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Watkins JA, Hatcher H, Malhotra S, Amen F, Bruty J, Trotman J, Tarpey P, Tadross JA. Identification of an Activating PDGFRA Deletion in a Novel Sinonasal Soft Tissue Neoplasm. Head Neck Pathol 2023; 17:576-580. [PMID: 36723852 PMCID: PMC10293132 DOI: 10.1007/s12105-023-01526-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/07/2023] [Indexed: 02/02/2023]
Abstract
BACKGROUND Spindle cell tumours in the sinonasal area are diagnostically challenging. We identified a neoplasm that defied histopathological classification using current criteria. METHODS The case was subjected to histopathological, immunohistochemical and molecular analysis using a large small variant DNA panel. RESULTS The tumour comprised cytologically bland epithelioid spindle cells with a rich vasculature, which lack expression of actin and other smooth muscle markers, CD34 and beta-catenin. An activating insertion/deletion in exon 12 of the PDGFRA gene was detected. This alteration has previously been described in gastrointestinal stromal tumours and inflammatory fibroid polyps of the GI tract, but the site, histological, and immunophenotypic features in this tumour are distinct. CONCLUSION We describe a novel sinonasal spindle cell tumour characterised by an activating insertion/deletion in exon 12 of PDGFRA. The diagnosis of PDGFRA-activated sinonasal spindle cell tumour should be considered in difficult to classify mesenchymal lesions at this site.
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Affiliation(s)
- James A. Watkins
- Department of Histopathology, Level 5, Laboratory Block, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
- Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Helen Hatcher
- Department of Oncology, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Shalini Malhotra
- Department of Histopathology, Level 5, Laboratory Block, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
| | - Furrat Amen
- Department of Surgery, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Jonathan Bruty
- Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jamie Trotman
- Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Patrick Tarpey
- Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - John A. Tadross
- Department of Histopathology, Level 5, Laboratory Block, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
- Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
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El-Masry OS, Alamri AM, Alzahrani F, Alsamman K. ADAMTS14, ARHGAP22, and EPDR1 as potential novel targets in acute myeloid leukaemia. Heliyon 2022; 8:e09065. [PMID: 35299609 PMCID: PMC8920923 DOI: 10.1016/j.heliyon.2022.e09065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/13/2021] [Accepted: 03/03/2022] [Indexed: 11/25/2022] Open
Abstract
Acute myeloid leukaemia (AML) is a blood cancer with a heterogeneous genomic landscape. This study aimed to mine bioinformatics data generated by RNA sequencing to unveil an AML case transcriptome profile and identify novel therapeutic targets and markers. In this study, we have determined the transcriptomic profile and analysed gene variants of an AML patient at the time of diagnosis and validated some genes by quantitative reverse transcriptase polymerase chain reaction. ADAMTS14, ARHGAP22, and ependymin-related protein 1 (EPDR1) were markedly upregulated compared to the corresponding control. In addition, novel exonic single-nucleotide and insertion/deletion variants were identified in these genes. Hence, ADAMTS14, ARHGAP22, and EPDR1 can be proposed as potential novel targets in AML, and their exact roles should be further explored.
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Affiliation(s)
- Omar S El-Masry
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahaman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Ali M Alamri
- Department of Internal Medicine, King Fahd Hospital of the University, Imam Abdulrahaman Bin Faisal University, Alkhobar, 34445, Saudi Arabia
| | - Faisal Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahaman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Khaldoon Alsamman
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahaman Bin Faisal University, Dammam, 31441, Saudi Arabia
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Hubacek JA, Dusek L, Majek O, Adamek V, Cervinkova T, Dlouha D, Adamkova V. ACE I/D polymorphism in Czech first-wave SARS-CoV-2-positive survivors. Clin Chim Acta 2021; 519:206-209. [PMID: 33957095 PMCID: PMC8091801 DOI: 10.1016/j.cca.2021.04.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 04/29/2021] [Accepted: 04/29/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rapidly spread from China in 2019/2020 to all continents. Significant geographical and ethnic differences were described, and host genetic background seems to be important for the resistance to and mortality of COVID-19. Angiotensin-converting enzyme (ACE) insertion/deletion (I/D) polymorphism (rs4646994) is one of the candidates with the potential to affect infection symptoms and mortality. METHODS In our study, we successfully genotyped 408 SARS-CoV-2-positive COVID-19 survivors (163 asymptomatic and 245 symptomatic) and compared them with a population-based DNA bank of 2,559 subjects. RESULTS The frequency of ACE I/I homozygotes was significantly increased in COVID-19 patients compared with that in controls (26.2% vs. 21.2%; P = 0.02; OR [95% CI] = 1.55 [1.17-2.05]. Importantly, however, the difference was driven just by the symptomatic subjects (29.0% vs. 21.2% of the I/I homozygotes; P = 0.002; OR [95% CI] = 1.78 [1.22-2.60]). The genotype distribution of the ACE genotypes was almost identical in population controls and asymptomatic SARS-CoV-2-positive patients (P = 0.76). CONCLUSIONS We conclude that ACE I/D polymorphism could have the potential to predict the severity of COVID-19, with I/I homozygotes being at increased risk of symptomatic COVID-19.
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Affiliation(s)
- Jaroslav A. Hubacek
- Experimental Medicine Center, Institute for Clinical and Experimental Medicine, Videnska 1958/9, Prague, Czech Republic,Corresponding author at: IKEM-EMC, Videnska 1958/9, 14021 Prague 4, Czech Republic
| | - Ladislav Dusek
- Institute of Health Information and Statistics of the Czech Republic, Palackeho namesti 4, Prague, Czech Republic,Institute of Biostatistics and Analyses, Faculty of Medicine, Masaryk University, Kamenice753/5, Brno, Czech Republic
| | - Ondrej Majek
- Institute of Health Information and Statistics of the Czech Republic, Palackeho namesti 4, Prague, Czech Republic,Institute of Biostatistics and Analyses, Faculty of Medicine, Masaryk University, Kamenice753/5, Brno, Czech Republic
| | - Vaclav Adamek
- Czech Technical University, Faculty of Biomedical Engineering, Sítná 3105, Kladno, Czech Republic
| | - Tereza Cervinkova
- Department of Preventive Cardiology, Institute for Clinical and Experimental Medicine, Videnska 1958/9, Prague, Czech Republic
| | - Dana Dlouha
- Experimental Medicine Center, Institute for Clinical and Experimental Medicine, Videnska 1958/9, Prague, Czech Republic
| | - Vera Adamkova
- Czech Technical University, Faculty of Biomedical Engineering, Sítná 3105, Kladno, Czech Republic,Department of Preventive Cardiology, Institute for Clinical and Experimental Medicine, Videnska 1958/9, Prague, Czech Republic
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Ossa H, Posada Y, Trujillo N, Martínez B, Loiola S, Simão F, Ossa RH, Castillo A, Ibarra A, Marrugo J, de Carvalho EF, Vargas CI, Pereira R, Gusmão L. Patterns of genetic diversity in Colombia for 38 indels used in human identification. Forensic Sci Int Genet 2021; 53:102495. [PMID: 33743518 DOI: 10.1016/j.fsigen.2021.102495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/06/2021] [Indexed: 01/15/2023]
Abstract
The current population of Colombia has a genetic heterogeneity resulting from different migrations from other continents and within the country. In addition, there are small groups in their territory that have remained isolated and therefore have a different genetic pool in relation to that of the neighbouring urban populations. This population stratification must be considered in forensic analysis, being more complex for markers with marked intercontinental differentiation. In this study, population differentiation in Colombian admixed, native, and Afro-descendant populations was evaluated for a group of 38 indels described for forensic use. Allelic frequencies and parameters of forensic relevance were determined in each of the groups defined based on population differentiation analyses. In addition to the differences found between population groups, the results show that the set of 38 indels analysed could be useful in studies of individual identification in Colombia. The exclusion power presented by this set of markers suggests the need for joint use with other markers, being able to complement the STRs in paternity cases. High levels of both power of discrimination and exclusion were found when complementing the 38 HID-indels with a second multiplex, for a total of 83 indels.
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Wei C, Hou D, Feng Y, Li T, Jing Z, Li W, Han R, Li G, Sun G, Tian Y, Liu X, Kang X, Li Z. Molecular characterization and a duplicated 31-bp indel within the LDB2 gene and its associations with production performance in chickens. Gene 2020; 761:145046. [PMID: 32781192 DOI: 10.1016/j.gene.2020.145046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 08/01/2020] [Accepted: 08/06/2020] [Indexed: 02/06/2023]
Abstract
Many studies have shown that the LDB2 gene plays a regulatory role in retinal development and the cell cycle, but its biological role remains unclear. In this study, a 31-bp indel in the LDB2 gene was found for the first time on the basis of 2797 individuals from 10 different breeds, which led to different genotypes among individuals (II, ID and DD). Among these genotypes, DD was the most dominant. Association analysis of an F2 resource population crossed with the Gushi (GS) chicken and Anka chicken showed that the DD genotype conferred a significantly greater semi-evisceration weight (SEW, 1108.665 g ± 6.263), evisceration weight (EW, 927.455 g ± 5.424), carcass weight (CW, 1197.306 g ± 6.443), breast muscle weight (BMW, 71.05 g ± 0.574), and leg muscle weight (LMW, 100.303 g ± 0.677) than the ID genotype (SEW, 1059.079 g ± 16.86; EW, 879.459 g ± 14.446; CW, 1141.821 g ± 17.176; BMW, 67.164 g ± 1.523; and LMW, 96.163 g ± 1.823). In addition, LDB2 gene expression in different breeds was significantly higher in the breast muscles and leg muscles than in other tissues. The expression level in the breast muscle differed significantly among stages of GS chicken development, with the highest expression observed at 6 weeks. The expression levels in the pectoral muscles differed significantly among Ross 308 genotypes. In summary, we studied the relationships between a 31-bp indel in the LDB2 gene and economic traits in chickens. The indel was significantly correlated with multiple growth and carcass traits in the F2 resource population and affected the expression of the LDB2 gene in muscle tissue. In short, our study revealed that the LDB2 gene 31-bp indel can be used as a potential genetic marker for molecular breeding.
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Abdelrahman M, Nakabayashi R, Mori T, Ikeuchi T, Mori M, Murakami K, Ozaki Y, Matsumoto M, Uragami A, Tsujimoto H, Tran LSP, Kanno A. Comparative Metabolome and Transcriptome Analyses of Susceptible Asparagus officinalis and Resistant Wild A. kiusianus Reveal Insights into Stem Blight Disease Resistance. Plant Cell Physiol 2020; 61:1464-1476. [PMID: 32374863 DOI: 10.1093/pcp/pcaa054] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/18/2020] [Indexed: 05/23/2023]
Abstract
Phomopsis asparagi is one of the most serious fungal pathogens, which causes stem blight disease in Asparagus officinalis (AO), adversely affecting its production worldwide. Recently, the development of novel asparagus varieties using wild Asparagus genetic resources with natural P. asparagi resistance has become a priority in Japan due to the lack of resistant commercial AO cultivars. In this study, comparative metabolome and transcriptome analyses of susceptible AO and resistant wild Asparagus kiusianus (AK) 24 and 48 h postinoculated (AOI_24 hpi, AOI_48 hpi, AKI_24 hpi and AKI_48 hpi, respectively) with P. asparagi were conducted to gain insights into metabolic and expression changes associated with AK species. Following infection, the resistant wild AK showed rapid metabolic changes with increased levels of flavonoids and steroidal saponins and decreased asparagusic acid glucose ester content, compared with the susceptible AO plants. Transcriptome data revealed a total of 21 differentially expressed genes (DEGs) as the core gene set that displayed upregulation in the resistant AK versus susceptible AO after infection with P. asparagi. Kyoto Encyclopedia of Genes and Genomes pathway analysis of these DEGs identified 11 significantly enriched pathways, including flavonoid biosynthesis and primary metabolite metabolism, in addition to plant signaling and defense-related pathways. In addition, comparative single-nucleotide polymorphism and Indel distributions in susceptible AO and resistant AK plants were evaluated using the latest AO reference genome Aspof.V1. The data generated in this study are important resources for advancing Asparagus breeding programs and for investigations of genetic linkage mapping, phylogenetic diversity and plant defense-related genes.
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Affiliation(s)
- Mostafa Abdelrahman
- Botany Department, Faculty of Sciences, Aswan University, Aswan 81528, Egypt
- Arid Land Research Center, Tottori University, Tottori, 680-0001 Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
| | - Ryo Nakabayashi
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Tetsuya Mori
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Takao Ikeuchi
- Kagawa Prefectural Agricultural Experiment Station, 1534-1 Ayagawa, Ayauta, Kagawa, 761-2306 Japan
| | - Mitsutaka Mori
- Kagawa Prefectural Agricultural Experiment Station, 1534-1 Ayagawa, Ayauta, Kagawa, 761-2306 Japan
| | - Kyoko Murakami
- Kagawa Prefectural Agricultural Experiment Station, 1534-1 Ayagawa, Ayauta, Kagawa, 761-2306 Japan
| | - Yukio Ozaki
- Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395 Japan
| | - Masaru Matsumoto
- Institute of Tropical Agriculture, Kyushu University, Fukuoka, 819-0395 Japan
| | - Atsuko Uragami
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Ibaraki, 305-8519 Japan
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori, 680-0001 Japan
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, Vietnam
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama, 230-0045 Japan
| | - Akira Kanno
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
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Liang K, Wang X, Tian X, Geng R, Li W, Jing Z, Han R, Tian Y, Liu X, Kang X, Li Z. Molecular characterization and an 80-bp indel polymorphism within the prolactin receptor ( PRLR) gene and its associations with chicken growth and carcass traits. 3 Biotech 2019; 9:296. [PMID: 31321200 DOI: 10.1007/s13205-019-1827-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/07/2019] [Indexed: 01/09/2023] Open
Abstract
The prolactin receptor (PRLR), a type I cytokine receptor, must bind prolactin (PRL) to act on target cells to mediate various physiological functions, including reproduction and lactation. This study identified an 80-bp insertion/deletion (indel) polymorphism in the 3'-untranslated region (3'-UTR) of the chicken PRLR gene in 3736 individuals from 15 breeds and analyzed its associations with growth and carcass traits in an F2 resource population. The results of the association analysis indicated that the 80-bp indel polymorphism was significantly (P < 0.05) or very significantly (P < 0.01) associated with multiple growth and carcass traits, such as body weight, leg weight, and shank length. In addition, we found that during the breeding process of commercial laying hens and commercial broilers, the 80-bp indel locus was artificially selected for the II genotype. Together, our findings reveal that this 80-bp indel polymorphism has potential as a new molecular marker for marker-assisted selection of chicken growth and carcass traits.
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Affiliation(s)
- Ke Liang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Xiangnan Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Xiaoxiao Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Rui Geng
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Wenya Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Zhenzhu Jing
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Xiaojun Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046 China
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Zhang H, He G, Guo J, Ren Z, Zhang H, Wang Q, Ji J, Yang M, Huang J, Wang CC. Genetic diversity, structure and forensic characteristics of Hmong-Mien-speaking Miao revealed by autosomal insertion/deletion markers. Mol Genet Genomics 2019; 294:1487-98. [PMID: 31312894 DOI: 10.1007/s00438-019-01591-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/22/2019] [Indexed: 02/08/2023]
Abstract
Insertion/deletion (Indel) genetic markers have special features compared to other forensic-related markers, such as the low mutation rate and di-allelic markers with length polymorphism, playing an indispensable role in the forensic and population genetics, molecular anthropology and evolutionary biology. However, the genetic diversity, allelic frequency, forensic parameters and population genetic characteristics of the Indel markers in Hmong-Mien-speaking Guizhou Miao people are unclear due to the sparse sampling. Thus, we genotyped 30 forensic-related Indel markers in 311 unrelated healthy Miao individuals (149 females and 161 males) residing in the Guizhou Province in Southwest China using the Investigator DIPplex amplification system. All 30 Indels are in accordance with the no departures of Hardy-Weinberg equilibrium and linkage disequilibrium. The combined probability of discrimination and the probability of exclusion in Guizhou Miao population are 0.999999999948 and 0.9843, respectively. This observed ideal forensic parameter estimates indicate that this di-allelic Indel panel can be used as a supplementary tool in forensic retinue personal identification and complemented for autosomal STRs in the parentage testing in Miao population, especially used as the main tool in old or highly degraded samples in disaster victim identification. Eleven Indels show a high allele frequency difference between different continental populations and could be used as ancestry-informative markers in forensic ancestry inference. Phylogenetic relationships between Guizhou Miao and 68 worldwide populations based on the genetic polymorphisms of Indels are investigated via three different pairwise genetic distances, principal component analysis, multidimensional scaling analysis and phylogenetic relationship reconstructions. Analyses of the comprehensive population genetic relationship comparison reveal significant genetic differentiation of Chinese groups. Our results demonstrate that Guizhou Miao people are genetically closer related to the geographically adjacent populations, especially with Liangshan Yi, Guangxi Miao and Dong, but genetically distinct with Turkic-speaking populations. Comprehensive and precise genetic admixture and divergence history of Guizhou Miao and neighboring populations are needed to further investigate and reconstruct via high-density marker panel or whole-genome sequencing of modern or ancient Miao samples.
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9
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Yang Z, Yang Z, Yang C, Wang Z, Chen D, Xie Y, Wu Y. Identification and genetic analysis of alternative splicing of long non-coding RNAs in tomato initial flowering stage. Genomics 2019; 112:897-907. [PMID: 31175976 DOI: 10.1016/j.ygeno.2019.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/19/2019] [Accepted: 06/04/2019] [Indexed: 01/07/2023]
Abstract
Alternative splicing (AS) is a key modulator of development in many eukaryotic organisms. Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs that play essential regulatory roles in various developmental processes and stress responses. However, the functions of AS lncRNAs during the initial flowering of tomato are largely unknown. This study was designed to investigate the AS pattern of lncRNAs in tomato flower, leaf, and root tissues at the initial flowering stage. Using RNA-Seq, we found that 72.55% of lncRNAs underwent AS in these tissues, yielding a total of 16,995 AS events. Among them, the main type of AS event is alternative first exon (AFE), followed by retained intron (RI). We performed candidate target genes analysis on tissue-specific AS lncRNA, and the results indicated that the candidate target genes of these lncRNAs may be involved in the regulation of circadian rhythm, plant immunity, cellulose synthesis and phosphate-containing compound metabolic process. Moreover, a total of 73,085 putative SNPs and 15,679 InDels were detected, and the potential relationship between the AS of lncRNAs and interesting SNP and InDel loci, as well as their numbers, revealed their effects on tomato genetic diversity and genomic stability. Our data provide new insights into the complexity of the transcriptome and the regulation of AS.
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Affiliation(s)
- Zhenchao Yang
- College of Horticulture, College of Life Sciences, College of Science, Northwest A&F University, Yangling, Shaan Xi, China
| | - Zhao Yang
- College of Horticulture, College of Life Sciences, College of Science, Northwest A&F University, Yangling, Shaan Xi, China
| | - Chengcheng Yang
- College of Horticulture, College of Life Sciences, College of Science, Northwest A&F University, Yangling, Shaan Xi, China
| | - Zhengyan Wang
- College of Horticulture, College of Life Sciences, College of Science, Northwest A&F University, Yangling, Shaan Xi, China
| | - Danyan Chen
- College of Horticulture, College of Life Sciences, College of Science, Northwest A&F University, Yangling, Shaan Xi, China
| | - Yingge Xie
- College of Horticulture, College of Life Sciences, College of Science, Northwest A&F University, Yangling, Shaan Xi, China.
| | - Yongjun Wu
- College of Horticulture, College of Life Sciences, College of Science, Northwest A&F University, Yangling, Shaan Xi, China.
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10
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Du W, Feng C, Yao T, Xiao C, Huang H, Wu W, Zhu L, Qiao H, Liu C, Chen L. Genetic variation and forensic efficiency of 30 indels for three ethnic groups in Guangxi: relationships with other populations. PeerJ 2019; 7:e6861. [PMID: 31110924 PMCID: PMC6501771 DOI: 10.7717/peerj.6861] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 03/28/2019] [Indexed: 02/06/2023] Open
Abstract
Aim In this study, we used a series of diallelic genetic marker insertion/deletion polymorphism (indel) to investigate three populations of Yao, Kelao, and Zhuang groups in the Guangxi region of China and to evaluate their efficiency in forensic application. Result No deviations for all 30 loci were observed from the Hardy–Weinberg equilibrium after Bonferroni correction (p > 0.05/30 = 0.0017). The allele frequencies of the short allele (DIP-) for the above three populations were in the range of 0.0520–0.9480, 0.0950–0.8780, and 0.0850–0.915, respectively. The observed heterozygosity of the 30 loci for the three populations was in the ranges 0.0802–0.5802, 0.1908–0.6053, and 0.1400–0.5600, respectively. The cumulative power of exclusion and combined discrimination power for Yao, Kelao, and Zhuang groups were (0.9843 and 0.9999999999433), (0.9972 and 0.9999999999184), and (0.9845 and 0.9999999999608), respectively. The DA distance, principal component analysis, and cluster analysis indicated a clear regional distribution. In addition, Zhuang groups had close genetic relationships with the Yao and Kelao populations in the Guangxi region. Conclusion This study indicated that the 30 loci were qualified for personal identification; moreover, they could be used as complementary genetic markers for paternity testing in forensic cases for the studied populations.
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Affiliation(s)
- Weian Du
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Guangdong Homy Genetics Incorporation, Foshan, China
| | - Chunlei Feng
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Ting Yao
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Cheng Xiao
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Hongyan Huang
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Weibin Wu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Linnan Zhu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Honghua Qiao
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Chao Liu
- School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Guangzhou Forensic Science Institute, Guangzhou, China
| | - Ling Chen
- School of Forensic Medicine, Southern Medical University, Guangzhou, China
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11
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Abdelrahman M, Mitoma M, Ikeuchi T, Mori M, Murakami K, Ozaki Y, Matsumoto M, Uragami A, Kanno A. Differential gene expression analysis and SNP/InDel marker discovery in resistant wild Asparagus kiusianus and susceptible A. officinalis in response to Phomopsis asparagi infection. Data Brief 2018; 21:2117-2121. [PMID: 30533460 PMCID: PMC6262200 DOI: 10.1016/j.dib.2018.11.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 11/04/2018] [Accepted: 11/08/2018] [Indexed: 12/02/2022] Open
Abstract
This data article reports de novo transcriptome analysis of resistant wild Asparagus kiusianus and susceptible A. officinalis plants 24 and 48 h post-inoculation (24 and 48 hpi) with Phomopsis asparagi. Differential gene expression (DGE) analysis demonstrated that several genes involved in secondary metabolites and plant-pathogen interactions are up-regulated in resistant wild A. kiusianus relative to susceptible A. officinalis. The assembled contig sequences generated in this study were used to search single nucleotide polymorphism (SNP) and insertion/deletion (InDel) distribution in A. kiusianus and A. officinalis plants. SNP and InDel data developed from this transcriptome analysis will be used to generate a high-density linkage map to facilitate further development of molecular marker-assisted selection in A. officinalis.
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Affiliation(s)
- Mostafa Abdelrahman
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan.,Botany Department, Faculty of Sciences, Aswan University, Aswan 81528, Egypt
| | - Mai Mitoma
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan
| | - Takao Ikeuchi
- Kagawa Prefectural Agricultural Experiment Station, 1534-1 Ayagawa, Ayauta, Kagawa 761-2306, Japan
| | - Mitsutaka Mori
- Kagawa Prefectural Agricultural Experiment Station, 1534-1 Ayagawa, Ayauta, Kagawa 761-2306, Japan
| | - Kyoko Murakami
- Kagawa Prefectural Agricultural Experiment Station, 1534-1 Ayagawa, Ayauta, Kagawa 761-2306, Japan
| | - Yukio Ozaki
- Faculty of Agriculture, Kyushu University, Fukuoka 811-2307, Japan
| | - Masaru Matsumoto
- Institute of Tropical Agriculture, Kyushu University, Fukuoka 812-8581, Japan
| | - Atsuko Uragami
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Ibaraki 305-8519, Japan
| | - Akira Kanno
- Arid Land Research Center, Tottori University, Tottori 680-0001, Japan
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Prodduturi N, Bhagwate A, Kocher JPA, Sun Z. Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine. BMC Med Genomics 2018; 11:67. [PMID: 30255803 PMCID: PMC6157028 DOI: 10.1186/s12920-018-0391-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background RNA-seq is the most commonly used sequencing application. Not only does it measure gene expression but it is also an excellent media to detect important structural variants such as single nucleotide variants (SNVs), insertion/deletion (Indels) or fusion transcripts. However, detection of these variants is challenging and complex from RNA-seq. Here we describe a sensitive and accurate analytical pipeline which detects various mutations at once for translational precision medicine. Methods The pipeline incorporates most sensitive aligners for Indels in RNA-Seq, the best practice for data preprocessing and variant calling, and STAR-fusion is for chimeric transcripts. Variants/mutations are annotated, and key genes can be extracted for further investigation and clinical actions. Three datasets were used to evaluate the performance of the pipeline for SNVs, indels and fusion transcripts. Results For the well-defined variants from NA12878 by GIAB project, about 95% and 80% of sensitivities were obtained for SNVs and indels, respectively, in matching RNA-seq. Comparison with other variant specific tools showed good performance of the pipeline. For the lung cancer dataset with 41 known and oncogenic mutations, 39 were detected by the pipeline with STAR aligner and all by the GSNAP aligner. An actionable EML4 and ALK fusion was also detected in one of the tumors, which also demonstrated outlier ALK expression. For 9 fusions spiked-into RNA-seq libraries with different concentrations, the pipeline was able to detect all in unfiltered results although some at very low concentrations may be missed when filtering was applied. Conclusions The new RNA-seq workflow is an accurate and comprehensive mutation profiler from RNA-seq. Key or actionable mutations are reliably detected from RNA-seq, which makes it a practical alternative source for personalized medicine. Electronic supplementary material The online version of this article (10.1186/s12920-018-0391-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Naresh Prodduturi
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
| | - Aditya Bhagwate
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
| | - Jean-Pierre A Kocher
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
| | - Zhifu Sun
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA.
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Oldoni F, Castella V, Hall D. A novel set of DIP-STR markers for improved analysis of challenging DNA mixtures. Forensic Sci Int Genet 2015; 19:156-64. [PMID: 26232274 DOI: 10.1016/j.fsigen.2015.07.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 07/09/2015] [Accepted: 07/13/2015] [Indexed: 01/09/2023]
Abstract
Currently available molecular biology tools allow forensic scientists to characterize DNA evidence found at crime scenes for a large variety of samples, including those of limited quantity and quality, and achieve high levels of individualization. Yet, standard forensic markers provide limited or no results when applied to mixed DNA samples where the contributors are present in very different proportions (unbalanced DNA mixtures). This becomes an issue mostly for the analysis of trace samples collected on the victim or from touched objects. To this end, we recently proposed an innovative type of genetic marker, named DIP-STR that relies on pairing deletion/insertion polymorphisms (DIP) with standard short tandem repeats (STR). This novel compound marker allows detection of the minor DNA contributor in a DNA mixture of any gender and cellular origin with unprecedented resolution (beyond a DNA ratio of 1:1000). To provide a novel analytical tool useful in practice to common forensic laboratories, this article describes the first set of 10 DIP-STR markers selected according to forensic technical standards. The novel DIP-STR regions are short (between 146 and 271 bp), include only highly polymorphic tri-, tetra- and pentanucleotide tandem repeats and are located on different chromosomes or chromosomal arms to provide statistically independent results. This novel set of DIP-STR can target the amplification of 0.03-0.1 ng of DNA when mixed with a 1000-fold excess of major DNA. DIP-STR relative allele frequencies are estimated based on a survey of 103 Swiss individuals. Finally, this study provides an estimate of the occurrence of informative alleles and a calculation of the corresponding random match probability of the detected minor DIP-STR genotype assessed across 10,506 pairwise conceptual mixtures.
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Abstract
Oregano (Origanum vulgare L., Lamiaceae) is a medicinal and aromatic plant maybe best known for flavouring pizza. New applications e.g. as natural antioxidants for food are emerging due to the plants' high antibacterial and antioxidant activity. The complete chloroplast (cp) genome of Origanum vulgare (GenBank/EBML/DDBJ accession number: JX880022) consists of 151,935 bp and includes a pair of inverted repeats (IR) of 25,527 bp separated by one small and one large single copy region (SSC and LSC) of 17,745 and 83,136 bp, respectively. The genome with an overall GC content of 38% hosts 114 genes that covering 63% of the genome of which 8% were introns. The comparison of the Origanum cp genome with the cp genomes of two other core lamiales (Salvia miltiorrhiza Bunge and Sesamum indicum L.) revealed completely conserved protein-coding regions in the IR region but also in the LSC and SSC regions. Phylogenetic analysis of the lamiids based on 56 protein-coding genes give a hint at the basic structure of the Lamiales. However, further genomes will be necessary to clarify this taxonomically complicated order. The variability of the cp within the genus Origanum, studied exemplarily on 16 different chloroplast DNA regions, demonstrated that in 14 regions analyzed, the variability was extremely low (max. 0.7%), while only two regions showed a moderate variability of up to 2.3%. The cp genome of Origanum vulgare contains 27 perfect mononucleotide repeats (number of repeats>9) consisting exclusively of the nucleotides A or T. 34 perfect repeats (repeat lengths>1 and number of repeats>3) were found, of which 32 were di-, and 2 were trinucleotide repeats.
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Affiliation(s)
- Brigitte Lukas
- Institute for Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria.
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