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Esteller-Cucala P, Palmada-Flores M, Kuderna LFK, Fontsere C, Serres-Armero A, Dabad M, Torralvo M, Faella A, Ferrández-Peral L, Llovera L, Fornas O, Julià E, Ramírez E, González I, Hecht J, Lizano E, Juan D, Marquès-Bonet T. Y chromosome sequence and epigenomic reconstruction across human populations. Commun Biol 2023; 6:623. [PMID: 37296226 PMCID: PMC10256797 DOI: 10.1038/s42003-023-05004-9] [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: 12/21/2022] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
Recent advances in long-read sequencing technologies have allowed the generation and curation of more complete genome assemblies, enabling the analysis of traditionally neglected chromosomes, such as the human Y chromosome (chrY). Native DNA was sequenced on a MinION Oxford Nanopore Technologies sequencing device to generate genome assemblies for seven major chrY human haplogroups. We analyzed and compared the chrY enrichment of sequencing data obtained using two different selective sequencing approaches: adaptive sampling and flow cytometry chromosome sorting. We show that adaptive sampling can produce data to create assemblies comparable to chromosome sorting while being a less expensive and time-consuming technique. We also assessed haplogroup-specific structural variants, which would be otherwise difficult to study using short-read sequencing data only. Finally, we took advantage of this technology to detect and profile epigenetic modifications among the considered haplogroups. Altogether, we provide a framework to study complex genomic regions with a simple, fast, and affordable methodology that could be applied to larger population genomics datasets.
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Affiliation(s)
- Paula Esteller-Cucala
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Doctor Aiguader 88, Barcelona, Spain.
| | - Marc Palmada-Flores
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Doctor Aiguader 88, Barcelona, Spain
| | - Lukas F K Kuderna
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Doctor Aiguader 88, Barcelona, Spain
| | - Claudia Fontsere
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Doctor Aiguader 88, Barcelona, Spain
| | - Aitor Serres-Armero
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Doctor Aiguader 88, Barcelona, Spain
| | - Marc Dabad
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona, Spain
| | - María Torralvo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Doctor Aiguader 88, Barcelona, Spain
| | - Armida Faella
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Doctor Aiguader 88, Barcelona, Spain
| | - Luis Ferrández-Peral
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Doctor Aiguader 88, Barcelona, Spain
| | - Laia Llovera
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Doctor Aiguader 88, Barcelona, Spain
| | - Oscar Fornas
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Doctor Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, Barcelona, Spain
| | - Eva Julià
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Doctor Aiguader 88, Barcelona, Spain
| | - Erika Ramírez
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Doctor Aiguader 88, Barcelona, Spain
| | - Irene González
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Doctor Aiguader 88, Barcelona, Spain
| | - Jochen Hecht
- Centre for Genomic Regulation (CRG), Barcelona Institute for Science and Technology (BIST), Doctor Aiguader 88, Barcelona, Spain
| | - Esther Lizano
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Doctor Aiguader 88, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Cerdanyola del Vallès, Spain
| | - David Juan
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Doctor Aiguader 88, Barcelona, Spain
| | - Tomàs Marquès-Bonet
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Doctor Aiguader 88, Barcelona, Spain.
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, Barcelona, Spain.
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Cerdanyola del Vallès, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, Spain.
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2
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A high-throughput real-time PCR tissue-of-origin test to distinguish blood from lymphoblastoid cell line DNA for (epi)genomic studies. Sci Rep 2022; 12:4684. [PMID: 35304543 PMCID: PMC8933453 DOI: 10.1038/s41598-022-08663-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
Lymphoblastoid cell lines (LCLs) derive from blood infected in vitro by Epstein–Barr virus and were used in several genetic, transcriptomic and epigenomic studies. Although few changes were shown between LCL and blood genotypes (SNPs) validating their use in genetics, more were highlighted for other genomic features and/or in their transcriptome and epigenome. This could render them less appropriate for these studies, notably when blood DNA could still be available. Here we developed a simple, high-throughput and cost-effective real-time PCR approach allowing to distinguish blood from LCL DNA samples based on the presence of EBV relative load and rearranged T-cell receptors γ and β. Our approach was able to achieve 98.5% sensitivity and 100% specificity on DNA of known origin (458 blood and 316 LCL DNA). It was further applied to 1957 DNA samples from the CEPH Aging cohort comprising DNA of uncertain origin, identifying 784 blood and 1016 LCL DNA. A subset of these DNA was further analyzed with an epigenetic clock indicating that DNA extracted from blood should be preferred to LCL for DNA methylation-based age prediction analysis. Our approach could thereby be a powerful tool to ascertain the origin of DNA in old collections prior to (epi)genomic studies.
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3
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Liu C, Fetterman JL, Sun X, Yan K, Liu P, Luo Y, Ding J, Zhu J, Levy D. Comparison of mitochondrial DNA sequences from whole blood and lymphoblastoid cell lines. Sci Rep 2022; 12:1801. [PMID: 35110616 PMCID: PMC8810874 DOI: 10.1038/s41598-022-05814-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/10/2022] [Indexed: 01/19/2023] Open
Abstract
Lymphoblastoid cell lines (LCLs) provide an unlimited source of genomic DNA for genetic studies. Here, we compared mtDNA sequence variants, heteroplasmic or homplasmic, between LCL (sequenced by mitoRCA-seq method) and whole blood samples (sequenced through whole genome sequencing approach) of the same 130 participants in the Framingham Heart Study. We applied harmonization of sequence coverages and consistent quality control to mtDNA sequences. We identified 866 variation sites in the 130 LCL samples and 666 sites in the 130 blood samples. More than 94% of the identified homoplasmies were present in both LCL and blood samples while more than 70% of heteroplasmic sites were uniquely present either in LCL or in blood samples. The LCL and whole blood samples carried a similar number of homoplasmic variants (p = 0.45) per sample while the LCL carried a greater number of heteroplasmic variants than whole blood per sample (p < 2.2e-16). Furthermore, the LCL samples tended to accumulate low level heteroplasmies (heteroplasmy level in 3-25%) than their paired blood samples (p = 0.001). These results suggest that cautions should be taken in the interpretation and comparison of findings when different tissues/cell types or different sequencing technologies are applied to obtain mtDNA sequences.
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Affiliation(s)
- Chunyu Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, 02118, USA.
| | | | - Xianbang Sun
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, 02118, USA
| | - Kaiyu Yan
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, 02118, USA
| | - Poching Liu
- DNA Sequencing and Genomics Core, NHLBI/NIH, Bethesda, MD, 20892, USA
| | - Yan Luo
- DNA Sequencing and Genomics Core, NHLBI/NIH, Bethesda, MD, 20892, USA
| | - Jun Ding
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA
| | - Jun Zhu
- System Biology Center, NHLBI/NIH, Bethesda, MD, 20892, USA
| | - Daniel Levy
- Population Sciences Branch, NHLBI/NIH, Bethesda, MD, 20892, USA.
- Framingham Heart Study, Framingham, MA, 01702, USA.
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4
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Rodriguez OL, Sharp AJ, Watson CT. Limitations of lymphoblastoid cell lines for establishing genetic reference datasets in the immunoglobulin loci. PLoS One 2021; 16:e0261374. [PMID: 34898642 PMCID: PMC8668129 DOI: 10.1371/journal.pone.0261374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/30/2021] [Indexed: 11/18/2022] Open
Abstract
Lymphoblastoid cell lines (LCLs) have been critical to establishing genetic resources for biomedical science. They have been used extensively to study human genetic diversity, genome function, and inform the development of tools and methodologies for augmenting disease genetics research. While the validity of variant callsets from LCLs has been demonstrated for most of the genome, previous work has shown that DNA extracted from LCLs is modified by V(D)J recombination within the immunoglobulin (IG) loci, regions that harbor antibody genes critical to immune system function. However, the impacts of V(D)J on short read sequencing data generated from LCLs has not been extensively investigated. In this study, we used LCL-derived short read sequencing data from the 1000 Genomes Project (n = 2,504) to identify signatures of V(D)J recombination. Our analyses revealed sample-level impacts of V(D)J recombination that varied depending on the degree of inferred monoclonality. We showed that V(D)J associated somatic deletions impacted genotyping accuracy, leading to adulterated population-level estimates of allele frequency and linkage disequilibrium. These findings illuminate limitations of using LCLs and short read data for building genetic resources in the IG loci, with implications for interpreting previous disease association studies in these regions.
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Affiliation(s)
- Oscar L. Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States of America
| | - Andrew J. Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States of America
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5
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Trost B, Loureiro LO, Scherer SW. Discovery of genomic variation across a generation. Hum Mol Genet 2021; 30:R174-R186. [PMID: 34296264 PMCID: PMC8490016 DOI: 10.1093/hmg/ddab209] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 11/12/2022] Open
Abstract
Over the past 30 years (the timespan of a generation), advances in genomics technologies have revealed tremendous and unexpected variation in the human genome and have provided increasingly accurate answers to long-standing questions of how much genetic variation exists in human populations and to what degree the DNA complement changes between parents and offspring. Tracking the characteristics of these inherited and spontaneous (or de novo) variations has been the basis of the study of human genetic disease. From genome-wide microarray and next-generation sequencing scans, we now know that each human genome contains over 3 million single nucleotide variants when compared with the ~ 3 billion base pairs in the human reference genome, along with roughly an order of magnitude more DNA—approximately 30 megabase pairs (Mb)—being ‘structurally variable’, mostly in the form of indels and copy number changes. Additional large-scale variations include balanced inversions (average of 18 Mb) and complex, difficult-to-resolve alterations. Collectively, ~1% of an individual’s genome will differ from the human reference sequence. When comparing across a generation, fewer than 100 new genetic variants are typically detected in the euchromatic portion of a child’s genome. Driven by increasingly higher-resolution and higher-throughput sequencing technologies, newer and more accurate databases of genetic variation (for instance, more comprehensive structural variation data and phasing of combinations of variants along chromosomes) of worldwide populations will emerge to underpin the next era of discovery in human molecular genetics.
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Affiliation(s)
- Brett Trost
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Livia O Loureiro
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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6
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Ishida N, Aoki Y, Katsuoka F, Nishijima I, Nobukuni T, Anzawa H, Bin L, Tsuda M, Kumada K, Kudo H, Terakawa T, Otsuki A, Kinoshita K, Yamashita R, Minegishi N, Yamamoto M. Landscape of electrophilic and inflammatory stress-mediated gene regulation in human lymphoblastoid cell lines. Free Radic Biol Med 2020; 161:71-83. [PMID: 33011271 DOI: 10.1016/j.freeradbiomed.2020.09.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 09/26/2020] [Indexed: 02/08/2023]
Abstract
Human lymphoblastoid cell lines (LCLs) are valuable for the functional analyses of diseases. We have established more than 4200 LCLs as one of the resources of an integrated biobank. While oxidative and inflammatory stresses play critical roles in the onset and progression of various diseases, the responsiveness of LCLs, especially that of biobank-made LCLs, to these stresses has not been established. To address how LCLs respond to these stresses, in this study, we performed RNA sequencing of eleven human LCLs that were treated with an electrophile, diethyl maleate (DEM) and/or an inflammatory mediator, lipopolysaccharide (LPS). We found that over two thousand genes, including those regulated by a master regulator of the electrophilic/oxidative stress response, NRF2, were upregulated in LCLs treated with DEM, while approximately three hundred genes, including inflammation-related genes, were upregulated in LPS-treated LCLs. Of the LPS-induced genes, a subset of proinflammatory genes was repressed by DEM, supporting the notion that DEM suppresses the expression of proinflammatory genes through NRF2 activation. Conversely, a part of DEM-induced gene was repressed by LPS, suggesting reciprocal interference between electrophilic and inflammatory stress-mediated pathways. These data clearly demonstrate that LCLs maintain, by and large, responsive pathways against oxidative and inflammatory stresses and further endorse the usefulness of the LCL supply from the biobank.
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Affiliation(s)
- Noriko Ishida
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Yuichi Aoki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan; Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Ichiko Nishijima
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Takahiro Nobukuni
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Hayato Anzawa
- Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Li Bin
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan; Advanced Research Center for Innovations in Next Generation Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Miyuki Tsuda
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Kazuki Kumada
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Hisaaki Kudo
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Takahiro Terakawa
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Akihito Otsuki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan; Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Riu Yamashita
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan; Division of Translational Informatics, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Naoko Minegishi
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan; Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.
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7
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Diagnosing Cornelia de Lange syndrome and related neurodevelopmental disorders using RNA sequencing. Genet Med 2020; 22:927-936. [PMID: 31911672 DOI: 10.1038/s41436-019-0741-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/19/2019] [Indexed: 01/05/2023] Open
Abstract
PURPOSE Neurodevelopmental disorders represent a frequent indication for clinical exome sequencing. Fifty percent of cases, however, remain undiagnosed even upon exome reanalysis. Here we show RNA sequencing (RNA-seq) on human B-lymphoblastoid cell lines (LCL) is highly suitable for neurodevelopmental Mendelian gene testing and demonstrate the utility of this approach in suspected cases of Cornelia de Lange syndrome (CdLS). METHODS Genotype-Tissue Expression project transcriptome data for LCL, blood, and brain were assessed for neurodevelopmental Mendelian gene expression. Detection of abnormal splicing and pathogenic variants in these genes was performed with a novel RNA-seq diagnostic pipeline and using a validation CdLS-LCL cohort (n = 10) and test cohort of patients who carry a clinical diagnosis of CdLS but negative genetic testing (n = 5). RESULTS LCLs share isoform diversity of brain tissue for a large subset of neurodevelopmental genes and express 1.8-fold more of these genes compared with blood (LCL, n = 1706; whole blood, n = 917). This enables testing of more than 1000 genetic syndromes. The RNA-seq pipeline had 90% sensitivity for detecting pathogenic events and revealed novel diagnoses such as abnormal splice products in NIPBL and pathogenic coding variants in BRD4 and ANKRD11. CONCLUSION The LCL transcriptome enables robust frontline and/or reflexive diagnostic testing for neurodevelopmental disorders.
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8
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Minegishi N, Nishijima I, Nobukuni T, Kudo H, Ishida N, Terakawa T, Kumada K, Yamashita R, Katsuoka F, Ogishima S, Suzuki K, Sasaki M, Satoh M, Tohoku Medical Megabank Project Study Group, Yamamoto M. Biobank Establishment and Sample Management in the Tohoku Medical Megabank Project. TOHOKU J EXP MED 2019; 248:45-55. [PMID: 31130587 DOI: 10.1620/tjem.248.45] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Tohoku Medical Megabank biobank (TMM biobank) is the first major population-based biobank established in Japan. The TMM biobank was established based on two population cohorts and is a reconstruction program from the Great East Japan Earthquake and Tsunami of 2011. The biobank stores more than 3.4 million tubes of biospecimens and associated health and analytic data obtained from approximately 150,000 TMM cohort participants between May 2013 and December 2018, and the TMM biobank currently shares high-quality specimens and data. Various biospecimens, including peripheral and cord blood mononuclear cells, buffy coat, plasma, serum, urine, breast milk and saliva have been collected in the TMM biobank. To minimize human error and maintain the quality of data and specimens, we have been utilizing laboratory information management system into various biobank procedures from registration to storage with various automation systems, such as liquid dispensing, DNA extraction and their storage. The biobank procedures for the quality management system (ISO 9001:2015) and information security management system (ISO 27001:2013) are certified by the International Organization for Standardization. The quality of our biobank samples fulfills the pre-analytical requirements for researchers conducting next-generation whole genome sequencing, DNA array analyses, proteomics, metabolomics, etc. We established analytical centers to conduct standard genomic and multiomic analyses in-house and share the generated data. Additionally, we generate thousands of Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines and proliferating T cells for functional studies. The TMM biobank serves as an indispensable infrastructure for academic, clinical and industrial research to actualize next-generation medicine in Japan.
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Affiliation(s)
- Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Ichiko Nishijima
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Takahiro Nobukuni
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Hisaaki Kudo
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Noriko Ishida
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Takahiro Terakawa
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Kazuki Kumada
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Riu Yamashita
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Kichiya Suzuki
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,School of Medicine, Iwate Medical University
| | - Mamoru Satoh
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,School of Medicine, Iwate Medical University
| | | | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
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9
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Extensive epigenetic and transcriptomic variability between genetically identical human B-lymphoblastoid cells with implications in pharmacogenomics research. Sci Rep 2019; 9:4889. [PMID: 30894562 PMCID: PMC6426863 DOI: 10.1038/s41598-019-40897-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/20/2019] [Indexed: 12/12/2022] Open
Abstract
Genotyped human B-lymphoblastoid cell lines (LCLs) are widely used models in mapping quantitative trait loci for chromatin features, gene expression, and drug response. The extent of genotype-independent functional genomic variability of the LCL model, although largely overlooked, may inform association study design. In this study, we use flow cytometry, chromatin immunoprecipitation sequencing and mRNA sequencing to study surface marker patterns, quantify genome-wide chromatin changes (H3K27ac) and transcriptome variability, respectively, among five isogenic LCLs derived from the same individual. Most of the studied LCLs were non-monoclonal and had mature B cell phenotypes. Strikingly, nearly one-fourth of active gene regulatory regions showed significantly variable H3K27ac levels, especially enhancers, among which several were classified as clustered enhancers. Large, contiguous genomic regions showed signs of coordinated activity change. Regulatory differences were mirrored by mRNA expression changes, preferentially affecting hundreds of genes involved in specialized cellular processes including immune and drug response pathways. Differential expression of DPYD, an enzyme involved in 5-fluorouracil (5-FU) catabolism, was associated with variable LCL growth inhibition mediated by 5-FU. The extent of genotype-independent functional genomic variability might highlight the need to revisit study design strategies for LCLs in pharmacogenomics.
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10
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Vadgama N, Pittman A, Simpson M, Nirmalananthan N, Murray R, Yoshikawa T, De Rijk P, Rees E, Kirov G, Hughes D, Fitzgerald T, Kristiansen M, Pearce K, Cerveira E, Zhu Q, Zhang C, Lee C, Hardy J, Nasir J. De novo single-nucleotide and copy number variation in discordant monozygotic twins reveals disease-related genes. Eur J Hum Genet 2019; 27:1121-1133. [PMID: 30886340 DOI: 10.1038/s41431-019-0376-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/18/2019] [Accepted: 03/01/2019] [Indexed: 01/11/2023] Open
Abstract
Recent studies have demonstrated genetic differences between monozygotic (MZ) twins. To test the hypothesis that early post-twinning mutational events associate with phenotypic discordance, we investigated a cohort of 13 twin pairs (n = 26) discordant for various clinical phenotypes using whole-exome sequencing and screened for copy number variation (CNV). We identified a de novo variant in PLCB1, a gene involved in the hydrolysis of lipid phosphorus in milk from dairy cows, associated with lactase non-persistence, and a variant in the mitochondrial complex I gene MT-ND5 associated with amyotrophic lateral sclerosis (ALS). We also found somatic variants in multiple genes (TMEM225B, KBTBD3, TUBGCP4, TFIP11) in another MZ twin pair discordant for ALS. Based on the assumption that discordance between twins could be explained by a common variant with variable penetrance or expressivity, we screened the twin samples for known pathogenic variants that are shared and identified a rare deletion overlapping ARHGAP11B, in the twin pair manifesting with either schizotypal personality disorder or schizophrenia. Parent-offspring trio analysis was implemented for two twin pairs to assess potential association of variants of parental origin with susceptibility to disease. We identified a de novo variant in RASD2 shared by 8-year-old male twins with a suspected diagnosis of autism spectrum disorder (ASD) manifesting as different traits. A de novo CNV duplication was also identified in these twins overlapping CD38, a gene previously implicated in ASD. In twins discordant for Tourette's syndrome, a paternally inherited stop loss variant was detected in AADAC, a known candidate gene for the disorder.
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Affiliation(s)
- Nirmal Vadgama
- Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Alan Pittman
- Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Michael Simpson
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | | | - Robin Murray
- Institute of Psychiatry, Psychology, and Neuroscience, King's College, London, UK
| | - Takeo Yoshikawa
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
| | - Peter De Rijk
- Applied Molecular Genomics Group, University of Antwerp, Antwerp, Belgium
| | - Elliott Rees
- Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - George Kirov
- Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Deborah Hughes
- Institute of Neurology, University College London, London, WC1N 3BG, UK
| | | | - Mark Kristiansen
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Kerra Pearce
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Eliza Cerveira
- Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Qihui Zhu
- Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Chengsheng Zhang
- Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Charles Lee
- Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - John Hardy
- Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Jamal Nasir
- Cell Biology and Genetics Research Centre, St. George's University of London, London, UK. .,Molecular Biosciences Research Group, University of Northampton, Northampton, NN1 5PH, UK.
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11
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Investigating mitonuclear interactions in human admixed populations. Nat Ecol Evol 2019; 3:213-222. [PMID: 30643241 PMCID: PMC6925600 DOI: 10.1038/s41559-018-0766-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/22/2018] [Indexed: 12/13/2022]
Abstract
To function properly, mitochondria utilize products of 37 mitochondrial and >1,000 nuclear genes, which should be compatible with each other. Discordance between mitochondrial and nuclear genetic ancestry could contribute to phenotypic variation in admixed populations. Here, we explored potential mitonuclear incompatibility in six admixed human populations from the Americas: African Americans, African Caribbeans, Colombians, Mexicans, Peruvians and Puerto Ricans. By comparing nuclear versus mitochondrial ancestry in these populations, we first show that mitochondrial DNA (mtDNA) copy number decreases with increasing discordance between nuclear and mtDNA ancestry. The direction of this effect is consistent across mtDNA haplogroups of different geographic origins. This observation indicates suboptimal regulation of mtDNA replication when its components are encoded by nuclear and mtDNA genes with different ancestry. Second, while most populations analysed exhibit no such trend, in African Americans and Puerto Ricans, we find a significant enrichment of ancestry at nuclear-encoded mitochondrial genes towards the source populations contributing the most prevalent mtDNA haplogroups (African and Native American, respectively). This possibly reflects compensatory effects of selection in recovering mitonuclear interactions optimized in the source populations. Our results provide evidence of mitonuclear interactions in human admixed populations and we discuss their implications for human health and disease.
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12
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Algady W, Louzada S, Carpenter D, Brajer P, Färnert A, Rooth I, Ngasala B, Yang F, Shaw MA, Hollox EJ. The Malaria-Protective Human Glycophorin Structural Variant DUP4 Shows Somatic Mosaicism and Association with Hemoglobin Levels. Am J Hum Genet 2018; 103:769-776. [PMID: 30388403 PMCID: PMC6218809 DOI: 10.1016/j.ajhg.2018.10.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/04/2018] [Indexed: 01/23/2023] Open
Abstract
Glycophorin A and glycophorin B are red blood cell surface proteins and are both receptors for the parasite Plasmodium falciparum, which is the principal cause of malaria in sub-Saharan Africa. DUP4 is a complex structural genomic variant that carries extra copies of a glycophorin A-glycophorin B fusion gene and has a dramatic effect on malaria risk by reducing the risk of severe malaria by up to 40%. Using fiber-FISH and Illumina sequencing, we validate the structural arrangement of the glycophorin locus in the DUP4 variant and reveal somatic variation in copy number of the glycophorin B-glycophorin A fusion gene. By developing a simple, specific, PCR-based assay for DUP4, we show that the DUP4 variant reaches a frequency of 13% in the population of a malaria-endemic village in south-eastern Tanzania. We genotype a substantial proportion of that village and demonstrate an association of DUP4 genotype with hemoglobin levels, a phenotype related to malaria, using a family-based association test. Taken together, we show that DUP4 is a complex structural variant that may be susceptible to somatic variation and show that DUP4 is associated with a malarial-related phenotype in a longitudinally followed population.
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Affiliation(s)
- Walid Algady
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Sandra Louzada
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Danielle Carpenter
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Paulina Brajer
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Anna Färnert
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, 17176 Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Ingegerd Rooth
- Nyamisati Malaria Research, Rufiji, National Institute for Medical Research, Dar-es-Salaam, Tanzania
| | - Billy Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania; Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala Universitet, 75185 Uppsala, Sweden
| | - Fengtang Yang
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Marie-Anne Shaw
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds LS9 7TF, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK.
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13
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Jia X, Madireddy L, Caillier S, Santaniello A, Esposito F, Comi G, Stuve O, Zhou Y, Taylor B, Kilpatrick T, Martinelli-Boneschi F, Cree BAC, Oksenberg JR, Hauser SL, Baranzini SE. Genome sequencing uncovers phenocopies in primary progressive multiple sclerosis. Ann Neurol 2018; 84:51-63. [PMID: 29908077 PMCID: PMC6119489 DOI: 10.1002/ana.25263] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 01/06/2023]
Abstract
Objective Primary progressive multiple sclerosis (PPMS) causes accumulation of neurological disability from disease onset without clinical attacks typical of relapsing multiple sclerosis (RMS). However, whether genetic variation influences the disease course remains unclear. We aimed to determine whether mutations causative of neurological disorders that share features with multiple sclerosis (MS) contribute to risk for developing PPMS. Methods We examined whole‐genome sequencing (WGS) data from 38 PPMS and 81 healthy subjects of European ancestry. We selected pathogenic variants exclusively found in PPMS patients that cause monogenic neurological disorders and performed two rounds of replication genotyping in 746 PPMS, 3,049 RMS, and 1,000 healthy subjects. To refine our findings, we examined the burden of rare, potentially pathogenic mutations in 41 genes that cause hereditary spastic paraplegias (HSPs) in PPMS (n = 314), secondary progressive multiple sclerosis (SPMS; n = 587), RMS (n = 2,248), and healthy subjects (n = 987) genotyped using the MS replication chip. Results WGS and replication studies identified three pathogenic variants in PPMS patients that cause neurological disorders sharing features with MS: KIF5A p.Ala361Val in spastic paraplegia 10; MLC1 p.Pro92Ser in megalencephalic leukodystrophy with subcortical cysts, and REEP1 c.606 + 43G>T in Spastic Paraplegia 31. Moreover, we detected a significant enrichment of HSP‐related mutations in PPMS patients compared to controls (risk ratio [RR] = 1.95; 95% confidence interval [CI], 1.27–2.98; p = 0.002), as well as in SPMS patients compared to controls (RR = 1.57; 95% CI, 1.18–2.10; p = 0.002). Importantly, this enrichment was not detected in RMS. Interpretation This study provides evidence to support the hypothesis that rare Mendelian genetic variants contribute to the risk for developing progressive forms of MS. Ann Neurol 2018;83:51–63
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Affiliation(s)
- Xiaoming Jia
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA.,Department of Neurology, University of California San Francisco, San Francisco, CA
| | - Lohith Madireddy
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA.,Department of Neurology, University of California San Francisco, San Francisco, CA
| | - Stacy Caillier
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA.,Department of Neurology, University of California San Francisco, San Francisco, CA
| | - Adam Santaniello
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA.,Department of Neurology, University of California San Francisco, San Francisco, CA
| | - Federica Esposito
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSpe), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy.,Department of Neurology and Neuro-rehabilitation, San Raffaele Scientific Institute, Milan, Italy
| | - Giancarlo Comi
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSpe), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy.,Department of Neurology and Neuro-rehabilitation, San Raffaele Scientific Institute, Milan, Italy
| | - Olaf Stuve
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical, Dallas, TX
| | - Yuan Zhou
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Bruce Taylor
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Trevor Kilpatrick
- Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, VIC, Australia
| | - Filippo Martinelli-Boneschi
- Laboratory of Genomics of Neurological Diseases and Department of Neurology, Policlinico San Donato Hospital and Scientific Institute, San Donato Milanese, Italy.,Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milan, Italy.,Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSpe), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Bruce A C Cree
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA.,Department of Neurology, University of California San Francisco, San Francisco, CA
| | - Jorge R Oksenberg
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA.,Department of Neurology, University of California San Francisco, San Francisco, CA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA
| | - Stephen L Hauser
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA.,Department of Neurology, University of California San Francisco, San Francisco, CA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA
| | - Sergio E Baranzini
- UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA.,Department of Neurology, University of California San Francisco, San Francisco, CA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA.,Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA
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14
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Frye RE, Nankova B, Bhattacharyya S, Rose S, Bennuri SC, MacFabe DF. Modulation of Immunological Pathways in Autistic and Neurotypical Lymphoblastoid Cell Lines by the Enteric Microbiome Metabolite Propionic Acid. Front Immunol 2017; 8:1670. [PMID: 29312285 PMCID: PMC5744079 DOI: 10.3389/fimmu.2017.01670] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/14/2017] [Indexed: 12/20/2022] Open
Abstract
Propionic acid (PPA) is a ubiquitous short-chain fatty acid which is a fermentation product of the enteric microbiome and present or added to many foods. While PPA has beneficial effects, it is also associated with human disorders, including autism spectrum disorders (ASDs). We previously demonstrated that PPA modulates mitochondrial dysfunction differentially in subsets of lymphoblastoid cell lines (LCLs) derived from patients with ASD. Specifically, PPA significantly increases mitochondrial function in LCLs that have mitochondrial dysfunction at baseline [individuals with autistic disorder with atypical mitochondrial function (AD-A) LCLs] as compared to ASD LCLs with normal mitochondrial function [individuals with autistic disorder with normal mitochondrial function (AD-N) LCLs] and control (CNT) LCLs. PPA at 1 mM was found to have a minimal effect on expression of immune genes in CNT and AD-N LCLs. However, as hypothesized, Panther analysis demonstrated that 1 mM PPA exposure at 24 or 48 h resulted in significant activation of the immune system genes in AD-A LCLs. When the effect of PPA on ASD LCLs were compared to the CNT LCLs, both ASD groups demonstrated immune pathway activation, although the AD-A LCLs demonstrate a wider activation of immune genes. Ingenuity Pathway Analysis identified several immune-related pathways as key Canonical Pathways that were differentially regulated, specifically human leukocyte antigen expression and immunoglobulin production genes were upregulated. These data demonstrate that the enteric microbiome metabolite PPA can evoke atypical immune activation in LCLs with an underlying abnormal metabolic state. As PPA, as well as enteric bacteria which produce PPA, have been implicated in a wide variety of diseases which have components of immune dysfunction, including ASD, diabetes, obesity, and inflammatory diseases, insight into this metabolic modulator may have wide applications for both health and disease.
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Affiliation(s)
- Richard E Frye
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Autism Research Program, Arkansas Children's Research Institute, Little Rock, AR, United States
| | | | - Sudeepa Bhattacharyya
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Autism Research Program, Arkansas Children's Research Institute, Little Rock, AR, United States
| | - Shannon Rose
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Autism Research Program, Arkansas Children's Research Institute, Little Rock, AR, United States
| | - Sirish C Bennuri
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Autism Research Program, Arkansas Children's Research Institute, Little Rock, AR, United States
| | - Derrick F MacFabe
- Kilee Patchell-Evans Autism Research Group, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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15
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Frye RE, Rose S, Wynne R, Bennuri SC, Blossom S, Gilbert KM, Heilbrun L, Palmer RF. Oxidative Stress Challenge Uncovers Trichloroacetaldehyde Hydrate-Induced Mitoplasticity in Autistic and Control Lymphoblastoid Cell Lines. Sci Rep 2017; 7:4478. [PMID: 28667285 PMCID: PMC5493637 DOI: 10.1038/s41598-017-04821-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/19/2017] [Indexed: 12/11/2022] Open
Abstract
Mitoplasticity occurs when mitochondria adapt to tolerate stressors. Previously we hypothesized that a subset of lymphoblastoid cell lines (LCLs) from children with autistic disorder (AD) show mitoplasticity (AD-A), presumably due to previous environmental exposures; another subset of AD LCLs demonstrated normal mitochondrial activity (AD-N). To better understand mitoplasticity in the AD-A LCLs we examined changes in mitochondrial function using the Seahorse XF96 analyzer in AD and Control LCLs after exposure to trichloroacetaldehyde hydrate (TCAH), an in vivo metabolite of the environmental toxicant and common environmental pollutant trichloroethylene. To better understand the role of reactive oxygen species (ROS) in mitoplasticity, TCAH exposure was followed by acute exposure to 2,3-dimethoxy-1,4-napthoquinone (DMNQ), an agent that increases ROS. TCAH exposure by itself resulted in a decline in mitochondrial respiration in all LCL groups. This effect was mitigated when TCAH was followed by acute DMNQ exposure but this varied across LCL groups. DMNQ did not affect AD-N LCLs, while it neutralized the detrimental effect of TCAH in Control LCLs and resulted in a increase in mitochondrial respiration in AD-A LCLs. These data suggest that acute increases in ROS can activate mitochondrial protective pathways and that AD-A LCLs are better able to activate these protective pathways.
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Affiliation(s)
- Richard Eugene Frye
- Arkansas Children's Research Institute, Little Rock, AR, USA. .,Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| | - Shannon Rose
- Arkansas Children's Research Institute, Little Rock, AR, USA.,Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Rebecca Wynne
- Arkansas Children's Research Institute, Little Rock, AR, USA.,Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Sirish C Bennuri
- Arkansas Children's Research Institute, Little Rock, AR, USA.,Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Sarah Blossom
- Arkansas Children's Research Institute, Little Rock, AR, USA.,Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Kathleen M Gilbert
- Arkansas Children's Research Institute, Little Rock, AR, USA.,Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Lynne Heilbrun
- Department of Family and Community Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Raymond F Palmer
- Department of Family and Community Medicine, University of Texas Health Science Center, San Antonio, TX, USA
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16
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Joesch-Cohen LM, Glusman G. Differences between the genomes of lymphoblastoid cell lines and blood-derived samples. ADVANCES IN GENOMICS AND GENETICS 2017; 7:1-9. [PMID: 28736497 PMCID: PMC5520659 DOI: 10.2147/agg.s128824] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Lymphoblastoid cell lines (LCLs) represent a convenient research tool for expanding the amount of biologic material available from an individual. LCLs are commonly used as reference materials, most notably from the Genome in a Bottle Consortium. However, the question remains how faithfully LCL-derived genome assemblies represent the germline genome of the donor individual as compared to the genome assemblies derived from peripheral blood mononuclear cells. We present an in-depth comparison of a large collection of LCL- and peripheral blood mononuclear cell-derived genomes in terms of distributions of coverage and copy number alterations. We found significant differences in the depth of coverage and copy number calls, which may be driven by differential replication timing. Importantly, these copy number changes preferentially affect regions closer to genes and with higher GC content. This suggests that genomic studies based on LCLs may display locus-specific biases, and that conclusions based on analysis of depth of coverage and copy number variation may require further scrutiny.
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17
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Frye RE, Rose S, Chacko J, Wynne R, Bennuri SC, Slattery JC, Tippett M, Delhey L, Melnyk S, Kahler SG, MacFabe DF. Modulation of mitochondrial function by the microbiome metabolite propionic acid in autism and control cell lines. Transl Psychiatry 2016; 6:e927. [PMID: 27779624 PMCID: PMC5290345 DOI: 10.1038/tp.2016.189] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 07/26/2016] [Accepted: 08/02/2016] [Indexed: 12/12/2022] Open
Abstract
Propionic acid (PPA) is a ubiquitous short-chain fatty acid, which is a major fermentation product of the enteric microbiome. PPA is a normal intermediate of metabolism and is found in foods, either naturally or as a preservative. PPA and its derivatives have been implicated in both health and disease. Whereas PPA is an energy substrate and has many proposed beneficial effects, it is also associated with human disorders involving mitochondrial dysfunction, including propionic acidemia and autism spectrum disorders (ASDs). We aimed to investigate the dichotomy between the health and disease effects of PPA by measuring mitochondrial function in ASD and age- and gender-matched control lymphoblastoid cell lines (LCLs) following incubation with PPA at several concentrations and durations both with and without an in vitro increase in reactive oxygen species (ROS). Mitochondrial function was optimally increased at particular exposure durations and concentrations of PPA with ASD LCLs, demonstrating a greater enhancement. In contrast, increasing ROS negated the positive PPA effect with the ASD LCLs, showing a greater detriment. These data demonstrate that enteric microbiome metabolites such as PPA can have both beneficial and toxic effects on mitochondrial function, depending on concentration, exposure duration and microenvironment redox state with these effects amplified in LCLs derived from individuals with ASD. As PPA, as well as enteric bacteria, which produce PPA, have been implicated in a wide variety of diseases, including ASD, diabetes, obesity and inflammatory diseases, insight into this metabolic modulator from the host microbiome may have wide applications for both health and disease.
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Affiliation(s)
- R E Frye
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA,Arkansas Children's Research Institute, Little Rock, AR, USA,Arkansas Children's Research Institute, Slot 512-41B, 13 Children's Way, Little Rock, AR 72202, USA. E-mail:
| | - S Rose
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA,Arkansas Children's Research Institute, Little Rock, AR, USA
| | - J Chacko
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - R Wynne
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA,Arkansas Children's Research Institute, Little Rock, AR, USA
| | - S C Bennuri
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA,Arkansas Children's Research Institute, Little Rock, AR, USA
| | - J C Slattery
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA,Arkansas Children's Research Institute, Little Rock, AR, USA
| | - M Tippett
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA,Arkansas Children's Research Institute, Little Rock, AR, USA
| | - L Delhey
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA,Arkansas Children's Research Institute, Little Rock, AR, USA
| | - S Melnyk
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA,Arkansas Children's Research Institute, Little Rock, AR, USA
| | - S G Kahler
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA,Arkansas Children's Research Institute, Little Rock, AR, USA
| | - D F MacFabe
- Kilee Patchell-Evans Autism Research Group, Division of Developmental Disabilities, Department of Psychology/Psychiatry, University of Western Ontario, London, ON, Canada
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18
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Chen J, Calhoun VD, Perrone-Bizzozero NI, Pearlson GD, Sui J, Du Y, Liu J. A pilot study on commonality and specificity of copy number variants in schizophrenia and bipolar disorder. Transl Psychiatry 2016; 6:e824. [PMID: 27244233 PMCID: PMC5545651 DOI: 10.1038/tp.2016.96] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 03/17/2016] [Indexed: 12/11/2022] Open
Abstract
Schizophrenia (SZ) and bipolar disorder (BD) are known to share genetic risks. In this work, we conducted whole-genome scanning to identify cross-disorder and disorder-specific copy number variants (CNVs) for these two disorders. The Database of Genotypes and Phenotypes (dbGaP) data were used for discovery, deriving from 2416 SZ patients, 592 BD patients and 2393 controls of European Ancestry, as well as 998 SZ patients, 121 BD patients and 822 controls of African Ancestry. PennCNV and Birdsuite detected high-confidence CNVs that were aggregated into CNV regions (CNVRs) and compared with the database of genomic variants for confirmation. Then, large (size⩾500 kb) and small common CNVRs (size <500 kb, frequency⩾1%) were examined for their associations with SZ and BD. Particularly for the European Ancestry samples, the dbGaP findings were further evaluated in the Wellcome Trust Case Control Consortium (WTCCC) data set for replication. Previously implicated variants (1q21.1, 15q13.3, 16p11.2 and 22q11.21) were replicated. Some cross-disorder variants were noted to differentially affect SZ and BD, including CNVRs in chromosomal regions encoding immunoglobulins and T-cell receptors that were associated more with SZ, and the 10q11.21 small CNVR (GPRIN2) associated more with BD. Disorder-specific CNVRs were also found. The 22q11.21 CNVR (COMT) and small CNVRs in 11p15.4 (TRIM5) and 15q13.2 (ARHGAP11B and FAN1) appeared to be SZ-specific. CNVRs in 17q21.2, 9p21.3 and 9q21.13 might be BD-specific. Overall, our primary findings in individual disorders largely echo previous reports. In addition, the comparison between SZ and BD reveals both specific and common risk CNVs. Particularly for the latter, differential involvement is noted, motivating further comparative studies and quantitative models.
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Affiliation(s)
- J Chen
- The Mind Research Network, Albuquerque, NM, USA
| | - V D Calhoun
- The Mind Research Network, Albuquerque, NM, USA
- Department of Electrical Engineering, University of New Mexico, Albuquerque, NM, USA
| | - N I Perrone-Bizzozero
- Departments of Neurosciences and Psychiatry, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - G D Pearlson
- Olin Neuropsychiatry Research Center, Institute of Living, Hartford, CT, USA
- Departments of Psychiatry and Neurobiology, Yale University, New Haven, CT, USA
| | - J Sui
- The Mind Research Network, Albuquerque, NM, USA
- Brainnetome Center and National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Y Du
- The Mind Research Network, Albuquerque, NM, USA
| | - J Liu
- The Mind Research Network, Albuquerque, NM, USA
- Department of Electrical Engineering, University of New Mexico, Albuquerque, NM, USA
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19
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McCarthy NS, Allan SM, Chandler D, Jablensky A, Morar B. Integrity of genome-wide genotype data from low passage lymphoblastoid cell lines. GENOMICS DATA 2016; 9:18-21. [PMID: 27330997 PMCID: PMC4909818 DOI: 10.1016/j.gdata.2016.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/09/2016] [Accepted: 05/09/2016] [Indexed: 01/08/2023]
Abstract
We compared genotype data from the HumanExomeCore Array in peripheral blood mononuclear cells and low passage lymphoblastoid cell lines from the same 24 individuals to test for genotypic errors caused by the Epstein–Barr Virus transformation process. Genotype concordance across the 24 comparisons was 99.57% for unfiltered genotype data, and 99.63% following standard genotype quality control filters. Mendelian error rates and levels of heterozygosity were not significantly different between lymphoblastoid cell lines and their parent peripheral blood mononuclear cells. These results show that at low passage numbers, genotype discrepancies are minimal even before stringent quality control, and extend current evidence qualifying the use of low-passage lymphoblastoid cell lines as a reliable DNA source for genotype analysis.
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Affiliation(s)
- Nina S McCarthy
- Centre for the Genetic Origins of Health and Disease, The University of Western Australia, Perth, Australia; Centre for Clinical Research in Neuropsychiatry, School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Perth, Australia; Cooperative Research Centre for Mental Health, Carlton South, Victoria, Australia
| | - Spencer M Allan
- Centre for the Genetic Origins of Health and Disease, The University of Western Australia, Perth, Australia
| | - David Chandler
- Centre for Clinical Research in Neuropsychiatry, School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Perth, Australia
| | - Assen Jablensky
- Centre for Clinical Research in Neuropsychiatry, School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Perth, Australia; Cooperative Research Centre for Mental Health, Carlton South, Victoria, Australia
| | - Bharti Morar
- Centre for Clinical Research in Neuropsychiatry, School of Psychiatry and Clinical Neurosciences, The University of Western Australia, Perth, Australia; Cooperative Research Centre for Mental Health, Carlton South, Victoria, Australia; Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Perth, Australia
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20
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Niu N, Wang L. In vitro human cell line models to predict clinical response to anticancer drugs. Pharmacogenomics 2015; 16:273-85. [PMID: 25712190 DOI: 10.2217/pgs.14.170] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In vitro human cell line models have been widely used for cancer pharmacogenomic studies to predict clinical response, to help generate pharmacogenomic hypothesis for further testing, and to help identify novel mechanisms associated with variation in drug response. Among cell line model systems, immortalized cell lines such as Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) have been used most often to test the effect of germline genetic variation on drug efficacy and toxicity. Another model, especially in cancer research, uses cancer cell lines such as the NCI-60 panel. These models have been used mainly to determine the effect of somatic alterations on response to anticancer therapy. Even though these cell line model systems are very useful for initial screening, results from integrated analyses of multiple omics data and drug response phenotypes using cell line model systems still need to be confirmed by functional validation and mechanistic studies, as well as validation studies using clinical samples. Future models might include the use of patient-specific inducible pluripotent stem cells and the incorporation of 3D culture which could further optimize in vitro cell line models to improve their predictive validity.
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Affiliation(s)
- Nifang Niu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
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21
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Duan J, Sanders AR, Moy W, Drigalenko EI, Brown EC, Freda J, Leites C, Göring HHH, Gejman PV. Transcriptome outlier analysis implicates schizophrenia susceptibility genes and enriches putatively functional rare genetic variants. Hum Mol Genet 2015; 24:4674-85. [PMID: 26022996 DOI: 10.1093/hmg/ddv199] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 05/26/2015] [Indexed: 02/06/2023] Open
Abstract
We searched a gene expression dataset comprised of 634 schizophrenia (SZ) cases and 713 controls for expression outliers (i.e., extreme tails of the distribution of transcript expression values) with SZ cases overrepresented compared with controls. These outlier genes were enriched for brain expression and for genes known to be associated with neurodevelopmental disorders. SZ cases showed higher outlier burden (i.e., total outlier events per subject) than controls for genes within copy number variants (CNVs) associated with SZ or neurodevelopmental disorders. Outlier genes were enriched for CNVs and for rare putative regulatory variants, but this only explained a small proportion of the outlier subjects, highlighting the underlying presence of additional genetic and potentially, epigenetic mechanisms.
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Affiliation(s)
- Jubao Duan
- Center for Psychiatric Genetics and Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA,
| | - Alan R Sanders
- Center for Psychiatric Genetics and Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA
| | - Winton Moy
- Center for Psychiatric Genetics and Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA
| | - Eugene I Drigalenko
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA and
| | - Eric C Brown
- Center for Biomedical Research Informatics, NorthShore University HealthSystem, Evanston, IL, USA
| | | | | | - Harald H H Göring
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA and
| | | | - Pablo V Gejman
- Center for Psychiatric Genetics and Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA
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Increased susceptibility to ethylmercury-induced mitochondrial dysfunction in a subset of autism lymphoblastoid cell lines. J Toxicol 2015; 2015:573701. [PMID: 25688267 PMCID: PMC4320799 DOI: 10.1155/2015/573701] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/12/2014] [Accepted: 12/13/2014] [Indexed: 12/21/2022] Open
Abstract
The association of autism spectrum disorders with oxidative stress, redox imbalance, and mitochondrial dysfunction has become increasingly recognized. In this study, extracellular flux analysis was used to compare mitochondrial respiration in lymphoblastoid cell lines (LCLs) from individuals with autism and unaffected controls exposed to ethylmercury, an environmental toxin known to deplete glutathione and induce oxidative stress and mitochondrial dysfunction. We also tested whether pretreating the autism LCLs with N-acetyl cysteine (NAC) to increase glutathione concentrations conferred protection from ethylmercury. Examination of 16 autism/control LCL pairs revealed that a subgroup (31%) of autism LCLs exhibited a greater reduction in ATP-linked respiration, maximal respiratory capacity, and reserve capacity when exposed to ethylmercury, compared to control LCLs. These respiratory parameters were significantly elevated at baseline in the ethylmercury-sensitive autism subgroup as compared to control LCLs. NAC pretreatment of the sensitive subgroup reduced (normalized) baseline respiratory parameters and blunted the exaggerated ethylmercury-induced reserve capacity depletion. These findings suggest that the epidemiological link between environmental mercury exposure and an increased risk of developing autism may be mediated through mitochondrial dysfunction and support the notion that a subset of individuals with autism may be vulnerable to environmental influences with detrimental effects on development through mitochondrial dysfunction.
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Gibbons JG, Branco AT, Yu S, Lemos B. Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans. Nat Commun 2014; 5:4850. [DOI: 10.1038/ncomms5850] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 07/30/2014] [Indexed: 01/26/2023] Open
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Li H. Toward better understanding of artifacts in variant calling from high-coverage samples. ACTA ACUST UNITED AC 2014; 30:2843-51. [PMID: 24974202 DOI: 10.1093/bioinformatics/btu356] [Citation(s) in RCA: 546] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
MOTIVATION Whole-genome high-coverage sequencing has been widely used for personal and cancer genomics as well as in various research areas. However, in the lack of an unbiased whole-genome truth set, the global error rate of variant calls and the leading causal artifacts still remain unclear even given the great efforts in the evaluation of variant calling methods. RESULTS We made 10 single nucleotide polymorphism and INDEL call sets with two read mappers and five variant callers, both on a haploid human genome and a diploid genome at a similar coverage. By investigating false heterozygous calls in the haploid genome, we identified the erroneous realignment in low-complexity regions and the incomplete reference genome with respect to the sample as the two major sources of errors, which press for continued improvements in these two areas. We estimated that the error rate of raw genotype calls is as high as 1 in 10-15 kb, but the error rate of post-filtered calls is reduced to 1 in 100-200 kb without significant compromise on the sensitivity. AVAILABILITY AND IMPLEMENTATION BWA-MEM alignment and raw variant calls are available at http://bit.ly/1g8XqRt scripts and miscellaneous data at https://github.com/lh3/varcmp. CONTACT hengli@broadinstitute.org SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Heng Li
- Medical Population Genetics Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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Diroma MA, Calabrese C, Simone D, Santorsola M, Calabrese FM, Gasparre G, Attimonelli M. Extraction and annotation of human mitochondrial genomes from 1000 Genomes Whole Exome Sequencing data. BMC Genomics 2014; 15 Suppl 3:S2. [PMID: 25077682 PMCID: PMC4083402 DOI: 10.1186/1471-2164-15-s3-s2] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Whole Exome Sequencing (WES) is one of the most used and cost-effective next generation technologies that allows sequencing of all nuclear exons. Off-target regions may be captured if they present high sequence similarity with baits. Bioinformatics tools have been optimized to retrieve a large amount of WES off-target mitochondrial DNA (mtDNA), by exploiting the aspecificity of probes, partially overlapping to Nuclear mitochondrial Sequences (NumtS). The 1000 Genomes project represents one of the widest resources to extract mtDNA sequences from WES data, considering the large effort the scientific community is undertaking to reconstruct human population history using mtDNA as marker, and the involvement of mtDNA in pathology. Results A previously published pipeline aimed at assembling mitochondrial genomes from off-target WES reads and further improved to detect insertions and deletions (indels) and heteroplasmy in a dataset of 1242 samples from the 1000 Genomes project, enabled to obtain a nearly complete mitochondrial genome from 943 samples (76% analyzed exomes). The robustness of our computational strategy was highlighted by the reduction of reads amount recognized as mitochondrial in the original annotation produced by the Consortium, due to NumtS filtering. An accurate survey was carried out on 1242 individuals. 215 indels, mostly heteroplasmic, and 3407 single base variants were mapped. A homogeneous mismatches distribution was observed along the whole mitochondrial genome, while a lower frequency of indels was found within protein-coding regions, where frameshift mutations may be deleterious. The majority of indels and mismatches found were not previously annotated in mitochondrial databases since conventional sequencing methods were limited to homoplasmy or quasi-homoplasmy detection. Intriguingly, upon filtering out non haplogroup-defining variants, we detected a widespread population occurrence of rare events predicted to be damaging. Eventually, samples were stratified into blood- and lymphoblastoid-derived to detect possibly different trends of mutability in the two datasets, an analysis which did not yield significant discordances. Conclusions To the best of our knowledge, this is likely the most extended population-scale mitochondrial genotyping in humans enriched with the estimation of heteroplasmies.
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Oxidative stress induces mitochondrial dysfunction in a subset of autistic lymphoblastoid cell lines. Transl Psychiatry 2014; 4:e377. [PMID: 24690598 PMCID: PMC4012280 DOI: 10.1038/tp.2014.15] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/31/2014] [Accepted: 02/02/2014] [Indexed: 11/10/2022] Open
Abstract
There is an increasing recognition that mitochondrial dysfunction is associated with autism spectrum disorders. However, little attention has been given to the etiology of mitochondrial dysfunction and how mitochondrial abnormalities might interact with other physiological disturbances such as oxidative stress. Reserve capacity is a measure of the ability of the mitochondria to respond to physiological stress. In this study, we demonstrate, for the first time, that lymphoblastoid cell lines (LCLs) derived from children with autistic disorder (AD) have an abnormal mitochondrial reserve capacity before and after exposure to reactive oxygen species (ROS). Ten (44%) of 22 AD LCLs exhibited abnormally high reserve capacity at baseline and a sharp depletion of reserve capacity when challenged with ROS. This depletion of reserve capacity was found to be directly related to an atypical simultaneous increase in both proton-leak respiration and adenosine triphosphate-linked respiration in response to increased ROS in this AD LCL subgroup. In this AD LCL subgroup, 48-hour pretreatment with N-acetylcysteine, a glutathione precursor, prevented these abnormalities and improved glutathione metabolism, suggesting a role for altered glutathione metabolism associated with this type of mitochondrial dysfunction. The results of this study suggest that a significant subgroup of AD children may have alterations in mitochondrial function, which could render them more vulnerable to a pro-oxidant microenvironment as well as intrinsic and extrinsic sources of ROS such as immune activation and pro-oxidant environmental toxins. These findings are consistent with the notion that AD is caused by a combination of genetic and environmental factors.
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Rose S, Frye RE, Slattery J, Wynne R, Tippett M, Pavliv O, Melnyk S, James SJ. Oxidative stress induces mitochondrial dysfunction in a subset of autism lymphoblastoid cell lines in a well-matched case control cohort. PLoS One 2014; 9:e85436. [PMID: 24416410 PMCID: PMC3885720 DOI: 10.1371/journal.pone.0085436] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 11/26/2013] [Indexed: 01/26/2023] Open
Abstract
There is increasing recognition that mitochondrial dysfunction is associated with the autism spectrum disorders. However, little attention has been given to the etiology of mitochondrial dysfunction or how mitochondrial abnormalities might interact with other physiological disturbances associated with autism, such as oxidative stress. In the current study we used respirometry to examine reserve capacity, a measure of the mitochondrial ability to respond to physiological stress, in lymphoblastoid cell lines (LCLs) derived from children with autistic disorder (AD) as well as age and gender-matched control LCLs. We demonstrate, for the first time, that LCLs derived from children with AD have an abnormal mitochondrial reserve capacity before and after exposure to increasingly higher concentrations of 2,3-dimethoxy-1,4-napthoquinone (DMNQ), an agent that increases intracellular reactive oxygen species (ROS). Specifically, the AD LCLs exhibit a higher reserve capacity at baseline and a sharper depletion of reserve capacity when ROS exposure is increased, as compared to control LCLs. Detailed investigation indicated that reserve capacity abnormalities seen in AD LCLs were the result of higher ATP-linked respiration and maximal respiratory capacity at baseline combined with a marked increase in proton leak respiration as ROS was increased. We further demonstrate that these reserve capacity abnormalities are driven by a subgroup of eight (32%) of 25 AD LCLs. Additional investigation of this subgroup of AD LCLs with reserve capacity abnormalities revealed that it demonstrated a greater reliance on glycolysis and on uncoupling protein 2 to regulate oxidative stress at the inner mitochondria membrane. This study suggests that a significant subgroup of AD children may have alterations in mitochondrial function which could render them more vulnerable to a pro-oxidant microenvironment derived from intrinsic and extrinsic sources of ROS such as immune activation and pro-oxidant environmental toxicants. These findings are consistent with the notion that AD is caused by a combination of genetic and environmental factors.
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Affiliation(s)
- Shannon Rose
- Department of Pediatrics, Arkansas Children's Hospital Research Institute, Little Rock, Arkansas, United States of America
| | - Richard E. Frye
- Department of Pediatrics, Arkansas Children's Hospital Research Institute, Little Rock, Arkansas, United States of America
- * E-mail:
| | - John Slattery
- Department of Pediatrics, Arkansas Children's Hospital Research Institute, Little Rock, Arkansas, United States of America
| | - Rebecca Wynne
- Department of Pediatrics, Arkansas Children's Hospital Research Institute, Little Rock, Arkansas, United States of America
| | - Marie Tippett
- Department of Pediatrics, Arkansas Children's Hospital Research Institute, Little Rock, Arkansas, United States of America
| | - Oleksandra Pavliv
- Department of Pediatrics, Arkansas Children's Hospital Research Institute, Little Rock, Arkansas, United States of America
| | - Stepan Melnyk
- Department of Pediatrics, Arkansas Children's Hospital Research Institute, Little Rock, Arkansas, United States of America
| | - S. Jill James
- Department of Pediatrics, Arkansas Children's Hospital Research Institute, Little Rock, Arkansas, United States of America
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28
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Boland JF, Chung CC, Roberson D, Mitchell J, Zhang X, Im KM, He J, Chanock SJ, Yeager M, Dean M. The new sequencer on the block: comparison of Life Technology's Proton sequencer to an Illumina HiSeq for whole-exome sequencing. Hum Genet 2013; 132:1153-63. [PMID: 23757002 PMCID: PMC4564298 DOI: 10.1007/s00439-013-1321-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 05/26/2013] [Indexed: 02/07/2023]
Abstract
We assessed the performance of the new Life Technologies Proton sequencer by comparing whole-exome sequence data in a Centre d'Etude du Polymorphisme Humain trio (family 1463) to the Illumina HiSeq instrument. To simulate a typical user's results, we utilized the standard capture, alignment and variant calling methods specific to each platform. We restricted data analysis to include the capture region common to both methods. The Proton produced high quality data at a comparable average depth and read length, and the Ion Reporter variant caller identified 96 % of single nucleotide polymorphisms (SNPs) detected by the HiSeq and GATK pipeline. However, only 40 % of small insertion and deletion variants (indels) were identified by both methods. Usage of the trio structure and segregation of platform-specific alleles supported this result. Further comparison of the trio data with Complete Genomics sequence data and Illumina SNP microarray genotypes documented high concordance and accurate SNP genotyping of both Proton and Illumina platforms. However, our study underscored the problem of accurate detection of indels for both the Proton and HiSeq platforms.
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Affiliation(s)
- Joseph F. Boland
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, 8717 Grovemont Circle, Gaithersburg, MD 20877, USA. Frederick National Laboratory for Cancer Research, SAIC-Frederick Inc, Gaithersburg, USA
| | - Charles C. Chung
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, 8717 Grovemont Circle, Gaithersburg, MD 20877, USA. Frederick National Laboratory for Cancer Research, SAIC-Frederick Inc, Gaithersburg, USA
| | - David Roberson
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, 8717 Grovemont Circle, Gaithersburg, MD 20877, USA. Frederick National Laboratory for Cancer Research, SAIC-Frederick Inc, Gaithersburg, USA
| | - Jason Mitchell
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, 8717 Grovemont Circle, Gaithersburg, MD 20877, USA. Frederick National Laboratory for Cancer Research, SAIC-Frederick Inc, Gaithersburg, USA
| | - Xijun Zhang
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, 8717 Grovemont Circle, Gaithersburg, MD 20877, USA. Frederick National Laboratory for Cancer Research, SAIC-Frederick Inc, Gaithersburg, USA
| | - Kate M. Im
- Laboratory of Experimental Immunology, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick, MD 21702, USA
| | - Ji He
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, 8717 Grovemont Circle, Gaithersburg, MD 20877, USA. Frederick National Laboratory for Cancer Research, SAIC-Frederick Inc, Gaithersburg, USA
| | - Stephen J. Chanock
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, 8717 Grovemont Circle, Gaithersburg, MD 20877, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, 8717 Grovemont Circle, Gaithersburg, MD 20877, USA. Frederick National Laboratory for Cancer Research, SAIC-Frederick Inc, Gaithersburg, USA
| | - Michael Dean
- Laboratory of Experimental Immunology, Center for Cancer Research, National Cancer Institute, NIH, DHHS, Frederick, MD 21702, USA
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