulting datasets. RESULTS We found that for large deletions and duplications (>50 kb), the existing software performed worse than for smaller ones, in terms of both sensitivity and specificity, and newer tools had not improved this. Our novel software, disCoverage, could polish variant callers' results, improving specificity by up to 62% and sensitivity by 15%, the latter requiring other data or samples. CONCLUSION We analyzed the current situation of >50-kb copy number variants with nanopore sequencing, which could be improved. The methods presented in this work could help to identify the known deletions and duplications in a set of patients, while also helping to filter out erroneous calls for these variants, which might aid the efforts to characterize a not-yet well-known fraction of genetic variability in the human genome.
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19
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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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20
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Rastorgueva E, Liamina D, Panchenko I, Iurova E, Beloborodov E, Pogodina E, Dmitrii S, Slesarev S, Saenko Y. The effect of chromosome abnormalities on expression of SnoRNA in radioresistant and radiosensitive cell lines after irradiation. Cancer Biomark 2022; 34:545-553. [PMID: 35275519 DOI: 10.3233/cbm-210092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
In this paper, we have studied the role of chromosomal abnormalities in the expression of small nucleolar RNAs (snoRNAs) of radioresistant (K562) and radiosensitive (HL-60) leukemia cell line. Cells were exposed to an X-ray dose of 4 Gy. SnoRNA expression was investigated using NGS sequencing. The distribution of expressed snoRNAs on chromosomes has been found to be different for two cell lines. The most significant differences in the expression of snoRNAs were found in the K562 cell line based on the analysis of the dynamics of log2fc values. The type of clustering, the number and type of snoRNAs slightly differed in the chromosomes with trisomy and monosomy and had a pronounced difference in pairs with marker chromosomes in both cell lines. In this study, we have demonstrated that chromosomal abnormalities alter the expression of snoRNA after irradiation. Trisomies and monosomies do not have such a noticeable effect on the expression of snoRNAs as the presence of marker chromosomes.
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Affiliation(s)
- Eugenia Rastorgueva
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian.,Department of General and Clinical Pharmacology and Microbiology, Faculty of Medicine, Ulyanovsk State University, Ulyanovsk, Russian
| | - Daria Liamina
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
| | - Ivan Panchenko
- Second Surgical Department, Ulyanovsk Oncology Center, Ulyanovsk, Russian
| | - Elena Iurova
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
| | - Evgenii Beloborodov
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
| | - Evgeniya Pogodina
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
| | - Sugak Dmitrii
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
| | - Sergei Slesarev
- Department of Biology, Ecology and Natural Resources Management, Faculty of Ecology, Ulyanovsk State University, Ulyanovsk, Russia
| | - Yury Saenko
- Laboratory of Molecular and Cell Biology, S.P. Kapitsa Research Institute of Technology, Ulyanovsk State University, Ulyanovsk, Russian
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21
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Song P, Wu LR, Yan YH, Zhang JX, Chu T, Kwong LN, Patel AA, Zhang DY. Limitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics. Nat Biomed Eng 2022; 6:232-245. [PMID: 35102279 PMCID: PMC9336539 DOI: 10.1038/s41551-021-00837-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 05/27/2021] [Indexed: 12/15/2022]
Abstract
Cell-free DNA (cfDNA) in the circulating blood plasma of patients with cancer contains tumour-derived DNA sequences that can serve as biomarkers for guiding therapy, for the monitoring of drug resistance, and for the early detection of cancers. However, the analysis of cfDNA for clinical diagnostic applications remains challenging because of the low concentrations of cfDNA, and because cfDNA is fragmented into short lengths and is susceptible to chemical damage. Barcodes of unique molecular identifiers have been implemented to overcome the intrinsic errors of next-generation sequencing, which is the prevailing method for highly multiplexed cfDNA analysis. However, a number of methodological and pre-analytical factors limit the clinical sensitivity of the cfDNA-based detection of cancers from liquid biopsies. In this Review, we describe the state-of-the-art technologies for cfDNA analysis, with emphasis on multiplexing strategies, and discuss outstanding biological and technical challenges that, if addressed, would substantially improve cancer diagnostics and patient care.
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Affiliation(s)
- Ping Song
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Lucia Ruojia Wu
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | | | - Tianqing Chu
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lawrence N Kwong
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
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22
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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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23
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MYCN in Neuroblastoma: "Old Wine into New Wineskins". Diseases 2021; 9:diseases9040078. [PMID: 34842635 PMCID: PMC8628738 DOI: 10.3390/diseases9040078] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
MYCN Proto-Oncogene, BHLH Transcription Factor (MYCN) has been one of the most studied genes in neuroblastoma. It is known for its oncogenetic mechanisms, as well as its role in the prognosis of the disease and it is considered one of the prominent targets for neuroblastoma therapy. In the present work, we attempted to review the literature, on the relation between MYCN and neuroblastoma from all possible mechanistic sites. We have searched the literature for the role of MYCN in neuroblastoma based on the following topics: the references of MYCN in the literature, the gene's anatomy, along with its transcripts, the protein's anatomy, the epigenetic mechanisms regulating MYCN expression and function, as well as MYCN amplification. MYCN plays a significant role in neuroblastoma biology. Its functions and properties range from the forming of G-quadraplexes, to the interaction with miRNAs, as well as the regulation of gene methylation and histone acetylation and deacetylation. Although MYCN is one of the most primary genes studied in neuroblastoma, there is still a lot to be learned. Our knowledge on the exact mechanisms of MYCN amplification, etiology and potential interventions is still limited. The knowledge on the molecular mechanisms of MYCN in neuroblastoma, could have potential prognostic and therapeutic advantages.
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24
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Liehr T. Molecular Cytogenetics in the Era of Chromosomics and Cytogenomic Approaches. Front Genet 2021; 12:720507. [PMID: 34721522 PMCID: PMC8548727 DOI: 10.3389/fgene.2021.720507] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/22/2021] [Indexed: 02/04/2023] Open
Abstract
Here the role of molecular cytogenetics in the context of yet available all other cytogenomic approaches is discussed. A short introduction how cytogenetics and molecular cytogenetics were established is followed by technical aspects of fluorescence in situ hybridization (FISH). The latter contains the methodology itself, the types of probe- and target-DNA, as well as probe sets. The main part deals with examples of modern FISH-applications, highlighting unique possibilities of the approach, like the possibility to study individual cells and even individual chromosomes. Different variants of FISH can be used to retrieve information on genomes from (almost) base pair to whole genomic level, as besides only second and third generation sequencing approaches can do. Here especially highlighted variations of FISH are molecular combing, chromosome orientation-FISH (CO-FISH), telomere-FISH, parental origin determination FISH (POD-FISH), FISH to resolve the nuclear architecture, multicolor-FISH (mFISH) approaches, among other applied in chromoanagenesis studies, Comet-FISH, and CRISPR-mediated FISH-applications. Overall, molecular cytogenetics is far from being outdated and actively involved in up-to-date diagnostics and research.
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Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Jena, Germany
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25
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Atlas G, Sreenivasan R, Sinclair A. Targeting the Non-Coding Genome for the Diagnosis of Disorders of Sex Development. Sex Dev 2021; 15:392-410. [PMID: 34634785 DOI: 10.1159/000519238] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/12/2021] [Indexed: 11/19/2022] Open
Abstract
Disorders of sex development (DSD) are a complex group of conditions with highly variable clinical phenotypes, most often caused by failure of gonadal development. DSD are estimated to occur in around 1.7% of all live births. Whilst the understanding of genes involved in gonad development has increased exponentially, approximately 50% of patients with a DSD remain without a genetic diagnosis, possibly implicating non-coding genomic regions instead. Here, we review how variants in the non-coding genome of DSD patients can be identified using techniques such as array comparative genomic hybridization (CGH) to detect copy number variants (CNVs), and more recently, whole genome sequencing (WGS). Once a CNV in a patient's non-coding genome is identified, putative regulatory elements such as enhancers need to be determined within these vast genomic regions. We will review the available online tools and databases that can be used to refine regions with potential enhancer activity based on chromosomal accessibility, histone modifications, transcription factor binding site analysis, chromatin conformation, and disease association. We will also review the current in vitro and in vivo techniques available to demonstrate the functionality of the identified enhancers. The review concludes with a clinical update on the enhancers linked to DSD.
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Affiliation(s)
- Gabby Atlas
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia, .,Department of Endocrinology and Diabetes, Royal Children's Hospital, Melbourne, Victoria, Australia, .,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia,
| | - Rajini Sreenivasan
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew Sinclair
- Reproductive Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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Critical evaluation of CNA estimators for DNA data using matching confidence masks and WGS technology. Biomed Signal Process Control 2021. [DOI: 10.1016/j.bspc.2021.103004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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27
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de Castro Fonseca M, de Oliveira JF, Araujo BHS, Canateli C, do Prado PFV, Amorim Neto DP, Bosque BP, Rodrigues PV, de Godoy JVP, Tostes K, Filho HVR, Nascimento AFZ, Saito A, Tonoli CCC, Batista FAH, de Oliveira PSL, Figueira AC, Souza da Costa S, Krepischi ACV, Rosenberg C, Westfahl H, da Silva AJR, Franchini KG. Molecular and cellular basis of hyperassembly and protein aggregation driven by a rare pathogenic mutation in DDX3X. iScience 2021; 24:102841. [PMID: 34381968 PMCID: PMC8335631 DOI: 10.1016/j.isci.2021.102841] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/21/2021] [Accepted: 07/08/2021] [Indexed: 12/30/2022] Open
Abstract
Current studies estimate that 1–3% of females with unexplained intellectual disability (ID) present de novo splice site, nonsense, frameshift, or missense mutations in the DDX3X protein (DEAD-Box Helicase 3 X-Linked). However, the cellular and molecular mechanisms by which DDX3X mutations impair brain development are not fully comprehended. Here, we show that the ID-linked missense mutation L556S renders DDX3X prone to aggregation. By using a combination of biophysical assays and imaging approaches, we demonstrate that this mutant assembles solid-like condensates and amyloid-like fibrils. Although we observed greatly reduced expression of the mutant allele in a patient who exhibits skewed X inactivation, this appears to be enough to sequestrate healthy proteins into solid-like ectopic granules, compromising cell function. Therefore, our data suggest ID-linked DDX3X L556S mutation as a disorder arising from protein misfolding and aggregation. DDX3X mutations skew X-inactivation and are found in 1-3% of unexplained ID in females DDX3X mutant proteins assemble solid-like condensates and amyloid-like fibrils Aberrant granules formed by DDX3X mutants sequestrate healthy DDX3X protein ID-linked DDX3X L556S mutation decreases cell viability and induces apoptosis
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Affiliation(s)
- Matheus de Castro Fonseca
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Juliana Ferreira de Oliveira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Bruno Henrique Silva Araujo
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Camila Canateli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Paula Favoretti Vital do Prado
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Dionísio Pedro Amorim Neto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Beatriz Pelegrini Bosque
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Paulla Vieira Rodrigues
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - João Vitor Pereira de Godoy
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Katiane Tostes
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Helder Veras Ribeiro Filho
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Andrey Fabricio Ziem Nascimento
- Brazilian Synchrotron Light National Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Angela Saito
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Celisa Caldana Costa Tonoli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Fernanda Aparecida Heleno Batista
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Paulo Sergio Lopes de Oliveira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Ana Carolina Figueira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil
| | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Harry Westfahl
- Brazilian Synchrotron Light National Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Antônio José Roque da Silva
- Brazilian Synchrotron Light National Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Kleber Gomes Franchini
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 10000 Giuseppe Maximo Scolfaro St., Campinas, São Paulo 13083-100, Brazil.,Department of Internal Medicine, School of Medicine, University of Campinas, Campinas, Brazil
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Zenda T, Liu S, Dong A, Duan H. Advances in Cereal Crop Genomics for Resilience under Climate Change. Life (Basel) 2021; 11:502. [PMID: 34072447 PMCID: PMC8228855 DOI: 10.3390/life11060502] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022] Open
Abstract
Adapting to climate change, providing sufficient human food and nutritional needs, and securing sufficient energy supplies will call for a radical transformation from the current conventional adaptation approaches to more broad-based and transformative alternatives. This entails diversifying the agricultural system and boosting productivity of major cereal crops through development of climate-resilient cultivars that can sustainably maintain higher yields under climate change conditions, expanding our focus to crop wild relatives, and better exploitation of underutilized crop species. This is facilitated by the recent developments in plant genomics, such as advances in genome sequencing, assembly, and annotation, as well as gene editing technologies, which have increased the availability of high-quality reference genomes for various model and non-model plant species. This has necessitated genomics-assisted breeding of crops, including underutilized species, consequently broadening genetic variation of the available germplasm; improving the discovery of novel alleles controlling important agronomic traits; and enhancing creation of new crop cultivars with improved tolerance to biotic and abiotic stresses and superior nutritive quality. Here, therefore, we summarize these recent developments in plant genomics and their application, with particular reference to cereal crops (including underutilized species). Particularly, we discuss genome sequencing approaches, quantitative trait loci (QTL) mapping and genome-wide association (GWAS) studies, directed mutagenesis, plant non-coding RNAs, precise gene editing technologies such as CRISPR-Cas9, and complementation of crop genotyping by crop phenotyping. We then conclude by providing an outlook that, as we step into the future, high-throughput phenotyping, pan-genomics, transposable elements analysis, and machine learning hold much promise for crop improvements related to climate resilience and nutritional superiority.
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Affiliation(s)
- Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Science, Faculty of Agriculture and Environmental Science, Bindura University of Science Education, Bindura P. Bag 1020, Zimbabwe
| | - Songtao Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Anyi Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, China; (S.L.); (A.D.)
- North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, Hebei Agricultural University, Baoding 071001, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
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Fernandes AC, da Silva VH, Goes CP, Moreira GCM, Godoy TF, Ibelli AMG, Peixoto JDO, Cantão ME, Ledur MC, de Rezende FM, Coutinho LL. Genome-wide detection of CNVs and their association with performance traits in broilers. BMC Genomics 2021; 22:354. [PMID: 34001004 PMCID: PMC8130382 DOI: 10.1186/s12864-021-07676-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 05/05/2021] [Indexed: 12/12/2022] Open
Abstract
Background Copy number variations (CNVs) are a major type of structural genomic variants that underlie genetic architecture and phenotypic variation of complex traits, not only in humans, but also in livestock animals. We identified CNVs along the chicken genome and analyzed their association with performance traits. Genome-wide CNVs were inferred from Affymetrix® high density SNP-chip data for a broiler population. CNVs were concatenated into segments and association analyses were performed with linear mixed models considering a genomic relationship matrix, for birth weight, body weight at 21, 35, 41 and 42 days, feed intake from 35 to 41 days, feed conversion ratio from 35 to 41 days and, body weight gain from 35 to 41 days of age. Results We identified 23,214 autosomal CNVs, merged into 5042 distinct CNV regions (CNVRs), covering 12.84% of the chicken autosomal genome. One significant CNV segment was associated with BWG on GGA3 (q-value = 0.00443); one significant CNV segment was associated with BW35 (q-value = 0.00571), BW41 (q-value = 0.00180) and BW42 (q-value = 0.00130) on GGA3, and one significant CNV segment was associated with BW on GGA5 (q-value = 0.00432). All significant CNV segments were verified by qPCR, and a validation rate of 92.59% was observed. These CNV segments are located nearby genes, such as KCNJ11, MyoD1 and SOX6, known to underlie growth and development. Moreover, gene-set analyses revealed terms linked with muscle physiology, cellular processes regulation and potassium channels. Conclusions Overall, this CNV-based GWAS study unravels potential candidate genes that may regulate performance traits in chickens. Our findings provide a foundation for future functional studies on the role of specific genes in regulating performance in chickens. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07676-1.
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Affiliation(s)
- Anna Carolina Fernandes
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - Vinicius Henrique da Silva
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | - Carolina Purcell Goes
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | | | - Thaís Fernanda Godoy
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil
| | | | - Jane de Oliveira Peixoto
- Embrapa Suínos e Aves: Empresa Brasileira de Pesquisa Agropecuária Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | - Maurício Egídio Cantão
- Embrapa Suínos e Aves: Empresa Brasileira de Pesquisa Agropecuária Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | - Mônica Corrêa Ledur
- Embrapa Suínos e Aves: Empresa Brasileira de Pesquisa Agropecuária Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | | | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, 13418-900, Brazil.
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30
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Gao B, Baudis M. Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes. Front Genet 2021; 12:654887. [PMID: 34054918 PMCID: PMC8155688 DOI: 10.3389/fgene.2021.654887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/15/2021] [Indexed: 12/13/2022] Open
Abstract
Copy number aberrations (CNA) are one of the most important classes of genomic mutations related to oncogenetic effects. In the past three decades, a vast amount of CNA data has been generated by molecular-cytogenetic and genome sequencing based methods. While this data has been instrumental in the identification of cancer-related genes and promoted research into the relation between CNA and histo-pathologically defined cancer types, the heterogeneity of source data and derived CNV profiles pose great challenges for data integration and comparative analysis. Furthermore, a majority of existing studies have been focused on the association of CNA to pre-selected "driver" genes with limited application to rare drivers and other genomic elements. In this study, we developed a bioinformatics pipeline to integrate a collection of 44,988 high-quality CNA profiles of high diversity. Using a hybrid model of neural networks and attention algorithm, we generated the CNA signatures of 31 cancer subtypes, depicting the uniqueness of their respective CNA landscapes. Finally, we constructed a multi-label classifier to identify the cancer type and the organ of origin from copy number profiling data. The investigation of the signatures suggested common patterns, not only of physiologically related cancer types but also of clinico-pathologically distant cancer types such as different cancers originating from the neural crest. Further experiments of classification models confirmed the effectiveness of the signatures in distinguishing different cancer types and demonstrated their potential in tumor classification.
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Affiliation(s)
- Bo Gao
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Michael Baudis
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
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31
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Abstract
Non-Hodgkin lymphoma encompasses a diverse group of B-cell and T-cell neoplasms. Current classification is based on clinical information, histologic assessment, immunophenotypic characteristics, and molecular alterations. A wide range of genetic alterations, including large chromosomal structural rearrangements, aneuploidies, point mutations, and copy number alterations, have been reported across all types of lymphomas. Many of these are now incorporated into the World Health Organization-defined criteria for the diagnostic evaluation of patients with lymphoid proliferations and, therefore, their accurate identification is paramount for diagnosis, subclassification, and selection of treatment. In addition to their value in the diagnostic setting, many alterations that are not routinely evaluated in standard clinical practice may still define specific disease entities as they have important implications in risk stratification, as well as roles in emerging alternate therapies and disease monitoring. Because of the complexity and range of alterations, their accurate and sensitive assessment requires a careful selection of technology. Here, we discuss the most commonly used molecular techniques in current clinical practice and highlight some of the benefits and pitfalls based on the type of alteration.
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Le L, Luo J, Wu H, Chen L, Tang X, Fu F. Overexpression of <em>MYBL2</em> predicts poor prognosis and promotes oncogenesis in endometrial carcinoma. Eur J Histochem 2021; 65. [PMID: 33782625 PMCID: PMC8054569 DOI: 10.4081/ejh.2021.3226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 03/20/2021] [Indexed: 11/23/2022] Open
Abstract
Endometrial cancer (EC) is the most common gynecologic malignancy and still remains clinically challenging. We aimed to explore the potential biomarkers of EC and provide a theoretical basis for early screening and targeted therapy. The available transcriptome data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were analyzed to identify differentially expressed genes. Immunohistochemistry was performed to detect gene expression. We analyzed the associations of MYBL2 with clinicopathological features and survival time and the biological effect of MYBL2 on the proliferation of EC cells. The effect of MYBL2 silencing on the transcriptome of EC cell model was analyzed by RNA-Seq. MYBL2 was significantly upregulated with obvious copy number alteration in EC. Copy number amplification significantly increased MYBL2 mRNA expression, which led to a poor prognosis and severe pathological types of EC. Additionally, MYBL2 silencing significantly inhibited proliferation and induced apoptosis and G1-phase cell cycle arrest in EC cell lines. Our results indicate that MYBL2 is closely related to the cell cycle and apoptosis pathways in EC. The findings in this study provide evidence that MYBL2 can serve as a new candidate prognostic marker and a target for future therapeutic intervention in EC.
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Affiliation(s)
- Lulu Le
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province.
| | - Ji Luo
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province.
| | - Haifang Wu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province.
| | - Ling Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province.
| | - Xiaoli Tang
- College of Basic Medical Science, Nanchang University, Nanchang, Jiangxi Province.
| | - Fen Fu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province.
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Liu J, Zhang J. Elevated EXO1 expression is associated with breast carcinogenesis and poor prognosis. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:135. [PMID: 33569437 PMCID: PMC7867906 DOI: 10.21037/atm-20-7922] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background Breast cancer is the most common cancer and leading cause of cancer mortality in women worldwide. Exonuclease 1 (EXO1), a protein with 5' to 3' exonuclease and RNase H activity, could be involved in mismatch repair and recombination. This study aims to investigate the prognostic value of EXO1 in breast cancer and explore the association between EXO1 expression and breast carcinogenesis. Methods The data of 1,215 breast cancer susceptibility gene (BRCA) samples were obtained from The Cancer Genome Atlas (TCGA). Real-time quantitative polymerase chain reaction (RT-qPCR) further verified the elevated mRNA expression level of EXO1 in human BRCA cells MDA-MB231 compared with that in human breast epithelial cells MCF-10A. EXO1 copy number was proved to be correlated with its expression level. Besides, Kaplan-Meier analysis, differentially expressed genes and function enrichment analysis were performed. Results Analysis of data from The Cancer Genome Atlas (TCGA) revealed that the EXO1 expression level in breast cancer tissues was significantly increased. Real-time quantitative polymerase chain reaction (RT-qPCR) supported the elevated mRNA expression level of EXO1 in human breast cancer cells MDA-MB231 compared with that in human breast epithelial cells MCF-10A. EXO1 copy number was shown to be correlated with its expression level. Kaplan-Meier analysis showed that elevated EXO1 was an indicator of poor breast cancer prognosis. Furthermore, differentially expressed genes and function enrichment analysis indicated that the cell cycle pathway and cardiac muscle contraction pathway were activated and inhibited respectively in breast cancer samples with high EXO1 expression. Conclusions Therefore, this study shows that elevated EXO1 expression is associated with carcinogenesis and poor prognosis in breast cancer, and might be a biomarker for breast cancer treatment.
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Affiliation(s)
- Jingjing Liu
- 3rd Department of Breast Cancer, China Tianjin Breast Cancer Prevention, Treatment and Research Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy of Ministry of Education, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Jin Zhang
- 3rd Department of Breast Cancer, China Tianjin Breast Cancer Prevention, Treatment and Research Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy of Ministry of Education, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
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Xavier MJ, Salas-Huetos A, Oud MS, Aston KI, Veltman JA. Disease gene discovery in male infertility: past, present and future. Hum Genet 2021; 140:7-19. [PMID: 32638125 PMCID: PMC7864819 DOI: 10.1007/s00439-020-02202-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/26/2020] [Indexed: 12/13/2022]
Abstract
Identifying the genes causing male infertility is important to increase our biological understanding as well as the diagnostic yield and clinical relevance of genetic testing in this disorder. While significant progress has been made in some areas, mainly in our knowledge of the genes underlying rare qualitative sperm defects, the same cannot be said for the genetics of quantitative sperm defects. Technological advances and approaches in genomics are critical for the process of disease gene identification. In this review we highlight the impact of various technological developments on male infertility gene discovery as well as functional validation, going from the past to the present and the future. In particular, we draw attention to the use of unbiased genomics approaches, the development of increasingly relevant functional assays and the importance of large-scale international collaboration to advance disease gene identification in male infertility.
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Affiliation(s)
- M J Xavier
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - A Salas-Huetos
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah, Salt Lake City, USA
| | - M S Oud
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - K I Aston
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah, Salt Lake City, USA.
| | - J A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK.
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Yin SJ, Lee JR, Hahn MJ, Yang JM, Qian GY, Park YD. Tyrosinase-mediated melanogenesis in melanoma cells: Array comparative genome hybridization integrating proteomics and bioinformatics studies. Int J Biol Macromol 2020; 170:150-163. [PMID: 33359255 DOI: 10.1016/j.ijbiomac.2020.12.146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/17/2022]
Abstract
We investigated the tyrosinase-associated melanogenesis in melanoma cells by using OMICS techniques. We characterized the chromosome copy numbers, including Chr 11q21 where the tyrosinase gene is located, from several melanoma cell lines (TXM13, G361, and SK-MEL-28) by using array CGH. We revealed that 11q21 is stable in TXM13 cells, which is directly related to a spontaneous high melanin pigment production. Meanwhile, significant loss of copy number of 11q21 was found in G361 and SK-MEL-28. We further profiled the proteome of TXM13 cells by LC-ESI-MSMS and detected more than 900 proteins, then predicted 11 hub proteins (YWHAZ; HSP90AA1; HSPA5; HSPA1L; HSPA9; HSP90B1; HSPA1A; HSPA8; FKSG30; ACTB; DKFZp686DQ972) by using an interactomic algorithm. YWHAZ (25% interaction in the network) is thought to be a most important protein as a linking factor between tyrosinase-triggered melanogenesis and melanoma growth. Bioinformatic tools were further applied for revealing various physiologic mechanisms and functional classification. The results revealed clues for the spontaneous pigmentation capability of TXM13 cells, contrary to G361 and SK-MEL-28 cells, which commonly have depigmentation properties during subculture. Our study comparatively conducted the genome-wide screening and proteomic profiling integrated interactomics prediction for TXM13 cells and suggests new insights for studying both melanogenesis and melanoma.
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Affiliation(s)
- Shang-Jun Yin
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jae-Rin Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Myong-Joon Hahn
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Jun-Mo Yang
- Department of Dermatology, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul 135-710, South Korea
| | - Guo-Ying Qian
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China.
| | - Yong-Doo Park
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China; Skin Diseases Research Center, Yangtze Delta Region Institute of Tsinghua University, 705 Yatai Road, Jiaxing 314006, PR China; Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, 705 Yatai Road, Jiaxing 314006, PR China.
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36
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Cho SB. Set-Wise Differential Interaction Between Copy Number Alterations and Gene Expressions of Lower-Grade Glioma Reveals Prognosis-Associated Pathways. ENTROPY 2020; 22:e22121434. [PMID: 33353229 PMCID: PMC7765960 DOI: 10.3390/e22121434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/30/2020] [Accepted: 12/16/2020] [Indexed: 12/22/2022]
Abstract
The integrative analysis of copy number alteration (CNA) and gene expression (GE) is an essential part of cancer research considering the impact of CNAs on cancer progression and prognosis. In this research, an integrative analysis was performed with generalized differentially coexpressed gene sets (gdCoxS), which is a modification of dCoxS. In gdCoxS, set-wise interaction is measured using the correlation of sample-wise distances with Renyi’s relative entropy, which requires an estimation of sample density based on omics profiles. To capture correlations between the variables, multivariate density estimation with covariance was applied. In the simulation study, the power of gdCoxS outperformed dCoxS that did not use the correlations in the density estimation explicitly. In the analysis of the lower-grade glioma of the cancer genome atlas program (TCGA-LGG) data, the gdCoxS identified 577 pathway CNAs and GEs pairs that showed significant changes of interaction between the survival and non-survival group, while other benchmark methods detected lower numbers of such pathways. The biological implications of the significant pathways were well consistent with previous reports of the TCGA-LGG. Taken together, the gdCoxS is a useful method for an integrative analysis of CNAs and GEs.
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Affiliation(s)
- Seong Beom Cho
- Department of Biomedical Informatics, College of Medicine, Gachon University, Seongnam-Daero 1342, Korea
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37
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Cascione L, Aresu L, Baudis M, Bertoni F. DNA Copy Number Changes in Diffuse Large B Cell Lymphomas. Front Oncol 2020; 10:584095. [PMID: 33344238 PMCID: PMC7740002 DOI: 10.3389/fonc.2020.584095] [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: 07/16/2020] [Accepted: 10/29/2020] [Indexed: 12/24/2022] Open
Abstract
Copy number aberrations (CNV/CNA) represent a major contribution to the somatic mutation landscapes in cancers, and their identification can lead to the discovery of oncogenetic targets as well as improved disease (sub-) classification. Diffuse large B cell lymphoma (DLBCL) is the most common lymphoma in Western Countries and up to 40% of the affected individuals still succumb to the disease. DLBCL is an heterogenous group of disorders, and we call DLBCL today is not necessarily the same disease of a few years ago. This review focuses on types and frequencies of regional DNA CNVs in DLBCL, not otherwise specified, and in two particular conditions, the transformation from indolent lymphomas and the DLBCL in individuals with immunodeficiency.
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Affiliation(s)
- Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Luca Aresu
- Department of Veterinary Science, University of Turin, Grugliasco, Italy
| | - Michael Baudis
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Molecular Life Science, University of Zurich, Zurich, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland.,Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
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38
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Fusion genes as biomarkers in pediatric cancers: A review of the current state and applicability in diagnostics and personalized therapy. Cancer Lett 2020; 499:24-38. [PMID: 33248210 DOI: 10.1016/j.canlet.2020.11.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/13/2022]
Abstract
The incidence of pediatric cancers is rising steadily across the world, along with the challenges in understanding the molecular mechanisms and devising effective therapeutic strategies. Pediatric cancers are presented with diverse molecular characteristics and more distinct subtypes when compared to adult cancers. Recent studies on the genomic landscape of pediatric cancers using next-generation sequencing (NGS) approaches have redefined this field by providing better subtype characterization and novel actionable targets. Since early identification and personalized treatment strategies influence therapeutic outcomes, survival, and quality of life in pediatric cancer patients, the quest for actionable biomarkers is of great value in this field. Fusion genes that are prevalent and recurrent in several pediatric cancers are ideally suited in this context due to their disease-specific occurrence. In this review, we explore the current status of fusion genes in pediatric cancer subtypes and their use as biomarkers for diagnosis and personalized therapy. We discuss the technological advancements made in recent years in NGS sequencing and their impact on fusion detection algorithms that have revolutionized this field. Finally, we also discuss the advantages of pairing liquid biopsy protocols for fusion detection and their eventual use in diagnosis and treatment monitoring.
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Rao J, Peng L, Liang X, Jiang H, Geng C, Zhao X, Liu X, Fan G, Chen F, Mu F. Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms. BMC Bioinformatics 2020; 21:518. [PMID: 33176676 PMCID: PMC7659224 DOI: 10.1186/s12859-020-03859-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 11/03/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND DNBSEQ™ platforms are new massively parallel sequencing (MPS) platforms that use DNA nanoball technology. Use of data generated from DNBSEQ™ platforms to detect single nucleotide variants (SNVs) and small insertions and deletions (indels) has proven to be quite effective, while the feasibility of copy number variants (CNVs) detection is unclear. RESULTS Here, we first benchmarked different CNV detection tools based on Illumina whole-genome sequencing (WGS) data of NA12878 and then assessed these tools in CNV detection based on DNBSEQ™ sequencing data from the same sample. When the same tool was used, the CNVs detected based on DNBSEQ™ and Illumina data were similar in quantity, length and distribution, while great differences existed within results from different tools and even based on data from a single platform. We further estimated the CNV detection power based on available CNV benchmarks of NA12878 and found similar precision and sensitivity between the DNBSEQ™ and Illumina platforms. We also found higher precision of CNVs shorter than 1 kbp based on DNBSEQ™ platforms than those based on Illumina platforms by using Pindel, DELLY and LUMPY. We carefully compared these two available benchmarks and found a large proportion of specific CNVs between them. Thus, we constructed a more complete CNV benchmark of NA12878 containing 3512 CNV regions. CONCLUSIONS We assessed and benchmarked CNV detections based on WGS with DNBSEQ™ platforms and provide guidelines for future studies.
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Affiliation(s)
- Junhua Rao
- MGI, BGI-Shenzhen, Shenzhen, 518083, China
| | | | | | - Hui Jiang
- MGI, BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Xia Zhao
- MGI, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, 518083, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, Shandong, China.,IGDB-BGI Joint Center for Omics, BGI-Shenzhen, Shenzhen, 518083, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, Shandong, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Fang Chen
- MGI, BGI-Shenzhen, Shenzhen, 518083, China. .,BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Feng Mu
- MGI, BGI-Shenzhen, Shenzhen, 518083, China. .,MGI-Wuhan, BGI-Shenzhen, Wuhan, 430074, China.
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40
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Salgado D, Armean IM, Baudis M, Beltran S, Capella-Gutierrez S, Carvalho-Silva D, Dominguez Del Angel V, Dopazo J, Furlong LI, Gao B, Garcia L, Gerloff D, Gut I, Gyenesei A, Habermann N, Hancock JM, Hanauer M, Hovig E, Johansson LF, Keane T, Korbel J, Lauer KB, Laurie S, Leskošek B, Lloyd D, Marques-Bonet T, Mei H, Monostory K, Piñero J, Poterlowicz K, Rath A, Samarakoon P, Sanz F, Saunders G, Sie D, Swertz MA, Tsukanov K, Valencia A, Vidak M, Yenyxe González C, Ylstra B, Béroud C. The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. F1000Res 2020; 9. [PMID: 34367618 PMCID: PMC8311797 DOI: 10.12688/f1000research.24887.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/27/2020] [Indexed: 02/02/2023] Open
Abstract
Copy number variations (CNVs) are major causative contributors both in the genesis of genetic diseases and human neoplasias. While “High-Throughput” sequencing technologies are increasingly becoming the primary choice for genomic screening analysis, their ability to efficiently detect CNVs is still heterogeneous and remains to be developed. The aim of this white paper is to provide a guiding framework for the future contributions of ELIXIR’s recently established
human CNV Community, with implications beyond human disease diagnostics and population genomics. This white paper is the direct result of a strategy meeting that took place in September 2018 in Hinxton (UK) and involved representatives of 11 ELIXIR Nodes. The meeting led to the definition of priority objectives and tasks, to address a wide range of CNV-related challenges ranging from detection and interpretation to sharing and training. Here, we provide suggestions on how to align these tasks within the ELIXIR Platforms strategy, and on how to frame the activities of this new ELIXIR Community in the international context.
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Affiliation(s)
| | - Irina M Armean
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Michael Baudis
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, Barcelona 08028, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Salvador Capella-Gutierrez
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Spanish National Bioinformatics Institute (INB)/ELIXIR-ES, Barcelona, Spain
| | - Denise Carvalho-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | | | - Joaquin Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud, CDCA, Hospital Virgen del Rocio, Sevilla, Spain
| | - Laura I Furlong
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
| | - Bo Gao
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Leyla Garcia
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.,ZB MED Information Centre for Life Sciences, Cologne, Germany.,ELIXIR Hub, Hinxton, UK
| | - Dietlind Gerloff
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, Barcelona 08028, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Attila Gyenesei
- Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Nina Habermann
- Genome Biology, European Molecular Biological Laboratory, Heidelberg, Germany
| | | | | | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Centre for bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Lennart F Johansson
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Thomas Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jan Korbel
- Genome Biology, European Molecular Biological Laboratory, Heidelberg, Germany
| | | | - Steve Laurie
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 4, Barcelona 08028, Spain
| | - Brane Leskošek
- Faculty of Medicine - ELIXIR Slovenia, University of Ljubljana, Ljubljana, Slovenia
| | | | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
| | - Katalin Monostory
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Janet Piñero
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
| | | | | | - Pubudu Samarakoon
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
| | | | - Daoud Sie
- Department of Clinical Genetics, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kirill Tsukanov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Spanish National Bioinformatics Institute (INB)/ELIXIR-ES, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies, Barcelona, Spain
| | - Marko Vidak
- Faculty of Medicine - ELIXIR Slovenia, University of Ljubljana, Ljubljana, Slovenia
| | - Cristina Yenyxe González
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Bauke Ylstra
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Christophe Béroud
- Aix Marseille Univ, INSERM, MMG, Marseille, France.,Département de Génétique Médicale et de Biologie Cellulaire, APHM, Hôpital d'enfants de la Timone, 13385 Marseille, France
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41
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SOX2 and squamous cancers. Semin Cancer Biol 2020; 67:154-167. [PMID: 32905832 DOI: 10.1016/j.semcancer.2020.05.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 11/10/2019] [Accepted: 05/09/2020] [Indexed: 12/20/2022]
Abstract
SOX2 is a pleiotropic nuclear transcription factor with major roles in stem cell biology and in development. Over the last 10 years SOX2 has also been implicated as a lineage-specific oncogene, notably in squamous carcinomas but also neurological tumours, particularly glioblastoma. Squamous carcinomas (SQCs) comprise a common group of malignancies for which there are no targeted therapeutic interventions. In this article we review the molecular epidemiological and laboratory evidence linking SOX2 with squamous carcinogenesis, explore in detail the multifaceted impact of SOX2 in SQC, describe areas of uncertainty and highlight areas for potential future research.
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Akar OS, Gunes S, Abur U, Altundag E, Asci R, Onat OE, Ozcelik T, Ogur G. Multiscale analysis of SRY-positive 46,XX testicular disorder of sex development: Presentation of nine cases. Andrologia 2020; 52:e13739. [PMID: 32882067 DOI: 10.1111/and.13739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/16/2020] [Accepted: 06/04/2020] [Indexed: 12/18/2022] Open
Abstract
46,XX testicular disorder of sex development (46,XX TDSD) is a relatively rare condition characterised by the presence of testicular tissue with 46,XX karyotype. The present study aims to reveal the phenotype to genotype correlation in a series of sex-determining region Y (SRY)-positive 46,XX TDSD cases. We present the clinical findings, hormone profiles and genetic test results of six patients with SRY-positive 46,XX TDSD and give the details and follow-up findings of our three of previously published patients. All patients presented common characteristics such as azoospermia, hypergonadotropic hypogonadism and an SRY gene translocated on the terminal part of the short arm of one of the X chromosomes. Mean ± standard deviation (SD) height of the patients was 164.78 ± 8.0 cm. Five patients had decreased secondary sexual characteristics, and three patients had gynaecomastia with varying degrees. Five of the seven patients revealed a translocation between protein kinase X (PRKX) and inverted protein kinase Y (PRKY) genes, and the remaining two patients showed a translocation between the pseudoautosomal region 1 (PAR1) of X chromosome and the differential region of Y chromosome. X chromosome inactivation (XCI) analysis results demonstrated random and skewed XCI in 5 cases and 1 case, respectively. In brief, we delineate the phenotypic spectrum of patients with SRY-positive 46,XX TDSD and the underlying mechanisms of Xp;Yp translocations.
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Affiliation(s)
- Omer Salih Akar
- Department of Medical Genetics, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Sezgin Gunes
- Department of Medical Biology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Ummet Abur
- Department of Medical Genetics, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Engin Altundag
- Department of Medical Genetics, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Ramazan Asci
- Department of Urology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Onur Emre Onat
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Tayfun Ozcelik
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Gonul Ogur
- Department of Medical Genetics, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
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43
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Thermodynamic energetics underlying genomic instability and whole-genome doubling in cancer. Proc Natl Acad Sci U S A 2020; 117:18880-18890. [PMID: 32694208 DOI: 10.1073/pnas.1920870117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genomic instability contributes to tumorigenesis through the amplification and deletion of cancer driver genes. DNA copy number (CN) profiling of ensembles of tumors allows a thermodynamic analysis of the profile for each tumor. The free energy of the distribution of CNs is found to be a monotonically increasing function of the average chromosomal ploidy. The dependence is universal across several cancer types. Surprisal analysis distinguishes two main known subgroups: tumors with cells that have or have not undergone whole-genome duplication (WGD). The analysis uncovers that CN states having a narrower distribution are energetically more favorable toward the WGD transition. Surprisal analysis also determines the deviations from a fully stable-state distribution. These deviations reflect constraints imposed by tumor fitness selection pressures. The results point to CN changes that are more common in high-ploidy tumors and thus support altered selection pressures upon WGD.
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44
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Through the looking glass and what you find there: making sense of comparative genomic hybridization and fluorescence in situ hybridization for melanoma diagnosis. Mod Pathol 2020; 33:1318-1330. [PMID: 32066861 DOI: 10.1038/s41379-020-0490-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 12/11/2022]
Abstract
Melanoma is the leading cause of death among cutaneous neoplasms. Best outcome relies on early detection and accurate pathologic diagnosis. For the great majority of melanocytic tumors, histopathologic examination can reliably distinguish nevi from melanomas. However, there is a subset of melanocytic tumors that cannot be definitively classified as benign or malignant using histopathological criteria alone. These tumors are usually diagnosed using terms that imply various degrees of uncertainty in regards to their malignant potential and create the possibility for over or undertreatment. For such tumors, additional ancillary tests would be beneficial in adjudicating a more definitive diagnosis. In recent years, DNA-based molecular ancillary tests, specifically comparative genomic hybridization and fluorescence in situ hybridization, have been developed to help guide the diagnosis of ambiguous melanocytic proliferations. This study will present an updated overview of these two major ancillary tests, which are currently being used in clinical practice to assist in the diagnosis of challenging melanocytic neoplasms.
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45
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Oncogene PRR14 promotes breast cancer through activation of PI3K signal pathway and inhibition of CHEK2 pathway. Cell Death Dis 2020; 11:464. [PMID: 32541902 PMCID: PMC7296039 DOI: 10.1038/s41419-020-2640-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/28/2022]
Abstract
Nuclear envelope component PRR14 has been detected to be upregulated in varieties of cancers, especially in breast cancer. But its role in breast carcinogenesis is poorly understood. In this study, we show PRR14 contributes to breast carcinogenesis mainly through overexpression, which derives from elevated transcription and gene amplification. Increased PRR14 expression promotes breast cancer cell proliferation and tumor formation. Biochemical analysis reveals, in addition to previously reported activation of PI3-kinase/Akt/mTOR pathway, PRR14 overexpression regulates cell cycle in breast cancer by inhibiting CHEK2’s activation, followed with the deregulation of DNA damage pathway. In correspondence, CHEK2 and PRR14 show opposite impact on breast cancer patients receiving chemotherapy. Collectively, our study is the first to document the oncogenetic role of PRR14 in breast cancer, which protects cells from apoptosis and stimulates proliferation by activating the PI3-kinase/Akt/mTOR pathway and inhibiting the CHEK2 pathway. Both of these pathways are of great influence in breast cancer and PRR14 appears to be their novel interacting node, which renders patients more resistance to chemotherapy and provides a potential therapeutic target in breast cancer.
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46
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Gao B, Baudis M. Minimum error calibration and normalization for genomic copy number analysis. Genomics 2020; 112:3331-3341. [PMID: 32413400 DOI: 10.1016/j.ygeno.2020.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 11/25/2022]
Abstract
BACKGROUND Copy number variations (CNV) are regional deviations from the normal autosomal bi-allelic DNA content. While germline CNVs are a major contributor to genomic syndromes and inherited diseases, the majority of cancers accumulate extensive "somatic" CNV (sCNV or CNA) during the process of oncogenetic transformation and progression. While specific sCNV have closely been associated with tumorigenesis, intriguingly many neoplasias exhibit recurrent sCNV patterns beyond the involvement of a few cancer driver genes. Currently, CNV profiles of tumor samples are generated using genomic micro-arrays or high-throughput DNA sequencing. Regardless of the underlying technology, genomic copy number data is derived from the relative assessment and integration of multiple signals, with the data generation process being prone to contamination from several sources. Estimated copy number values have no absolute or strictly linear correlation to their corresponding DNA levels, and the extent of deviation differs between sample profiles, which poses a great challenge for data integration and comparison in large scale genome analysis. RESULTS In this study, we present a novel method named "Minimum Error Calibration and Normalization for Copy Numbers Analysis" (Mecan4CNA). It only requires CNV segmentation files as input, is platform independent, and has a high performance with limited hardware requirements. For a given multi-sample copy number dataset, Mecan4CNA can batch-normalize all samples to the corresponding true copy number levels of the main tumor clones. Experiments of Mecan4CNA on simulated data showed an overall accuracy of 93% and 91% in determining the normal level and single copy alteration (i.e. duplication or loss of one allele), respectively. Comparison of estimated normal levels and single copy alternations with existing methods and karyotyping data on the NCI-60 tumor cell line produced coherent results. To estimate the method's impact on downstream analyses, we performed GISTIC analyses on the original and Mecan4CNA normalized data from the Cancer Genome Atlas (TCGA) where the normalized data showed prominent improvements of both sensitivity and specificity in detecting focal regions. CONCLUSIONS Mecan4CNA provides an advanced method for CNA data normalization, especially in meta-analyses involving large profile numbers and heterogeneous source data quality. With its informative output and visualization options, Mecan4CNA also can improve the interpretation of individual CNA profiles. Mecan4CNA is freely available as a Python package and through its code repository on Github.
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Affiliation(s)
- Bo Gao
- Department of Molecular Life Sciences, University of Zurich, Switzerland; Swiss Institute of Bioinformatics, Switzerland
| | - Michael Baudis
- Department of Molecular Life Sciences, University of Zurich, Switzerland; Swiss Institute of Bioinformatics, Switzerland.
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47
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Li L, Yang P, Shi S, Zhang Z, Shi Q, Xu J, He H, Lei C, Wang E, Chen H, Huang Y. Association Analysis to Copy Number Variation (CNV) of Opn4 Gene with Growth Traits of Goats. Animals (Basel) 2020; 10:ani10030441. [PMID: 32155759 PMCID: PMC7143651 DOI: 10.3390/ani10030441] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/11/2020] [Accepted: 03/05/2020] [Indexed: 01/03/2023] Open
Abstract
Simple Summary Copy number variation is a common genetic polymorphism and is mainly represented by submicroscopic levels of deletion and duplication which are caused by rearrangement of the genome. It is well known that copy number variations of genes are associated with growth traits of livestock. In this study, we detected the correlation between the copy number variation of the Opn4 gene and growth traits of Guizhou goats. We found that the copy number variation of the Opn4 gene had a significant influence on the body length and body weight of Guizhou goats. The results may provide preliminary suggestions into Guizhou goat breeding and new insights into the future of CNV as a new promising molecular marker in animal breeding. Abstract Extensive research has been carried out regarding the correlation between the growth traits of livestock and genetic polymorphisms, including single nucleotide polymorphisms and copy number variations (CNV). The purpose of this study was to analyze the CNV and its genetic effects of the Opn4 gene in 284 Guizhou goats (Guizhou black goat: n = 186, Guizhou white goat: n = 98). We used qPCR to detect the CNV of the Opn4 gene in Guizhou goats, and the classification results were correlated with the corresponding individual growth traits by SPSS software. The results showed that the Opn4 gene had a superior effect on growth traits with multiple copy variants in Guizhou black goats, and there was a significant correlation between copy number variation sites and body length traits. Contrary to the former conclusion, in Guizhou white goats, individuals with the Normal copy number type showed superior growth traits and copy number variant sites were significantly associated with body weight traits. Therefore, the CNV of the Opn4 gene can be used as a candidate molecular genetic marker to improve goat growth traits, speeding up the breeding process of goat elite varieties.
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Affiliation(s)
- LiJuan Li
- Institute of Bijie Test Area, Guizhou University of Engineering Science, Bijie, Guizhou 551700, China; (L.L.)
| | - Peng Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China; (P.Y.)
| | - ShuYue Shi
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China; (P.Y.)
| | - ZiJing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 45002, China; (Z.Z.); (Q.S.)
| | - QiaoTing Shi
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 45002, China; (Z.Z.); (Q.S.)
| | - JiaWei Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China; (P.Y.)
| | - Hua He
- Institute of Bijie Test Area, Guizhou University of Engineering Science, Bijie, Guizhou 551700, China; (L.L.)
- College of Veterinary Medicine, Northwest A&F University, Yangling Shaanxi 712100, China
| | - ChuZhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China; (P.Y.)
| | - ErYao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 45002, China; (Z.Z.); (Q.S.)
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China; (P.Y.)
| | - YongZhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China; (P.Y.)
- Correspondence: ; Tel.: +86-29-87092102; Fax: +86-29-87092164
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Xing Y, Dabney AR, Li X, Wang G, Gill CA, Casola C. SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference Genomes. Front Genet 2020; 11:82. [PMID: 32153642 PMCID: PMC7046838 DOI: 10.3389/fgene.2020.00082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/24/2020] [Indexed: 01/26/2023] Open
Abstract
Copy number variants are duplications and deletions of the genome that play an important role in phenotypic changes and human disease. Many software applications have been developed to detect copy number variants using either whole-genome sequencing or whole-exome sequencing data. However, there is poor agreement in the results from these applications. Simulated datasets containing copy number variants allow comprehensive comparisons of the operating characteristics of existing and novel copy number variant detection methods. Several software applications have been developed to simulate copy number variants and other structural variants in whole-genome sequencing data. However, none of the applications reliably simulate copy number variants in whole-exome sequencing data. We have developed and tested Simulator of Exome Copy Number Variants (SECNVs), a fast, robust and customizable software application for simulating copy number variants and whole-exome sequences from a reference genome. SECNVs is easy to install, implements a wide range of commands to customize simulations, can output multiple samples at once, and incorporates a pipeline to output rearranged genomes, short reads and BAM files in a single command. Variants generated by SECNVs are detected with high sensitivity and precision by tools commonly used to detect copy number variants. SECNVs is publicly available at https://github.com/YJulyXing/SECNVs.
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Affiliation(s)
- Yue Xing
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX, United States
- Department of Statistics, Texas A&M University, College Station, TX, United States
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Alan R. Dabney
- Department of Statistics, Texas A&M University, College Station, TX, United States
| | - Xiao Li
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, United States
| | - Guosong Wang
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Clare A. Gill
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Claudio Casola
- Department of Ecosystem Science and Management, Texas A&M University, College Station, TX, United States
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Contreras AL, Andal JJL, Lo RM, Ang DC. Pre-analytics, Current Testing Technologies, and Limitations of Testing. Genomic Med 2020. [DOI: 10.1007/978-3-030-22922-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Mabire C, Duarte J, Darracq A, Pirani A, Rimbert H, Madur D, Combes V, Vitte C, Praud S, Rivière N, Joets J, Pichon JP, Nicolas SD. High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix® axiom® array. BMC Genomics 2019; 20:848. [PMID: 31722668 PMCID: PMC6854671 DOI: 10.1186/s12864-019-6136-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 09/23/2019] [Indexed: 12/19/2022] Open
Abstract
Background Insertions/deletions (InDels) and more specifically presence/absence variations (PAVs) are pervasive in several species and have strong functional and phenotypic effect by removing or drastically modifying genes. Genotyping of such variants on large panels remains poorly addressed, while necessary for approaches such as association mapping or genomic selection. Results We have developed, as a proof of concept, a new high-throughput and affordable approach to genotype InDels. We first identified 141,000 InDels by aligning reads from the B73 line against the genome of three temperate maize inbred lines (F2, PH207, and C103) and reciprocally. Next, we designed an Affymetrix® Axiom® array to target these InDels, with a combination of probes selected at breakpoint sites (13%) or within the InDel sequence, either at polymorphic (25%) or non-polymorphic sites (63%) sites. The final array design is composed of 662,772 probes and targets 105,927 InDels, including PAVs ranging from 35 bp to 129kbp. After Affymetrix® quality control, we successfully genotyped 86,648 polymorphic InDels (82% of all InDels interrogated by the array) on 445 maize DNA samples with 422,369 probes. Genotyping InDels using this approach produced a highly reliable dataset, with low genotyping error (~ 3%), high call rate (~ 98%), and high reproducibility (> 95%). This reliability can be further increased by combining genotyping of several probes calling the same InDels (< 0.1% error rate and > 99.9% of call rate for 5 probes). This “proof of concept” tool was used to estimate the kinship matrix between 362 maize lines with 57,824 polymorphic InDels. This InDels kinship matrix was highly correlated with kinship estimated using SNPs from Illumina 50 K SNP arrays. Conclusions We efficiently genotyped thousands of small to large InDels on a sizeable number of individuals using a new Affymetrix® Axiom® array. This powerful approach opens the way to studying the contribution of InDels to trait variation and heterosis in maize. The approach is easily extendable to other species and should contribute to decipher the biological impact of InDels at a larger scale.
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Affiliation(s)
- Clément Mabire
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Jorge Duarte
- Biogemma - Centre de Recherche de Chappes, CS 90126, 63720, Chappes, France
| | - Aude Darracq
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Ali Pirani
- Thermo Fisher Scientific, 3450 Central Expressway, Santa Clara, CA, 95051, USA
| | - Hélène Rimbert
- Biogemma - Centre de Recherche de Chappes, CS 90126, 63720, Chappes, France.,Present address: GDEC, INRA, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Delphine Madur
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Valérie Combes
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Clémentine Vitte
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Sébastien Praud
- Biogemma - Centre de Recherche de Chappes, CS 90126, 63720, Chappes, France
| | - Nathalie Rivière
- Biogemma - Centre de Recherche de Chappes, CS 90126, 63720, Chappes, France
| | - Johann Joets
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | | | - Stéphane D Nicolas
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France.
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