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Meng X, Wang M, Luo M, Sun L, Yan Q, Liu Y. Systematic evaluation of multiple NGS platforms for structural variants detection. J Biol Chem 2023; 299:105436. [PMID: 37944616 PMCID: PMC10724692 DOI: 10.1016/j.jbc.2023.105436] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Structural variations (SV) are critical genome changes affecting human diseases. Although many hybridization-based methods exist, evaluating SVs through next-generation sequencing (NGS) data is still necessary for broader research exploration. Here, we comprehensively compared the performance of 16 SV callers and multiple NGS platforms using NA12878 whole genome sequencing (WGS) datasets. The results indicated that several SV callers performed well relatively, such as Manta, GRIDSS, LUMPY, TARDIS, FermiKit, and Wham. Meanwhile, all NGS platforms have a similar performance using a single software. Additionally, we found that the source of undetected SVs was mostly from long reads datasets, therefore, the more appropriate strategy for accurate SV detection will be an integration of long and shorter reads in the future. At present, in the period of NGS as a mainstream method in bioinformatics, our study would provide helpful and comprehensive guidelines for specific categories of SV research.
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Affiliation(s)
- Xuan Meng
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Miao Wang
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China
| | - Mingjie Luo
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China
| | - Lei Sun
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China
| | - Qin Yan
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China
| | - Yongfeng Liu
- Research Cooperation Department, GeneMind Biosciences Company Limited, Shenzhen, China.
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2
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Rodríguez-López R, Gimeno-Ferrer F, do Santos DA, Ferrer-Bolufer I, Luján CG, Alcalá OZ, García-Banacloy A, Cogollos VB, Juan CS. Reviewed and updated Algorithm for Genetic Characterization of Syndromic Obesity Phenotypes. Curr Genomics 2022; 23:147-162. [PMID: 36777005 PMCID: PMC9878830 DOI: 10.2174/1389202923666220426093436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/30/2021] [Accepted: 02/01/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Individuals with a phenotype of early-onset severe obesity associated with intellectual disability can have molecular diagnoses ranging from monogenic to complex genetic traits. Severe overweight is the major sign of a syndromic physical appearance and predicting the influence of a single gene and/or polygenic risk profile is extremely complicated among the majority of the cases. At present, considering rare monogenic bases as the principal etiology for the majority of obesity cases associated with intellectual disability is scientifically poor. The diversity of the molecular bases responsible for the two entities makes the appliance of the current routinely powerful genomics diagnostic tools essential. Objective: Clinical investigation of these difficult-to-diagnose patients requires pediatricians and neurologists to use optimized descriptions of signs and symptoms to improve genotype correlations. Methods: The use of modern integrated bioinformatics strategies which are conducted by experienced multidisciplinary clinical teams. Evaluation of the phenotype of the patient's family is also of importance. Results: The next step involves discarding the monogenic canonical obesity syndromes and considering infrequent unique molecular cases, and/or then polygenic bases. Adequate management of the application of the new technique and its diagnostic phases is essential for achieving good cost/efficiency balances. Conclusion: With the current clinical management, it is necessary to consider the potential coincidence of risk mutations for obesity in patients with genetic alterations that induce intellectual disability. In this review, we describe an updated algorithm for the molecular characterization and diagnosis of patients with a syndromic obesity phenotype.
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Affiliation(s)
- Raquel Rodríguez-López
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain;,Address correspondence to this author at the Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Avenida de las Tres Cruces no. 2 46014, Valencia, Spain; Tel: 0034 963 131 800 – 437317; Fax: 0034 963 131 979; E-mail:
| | - Fátima Gimeno-Ferrer
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | - David Albuquerque do Santos
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | - Irene Ferrer-Bolufer
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | - Carola Guzmán Luján
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | - Otilia Zomeño Alcalá
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | - Amor García-Banacloy
- Laboratory of Molecular Genetics, Clinical Analysis Service, General Hospital Consortium of Valencia, Valencia, Spain
| | | | - Carlos Sánchez Juan
- Endocrinology Service, General Hospital Consortium of Valencia, Valencia, Spain
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3
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Hehir-Kwa JY, Koudijs MJ, Verwiel ETP, Kester LA, van Tuil M, Strengman E, Buijs A, Kranendonk MEG, Hiemcke-Jiwa LS, de Haas V, van de Geer E, de Leng W, van der Lugt J, Lijnzaad P, Holstege FCP, Kemmeren P, Tops BBJ. Improved Gene Fusion Detection in Childhood Cancer Diagnostics Using RNA Sequencing. JCO Precis Oncol 2022; 6:e2000504. [PMID: 35085008 PMCID: PMC8830514 DOI: 10.1200/po.20.00504] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 08/27/2021] [Accepted: 12/03/2021] [Indexed: 12/16/2022] Open
Abstract
PURPOSE Gene fusions play a significant role in cancer etiology, making their detection crucial for accurate diagnosis, prognosis, and determining therapeutic targets. Current diagnostic methods largely focus on either targeted or low-resolution genome-wide techniques, which may be unable to capture rare events or both fusion partners. We investigate if RNA sequencing can overcome current limitations with traditional diagnostic techniques to identify gene fusion events. METHODS We first performed RNA sequencing on a validation cohort of 24 samples with a known gene fusion event, after which a prospective pan-pediatric cancer cohort (n = 244) was tested by RNA sequencing in parallel to existing diagnostic procedures. This cohort included hematologic malignancies, tumors of the CNS, solid tumors, and suspected neoplastic samples. All samples were processed in the routine diagnostic workflow and analyzed for gene fusions using standard-of-care methods and RNA sequencing. RESULTS We identified a clinically relevant gene fusion in 83 of 244 cases in the prospective cohort. Sixty fusions were detected by both routine diagnostic techniques and RNA sequencing, and one fusion was detected only in routine diagnostics, but an additional 24 fusions were detected solely by RNA sequencing. RNA sequencing, therefore, increased the diagnostic yield by 38%-39%. In addition, RNA sequencing identified both gene partners involved in the gene fusion, in contrast to most routine techniques. For two patients, the newly identified fusion by RNA sequencing resulted in treatment with targeted agents. CONCLUSION We show that RNA sequencing is sufficiently robust for gene fusion detection in routine diagnostics of childhood cancers and can make a difference in treatment decisions.
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Affiliation(s)
| | - Marco J. Koudijs
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Department of Laboratories, Pharmacy and Biomedical Genetics, Section of Genome Diagnostics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Lennart A. Kester
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Marc van Tuil
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Eric Strengman
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Arjan Buijs
- Department of Laboratories, Pharmacy and Biomedical Genetics, Section of Genome Diagnostics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | - Valerie de Haas
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Ellen van de Geer
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Wendy de Leng
- Department of Laboratories, Pharmacy and Biomedical Genetics, Section Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Philip Lijnzaad
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
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Mojidra R, Hole A, Iwasaki K, Noothalapati H, Yamamoto T, C MK, Govekar R. DNA Fingerprint Analysis of Raman Spectra Captures Global Genomic Alterations in Imatinib-Resistant Chronic Myeloid Leukemia: A Potential Single Assay for Screening Imatinib Resistance. Cells 2021; 10:cells10102506. [PMID: 34685486 PMCID: PMC8533852 DOI: 10.3390/cells10102506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/15/2021] [Accepted: 09/18/2021] [Indexed: 11/29/2022] Open
Abstract
Monitoring the development of resistance to the tyrosine kinase inhibitor (TKI) imatinib in chronic myeloid leukemia (CML) patients in the initial chronic phase (CP) is crucial for limiting the progression of unresponsive patients to terminal phase of blast crisis (BC). This study for the first time demonstrates the potential of Raman spectroscopy to sense the resistant phenotype. Currently recommended resistance screening strategy include detection of BCR-ABL1 transcripts, kinase domain mutations, complex chromosomal abnormalities and BCR-ABL1 gene amplification. The techniques used for these tests are expensive, technologically demanding and have limited availability in resource-poor countries. In India, this could be a reason for more patients reporting to clinics with advanced disease. A single method which can identify resistant cells irrespective of the underlying mechanism would be a practical screening strategy. During our analysis of imatinib-sensitive and -resistant K562 cells, by array comparative genomic hybridization (aCGH), copy number variations specific to resistant cells were detected. aCGH is technologically demanding, expensive and therefore not suitable to serve as a single economic test. We therefore explored whether DNA finger-print analysis of Raman hyperspectral data could capture these alterations in the genome, and demonstrated that it could indeed segregate imatinib-sensitive and -resistant cells. Raman spectroscopy, due to availability of portable instruments, ease of spectrum acquisition and possibility of centralized analysis of transmitted data, qualifies as a preliminary screening tool in resource-poor countries for imatinib resistance in CML. This study provides a proof of principle for a single assay for monitoring resistance to imatinib, available for scrutiny in clinics.
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Affiliation(s)
- Rahul Mojidra
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai 410210, India; (R.M.); (A.H.)
- Homi Bhabha National Institute, BARC Training School Complex, Mumbai 400094, India
| | - Arti Hole
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai 410210, India; (R.M.); (A.H.)
| | - Keita Iwasaki
- The United Graduate School of Agricultural Sciences, Tottori University, Tottori 680-8550, Japan;
| | - Hemanth Noothalapati
- Faculty of Life and Environmental Sciences, Shimane University, Matsue 690-8504, Japan;
- Raman Project Center for Medical and Biological Applications, Shimane University, Matsue 690-8504, Japan
| | - Tatsuyuki Yamamoto
- Faculty of Life and Environmental Sciences, Shimane University, Matsue 690-8504, Japan;
- Raman Project Center for Medical and Biological Applications, Shimane University, Matsue 690-8504, Japan
- Correspondence: (T.Y.); (M.K.C.); (R.G.)
| | - Murali Krishna C
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai 410210, India; (R.M.); (A.H.)
- Homi Bhabha National Institute, BARC Training School Complex, Mumbai 400094, India
- Correspondence: (T.Y.); (M.K.C.); (R.G.)
| | - Rukmini Govekar
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai 410210, India; (R.M.); (A.H.)
- Homi Bhabha National Institute, BARC Training School Complex, Mumbai 400094, India
- Correspondence: (T.Y.); (M.K.C.); (R.G.)
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Next Generation Sequencing Technology in the Clinic and Its Challenges. Cancers (Basel) 2021; 13:cancers13081751. [PMID: 33916923 PMCID: PMC8067551 DOI: 10.3390/cancers13081751] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/30/2021] [Accepted: 04/05/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Precise identification and annotation of mutations are of utmost importance in clinical oncology. Insights of the DNA sequence can provide meaningful knowledge to unravel the underlying genetics of disease. Hence, tailoring of personalized medicine often relies on specific genomic alteration for treatment efficacy. The aim of this review is to highlight that sequencing harbors much more than just four nucleotides. Moreover, the gradual transition from first to second generation sequencing technologies has led to awareness for choosing the most appropriate bioinformatic analytic tools based on the aim, quality and demand for a specific purpose. Thus, the same raw data can lead to various results reflecting the intrinsic features of different datamining pipelines. Abstract Data analysis has become a crucial aspect in clinical oncology to interpret output from next-generation sequencing-based testing. NGS being able to resolve billions of sequencing reactions in a few days has consequently increased the demand for tools to handle and analyze such large data sets. Many tools have been developed since the advent of NGS, featuring their own peculiarities. Increased awareness when interpreting alterations in the genome is therefore of utmost importance, as the same data using different tools can provide diverse outcomes. Hence, it is crucial to evaluate and validate bioinformatic pipelines in clinical settings. Moreover, personalized medicine implies treatment targeting efficacy of biological drugs for specific genomic alterations. Here, we focused on different sequencing technologies, features underlying the genome complexity, and bioinformatic tools that can impact the final annotation. Additionally, we discuss the clinical demand and design for implementing NGS.
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Ahmad R, Singh JK, Wunnava A, Al-Obeed O, Abdulla M, Srivastava SK. Emerging trends in colorectal cancer: Dysregulated signaling pathways (Review). Int J Mol Med 2021; 47:14. [PMID: 33655327 PMCID: PMC7834960 DOI: 10.3892/ijmm.2021.4847] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the third most frequently detected type of cancer, and the second most common cause of cancer‑related mortality globally. The American Cancer Society predicted that approximately 147,950 individuals would be diagnosed with CRC, out of which 53,200 individuals would succumb to the disease in the USA alone in 2020. CRC‑related mortality ranks third among both males and females in the USA. CRC arises from 3 major pathways: i) The adenoma‑carcinoma sequence; ii) serrated pathway; and iii) the inflammatory pathway. The majority of cases of CRC are sporadic and result from risk factors, such as a sedentary lifestyle, obesity, processed diets, alcohol consumption and smoking. CRC is also a common preventable cancer. With widespread CRC screening, the incidence and mortality from CRC have decreased in developed countries. However, over the past few decades, CRC cases and mortality have been on the rise in young adults (age, <50 years). In addition, CRC cases are increasing in developing countries with a low gross domestic product (GDP) due to lifestyle changes. CRC is an etiologically heterogeneous disease classified by tumor location and alterations in global gene expression. Accumulating genetic and epigenetic perturbations and aberrations over time in tumor suppressor genes, oncogenes and DNA mismatch repair genes could be a precursor to the onset of colorectal cancer. CRC can be divided as sporadic, familial, and inherited depending on the origin of the mutation. Germline mutations in APC and MLH1 have been proven to play an etiological role, resulting in the predisposition of individuals to CRC. Genetic alterations cause the dysregulation of signaling pathways leading to drug resistance, the inhibition of apoptosis and the induction of proliferation, invasion and migration, resulting in CRC development and metastasis. Timely detection and effective precision therapies based on the present knowledge of CRC is essential for successful treatment and patient survival. The present review presents the CRC incidence, risk factors, dysregulated signaling pathways and targeted therapies.
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Affiliation(s)
- Rehan Ahmad
- Colorectal Research Chair, Department of Surgery, King Saud University College of Medicine, Riyadh 11472, Saudi Arabia
| | - Jaikee Kumar Singh
- Department of Biosciences, Manipal University Jaipur, Jaipur, Rajasthan 303007, India
| | - Amoolya Wunnava
- Department of Biosciences, Manipal University Jaipur, Jaipur, Rajasthan 303007, India
| | - Omar Al-Obeed
- Colorectal Research Chair, Department of Surgery, King Saud University College of Medicine, Riyadh 11472, Saudi Arabia
| | - Maha Abdulla
- Colorectal Research Chair, Department of Surgery, King Saud University College of Medicine, Riyadh 11472, Saudi Arabia
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Zhuang X, Ye R, So MT, Lam WY, Karim A, Yu M, Ngo ND, Cherny SS, Tam PKH, Garcia-Barcelo MM, Tang CSM, Sham PC. A random forest-based framework for genotyping and accuracy assessment of copy number variations. NAR Genom Bioinform 2020; 2:lqaa071. [PMID: 33575619 PMCID: PMC7671382 DOI: 10.1093/nargab/lqaa071] [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: 03/25/2020] [Revised: 08/18/2020] [Accepted: 08/26/2020] [Indexed: 12/24/2022] Open
Abstract
Detection of copy number variations (CNVs) is essential for uncovering genetic factors underlying human diseases. However, CNV detection by current methods is prone to error, and precisely identifying CNVs from paired-end whole genome sequencing (WGS) data is still challenging. Here, we present a framework, CNV-JACG, for Judging the Accuracy of CNVs and Genotyping using paired-end WGS data. CNV-JACG is based on a random forest model trained on 21 distinctive features characterizing the CNV region and its breakpoints. Using the data from the 1000 Genomes Project, Genome in a Bottle Consortium, the Human Genome Structural Variation Consortium and in-house technical replicates, we show that CNV-JACG has superior sensitivity over the latest genotyping method, SV2, particularly for the small CNVs (≤1 kb). We also demonstrate that CNV-JACG outperforms SV2 in terms of Mendelian inconsistency in trios and concordance between technical replicates. Our study suggests that CNV-JACG would be a useful tool in assessing the accuracy of CNVs to meet the ever-growing needs for uncovering the missing heritability linked to CNVs.
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Affiliation(s)
- Xuehan Zhuang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Rui Ye
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Man-Ting So
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Wai-Yee Lam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Anwarul Karim
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Michelle Yu
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ngoc Diem Ngo
- National Hospital of Pediatrics, Ha Noi 100000, Vietnam
| | - Stacey S Cherny
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Paul Kwong-Hang Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | | | - Clara Sze-Man Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Pak Chung Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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Abstract
Diversity within the fungal kingdom is evident from the wide range of morphologies fungi display as well as the various ecological roles and industrial purposes they serve. Technological advances, particularly in long-read sequencing, coupled with the increasing efficiency and decreasing costs across sequencing platforms have enabled robust characterization of fungal genomes. These sequencing efforts continue to reveal the rampant diversity in fungi at the genome level. Here, we discuss studies that have furthered our understanding of fungal genetic diversity and genomic evolution. These studies revealed the presence of both small-scale and large-scale genomic changes. In fungi, research has recently focused on many small-scale changes, such as how hypermutation and allelic transmission impact genome evolution as well as how and why a few specific genomic regions are more susceptible to rapid evolution than others. High-throughput sequencing of a diverse set of fungal genomes has also illuminated the frequency, mechanisms, and impacts of large-scale changes, which include chromosome structural variation and changes in chromosome number, such as aneuploidy, polyploidy, and the presence of supernumerary chromosomes. The studies discussed herein have provided great insight into how the architecture of the fungal genome varies within species and across the kingdom and how modern fungi may have evolved from the last common fungal ancestor and might also pave the way for understanding how genomic diversity has evolved in all domains of life.
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Affiliation(s)
- Shelby J. Priest
- Department of Molecular Genetics and Microbiology, Duke University Medical Centre, Durham, NC, USA
| | - Vikas Yadav
- Department of Molecular Genetics and Microbiology, Duke University Medical Centre, Durham, NC, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Centre, Durham, NC, USA
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Hu Q, Maurais EG, Ly P. Cellular and genomic approaches for exploring structural chromosomal rearrangements. Chromosome Res 2020; 28:19-30. [PMID: 31933061 PMCID: PMC7131874 DOI: 10.1007/s10577-020-09626-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/20/2019] [Accepted: 01/01/2020] [Indexed: 12/13/2022]
Abstract
Human chromosomes are arranged in a linear and conserved sequence order that undergoes further spatial folding within the three-dimensional space of the nucleus. Although structural variations in this organization are an important source of natural genetic diversity, cytogenetic aberrations can also underlie a number of human diseases and disorders. Approaches for studying chromosome structure began half a century ago with karyotyping of Giemsa-banded chromosomes and has now evolved to encompass high-resolution fluorescence microscopy, reporter-based assays, and next-generation DNA sequencing technologies. Here, we provide a general overview of experimental methods at different resolution and sensitivity scales and discuss how they can be complemented to provide synergistic insight into the study of human chromosome structural rearrangements. These approaches range from kilobase-level resolution DNA fluorescence in situ hybridization (FISH)-based imaging approaches of individual cells to genome-wide sequencing strategies that can capture nucleotide-level information from diverse sample types. Technological advances coupled to the combinatorial use of multiple methods have resulted in the discovery of new rearrangement classes along with mechanistic insights into the processes that drive structural alterations in the human genome.
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Affiliation(s)
- Qing Hu
- Department of Pathology, Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elizabeth G Maurais
- Department of Pathology, Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peter Ly
- Department of Pathology, Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Combinations of exonic deletions and rare mutations lead to misdiagnosis of propionic acidemia. Clin Chim Acta 2020; 502:153-158. [DOI: 10.1016/j.cca.2019.12.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 12/17/2019] [Accepted: 12/25/2019] [Indexed: 12/23/2022]
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Ou J, Yang C, Cui X, Chen C, Ye S, Zhang C, Wang K, Chen J, Zhang Q, Qian C, Fang G, Zhang W. Successful pregnancy after prenatal diagnosis by NGS for a carrier of complex chromosome rearrangements. Reprod Biol Endocrinol 2020; 18:15. [PMID: 32113484 PMCID: PMC7049181 DOI: 10.1186/s12958-020-00572-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/10/2020] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The study is aimed to provide prediction for fertility risk in the setting of assisted reproduction for a woman with complex chromosomal rearrangements (CCRs). METHODS We implemented a robust approach, which combined whole-genome low-coverage mate-pair sequencing (WGL-MPS), junction-spanning PCR and preimplantation genetic testing for aneuploidy (PGT-A) method to provide accurate chromosome breakpoint junctional sequences in the embryo selection process in the setting of assisted reproduction for a couple with recurrent abortions due to CCRs. RESULT WGL-MPS was applied to a female carrying CCRs which consisted of 9 breakpoints and 1 cryptic deletion related to fertility risks. Sequencing data provided crucial information for designing junction-spanning PCR and PGT-A process, which was performed on the 11 embryos cultivated. One embryo was considered qualified for transplanting, which carried the exact same CCRs as the female carrier, whose phenotype was normal. The amniotic fluid was also investigated by WGL-MPS and karyotyping at 19 weeks' gestation, which verified the results that the baby carried the same CCRs. A healthy baby was born at 39 weeks' gestation by vaginal delivery. CONCLUSION(S) Our study illustrates the WGL-MPS approach combining with junction-spanning PCR and PGT-A is a powerful and practical method in the setting of assisted reproduction for couples with recurrent miscarriage due to chromosomal abnormalities, especially CCRs carriers.
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Affiliation(s)
- Jian Ou
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, 215002, China
| | - Chuanchun Yang
- CheerLand Biological Technology Co., Ltd, Shenzhen, 518000, China
| | - Xiaoli Cui
- CheerLand Biological Technology Co., Ltd, Shenzhen, 518000, China
| | - Chuan Chen
- CheerLand Biological Technology Co., Ltd, Shenzhen, 518000, China
| | - Suyan Ye
- Shenzhen Dapeng New District Maternity & Child Health Hospital Department of Gynecology, Shenzhen, China
| | - Cai Zhang
- CheerLand Biological Technology Co., Ltd, Shenzhen, 518000, China
| | - Kai Wang
- CheerLand Biological Technology Co., Ltd, Shenzhen, 518000, China
| | - Jianguo Chen
- CheerLand Biological Technology Co., Ltd, Shenzhen, 518000, China
| | - Qin Zhang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, 215002, China
| | - Chunfeng Qian
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, 215002, China
| | - Guangguang Fang
- Shenzhen Dapeng New District Maternity & Child Health Hospital Department of Gynecology, Shenzhen, China.
- Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.
| | - Wenyong Zhang
- Southern University of Science and Technology-CheerLand Institute of Precision Medicine, Shenzhen, China.
- School of Medicine, Southern University of Science and Technology, Shenzhen, China.
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Yoshihara M, Oguchi A, Murakawa Y. Genomic Instability of iPSCs and Challenges in Their Clinical Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1201:23-47. [PMID: 31898780 DOI: 10.1007/978-3-030-31206-0_2] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Generation of human-induced pluripotent stem cells (iPSCs) from somatic cells has opened the possibility to design novel therapeutic approaches. In 2014, the first-in-human clinical trial of iPSC-based therapy was conducted. However, the transplantation for the second patient was discontinued at least in part due to genetic aberrations detected in iPSCs. Moreover, many studies have reported genetic aberrations in iPSCs with the rapid progress in genomic technologies. The presence of genomic instability raises serious safety concerns and can hamper the advancement of iPSC-based therapies. Here, we summarize our current knowledge on genomic instability of iPSCs and challenges in their clinical applications. In view of the recent expansion of stem cell therapies, it is crucial to gain deeper mechanistic insights into the genetic aberrations, ranging from chromosomal aberrations, copy number variations to point mutations. On the basis of their origin, these genetic aberrations in iPSCs can be classified as (i) preexisting mutations in parental somatic cells, (ii) reprogramming-induced mutations, and (iii) mutations that arise during in vitro culture. However, it is still unknown whether these genetic aberrations in iPSCs can be an actual risk factor for adverse effects. Intersection of the genomic data on iPSCs with the patients' clinical follow-up data will help to produce evidence-based criteria for clinical application. Furthermore, we discuss novel approaches to generate iPSCs with fewer genetic aberrations. Better understanding of iPSCs from both basic and clinical aspects will pave the way for iPSC-based therapies.
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Affiliation(s)
- Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Akiko Oguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy.
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Rojano E, Seoane P, Ranea JAG, Perkins JR. Regulatory variants: from detection to predicting impact. Brief Bioinform 2019; 20:1639-1654. [PMID: 29893792 PMCID: PMC6917219 DOI: 10.1093/bib/bby039] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/18/2018] [Indexed: 02/01/2023] Open
Abstract
Variants within non-coding genomic regions can greatly affect disease. In recent years, increasing focus has been given to these variants, and how they can alter regulatory elements, such as enhancers, transcription factor binding sites and DNA methylation regions. Such variants can be considered regulatory variants. Concurrently, much effort has been put into establishing international consortia to undertake large projects aimed at discovering regulatory elements in different tissues, cell lines and organisms, and probing the effects of genetic variants on regulation by measuring gene expression. Here, we describe methods and techniques for discovering disease-associated non-coding variants using sequencing technologies. We then explain the computational procedures that can be used for annotating these variants using the information from the aforementioned projects, and prediction of their putative effects, including potential pathogenicity, based on rule-based and machine learning approaches. We provide the details of techniques to validate these predictions, by mapping chromatin-chromatin and chromatin-protein interactions, and introduce Clustered Regularly Interspaced Short Palindromic Repeats-Associated Protein 9 (CRISPR-Cas9) technology, which has already been used in this field and is likely to have a big impact on its future evolution. We also give examples of regulatory variants associated with multiple complex diseases. This review is aimed at bioinformaticians interested in the characterization of regulatory variants, molecular biologists and geneticists interested in understanding more about the nature and potential role of such variants from a functional point of views, and clinicians who may wish to learn about variants in non-coding genomic regions associated with a given disease and find out what to do next to uncover how they impact on the underlying mechanisms.
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Affiliation(s)
- Elena Rojano
- Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain
| | - Pedro Seoane
- Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain
| | - Juan A G Ranea
- CIBER de Enfermedades Raras, ISCIII, Madrid, Spain and Department of Molecular Biology and Biochemistry, University of Malaga (UMA), 29010 Malaga, Spain
| | - James R Perkins
- Research laboratory, IBIMA-Regional University Hospital of Malaga, UMA, Malaga 29009, Spain
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14
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Dutta UR, Rao SN, Pidugu VK, V.S. V, Bhattacherjee A, Bhowmik AD, Ramaswamy SK, Singh KG, Dalal A. Breakpoint mapping of a novel de novo translocation t(X;20)(q11.1;p13) by positional cloning and long read sequencing. Genomics 2019; 111:1108-1114. [DOI: 10.1016/j.ygeno.2018.07.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/21/2018] [Accepted: 07/06/2018] [Indexed: 01/20/2023]
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15
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Liu M, Fang L, Liu S, Pan MG, Seroussi E, Cole JB, Ma L, Chen H, Liu GE. Array CGH-based detection of CNV regions and their potential association with reproduction and other economic traits in Holsteins. BMC Genomics 2019; 20:181. [PMID: 30845913 PMCID: PMC6407259 DOI: 10.1186/s12864-019-5552-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/21/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy number variations (CNVs) are structural variants consisting of large-scale insertions and deletions of genomic fragments. Exploring CNVs and estimating their effects on phenotypes are useful for genome selection but remain challenging in the livestock. RESULTS We identified 1043 CNV regions (CNVRs) from array comparative genomic hybridization (CGH) data of 47 Holstein bulls. Using a probe-based CNV association approach, we detected 87 CNVRs significantly (Bonferroni-corrected P value < 0.05) associated with at least one out of 41 complex traits. Within them, 39 CNVRs were simultaneously associated with at least 2 complex traits. Notably, 24 CNVRs were markedly related to daughter pregnancy rate (DPR). For example, CNVR661 containing CYP4A11 and CNVR213 containing CTR9, respectively, were associated with DPR and other traits related to reproduction, production, and body conformation. CNVR758 was also significantly related to DPR, with a nearby gene CAPZA3, encoding one of F-actin-capping proteins which play a role in determining sperm architecture and male fertility. We corroborated these CNVRs by examining their overlapped quantitative trait loci and comparing with previously published CNV results. CONCLUSION To our knowledge, this is one of the first genome-wide association studies based on CNVs called by array CGH in Holstein cattle. Our results contribute substantial information about the potential CNV impacts on reproduction, health, production, and body conformation traits, which lay the foundation for incorporating CNV into the future dairy cattle breeding program.
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Affiliation(s)
- Mei Liu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, 712100 Shaanxi China
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Lingzhao Fang
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD USA
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Michael G. Pan
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Eyal Seroussi
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, Department of Quantitative and Molecular Genetics, HaMaccabim Road, P.O.B 15159, 7528809 Rishon LeTsiyon, Israel
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD USA
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, 712100 Shaanxi China
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
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16
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Murcia Pienkowski V, Kucharczyk M, Młynek M, Szczałuba K, Rydzanicz M, Poszewiecka B, Skórka A, Sykulski M, Biernacka A, Koppolu AA, Posmyk R, Walczak A, Kosińska J, Krajewski P, Castaneda J, Obersztyn E, Jurkiewicz E, Śmigiel R, Gambin A, Chrzanowska K, Krajewska-Walasek M, Płoski R. Mapping of breakpoints in balanced chromosomal translocations by shallow whole-genome sequencing points to EFNA5, BAHD1 and PPP2R5E as novel candidates for genes causing human Mendelian disorders. J Med Genet 2018; 56:104-112. [PMID: 30352868 DOI: 10.1136/jmedgenet-2018-105527] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/04/2022]
Abstract
BACKGROUND Mapping the breakpoints in de novo balanced chromosomal translocations (BCT) in symptomatic individuals provides a unique opportunity to identify in an unbiased way the likely causative genetic defect and thus find novel human disease candidate genes. Our aim was to fine-map breakpoints of de novo BCTs in a case series of nine patients. METHODS Shallow whole-genome mate pair sequencing (SGMPS) together with long-range PCR and Sanger sequencing. In one case (BCT disrupting BAHD1 and RET) cDNA analysis was used to verify expression of a fusion transcript in cultured fibroblasts. RESULTS In all nine probands 11 disrupted genes were found, that is, EFNA5, EBF3, LARGE, PPP2R5E, TXNDC5, ZNF423, NIPBL, BAHD1, RET, TRPS1 and SLC4A10. Five subjects had translocations that disrupted genes with so far unknown (EFNA5, BAHD1, PPP2R5E, TXNDC5) or poorly delineated impact on the phenotype (SLC4A10, two previous reports of BCT disrupting the gene). The four genes with no previous disease associations (EFNA5, BAHD1, PPP2R5E, TXNDC5), when compared with all human genes by a bootstrap test, had significantly higher pLI (p<0.017) and DOMINO (p<0.02) scores indicating enrichment in genes likely to be intolerant to single copy damage. Inspection of individual pLI and DOMINO scores, and local topologically associating domain structure suggested that EFNA5, BAHD1 and PPP2R5E were particularly good candidates for novel disease loci. The pathomechanism for BAHD1 may involve deregulation of expression due to fusion with RET promoter. CONCLUSION SGMPS in symptomatic carriers of BCTs is a powerful approach to delineate novel human gene-disease associations.
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Affiliation(s)
- Victor Murcia Pienkowski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Marzena Kucharczyk
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Marlena Młynek
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | | | - Barbara Poszewiecka
- Faculty of Mathematics, Informatics and Mechanics, Institute of Informatics, University of Warsaw, Warsaw, Poland
| | - Agata Skórka
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland.,Department of Pediatrics, Medical University of Warsaw, Warsaw, Poland
| | - Maciej Sykulski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,genXone, Poznan, Poland
| | - Anna Biernacka
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Anna Koppolu
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Renata Posmyk
- Department of Clinical Genetics, Podlaskie Medical Center, Bialystok, Poland.,Department of Perinatology, Medical University of Bialystok, Bialystok, Poland
| | - Anna Walczak
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Joanna Kosińska
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Paweł Krajewski
- Department of Forensic Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Jennifer Castaneda
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Ewa Obersztyn
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Elżbieta Jurkiewicz
- Department of Diagnostic Imaging, The Children's Memorial Health Institute, Warsaw, Poland
| | - Robert Śmigiel
- Department of Pediatrics and Rare Disorder, Wroclaw Medical University, Wroclaw, Poland
| | - Anna Gambin
- Faculty of Mathematics, Informatics and Mechanics, Institute of Informatics, University of Warsaw, Warsaw, Poland
| | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | | | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
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17
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Sgardioli IC, Lustosa-Mendes E, dos Santos AP, Vieira TP, Gil-da-Silva-Lopes VL. A Rare Case of Concomitant Deletions in 15q11.2 and 19p13.3. Cytogenet Genome Res 2018; 156:80-86. [DOI: 10.1159/000493283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2018] [Indexed: 01/29/2023] Open
Abstract
A female individual with concomitant deletions in 15q11.2 and 19p13.3 is reported. She presents facial dysmorphisms, motor delay, learning difficulties, and mild behavioral impairment. After chromosomal microarray analysis, the final karyotype was established as 46,XX.arr[GRCh37] 15q11.2 (22770421_23282798)×1,19p13.3(3793904_4816330)×1. The deletion in 15q11.2 is 507 kb in size involving 7 non-imprinted genes, 4 of which are registered in the OMIM database and are implicated in neuropsychiatric or neurodevelopmental disorders. The deletion in 19p13.3 is 1,022 kb in size and encompasses 47 genes, most of which do not have a well-known function. The genotype-phenotype correlation is discussed, and most of the features could be related to the 19p13.3 deletion, except for velopharyngeal insufficiency. Other genes encompassed in the deleted region, as well as unrecognized epistatic factors could also be involved. Nevertheless, the two-hit model related to the 15q11.2 deletion would be an important hypothesis to be considered.
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18
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Next-generation sequencing approaches for the study of genome and epigenome toxicity induced by sulfur mustard. Arch Toxicol 2018; 92:3443-3457. [PMID: 30155719 DOI: 10.1007/s00204-018-2294-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/20/2018] [Indexed: 12/19/2022]
Abstract
Sulfur mustard (SM) is an extensive nucleophilic and alkylating agent that targets different tissues. The genotoxic property of SM is the most threatening effect, because it is associated with detrimental inflammations and susceptibility to several kinds of cancer. Moreover, SM causes a wide variety of adverse effects on DNA which result in accumulation of DNA adducts, multiple mutations, aneuploidies, and epigenetic aberrations in the genome. However, these adverse effects are still not known well, possibly because no valid biomarkers have been developed for detecting them. The advent of next-generation sequencing (NGS) has provided opportunities for the characterization of these alterations with a higher level of molecular detail and cost-effectivity. The present review introduces NGS approaches for the detection of SM-induced DNA adducts, mutations, chromosomal structural variation, and epigenetic aberrations, and also comparing and contrasting them with regard to which might be most advantageous.
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19
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Adega F, Matoso Silva R, Kjöllerström HJ, Vercammen P, Raudsepp T, Collares-Pereira MJ, Fernandes C, do Mar Oom M, Chaves R. Comparative Chromosome Painting in Genets (Carnivora, Viverridae, Genetta), the Only Known Feliforms with a Highly Rearranged Karyotype. Cytogenet Genome Res 2018; 156:35-44. [PMID: 30086546 DOI: 10.1159/000491868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2018] [Indexed: 11/19/2022] Open
Abstract
Mammalian carnivores have been extensively studied by cross-species chromosome painting, which indicated a high degree of karyotypic conservatism in the cat-like suborder Feliformia relative to the ancestral carnivore karyotype (ACK). The first exception to this high degree of karyotypic conservation in feliforms was recently confirmed in genets, mesocarnivores belonging to the basal family Viverridae. Here, we present a comparative analysis of the chromosome rearrangements among 2 subspecies of the small-spotted genet Genetta genetta (the Iberian nominate and the Arabian grantii) and the panther genet G. maculata, the 2 most common and widespread genets, using whole-chromosome paints from the domestic cat (Felis catus). The chromosome homology maps and the presence of numerous interstitial telomeric sites in both genet species strengthen the hypothesis that a highly rearranged karyotype compared to the ACK may occur throughout Genetta. The karyotype of G. maculata appears to have undergone more rearrangements than that of G. genetta, which is an older lineage. Notably, we identified a tandem fusion distinguishing G. g. genetta and G. g.grantii. As G. g. grantii is morphologically and genetically distinctive, and tandem fusions have been associated with substantial postzygotic isolation in mammals, this cytogenetic finding flags the subspecies for future taxonomic investigations.
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20
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Baumgartner A, Ferlatte Hartshorne C, Polyzos AA, Weier HUG, Weier JF, O’Brien B. Full Karyotype Interphase Cell Analysis. J Histochem Cytochem 2018; 66:595-606. [PMID: 29672206 PMCID: PMC6071177 DOI: 10.1369/0022155418771613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/15/2018] [Indexed: 11/22/2022] Open
Abstract
Aneuploidy seems to play not only a decisive role in embryonal development but also in tumorigenesis where chromosomal and genomic instability reflect a universal feature of malignant tumors. The cost of whole genome sequencing has fallen significantly, but it is still prohibitive for many institutions and clinical settings. No applied, cost-effective, and efficient technique has been introduced yet aiming at research to assess the ploidy status of all 24 different human chromosomes in interphases simultaneously, especially in single cells. Here, we present the selection of human probe DNA and a technique using multistep fluorescence in situ hybridization (FISH) employing four sets of six labeled FISH probes able to delineate all 24 human chromosomes in interphase cells. This full karyotype analysis approach will provide additional diagnostic potential for single cell analysis. The use of spectral imaging (SIm) has enabled the use of up to eight different fluorochrome labels simultaneously. Thus, scoring can be easily assessed by visual inspection, because SIm permits computer-assigned and distinguishable pseudo-colors to each probe during image processing. This enables full karyotype analysis by FISH of single-cell interphase nuclei.
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Affiliation(s)
- Adi Baumgartner
- Department of Obstetrics, Gynecology and
Reproductive Sciences, University of California, San Francisco,
California
- Life Sciences Division, E.O. Lawrence Berkeley
National Laboratory, Berkeley, California
- Biomedical Science, School of Health Sciences,
York St John University, York, United Kingdom
| | - Christy Ferlatte Hartshorne
- Department of Obstetrics, Gynecology and
Reproductive Sciences, University of California, San Francisco,
California
| | - Aris A. Polyzos
- Life Sciences Division, E.O. Lawrence Berkeley
National Laboratory, Berkeley, California
| | - Heinz-Ulrich G. Weier
- Life Sciences Division, E.O. Lawrence Berkeley
National Laboratory, Berkeley, California
| | - Jingly Fung Weier
- Department of Obstetrics, Gynecology and
Reproductive Sciences, University of California, San Francisco,
California
- Dermatopathology Service, University of
California, San Francisco, California
- Life Sciences Division, E.O. Lawrence Berkeley
National Laboratory, Berkeley, California
| | - Ben O’Brien
- Life Sciences Division, E.O. Lawrence Berkeley
National Laboratory, Berkeley, California
- Department of Perioperative Medicine, St
Bartholomew’s Hospital & Barts Heart Centre, London, United
Kingdom
- Outcomes Research Consortium, Cleveland Clinic,
Cleveland, Ohio
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Marajó L, Viana PF, Ferreira M, Py-Daniel LHR, Feldberg E. Cytogenetics of two Farlowella species (Loricariidae: Loricariinae): implications on the taxonomic status of the species. NEOTROPICAL ICHTHYOLOGY 2018. [DOI: 10.1590/1982-0224-20180029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
ABSTRACT Farlowella is one of the most diverse genera of the Loricariinae, restricted to South America rivers. The taxonomic and phylogenetic relationships among its species are contentious and, while genetic studies would contribute to the understanding of their relationships, the only available datum refer to the karyotype description of only one species. In the present study two Amazonian species, Farlowella cf. amazonum and F. schreitmuelleri, were analyzed using conventional and molecular cytogenetic procedures. Both species had diploid chromosome number 58, but different fundamental numbers (NF) 116 and 112, respectively, indicative of chromosomal rearrangements. C-banding is almost poor, especially in F. cf. amazonum, and occurs predominantly in the centromeric and in some telomeric regions, although genome of F. schreitmuelleri possessed a much larger heterochromatin amount then those of F. cf. amazonum. The chromosomes bearing the NOR sites were likely the same for both species, corresponding to the 1st metacentric pair in F. cf. amazonum and to the 28th acrocentric in F. schreitmuelleri. The location of the 5S rDNA was species-specific marker. This study expanded the available cytogenetic data for Farlowella species and pointed the remarkable karyotype diversity among species/populations, indicating a possible species complex within genus.
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22
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Yoshihara M, Hayashizaki Y, Murakawa Y. Genomic Instability of iPSCs: Challenges Towards Their Clinical Applications. Stem Cell Rev Rep 2017; 13:7-16. [PMID: 27592701 PMCID: PMC5346115 DOI: 10.1007/s12015-016-9680-6] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Induced pluripotent stem cells (iPSCs) are a type of pluripotent stem cells generated directly from mature cells through the introduction of key transcription factors. iPSCs can be propagated and differentiated into many cell types in the human body, holding enormous potential in the field of regenerative medicine. However, genomic instability of iPSCs has been reported with the advent of high-throughput technologies such as next-generation sequencing. The presence of genetic variations in iPSCs has raised serious safety concerns, hampering the advancement of iPSC-based novel therapies. Here we summarize our current knowledge on genomic instability of iPSCs, with a particular focus on types of genetic variations and their origins. Importantly, it remains elusive whether genetic variations in iPSCs can be an actual risk factor for adverse effects including malignant outgrowth. Furthermore, we discuss novel approaches to generate iPSCs with fewer genetic variations. Lastly, we outline the safety issues and monitoring strategies of iPSCs in clinical settings.
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Affiliation(s)
- Masahito Yoshihara
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan.,Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | | | - Yasuhiro Murakawa
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan. .,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan.
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23
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Abstract
PurposeCurrent clinical genomics assays primarily utilize short-read sequencing (SRS), but SRS has limited ability to evaluate repetitive regions and structural variants. Long-read sequencing (LRS) has complementary strengths, and we aimed to determine whether LRS could offer a means to identify overlooked genetic variation in patients undiagnosed by SRS.MethodsWe performed low-coverage genome LRS to identify structural variants in a patient who presented with multiple neoplasia and cardiac myxomata, in whom the results of targeted clinical testing and genome SRS were negative.ResultsThis LRS approach yielded 6,971 deletions and 6,821 insertions > 50 bp. Filtering for variants that are absent in an unrelated control and overlap a disease gene coding exon identified three deletions and three insertions. One of these, a heterozygous 2,184 bp deletion, overlaps the first coding exon of PRKAR1A, which is implicated in autosomal dominant Carney complex. RNA sequencing demonstrated decreased PRKAR1A expression. The deletion was classified as pathogenic based on guidelines for interpretation of sequence variants.ConclusionThis first successful application of genome LRS to identify a pathogenic variant in a patient suggests that LRS has significant potential for the identification of disease-causing structural variation. Larger studies will ultimately be required to evaluate the potential clinical utility of LRS.
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Ahram DF, Al-Sarraj Y, Taha RZ, Elhag SF, Al-Shaban FA, El-Shanti H, Kambouris M. A chromosomal microdeletion of 15q in a female patient with epilepsy, ID, and autism spectrum disorder: a case report. Clin Case Rep 2017; 5:1013-1017. [PMID: 28588858 PMCID: PMC5457985 DOI: 10.1002/ccr3.945] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/19/2017] [Accepted: 03/09/2017] [Indexed: 11/15/2022] Open
Abstract
15q deletions have been described in association with intellectual disability and autism spectrum disorder (ASD). Previous reports have supported the role of 15q24 low copy repeats (LCRs) in mediating alternatively sized genomic rearrangements. Based on our reported finding of a 15q24 deletion coinciding with two LCR regions in a patient with epilepsy and ASD, we recommend that patients with 15q24 deletions be evaluated for ASD for early institution of therapy.
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Affiliation(s)
- Dina F Ahram
- Division of Nephrology College of Physicians and Surgeons Columbia University New York City New York
| | - Yasser Al-Sarraj
- Medical Genetics Center Qatar Biomedical Research Institute Hamad Bin Khalifa University Doha Qatar
| | - Rowaida Z Taha
- Medical Genetics Center Qatar Biomedical Research Institute Hamad Bin Khalifa University Doha Qatar
| | - Saba F Elhag
- Medical Genetics Center Qatar Biomedical Research Institute Hamad Bin Khalifa University Doha Qatar
| | - Fouad A Al-Shaban
- Medical Genetics Center Qatar Biomedical Research Institute Hamad Bin Khalifa University Doha Qatar
| | - Hatem El-Shanti
- Pediatrics University of Jordan Amman Jordan.,Pediatrics University of Iowa Iowa City Iowa
| | - Marios Kambouris
- Pathology-Genetics Sidra Medical and Research Center Doha Qatar.,Genetics Yale University School of Medicine New Haven Connecticut
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25
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Accurate Breakpoint Mapping in Apparently Balanced Translocation Families with Discordant Phenotypes Using Whole Genome Mate-Pair Sequencing. PLoS One 2017; 12:e0169935. [PMID: 28072833 PMCID: PMC5225008 DOI: 10.1371/journal.pone.0169935] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/22/2016] [Indexed: 12/21/2022] Open
Abstract
Familial apparently balanced translocations (ABTs) segregating with discordant phenotypes are extremely challenging for interpretation and counseling due to the scarcity of publications and lack of routine techniques for quick investigation. Recently, next generation sequencing has emerged as an efficacious methodology for precise detection of translocation breakpoints. However, studies so far have mainly focused on de novo translocations. The present study focuses specifically on familial cases in order to shed some light to this diagnostic dilemma. Whole-genome mate-pair sequencing (WG-MPS) was applied to map the breakpoints in nine two-way ABT carriers from four families. Translocation breakpoints and patient-specific structural variants were validated by Sanger sequencing and quantitative Real Time PCR, respectively. Identical sequencing patterns and breakpoints were identified in affected and non-affected members carrying the same translocations. PTCD1, ATP5J2-PTCD1, CADPS2, and STPG1 were disrupted by the translocations in three families, rendering them initially as possible disease candidate genes. However, subsequent mutation screening and structural variant analysis did not reveal any pathogenic mutations or unique variants in the affected individuals that could explain the phenotypic differences between carriers of the same translocations. In conclusion, we suggest that NGS-based methods, such as WG-MPS, can be successfully used for detailed mapping of translocation breakpoints, which can also be used in routine clinical investigation of ABT cases. Unlike de novo translocations, no associations were determined here between familial two-way ABTs and the phenotype of the affected members, in which the presence of cryptic imbalances and complex chromosomal rearrangements has been excluded. Future whole-exome or whole-genome sequencing will potentially reveal unidentified mutations in the patients underlying the discordant phenotypes within each family. In addition, larger studies are needed to determine the exact percentage for phenotypic risk in families with ABTs.
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Stočes Š, Ruttink T, Bartoš J, Studer B, Yates S, Zwierzykowski Z, Abrouk M, Roldán-Ruiz I, Książczyk T, Rey E, Doležel J, Kopecký D. Orthology Guided Transcriptome Assembly of Italian Ryegrass and Meadow Fescue for Single-Nucleotide Polymorphism Discovery. THE PLANT GENOME 2016; 9. [PMID: 27902806 DOI: 10.3835/plantgenome2016.02.0017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Single-nucleotide polymorphisms (SNPs) represent natural DNA sequence variation. They can be used for various applications including the construction of high-density genetic maps, analysis of genetic variability, genome-wide association studies, and map-based cloning. Here we report on transcriptome sequencing in the two forage grasses, meadow fescue ( Huds.) and Italian ryegrass ( Lam.), and identification of various classes of SNPs. Using the Orthology Guided Assembly (OGA) strategy, we assembled and annotated a total of 18,952 and 19,036 transcripts for Italian ryegrass and meadow fescue, respectively. In addition, we used transcriptome sequence data of perennial ryegrass ( L.) from a previous study to identify 16,613 transcripts shared across all three species. Large numbers of intraspecific SNPs were identified in all three species: 248,000 in meadow fescue, 715,000 in Italian ryegrass, and 529,000 in perennial ryegrass. Moreover, we identified almost 25,000 interspecific SNPs located in 5343 genes that can distinguish meadow fescue from Italian ryegrass and 15,000 SNPs located in 3976 genes that discriminate meadow fescue from both species. All identified SNPs were positioned in silico on the seven linkage groups (LGs) of using the GenomeZipper approach. With the identification and positioning of interspecific SNPs, our study provides a valuable resource for the grass research and breeding community and will enable detailed characterization of genomic composition and gene expression analysis in prospective × hybrids.
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The genetics of nonsyndromic bilateral Duane retraction syndrome. J AAPOS 2016; 20:396-400.e2. [PMID: 27658539 DOI: 10.1016/j.jaapos.2016.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 06/01/2016] [Accepted: 06/10/2016] [Indexed: 11/20/2022]
Abstract
PURPOSE To assess the importance of monogenic mutations and chromosomal copy number variants (CNVs) in the occurrence of nonsyndromic bilateral Duane retraction syndrome (bilateral nsDRS). METHODS The medical records of 12 patients with bilateral nsDRS were reviewed. Genes associated with DRS and associated congenital cranial dysinnervation disorders (SALL4, CHN1, HOXA1, TUBB3, and KIF21A) were sequenced in the standard fashion in each patient. Array comparative genomic hybridization (array CGH) was performed using Affymetrix Cytogenetics Whole-Genome 2.7M array, and the results were analyzed using Affymetrix Chromosome Analysis Suite v1.2. CNVs were assessed as unlikely to be pathologic if they were also present in the Database of Genomic Variants (DGV) or our local database of array CGH results in 150 normal individuals of Middle Eastern ethnicity. RESULTS No patient had a sequence mutation in SALL4, CHN1, HOXA1, TUBB3, or KIF21A. These 12 patients each had 36-42 chromosomal deletions and/or duplications (mean with standard deviation, 26.25 ± 6.77), but all of these CNVs were present either in the DGV or in our local database of normal individuals of similar ethnicity and, therefore, are considered nonpathogenic. CONCLUSIONS The results reported here suggest that bilateral nsDRS is not usually associated with mutations in these genes or with chromosomal CNVs. Current evidence suggests other factors such as epigenetic and/or teratogenic abnormalities may be a potential cause of bilateral nsDRS.
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Du C, Pusey BN, Adams CJ, Lau CC, Bone WP, Gahl WA, Markello TC, Adams DR. Explorations to improve the completeness of exome sequencing. BMC Med Genomics 2016; 9:56. [PMID: 27568008 PMCID: PMC5002202 DOI: 10.1186/s12920-016-0216-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 08/05/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Exome sequencing has advanced to clinical practice and proven useful for obtaining molecular diagnoses in rare diseases. In approximately 75 % of cases, however, a clinical exome study does not produce a definitive molecular diagnosis. These residual cases comprise a new diagnostic challenge for the genetics community. The Undiagnosed Diseases Program of the National Institutes of Health routinely utilizes exome sequencing for refractory clinical cases. Our preliminary data suggest that disease-causing variants may be missed by current standard-of-care clinical exome analysis. Such false negatives reflect limitations in experimental design, technical performance, and data analysis. RESULTS We present examples from our datasets to quantify the analytical performance associated with current practices, and explore strategies to improve the completeness of data analysis. In particular, we focus on patient ascertainment, exome capture, inclusion of intronic variants, and evaluation of medium-sized structural variants. CONCLUSIONS The strategies we present may recover previously-missed, disease causing variants in second-pass exome analysis. Understanding the limitations of the current clinical exome search space provides a rational basis to improve methods for disease variant detection using genome-scale sequencing techniques.
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Affiliation(s)
- Chen Du
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Barbara N Pusey
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Christopher J Adams
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - C Christopher Lau
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - William P Bone
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Thomas C Markello
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - David R Adams
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA.
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Marczok S, Bortz B, Wang C, Pospisil H. Comprehensive Analysis of Genome Rearrangements in Eight Human Malignant Tumor Tissues. PLoS One 2016; 11:e0158995. [PMID: 27391163 PMCID: PMC4938598 DOI: 10.1371/journal.pone.0158995] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 06/25/2016] [Indexed: 11/19/2022] Open
Abstract
Carcinogenesis is a complex multifactorial, multistage process, but the precise mechanisms are not well understood. In this study, we performed a genome-wide analysis of the copy number variation (CNV), breakpoint region (BPR) and fragile sites in 2,737 tumor samples from eight tumor entities and in 432 normal samples. CNV detection and BPR identification revealed that BPRs tended to accumulate in specific genomic regions in tumor samples whereas being dispersed genome-wide in the normal samples. Hotspots were observed, at which segments with similar alteration in copy number were overlapped along with BPRs adjacently clustered. Evaluation of BPR occurrence frequency showed that at least one was detected in about and more than 15% of samples for each tumor entity while BPRs were maximal in 12% of the normal samples. 127 of 2,716 tumor-relevant BPRs (termed 'common BPRs') exhibited also a noticeable occurrence frequency in the normal samples. Colocalization assessment identified 20,077 CNV-affecting genes and 169 of these being known tumor-related genes. The most noteworthy genes are KIAA0513 important for immunologic, synaptic and apoptotic signal pathways, intergenic non-coding RNA RP11-115C21.2 possibly acting as oncogene or tumor suppressor by changing the structure of chromatin, and ADAM32 likely importance in cancer cell proliferation and progression by ectodomain-shedding of diverse growth factors, and the well-known tumor suppressor gene p53. The BPR distributions indicate that CNV mutations are likely non-random in tumor genomes. The marked recurrence of BPRs at specific regions supports common progression mechanisms in tumors. The presence of hotspots together with common BPRs, despite its small group size, imply a relation between fragile sites and cancer-gene alteration. Our data further suggest that both protein-coding and non-coding genes possessing a range of biological functions might play a causative or functional role in tumor biology. This research enhances our understanding of the mechanisms for tumorigenesis and progression.
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Affiliation(s)
- Stefanie Marczok
- University of Applied Sciences Wildau, High Performance Computing in Life Sciences, Institute for Applied Biosciences, Wildau, Germany
| | - Birgit Bortz
- University of Applied Sciences Wildau, High Performance Computing in Life Sciences, Institute for Applied Biosciences, Wildau, Germany
| | - Chong Wang
- University of Applied Sciences Wildau, High Performance Computing in Life Sciences, Institute for Applied Biosciences, Wildau, Germany
| | - Heike Pospisil
- University of Applied Sciences Wildau, High Performance Computing in Life Sciences, Institute for Applied Biosciences, Wildau, Germany
- * E-mail:
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Zhu J, Liu H, Tang J, Riaz Khan M, Wang B, Bukhari I. Identification of minor chromosomal defects causing abnormal foetus and spontaneous abortions. Br J Biomed Sci 2016; 73:67-73. [PMID: 27181173 DOI: 10.1080/09674845.2016.1157919] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND Chromosomal abnormalities are the most common cause of recurrent abortions and miscarriages (RAM), but micro-variations on chromosomes causing RAM have never been previously studied. Single nucleotide polymorphisms (SNPs) are the single nucleotide variations frequently present at genome with the density of at least one common (>20% allele frequency) SNP per kilobase pair. It has already been reported that SNP array examination for chromosomal abnormalities has better performance than the conventional cytogenetic karyotyping. METHODS We applied SNP array to detect the chromosomal defects in 80 placental villi and foetal tissues of abnormal foetus and spontaneous abortions. RESULTS The analyses of data revealed that total 52.5% (42/80) cases were found to have chromosomal abnormalities. The trisomies were most commonly found 26/42 (61.9%) in current samples. Total 8/42 (19.1%) cases were found to have other structural aberrations including translocations in 2/8 (25%), duplications and deletions in 3/8 (37.5%) cases, respectively. SNP analysis also successfully detected triploidy 69,XXX and tetraploidy 92,XXXY. Total 12/80 cases were performed by cytogenetic karyotyping and results were compared with SNP data. Total 5/12 (41.7%) cases were found to have same findings with SNP data while results of 2/12 (16.7%) cases had partial similarity between both techniques. Four cases were declared as karyotypically normal (46,XY or 46,XX) by cytogenetic examination, but later on these four cases were found to have small chromosomal variation which could be the cause of RAM in women. CONCLUSION Therefore, we conclude that use of a high-density SNP platform in diagnosis can give better understanding of molecular causes of pregnancy loss and foetal abnormalities.
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Affiliation(s)
- Jiansheng Zhu
- a Maternity and Child Health Hospital of Anhui Province, The Maternal and Child Health Clinical College, Anhui Medical University , Hefei , China.,b Department of Laboratory Medicines , Anhui Provincial Hospital, Anhui Medical University , Hefei , China
| | - Hui Liu
- a Maternity and Child Health Hospital of Anhui Province, The Maternal and Child Health Clinical College, Anhui Medical University , Hefei , China
| | - Junxiang Tang
- a Maternity and Child Health Hospital of Anhui Province, The Maternal and Child Health Clinical College, Anhui Medical University , Hefei , China
| | - Muhammad Riaz Khan
- c School of life sciences , University of Science and Technology of China , Hefei , China
| | - Baolong Wang
- b Department of Laboratory Medicines , Anhui Provincial Hospital, Anhui Medical University , Hefei , China
| | - Ihtisham Bukhari
- c School of life sciences , University of Science and Technology of China , Hefei , China
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Potapova TA, Unruh JR, Box AC, Bradford WD, Seidel CW, Slaughter BD, Sivagnanam S, Wu Y, Li R. Karyotyping human and mouse cells using probes from single-sorted chromosomes and open source software. Biotechniques 2015; 59:335-6, 338, 340-2 passim. [PMID: 26651513 DOI: 10.2144/000114362] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 08/05/2015] [Indexed: 11/23/2022] Open
Abstract
Multispectral karyotyping analyzes all chromosomes in a single cell by labeling them with chromosome-specific probes conjugated to unique combinations of fluorophores. Currently available multispectral karyotyping systems require the purchase of specialized equipment and reagents. However, conventional laser scanning confocal microscopes that are capable of separating multiple overlapping emission spectra through spectral imaging and linear unmixing can be utilized for classifying chromosomes painted with multicolor probes. Here, we generated multicolor chromosome paints from single-sorted human and mouse chromosomes and developed the Karyotype Identification via Spectral Separation (KISS) analysis package, a set of freely available open source ImageJ tools for spectral unmixing and karyotyping. Chromosome spreads painted with our multispectral probe sets can be imaged on widely available spectral laser scanning confocal microscopes and analyzed using our ImageJ tools. Together, our probes and software enable academic labs with access to a laser-scanning spectral microscope to perform multicolor karyotyping in a cost-effective manner.
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Affiliation(s)
| | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO
| | - Andrew C Box
- Stowers Institute for Medical Research, Kansas City, MO
| | | | | | | | | | - Yuping Wu
- Stowers Institute for Medical Research, Kansas City, MO
| | - Rong Li
- Stowers Institute for Medical Research, Kansas City, MO.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS.,Department of Cell Biology, Johns Hopkins University School of Medicine, 855, N. Wolfe Street, 21205, Baltimore, MD
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Cytogenomics of Feline Cancers: Advances and Opportunities. Vet Sci 2015; 2:246-258. [PMID: 29061944 PMCID: PMC5644630 DOI: 10.3390/vetsci2030246] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 08/26/2015] [Indexed: 12/16/2022] Open
Abstract
Relative to the dog, integration of the cat into the “One Health” concept has been more restricted, particularly in the field of molecular oncology. Beyond the continual need to enhance the sophistication of feline healthcare per se, the unique spectrum of naturally-occurring cancers in the cat offers tremendous opportunities for comparative and translational advances that may have mutual benefit for human and veterinary medicine. The study of feline cancers additionally may generate new insight into underexplored aspects of tumor biology that are less accessible in other species, such as the relationship between chronic inflammation and neoplasia, and the role of viruses in malignant transformation. Several factors that have hindered molecular studies of feline cancers have now been surmounted, with the most fundamental step forward coming from the development of a high-quality reference genome sequence assembly for the cat. This article reviews landmark studies that have led to our current appreciation of feline genome architecture, and outlines techniques used in cancer cytogenomics, from conventional karyotyping analysis through to the development of genomic microarrays and beyond. A summary of progress in the identification and characterization of chromosomal aberrations in feline cancers is provided using examples from studies of injection-site sarcomas, lymphomas and mammary tumors.
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Pirooznia M, Goes FS, Zandi PP. Whole-genome CNV analysis: advances in computational approaches. Front Genet 2015; 6:138. [PMID: 25918519 PMCID: PMC4394692 DOI: 10.3389/fgene.2015.00138] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/23/2015] [Indexed: 01/04/2023] Open
Abstract
Accumulating evidence indicates that DNA copy number variation (CNV) is likely to make a significant contribution to human diversity and also play an important role in disease susceptibility. Recent advances in genome sequencing technologies have enabled the characterization of a variety of genomic features, including CNVs. This has led to the development of several bioinformatics approaches to detect CNVs from next-generation sequencing data. Here, we review recent advances in CNV detection from whole genome sequencing. We discuss the informatics approaches and current computational tools that have been developed as well as their strengths and limitations. This review will assist researchers and analysts in choosing the most suitable tools for CNV analysis as well as provide suggestions for new directions in future development.
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Affiliation(s)
- Mehdi Pirooznia
- Mood Disorders Center, Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University Baltimore, MD, USA
| | - Fernando S Goes
- Mood Disorders Center, Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University Baltimore, MD, USA
| | - Peter P Zandi
- Mood Disorders Center, Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University Baltimore, MD, USA ; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health Baltimore, MD, USA USA
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Durmaz AA, Karaca E, Demkow U, Toruner G, Schoumans J, Cogulu O. Evolution of genetic techniques: past, present, and beyond. BIOMED RESEARCH INTERNATIONAL 2015; 2015:461524. [PMID: 25874212 PMCID: PMC4385642 DOI: 10.1155/2015/461524] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/05/2014] [Indexed: 12/05/2022]
Abstract
Genetics is the study of heredity, which means the study of genes and factors related to all aspects of genes. The scientific history of genetics began with the works of Gregor Mendel in the mid-19th century. Prior to Mendel, genetics was primarily theoretical whilst, after Mendel, the science of genetics was broadened to include experimental genetics. Developments in all fields of genetics and genetic technology in the first half of the 20th century provided a basis for the later developments. In the second half of the 20th century, the molecular background of genetics has become more understandable. Rapid technological advancements, followed by the completion of Human Genome Project, have contributed a great deal to the knowledge of genetic factors and their impact on human life and diseases. Currently, more than 1800 disease genes have been identified, more than 2000 genetic tests have become available, and in conjunction with this at least 350 biotechnology-based products have been released onto the market. Novel technologies, particularly next generation sequencing, have dramatically accelerated the pace of biological research, while at the same time increasing expectations. In this paper, a brief summary of genetic history with short explanations of most popular genetic techniques is given.
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Affiliation(s)
- Asude Alpman Durmaz
- Department of Medical Genetics, Ege University Faculty of Medicine, 35100 Izmir, Turkey
| | - Emin Karaca
- Department of Medical Genetics, Ege University Faculty of Medicine, 35100 Izmir, Turkey
| | - Urszula Demkow
- Department of Laboratory Diagnostics and Clinical Immunology, Warsaw University Faculty of Medicine, 61 02-091 Warsaw, Poland
| | - Gokce Toruner
- Institute of Genomic Medicine, UMDNJ-NJ Medical School, Newark, NJ 07103, USA
| | - Jacqueline Schoumans
- Department of Medical Genetics, Cancer Cytogenetic Unit, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Ozgur Cogulu
- Department of Medical Genetics, Ege University Faculty of Medicine, 35100 Izmir, Turkey
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The molecular landscape of pediatric brain tumors in the next-generation sequencing era. Curr Neurol Neurosci Rep 2015; 14:474. [PMID: 25037717 DOI: 10.1007/s11910-014-0474-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Pediatric brain tumors are a leading cause of cancer-related death in children. In recent years, the application of next-generation sequencing and other high-throughput technologies to analysis of pediatric brain tumors has generated an abundance of molecular information. This has provided an unprecedented understanding of their biology and is refining tumor classification into clinically relevant subgroups. In this review, we provide an overview of our evolving molecular knowledge of the commonest pediatric brain tumors, pilocytic astrocytomas, ependymomas, medulloblastomas, and pediatric glioblastomas, as well as the biological and potential clinical implications of this new knowledge. Studies aimed at investigating intratumoral heterogeneity are also discussed.
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Liehr T, Othman MAK, Rittscher K, Alhourani E. The current state of molecular cytogenetics in cancer diagnosis. Expert Rev Mol Diagn 2015; 15:517-26. [PMID: 25664836 DOI: 10.1586/14737159.2015.1013032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Cytogenetics and molecular cytogenetics are and will continue to be indispensable tools in cancer diagnostics. Leukemia and lymphoma diagnostics are still emphases of routine (molecular) cytogenetics and corresponding studies of solid tumors gain more and more prominence. Here, first a historical perspective of molecular tumor cytogenetics is provided, which is followed by the basic principles of the fluorescence in situ hybridization (FISH) approach. Finally the current state of molecular cytogenetics in cancer diagnostics is discussed. Nowadays routine diagnostics includes basic FISH approaches rather than multicolor-FISH. The latter together with modern high-throughput methods have their impact on research to identify new tumor-associated genomic regions.
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Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, Postfach, D-07743 Jena, Germany
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Xu C, Zhang J, Wang YP, Deng HW, Li J. Characterization of human chromosomal material exchange with regard to the chromosome translocations using next-generation sequencing data. Genome Biol Evol 2014; 6:3015-24. [PMID: 25349267 PMCID: PMC4255766 DOI: 10.1093/gbe/evu234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
As an important subtype of structural variations, chromosomal translocation is associated with various diseases, especially cancers, by disrupting gene structures and functions. Traditional methods for identifying translocations are time consuming and have limited resolutions. Recently, a few studies have employed next-generation sequencing (NGS) technology for characterizing chromosomal translocations on human genome, obtaining high-throughput results with high resolutions. However, these studies are mainly focused on mechanism-specific or site-specific translocation mapping. In this study, we conducted a comprehensive genome-wide analysis on the characterization of human chromosomal material exchange with regard to the chromosome translocations. Using NGS data of 1,481 subjects from the 1000 Genomes Project, we identified 15,349,092 translocated DNA fragment pairs, ranging from 65 to 1,886 bp and with an average size of approximately 102 bp. On average, each individual genome carried about 10,364 pairs, covering approximately 0.069% of the genome. We identified 16 translocation hot regions, among which two regions did not contain repetitive fragments. Results of our study overlapped with a majority of previous results, containing approximately 79% of approximately 2,340 translocations characterized in three available translocation databases. In addition, our study identified five novel potential recurrent chromosomal material exchange regions with greater than 20% detection rates. Our results will be helpful for an accurate characterization of translocations in human genomes, and contribute as a resource for future studies of the roles of translocations in human disease etiology and mechanisms.
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Affiliation(s)
- Chao Xu
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University
| | - Jigang Zhang
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University
| | - Yu-Ping Wang
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University Department of Biomedical Engineering, School of Science and Engineering, Tulane University
| | - Hong-Wen Deng
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University Third Affiliated Hospital, China Southern Medical University, Guang Zhou, 510000, P. R. China
| | - Jian Li
- Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University
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Oliveira PH, da Silva CL, Cabral JM. Concise Review: Genomic Instability in Human Stem Cells: Current Status and Future Challenges. Stem Cells 2014; 32:2824-32. [DOI: 10.1002/stem.1796] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/03/2014] [Accepted: 06/09/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Pedro H. Oliveira
- Institut Pasteur; Microbial Evolutionary Genomics, Département Génomes et Génétique; Paris France
- CNRS; UMR3525 Paris France
| | - Cláudia Lobato da Silva
- Institute for Biotechnology and Bioengineering, Department of Bioengineering; Instituto Superior Técnico, Universidade de Lisboa; Lisboa Portugal
| | - Joaquim M.S. Cabral
- Institute for Biotechnology and Bioengineering, Department of Bioengineering; Instituto Superior Técnico, Universidade de Lisboa; Lisboa Portugal
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Wakui K. Study of structural chromosome abnormalities to increase the understanding of human genetic diversity: a commentary on signature of backward replication slippage at the copy number variation junction. J Hum Genet 2014; 59:591-2. [PMID: 25296582 DOI: 10.1038/jhg.2014.83] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Keiko Wakui
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
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Yenamandra A, Wheeler F, Hollis A, Barba L, Wang Y, Geng L. Detection of Genomic Imbalances Involved in Common Chromosomal Rearrangements of Acute Leukemia by Cytogenomic SNP Microarray Analysis. Cancer Genet 2014. [DOI: 10.1016/j.cancergen.2014.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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da Silva M, Ribeiro ED, Matoso DA, Sousa LM, Hrbek T, Py-Daniel LR, Feldberg E. Chromosomal polymorphism in two species of Hypancistrus (Siluriformes: Loricariidae): an integrative approach for understanding their biodiversity. Genetica 2014; 142:127-39. [PMID: 24682750 DOI: 10.1007/s10709-014-9760-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 03/14/2014] [Indexed: 10/25/2022]
Abstract
Structural chromosome changes are widely described in different vertebrate groups and generate genetic, phenotypic and behavioral diversity. During the evolution of loricariids, several rearrangements (fissions, fusions, inversions) seem to have occurred. Hypancistrus, tribe Ancistrini, are highly demanded for fishkeeping around the world. In this tribe, the diploid chromosome number 2n = 52 is considered a synapomorphy, and paracentric-type inversions appear to be involved in the chromosomal evolution of the tribe. The present study investigated the karyotypes of H. zebra and H. cf. debilittera using cytogenetic, classical and molecular tools, as well as DNA barcoding. Data reveal that, although diploid number in both species corroborates the proposed synapomorphy for the tribe, there is a complex karyotype dynamics, reflected in the intense chromosomal polymorphism, resulting from rearrangements involving ribosomal regions (5S and 18S rDNA), which are suggested to be paracentric inversions. Besides, DNA barcode confirms reciprocal monophyletism between the species, validating the existence of two species, only. This scenario, coupled with genomic instability caused by exogenous sequences such as Rex-3 retrotransposons and the species' sedentary lifestyle, which helps the fast polymorphism fixation, may reflect different phenotypic color patterns in natural populations, as observed in H. cf. debilittera.
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Affiliation(s)
- Maelin da Silva
- Programa de Pós Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo 2936, Petrópolis, Manaus, Amazonas, CEP 69067-375, Brazil,
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Utami KH, Hillmer AM, Aksoy I, Chew EGY, Teo ASM, Zhang Z, Lee CWH, Chen PJ, Seng CC, Ariyaratne PN, Rouam SL, Soo LS, Yousoof S, Prokudin I, Peters G, Collins F, Wilson M, Kakakios A, Haddad G, Menuet A, Perche O, Tay SKH, Sung KWK, Ruan X, Ruan Y, Liu ET, Briault S, Jamieson RV, Davila S, Cacheux V. Detection of chromosomal breakpoints in patients with developmental delay and speech disorders. PLoS One 2014; 9:e90852. [PMID: 24603971 PMCID: PMC3946304 DOI: 10.1371/journal.pone.0090852] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 02/04/2014] [Indexed: 01/25/2023] Open
Abstract
Delineating candidate genes at the chromosomal breakpoint regions in the apparently balanced chromosome rearrangements (ABCR) has been shown to be more effective with the emergence of next-generation sequencing (NGS) technologies. We employed a large-insert (7-11 kb) paired-end tag sequencing technology (DNA-PET) to systematically analyze genome of four patients harbouring cytogenetically defined ABCR with neurodevelopmental symptoms, including developmental delay (DD) and speech disorders. We characterized structural variants (SVs) specific to each individual, including those matching the chromosomal breakpoints. Refinement of these regions by Sanger sequencing resulted in the identification of five disrupted genes in three individuals: guanine nucleotide binding protein, q polypeptide (GNAQ), RNA-binding protein, fox-1 homolog (RBFOX3), unc-5 homolog D (C.elegans) (UNC5D), transmembrane protein 47 (TMEM47), and X-linked inhibitor of apoptosis (XIAP). Among them, XIAP is the causative gene for the immunodeficiency phenotype seen in the patient. The remaining genes displayed specific expression in the fetal brain and have known biologically relevant functions in brain development, suggesting putative candidate genes for neurodevelopmental phenotypes. This study demonstrates the application of NGS technologies in mapping individual gene disruptions in ABCR as a resource for deciphering candidate genes in human neurodevelopmental disorders (NDDs).
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Affiliation(s)
- Kagistia H. Utami
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Axel M. Hillmer
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore
| | - Irene Aksoy
- Stem Cells and Developmental Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Elaine G. Y. Chew
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore
| | - Audrey S. M. Teo
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore
| | - Zhenshui Zhang
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore
| | - Charlie W. H. Lee
- Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Pauline J. Chen
- Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Chan Chee Seng
- Scientific & Research Computing, Genome Institute of Singapore, Singapore, Singapore
| | - Pramila N. Ariyaratne
- Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Sigrid L. Rouam
- Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Lim Seong Soo
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Saira Yousoof
- Eye and Developmental Genetics Research, The Children’s Hospital at Westmead, Children’s Medical Research Institute and Save Sight Institute, Sydney, New South Wales, Australia
- Disciplines of Paediatrics and Child Health and Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Ivan Prokudin
- Eye and Developmental Genetics Research, The Children’s Hospital at Westmead, Children’s Medical Research Institute and Save Sight Institute, Sydney, New South Wales, Australia
- Disciplines of Paediatrics and Child Health and Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Gregory Peters
- Department of Cytogenetics, The Children’s Hospital at Westmead, Sydney, New South Wales, Australia
| | - Felicity Collins
- Department of Clinical Genetics, The Children’s Hospital at Westmead, Sydney, New South Wales, Australia
| | - Meredith Wilson
- Department of Clinical Genetics, The Children’s Hospital at Westmead, Sydney, New South Wales, Australia
| | - Alyson Kakakios
- Department of Immunology, The Children’s Hospital at Westmead, Sydney, New South Wales, Australia
| | | | - Arnaud Menuet
- Service de Genetique INEM UMR7355 CNRS-University, Centre Hospitalier Régional d’Orléans, Orléans, France
| | - Olivier Perche
- Service de Genetique INEM UMR7355 CNRS-University, Centre Hospitalier Régional d’Orléans, Orléans, France
| | - Stacey Kiat Hong Tay
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ken W. K. Sung
- Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Xiaoan Ruan
- Genome Technology and Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Yijun Ruan
- Genome Technology and Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Edison T. Liu
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore, Singapore
| | - Sylvain Briault
- Service de Genetique INEM UMR7355 CNRS-University, Centre Hospitalier Régional d’Orléans, Orléans, France
| | - Robyn V. Jamieson
- Eye and Developmental Genetics Research, The Children’s Hospital at Westmead, Children’s Medical Research Institute and Save Sight Institute, Sydney, New South Wales, Australia
| | - Sonia Davila
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Valere Cacheux
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
- * E-mail:
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Abstract
The field of cytogenetics has focused on studying the number, structure, function and origin of chromosomal abnormalities and the evolution of chromosomes. The development of fluorescent molecules that either directly or via an intermediate molecule bind to DNA has led to the development of fluorescent in situ hybridization (FISH), a technology linking cytogenetics to molecular genetics. This technique has a wide range of applications that increased the dimension of chromosome analysis. The field of cytogenetics is particularly important for medical diagnostics and research as well as for gene ordering and mapping. Furthermore, the increased application of molecular biology techniques, such as array-based technologies, has led to improved resolution, extending the recognized range of microdeletion/microduplication syndromes and genomic disorders. In adopting these newly expanded methods, cytogeneticists have used a range of technologies to study the association between visible chromosome rearrangements and defects at the single nucleotide level. Overall, molecular cytogenetic techniques offer a remarkable number of potential applications, ranging from physical mapping to clinical and evolutionary studies, making a powerful and informative complement to other molecular and genomic approaches. This manuscript does not present a detailed history of the development of molecular cytogenetics; however, references to historical reviews and experiments have been provided whenever possible. Herein, the basic principles of molecular cytogenetics, the technologies used to identify chromosomal rearrangements and copy number changes, and the applications for cytogenetics in biomedical diagnosis and research are presented and discussed.
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Affiliation(s)
- Mariluce Riegel
- Serviço de Genética Médica, Hospital de Clínicas, Porto Alegre, RS, Brazil . ; Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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Abu-Amero KK, Bosley TM, Kondkar AA, Oystreck DT, Khan AO. CCDD Phenotype Associated with a Small Chromosome 2 Deletion. Semin Ophthalmol 2014; 30:435-42. [PMID: 24475916 DOI: 10.3109/08820538.2013.874474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE Some individuals are born with congenital limitation of ocular motility, often associated with ptosis and retraction of the globe. Many of these disorders are now known as the congenital cranial dysinnervation disorders (CCDDs). While several genes have been associated with CCDD phenotypes, there are still patients for whom the genetic basis has not been identified. METHODS Clinical evaluation and neuroimaging, sequencing of candidate genes, and array comparative genomic hybridization (array CGH). RESULTS The patient was a four-year-old girl with mild dysmorphism; bilateral mild ptosis; substantial limitation of abduction OS with milder limitations of abduction OD, adduction OS, and vertical gaze OS; and retraction OS > OD on attempted adduction. No mutations were detected in the HOXA1, KIF21A, SALL4, TUBB3, and CHN1 genes. Array CGH revealed a 8 Kb de novo deletion on chromosome 2 (2q24.3) that encompassed a portion of only one gene, the Xin Actin-binding Repeat containing 2 (Gene Symbol XIRP2; NM_001079810). This gene encodes a protein that is involved in muscle development and protecting actin filaments from depolymerization. It interacts functionally with 10 other proteins playing a similar role in muscle development. CONCLUSIONS This patient's chromosomal abnormality affected only one gene that currently seems involved only in muscle development. All other genes currently associated with the CCDDs affect neurologic development. Genetic information from this patient implies that genes involved in development and maintenance of extraocular muscles can cause congenital ocular motility disorders as well.
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Affiliation(s)
- Khaled K Abu-Amero
- a Department of Ophthalmology , College of Medicine, King Saud University , Riyadh , Saudi Arabia .,b Department of Ophthalmology , College of Medicine, University of Florida , Jacksonville , Florida , USA
| | - Thomas M Bosley
- a Department of Ophthalmology , College of Medicine, King Saud University , Riyadh , Saudi Arabia
| | - Altaf A Kondkar
- a Department of Ophthalmology , College of Medicine, King Saud University , Riyadh , Saudi Arabia
| | - Darren T Oystreck
- a Department of Ophthalmology , College of Medicine, King Saud University , Riyadh , Saudi Arabia .,c Division of Ophthalmology, Faculty of Health Sciences , University of Stellenbosch , Tygerberg , South Africa , and
| | - Arif O Khan
- d Division of Pediatric Ophthalmology , King Khaled Eye Specialist Hospital , Riyadh , Saudi Arabia
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Gatinois V, Puechberty J, Lefort G, Geneviève D, Pellestor F. Les remaniements chromosomiques complexes. Med Sci (Paris) 2014; 30:55-63. [DOI: 10.1051/medsci/20143001014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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Tzetis M, Kitsiou-Tzeli S, Frysira H, Xaidara A, Kanavakis E. The clinical utility of molecular karyotyping using high-resolution array-comparative genomic hybridization. Expert Rev Mol Diagn 2014; 12:449-57. [DOI: 10.1586/erm.12.40] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Maria Tzetis
- Department of Medical Genetics, Aghia Sophia Childrens Hospital, Thivon & Levadias, Medical School, University of Athens, 11527, Athens, Greece
- Department of Medical Genetics, Aghia Sophia Childrens Hospital, Thivon & Levadias, Medical School, University of Athens, 11527, Athens, Greece
| | - Sofia Kitsiou-Tzeli
- Department of Medical Genetics, Aghia Sophia Childrens Hospital, Thivon & Levadias, Medical School, University of Athens, 11527, Athens, Greece
| | - Helen Frysira
- Department of Medical Genetics, Aghia Sophia Childrens Hospital, Thivon & Levadias, Medical School, University of Athens, 11527, Athens, Greece
| | - Athena Xaidara
- First Department of Pediatrics, Aghia Sophia, Children’s Hospital, Medical School, University of Athens, Greece
| | - Emmanuel Kanavakis
- Department of Medical Genetics, Aghia Sophia Childrens Hospital, Thivon & Levadias, Medical School, University of Athens, 11527, Athens, Greece
- Research Institute for the Study of Genetic and Malignant Disorders in Childhood, Aghia Sophia, Children’s Hospital, Athens, Greece
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Idris SF, Ahmad SS, Scott MA, Vassiliou GS, Hadfield J. The role of high-throughput technologies in clinical cancer genomics. Expert Rev Mol Diagn 2014; 13:167-81. [DOI: 10.1586/erm.13.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Abu-Amero KK, Kondkar A, Hellani AM, Oystreck DT, Khan AO, Bosley TM. Nicotinic Receptor Mutation in a Mildly Dysmorphic Girl with Duane Retraction Syndrome. Ophthalmic Genet 2013; 36:99-104. [DOI: 10.3109/13816810.2013.835431] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Khaled K Abu-Amero
- Department of Ophthalmology, College of Medicine, King Saud University , Riyadh , Saudi Arabia
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Abu-Amero KK, Kondkar AA, Al Otaibi A, Alorainy IA, Khan AO, Hellani AM, Oystreck DT, Bosley TM. Partial duplication of chromosome 19 associated with syndromic duane retraction syndrome. Ophthalmic Genet 2013; 36:14-20. [PMID: 23952617 DOI: 10.3109/13816810.2013.827218] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND To evaluate possible monogenic and chromosomal anomalies in a patient with unilateral Duane retraction syndrome, modest dysmorphism, cerebral white matter abnormalities, and normal cognitive function. MATERIALS AND METHODS Performing high-resolution array comparative genomic hybridization (array CGH) and sequencing of HOXA1, KIF21A, SALL4, and CHN1 genes. RESULTS The proband had unilateral Duane retraction syndrome (DRS) type III on the right with low-set ears, prominent forehead, clinodactyly, and a history of frequent infections during early childhood. Motor development and cognitive function were normal. Parents were not related, and no other family member was similarly affected. MRI revealed multiple small areas of high signal on T2 weighted images in cerebral white matter oriented along white matter tracts. Sequencing of HOXA1, KIF21A, SALL4, and CHN1 did not reveal any mutation(s). Array CGH showed a 95 Kb de novo duplication on chromosome 19q13.4 encompassing four killer cell immunoglobulin-like receptor (KIR) genes. Conclusions. KIR genes have not previously been linked to a developmental syndrome, although they are known to be expressed in the human brain and brainstem and to be associated with certain infections and autoimmune diseases, including some affecting the nervous system. DRS and brain neuroimaging abnormalities may imply a central and peripheral oligodendrocyte abnormality related in some fashion to an immunomodulatory disturbance.
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Affiliation(s)
- Khaled K Abu-Amero
- Department of Ophthalmology, College of Medicine, King Saud University , Riyadh , Saudi Arabia
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Benn P, Cuckle H, Pergament E. Non-invasive prenatal testing for aneuploidy: current status and future prospects. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2013; 42:15-33. [PMID: 23765643 DOI: 10.1002/uog.12513] [Citation(s) in RCA: 225] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 05/13/2013] [Accepted: 05/14/2013] [Indexed: 05/09/2023]
Abstract
Non-invasive prenatal testing (NIPT) for aneuploidy using cell-free DNA in maternal plasma is revolutionizing prenatal screening and diagnosis. We review NIPT in the context of established screening and invasive technologies, the range of cytogenetic abnormalities detectable, cost, counseling and ethical issues. Current NIPT approaches involve whole-genome sequencing, targeted sequencing and assessment of single nucleotide polymorphism (SNP) differences between mother and fetus. Clinical trials have demonstrated the efficacy of NIPT for Down and Edwards syndromes, and possibly Patau syndrome, in high-risk women. Universal NIPT is not cost-effective, but using NIPT contingently in women found at moderate or high risk by conventional screening is cost-effective. Positive NIPT results must be confirmed using invasive techniques. Established screening, fetal ultrasound and invasive procedures with microarray testing allow the detection of a broad range of additional abnormalities not yet detectable by NIPT. NIPT approaches that take advantage of SNP information potentially allow the identification of parent of origin for imbalances, triploidy, uniparental disomy and consanguinity, and separate evaluation of dizygotic twins. Fetal fraction enrichment, improved sequencing and selected analysis of the most informative sequences should result in tests for additional chromosomal abnormalities. Providing adequate prenatal counseling poses a substantial challenge given the broad range of prenatal testing options now available.
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Affiliation(s)
- P Benn
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT, USA.
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