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Liu K, Xie N. Pipeline for developing polymorphic microsatellites in species without reference genomes. 3 Biotech 2022; 12:248. [PMID: 36039078 PMCID: PMC9418399 DOI: 10.1007/s13205-022-03313-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/16/2022] [Indexed: 11/01/2022] Open
Abstract
Microsatellites, also known as simple sequence repeats (SSRs), are the preferred type of marker for many genetic applications. In conjunction with the ongoing development of next-generation sequencing, several bioinformatic tools have been developed for identifying SSRs from genomic or transcriptomic sequences. Although these tools are handy for generating polymorphic SSRs, their application almost always depends on an existing reference genome or self-assembly of the reference genome. With this in mind, we propose a pipeline for developing polymorphic SSRs that may be applied to species without reference genomes. Using a species without a reference genome (black Amur bream; Megalobrama terminalis Richardson, 1846) as a model, our pipeline was able to effectively discover polymorphic SSRs. Under different R parameters of a reference-free single nucleotide polymorphisms (SNPs) caller (ebwt2InDel), a total of 258, 208, 102, and 11 polymorphic SSRs were mined. To quantify the accuracy of the polymorphic SSRs detected using our pipeline, we analyzed 25 SSRs with PCR experiments. All primers were successfully amplified, and most SSRs (23 SSRs, 92%) were polymorphic. From the 36 individual black Amur bream, we acquired an average of 3.36 alleles per locus, ranging from one to 11. This demonstrates the effectiveness of our pipeline in identifying polymorphic SSRs and designing primers for SSR genotyping. Ultimately, our pipeline can effectively mine polymorphic SSRs for species without reference genomes, complementing SSR mining approaches based on reference genomes and helping to resolve biological issues that accompany these methods. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03313-0.
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Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang China
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang China
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2
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Tian HF, Hu QM, Li Z. Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in swamp eel (Monopterus albus). Sci Prog 2021; 104:368504211035597. [PMID: 34375541 PMCID: PMC10358632 DOI: 10.1177/00368504211035597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Swamp eel is one model species for sexual reversion and an aquaculture fish in China. One local strain with deep yellow and big spots of Monopterus albus has been selected for consecutive selective breeding. The objectives of this study were characterizing the Simple Sequence Repeats (SSRs) of M. albus in the assembled genome obtained recently, and developing polymorphic SSRs for future breeding programs. METHODS The genome wide SSRs were mined by using MISA software, and their types and genomic distribution patterns were investigated. Based on the available flanking sequences, primer pairs were batched developed, and Polymorphic SSRs were identified by using Polymorphic SSR Retrieval tool. The obtained polymorphic SSRs were validated by using e-PCR and capillary electrophoresis, then they were used to investigate genetic diversity of one breeding population. RESULTS A total of 364,802 SSRs were identified in assembled M. albus genome. The total length, density and frequency of SSRs were 8,204,641 bp, 10,259 bp/Mb, and 456.16 loci/Mb, respectively. Mononucleotide repeats were predominant among SSRs (33.33%), and AC and AAT repeats were the most abundant di- and tri-nucleotide repeats motifs. A total of 287,189 primer pairs were designed, and a high-density physical map was constructed (359.11 markers per Mb). A total of 871 polymorphic SSRs were identified, and 38 SSRs of 101 randomly selected ones were validated by using e-PCR and capillary electrophoresis. Using these 38 polymorphic SSRs, 201 alleles were detected and genetic diversity level (Na, PIC, HO, and He) was evaluated. CONCLUSIONS The genome-wide SSRs and newly developed SSR markers will provide a useful tool for genetic mapping, diversity analysis studies in swamp eel in the future. The high level of genetic diversity (Na = 5.29, PIC = 0.5068, HO = 0.4665, He = 0.5525) but excess of homozygotes (FIS = 0.155) in one breeding population provide baseline information for future breeding program.
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Affiliation(s)
- Hai-feng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, China
| | - Qiao-mu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, China
| | - Zhong Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, China
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3
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Chen T, Zeng R, Cai W, Xiong X, Fu W, Mipam TD, Li J, Lan D. Systematic selection of microsatellite for paternity testing of yak. Anim Genet 2021; 52:572-573. [PMID: 33999441 DOI: 10.1111/age.13080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Tong Chen
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, 610041, China.,Key Laboratory of Animal Science of State Ethnic Affairs Commission, Southwest Minzu University, Chengdu, 610041, China
| | - Ruilin Zeng
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, 610041, China.,Key Laboratory of Animal Science of State Ethnic Affairs Commission, Southwest Minzu University, Chengdu, 610041, China
| | - Wenyi Cai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, 610041, China.,Key Laboratory of Animal Science of State Ethnic Affairs Commission, Southwest Minzu University, Chengdu, 610041, China
| | - Xianrong Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, 610041, China.,Key Laboratory of Animal Science of State Ethnic Affairs Commission, Southwest Minzu University, Chengdu, 610041, China.,College of Animal and Verterinary Sciences, Southwest Minzu University, Chengdu, 610041, China
| | - Wei Fu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, 610041, China.,Key Laboratory of Animal Science of State Ethnic Affairs Commission, Southwest Minzu University, Chengdu, 610041, China.,College of Animal and Verterinary Sciences, Southwest Minzu University, Chengdu, 610041, China
| | - Tserang-Donko Mipam
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, 610041, China.,Key Laboratory of Animal Science of State Ethnic Affairs Commission, Southwest Minzu University, Chengdu, 610041, China.,Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610041, China
| | - Jian Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, 610041, China.,Key Laboratory of Animal Science of State Ethnic Affairs Commission, Southwest Minzu University, Chengdu, 610041, China.,College of Animal and Verterinary Sciences, Southwest Minzu University, Chengdu, 610041, China
| | - Daoliang Lan
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Ministry of Education, Southwest Minzu University, Chengdu, 610041, China.,Key Laboratory of Animal Science of State Ethnic Affairs Commission, Southwest Minzu University, Chengdu, 610041, China.,College of Animal and Verterinary Sciences, Southwest Minzu University, Chengdu, 610041, China
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4
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The Potential of HTS Approaches for Accurate Genotyping in Grapevine ( Vitis vinifera L.). Genes (Basel) 2020; 11:genes11080917. [PMID: 32785184 PMCID: PMC7464945 DOI: 10.3390/genes11080917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 11/16/2022] Open
Abstract
The main challenge associated with genotyping based on conventional length polymorphisms is the cross-laboratory standardization of allele sizes. This step requires the inclusion of standards and manual sizing to avoid false results. Capillary electrophoresis (CE) approaches limit the information to the length polymorphism and do not allow the determination of a complete marker sequence. As an alternative, high-throughput sequencing (HTS) offers complete information regarding marker sequences and their flanking regions. In this work, we investigated the suitability of a semi-quantitative sequencing approach for microsatellite genotyping using Illumina paired-end technology. Twelve microsatellite loci that are well established for grapevine CE typing were analysed on 96 grapevine samples from six different countries. We redesigned primers to the length of the amplicon for short sequencing (~100 bp). The primer pair was flanked with a 10 bp overhang for the introduction of barcodes on both sides of the amplicon to enable high multiplexing. The highest data peaks were determined as simple sequence repeat (SSR) alleles and compared with the CE dataset based on 12 reference samples. The comparison showed that HTS SSR genotyping can successfully replace the CE system in further experiments. We believe that, with next-generation sequencing, genotyping can be improved in terms of its speed, accuracy, and price.
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Guo L, Yang Q, Yang JW, Zhang N, Liu BS, Zhu KC, Guo HY, Jiang SG, Zhang DC. MultiplexSSR: A pipeline for developing multiplex SSR-PCR assays from resequencing data. Ecol Evol 2020; 10:3055-3067. [PMID: 32211176 PMCID: PMC7083706 DOI: 10.1002/ece3.6121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 02/02/2020] [Accepted: 02/05/2020] [Indexed: 12/15/2022] Open
Abstract
Next-generation sequencing has greatly promoted the investigation of single nucleotide polymorphisms, while studies of simple sequence repeats are sharply decreasing. However, simple sequence repeats still present some advantages in conservation genetics. In this study, an end-to-end pipeline referred to as MultiplexSSR was established to develop multiplex PCR assays in batches with highly polymorphic simple sequence repeats for capillary platforms from resequencing data. The distribution of single sequence repeats in the genome, the error profiles of genotypes and allelotypes, and the increase in the allele length range depending on the number of individuals were investigated. A total of 98% of single sequence repeats presented lengths of less than 100 bp. The error rate of the genotyping and allelotyping of dimeric patterns was ten times higher than those for other patterns. The error rate of allelotyping was less than that of genotyping. The allele length range reached approximate saturation with 10 individuals. This pipeline uses allele numbers to select highly polymorphic loci, masks loci with variation, and applies in silico PCR to improve primer specificity. The application of the developed multiplex SSR-PCR assays validated the pipeline's robustness, showing higher polymorphism and stability for the developed simple sequence repeats and a lower cost for genotyping and providing low-depth resequencing data from less than a dozen individuals for the development of markers. This pipeline fills the gap between next-generation sequencing and multiplex SSR-PCR.
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Affiliation(s)
- Liang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
| | - Quan Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
- National Demonstration Center for Experimental Fisheries Science Education Shanghai Ocean University Shanghai China
| | - Jing-Wen Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
| | - Bao-Suo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
| | - Ke-Cheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
| | - Hua-Yang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
| | - Shi-Gui Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou China
- Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry Guangzhou China
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6
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Guo L, Yao H, Shepherd B, Sepulveda-Villet OJ, Zhang DC, Wang HP. Development of a Genomic Resource and Identification of Nucleotide Diversity of Yellow Perch by RAD Sequencing. Front Genet 2019; 10:992. [PMID: 31681426 PMCID: PMC6802114 DOI: 10.3389/fgene.2019.00992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 09/18/2019] [Indexed: 01/28/2023] Open
Affiliation(s)
- Liang Guo
- Aquatic Genetics and Breeding Laboratory, Ohio State University South Centers, Piketon, OH, United States.,Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institutes, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Hong Yao
- Aquatic Genetics and Breeding Laboratory, Ohio State University South Centers, Piketon, OH, United States
| | - Brian Shepherd
- USDA-ARS-School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | - Osvaldo J Sepulveda-Villet
- USDA-ARS-School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States.,School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institutes, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Han-Ping Wang
- Aquatic Genetics and Breeding Laboratory, Ohio State University South Centers, Piketon, OH, United States
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Yasodha R, Vasudeva R, Balakrishnan S, Sakthi AR, Abel N, Binai N, Rajashekar B, Bachpai VKW, Pillai C, Dev SA. Draft genome of a high value tropical timber tree, Teak (Tectona grandis L. f): insights into SSR diversity, phylogeny and conservation. DNA Res 2018; 25:409-419. [PMID: 29800113 PMCID: PMC6105116 DOI: 10.1093/dnares/dsy013] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/19/2018] [Indexed: 12/31/2022] Open
Abstract
Teak (Tectona grandis L. f.) is one of the precious bench mark tropical hardwood having qualities of durability, strength and visual pleasantries. Natural teak populations harbour a variety of characteristics that determine their economic, ecological and environmental importance. Sequencing of whole nuclear genome of teak provides a platform for functional analyses and development of genomic tools in applied tree improvement. A draft genome of 317 Mb was assembled at 151× coverage and annotated 36, 172 protein-coding genes. Approximately about 11.18% of the genome was repetitive. Microsatellites or simple sequence repeats (SSRs) are undoubtedly the most informative markers in genotyping, genetics and applied breeding applications. We generated 182,712 SSRs at the whole genome level, of which, 170,574 perfect SSRs were found; 16,252 perfect SSRs showed in silico polymorphisms across six genotypes suggesting their promising use in genetic conservation and tree improvement programmes. Genomic SSR markers developed in this study have high potential in advancing conservation and management of teak genetic resources. Phylogenetic studies confirmed the taxonomic position of the genus Tectona within the family Lamiaceae. Interestingly, estimation of divergence time inferred that the Miocene origin of the Tectona genus to be around 21.4508 million years ago.
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Affiliation(s)
- Ramasamy Yasodha
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Ramesh Vasudeva
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala, India
| | - Swathi Balakrishnan
- Department of Forest Biology and Tree Improvement, University of Agricultural Sciences, College of Forestry, Sirsi, Uttara Kannada, Karnataka, India
| | - Ambothi Rathnasamy Sakthi
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Nicodemus Abel
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Nagarajan Binai
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Balaji Rajashekar
- Genotypic Technology Private Limited, Bengaluru, Karnataka, India.,Institute of Computer Science, University of Tartu, Estonia
| | - Vijay Kumar Waman Bachpai
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Chandrasekhara Pillai
- Department of Forest Biology and Tree Improvement, University of Agricultural Sciences, College of Forestry, Sirsi, Uttara Kannada, Karnataka, India
| | - Suma Arun Dev
- Department of Forest Biology and Tree Improvement, University of Agricultural Sciences, College of Forestry, Sirsi, Uttara Kannada, Karnataka, India
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8
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Taheri S, Lee Abdullah T, Yusop MR, Hanafi MM, Sahebi M, Azizi P, Shamshiri RR. Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants. Molecules 2018; 23:E399. [PMID: 29438290 PMCID: PMC6017569 DOI: 10.3390/molecules23020399] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/11/2018] [Accepted: 01/13/2018] [Indexed: 11/17/2022] Open
Abstract
Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.
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Affiliation(s)
- Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Thohirah Lee Abdullah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohd Rafii Yusop
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohamed Musa Hanafi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Parisa Azizi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Redmond Ramin Shamshiri
- Smart Farming Technology Research Center, Department of Biological and Agricultural Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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Walker CJ, Miranda MA, O'Hern MJ, Blachly JS, Moyer CL, Ivanovich J, Kroll KW, Eisfeld AK, Sapp CE, Mutch DG, Cohn DE, Bundschuh R, Goodfellow PJ. MonoSeq Variant Caller Reveals Novel Mononucleotide Run Indel Mutations in Tumors with Defective DNA Mismatch Repair. Hum Mutat 2016; 37:1004-12. [PMID: 27346418 DOI: 10.1002/humu.23036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 06/07/2016] [Indexed: 01/23/2023]
Abstract
Next-generation sequencing has revolutionized cancer genetics, but accurately detecting mutations in repetitive DNA sequences, especially mononucleotide runs, remains a challenge. This is a particular concern for tumors with defective mismatch repair (MMR) that accumulate strand-slippage mutations. We developed MonoSeq to improve indel mutation detection in mononucleotide runs, and used MonoSeq to investigate strand-slippage mutations in endometrial cancers, a tumor type that has frequent loss of MMR. We performed extensive Sanger sequencing to validate both clonal and subclonal MonoSeq mutation calls. Eighty-one regions containing mononucleotide runs were sequenced in 540 primary endometrial cancers (223 with defective MMR). Our analyses revealed that the overall mutation rate in MMR-deficient tumors was 20-30-fold higher than in MMR-normal tumors. MonoSeq analysis identified several previously unreported mutations, including a novel hotspot in an A7 run in the terminal exon of ARID5B.The ARID5B indel mutations were seen in both MMR-deficient and MMR-normal tumors, suggesting biologic selection. The analysis of tumor mRNAs revealed the presence of mutant transcripts that could result in translation of neopeptides. Improved detection of mononucleotide run strand-slippage mutations has clear implications for comprehensive mutation detection in tumors with defective MMR. Indel frameshift mutations and the resultant antigenic peptides could help guide immunotherapy strategies.
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Affiliation(s)
- Christopher J Walker
- James Comprehensive Cancer Center and the Department of Obstetrics and Gynecology, Ohio State University, Columbus, OH
| | - Mario A Miranda
- James Comprehensive Cancer Center and the Department of Obstetrics and Gynecology, Ohio State University, Columbus, OH
| | - Matthew J O'Hern
- James Comprehensive Cancer Center and the Department of Obstetrics and Gynecology, Ohio State University, Columbus, OH
| | - James S Blachly
- James Comprehensive Cancer Center and the Department of Internal Medicine, Ohio State University, Columbus, Ohio
| | - Cassandra L Moyer
- James Comprehensive Cancer Center and the Department of Obstetrics and Gynecology, Ohio State University, Columbus, OH
| | - Jennifer Ivanovich
- Siteman Cancer Center and the Department of Surgery, Washington University School of Medicine, St. Louis, MO
| | - Karl W Kroll
- James Comprehensive Cancer Center, Ohio State University, Columbus, OH
| | | | - Caroline E Sapp
- James Comprehensive Cancer Center and the Department of Obstetrics and Gynecology, Ohio State University, Columbus, OH
| | - David G Mutch
- Siteman Cancer Center and the Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO
| | - David E Cohn
- James Comprehensive Cancer Center and the Department of Obstetrics and Gynecology, Ohio State University, Columbus, OH
| | - Ralf Bundschuh
- Department of Physics, Department of Chemistry and Biochemistry, Department of Internal Medicine, Ohio State University, Columbus, OH
| | - Paul J Goodfellow
- James Comprehensive Cancer Center and the Department of Obstetrics and Gynecology, Ohio State University, Columbus, OH.
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