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Li J, Lin Y, Li D, He M, Kui H, Bai J, Chen Z, Gou Y, Zhang J, Wang T, Tang Q, Kong F, Jin L, Li M. Building Haplotype-Resolved 3D Genome Maps of Chicken Skeletal Muscle. Adv Sci (Weinh) 2024:e2305706. [PMID: 38582509 DOI: 10.1002/advs.202305706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 03/07/2024] [Indexed: 04/08/2024]
Abstract
Haplotype-resolved 3D chromatin architecture related to allelic differences in avian skeletal muscle development has not been addressed so far, although chicken husbandry for meat consumption has been prevalent feature of cultures on every continent for more than thousands of years. Here, high-resolution Hi-C diploid maps (1.2-kb maximum resolution) are generated for skeletal muscle tissues in chicken across three developmental stages (embryonic day 15 to day 30 post-hatching). The sequence features governing spatial arrangement of chromosomes and characterize homolog pairing in the nucleus, are identified. Multi-scale characterization of chromatin reorganization between stages from myogenesis in the fetus to myofiber hypertrophy after hatching show concordant changes in transcriptional regulation by relevant signaling pathways. Further interrogation of parent-of-origin-specific chromatin conformation supported that genomic imprinting is absent in birds. This study also reveals promoter-enhancer interaction (PEI) differences between broiler and layer haplotypes in skeletal muscle development-related genes are related to genetic variation between breeds, however, only a minority of breed-specific variations likely contribute to phenotypic divergence in skeletal muscle potentially via allelic PEI rewiring. Beyond defining the haplotype-specific 3D chromatin architecture in chicken, this study provides a rich resource for investigating allelic regulatory divergence among chicken breeds.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Mengnan He
- Wildlife Conservation Research Department, Chengdu Research Base of Giant Panda Breeding, Chengdu, 610057, China
| | - Hua Kui
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jingyi Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ziyu Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuwei Gou
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiaman Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tao Wang
- School of Pharmacy, Chengdu University, Chengdu, 610106, China
| | - Qianzi Tang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fanli Kong
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Long Jin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mingzhou Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
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Asia LK, Van Vuren EJ, Kruger IM, Williams ME. A Pilot Investigation of the Association Between Vpr Amino Acid Substitutions and Peripheral Immune Marker Levels in People With Human Immunodeficiency Virus: Implications for Neurocognitive Impairment. Open Forum Infect Dis 2024; 11:ofae111. [PMID: 38524224 PMCID: PMC10960601 DOI: 10.1093/ofid/ofae111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/23/2024] [Indexed: 03/26/2024] Open
Abstract
Background Subtype-specific amino acid variations in viral proteins of human immunodeficiency virus type 1 (HIV-1) influence disease progression. Furthermore, Vpr sequence variation correlates with chronic inflammation, a central mechanism in HIV-1 (neuro)pathogenesis. Nevertheless, no clinical study has investigated the link between Vpr sequence variation and peripheral inflammation in people with HIV (PWH). The aim of this pilot study was to ascertain whether specific Vpr amino acid variants were associated with immune markers in PWH. Methods We included a unique cohort of 48 treatment-naive South African PWH to determine the association between blood-derived Vpr sequence variation and peripheral immune marker levels using Sanger sequencing and enzyme-linked immunosorbent assay analysis, respectively. Results Our findings indicate that among the many neuropathogenic Vpr amino acid variants and immune markers examined, after applying Bonferroni corrections (P = .05/3) and adjusting for sex and locality, soluble urokinase plasminogen activator receptor (suPAR) was nearing significance for higher levels in participants with the G41 amino acid variant compared to those with the S41 variant (P = .035). Furthermore, amino acid variations at position 41 (between G41 and S41) exhibited a significant association with suPAR (adjusted R2 = 0.089, β = .386 [95% confidence interval, .125-3.251]; P = .035). Conclusions These findings suggest that Vpr amino acid sequence variations might contribute to dysregulated inflammation, which could explain the observed association between specific Vpr variants and HIV-1 (neuro)pathogenesis found in prior research. These Vpr variants merit further investigation to fully understand their roles in HIV-1 pathogenesis and neuropathogenesis.
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Affiliation(s)
- Levanco K Asia
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Esmé Jansen Van Vuren
- Hypertension in Africa Research Team, North-West University, Potchefstroom, South Africa
- South African Medical Research Council, Unit for Hypertension and Cardiovascular Disease, North-West University, Potchefstroom, South Africa
| | - Iolanthé M Kruger
- Africa Unit for Transdisciplinary Health Research, North-West University, Potchefstroom, South Africa
| | - Monray E Williams
- Human Metabolomics, North-West University, Potchefstroom, South Africa
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Srivastava P, Bamba C, Chopra S, Rohilla M, Chaudhry C, Kaur A, Panigrahi I, Mandal K. Identification of genetic alterations in couples and their products of conceptions from recurrent pregnancy loss in North Indian population. Front Genet 2023; 14:1155211. [PMID: 37260775 PMCID: PMC10227573 DOI: 10.3389/fgene.2023.1155211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/02/2023] [Indexed: 06/02/2023] Open
Abstract
Background: Recurrent pregnancy loss (RPL) is one of the most common pregnancy-related complications, which can be stressful and emotionally draining for a couple. Genetic alterations, which are responsible for RPL, can be present in either of the three genomes: mother, father, or their fetuses. In addition, environmental factors interacting with these three genomes can affect germline cells. With this aim, the present study was conducted to understand the underlying etiology of RPL using Next-generation sequencing (NGS; couple exome and TRIO exomes) in combination with cytogenetic tests [karyotyping and chromosomal microarray (CMA)]. Material & Methods: In present study we recruited 61 couples with RPL (history of ≥ 2 abortions) and 31 products of conceptions (POCs). For all couples karyotyping was done at the time of recruitment, followed by collection of POC samples and parental blood samples. Before processing POC samples for CMA, they were checked for maternal cell contamination (MCC) by QF-PCR. In POC samples with no pathogenic variant, TRIO exome sequencing was done. Further, in case of unavailability of POC sample, couple exome sequencing was done for RPL couples. Results: In six individuals out of 61 couples (5%), abnormality in karyotypes was detected. Among 116 normal karyotypes, there were 11 heteromorphisms (9.5%), for which the couples had to be counselled and reassured. Out of the 31 POCs, 10 were excluded because of MCC (around 30%) and one had major aneuploidy. CMA in POCs identified pathogenic copy number variations (CNVs) in 25% of cases (5/20) and variant of unknown significance (VUS) in 20% of cases (4/20). Autosomal trisomy was the most frequent chromosomal abnormality diagnosed. NGS was performed to establish single-gene causes of RPL. Couple exome sequencing was performed in 20 couples, and 14 were found to be carriers for autosomal recessive conditions. A total of 50 potential disease-causing variants in 40 genes were identified in 33 of 40 individuals (82.5%). Putative causative variants were identified in 37.5% of the TRIO cases (3/8). Mutations in few important genes (SRP54, ERBB4, NEB, ALMS, ALAD, MTHFR, F5, and APOE), which are involved in vital pathways, early embryonic development, and fetal demise, were identified in the POCs. Conclusion: It enhances our understanding of prenatal phenotypes of many Mendelian disorders. These mutated genes may play an auxiliary role in the development of treatment strategies for RPL. There was no correlation of the number of abortions with etiological yield of any technique to detect the cause of RPL. This study shows the utilization of combination of techniques in improving our understanding of the cause of early embryonic lethality in humans.
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Affiliation(s)
- Priyanka Srivastava
- Genetic Metabolic Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Chitra Bamba
- Genetic Metabolic Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Seema Chopra
- Department of Obstetrics and Gynaecology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Minakshi Rohilla
- Department of Obstetrics and Gynaecology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Chakshu Chaudhry
- Genetic Metabolic Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Anupriya Kaur
- Genetic Metabolic Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Inusha Panigrahi
- Genetic Metabolic Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow, India
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Dharanipragada P, Parekh N. In Silico Identification and Functional Characterization of Genetic Variations across DLBCL Cell Lines. Cells 2023; 12:cells12040596. [PMID: 36831263 PMCID: PMC9954129 DOI: 10.3390/cells12040596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/12/2023] [Accepted: 01/29/2023] [Indexed: 02/15/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common form of non-Hodgkin lymphoma and frequently develops through the accumulation of several genetic variations. With the advancement in high-throughput techniques, in addition to mutations and copy number variations, structural variations have gained importance for their role in genome instability leading to tumorigenesis. In this study, in order to understand the genetics of DLBCL pathogenesis, we carried out a whole-genome mutation profile analysis of eleven human cell lines from germinal-center B-cell-like (GCB-7) and activated B-cell-like (ABC-4) subtypes of DLBCL. Analysis of genetic variations including small sequence variants and large structural variations across the cell lines revealed distinct variation profiles indicating the heterogeneous nature of DLBCL and the need for novel patient stratification methods to design potential intervention strategies. Validation and prognostic significance of the variants was assessed using annotations provided for DLBCL samples in cBioPortal for Cancer Genomics. Combining genetic variations revealed new subgroups between the subtypes and associated enriched pathways, viz., PI3K-AKT signaling, cell cycle, TGF-beta signaling, and WNT signaling. Mutation landscape analysis also revealed drug-variant associations and possible effectiveness of known and novel DLBCL treatments. From the whole-genome-based mutation analysis, our findings suggest putative molecular genetics of DLBCL lymphomagenesis and potential genomics-driven precision treatments.
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Deutsch N, Pajkos M, Erdős G, Dosztányi Z. DisCanVis: Visualizing integrated structural and functional annotations to better understand the effect of cancer mutations located within disordered proteins. Protein Sci 2023; 32:e4522. [PMID: 36452990 PMCID: PMC9793970 DOI: 10.1002/pro.4522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
Abstract
Intrinsically disordered proteins (IDPs) play important roles in a wide range of biological processes and have been associated with various diseases, including cancer. In the last few years, cancer genome projects have systematically collected genetic variations underlying multiple cancer types. In parallel, the number and different types of disordered proteins characterized by experimental methods have also significantly increased. Nevertheless, the role of IDPs in various types of cancer is still not well understood. In this work, we present DisCanVis, a novel visualization tool for cancer mutations with a special focus on IDPs. In order to aid the interpretation of observed mutations, genome level information is combined with information about the structural and functional properties of proteins. The web server enables users to inspect individual proteins, collect examples with existing annotations of protein disorder and associated function or to discover currently uncharacterized examples with likely disease relevance. Through a REST API interface and precompiled tables the analysis can be extended to a group of proteins.
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Affiliation(s)
- Norbert Deutsch
- Department of BiochemistryInstitute of Biology, ELTE Eötvös Loránd UniversityBudapestHungary
| | - Mátyás Pajkos
- Department of BiochemistryInstitute of Biology, ELTE Eötvös Loránd UniversityBudapestHungary
| | - Gábor Erdős
- Department of BiochemistryInstitute of Biology, ELTE Eötvös Loránd UniversityBudapestHungary
| | - Zsuzsanna Dosztányi
- Department of BiochemistryInstitute of Biology, ELTE Eötvös Loránd UniversityBudapestHungary
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Rai A, Patil SJ, Srivastava P, Gaurishankar K, Phadke SR. Clinical and molecular characterization of four patients with Robinow syndrome from different families. Am J Med Genet A 2021; 185:1105-1112. [PMID: 33496066 DOI: 10.1002/ajmg.a.62082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 11/11/2022]
Abstract
Robinow syndrome (RS) is a rare heterogeneous disorder characterized by short stature, short-limbs, craniofacial, oro-dental abnormalities, vertebral segmentation defects, and frequently genital hypoplasia. Both autosomal dominant and recessive patterns of inheritance are observed with many causative genes. Here, we present the phenotypes and genotypes of four children with RS from different Indian families. Sequence variants were identified in genes ROR2, DVL1, and DVL3. Our results expand the mutational spectrum of RS and we also highlight the radiological changes in the radius and ulna in patients with ROR2 sequence variants which are primarily characteristic for ROR2 related RS but have been reported in WNT5A related RS.
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Affiliation(s)
- Archana Rai
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Siddaramappa J Patil
- Division of Medical Genetics, Narayana Hrudayalaya Hospitals, Mazumdar-Shaw Medical Center, Bangalore, India
| | - Priyanka Srivastava
- Genetic Metabolic Unit, Department of Pediatrics, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Kalpana Gaurishankar
- Department of Medical Genetics, Apollo Hospitals and Kanchi Kamakoti Childs Trust Hospital, Chennai, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
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Abstract
Proteoforms are the workhorses of the cell, and subtle differences between their amino acid sequences or post-translational modifications (PTMs) can change their biological function. To most effectively identify and quantify proteoforms in genetically diverse samples by mass spectrometry (MS), it is advantageous to search the MS data against a sample-specific protein database that is tailored to the sample being analyzed, in that it contains the correct amino acid sequences and relevant PTMs for that sample. To this end, we have developed Spritz (https://smith-chem-wisc.github.io/Spritz/), an open-source software tool for generating protein databases annotated with sequence variations and PTMs. We provide a simple graphical user interface for Windows and scripts that can be run on any operating system. Spritz automatically sets up and executes approximately 20 tools, which enable the construction of a proteogenomic database from only raw RNA sequencing data. Sequence variations that are discovered in RNA sequencing data upon comparison to the Ensembl reference genome are annotated on proteins in these databases, and PTM annotations are transferred from UniProt. Modifications can also be discovered and added to the database using bottom-up mass spectrometry data and global PTM discovery in MetaMorpheus. We demonstrate that such sample-specific databases allow the identification of variant peptides, modified variant peptides, and variant proteoforms by searching bottom-up and top-down proteomic data from the Jurkat human T lymphocyte cell line and demonstrate the identification of phosphorylated variant sites with phosphoproteomic data from the U2OS human osteosarcoma cell line.
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Affiliation(s)
- Anthony J Cesnik
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm 17121, Sweden.,Department of Genetics, Stanford University, Stanford, California 94305, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Rachel M Miller
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Khairina Ibrahim
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lei Lu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Robert J Millikin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Brian L Frey
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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Huang Q, Liu X, Brisse M, Ly H, Liang Y. Effect of Strain Variations on Lassa Virus Z Protein-Mediated Human RIG-I Inhibition. Viruses 2020; 12:E907. [PMID: 32824946 PMCID: PMC7551410 DOI: 10.3390/v12090907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/12/2020] [Accepted: 08/16/2020] [Indexed: 11/21/2022] Open
Abstract
Mammarenaviruses include several known human pathogens, such as the prototypic lymphocytic choriomeningitis virus (LCMV) that can cause neurological diseases and Lassa virus (LASV) that causes endemic hemorrhagic fever infection. LASV-infected patients show diverse clinical manifestations ranging from asymptomatic infection to hemorrhage, multi-organ failures and death, the mechanisms of which have not been well characterized. We have previously shown that the matrix protein Z of pathogenic arenaviruses, including LASV and LCMV, can strongly inhibit the ability of the innate immune protein RIG-I to suppress type I interferon (IFN-I) expression, which serves as a mechanism of viral immune evasion and virulence. Here, we show that Z proteins of diverse LASV isolates derived from rodents and humans have a high degree of sequence variations at their N- and C-terminal regions and produce variable degrees of inhibition of human RIG-I (hRIG-I) function in an established IFN-β promoter-driven luciferase (LUC) reporter assay. Additionally, we show that Z proteins of four known LCMV strains can also inhibit hRIG-I at variable degrees of efficiency. Collectively, our results confirm that Z proteins of pathogenic LASV and LCMV can inhibit hRIG-I and suggest that strain variations of the Z proteins can influence their efficiency to suppress host innate immunity that might contribute to viral virulence and disease heterogeneity.
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Affiliation(s)
| | | | | | | | - Yuying Liang
- Correspondence: ; Tel.: +1-612-625-3376; Fax: +1-612-625-0204
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Shahid M, Firasat S, Satti HS, Satti TM, Ghafoor T, Sharif I, Afshan K. Screening of the FANCA gene mutational hotspots in the Pakistani fanconi anemia patients revealed 19 sequence variations. Congenit Anom (Kyoto) 2020; 60:32-39. [PMID: 30809872 DOI: 10.1111/cga.12331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/04/2019] [Accepted: 02/21/2019] [Indexed: 02/06/2023]
Abstract
Fanconi anemia (FA) is a recessive disorder that predispose to bone marrow failure and multiple congenital anomalies in affected individuals worldwide. To date, 22 FA genes are known to harbor sequence variations in disease phenotype. Among these, mutations in the FANCA gene are associated with 60% to 70% of FA cases. The aim of the present study was to screen FA cases belonging to consanguineous Pakistani families for selected exons of FANCA gene which are known mutational hotspots for Asian populations. Blood samples were collected from 20 FA cases and 20 controls. RNA was extracted and cDNA was synthesized from blood samples of cases. DNA was extracted from blood samples of cases and ethnically matched healthy controls. Sanger's sequencing of the nine selected exons of FANCA gene in FA cases revealed 19 genetic alterations of which 15 were single nucleotide variants, three were insertions and one was microdeletion. Of the total 19 sequence changes, 13 were novel and six were previously reported. All identified variants were evaluated by computational programs including SIFT, PolyPhen-2 and Mutation taster. Seven out of 20 analyzed patients were carrying homozygous novel sequence variations, predicted to be associated with FA. These disease associated novel variants were not detected in ethnically matched controls and depict genetic heterogeneity of disease.
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Affiliation(s)
- Muhammad Shahid
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sabika Firasat
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Humayoon Shafique Satti
- Armed Forces Bone Marrow Transplant Centre (AFBMTC), CMH Medical Complex, Rawalpindi, Pakistan
| | - Tariq Mahmood Satti
- Armed Forces Bone Marrow Transplant Centre (AFBMTC), CMH Medical Complex, Rawalpindi, Pakistan
| | - Tariq Ghafoor
- Armed Forces Bone Marrow Transplant Centre (AFBMTC), CMH Medical Complex, Rawalpindi, Pakistan
| | - Imtenan Sharif
- Department of Community Medicine, Army Medical College (AMC), National University of Medical Sciences, Rawalpindi, Pakistan
| | - Kiran Afshan
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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Dorn C, Grunert M, Sperling SR. Application of high-throughput sequencing for studying genomic variations in congenital heart disease. Brief Funct Genomics 2013; 13:51-65. [PMID: 24095982 DOI: 10.1093/bfgp/elt040] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Congenital heart diseases (CHD) represent the most common birth defect in human. The majority of cases are caused by a combination of complex genetic alterations and environmental influences. In the past, many disease-causing mutations have been identified; however, there is still a large proportion of cardiac malformations with unknown precise origin. High-throughput sequencing technologies established during the last years offer novel opportunities to further study the genetic background underlying the disease. In this review, we provide a roadmap for designing and analyzing high-throughput sequencing studies focused on CHD, but also with general applicability to other complex diseases. The three main next-generation sequencing (NGS) platforms including their particular advantages and disadvantages are presented. To identify potentially disease-related genomic variations and genes, different filtering steps and gene prioritization strategies are discussed. In addition, available control datasets based on NGS are summarized. Finally, we provide an overview of current studies already using NGS technologies and showing that these techniques will help to further unravel the complex genetics underlying CHD.
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Affiliation(s)
- Cornelia Dorn
- Department of Cardiovascular Genetics, Experimental and Clinical Research Center (ECRC), Charité-University Medicine Berlin and Max Delbrück Center (MDC) for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany. Department of Biochemistry, Free University Berlin, Berlin, Germany. Tel.: +49-(0)30-450540123; Fax: +49-(0)30-84131699;
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Li XY, Bian QQ, Zhao GH. Phylogenetic analysis of Pomacea canaliculata isolates collected from rice fields in different origins of China by combined mitochondrial 12S and 16S genes. Mitochondrial DNA 2013; 26:27-31. [PMID: 23876192 DOI: 10.3109/19401736.2013.809452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
To study the genetic relationships of Pomacea canaliculata collected from rice fields in China, the mitochondrial (mt) 12S and 16S of 9 P. canaliculata isolates from 5 southern provinces in China were sequenced and analyzed. The intra-specific sequence variations of P. canaliculata were 0-1.1% for 12S and 0--0.6% for 16S, while the inter-specific variations among common Pomacea species in mt 12S and 16S were 3.0-11.7% and 2.3-10.1%, respectively. Phylogenetic analysis based on combined sequences of mt 12S and 16S revealed complex genetic structure of P. canaliculata in China. Two phylogenetic groups of P. canaliculata were indicated in China with one group sistered to P. canaliculata isolates from USA, and two groups were even found in the same province. The phylogenetic relationships of Pomacea spp. also could be effectively inferred by combined sequences of mt 12S and 16S. These findings provided basic information for further study of population genetics and diffusion pattern of P. canaliculata in China as well as in the world.
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Affiliation(s)
- Xiao-Yan Li
- Northwest A&F University , Yangling, Shaanxi Province 712100 , People's Republic of China
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Zhao ZH, Bian QQ, Ren WX, Cheng WY, Jia YQ, Fang YQ, Zhao GH. Genetic variability of Baylisascaris schroederi from the Qinling subspecies of the giant panda in China revealed by sequences of three mitochondrial genes. ACTA ACUST UNITED AC 2013; 25:212-7. [PMID: 23656289 DOI: 10.3109/19401736.2013.792074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The present study examined the variations in three mitochondrial (mt) DNA sequences, namely cytochrome b (cytb), cytochrome c oxidase subunit 3 (cox3) and NADH dehydrogenase subunit 5 (nad5), among Baylisascaris schroederi isolates from the Qinling subspecies of the giant panda in Shaanxi province, northwestern China. No differences in length were detected in the three mt fragments from different isolates. The intra-specific sequence variations within all B. schroederi samples were 0-2.6% for pcytb, 0-1.8% for pcox3 and 0-2.1% for pnad5, while the inter-specific sequence differences among members of the genus Baylisascaris were 8.2-15.2%, 6.2-15.9% and 8.4-16.0% for pcytb, pcox3, pnad5, respectively. A phylogenetic analysis of the combined sequences of pcytb, pcox3 and pnad 5 showed that all B. schroederi samples in the present study were located in two large clusters, with one cluster containing samples from giant pandas in Sichuan province. These findings provide basic information for further study of molecular epidemiology and control of B. schroederi infection in the Qinling subspecies of the giant panda and throughout China.
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Affiliation(s)
- Zhong-Hui Zhao
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi Province , People's Republic of China
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