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Lei Y, Meng Y, Guo X, Ning K, Bian Y, Li L, Hu Z, Anashkina AA, Jiang Q, Dong Y, Zhu X. Overview of structural variation calling: Simulation, identification, and visualization. Comput Biol Med 2022; 145:105534. [DOI: 10.1016/j.compbiomed.2022.105534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/09/2022] [Accepted: 04/14/2022] [Indexed: 12/11/2022]
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Boehlke C, Rupf S, Tenniswood M, Chittur SV, Hannig C, Zierau O. Caries and periodontitis associated bacteria are more abundant in human saliva compared to other great apes. Arch Oral Biol 2020; 111:104648. [PMID: 31927405 DOI: 10.1016/j.archoralbio.2020.104648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/29/2019] [Accepted: 01/01/2020] [Indexed: 01/09/2023]
Abstract
OBJECTIVE Caries and periodontitis are uncommon in free ranging great apes but a major oral disease in humans. The aim was to analyze abundance and diversity of oral bacteria of western humans and their closest relatives, to examine if zoo apes feeding on diet other than in their natural habitat show caries and periodontitis associated salivary bacteria and comparable susceptibility for oral civilization diseases as humans. DESIGN Bacterial composition of human and great ape saliva samples were compared by analyzing the V3 region of the bacteria 16S rRNA gene by Next Generation Sequencing with Ion Torrent. RESULTS Results show species-specific differences in the salivary bacteria phyla and genera composition among all apes. Moreover, salivary bacterial composition within non-human apes showed higher intra-individual differences than within humans. Human saliva exhibited lowest bacteria diversity. Different behavioral patterns including (oral) hygiene standards of humans and non-human apes might cause differences. All species differed in diversity and abundance of caries associated bacteria genera. Human saliva revealed higher abundance of caries and periodontitis relevant bacteria in contrast to other great apes, which might be supported by higher consume of refined cariogenic food items, possibly raising their risk for oral disease susceptibility. CONCLUSIONS The study offers first clues on caries and periodontitis relevant bacteria of captive great ape species in comparison to humans. Higher susceptibility to oral diseases for humans than for their closest relatives, leads to the question, if the oral microbiome changed during evolution and how it is influenced by the human life style.
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Affiliation(s)
- Carolin Boehlke
- Faculty of Biology, Institute of Zoology, Molecular Cell Physiology and Endocrinology, Technische Universität Dresden, 01217 Dresden, Germany; Policlinic of Operative and Pediatric Dentistry, Faculty of Medicine ´Carl Gustav Carus´, Technische Universität Dresden, 01307 Dresden, Germany.
| | - Stefan Rupf
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, 66424 Homburg/Saar, Germany.
| | - Martin Tenniswood
- Department of Biomedical Sciences, School of Public Health, University at Albany, Rensselaer, NY, 12144-2345, USA.
| | - Sridar V Chittur
- Department of Biomedical Sciences, School of Public Health, University at Albany, Rensselaer, NY, 12144-2345, USA; Center for Functional Genomics, University at Albany, Rensselaer, NY, 12144-2345, USA.
| | - Christian Hannig
- Policlinic of Operative and Pediatric Dentistry, Faculty of Medicine ´Carl Gustav Carus´, Technische Universität Dresden, 01307 Dresden, Germany.
| | - Oliver Zierau
- Faculty of Biology, Institute of Zoology, Molecular Cell Physiology and Endocrinology, Technische Universität Dresden, 01217 Dresden, Germany.
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Udagawa C, Sasaki Y, Suemizu H, Ohnishi Y, Ohnishi H, Tokino T, Zembutsu H. Targeted sequencing reveals genetic variants associated with sensitivity of 79 human cancer xenografts to anticancer drugs. Exp Ther Med 2017; 15:1339-1359. [PMID: 29434720 PMCID: PMC5774388 DOI: 10.3892/etm.2017.5533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/28/2017] [Indexed: 02/07/2023] Open
Abstract
Although there has been progress moving from a 'one-size-fits-all' cytotoxic approach to personalized molecular medicine, the majority of patients with cancer receive chemotherapy using cytotoxic anticancer drugs. The sequencing analysis of 409 genes associated with cancer was conducted in the present study using 59 DNA sequences extracted from human cancer xenografts implanted into nude mice, of which sensitivity to 9 cytotoxic anticancer drugs [5-fluorouracil, nimustine, adriamycin, cyclophosphamide, cisplatin, mitomycin C (MMC), methotrexate, vincristine (VCR), and vinblastine] was examined. The present study investigated the association between the sensitivities of the xenografts to the 9 anticancer drugs and the frequency of single nucleotide variants (SNV). The correlation between the expression level of the genes and sensitivities to the 9 drugs in the above xenografts was also estimated. In the screening study using 59 xenografts, 3 SNVs (rs1805321, rs62456182 in PMS1 Homolog 2, Mismatch Repair System Component and rs13382825 in LDL Receptor Related Protein 1B), were associated with sensitivity to VCR and MMC, respectively (P<0.001). A replication study of 596 SNVs was subsequently performed, which indicated P<0.05 in the screening study using independent samples of 20 xenografts. A combined result of the screening and replication studies indicated that 35 SNVs were potentially associated with sensitivities to one or more of the nine anticancer drugs (Pcombined=0.0011-0.035). Of the 35 SNVs, rs16903989 and rs201432181 in Leukemia Inhibitory Factor Receptor α and Adhesion G Protein-Coupled Receptor A2 were commonly associated with sensitivity to 2 or 4 anticancer drugs, respectively. These findings provide novel insights which may benefit the development of personalized anticancer therapy for patients with cancer in the future.
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Affiliation(s)
- Chihiro Udagawa
- Liquid Biopsy Development Group, Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan.,Division of Genetics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yasushi Sasaki
- Department of Medical Genome Science, Research Institute for Frontier Medicine, Sapporo Medical University, School of Medicine, Hokkaido 060-8556, Japan
| | - Hiroshi Suemizu
- Laboratory Animal Research Department, Central Institute for Experimental Animals, Kawasaki, 210-0821, Japan
| | - Yasuyuki Ohnishi
- Laboratory Animal Research Department, Central Institute for Experimental Animals, Kawasaki, 210-0821, Japan
| | - Hiroshi Ohnishi
- Liquid Biopsy Development Group, Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Takashi Tokino
- Department of Medical Genome Science, Research Institute for Frontier Medicine, Sapporo Medical University, School of Medicine, Hokkaido 060-8556, Japan
| | - Hitoshi Zembutsu
- Liquid Biopsy Development Group, Project for Development of Liquid Biopsy Diagnosis, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan.,Division of Genetics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
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Burnicka-Turek O, Steimle JD, Huang W, Felker L, Kamp A, Kweon J, Peterson M, Reeves RH, Maslen CL, Gruber PJ, Yang XH, Shendure J, Moskowitz IP. Cilia gene mutations cause atrioventricular septal defects by multiple mechanisms. Hum Mol Genet 2016; 25:3011-3028. [PMID: 27340223 DOI: 10.1093/hmg/ddw155] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 05/13/2016] [Accepted: 05/18/2016] [Indexed: 01/13/2023] Open
Abstract
Atrioventricular septal defects (AVSDs) are a common severe form of congenital heart disease (CHD). In this study we identified deleterious non-synonymous mutations in two cilia genes, Dnah11 and Mks1, in independent N-ethyl-N-nitrosourea-induced mouse mutant lines with heritable recessive AVSDs by whole-exome sequencing. Cilia are required for left/right body axis determination and second heart field (SHF) Hedgehog (Hh) signaling, and we find that cilia mutations affect these requirements differentially. Dnah11avc4 did not disrupt SHF Hh signaling and caused AVSDs only concurrently with heterotaxy, a left/right axis abnormality. In contrast, Mks1avc6 disrupted SHF Hh signaling and caused AVSDs without heterotaxy. We performed unbiased whole-genome SHF transcriptional profiling and found that cilia motility genes were not expressed in the SHF whereas cilia structural and signaling genes were highly expressed. SHF cilia gene expression predicted the phenotypic concordance between AVSDs and heterotaxy in mice and humans with cilia gene mutations. A two-step model of cilia action accurately predicted the AVSD/heterotaxyu phenotypic expression pattern caused by cilia gene mutations. We speculate that cilia gene mutations contribute to both syndromic and non-syndromic AVSDs in humans and provide a model that predicts the phenotypic consequences of specific cilia gene mutations.
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Affiliation(s)
- Ozanna Burnicka-Turek
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA,
| | - Jeffrey D Steimle
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Wenhui Huang
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Lindsay Felker
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Anna Kamp
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Junghun Kweon
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Michael Peterson
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Roger H Reeves
- Department of Physiology and Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Cheryl L Maslen
- Knight Cardiovascular Institute and Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA and
| | - Peter J Gruber
- Department of Cardiothoracic Surgery, University of Iowa, Iowa City, IA 52245, USA
| | - Xinan H Yang
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Ivan P Moskowitz
- Departments of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL 60637, USA,
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Brezina PR, Anchan R, Kearns WG. Preimplantation genetic testing for aneuploidy: what technology should you use and what are the differences? J Assist Reprod Genet 2016; 33:823-32. [PMID: 27299602 DOI: 10.1007/s10815-016-0740-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/02/2016] [Indexed: 11/30/2022] Open
Abstract
PURPOSE The purpose of the review was to define the various diagnostic platforms currently available to perform preimplantation genetic testing for aneuploidy and describe in a clear and balanced manner the various strengths and weaknesses of these technologies. METHODS A systematic literature review was conducted. We used the terms "preimplantation genetic testing," "preimplantation genetic diagnosis," "preimplantation genetic screening," "preimplantation genetic diagnosis for aneuploidy," "PGD," "PGS," and "PGD-A" to search through PubMed, ScienceDirect, and Google Scholar from the year 2000 to April 2016. Bibliographies of articles were also searched for relevant studies. When possible, larger randomized controlled trials were used. However, for some emerging data, only data from meeting abstracts were available. RESULTS PGS is emerging as one of the most valuable tools to enhance pregnancy success with assisted reproductive technologies. While all of the current diagnostic platforms currently available have various advantages and disadvantages, some platforms, such as next-generation sequencing (NGS), are capable of evaluating far more data points than has been previously possible. The emerging complexity of different technologies, especially with the utilization of more sophisticated tools such as NGS, requires an understanding by clinicians in order to request the best test for their patients.. CONCLUSION Ultimately, the choice of which diagnostic platform is utilized should be individualized to the needs of both the clinic and the patient. Such a decision must incorporate the risk tolerance of both the patient and provider, fiscal considerations, and other factors such as the ability to counsel patients on their testing results and how these may or may not impact clinical outcomes.
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Affiliation(s)
- Paul R Brezina
- Department of OB/GYN, Vanderbilt University School of Medicine, Nashville, TN, USA.,AdvaGenix, Rockville, MD, USA.,Fertility Associates of Memphis, Memphis, TN, USA
| | - Raymond Anchan
- Department of OB/GYN, Division of Reproductive Endocrinology and Infertility, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - William G Kearns
- AdvaGenix, Rockville, MD, USA. .,Department of OB/GYN, GENETICS, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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CRISPR/Cas9-Mediated Rapid Generation of Multiple Mouse Lines Identified Ccdc63 as Essential for Spermiogenesis. Int J Mol Sci 2015; 16:24732-50. [PMID: 26501274 PMCID: PMC4632774 DOI: 10.3390/ijms161024732] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 09/30/2015] [Accepted: 10/09/2015] [Indexed: 12/14/2022] Open
Abstract
Spermatozoa are flagellated cells whose role in fertilization is dependent on their ability to move towards an oocyte. The structure of the sperm flagella is highly conserved across species, and much of what is known about this structure is derived from studies utilizing animal models. One group of proteins essential for the movement of the flagella are the dyneins. Using the advanced technology of CRISPR/Cas9 we have targeted three dynein group members; Dnaic1, Wdr63 and Ccdc63 in mice. All three of these genes are expressed strongly in the testis. We generated mice with amino acid substitutions in Dnaic1 to analyze two specific phosphorylation events at S124 and S127, and generated simple knockouts of Wdr63 and Ccdc63. We found that the targeted phosphorylation sites in Dnaic1 were not essential for male fertility. Similarly, Wdr63 was not essential for male fertility; however, Ccdc63 removal resulted in sterile male mice due to shortened flagella. This study demonstrates the versatility of the CRISPR/Cas9 system to generate animal models of a highly complex system by introducing point mutations and simple knockouts in a fast and efficient manner.
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7
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Ikeda H, Ishiguro K, Igarashi T, Aoki Y, Hayashi T, Ishida T, Sasaki Y, Tokino T, Shinomura Y. Molecular diagnostics of a single drug-resistant multiple myeloma case using targeted next-generation sequencing. Onco Targets Ther 2015; 8:2805-15. [PMID: 26491355 PMCID: PMC4599646 DOI: 10.2147/ott.s86515] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A 69-year-old man was diagnosed with IgG λ-type multiple myeloma (MM), Stage II in October 2010. He was treated with one cycle of high-dose dexamethasone. After three cycles of bortezomib, the patient exhibited slow elevations in the free light-chain levels and developed a significant new increase of serum M protein. Bone marrow cytogenetic analysis revealed a complex karyotype characteristic of malignant plasma cells. To better understand the molecular pathogenesis of this patient, we sequenced for mutations in the entire coding regions of 409 cancer-related genes using a semiconductor-based sequencing platform. Sequencing analysis revealed eight nonsynonymous somatic mutations in addition to several copy number variants, including CCND1 and RB1. These alterations may play roles in the pathobiology of this disease. This targeted next-generation sequencing can allow for the prediction of drug resistance and facilitate improvements in the treatment of MM patients.
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Affiliation(s)
- Hiroshi Ikeda
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University, Sapporo, Japan
| | - Kazuya Ishiguro
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University, Sapporo, Japan
| | - Tetsuyuki Igarashi
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University, Sapporo, Japan
| | - Yuka Aoki
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University, Sapporo, Japan
| | - Toshiaki Hayashi
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University, Sapporo, Japan
| | - Tadao Ishida
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University, Sapporo, Japan
| | - Yasushi Sasaki
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University, Sapporo, Japan ; Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Takashi Tokino
- Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Yasuhisa Shinomura
- Department of Gastroenterology, Rheumatology and Clinical Immunology, Sapporo Medical University, Sapporo, Japan
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8
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Activation and function of murine primary microglia in the absence of the prion protein. J Neuroimmunol 2015; 286:25-32. [PMID: 26298321 DOI: 10.1016/j.jneuroim.2015.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 07/02/2015] [Accepted: 07/04/2015] [Indexed: 11/21/2022]
Abstract
The prion protein (PrP(C)) is predominantly expressed in the nervous and immune systems and is involved in relevant cell signaling. Microglia participate in neuroimmune interactions, and their regulatory mechanisms are critical for both health and disease. Despite recent reports with a microglial cell line, little is known about the relevance of PrP(C) in brain microglia. We investigated the role of PrP(C) in mouse primary microglia, and found no differences between wild type and Prnp-null cells in cell morphology or the expression of a microglial marker. Translocation of NF-κB to the nucleus also did not differ, nor did cytokine production. The levels of iNOS were also similar and, finally, microglia of either genotype showed no differences in either rates of phagocytosis or migration, even following activation. Thus, functional roles of PrP(C) in primary microglial cells are - if present - much more subtle than in transformed microglial cell lines.
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9
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Li Y, Klena NT, Gabriel GC, Liu X, Kim AJ, Lemke K, Chen Y, Chatterjee B, Devine W, Damerla RR, Chang C, Yagi H, San Agustin JT, Thahir M, Anderton S, Lawhead C, Vescovi A, Pratt H, Morgan J, Haynes L, Smith CL, Eppig JT, Reinholdt L, Francis R, Leatherbury L, Ganapathiraju MK, Tobita K, Pazour GJ, Lo CW. Global genetic analysis in mice unveils central role for cilia in congenital heart disease. Nature 2015; 521:520-4. [PMID: 25807483 DOI: 10.1038/nature14269] [Citation(s) in RCA: 297] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/26/2015] [Indexed: 01/20/2023]
Abstract
Congenital heart disease (CHD) is the most prevalent birth defect, affecting nearly 1% of live births; the incidence of CHD is up to tenfold higher in human fetuses. A genetic contribution is strongly suggested by the association of CHD with chromosome abnormalities and high recurrence risk. Here we report findings from a recessive forward genetic screen in fetal mice, showing that cilia and cilia-transduced cell signalling have important roles in the pathogenesis of CHD. The cilium is an evolutionarily conserved organelle projecting from the cell surface with essential roles in diverse cellular processes. Using echocardiography, we ultrasound scanned 87,355 chemically mutagenized C57BL/6J fetal mice and recovered 218 CHD mouse models. Whole-exome sequencing identified 91 recessive CHD mutations in 61 genes. This included 34 cilia-related genes, 16 genes involved in cilia-transduced cell signalling, and 10 genes regulating vesicular trafficking, a pathway important for ciliogenesis and cell signalling. Surprisingly, many CHD genes encoded interacting proteins, suggesting that an interactome protein network may provide a larger genomic context for CHD pathogenesis. These findings provide novel insights into the potential Mendelian genetic contribution to CHD in the fetal population, a segment of the human population not well studied. We note that the pathways identified show overlap with CHD candidate genes recovered in CHD patients, suggesting that they may have relevance to the more complex genetics of CHD overall. These CHD mouse models and >8,000 incidental mutations have been sperm archived, creating a rich public resource for human disease modelling.
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Affiliation(s)
- You Li
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA
| | - Nikolai T Klena
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA
| | - George C Gabriel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA
| | - Xiaoqin Liu
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA
| | - Andrew J Kim
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA
| | - Kristi Lemke
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA
| | - Yu Chen
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA
| | - Bishwanath Chatterjee
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA
| | - William Devine
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
| | - Rama Rao Damerla
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA
| | - Chienfu Chang
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA
| | - Hisato Yagi
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA
| | - Jovenal T San Agustin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Mohamed Thahir
- 1] Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15206, USA [2] Intelligent Systems Program, School of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 16260, USA
| | - Shane Anderton
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA
| | - Caroline Lawhead
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA
| | - Anita Vescovi
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA
| | - Herbert Pratt
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Judy Morgan
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Leslie Haynes
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | - Janan T Eppig
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | - Richard Francis
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA
| | - Linda Leatherbury
- The Heart Center, Children's National Medical Center, Washington DC 20010, USA
| | - Madhavi K Ganapathiraju
- 1] Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15206, USA [2] Intelligent Systems Program, School of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 16260, USA
| | - Kimimasa Tobita
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15201, USA
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Galindo-González L, Pinzón-Latorre D, Bergen EA, Jensen DC, Deyholos MK. Ion Torrent sequencing as a tool for mutation discovery in the flax (Linum usitatissimum L.) genome. PLANT METHODS 2015; 11:19. [PMID: 25788971 PMCID: PMC4363359 DOI: 10.1186/s13007-015-0062-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/02/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Detection of induced mutations is valuable for inferring gene function and for developing novel germplasm for crop improvement. Many reverse genetics approaches have been developed to identify mutations in genes of interest within a mutagenized population, including some approaches that rely on next-generation sequencing (e.g. exome capture, whole genome resequencing). As an alternative to these genome or exome-scale methods, we sought to develop a scalable and efficient method for detection of induced mutations that could be applied to a small number of target genes, using Ion Torrent technology. We developed this method in flax (Linum usitatissimum), to demonstrate its utility in a crop species. RESULTS We used an amplicon-based approach in which DNA samples from an ethyl methanesulfonate (EMS)-mutagenized population were pooled and used as template in PCR reactions to amplify a region of each gene of interest. Barcodes were incorporated during PCR, and the pooled amplicons were sequenced using an Ion Torrent PGM. A pilot experiment with known SNPs showed that they could be detected at a frequency > 0.3% within the pools. We then selected eight genes for which we wanted to discover novel mutations, and applied our approach to screen 768 individuals from the EMS population, using either the Ion 314 or Ion 316 chips. Out of 29 potential mutations identified after processing the NGS reads, 16 mutations were confirmed using Sanger sequencing. CONCLUSIONS The methodology presented here demonstrates the utility of Ion Torrent technology in detecting mutation variants in specific genome regions for large populations of a species such as flax. The methodology could be scaled-up to test >100 genes using the higher capacity chips now available from Ion Torrent.
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Affiliation(s)
| | - David Pinzón-Latorre
- />Department of Biological Sciences, University of Alberta, Edmonton, AB Canada T6G 2E9
| | - Erik A Bergen
- />Department of Biological Sciences, University of Alberta, Edmonton, AB Canada T6G 2E9
| | - Dustin C Jensen
- />Department of Computing Sciences, Kings University College, Edmonton, AB Canada T6B 2H3
| | - Michael K Deyholos
- />IK Barber School of Arts & Sciences, University of British Columbia, Okanagan campus, Kelowna, BC Canada V1V 1 V7
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Podgorny OV, Polina NF, Babenko VV, Karpova IY, Kostryukova ES, Govorun VM, Lazarev VN. Isolation of single Chlamydia-infected cells using laser microdissection. J Microbiol Methods 2015; 109:123-8. [DOI: 10.1016/j.mimet.2014.12.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 12/12/2014] [Accepted: 12/23/2014] [Indexed: 11/15/2022]
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12
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Kremkow BG, Lee KH. Sequencing technologies for animal cell culture research. Biotechnol Lett 2014; 37:55-65. [DOI: 10.1007/s10529-014-1660-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/27/2014] [Indexed: 01/16/2023]
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13
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Validation of ambiguous MLPA results by targeted next-generation sequencing discloses a nonsense mutation in the DMD gene. Clin Chim Acta 2014; 436:155-9. [PMID: 24892813 DOI: 10.1016/j.cca.2014.05.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/22/2014] [Accepted: 05/23/2014] [Indexed: 01/16/2023]
Abstract
BACKGROUND Duchenne muscular dystrophy (DMD) is the most common inherited muscular disease and caused by mutations in the DMD gene on the X-chromosome. Multiplex ligation-dependent probe amplification (MLPA) is recognized as a convenient and reliable technique to detect exon deletion/duplication mutations in the DMD gene. Here, we applied targeted semi-conductor next-generation sequencing to clarify the cause of ambiguous MLPA results. METHODS Targeted semi-conductor next-generation sequencing was carried out using the Inherited Disease Panel (IDP) on the Ion Torrent Personal Genome Machine (PGM). RESULTS MLPA analysis disclosed unclassifiable relative peak ratio of exon 18 in a DMD boy. His female cousin was indicated to have exon 18 deletion in one allele. To validate these incompatible results, targeted next-generation sequencing was conducted. A nucleotide change, C.2227 C>T creating a premature stop codon, was in exon 18. Concomitantly, both C and T nucleotides were identified in his cousin's genome. Ambiguous values of the relative peak ratio in MLPA were considered due to the one nucleotide mismatch between the genomic sequence and the probe used in MLPA. CONCLUSION Analysis using IDP on PGM disclosed a nonsense mutation in the DMD gene as a cause of ambiguous results of MLPA.
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