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Han N, Oh JM, Kim IW. Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in Koreans. J Pers Med 2021; 11:33. [PMID: 33430289 PMCID: PMC7825650 DOI: 10.3390/jpm11010033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/16/2020] [Accepted: 01/04/2021] [Indexed: 12/12/2022] Open
Abstract
For predicting phenotypes and executing precision medicine, combination analysis of single nucleotide variants (SNVs) genotyping with copy number variations (CNVs) is required. The aim of this study was to discover SNVs or common copy CNVs and examine the combined frequencies of SNVs and CNVs in pharmacogenes using the Korean genome and epidemiology study (KoGES), a consortium project. The genotypes (N = 72,299) and CNV data (N = 1000) were provided by the Korean National Institute of Health, Korea Centers for Disease Control and Prevention. The allele frequencies of SNVs, CNVs, and combined SNVs with CNVs were calculated and haplotype analysis was performed. CYP2D6 rs1065852 (c.100C>T, p.P34S) was the most common variant allele (48.23%). A total of 8454 haplotype blocks in 18 pharmacogenes were estimated. DMD ranked the highest in frequency for gene gain (64.52%), while TPMT ranked the highest in frequency for gene loss (51.80%). Copy number gain of CYP4F2 was observed in 22 subjects; 13 of those subjects were carriers with CYP4F2*3 gain. In the case of TPMT, approximately one-half of the participants (N = 308) had loss of the TPMT*1*1 diplotype. The frequencies of SNVs and CNVs in pharmacogenes were determined using the Korean cohort-based genome-wide association study.
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Affiliation(s)
| | | | - In-Wha Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea; (N.H.); (J.M.O.)
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52
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Cheng YH, Liu CFJ, Yu YH, Jhou YT, Fujishima M, Tsai IJ, Leu JY. Genome plasticity in Paramecium bursaria revealed by population genomics. BMC Biol 2020; 18:180. [PMID: 33250052 PMCID: PMC7702705 DOI: 10.1186/s12915-020-00912-2] [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: 10/22/2019] [Accepted: 10/29/2020] [Indexed: 11/25/2022] Open
Abstract
Background Ciliates are an ancient and diverse eukaryotic group found in various environments. A unique feature of ciliates is their nuclear dimorphism, by which two types of nuclei, the diploid germline micronucleus (MIC) and polyploidy somatic macronucleus (MAC), are present in the same cytoplasm and serve different functions. During each sexual cycle, ciliates develop a new macronucleus in which newly fused genomes are extensively rearranged to generate functional minichromosomes. Interestingly, each ciliate species seems to have its way of processing genomes, providing a diversity of resources for studying genome plasticity and its regulation. Here, we sequenced and analyzed the macronuclear genome of different strains of Paramecium bursaria, a highly divergent species of the genus Paramecium which can stably establish endosymbioses with green algae. Results We assembled a high-quality macronuclear genome of P. bursaria and further refined genome annotation by comparing population genomic data. We identified several species-specific expansions in protein families and gene lineages that are potentially associated with endosymbiosis. Moreover, we observed an intensive chromosome breakage pattern that occurred during or shortly after sexual reproduction and contributed to highly variable gene dosage throughout the genome. However, patterns of copy number variation were highly correlated among genetically divergent strains, suggesting that copy number is adjusted by some regulatory mechanisms or natural selection. Further analysis showed that genes with low copy number variation among populations tended to function in basic cellular pathways, whereas highly variable genes were enriched in environmental response pathways. Conclusions We report programmed DNA rearrangements in the P. bursaria macronuclear genome that allow cells to adjust gene copy number globally according to individual gene functions. Our results suggest that large-scale gene copy number variation may represent an ancient mechanism for cells to adapt to different environments. Supplementary information The online version contains supplementary material available at 10.1186/s12915-020-00912-2.
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Affiliation(s)
- Yu-Hsuan Cheng
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, 106, Taiwan.,Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan
| | - Chien-Fu Jeff Liu
- Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan
| | - Yen-Hsin Yu
- Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan
| | - Yu-Ting Jhou
- Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan
| | - Masahiro Fujishima
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi, 753-8512, Japan
| | - Isheng Jason Tsai
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, 106, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Jun-Yi Leu
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, 106, Taiwan. .,Institute of Molecular Biology, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei, 115, Taiwan.
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53
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Spealman P, Burrell J, Gresham D. Inverted duplicate DNA sequences increase translocation rates through sequencing nanopores resulting in reduced base calling accuracy. Nucleic Acids Res 2020; 48:4940-4945. [PMID: 32255181 PMCID: PMC7229812 DOI: 10.1093/nar/gkaa206] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/14/2020] [Accepted: 04/03/2020] [Indexed: 12/27/2022] Open
Abstract
Inverted duplicated DNA sequences are a common feature of structural variants (SVs) and copy number variants (CNVs). Analysis of CNVs containing inverted duplicated DNA sequences using nanopore sequencing identified recurrent aberrant behavior characterized by low confidence, incorrect and missed base calls. Inverted duplicate DNA sequences in both yeast and human samples were observed to have systematic elevation in the electrical current detected at the nanopore, increased translocation rates and decreased sampling rates. The coincidence of inverted duplicated DNA sequences with dramatically reduced sequencing accuracy and an increased translocation rate suggests that secondary DNA structures may interfere with the dynamics of transit of the DNA through the nanopore.
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Affiliation(s)
- Pieter Spealman
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Jaden Burrell
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - David Gresham
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
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54
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Nelson PT, Fardo DW, Katsumata Y. The MUC6/AP2A2 Locus and Its Relevance to Alzheimer's Disease: A Review. J Neuropathol Exp Neurol 2020; 79:568-584. [PMID: 32357373 PMCID: PMC7241941 DOI: 10.1093/jnen/nlaa024] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/10/2020] [Indexed: 12/11/2022] Open
Abstract
We recently reported evidence of Alzheimer's disease (AD)-linked genetic variation within the mucin 6 (MUC6) gene on chromosome 11p, nearby the adaptor-related protein complex 2 subunit alpha 2 (AP2A2) gene. This locus has interesting features related to human genomics and clinical research. MUC6 gene variants have been reported to potentially influence viral-including herpesvirus-immunity and the gut microbiome. Within the MUC6 gene is a unique variable number of tandem repeat (VNTR) region. We discovered an association between MUC6 VNTR repeat expansion and AD pathologic severity, particularly tau proteinopathy. Here, we review the relevant literature. The AD-linked VNTR polymorphism may also influence AP2A2 gene expression. AP2A2 encodes a polypeptide component of the adaptor protein complex, AP-2, which is involved in clathrin-coated vesicle function and was previously implicated in AD pathogenesis. To provide background information, we describe some key knowledge gaps in AD genetics research. The "missing/hidden heritability problem" of AD is highlighted. Extensive portions of the human genome, including the MUC6 VNTR, have not been thoroughly evaluated due to limitations of existing high-throughput sequencing technology. We present and discuss additional data, along with cautionary considerations, relevant to the hypothesis that MUC6 repeat expansion influences AD pathogenesis.
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Affiliation(s)
- Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
- Department of Pathology, University of Kentucky, Lexington, Kentucky
| | - David W Fardo
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky
| | - Yuriko Katsumata
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky
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55
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Blount ZD, Maddamsetti R, Grant NA, Ahmed ST, Jagdish T, Baxter JA, Sommerfeld BA, Tillman A, Moore J, Slonczewski JL, Barrick JE, Lenski RE. Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment. eLife 2020; 9:55414. [PMID: 32469311 PMCID: PMC7299349 DOI: 10.7554/elife.55414] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/28/2020] [Indexed: 12/27/2022] Open
Abstract
Evolutionary innovations allow populations to colonize new ecological niches. We previously reported that aerobic growth on citrate (Cit+) evolved in an Escherichia coli population during adaptation to a minimal glucose medium containing citrate (DM25). Cit+ variants can also grow in citrate-only medium (DM0), a novel environment for E. coli. To study adaptation to this niche, we founded two sets of Cit+ populations and evolved them for 2500 generations in DM0 or DM25. The evolved lineages acquired numerous parallel mutations, many mediated by transposable elements. Several also evolved amplifications of regions containing the maeA gene. Unexpectedly, some evolved populations and clones show apparent declines in fitness. We also found evidence of substantial cell death in Cit+ clones. Our results thus demonstrate rapid trait refinement and adaptation to the new citrate niche, while also suggesting a recalcitrant mismatch between E. coli physiology and growth on citrate.
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Affiliation(s)
- Zachary D Blount
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States.,The BEACON Center for the Study of Evolution in Action, East Lansing, United States
| | - Rohan Maddamsetti
- Department of Biomedical Engineering, Duke University, Durham, United States
| | - Nkrumah A Grant
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States.,The BEACON Center for the Study of Evolution in Action, East Lansing, United States
| | - Sumaya T Ahmed
- Department of Biology, Kenyon College, Gambier, United States
| | - Tanush Jagdish
- The BEACON Center for the Study of Evolution in Action, East Lansing, United States.,Program for Systems, Synthetic, and Quantitative Biology, Harvard University, Cambridge, United States
| | - Jessica A Baxter
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
| | - Brooke A Sommerfeld
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
| | - Alice Tillman
- Department of Biology, Kenyon College, Gambier, United States
| | - Jeremy Moore
- Department of Biology, Kenyon College, Gambier, United States
| | | | - Jeffrey E Barrick
- The BEACON Center for the Study of Evolution in Action, East Lansing, United States.,Department of Molecular Biosciences, The University of Texas, Austin, United States
| | - Richard E Lenski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States.,The BEACON Center for the Study of Evolution in Action, East Lansing, United States
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56
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Mechanisms of a near-orthogonal ultra-fast evolution of human behaviour as a source of culture development. Behav Brain Res 2020; 384:112521. [DOI: 10.1016/j.bbr.2020.112521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 12/15/2022]
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57
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Zhao Y, Long L, Wan J, Biliya S, Brady SC, Lee D, Ojemakinde A, Andersen EC, Vannberg FO, Lu H, McGrath PT. A spontaneous complex structural variant in rcan-1 increases exploratory behavior and laboratory fitness of Caenorhabditis elegans. PLoS Genet 2020; 16:e1008606. [PMID: 32092052 PMCID: PMC7058356 DOI: 10.1371/journal.pgen.1008606] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 03/05/2020] [Accepted: 01/11/2020] [Indexed: 01/02/2023] Open
Abstract
Over long evolutionary timescales, major changes to the copy number, function, and genomic organization of genes occur, however, our understanding of the individual mutational events responsible for these changes is lacking. In this report, we study the genetic basis of adaptation of two strains of C. elegans to laboratory food sources using competition experiments on a panel of 89 recombinant inbred lines (RIL). Unexpectedly, we identified a single RIL with higher relative fitness than either of the parental strains. This strain also displayed a novel behavioral phenotype, resulting in higher propensity to explore bacterial lawns. Using bulk-segregant analysis and short-read resequencing of this RIL, we mapped the change in exploration behavior to a spontaneous, complex rearrangement of the rcan-1 gene that occurred during construction of the RIL panel. We resolved this rearrangement into five unique tandem inversion/duplications using Oxford Nanopore long-read sequencing. rcan-1 encodes an ortholog to human RCAN1/DSCR1 calcipressin gene, which has been implicated as a causal gene for Down syndrome. The genomic rearrangement in rcan-1 creates two complete and two truncated versions of the rcan-1 coding region, with a variety of modified 5’ and 3’ non-coding regions. While most copy-number variations (CNVs) are thought to act by increasing expression of duplicated genes, these changes to rcan-1 ultimately result in the reduction of its whole-body expression due to changes in the upstream regions. By backcrossing this rearrangement into a common genetic background to create a near isogenic line (NIL), we demonstrate that both the competitive advantage and exploration behavioral changes are linked to this complex genetic variant. This NIL strain does not phenocopy a strain containing an rcan-1 loss-of-function allele, which suggests that the residual expression of rcan-1 is necessary for its fitness effects. Our results demonstrate how colonization of new environments, such as those encountered in the laboratory, can create evolutionary pressure to modify gene function. This evolutionary mismatch can be resolved by an unexpectedly complex genetic change that simultaneously duplicates and diversifies a gene into two uniquely regulated genes. Our work shows how complex rearrangements can act to modify gene expression in ways besides increased gene dosage. Evolution acts on genetic variants that modify phenotypes that increase the likelihood of staying alive and passing on these genetic changes to subsequent generations (i.e. fitness). There is general interest in understanding the types of genetic variants that can increase fitness in specific environments. One route that fitness can be increased is through changes in behavior, such as finding new food sources. Here, we identify a spontaneous genetic change that increases exploration behavior and fitness of animals in laboratory environments. Interestingly, this genetic change is not a simple genetic change that deletes or changes the sequence of a protein product, but rather a complex structural variant that simultaneously duplicates the rcan-1 gene and also modifies its expression in a number of tissues. Our work demonstrates how a complex structural change can duplicate a gene, modify the DNA control regions that determine its cellular sites of action, and confer a fitness advantage that could lead to its spread in a population.
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Affiliation(s)
- Yuehui Zhao
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Lijiang Long
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Jason Wan
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
| | - Shweta Biliya
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Shannon C. Brady
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Daehan Lee
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Akinade Ojemakinde
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Erik C. Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, United States of America
| | - Fredrik O. Vannberg
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Hang Lu
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Patrick T. McGrath
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
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