1
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Haderk F, Chou YT, Cech L, Fernández-Méndez C, Yu J, Olivas V, Meraz IM, Barbosa Rabago D, Kerr DL, Gomez C, Allegakoen DV, Guan J, Shah KN, Herrington KA, Gbenedio OM, Nanjo S, Majidi M, Tamaki W, Pourmoghadam YK, Rotow JK, McCoach CE, Riess JW, Gutkind JS, Tang TT, Post L, Huang B, Santisteban P, Goodarzi H, Bandyopadhyay S, Kuo CJ, Roose JP, Wu W, Blakely CM, Roth JA, Bivona TG. Focal adhesion kinase-YAP signaling axis drives drug-tolerant persister cells and residual disease in lung cancer. Nat Commun 2024; 15:3741. [PMID: 38702301 PMCID: PMC11068778 DOI: 10.1038/s41467-024-47423-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/18/2024] [Indexed: 05/06/2024] Open
Abstract
Targeted therapy is effective in many tumor types including lung cancer, the leading cause of cancer mortality. Paradigm defining examples are targeted therapies directed against non-small cell lung cancer (NSCLC) subtypes with oncogenic alterations in EGFR, ALK and KRAS. The success of targeted therapy is limited by drug-tolerant persister cells (DTPs) which withstand and adapt to treatment and comprise the residual disease state that is typical during treatment with clinical targeted therapies. Here, we integrate studies in patient-derived and immunocompetent lung cancer models and clinical specimens obtained from patients on targeted therapy to uncover a focal adhesion kinase (FAK)-YAP signaling axis that promotes residual disease during oncogenic EGFR-, ALK-, and KRAS-targeted therapies. FAK-YAP signaling inhibition combined with the primary targeted therapy suppressed residual drug-tolerant cells and enhanced tumor responses. This study unveils a FAK-YAP signaling module that promotes residual disease in lung cancer and mechanism-based therapeutic strategies to improve tumor response.
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Affiliation(s)
- Franziska Haderk
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Yu-Ting Chou
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Lauren Cech
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Celia Fernández-Méndez
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científícas (CSIC) y Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Johnny Yu
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Victor Olivas
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Ismail M Meraz
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dora Barbosa Rabago
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - D Lucas Kerr
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Carlos Gomez
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - David V Allegakoen
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Juan Guan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Khyati N Shah
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Kari A Herrington
- Center for Advanced Light Microscopy, University of California, San Francisco, San Francisco, CA, USA
| | | | - Shigeki Nanjo
- Division of Medical Oncology, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Mourad Majidi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Whitney Tamaki
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yashar K Pourmoghadam
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Julia K Rotow
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Caroline E McCoach
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan W Riess
- University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - J Silvio Gutkind
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Tracy T Tang
- Vivace Therapeutics, Inc., 1500 Fashion Island Blvd., Suite 102, San Mateo, CA, USA
| | - Leonard Post
- Vivace Therapeutics, Inc., 1500 Fashion Island Blvd., Suite 102, San Mateo, CA, USA
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Pilar Santisteban
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científícas (CSIC) y Universidad Autónoma de Madrid (UAM), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Hani Goodarzi
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Sourav Bandyopadhyay
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeroen P Roose
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Collin M Blakely
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jack A Roth
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
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2
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Morelli M, Lessi F, Franceschi S, Ferri G, Giacomarra M, Menicagli M, Gambacciani C, Pieri F, Pasqualetti F, Montemurro N, Aretini P, Santonocito OS, Di Stefano AL, Mazzanti CM. Exploring Regorafenib Responsiveness and Uncovering Molecular Mechanisms in Recurrent Glioblastoma Tumors through Longitudinal In Vitro Sampling. Cells 2024; 13:487. [PMID: 38534332 PMCID: PMC10968984 DOI: 10.3390/cells13060487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024] Open
Abstract
Glioblastoma, a deadly brain tumor, shows limited response to standard therapies like temozolomide (TMZ). Recent findings from the REGOMA trial underscore a significant survival improvement offered by Regorafenib (REGO) in recurrent glioblastoma. Our study aimed to propose a 3D ex vivo drug response precision medicine approach to investigate recurrent glioblastoma sensitivity to REGO and elucidate the underlying molecular mechanisms involved in tumor resistance or responsiveness to treatment. Three-dimensional glioblastoma organoids (GB-EXPs) obtained from 18 patients' resected recurrent glioblastoma tumors were treated with TMZ and REGO. Drug responses were evaluated using NAD(P)H FLIM, stratifying tumors as responders (Resp) or non-responders (NRs). Whole-exome sequencing was performed on 16 tissue samples, and whole-transcriptome analysis on 13 GB-EXPs treated and untreated. We found 35% (n = 9) and 77% (n = 20) of tumors responded to TMZ and REGO, respectively, with no instances of TMZ-Resp being REGO-NRs. Exome analysis revealed a unique mutational profile in REGO-Resp tumors compared to NR tumors. Transcriptome analysis identified distinct expression patterns in Resp and NR tumors, impacting Rho GTPase and NOTCH signaling, known to be involved in drug response. In conclusion, recurrent glioblastoma tumors were more responsive to REGO compared to TMZ treatment. Importantly, our approach enables a comprehensive longitudinal exploration of the molecular changes induced by treatment, unveiling promising biomarkers indicative of drug response.
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Affiliation(s)
- Mariangela Morelli
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy; (F.L.); (S.F.); (M.G.); (C.M.M.)
| | - Francesca Lessi
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy; (F.L.); (S.F.); (M.G.); (C.M.M.)
| | - Sara Franceschi
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy; (F.L.); (S.F.); (M.G.); (C.M.M.)
| | - Gianmarco Ferri
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy; (F.L.); (S.F.); (M.G.); (C.M.M.)
| | - Manuel Giacomarra
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy; (F.L.); (S.F.); (M.G.); (C.M.M.)
| | - Michele Menicagli
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy; (F.L.); (S.F.); (M.G.); (C.M.M.)
| | - Carlo Gambacciani
- Neurosurgical Department of Spedali Riuniti di Livorno, 57124 Livorno, Italy (O.S.S.)
| | - Francesco Pieri
- Neurosurgical Department of Spedali Riuniti di Livorno, 57124 Livorno, Italy (O.S.S.)
| | - Francesco Pasqualetti
- Radiotherapy Department, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy
| | - Nicola Montemurro
- Department of Neurosurgery, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy;
| | - Paolo Aretini
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy; (F.L.); (S.F.); (M.G.); (C.M.M.)
| | | | - Anna Luisa Di Stefano
- Neurosurgical Department of Spedali Riuniti di Livorno, 57124 Livorno, Italy (O.S.S.)
| | - Chiara Maria Mazzanti
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy; (F.L.); (S.F.); (M.G.); (C.M.M.)
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3
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Jambulingam D, Rathinakannan VS, Heron S, Schleutker J, Fey V. Kuura-An automated workflow for analyzing WES and WGS data. PLoS One 2024; 19:e0296785. [PMID: 38236904 PMCID: PMC10796025 DOI: 10.1371/journal.pone.0296785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 12/19/2023] [Indexed: 01/22/2024] Open
Abstract
The advent of high-throughput sequencing technologies has revolutionized the field of genomic sciences by cutting down the cost and time associated with standard sequencing methods. This advancement has not only provided the research community with an abundance of data but has also presented the challenge of analyzing it. The paramount challenge in analyzing the copious amount of data is in using the optimal resources in terms of available tools. To address this research gap, we propose "Kuura-An automated workflow for analyzing WES and WGS data", which is optimized for both whole exome and whole genome sequencing data. This workflow is based on the nextflow pipeline scripting language and uses docker to manage and deploy the workflow. The workflow consists of four analysis stages-quality control, mapping to reference genome & quality score recalibration, variant calling & variant recalibration and variant consensus & annotation. An important feature of the DNA-seq workflow is that it uses the combination of multiple variant callers (GATK Haplotypecaller, DeepVariant, VarScan2, Freebayes and Strelka2), generating a list of high-confidence variants in a consensus call file. The workflow is flexible as it integrates the fragmented tools and can be easily extended by adding or updating tools or amending the parameters list. The use of a single parameters file enhances reproducibility of the results. The ease of deployment and usage of the workflow further increases computational reproducibility providing researchers with a standardized tool for the variant calling step in different projects. The source code, instructions for installation and use of the tool are publicly available at our github repository https://github.com/dhanaprakashj/kuura_pipeline.
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Affiliation(s)
- Dhanaprakash Jambulingam
- Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
| | - Venkat Subramaniam Rathinakannan
- Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
| | - Samuel Heron
- Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
| | - Johanna Schleutker
- Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
- Department of Genomics, Laboratory Division, Turku University Hospital, Turku, Finland
| | - Vidal Fey
- Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland
- Faculty of Medicine and Health Technology/BioMediTech, Tampere University, Tampere, Finland
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4
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Li M, Hao N, Jiang Y, Xue H, Dai Y, Wang M, Bai J, Lv Y, Qi Q, Zhou X. Contribution of uniparental disomy to fetal growth restriction: a whole-exome sequencing series in a prenatal setting. Sci Rep 2024; 14:238. [PMID: 38168635 PMCID: PMC10762123 DOI: 10.1038/s41598-023-50584-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
Fetal growth restriction (FGR), a leading cause of perinatal morbidity and mortality, is caused by fetal, maternal, and placental factors. Uniparental disomy (UPD) is a rare condition that leads to imprinting effects, low-level mosaic aneuploidies and homozygosity for pathogenic variants. In the present study, UPD events were detected in 5 women with FGR by trio exome sequencing (trio-WES) of a cohort of 150 FGR cases. Furthermore, noninvasive prenatal testing results of the 5 patients revealed a high risk of rare autosomal trisomy. Trio-WES showed no copy-number variations (CNVs) or nondisease-causing mutations associated with FGR. Among the 5 women with FGR, two showed gene imprinting, and two exhibited confined placental mosaicism (CPM) by copy number variant sequencing (CNV-seq). The present study showed that in FGR patients with UPD, the detection of imprinted genes and CPM could enhance the genetic diagnosis of FGR.
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Affiliation(s)
- Mengmeng Li
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Na Hao
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yulin Jiang
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Huili Xue
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian, 350001, China
| | - Yifang Dai
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian, 350001, China
| | - Mingming Wang
- GenoDecode (Beijing) Co. Ltd., Beijing, 101160, China
| | - Junjie Bai
- Be Creative Lab (Beijing) Co. Ltd., Beijing, 100176, China
| | - Yan Lv
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Qingwei Qi
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xiya Zhou
- National Clinical Research Centre for Obstetric & Gynecologic Diseases, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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5
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Cullen JN, Friedenberg SG. Whole Animal Genome Sequencing: user-friendly, rapid, containerized pipelines for processing, variant discovery, and annotation of short-read whole genome sequencing data. G3 (BETHESDA, MD.) 2023; 13:jkad117. [PMID: 37243692 PMCID: PMC10411559 DOI: 10.1093/g3journal/jkad117] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 02/24/2023] [Accepted: 05/20/2023] [Indexed: 05/29/2023]
Abstract
Advancements in massively parallel short-read sequencing technologies and the associated decreasing costs have led to large and diverse variant discovery efforts across species. However, processing high-throughput short-read sequencing data can be challenging with potential pitfalls and bioinformatics bottlenecks in generating reproducible results. Although a number of pipelines exist that address these challenges, these are often geared toward human or traditional model organism species and can be difficult to configure across institutions. Whole Animal Genome Sequencing (WAGS) is an open-source set of user-friendly, containerized pipelines designed to simplify the process of identifying germline short (SNP and indel) and structural variants (SVs) geared toward the veterinary community but adaptable to any species with a suitable reference genome. We present a description of the pipelines [adapted from the best practices of the Genome Analysis Toolkit (GATK)], along with benchmarking data from both the preprocessing and joint genotyping steps, consistent with a typical user workflow.
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Affiliation(s)
- Jonah N Cullen
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, 1352 Boyd Ave, Saint Paul, MN 55108, USA
| | - Steven G Friedenberg
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, 1352 Boyd Ave, Saint Paul, MN 55108, USA
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Lessi F, Morelli M, Franceschi S, Aretini P, Menicagli M, Marranci A, Pasqualetti F, Gambacciani C, Pieri F, Grimod G, Zucchi V, Cupini S, Di Stefano AL, Santonocito OS, Mazzanti CM. Innovative Approach to Isolate and Characterize Glioblastoma Circulating Tumor Cells and Correlation with Tumor Mutational Status. Int J Mol Sci 2023; 24:10147. [PMID: 37373295 DOI: 10.3390/ijms241210147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Circulating tumor cells (CTCs) are one of the most important causes of tumor recurrence and distant metastases. Glioblastoma (GBM) has been considered restricted to the brain for many years. Nevertheless, in the past years, several pieces of evidence indicate that hematogenous dissemination is a reality, and this is also in the caseof GBM. Our aim was to optimize CTCs' detection in GBM and define the genetic background of single CTCs compared to the primary GBM tumor and its recurrence to demonstrate that CTCs are indeed derived from the parental tumor. We collected blood samples from a recurrent IDH wt GBM patient. We genotyped the parental recurrent tumor tissue and the respective primary GBM tissue. CTCs were analyzed using the DEPArray system. CTCs Copy Number Alterations (CNAs) and sequencing analyses were performed to compare CTCs' genetic background with the same patient's primary and recurrent GBM tissues. We identified 210 common mutations in the primary and recurrent tumors. Among these, three somatic high-frequency mutations (in PRKCB, TBX1, and COG5 genes) were selected to investigate their presence in CTCs. Almost all sorted CTCs (9/13) had at least one of the mutations tested. The presence of TERT promoter mutations was also investigated and C228T variation was found in parental tumors and CTCs (C228T heterozygous and homozygous, respectively). We were able to isolate and genotype CTCs from a patient with GBM. We found common mutations but also exclusive molecular characteristics.
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Affiliation(s)
- Francesca Lessi
- Section of Genomics and Transcriptomics, Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy
| | - Mariangela Morelli
- Section of Genomics and Transcriptomics, Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy
| | - Sara Franceschi
- Section of Genomics and Transcriptomics, Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy
| | - Paolo Aretini
- Section of Genomics and Transcriptomics, Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy
| | - Michele Menicagli
- Section of Genomics and Transcriptomics, Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy
| | - Andrea Marranci
- Section of Genomics and Transcriptomics, Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy
| | - Francesco Pasqualetti
- Department of Radiation Oncology, Azienda Ospedaliera Universitaria Pisana, University of Pisa, 56122 Pisa, Italy
| | - Carlo Gambacciani
- Division of Neurosurgery, Spedali Riuniti di Livorno-USL Toscana Nord-Ovest, 57124 Livorno, Italy
| | - Francesco Pieri
- Division of Neurosurgery, Spedali Riuniti di Livorno-USL Toscana Nord-Ovest, 57124 Livorno, Italy
| | - Gianluca Grimod
- Division of Neurosurgery, Spedali Riuniti di Livorno-USL Toscana Nord-Ovest, 57124 Livorno, Italy
| | - Vanna Zucchi
- Division of Pathology, Spedali Riuniti di Livorno-USL Toscana Nord-Ovest, 57124 Livorno, Italy
| | - Samanta Cupini
- Division of Oncology, Spedali Riuniti di Livorno-USL Toscana Nord-Ovest, 57124 Livorno, Italy
| | - Anna Luisa Di Stefano
- Division of Neurosurgery, Spedali Riuniti di Livorno-USL Toscana Nord-Ovest, 57124 Livorno, Italy
- Neurology Department, Foch Hospital, 92150 Suresnes, France
| | - Orazio Santo Santonocito
- Division of Neurosurgery, Spedali Riuniti di Livorno-USL Toscana Nord-Ovest, 57124 Livorno, Italy
| | - Chiara Maria Mazzanti
- Section of Genomics and Transcriptomics, Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy
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7
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Gaeta R, Morelli M, Lessi F, Mazzanti CM, Menicagli M, Capanna R, Andreani L, Coccoli L, Aretini P, Franchi A. Identification of New Potential Prognostic and Predictive Markers in High-Grade Osteosarcoma Using Whole Exome Sequencing. Int J Mol Sci 2023; 24:10086. [PMID: 37373240 DOI: 10.3390/ijms241210086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/08/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
Conventional high-grade osteosarcoma (OS) is the most common primary cancer of bone and it typically affects the extremities of adolescents. OS has a complex karyotype, and molecular mechanisms related to carcinogenesis, progression and resistance to therapy are still largely unknown. For this reason, the current standard of care is associated with considerable adverse effects. In this study, our aim was to identify gene alterations in OS patients using whole exome sequencing (WES) to find new potential prognostic biomarkers and therapeutic targets. We performed WES on formalin-fixed paraffin-embedded (FFPE) biopsy materials collected from 19 patients affected by conventional high-grade OS. The clinical and genetic data were analyzed according to response to therapy, presence of metastasis and disease status. By comparing good and poor responders to neoadjuvant therapy, we detected a clear prevalence of mutations in the ARID1A, CREBBP, BRCA2 and RAD50 genes in poor responders that negatively influence the progression-free survival time. Moreover, higher tumor mutational burden values correlated with worse prognosis. The identification of mutations in ARID1A, CREBBP, BRCA2 and RAD50 may support the use of a more specific therapy for tumors harboring these alterations. In particular, BRCA2 and RAD50 are involved in homologous recombination repair, and could thus be used as specific therapy targets of inhibitors of the enzyme Poly ADP Ribose Polymerase (PARP). Finally, tumor mutational burden is found to be a potential prognostic marker for OS.
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Affiliation(s)
- Raffaele Gaeta
- Section of Pathology, Department of Translational Research and of New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
| | | | - Francesca Lessi
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy
| | | | - Michele Menicagli
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy
| | - Rodolfo Capanna
- Section of Pathology, Department of Translational Research and of New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
| | - Lorenzo Andreani
- Department of Orthopedics and Trauma Surgery, Azienda Ospedaliera Universitaria Pisana, 56124 Pisa, Italy
| | - Luca Coccoli
- Pediatric Hematology Oncology Unit, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy
| | - Paolo Aretini
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy
| | - Alessandro Franchi
- Section of Pathology, Department of Translational Research and of New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
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Mattern L, Begemann M, Delbrück H, Holschbach P, Schröder S, Schacht SM, Kurth I, Elbracht M. Variant of the catalytic cysteine of UFSP2 leads to spondyloepimetaphyseal dysplasia type Di Rocco. Bone Rep 2023; 18:101683. [PMID: 37214758 PMCID: PMC10193157 DOI: 10.1016/j.bonr.2023.101683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
Spondyloepimetaphyseal dysplasia (SEMD) is characterized by vertebral, epiphyseal, and metaphyseal alterations. Patients become predominantly apparent with disproportionate short stature. The genetic background of SEMD is heterogeneous, with different modes of inheritance (autosomal dominant, autosomal recessive, and X-linked disorders). Amongst the genes in which variants are known to cause SEMD, UFM1-specific protease 2 (UFSP2) encodes a cysteine protease involved in the maturation of Ubiquitin-fold modifier 1 (UFM1). Heterozygous pathogenic variants affecting the C-terminal catalytic domain of UFSP2 are related to two entities of skeletal dysplasia, Beukes hip dysplasia (BHD) and SEMD type Di Rocco (SEMDDR). This is the first report of a de novo heterozygous variant affecting the catalytic Cys302 residue of UFSP2 (NM_018359.3:c.905G>C, p.(Cys302Ser)) causing SEMDDR. According to previously described patients with SEMDDR, our patient presented with disproportionate short stature, genu varum, gait instability, and radiologically detected epiphyseal and metaphyseal alterations. Additionally, a bell-shaped thorax, lumbar hyperlordosis, muscular hypotonia, and coxa vara were observed in the patient described in this study. Our findings underline the fundamental importance of an intact catalytic triad of the human UFSP2 for normal skeletal development and extend the phenotypical features of patients with UFSP2-related skeletal dysplasia.
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Affiliation(s)
- Larissa Mattern
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Matthias Begemann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Heide Delbrück
- Department of Orthopaedic, Trauma and Reconstructive Surgery, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Petra Holschbach
- Department of Pediatrics, Division of Neuropediatrics and Social Pediatrics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Silvia Schröder
- Department of Orthopaedic, Trauma and Reconstructive Surgery, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Sabine M. Schacht
- Department of Diagnostic and Interventional Radiology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Ingo Kurth
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
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Licata L, Via A, Turina P, Babbi G, Benevenuta S, Carta C, Casadio R, Cicconardi A, Facchiano A, Fariselli P, Giordano D, Isidori F, Marabotti A, Martelli PL, Pascarella S, Pinelli M, Pippucci T, Russo R, Savojardo C, Scafuri B, Valeriani L, Capriotti E. Resources and tools for rare disease variant interpretation. Front Mol Biosci 2023; 10:1169109. [PMID: 37234922 PMCID: PMC10206239 DOI: 10.3389/fmolb.2023.1169109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Collectively, rare genetic disorders affect a substantial portion of the world's population. In most cases, those affected face difficulties in receiving a clinical diagnosis and genetic characterization. The understanding of the molecular mechanisms of these diseases and the development of therapeutic treatments for patients are also challenging. However, the application of recent advancements in genome sequencing/analysis technologies and computer-aided tools for predicting phenotype-genotype associations can bring significant benefits to this field. In this review, we highlight the most relevant online resources and computational tools for genome interpretation that can enhance the diagnosis, clinical management, and development of treatments for rare disorders. Our focus is on resources for interpreting single nucleotide variants. Additionally, we present use cases for interpreting genetic variants in clinical settings and review the limitations of these results and prediction tools. Finally, we have compiled a curated set of core resources and tools for analyzing rare disease genomes. Such resources and tools can be utilized to develop standardized protocols that will enhance the accuracy and effectiveness of rare disease diagnosis.
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Affiliation(s)
- Luana Licata
- Department of Biology, University of Rome Tor Vergata, Roma, Italy
| | - Allegra Via
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome “La Sapienza”, Roma, Italy
| | - Paola Turina
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giulia Babbi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | - Claudio Carta
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Roma, Italy
| | - Rita Casadio
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Andrea Cicconardi
- Department of Physics, University of Genova, Genova, Italy
- Italiano di Tecnologia—IIT, Genova, Italy
| | - Angelo Facchiano
- National Research Council, Institute of Food Science, Avellino, Italy
| | - Piero Fariselli
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Deborah Giordano
- National Research Council, Institute of Food Science, Avellino, Italy
| | - Federica Isidori
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Anna Marabotti
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, Fisciano, SA, Italy
| | - Pier Luigi Martelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome “La Sapienza”, Roma, Italy
| | - Michele Pinelli
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
| | - Tommaso Pippucci
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Roberta Russo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, Napoli, Italy
| | - Castrense Savojardo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Bernardina Scafuri
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, Fisciano, SA, Italy
| | | | - Emidio Capriotti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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10
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Clonal Elimination of the Pathogenic Allele as Diagnostic Pitfall in SAMD9L-Associated Neuropathy. Genes (Basel) 2022; 13:genes13122356. [PMID: 36553623 PMCID: PMC9778166 DOI: 10.3390/genes13122356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Heterozygous gain-of-function variants in SAMD9L are associated with ataxia-pancytopenia syndrome (ATXPC) and monosomy 7 myelodysplasia and leukemia syndrome-1 (M7MLS1). Association with peripheral neuropathy has rarely been described. METHODS Whole-exome sequencing (WES) from DNA extracted from peripheral blood was performed in a 10-year-old female presenting with demyelinating neuropathy, her similarly affected mother and the unaffected maternal grandparents. In addition to evaluation of single nucleotide variants, thorough work-up of copy number and exome-wide variant allele frequency data was performed. RESULTS Combined analysis of the mother's and daughter's duo-exome data and analysis of the mother's and her parents' trio-exome data initially failed to detect a disease-associated variant. More detailed analysis revealed a copy number neutral loss of heterozygosity of 7q in the mother and led to reanalysis of the exome data for respective sequence variants. Here, a previously reported likely pathogenic variant in the SAMD9L gene on chromosome 7q (NM_152703.5:c.2956C>T; p.(Arg986Cys)) was identified that was not detected with standard filter settings because of a low percentage in blood cells (13%). The variant also showed up in the daughter at 32%, a proportion well below the expected 50%, which in each case can be explained by clonal selection processes in the blood due to this SAMD9L variant. CONCLUSION The report highlights the specific pitfalls of molecular genetic analysis of SAMD9L and, furthermore, shows that gain-of-function variants in this gene can lead to a clinical picture associated with the leading symptom of peripheral neuropathy. Due to clonal hematopoietic selection, displacement of the mutant allele occurred, making diagnosis difficult.
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11
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Liu J, Shen Q, Bao H. Comparison of seven SNP calling pipelines for the next-generation sequencing data of chickens. PLoS One 2022; 17:e0262574. [PMID: 35100292 PMCID: PMC8803190 DOI: 10.1371/journal.pone.0262574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 12/29/2021] [Indexed: 11/18/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are widely used in genome-wide association studies and population genetics analyses. Next-generation sequencing (NGS) has become convenient, and many SNP-calling pipelines have been developed for human NGS data. We took advantage of a gap knowledge in selecting the appropriated SNP calling pipeline to handle with high-throughput NGS data. To fill this gap, we studied and compared seven SNP calling pipelines, which include 16GT, genome analysis toolkit (GATK), Bcftools-single (Bcftools single sample mode), Bcftools-multiple (Bcftools multiple sample mode), VarScan2-single (VarScan2 single sample mode), VarScan2-multiple (VarScan2 multiple sample mode) and Freebayes pipelines, using 96 NGS data with the different depth gradients of approximately 5X, 10X, 20X, 30X, 40X, and 50X coverage from 16 Rhode Island Red chickens. The sixteen chickens were also genotyped with a 50K SNP array, and the sensitivity and specificity of each pipeline were assessed by comparison to the results of SNP arrays. For each pipeline, except Freebayes, the number of detected SNPs increased as the input read depth increased. In comparison with other pipelines, 16GT, followed by Bcftools-multiple, obtained the most SNPs when the input coverage exceeded 10X, and Bcftools-multiple obtained the most when the input was 5X and 10X. The sensitivity and specificity of each pipeline increased with increasing input. Bcftools-multiple had the highest sensitivity numerically when the input ranged from 5X to 30X, and 16GT showed the highest sensitivity when the input was 40X and 50X. Bcftools-multiple also had the highest specificity, followed by GATK, at almost all input levels. For most calling pipelines, there were no obvious changes in SNP numbers, sensitivities or specificities beyond 20X. In conclusion, (1) if only SNPs were detected, the sequencing depth did not need to exceed 20X; (2) the Bcftools-multiple may be the best choice for detecting SNPs from chicken NGS data, but for a single sample or sequencing depth greater than 20X, 16GT was recommended. Our findings provide a reference for researchers to select suitable pipelines to obtain SNPs from the NGS data of chickens or nonhuman animals.
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Affiliation(s)
- Jing Liu
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qingmiao Shen
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haigang Bao
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
- * E-mail:
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12
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Napolioni V, Fredericks CA, Kim Y, Channappa D, Khan RR, Kim LH, Zafar F, Couthouis J, Davidzon GA, Mormino EC, Gitler AD, Montine TJ, Schüle B, Greicius MD. Phenotypic Heterogeneity among GBA p.R202X Carriers in Lewy Body Spectrum Disorders. Biomedicines 2022; 10:biomedicines10010160. [PMID: 35052839 PMCID: PMC8774039 DOI: 10.3390/biomedicines10010160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/03/2022] [Accepted: 01/11/2022] [Indexed: 02/02/2023] Open
Abstract
We describe the clinical and neuropathologic features of patients with Lewy body spectrum disorder (LBSD) carrying a nonsense variant, c.604C>T; p.R202X, in the glucocerebrosidase 1 (GBA) gene. While this GBA variant is causative for Gaucher's disease, the pathogenic role of this mutation in LBSD is unclear. Detailed neuropathologic evaluation was performed for one index case and a structured literature review of other GBA p.R202X carriers was conducted. Through the systematic literature search, we identified three additional reported subjects carrying the same GBA mutation, including one Parkinson's disease (PD) patient with early disease onset, one case with neuropathologically-verified LBSD, and one unaffected relative of a Gaucher's disease patient. Among the affected subjects carrying the GBA p.R202X, all males were diagnosed with Lewy body dementia, while the two females presented as PD. The clinical penetrance of GBA p.R202X in LBSD patients and families argues strongly for a pathogenic role for this variant, although presenting with a striking phenotypic heterogeneity of clinical and pathological features.
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Affiliation(s)
- Valerio Napolioni
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; (C.A.F.); (Y.K.); (R.R.K.); (L.H.K.); (E.C.M.); (M.D.G.)
- Correspondence: ; Tel.: +1-(669)-287-2586
| | - Carolyn A. Fredericks
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; (C.A.F.); (Y.K.); (R.R.K.); (L.H.K.); (E.C.M.); (M.D.G.)
| | - Yongha Kim
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; (C.A.F.); (Y.K.); (R.R.K.); (L.H.K.); (E.C.M.); (M.D.G.)
| | - Divya Channappa
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; (D.C.); (F.Z.); (T.J.M.); (B.S.)
| | - Raiyan R. Khan
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; (C.A.F.); (Y.K.); (R.R.K.); (L.H.K.); (E.C.M.); (M.D.G.)
| | - Lily H. Kim
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; (C.A.F.); (Y.K.); (R.R.K.); (L.H.K.); (E.C.M.); (M.D.G.)
| | - Faria Zafar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; (D.C.); (F.Z.); (T.J.M.); (B.S.)
| | - Julien Couthouis
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; (J.C.); (A.D.G.)
| | - Guido A. Davidzon
- Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA;
| | - Elizabeth C. Mormino
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; (C.A.F.); (Y.K.); (R.R.K.); (L.H.K.); (E.C.M.); (M.D.G.)
| | - Aaron D. Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; (J.C.); (A.D.G.)
| | - Thomas J. Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; (D.C.); (F.Z.); (T.J.M.); (B.S.)
| | - Birgitt Schüle
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; (D.C.); (F.Z.); (T.J.M.); (B.S.)
| | - Michael D. Greicius
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; (C.A.F.); (Y.K.); (R.R.K.); (L.H.K.); (E.C.M.); (M.D.G.)
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13
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Ahmed Z, Renart EG, Mishra D, Zeeshan S. JWES: a new pipeline for whole genome/exome sequence data processing, management, and gene-variant discovery, annotation, prediction, and genotyping. FEBS Open Bio 2021; 11:2441-2452. [PMID: 34370400 PMCID: PMC8409305 DOI: 10.1002/2211-5463.13261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/18/2021] [Accepted: 08/02/2021] [Indexed: 01/07/2023] Open
Abstract
Whole genome and exome sequencing (WGS/WES) are the most popular next‐generation sequencing (NGS) methodologies and are at present often used to detect rare and common genetic variants of clinical significance. We emphasize that automated sequence data processing, management, and visualization should be an indispensable component of modern WGS and WES data analysis for sequence assembly, variant detection (SNPs, SVs), imputation, and resolution of haplotypes. In this manuscript, we present a newly developed findable, accessible, interoperable, and reusable (FAIR) bioinformatics‐genomics pipeline Java based Whole Genome/Exome Sequence Data Processing Pipeline (JWES) for efficient variant discovery and interpretation, and big data modeling and visualization. JWES is a cross‐platform, user‐friendly, product line application, that entails three modules: (a) data processing, (b) storage, and (c) visualization. The data processing module performs a series of different tasks for variant calling, the data storage module efficiently manages high‐volume gene‐variant data, and the data visualization module supports variant data interpretation with Circos graphs. The performance of JWES was tested and validated in‐house with different experiments, using Microsoft Windows, macOS Big Sur, and UNIX operating systems. JWES is an open‐source and freely available pipeline, allowing scientists to take full advantage of all the computing resources available, without requiring much computer science knowledge. We have successfully applied JWES for processing, management, and gene‐variant discovery, annotation, prediction, and genotyping of WGS and WES data to analyze variable complex disorders. In summary, we report the performance of JWES with some reproducible case studies, using open access and in‐house generated, high‐quality datasets.
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Affiliation(s)
- Zeeshan Ahmed
- Institute for Health, Health Care Policy and Aging Research, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.,Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers Biomedical and Health Sciences, New Brunswick, NJ, USA
| | - Eduard Gibert Renart
- Institute for Health, Health Care Policy and Aging Research, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Deepshikha Mishra
- Institute for Health, Health Care Policy and Aging Research, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Saman Zeeshan
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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14
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Lausberg E, Gießelmann S, Dewulf JP, Wiame E, Holz A, Salvarinova R, van Karnebeek CD, Klemm P, Ohl K, Mull M, Braunschweig T, Weis J, Sommer CJ, Demuth S, Haase C, Stollbrink-Peschgens C, Debray FG, Libioulle C, Choukair D, Oommen PT, Borkhardt A, Surowy H, Wieczorek D, Wagner N, Meyer R, Eggermann T, Begemann M, Van Schaftingen E, Häusler M, Tenbrock K, van den Heuvel L, Elbracht M, Kurth I, Kraft F. C2orf69 mutations disrupt mitochondrial function and cause a multisystem human disorder with recurring autoinflammation. J Clin Invest 2021; 131:143078. [PMID: 33945503 DOI: 10.1172/jci143078] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 04/29/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUNDDeciphering the function of the many genes previously classified as uncharacterized open reading frame (ORF) would complete our understanding of a cell's function and its pathophysiology.METHODSWhole-exome sequencing, yeast 2-hybrid and transcriptome analyses, and molecular characterization were performed in this study to uncover the function of the C2orf69 gene.RESULTSWe identified loss-of-function mutations in the uncharacterized C2orf69 gene in 8 individuals with brain abnormalities involving hypomyelination and microcephaly, liver dysfunction, and recurrent autoinflammation. C2orf69 contains an N-terminal signal peptide that is required and sufficient for mitochondrial localization. Consistent with mitochondrial dysfunction, the patients showed signs of respiratory chain defects, and a CRISPR/Cas9-KO cell model of C2orf69 had similar respiratory chain defects. Patient-derived cells revealed alterations in immunological signaling pathways. Deposits of periodic acid-Schiff-positive (PAS-positive) material in tissues from affected individuals, together with decreased glycogen branching enzyme 1 (GBE1) activity, indicated an additional impact of C2orf69 on glycogen metabolism.CONCLUSIONSOur study identifies C2orf69 as an important regulator of human mitochondrial function and suggests that this gene has additional influence on other metabolic pathways.
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Affiliation(s)
- Eva Lausberg
- Institute of Human Genetics, Medical Faculty, Rheinisch-Westfaelische Technische Hochschule (RWTH) Aachen University, Aachen, Germany
| | - Sebastian Gießelmann
- Institute of Human Genetics, Medical Faculty, Rheinisch-Westfaelische Technische Hochschule (RWTH) Aachen University, Aachen, Germany
| | - Joseph P Dewulf
- Laboratory of Physiological Chemistry, de Duve Institute and.,Department of Laboratory Medicine, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Elsa Wiame
- Laboratory of Physiological Chemistry, de Duve Institute and
| | - Anja Holz
- CeGaT GmbH and Praxis für Humangenetik, Tübingen, Germany
| | - Ramona Salvarinova
- Division of Biochemical Diseases, Department of Pediatrics, British Columbia Children's Hospital Vancouver, Vancouver, British Columbia, Canada.,British Columbia Children's Hospital Research Institute, University of British Columbia (UBC), Vancouver, British Columbia, Canada
| | - Clara D van Karnebeek
- Department of Pediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, Netherlands.,Department of Pediatrics, Centre for Molecular Medicine and Therapeutics, UBC, Vancouver, British Columbia, Canada
| | | | - Kim Ohl
- Department of Pediatrics, Medical Faculty
| | - Michael Mull
- Department of Diagnostic and Interventional Neuroradiology, Medical Faculty
| | | | - Joachim Weis
- Institute of Neuropathology, Medical Faculty, RWTH University, Aachen, Germany
| | - Clemens J Sommer
- Institute of Neuropathology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Claudia Haase
- HELIOS Klinikum Erfurt, Ambulanz für Angeborene Stoffwechselerkrankungen, Sozialpädiatrisches Zentrum, Erfurt, Germany
| | | | | | - Cecile Libioulle
- Department of Human Genetics, Centre Hospitalier Universitaire (CHU) de Liège, Liège, Belgium
| | - Daniela Choukair
- Department of General Pediatrics, University Children's Hospital, Heidelberg University, Heidelberg, Germany
| | - Prasad T Oommen
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, University Children's Hospital, Medical Faculty and
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, University Children's Hospital, Medical Faculty and
| | - Harald Surowy
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine University (HHU), Düsseldorf, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine University (HHU), Düsseldorf, Germany
| | | | - Robert Meyer
- Institute of Human Genetics, Medical Faculty, Rheinisch-Westfaelische Technische Hochschule (RWTH) Aachen University, Aachen, Germany
| | - Thomas Eggermann
- Institute of Human Genetics, Medical Faculty, Rheinisch-Westfaelische Technische Hochschule (RWTH) Aachen University, Aachen, Germany
| | - Matthias Begemann
- Institute of Human Genetics, Medical Faculty, Rheinisch-Westfaelische Technische Hochschule (RWTH) Aachen University, Aachen, Germany
| | | | | | | | - Lambert van den Heuvel
- Department of Pediatrics, Translational Metabolic Laboratory at the Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, Rheinisch-Westfaelische Technische Hochschule (RWTH) Aachen University, Aachen, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, Rheinisch-Westfaelische Technische Hochschule (RWTH) Aachen University, Aachen, Germany
| | - Florian Kraft
- Institute of Human Genetics, Medical Faculty, Rheinisch-Westfaelische Technische Hochschule (RWTH) Aachen University, Aachen, Germany
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15
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He X, Zhang Y, Yuan D, Han X, He J, Duan X, Liu S, Wang X, Niu B. DIVIS: Integrated and Customizable Pipeline for Cancer Genome Sequencing Analysis and Interpretation. Front Oncol 2021; 11:672597. [PMID: 34168993 PMCID: PMC8217664 DOI: 10.3389/fonc.2021.672597] [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: 02/26/2021] [Accepted: 04/27/2021] [Indexed: 11/13/2022] Open
Abstract
Next-generation sequencing (NGS) has drastically enhanced human cancer research, but diverse sequencing strategies, complicated open-source software, and the identification of massive numbers of mutations have limited the clinical application of NGS. Here, we first presented GPyFlow, a lightweight tool that flexibly customizes, executes, and shares workflows. We then introduced DIVIS, a customizable pipeline based on GPyFlow that integrates read preprocessing, alignment, variant detection, and annotation of whole-genome sequencing, whole-exome sequencing, and gene-panel sequencing. By default, DIVIS screens variants from multiple callers and generates a standard variant-detection format list containing caller evidence for each sample, which is compatible with advanced analyses. Lastly, DIVIS generates a statistical report, including command lines, parameters, quality-control indicators, and mutation summary. DIVIS substantially facilitates complex cancer genome sequencing analyses by means of a single powerful and easy-to-use command. The DIVIS code is freely available at https://github.com/niu-lab/DIVIS, and the docker image can be downloaded from https://hub.docker.com/repository/docker/sunshinerain/divis.
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Affiliation(s)
- Xiaoyu He
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu Zhang
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Danyang Yuan
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xinyin Han
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jiayin He
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Xiaohong Duan
- ChosenMed Technology (Beijing) Co., Ltd., Beijing, China
| | - Siyao Liu
- ChosenMed Technology (Beijing) Co., Ltd., Beijing, China
| | - Xintong Wang
- ChosenMed Technology (Beijing) Co., Ltd., Beijing, China
| | - Beifang Niu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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16
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Vollbach K, Trepels-Kottek S, Elbracht M, Kurth I, Wagner N, Orlikowsky T, Braunschweig T, Tenbrock K. Alveolar capillary dysplasia without misalignment of pulmonary veins, hyperinflammation, megalocornea and overgrowth - Association with a homozygous 2bp-insertion in LTBP2? Eur J Med Genet 2021; 64:104209. [PMID: 33766794 DOI: 10.1016/j.ejmg.2021.104209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 11/28/2022]
Abstract
We present a male infant with alveolar capillary dysplasia without misalignment of pulmonary veins, hyperinflammation, megalocornea and macrosomia/macrocephaly at birth. Whole-exome sequencing revealed a homozygous 2bp-insertion in the latent transforming growth factor-beta binding protein 2 (LTBP2) (c.278_279dup, p.(Ser94Glyfs*187)). So far, LTBP2-variants have been frequently reported with an eye-restricted phenotype including primary congenital glaucoma and megalocornea/microspherphakia and ectopia lentis with/without secondary glaucoma. Hitherto reported systemic phenotypes showed, among others, features as tall stature, finger anomalies, high-arched palate and cardiovascular anomalies. The main pathophysiological finding of our patient was an alveolar capillary dysplasia (with pulmonary arterial hypertension and right ventricular impairment but without misalignment of pulmonary veins) resulting in almost continuous oxygen demand and prolonged dependence on mechanical ventilation. He died of respiratory failure at the age of seven months. This patient may extend the LTBP2-related phenotype with resulting diagnostic implications.
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Affiliation(s)
- Kristina Vollbach
- Department of Pediatrics, RWTH Aachen University Hospital, Aachen, Germany.
| | - Sonja Trepels-Kottek
- Department of Pediatrics, Division of Neonatology, RWTH Aachen University Hospital, Aachen, Germany
| | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University Hospital, Aachen, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University Hospital, Aachen, Germany
| | - Norbert Wagner
- Department of Pediatrics, RWTH Aachen University Hospital, Aachen, Germany
| | - Thorsten Orlikowsky
- Department of Pediatrics, Division of Neonatology, RWTH Aachen University Hospital, Aachen, Germany
| | - Till Braunschweig
- Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany
| | - Klaus Tenbrock
- Department of Pediatrics, RWTH Aachen University Hospital, Aachen, Germany
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17
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Hedberg-Oldfors C, Meyer R, Nolte K, Abdul Rahim Y, Lindberg C, Karason K, Thuestad IJ, Visuttijai K, Geijer M, Begemann M, Kraft F, Lausberg E, Hitpass L, Götzl R, Luna EJ, Lochmüller H, Koschmieder S, Gramlich M, Gess B, Elbracht M, Weis J, Kurth I, Oldfors A, Knopp C. Loss of supervillin causes myopathy with myofibrillar disorganization and autophagic vacuoles. Brain 2020; 143:2406-2420. [PMID: 32779703 PMCID: PMC7447519 DOI: 10.1093/brain/awaa206] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 04/16/2020] [Accepted: 05/07/2020] [Indexed: 01/01/2023] Open
Abstract
The muscle specific isoform of the supervillin protein (SV2), encoded by the SVIL gene, is a large sarcolemmal myosin II- and F-actin-binding protein. Supervillin (SV2) binds and co-localizes with costameric dystrophin and binds nebulin, potentially attaching the sarcolemma to myofibrillar Z-lines. Despite its important role in muscle cell physiology suggested by various in vitro studies, there are so far no reports of any human disease caused by SVIL mutations. We here report four patients from two unrelated, consanguineous families with a childhood/adolescence onset of a myopathy associated with homozygous loss-of-function mutations in SVIL. Wide neck, anteverted shoulders and prominent trapezius muscles together with variable contractures were characteristic features. All patients showed increased levels of serum creatine kinase but no or minor muscle weakness. Mild cardiac manifestations were observed. Muscle biopsies showed complete loss of large supervillin isoforms in muscle fibres by western blot and immunohistochemical analyses. Light and electron microscopic investigations revealed a structural myopathy with numerous lobulated muscle fibres and considerable myofibrillar alterations with a coarse and irregular intermyofibrillar network. Autophagic vacuoles, as well as frequent and extensive deposits of lipoproteins, including immature lipofuscin, were observed. Several sarcolemma-associated proteins, including dystrophin and sarcoglycans, were partially mis-localized. The results demonstrate the importance of the supervillin (SV2) protein for the structural integrity of muscle fibres in humans and show that recessive loss-of-function mutations in SVIL cause a distinctive and novel myopathy.
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Affiliation(s)
- Carola Hedberg-Oldfors
- Department of Pathology and Genetics, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Robert Meyer
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Kay Nolte
- Institute of Neuropathology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Yassir Abdul Rahim
- Department of Pathology and Genetics, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Christopher Lindberg
- Department of Neurology, Neuromuscular Centre, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Kristjan Karason
- Department of Cardiology and Transplant Institute, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Kittichate Visuttijai
- Department of Pathology and Genetics, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mats Geijer
- Department of Radiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Matthias Begemann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Florian Kraft
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Eva Lausberg
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Lea Hitpass
- Department of Diagnostic and Interventional Radiology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Rebekka Götzl
- Department of Plastic Surgery, Hand and Burn Surgery, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Elizabeth J Luna
- Division of Cell Biology and Imaging, Department of Radiology, University of Massachusetts Medical School, Worcester, USA
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Canada.,Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Michael Gramlich
- Department of Invasive Electrophysiology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Burkhard Gess
- Department of Neurology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Joachim Weis
- Institute of Neuropathology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Anders Oldfors
- Department of Pathology and Genetics, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Cordula Knopp
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
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18
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Kanzi AM, San JE, Chimukangara B, Wilkinson E, Fish M, Ramsuran V, de Oliveira T. Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance. Front Genet 2020; 11:544162. [PMID: 33193618 PMCID: PMC7649788 DOI: 10.3389/fgene.2020.544162] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/21/2020] [Indexed: 12/29/2022] Open
Abstract
Mendelian and complex genetic trait diseases continue to burden and affect society both socially and economically. The lack of effective tests has hampered diagnosis thus, the affected lack proper prognosis. Mendelian diseases are caused by genetic mutations in a singular gene while complex trait diseases are caused by the accumulation of mutations in either linked or unlinked genomic regions. Significant advances have been made in identifying novel diseases associated mutations especially with the introduction of next generation and third generation sequencing. Regardless, some diseases are still without diagnosis as most tests rely on SNP genotyping panels developed from population based genetic analyses. Analysis of family genetic inheritance using whole genomes, whole exomes or a panel of genes has been shown to be effective in identifying disease-causing mutations. In this review, we discuss next generation and third generation sequencing platforms, bioinformatic tools and genetic resources commonly used to analyze family based genomic data with a focus on identifying inherited or novel disease-causing mutations. Additionally, we also highlight the analytical, ethical and regulatory challenges associated with analyzing personal genomes which constitute the data used for family genetic inheritance.
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Affiliation(s)
- Aquillah M. Kanzi
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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19
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Meyer R, Begemann M, Demuth S, Kraft F, Dey D, Schüler H, Busse S, Häusler M, Zerres K, Kurth I, Eggermann T, Elbracht M. Inherited cases of CNOT3-associated intellectual developmental disorder with speech delay, autism, and dysmorphic facies. Clin Genet 2020; 98:408-412. [PMID: 32720325 DOI: 10.1111/cge.13819] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/15/2020] [Accepted: 07/20/2020] [Indexed: 12/01/2022]
Abstract
De novo pathogenic variants in CNOT3 have recently been reported in a developmental delay disorder (intellectual developmental disorder with speech delay, autism, and dysmorphic facies [IDDSADF, OMIM: #618672]). The patients present with a variable degree of developmental delay and behavioral problems. To date, all reported disease-causing variants occurred de novo and no parent-child transmission was observed. We report for the first time autosomal dominant transmissions of the CNOT3-associated developmental disorder in two unrelated families. The clinical characteristics in our patients match the IDDSADF features reported so far and suggest substantial variability of the phenotype within the same family.
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Affiliation(s)
- Robert Meyer
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Matthias Begemann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | | | - Florian Kraft
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Daniela Dey
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Herdit Schüler
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Sabine Busse
- Division of Neuropediatrics and Social Pediatrics, Department of Pediatrics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Martin Häusler
- Division of Neuropediatrics and Social Pediatrics, Department of Pediatrics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Klaus Zerres
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Thomas Eggermann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
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20
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Hübner CT, Meyer R, Kenawy A, Ambrozaityte L, Matuleviciene A, Kraft F, Begemann M, Elbracht M, Eggermann T. HMGA2 Variants in Silver-Russell Syndrome: Homozygous and Heterozygous Occurrence. J Clin Endocrinol Metab 2020; 105:5839772. [PMID: 32421827 DOI: 10.1210/clinem/dgaa273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 05/13/2020] [Indexed: 02/06/2023]
Abstract
CONTEXT Silver-Russell syndrome (SRS) is a clinical and molecular heterogeneous disorder associated with short stature, typical facial gestalt, and body asymmetry. Though molecular causes of SRS can be identified in a significant number of patients, about one-half of patients currently remain without a molecular diagnosis. However, determination of the molecular cause is required for a targeted treatment and genetic counselling. OBJECTIVE The aim of this study was to corroborate the role of HMGA2 as an SRS-causing gene and reevaluate its mode of inheritance. DESIGN, SETTING, PATIENTS Patients were part of an ongoing study aiming on SRS-causing genes. They were classified according to the Netchine-Harbison clinical scoring system, and DNA samples were investigated by whole exome sequencing. Common molecular causes of SRS were excluded before. RESULTS Three novel pathogenic HMGA2 variants were identified in 5 patients from 3 SRS families, and fulfilling diagnostic criteria of SRS. For the first time, homozygosity for a variant in HMGA2 could be identified in a severely affected sibpair, whereas parents carrying heterozygous variants had a mild phenotype. Treatment with recombinant growth hormone led to a catch-up growth in 1 patient, whereas all others did not receive growth hormone and stayed small. One patient developed type 2 diabetes at age 30 years. CONCLUSIONS Identification of novel pathogenic variants confirms HMGA2 as an SRS-causing gene; thus, HMGA2 testing should be implemented in molecular SRS diagnostic workup. Furthermore, inheritance of HMGA2 is variable depending on the severity of the variant and its consequence for protein function.
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Affiliation(s)
| | - Robert Meyer
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Asmaa Kenawy
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Laima Ambrozaityte
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Ausra Matuleviciene
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Florian Kraft
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Matthias Begemann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Thomas Eggermann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
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21
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Abstract
Pheochromocytoma (PCC) is a rare, mostly benign tumour of the adrenal medulla. Hereditary PCC accounts for ~35% of cases and has been associated with germline mutations in several cancer susceptibility genes (e.g., KIF1B, SDHB, VHL, SDHD, RET). We performed whole-exome sequencing in a family with four PCC-affected patients in two consecutive generations and identified a potential novel candidate pathogenic variant in the REXO2 gene that affects splicing (c.531-1G>T (NM 015523.3)), which co-segregated with the phenotype in the family. REXO2 encodes for RNA exonuclease 2 protein and localizes to 11q23, a chromosomal region displaying allelic imbalance in PCC. REXO2 protein has been associated with DNA repair, replication and recombination processes and thus its inactivation may contribute to tumorigenesis. While the study suggests that this novel REXO2 gene variant underlies PCC in this family, additional functional studies are required in order to establish the putative role of the REXO2 gene in PCC predisposition.
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22
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Gaeta R, Lessi F, Mazzanti C, Modena M, Garaventa A, Boero S, Michelis MB, Capanna R, Aretini P, Franchi A. Diffuse bone and soft tissue angiomatosis with GNAQ mutation. Pathol Int 2020; 70:452-457. [PMID: 32314513 DOI: 10.1111/pin.12933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 12/15/2022]
Abstract
We describe a unique case of skeletal and extraskeletal angiomatosis complicated by Kasabach-Merritt syndrome. The patient was a 3-year-old boy, who presented with involvement of both femurs and left tibia, as well as with soft tissue lesions of the left thigh. At birth, multiple hemangiomas of the soft tissues of the frontal and parietal scalp had been identified, together with a space-occupying lesion of the lung. Histologically, the skeletal and soft tissue lesions consisted of a proliferation of thin-walled, dilated blood vessels, with an endothelial lining devoid of atypia and exhibiting immunoreactivity for CD31 and CD34, while podoplanin and GLUT1 were negative. Whole exome sequencing performed on samples from the lesion of the femur, the tibia and the skin of the thigh, showed a GNAQ (c.286A>T:p.T96S) variant in all specimens, that was confirmed with digital droplet PCR. This case expands the clinical and pathologic spectrum of vascular proliferations showing similar molecular biology, characterized by GNAQ, GNA11 or GNA14 mutations.
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Affiliation(s)
- Raffaele Gaeta
- Department of Translational Research and of New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy.,Genomic Section, Fondazione Pisana per la Scienza, Pisa, Italy
| | - Francesca Lessi
- Genomic Section, Fondazione Pisana per la Scienza, Pisa, Italy
| | - Chiara Mazzanti
- Genomic Section, Fondazione Pisana per la Scienza, Pisa, Italy
| | - Martina Modena
- Genomic Section, Fondazione Pisana per la Scienza, Pisa, Italy.,Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | | | - Silvio Boero
- Department of Paediatric Orthopaedics, IRCCS Istituto Giannina Gaslini, ItalyBond-ERN (European Reference Network for Bone and Muscoloskeletal Rare Disease), Genoa, Italy
| | - Maria Beatrice Michelis
- Department of Paediatric Orthopaedics, IRCCS Istituto Giannina Gaslini, ItalyBond-ERN (European Reference Network for Bone and Muscoloskeletal Rare Disease), Genoa, Italy
| | - Rodolfo Capanna
- Department of Translational Research and of New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Paolo Aretini
- Genomic Section, Fondazione Pisana per la Scienza, Pisa, Italy
| | - Alessandro Franchi
- Department of Translational Research and of New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
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23
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Modena M, Castiglione V, Aretini P, Mazzanti CM, Chiti E, Giannoni A, Emdin M, Di Paolo M. Unveiling a sudden unexplained death case by whole exome sequencing and bioinformatic analysis. Mol Genet Genomic Med 2020; 8:e1182. [PMID: 32101375 PMCID: PMC7196487 DOI: 10.1002/mgg3.1182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 01/12/2020] [Accepted: 01/30/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Sudden unexplained death (SUD) refers to cases of sudden death where autopsy fails to identify any cardiac or extracardiac underlying cause. Guideline-directed standard genetic testing identifies a disease-causing mutation in less than one-third of cases of SUD. Conversely, whole exome sequencing (WES) may provide the key to solve most cases of SUD even after several years from the subject's death. METHODS We report on a case of sudden unexpected death of a 37-year-old male, with inconclusive autopsy conducted 14 years ago. A recent reevaluation through WES was performed on DNA extracted from left ventricular samples. A multiple step process including several "in silico" tools was applied to identify potentially pathogenic variants. Data analysis was based on a 562 gene panel, including 234 candidate genes associated with sudden cardiac death or heart diseases, with the addition of 328 genes highly expressed in the heart. WebGestalt algorithms were used for association enrichment analysis of all genes with detected putative pathogenic variants. RESULTS WES analysis identified four potentially pathogenic variants: RYR2:c.12168G>T, TTN:c.11821C>T (rs397517804), MYBPC3:c.1255C>T (rs368770848), and ACADVL:c.848T>C (rs113994167). WebGestalt algorithms indicated that their combination holds an unfavorable arrhythmic susceptibility which conceivably caused the occurrence of the events leading to our subject's sudden death. CONCLUSION Associating WES technique with online prediction algorithms may allow the recognition of genetic mutations potentially responsible for otherwise unexplained deaths.
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Affiliation(s)
- Martina Modena
- Institute of Life SciencesScuola Superiore Sant'AnnaPisaItaly
- Fondazione Pisana per la Scienza ONLUSPisaItaly
| | - Vincenzo Castiglione
- Institute of Life SciencesScuola Superiore Sant'AnnaPisaItaly
- Cardiology DivisionUniversity of PisaPisaItaly
| | | | | | - Enrica Chiti
- Institute of Legal MedicineUniversity of PisaPisaItaly
| | - Alberto Giannoni
- Institute of Life SciencesScuola Superiore Sant'AnnaPisaItaly
- Fondazione Toscana Gabriele MonasterioPisaItaly
| | - Michele Emdin
- Institute of Life SciencesScuola Superiore Sant'AnnaPisaItaly
- Fondazione Toscana Gabriele MonasterioPisaItaly
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24
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Cetani F, Pardi E, Aretini P, Saponaro F, Borsari S, Mazoni L, Apicella M, Civita P, La Ferla M, Caligo MA, Lessi F, Mazzanti CM, Torregossa L, Oppo A, Marcocci C. Whole exome sequencing in familial isolated primary hyperparathyroidism. J Endocrinol Invest 2020; 43:231-245. [PMID: 31486992 DOI: 10.1007/s40618-019-01107-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/29/2019] [Indexed: 12/14/2022]
Abstract
PURPOSE Familial isolated hyperparathyroidism (FIHP) is a rare inherited disease accounting for 1% of all cases of primary hyperparathyroidism (PHPT). It is genetically heterogeneous being associated with mutations in different genes, including MEN1, CDC73, CASR, and recently GCM2. The aim of the study was to further investigate the molecular pathogenesis in Italian FIHP kindreds. METHODS We used whole exome sequencing (WES) in the probands of seven unrelated FIHP kindreds. We carried out a separate family-based exome analysis in a large family characterized by the co-occurrence of PHPT with multiple tumors apparently unrelated to the disease. Selected variants were also screened in 18 additional FIHP kindreds. The clinical, biochemical, and pathological characteristics of the families were also investigated. RESULTS Three different variants in GCM2 gene were found in two families, but only one (p.Tyr394Ser), already been shown to be pathogenic in vitro, segregated with the disease. Six probands carried seven heterozygous missense mutations segregating with the disease in the FAT3, PARK2, HDAC4, ITPR2 and TBCE genes. A genetic variant in the APC gene co-segregating with PHPT (p.Val530Ala) was detected in a family whose affected relatives had additional tumors, including colonic polyposis. CONCLUSION We confirm the role of GCM2 germline mutations in the pathogenesis of FIHP, although at a lower rate than in the previous WES study. Further studies are needed to establish the prevalence and the role in the predisposition to FIHP of the novel variants in additional genes.
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Affiliation(s)
- F Cetani
- University Hospital of Pisa, Endocrine Unit 2, Via Paradisa 2, 56124, Pisa, Italy.
| | - E Pardi
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - P Aretini
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - F Saponaro
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - S Borsari
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - L Mazoni
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - M Apicella
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - P Civita
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - M La Ferla
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - M A Caligo
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - F Lessi
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - C M Mazzanti
- Fondazione Pisana per la Scienza ONLUS, Pisa, Italy
| | - L Torregossa
- Division of Surgical Pathology, University Hospital of Pisa, Pisa, Italy
| | - A Oppo
- Endocrinology Unit, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - C Marcocci
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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25
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Garcia M, Juhos S, Larsson M, Olason PI, Martin M, Eisfeldt J, DiLorenzo S, Sandgren J, Díaz De Ståhl T, Ewels P, Wirta V, Nistér M, Käller M, Nystedt B. Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants. F1000Res 2020; 9:63. [PMID: 32269765 PMCID: PMC7111497 DOI: 10.12688/f1000research.16665.2] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and somatic mutations based on sequencing data from WGS, whole-exome sequencing (WES), or gene panels. Sarek features (i) easy installation, (ii) robust portability across different computer environments, (iii) comprehensive documentation, (iv) transparent and easy-to-read code, and (v) extensive quality metrics reporting. Sarek is implemented in the Nextflow workflow language and supports both Docker and Singularity containers as well as Conda environments, making it ideal for easy deployment on any POSIX-compatible computers and cloud compute environments. Sarek follows the GATK best-practice recommendations for read alignment and pre-processing, and includes a wide range of software for the identification and annotation of germline and somatic single-nucleotide variants, insertion and deletion variants, structural variants, tumour sample purity, and variations in ploidy and copy number. Sarek offers easy, efficient, and reproducible WGS analyses, and can readily be used both as a production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups. The Sarek source code, documentation and installation instructions are freely available at
https://github.com/nf-core/sarek and at
https://nf-co.re/sarek/.
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Affiliation(s)
- Maxime Garcia
- Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164, Sweden
| | - Szilveszter Juhos
- Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164, Sweden.,Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, Solna, 17121, Sweden.,Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37, Sweden
| | - Malin Larsson
- Department of Physics, Chemistry and Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Linköping University, Linköping, 58183, Sweden
| | - Pall I Olason
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37, Sweden
| | - Marcel Martin
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, Solna, 17121, Sweden
| | - Jesper Eisfeldt
- Clinical Genetics, Department of Molecular Medicine and Surgery, Karolinska Institutet, MMK L1:00, Karolinska University Hospital at Solna, Stockholm, 171 76, Sweden
| | - Sebastian DiLorenzo
- Department of Medical Sciences, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37, Sweden
| | - Johanna Sandgren
- Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164, Sweden
| | - Teresita Díaz De Ståhl
- Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164, Sweden
| | - Philip Ewels
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, Solna, 17121, Sweden
| | - Valtteri Wirta
- Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Facility, Science for Life Laboratory, Karolinska Institutet, Box 1031, Solna, 171 21, Sweden
| | - Monica Nistér
- Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164, Sweden
| | - Max Käller
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Box 1031, Solna, 17121, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37, Sweden
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26
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Garcia M, Juhos S, Larsson M, Olason PI, Martin M, Eisfeldt J, DiLorenzo S, Sandgren J, Díaz De Ståhl T, Ewels P, Wirta V, Nistér M, Käller M, Nystedt B. Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants. F1000Res 2020; 9:63. [PMID: 32269765 PMCID: PMC7111497 DOI: 10.12688/f1000research.16665.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 06/22/2024] Open
Abstract
Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and user-friendly workflows for WGS analyses poses a major challenge for many research groups and hampers scientific progress. Here we present Sarek, an open-source workflow to detect germline variants and somatic mutations based on sequencing data from WGS, whole-exome sequencing (WES), or gene panels. Sarek features (i) easy installation, (ii) robust portability across different computer environments, (iii) comprehensive documentation, (iv) transparent and easy-to-read code, and (v) extensive quality metrics reporting. Sarek is implemented in the Nextflow workflow language and supports both Docker and Singularity containers as well as Conda environments, making it ideal for easy deployment on any POSIX-compatible computers and cloud compute environments. Sarek follows the GATK best-practice recommendations for read alignment and pre-processing, and includes a wide range of software for the identification and annotation of germline and somatic single-nucleotide variants, insertion and deletion variants, structural variants, tumour sample purity, and variations in ploidy and copy number. Sarek offers easy, efficient, and reproducible WGS analyses, and can readily be used both as a production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups. The Sarek source code, documentation and installation instructions are freely available at https://github.com/nf-core/sarek and at https://nf-co.re/sarek/.
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Affiliation(s)
- Maxime Garcia
- Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164, Sweden
| | - Szilveszter Juhos
- Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164, Sweden
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, Solna, 17121, Sweden
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37, Sweden
| | - Malin Larsson
- Department of Physics, Chemistry and Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Linköping University, Linköping, 58183, Sweden
| | - Pall I. Olason
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37, Sweden
| | - Marcel Martin
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, Solna, 17121, Sweden
| | - Jesper Eisfeldt
- Clinical Genetics, Department of Molecular Medicine and Surgery, Karolinska Institutet, MMK L1:00, Karolinska University Hospital at Solna, Stockholm, 171 76, Sweden
| | - Sebastian DiLorenzo
- Department of Medical Sciences, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37, Sweden
| | - Johanna Sandgren
- Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164, Sweden
| | - Teresita Díaz De Ståhl
- Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164, Sweden
| | - Philip Ewels
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, Solna, 17121, Sweden
| | - Valtteri Wirta
- Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Facility, Science for Life Laboratory, Karolinska Institutet, Box 1031, Solna, 171 21, Sweden
| | - Monica Nistér
- Department of Oncology-Pathology, Karolinska Institutet, J5:30 BioClinicum, Visionsgatan 4, Karolinska University Hospital at Solna, Solna, 17164, Sweden
| | - Max Käller
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Box 1031, Solna, 17121, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Husargatan 3, Uppsala, 752 37, Sweden
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27
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Begemann M, Waszak SM, Robinson GW, Jäger N, Sharma T, Knopp C, Kraft F, Moser O, Mynarek M, Guerrini-Rousseau L, Brugieres L, Varlet P, Pietsch T, Bowers DC, Chintagumpala M, Sahm F, Korbel JO, Rutkowski S, Eggermann T, Gajjar A, Northcott P, Elbracht M, Pfister SM, Kontny U, Kurth I. Germline GPR161 Mutations Predispose to Pediatric Medulloblastoma. J Clin Oncol 2019; 38:43-50. [PMID: 31609649 PMCID: PMC6943973 DOI: 10.1200/jco.19.00577] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
PURPOSE The identification of a heritable tumor predisposition often leads to changes in management and increased surveillance of individuals who are at risk; however, for many rare entities, our knowledge of heritable predisposition is incomplete. METHODS Families with childhood medulloblastoma, one of the most prevalent childhood malignant brain tumors, were investigated to identify predisposing germline mutations. Initial findings were extended to genomes and epigenomes of 1,044 medulloblastoma cases from international multicenter cohorts, including retrospective and prospective clinical studies and patient series. RESULTS We identified heterozygous germline mutations in the G protein-coupled receptor 161 (GPR161) gene in six patients with infant-onset medulloblastoma (median age, 1.5 years). GPR161 mutations were exclusively associated with the sonic hedgehog medulloblastoma (MBSHH) subgroup and accounted for 5% of infant MBSHH cases in our cohorts. Molecular tumor profiling revealed a loss of heterozygosity at GPR161 in all affected MBSHH tumors, atypical somatic copy number landscapes, and no additional somatic driver events. Analysis of 226 MBSHH tumors revealed somatic copy-neutral loss of heterozygosity of chromosome 1q as the hallmark characteristic of GPR161 deficiency and the primary mechanism for biallelic inactivation of GPR161 in affected MBSHH tumors. CONCLUSION Here, we describe a novel brain tumor predisposition syndrome that is caused by germline GPR161 mutations and characterized by MBSHH in infants. Additional studies are needed to identify a potential broader tumor spectrum associated with germline GPR161 mutations.
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Affiliation(s)
| | | | | | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg, Heidelberg, Germany.,German Cancer Research Centre, Heidelberg, Germany
| | - Tanvi Sharma
- Hopp Children's Cancer Center Heidelberg, Heidelberg, Germany.,German Cancer Research Centre, Heidelberg, Germany
| | | | | | | | - Martin Mynarek
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | | | | | | | | | - Felix Sahm
- German Cancer Research Centre, Heidelberg, Germany.,University Hospital Heidelberg, Heidelberg, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | - Amar Gajjar
- St Jude Children's Research Hospital, Memphis, TN
| | | | | | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg, Heidelberg, Germany.,German Cancer Research Centre, Heidelberg, Germany.,University Hospital Heidelberg, Heidelberg, Germany
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28
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La Ferla M, Lessi F, Aretini P, Pellegrini D, Franceschi S, Tantillo E, Menicagli M, Marchetti I, Scopelliti C, Civita P, De Angelis C, Diodati L, Bertolini I, Roncella M, McDonnell LA, Hochman J, Del Re M, Scatena C, Naccarato AG, Fontana A, Mazzanti CM. ANKRD44 Gene Silencing: A Putative Role in Trastuzumab Resistance in Her2-Like Breast Cancer. Front Oncol 2019; 9:547. [PMID: 31297336 PMCID: PMC6607964 DOI: 10.3389/fonc.2019.00547] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/04/2019] [Indexed: 12/11/2022] Open
Abstract
Trastuzumab is an effective therapeutic treatment for Her2-like breast cancer; despite this most of these tumors develop resistance to therapy due to specific gene mutations or alterations in gene expression. Understanding the mechanisms of resistance to Trastuzumab could be a useful tool in order to identify combinations of drugs that elude resistance and allow a better response for the treated patients. Twelve primary biopsies of Her2+/hormone receptor negative (ER-/PgR-) breast cancer patients were selected based on the specific response to neoadjuvant therapy with Trastuzumab and their whole exome was sequenced leading to the identification of 18 informative gene mutations that discriminate patients selectively based on response to treatment. Among these genes, we focused on the study of the ANKRD44 gene to understand its role in the mechanism of resistance to Trastuzumab. The ANKRD44 gene was silenced in Her2-like breast cancer cell line (BT474), obtaining a partially Trastuzumab-resistant breast cancer cell line that constitutively activates the NF-kb protein via the TAK1/AKT pathway. Following this activation an increase in the level of glycolysis in resistant cells is promoted, also confirmed by the up-regulation of the LDHB protein and by an increased TROP2 protein expression, found generally associated with aggressive tumors. These results allow us to consider the ANKRD44 gene as a potential gene involved in Trastuzumab resistance.
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Affiliation(s)
- Marco La Ferla
- Fondazione Pisana per la Scienza - Genomic Section, Pisa, Italy
| | - Francesca Lessi
- Fondazione Pisana per la Scienza - Genomic Section, Pisa, Italy
| | - Paolo Aretini
- Fondazione Pisana per la Scienza - Genomic Section, Pisa, Italy
| | - Davide Pellegrini
- Fondazione Pisana per la Scienza - Proteomic Section, Pisa, Italy.,NEST, Scuola Normale Superiore, Pisa, Italy
| | - Sara Franceschi
- Fondazione Pisana per la Scienza - Genomic Section, Pisa, Italy
| | - Elena Tantillo
- Fondazione Pisana per la Scienza - Genomic Section, Pisa, Italy.,Scuola Normale Superiore, Pisa, Italy
| | | | - Ivo Marchetti
- Cytopathology Section, Azienda Ospedaliero-Universitaria Pisana (AOUP), Pisa, Italy
| | | | - Prospero Civita
- Fondazione Pisana per la Scienza - Genomic Section, Pisa, Italy
| | - Claudia De Angelis
- Medical Oncology Unit, Azienda Ospedaliero-Universitaria Pisana (AOUP), Pisa, Italy
| | - Lucrezia Diodati
- Medical Oncology Unit, Azienda Ospedaliero-Universitaria Pisana (AOUP), Pisa, Italy
| | - Ilaria Bertolini
- Medical Oncology Unit, Azienda Ospedaliero-Universitaria Pisana (AOUP), Pisa, Italy
| | - Manuela Roncella
- Breast Cancer Center, Azienda Ospedaliero-Universitaria Pisana (AOUP), Pisa, Italy
| | - Liam A McDonnell
- Fondazione Pisana per la Scienza - Proteomic Section, Pisa, Italy
| | - Jacob Hochman
- Department of Cell and Developmental Biology, the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Marzia Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Cristian Scatena
- Department of Translational Research and New Technologies in Medicine and Surgery, University Hospital of Pisa, Pisa, Italy
| | - Antonio G Naccarato
- Department of Translational Research and New Technologies in Medicine and Surgery, University Hospital of Pisa, Pisa, Italy
| | - Andrea Fontana
- Medical Oncology Unit, Azienda Ospedaliero-Universitaria Pisana (AOUP), Pisa, Italy
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29
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Next generation sequencing and imprinting disorders: Current applications and future perspectives: Lessons from Silver-Russell syndrome. Mol Cell Probes 2019; 44:1-7. [DOI: 10.1016/j.mcp.2018.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 12/05/2018] [Accepted: 12/22/2018] [Indexed: 12/28/2022]
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30
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Karsai G, Kraft F, Haag N, Korenke GC, Hänisch B, Othman A, Suriyanarayanan S, Steiner R, Knopp C, Mull M, Bergmann M, Schröder JM, Weis J, Elbracht M, Begemann M, Hornemann T, Kurth I. DEGS1-associated aberrant sphingolipid metabolism impairs nervous system function in humans. J Clin Invest 2019; 129:1229-1239. [PMID: 30620338 DOI: 10.1172/jci124159] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/21/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Sphingolipids are important components of cellular membranes and functionally associated with fundamental processes such as cell differentiation, neuronal signaling, and myelin sheath formation. Defects in the synthesis or degradation of sphingolipids leads to various neurological pathologies; however, the entire spectrum of sphingolipid metabolism disorders remains elusive. METHODS A combined approach of genomics and lipidomics was applied to identify and characterize a human sphingolipid metabolism disorder. RESULTS By whole-exome sequencing in a patient with a multisystem neurological disorder of both the central and peripheral nervous systems, we identified a homozygous p.Ala280Val variant in DEGS1, which catalyzes the last step in the ceramide synthesis pathway. The blood sphingolipid profile in the patient showed a significant increase in dihydro sphingolipid species that was further recapitulated in patient-derived fibroblasts, in CRISPR/Cas9-derived DEGS1-knockout cells, and by pharmacological inhibition of DEGS1. The enzymatic activity in patient fibroblasts was reduced by 80% compared with wild-type cells, which was in line with a reduced expression of mutant DEGS1 protein. Moreover, an atypical and potentially neurotoxic sphingosine isomer was identified in patient plasma and in cells expressing mutant DEGS1. CONCLUSION We report DEGS1 dysfunction as the cause of a sphingolipid disorder with hypomyelination and degeneration of both the central and peripheral nervous systems. TRIAL REGISTRATION Not applicable. FUNDING Seventh Framework Program of the European Commission, Swiss National Foundation, Rare Disease Initiative Zurich.
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Affiliation(s)
- Gergely Karsai
- Center for Integrative Human Physiology, University of Zürich, Zürich, Switzerland.,Institute for Clinical Chemistry, University Hospital, Zürich, Switzerland
| | - Florian Kraft
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Natja Haag
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - G Christoph Korenke
- Clinic for Neuropediatrics and Congenital Metabolic Diseases, University Clinic for Paediatrics and Adolescent Medicine, Oldenburg, Germany
| | - Benjamin Hänisch
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Alaa Othman
- Center for Integrative Human Physiology, University of Zürich, Zürich, Switzerland.,Institute for Clinical Chemistry, University Hospital, Zürich, Switzerland
| | - Saranya Suriyanarayanan
- Center for Integrative Human Physiology, University of Zürich, Zürich, Switzerland.,Institute for Clinical Chemistry, University Hospital, Zürich, Switzerland
| | - Regula Steiner
- Center for Integrative Human Physiology, University of Zürich, Zürich, Switzerland.,Institute for Clinical Chemistry, University Hospital, Zürich, Switzerland
| | - Cordula Knopp
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Michael Mull
- Department of Diagnostic and Interventional Neuroradiology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Markus Bergmann
- Institute for Neuropathology, Hospital Bremen-Mitte, Bremen, Germany
| | - J Michael Schröder
- Institute of Neuropathology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Joachim Weis
- Institute of Neuropathology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Matthias Begemann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Thorsten Hornemann
- Center for Integrative Human Physiology, University of Zürich, Zürich, Switzerland.,Institute for Clinical Chemistry, University Hospital, Zürich, Switzerland
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
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31
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Hebbar M, Shukla A, Nampoothiri S, Bielas S, Girisha KM. Locus and allelic heterogeneity in five families with hereditary spastic paraplegia. J Hum Genet 2018; 64:17-21. [PMID: 30337681 PMCID: PMC6344291 DOI: 10.1038/s10038-018-0523-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 09/12/2018] [Accepted: 10/08/2018] [Indexed: 01/29/2023]
Abstract
Hereditary spastic paraplegias are a group of genetically heterogeneous neurological disorders characterized by progressive weakness and spasticity of lower limbs. We ascertained five families with eight individuals with hereditary spastic paraplegia. Pathogenic variants were identified by exome sequencing of index cases. The cohort consists of three families with spastic paraplegia type 47 (AP4B1) with a common mutation in two families, a family with spastic paraplegia type 50 (AP4M1), and two male siblings with X-linked spastic paraplegia 2 (PLP1). This work illustrates locus and allelic heterogeneity in five families with hereditary spastic paraplegia.
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Affiliation(s)
- Malavika Hebbar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Ponekkara, Cochin, Kerala, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
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32
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Tessier L, Côté O, Bienzle D. Sequence variant analysis of RNA sequences in severe equine asthma. PeerJ 2018; 6:e5759. [PMID: 30324028 PMCID: PMC6186407 DOI: 10.7717/peerj.5759] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 09/15/2018] [Indexed: 12/13/2022] Open
Abstract
Background Severe equine asthma is a chronic inflammatory disease of the lung in horses similar to low-Th2 late-onset asthma in humans. This study aimed to determine the utility of RNA-Seq to call gene sequence variants, and to identify sequence variants of potential relevance to the pathogenesis of asthma. Methods RNA-Seq data were generated from endobronchial biopsies collected from six asthmatic and seven non-asthmatic horses before and after challenge (26 samples total). Sequences were aligned to the equine genome with Spliced Transcripts Alignment to Reference software. Read preparation for sequence variant calling was performed with Picard tools and Genome Analysis Toolkit (GATK). Sequence variants were called and filtered using GATK and Ensembl Variant Effect Predictor (VEP) tools, and two RNA-Seq predicted sequence variants were investigated with both PCR and Sanger sequencing. Supplementary analysis of novel sequence variant selection with VEP was based on a score of <0.01 predicted with Sorting Intolerant from Tolerant software, missense nature, location within the protein coding sequence and presence in all asthmatic individuals. For select variants, effect on protein function was assessed with Polymorphism Phenotyping 2 and screening for non-acceptable polymorphism 2 software. Sequences were aligned and 3D protein structures predicted with Geneious software. Difference in allele frequency between the groups was assessed using a Pearson’s Chi-squared test with Yates’ continuity correction, and difference in genotype frequency was calculated using the Fisher’s exact test for count data. Results RNA-Seq variant calling and filtering correctly identified substitution variants in PACRG and RTTN. Sanger sequencing confirmed that the PACRG substitution was appropriately identified in all 26 samples while the RTTN substitution was identified correctly in 24 of 26 samples. These variants of uncertain significance had substitutions that were predicted to result in loss of function and to be non-neutral. Amino acid substitutions projected no change of hydrophobicity and isoelectric point in PACRG, and a change in both for RTTN. For PACRG, no difference in allele frequency between the two groups was detected but a higher proportion of asthmatic horses had the altered RTTN allele compared to non-asthmatic animals. Discussion RNA-Seq was sensitive and specific for calling gene sequence variants in this disease model. Even moderate coverage (<10–20 counts per million) yielded correct identification in 92% of samples, suggesting RNA-Seq may be suitable to detect sequence variants in low coverage samples. The impact of amino acid alterations in PACRG and RTTN proteins, and possible association of the sequence variants with asthma, is of uncertain significance, but their role in ciliary function may be of future interest.
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Affiliation(s)
- Laurence Tessier
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada.,BenchSci, Toronto, ON, Canada
| | - Olivier Côté
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada.,BioAssay Works, Ijamsville, MD, USA
| | - Dorothee Bienzle
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
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33
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Osaki T, Uzel SGM, Kamm RD. Microphysiological 3D model of amyotrophic lateral sclerosis (ALS) from human iPS-derived muscle cells and optogenetic motor neurons. SCIENCE ADVANCES 2018; 4:eaat5847. [PMID: 30324134 PMCID: PMC6179377 DOI: 10.1126/sciadv.aat5847] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/05/2018] [Indexed: 05/04/2023]
Abstract
Amyotrophic lateral sclerosis (ALS), a progressive neurodegenerative disease involving loss of motor neurons (MNs) and muscle atrophy, still has no effective treatment, despite much research effort. To provide a platform for testing drug candidates and investigating the pathogenesis of ALS, we developed an ALS-on-a-chip technology (i.e., an ALS motor unit) using three-dimensional skeletal muscle bundles along with induced pluripotent stem cell (iPSC)-derived and light-sensitive channelrhodopsin-2-induced MN spheroids from a patient with sporadic ALS. Each tissue was cultured in a different compartment of a microfluidic device. Axon outgrowth formed neuromuscular junctions on the muscle fiber bundles. Light was used to activate muscle contraction, which was measured on the basis of pillar deflections. Compared to a non-ALS motor unit, the ALS motor unit generated fewer muscle contractions, there was MN degradation, and apoptosis increased in the muscle. Furthermore, the muscle contractions were recovered by single treatments and cotreatment with rapamycin (a mechanistic target of rapamycin inhibitor) and bosutinib (an Src/c-Abl inhibitor). This recovery was associated with up-regulation of autophagy and degradation of TAR DNA binding protein-43 in the MNs. Moreover, administering the drugs via an endothelial cell barrier decreased the expression of P-glycoprotein (an efflux pump that transports bosutinib) in the endothelial cells, indicating that rapamycin and bosutinib cotreatment has considerable potential for ALS treatment. This ALS-on-a-chip and optogenetics technology could help to elucidate the pathogenesis of ALS and to screen for drug candidates.
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Affiliation(s)
- Tatsuya Osaki
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 500 Technology Square, Room NE47-321, Cambridge, MA 02139, USA
| | - Sebastien G. M. Uzel
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 500 Technology Square, Room NE47-321, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Roger D. Kamm
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 500 Technology Square, Room NE47-321, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square, Room NE47-321, Cambridge, MA 02139, USA
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- Corresponding author.
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Tom N, Tom O, Malcikova J, Pavlova S, Kubesova B, Rausch T, Kolarik M, Benes V, Bystry V, Pospisilova S. ToTem: a tool for variant calling pipeline optimization. BMC Bioinformatics 2018; 19:243. [PMID: 29940847 PMCID: PMC6020218 DOI: 10.1186/s12859-018-2227-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/31/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND High-throughput bioinformatics analyses of next generation sequencing (NGS) data often require challenging pipeline optimization. The key problem is choosing appropriate tools and selecting the best parameters for optimal precision and recall. RESULTS Here we introduce ToTem, a tool for automated pipeline optimization. ToTem is a stand-alone web application with a comprehensive graphical user interface (GUI). ToTem is written in Java and PHP with an underlying connection to a MySQL database. Its primary role is to automatically generate, execute and benchmark different variant calling pipeline settings. Our tool allows an analysis to be started from any level of the process and with the possibility of plugging almost any tool or code. To prevent an over-fitting of pipeline parameters, ToTem ensures the reproducibility of these by using cross validation techniques that penalize the final precision, recall and F-measure. The results are interpreted as interactive graphs and tables allowing an optimal pipeline to be selected, based on the user's priorities. Using ToTem, we were able to optimize somatic variant calling from ultra-deep targeted gene sequencing (TGS) data and germline variant detection in whole genome sequencing (WGS) data. CONCLUSIONS ToTem is a tool for automated pipeline optimization which is freely available as a web application at https://totem.software .
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Affiliation(s)
- Nikola Tom
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, Medical Faculty, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Ondrej Tom
- Department of Computer Science, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Jitka Malcikova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, Medical Faculty, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Sarka Pavlova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, Medical Faculty, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Blanka Kubesova
- Department of Internal Medicine - Hematology and Oncology, Medical Faculty, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Tobias Rausch
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Miroslav Kolarik
- Department of Computer Science, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Vojtech Bystry
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine - Hematology and Oncology, Medical Faculty, Masaryk University and University Hospital Brno, Brno, Czech Republic
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35
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A biallelic 36-bp insertion in PIBF1 is associated with Joubert syndrome. J Hum Genet 2018; 63:935-939. [PMID: 29695797 PMCID: PMC6060014 DOI: 10.1038/s10038-018-0462-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 04/10/2018] [Accepted: 04/10/2018] [Indexed: 02/06/2023]
Abstract
Biallelic pathogenic variants in PIBF1 have been identified as one of the genetic etiologies of Joubert syndrome. We report a two-years-old girl with global developmental delay, facial dysmorphism, hypotonia, enlarged cystic kidneys, molar tooth sign and thinning of corpus callosum. A novel homozygous 36-bp insertion in PIBF1 (c.1181_1182ins36) was identified by exome sequencing as the likely cause of her condition. This is the second publication demonstrating the cause and effect relationship between PIBF1 and Joubert syndrome.
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36
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Clinical and genetic spectrum of AMPD2-related pontocerebellar hypoplasia type 9. Eur J Hum Genet 2018; 26:695-708. [PMID: 29463858 DOI: 10.1038/s41431-018-0098-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 12/28/2017] [Accepted: 01/09/2018] [Indexed: 11/08/2022] Open
Abstract
Pontocerebellar hypoplasia (PCH) represents a group of autosomal-recessive progressive neurodegenerative disorders of prenatal onset. Eleven PCH subtypes are classified according to clinical, neuroimaging and genetic findings. Individuals with PCH type 9 (PCH9) have a unique combination of postnatal microcephaly, hypoplastic cerebellum and pons, and hypoplastic or absent corpus callosum. PCH9 is caused by biallelic variants in AMPD2 encoding adenosine monophosphate deaminase 2; however, a homozygous AMPD2 frameshift variant has recently been reported in two family members with spastic paraplegia type 63 (SPG63). We identified homozygous or compound heterozygous AMPD2 variants in eight PCH-affected individuals from six families. The eight variants likely affect function and comprise one frameshift, one nonsense and six missense variants; seven of which were novel. The main clinical manifestations in the eight new patients and 17 previously reported individuals with biallelic AMPD2 variants were postnatal microcephaly, severe global developmental delay, spasticity, and central visual impairment. Brain imaging data identified hypomyelination, hypoplasia of the cerebellum and pons, atrophy of the cerebral cortex, complete or partial agenesis of the corpus callosum and the "figure 8" shape of the hypoplastic midbrain as consistent features. We broaden the AMPD2-related clinical spectrum by describing one individual without microcephaly and absence of the characteristic "figure 8" shape of the midbrain. The existence of various AMPD2 isoforms with different functions possibly explains the variability in phenotypes associated with AMPD2 variants: variants leaving some of the isoforms intact may cause SPG63, while those affecting all isoforms may result in the severe and early-onset PCH9.
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Dunn P, Albury CL, Maksemous N, Benton MC, Sutherland HG, Smith RA, Haupt LM, Griffiths LR. Next Generation Sequencing Methods for Diagnosis of Epilepsy Syndromes. Front Genet 2018; 9:20. [PMID: 29467791 PMCID: PMC5808353 DOI: 10.3389/fgene.2018.00020] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/16/2018] [Indexed: 12/28/2022] Open
Abstract
Epilepsy is a neurological disorder characterized by an increased predisposition for seizures. Although this definition suggests that it is a single disorder, epilepsy encompasses a group of disorders with diverse aetiologies and outcomes. A genetic basis for epilepsy syndromes has been postulated for several decades, with several mutations in specific genes identified that have increased our understanding of the genetic influence on epilepsies. With 70-80% of epilepsy cases identified to have a genetic cause, there are now hundreds of genes identified to be associated with epilepsy syndromes which can be analyzed using next generation sequencing (NGS) techniques such as targeted gene panels, whole exome sequencing (WES) and whole genome sequencing (WGS). For effective use of these methodologies, diagnostic laboratories and clinicians require information on the relevant workflows including analysis and sequencing depth to understand the specific clinical application and diagnostic capabilities of these gene sequencing techniques. As epilepsy is a complex disorder, the differences associated with each technique influence the ability to form a diagnosis along with an accurate detection of the genetic etiology of the disorder. In addition, for diagnostic testing, an important parameter is the cost-effectiveness and the specific diagnostic outcome of each technique. Here, we review these commonly used NGS techniques to determine their suitability for application to epilepsy genetic diagnostic testing.
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Affiliation(s)
- Paul Dunn
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Cassie L Albury
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Neven Maksemous
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Miles C Benton
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Heidi G Sutherland
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Robert A Smith
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Larisa M Haupt
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
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Li J, Shi L, Zhang K, Zhang Y, Hu S, Zhao T, Teng H, Li X, Jiang Y, Ji L, Sun Z. VarCards: an integrated genetic and clinical database for coding variants in the human genome. Nucleic Acids Res 2018; 46:D1039-D1048. [PMID: 29112736 PMCID: PMC5753295 DOI: 10.1093/nar/gkx1039] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 12/24/2022] Open
Abstract
A growing number of genomic tools and databases were developed to facilitate the interpretation of genomic variants, particularly in coding regions. However, these tools are separately available in different online websites or databases, making it challenging for general clinicians, geneticists and biologists to obtain the first-hand information regarding some particular variants and genes of interest. Starting with coding regions and splice sties, we artificially generated all possible single nucleotide variants (n = 110 154 363) and cataloged all reported insertion and deletions (n = 1 223 370). We then annotated these variants with respect to functional consequences from more than 60 genomic data sources to develop a database, named VarCards (http://varcards.biols.ac.cn/), by which users can conveniently search, browse and annotate the variant- and gene-level implications of given variants, including the following information: (i) functional effects; (ii) functional consequences through different in silico algorithms; (iii) allele frequencies in different populations; (iv) disease- and phenotype-related knowledge; (v) general meaningful gene-level information; and (vi) drug-gene interactions. As a case study, we successfully employed VarCards in interpretation of de novo mutations in autism spectrum disorders. In conclusion, VarCards provides an intuitive interface of necessary information for researchers to prioritize candidate variations and genes.
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Affiliation(s)
- Jinchen Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410078, China
- Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Leisheng Shi
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Kun Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Yi Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Shanshan Hu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Tingting Zhao
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Huajing Teng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianfeng Li
- Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Jiang
- Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Liying Ji
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Zhongsheng Sun
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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Meena N, Mathur P, Medicherla K, Suravajhala P. A Bioinformatics Pipeline for Whole Exome Sequencing: Overview of the Processing and Steps from Raw Data to Downstream Analysis. Bio Protoc 2018. [DOI: 10.21769/bioprotoc.2805] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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40
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Kleyner R, Malcolmson J, Tegay D, Ward K, Maughan A, Maughan G, Nelson L, Wang K, Robison R, Lyon GJ. KBG syndrome involving a single-nucleotide duplication in ANKRD11. Cold Spring Harb Mol Case Stud 2017; 2:a001131. [PMID: 27900361 PMCID: PMC5111005 DOI: 10.1101/mcs.a001131] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
KBG syndrome is a rare autosomal dominant genetic condition characterized by neurological involvement and distinct facial, hand, and skeletal features. More than 70 cases have been reported; however, it is likely that KBG syndrome is underdiagnosed because of lack of comprehensive characterization of the heterogeneous phenotypic features. We describe the clinical manifestations in a male currently 13 years of age, who exhibited symptoms including epilepsy, severe developmental delay, distinct facial features, and hand anomalies, without a positive genetic diagnosis. Subsequent exome sequencing identified a novel de novo heterozygous single base pair duplication (c.6015dupA) in ANKRD11, which was validated by Sanger sequencing. This single-nucleotide duplication is predicted to lead to a premature stop codon and loss of function in ANKRD11, thereby implicating it as contributing to the proband's symptoms and yielding a molecular diagnosis of KBG syndrome. Before molecular diagnosis, this syndrome was not recognized in the proband, as several key features of the disorder were mild and were not recognized by clinicians, further supporting the concept of variable expressivity in many disorders. Although a diagnosis of cerebral folate deficiency has also been given, its significance for the proband's condition remains uncertain.
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Affiliation(s)
- Robert Kleyner
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Janet Malcolmson
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;; Genetic Counseling Graduate Program, Long Island University (LIU), Brookville, New York 11548, USA
| | - David Tegay
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Kenneth Ward
- Affiliated Genetics, Inc., Salt Lake City, Utah 84109, USA
| | | | - Glenn Maughan
- KBG Syndrome Foundation, West Jordan, Utah 84088, USA
| | - Lesa Nelson
- Affiliated Genetics, Inc., Salt Lake City, Utah 84109, USA
| | - Kai Wang
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90089, USA;; Department of Psychiatry & Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA;; Utah Foundation for Biomedical Research, Salt Lake City, Utah 84107, USA
| | - Reid Robison
- Utah Foundation for Biomedical Research, Salt Lake City, Utah 84107, USA
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;; Utah Foundation for Biomedical Research, Salt Lake City, Utah 84107, USA
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41
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Hebbar M, Kanthi A, Shrikiran A, Patil S, Muranjan M, Francis F, Bhat B V, Girisha KM, Shukla A. p.Arg69Trp in RNASEH2C
is a founder variant in three Indian families with Aicardi-Goutières syndrome. Am J Med Genet A 2017; 176:156-160. [DOI: 10.1002/ajmg.a.38522] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 09/19/2017] [Accepted: 10/08/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Malavika Hebbar
- Department of Medical Genetics, Kasturba Medical College; Manipal University; Manipal India
| | - Anil Kanthi
- Department of Medical Genetics, Kasturba Medical College; Manipal University; Manipal India
| | - Aroor Shrikiran
- Department of Pediatrics, Kasturba Medical College; Manipal University; Manipal India
| | - Snehal Patil
- Department of Pediatrics; Seth GSMC and KEM Hospital; Mumbai India
| | - Mamta Muranjan
- Department of Pediatrics; Seth GSMC and KEM Hospital; Mumbai India
| | - Febi Francis
- Department of Neonatology; JIPMER; Pondicherry India
| | - Vishnu Bhat B
- Department of Neonatology; JIPMER; Pondicherry India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College; Manipal University; Manipal India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College; Manipal University; Manipal India
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Homozygosity for a nonsense variant in AIMP2 is associated with a progressive neurodevelopmental disorder with microcephaly, seizures, and spastic quadriparesis. J Hum Genet 2017; 63:19-25. [PMID: 29215095 DOI: 10.1038/s10038-017-0363-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/07/2017] [Accepted: 09/07/2017] [Indexed: 01/31/2023]
Abstract
We ascertained two unrelated consanguineous families with two affected children each having microcephaly, refractory seizures, intellectual disability, and spastic quadriparesis. Magnetic resonance imaging showed atrophy of cerebrum, cerebellum and spinal cord, prominent cisterna magna, symmetric T2 hypo-intensities in the bilateral basal ganglia and thinning of corpus callosum. Whole-exome sequencing of three affected individuals revealed c.105C>A [p.(Tyr35Ter)] variant in AIMP2. The variant lies in a common homozygous region of 940 kb on chromosome 7 and is likely to have been inherited from a common ancestor. The phenotype noted in our subjects' shares marked similarity with that of hypomyelinating leukodystrophy-3 caused by mutations in closely related gene AIMP1. We hereby report the first human disease associated with deleterious mutations in AIMP2.
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43
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Hebbar M, Girisha KM, Srivastava A, Bielas S, Shukla A. Homozygous c.359del variant in MGME1 is associated with early onset cerebellar ataxia. Eur J Med Genet 2017; 60:533-535. [PMID: 28711739 DOI: 10.1016/j.ejmg.2017.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/04/2017] [Accepted: 07/11/2017] [Indexed: 11/25/2022]
Abstract
We ascertained a child with early onset cerebellar ataxia and identified a novel frameshift deletion, c.359del [p. (Pro120Leufs*2), NM_052865.2] in exon 2 of MGME1 (mitochondrial genome maintenance exonuclease 1) by exome sequencing. Variations in MGME1 have been reported to cause mitochondrial DNA (mtDNA) depletion syndrome 11 (MIM #615084) in an earlier work. The phenotype included progressive external ophthalmoplegia, emaciation, respiratory failure and late onset progressive ataxia. However, the child presented here has early onset progressive ataxia, speech delay, microcephaly, cerebellar atrophy and fundus albipunctatus. This is the second report of a mutation in MGME1 and describes a more severe phenotype.
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Affiliation(s)
- Malavika Hebbar
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Anshika Srivastava
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India.
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44
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Requena T, Gallego-Martinez A, Lopez-Escamez JA. A pipeline combining multiple strategies for prioritizing heterozygous variants for the identification of candidate genes in exome datasets. Hum Genomics 2017; 11:11. [PMID: 28532469 PMCID: PMC5441048 DOI: 10.1186/s40246-017-0107-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/11/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The identification of disease-causing variants in autosomal dominant diseases using exome-sequencing data remains a difficult task in small pedigrees. We combined several strategies to improve filtering and prioritizing of heterozygous variants using exome-sequencing datasets in familial Meniere disease: an in-house Pathogenic Variant (PAVAR) score, the Variant Annotation Analysis and Search Tool (VAAST-Phevor), Exomiser-v2, CADD, and FATHMM. We also validated the method by a benchmarking procedure including causal mutations in synthetic exome datasets. RESULTS PAVAR and VAAST were able to select the same sets of candidate variants independently of the studied disease. In contrast, Exomiser V2 and VAAST-Phevor had a variable correlation depending on the phenotypic information available for the disease on each family. Nevertheless, all the selected diseases ranked a limited number of concordant variants in the top 10 ranking, using the three systems or other combined algorithm such as CADD or FATHMM. Benchmarking analyses confirmed that the combination of systems with different approaches improves the prediction of candidate variants compared with the use of a single method. The overall efficiency of combined tools ranges between 68 and 71% in the top 10 ranked variants. CONCLUSIONS Our pipeline prioritizes a short list of heterozygous variants in exome datasets based on the top 10 concordant variants combining multiple systems.
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Affiliation(s)
- Teresa Requena
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research – Pfizer/University of Granada/Junta de Andalucía, PTS, 18016 Granada, Spain
| | - Alvaro Gallego-Martinez
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research – Pfizer/University of Granada/Junta de Andalucía, PTS, 18016 Granada, Spain
| | - Jose A. Lopez-Escamez
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research – Pfizer/University of Granada/Junta de Andalucía, PTS, 18016 Granada, Spain
- Department of Otolaryngology, Complejo Hospitalario Universidad de Granada (CHUGRA), ibs.granada, 18014 Granada, Spain
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Shukla A, Hebbar M, Srivastava A, Kadavigere R, Upadhyai P, Kanthi A, Brandau O, Bielas S, Girisha KM. Homozygous p.(Glu87Lys) variant in ISCA1 is associated with a multiple mitochondrial dysfunctions syndrome. J Hum Genet 2017; 62:723-727. [PMID: 28356563 PMCID: PMC5484744 DOI: 10.1038/jhg.2017.35] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 02/06/2023]
Abstract
The iron-sulfur (Fe-S) cluster (ISC) biogenesis pathway is indispensable for many fundamental biological processes and pathogenic variations in genes encoding several components of the Fe-S biogenesis machinery, such as NFU1, BOLA3, IBA57 and ISCA2 are already implicated in causing four types of multiple mitochondrial dysfunctions syndromes (MMDS). We report on two unrelated families, with two affected children each with early onset neurological deterioration, seizures, extensive white matter abnormalities, cortical migrational abnormalities, lactic acidosis and early demise. Exome sequencing of two affected individuals, one from each family, revealed a homozygous c.259G>A [p.(Glu87Lys)] variant in ISCA1 and Mendelian segregation was confirmed in both families. The ISCA1 variant lies in the only shared region of homozygosity between the two families suggesting the possibility of a founder effect. In silico functional analyses and structural modeling of the protein predict the identified ISCA1 variant to be detrimental to protein stability and function. Notably the phenotype observed in all affected subjects with the ISCA1 pathogenic variant is similar to that previously described in all four types of MMDS. Our findings suggest association of a pathogenic variant in ISCA1 with another MMDS.
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Affiliation(s)
- Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Malavika Hebbar
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Anshika Srivastava
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Rajagopal Kadavigere
- Department of Radiodiagnosis and Imaging, Kasturba Medical College, Manipal, India
| | - Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Anil Kanthi
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | | | - Stephanie Bielas
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
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46
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A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data. Int J Genomics 2016; 2016:7983236. [PMID: 28070503 PMCID: PMC5192301 DOI: 10.1155/2016/7983236] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 10/26/2016] [Indexed: 12/31/2022] Open
Abstract
Whole Exome Sequencing (WES) is the application of the next-generation technology to determine the variations in the exome and is becoming a standard approach in studying genetic variants in diseases. Understanding the exomes of individuals at single base resolution allows the identification of actionable mutations for disease treatment and management. WES technologies have shifted the bottleneck in experimental data production to computationally intensive informatics-based data analysis. Novel computational tools and methods have been developed to analyze and interpret WES data. Here, we review some of the current tools that are being used to analyze WES data. These tools range from the alignment of raw sequencing reads all the way to linking variants to actionable therapeutics. Strengths and weaknesses of each tool are discussed for the purpose of helping researchers make more informative decisions on selecting the best tools to analyze their WES data.
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47
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Shi L, Guo Y, Dong C, Huddleston J, Yang H, Han X, Fu A, Li Q, Li N, Gong S, Lintner KE, Ding Q, Wang Z, Hu J, Wang D, Wang F, Wang L, Lyon GJ, Guan Y, Shen Y, Evgrafov OV, Knowles JA, Thibaud-Nissen F, Schneider V, Yu CY, Zhou L, Eichler EE, So KF, Wang K. Long-read sequencing and de novo assembly of a Chinese genome. Nat Commun 2016; 7:12065. [PMID: 27356984 PMCID: PMC4931320 DOI: 10.1038/ncomms12065] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 05/26/2016] [Indexed: 12/31/2022] Open
Abstract
Short-read sequencing has enabled the de novo assembly of several individual human genomes, but with inherent limitations in characterizing repeat elements. Here we sequence a Chinese individual HX1 by single-molecule real-time (SMRT) long-read sequencing, construct a physical map by NanoChannel arrays and generate a de novo assembly of 2.93 Gb (contig N50: 8.3 Mb, scaffold N50: 22.0 Mb, including 39.3 Mb N-bases), together with 206 Mb of alternative haplotypes. The assembly fully or partially fills 274 (28.4%) N-gaps in the reference genome GRCh38. Comparison to GRCh38 reveals 12.8 Mb of HX1-specific sequences, including 4.1 Mb that are not present in previously reported Asian genomes. Furthermore, long-read sequencing of the transcriptome reveals novel spliced genes that are not annotated in GENCODE and are missed by short-read RNA-Seq. Our results imply that improved characterization of genome functional variation may require the use of a range of genomic technologies on diverse human populations. Short-read sequencing has inherent limitations in the characterisation of long repeat elements. Shi and Guo et al. combine single-molecule real-time sequencing and IrysChip to construct a Chinese reference genome that fills many gaps in the reference genome, and identify novel spliced genes.
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Affiliation(s)
- Lingling Shi
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China.,Ministry of Education Joint International Research Laboratory of CNS Regeneration, Jinan University, Guangzhou 510632, China.,Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Yunfei Guo
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90089, USA
| | - Chengliang Dong
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90089, USA
| | - John Huddleston
- Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Hui Yang
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90089, USA
| | - Xiaolu Han
- Genetic, Molecular, and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Aisi Fu
- Wuhan Institute of Biotechnology, Wuhan 430000, China
| | - Quan Li
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90089, USA
| | - Na Li
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China
| | - Siyi Gong
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China
| | - Katherine E Lintner
- Department of Pediatrics, The Ohio State University, and The Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Qiong Ding
- Wuhan Institute of Biotechnology, Wuhan 430000, China
| | - Zou Wang
- Wuhan Institute of Biotechnology, Wuhan 430000, China
| | - Jiang Hu
- Nextomics Biosciences, Wuhan 430000, China
| | | | - Feng Wang
- School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430000, China
| | - Lin Wang
- Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, New York, New York 11797, USA
| | - Yongtao Guan
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yufeng Shen
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, New York 10032, USA
| | - Oleg V Evgrafov
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90089, USA.,Department of Psychiatry &Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - James A Knowles
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90089, USA.,Department of Psychiatry &Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, Maryland 20894, USA
| | - Valerie Schneider
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, Maryland 20894, USA
| | - Chack-Yung Yu
- Department of Pediatrics, The Ohio State University, and The Research Institute at Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Libing Zhou
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China.,Ministry of Education Joint International Research Laboratory of CNS Regeneration, Jinan University, Guangzhou 510632, China.,Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Evan E Eichler
- Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
| | - Kwok-Fai So
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China.,Ministry of Education Joint International Research Laboratory of CNS Regeneration, Jinan University, Guangzhou 510632, China.,Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China.,Department of Ophthalmology, The University of Hong Kong, Hong Kong, China.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, China
| | - Kai Wang
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90089, USA.,Department of Psychiatry &Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
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