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Lu M, Sun X, Zhao Y, Zheng L, Lin J, Tang C, Chao K, Chen Y, Li K, Zhou Y, Xiao J. Low cycle number multiplex PCR: A novel strategy for the construction of amplicon libraries for next-generation sequencing. Electrophoresis 2024. [PMID: 38533931 DOI: 10.1002/elps.202300160] [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: 03/14/2023] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 03/28/2024]
Abstract
Multiplex PCR is a critical step when preparing amplicon library for next-generation sequencing. However, there are several challenges related to multiplex PCR including poor uniformity, nonspecific amplification, and primer-dimers. To address these issues, we propose a novel solution strategy that involves using a low cycle number (<10 cycles) in multiplex PCR and then employing carrier DNAs and magnetic beads for the selection of targeted products. This technique improves the amplicon uniformity while also reducing primer-dimers and PCR artifacts. To evaluate our technique, we initially utilized 120 DNA fragments from mouse genome containing single nucleotide polymorphism (SNP) sites. Sequencing results demonstrated that with only 7 cycles of multiplex PCR, 95.8% of the targeted SNP sites were mapped, with a coverage of at least 1×. The average sequencing depth of all amplicons was 1705.79 ± 1205.30×; 87% of them reached a coverage depth that exceeded 0.2-fold of the average sequencing depth. Our method had a greater uniformity (87%) when compared to Hi-Plex PCR (53.3%). Furthermore, we validated our strategy by randomly selecting 90 primer pairs twice from the initial set of 120 primer-pairs. Next, we used the same protocol to prepare amplicon libraries. The two groups had an average sequencing depth of 1013.30 ± 585.57× and 219.10 ± 158.27×, respectively; over 84% of the amplicons had a sequencing depth that exceeded 0.2-fold of average depth. These results suggest that the use of a low cycle number in multiplex PCR is a cost-effective and efficient approach for the preparation of amplicon libraries.
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Affiliation(s)
- Meng Lu
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Xiuxiu Sun
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Yuxin Zhao
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Linlin Zheng
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Junjie Lin
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Chen Tang
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Kaiyue Chao
- Shanghai Biowing Biotechnology Application Co., Ltd, Shanghai, P. R. China
| | - Ye Chen
- Shanghai Biowing Biotechnology Application Co., Ltd, Shanghai, P. R. China
| | - Kai Li
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Yuxun Zhou
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
| | - Junhua Xiao
- College of Biological Science and Medical Engineering, Donghua University, Shanghai, P. R. China
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Ascari JP, Cazón LI, Rahnama M, Lamour K, Fernandes JMC, Farman ML, Ponte EMD. Pyricularia Are Mostly Host-Specialized with Limited Reciprocal Cross-Infection Between Wheat and Endemic Grasses in Minas Gerais, Brazil. PHYTOPATHOLOGY 2024; 114:226-240. [PMID: 37399001 DOI: 10.1094/phyto-01-23-0024-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Wheat blast, caused by Pyricularia oryzae Triticum (PoT), is an emerging threat to global wheat production. The current understanding of the population biology of the pathogen and epidemiology of the disease has been based on phylogenomic studies that compared the wheat blast pathogen with isolates collected from grasses that were invasive to Brazilian wheat fields. In this study, we performed a comprehensive sampling of blast lesions in wheat crops and endemic grasses found in and away from wheat fields in Minas Gerais. A total of 1,368 diseased samples were collected (976 leaves of wheat and grasses and 392 wheat heads), which yielded a working collection of 564 Pyricularia isolates. We show that, contrary to earlier implications, PoT was rarely found on endemic grasses, and, conversely, members of grass-adapted lineages were rarely found on wheat. Instead, most lineages were host-specialized, with constituent isolates usually grouping according to their host of origin. With regard to the dominant role proposed for signalgrass in wheat blast epidemiology, we found only one PoT member in 67 isolates collected from signalgrass grown away from wheat fields and only three members of Urochloa-adapted lineages among hundreds of isolates from wheat. Cross-inoculation assays on wheat and a signalgrass used in pastures (U. brizantha) suggested that the limited cross-infection observed in the field may be due to innate compatibility differences. Whether or not the observed level of cross-infection would be sufficient to provide an inoculum reservoir, or serve as a bridge between wheat growing regions, is questionable and, therefore, deserves further investigation.
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Affiliation(s)
- João P Ascari
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Luis I Cazón
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Mostafa Rahnama
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A
- Department of Biology, Tennessee Tech University, Cookeville, TN 38501, U.S.A
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, U.S.A
| | | | - Mark L Farman
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A
| | - Emerson M Del Ponte
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
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Ousmael K, Whetten RW, Xu J, Nielsen UB, Lamour K, Hansen OK. Identification and high-throughput genotyping of single nucleotide polymorphism markers in a non-model conifer (Abies nordmanniana (Steven) Spach). Sci Rep 2023; 13:22488. [PMID: 38110478 PMCID: PMC10728141 DOI: 10.1038/s41598-023-49462-x] [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: 05/01/2023] [Accepted: 12/08/2023] [Indexed: 12/20/2023] Open
Abstract
Single nucleotide polymorphism (SNP) markers are powerful tools for investigating population structures, linkage analysis, and genome-wide association studies, as well as for breeding and population management. The availability of SNP markers has been limited to the most commercially important timber species, primarily due to the cost of genome sequencing required for SNP discovery. In this study, a combination of reference-based and reference-free approaches were used to identify SNPs in Nordmann fir (Abies nordmanniana), a species previously lacking genomic sequence information. Using a combination of a genome assembly of the closely related Silver fir (Abies alba) species and a de novo assembly of low-copy regions of the Nordmann fir genome, we identified a high density of reliable SNPs. Reference-based approaches identified two million SNPs in common between the Silver fir genome and low-copy regions of Nordmann fir. A combination of one reference-free and two reference-based approaches identified 250 shared SNPs. A subset of 200 SNPs were used to genotype 342 individuals and thereby tested and validated in the context of identity analysis and/or clone identification. The tested SNPs successfully identified all ramets per clone and five mislabeled individuals via identity and genomic relatedness analysis. The identified SNPs will be used in ad hoc breeding of Nordmann fir in Denmark.
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Affiliation(s)
- Kedra Ousmael
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark.
| | - Ross W Whetten
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27606, USA
| | - Jing Xu
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
| | - Ulrik B Nielsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Ole K Hansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
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4
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Tandy P, Lamour K, Placidi de Bortoli C, Nagoshi R, Emrich SJ, Jurat-Fuentes JL. Screening for resistance alleles to Cry1 proteins through targeted sequencing in the native and invasive range of Spodoptera frugiperda (Lepidoptera: Noctuidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2023; 116:935-944. [PMID: 37311017 DOI: 10.1093/jee/toad061] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/02/2023] [Accepted: 03/30/2023] [Indexed: 06/15/2023]
Abstract
The fall armyworm, Spodoptera frugiperda (J. E. Smith), is a highly polyphagous pest native to the tropical Americas that has recently spread to become a global super-pest threatening food and fiber production. Transgenic crops producing insecticidal Cry and Vip3Aa proteins from Bacillus thuringiensis (Bt) are used for control of this pest in its native range. The evolution of practical resistance represents the greatest threat to sustainability of this technology and its potential efficacy in the S. frugiperda invasive range. Monitoring for resistance is vital to management approaches delaying S. frugiperda resistance to Bt crops. DNA-based resistance screening provides higher sensitivity and cost-effectiveness than currently used bioassay-based monitoring. So far, practical S. frugiperda resistance to Bt corn-producing Cry1F has been genetically linked to mutations in the SfABCC2 gene, providing a model to develop and test monitoring tools. In this study, we performed targeted SfABCC2 sequencing followed by Sanger sequencing to confirm the detection of known and candidate resistance alleles to Cry1F corn in field-collected S. frugiperda from continental USA, Puerto Rico, Africa (Ghana, Togo, and South Africa), and Southeast Asia (Myanmar). Results confirm that the distribution of a previously characterized resistance allele (SfABCC2mut) is limited to Puerto Rico and identify 2 new candidate SfABCC2 alleles for resistance to Cry1F, one of them potentially spreading along the S. frugiperda migratory route in North America. No candidate resistance alleles were found in samples from the invasive S. frugiperda range. These results provide support for the potential use of targeted sequencing in Bt resistance monitoring programs.
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Affiliation(s)
- Peter Tandy
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | | | - Rodney Nagoshi
- Center for Medical, Agricultural and Veterinary Entomology (CMAVE), United States Department of Agriculture-Agricultural Research Service, Gainesville, FL 32608, USA
| | - Scott J Emrich
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN 37996, USA
| | - Juan Luis Jurat-Fuentes
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
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Shumate S, Haylett M, Nelson B, Young N, Lamour K, Walsh D, Bradford B, Clements J. Using targeted sequencing and TaqMan approaches to detect acaricide (bifenthrin, bifenazate, and etoxazole) resistance associated SNPs in Tetranychus urticae collected from peppermint fields and hop yards. PLoS One 2023; 18:e0283211. [PMID: 36952542 PMCID: PMC10035822 DOI: 10.1371/journal.pone.0283211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 03/03/2023] [Indexed: 03/25/2023] Open
Abstract
Tetranychus urticae (Koch) is an economically important pest of many agricultural commodities world-wide. Multiple acaricides, including bifenazate, bifenthrin, and extoxazole, are currently registered to control T. urticae. However, populations of T. urticae in many different growing regions have developed acaricide resistance through multiple mechanisms. Within T. urticae, single nucleotide polymorphisms (SNPs) have been documented in different genes which are associated with acaricide resistance phenotypes. The detection of these mutations through TaqMan qPCR has been suggested as a practical, quick, and reliable tool to inform agricultural producers of acaricide resistance phenotypes present within their fields and have potential utility for making appropriate acaricide application and integrated pest management decisions. Within this investigation we examined the use of a TaqMan qPCR-based approach to determine genotypes which have been previously associated with acaricide resistance in field-collected populations of T. urticae from peppermint fields and hop yards in the Pacific Northwest of the United States and confirmed the results with a multiplex targeted sequencing. The results suggest that a TaqMan qPCR approach accurately genotypes T. urticae populations for SNPs that have been linked to Bifenazate, Bifenthrin, and Etoxazole resistance. The results also demonstrated that different populations of mites in Washington and Idaho displayed varying frequencies of the examined SNPs. While we were able to detect the SNPs associated with the examined acaricides, the mutation G126S was not an appropriate or accurate indicator for bifenazate resistance.
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Affiliation(s)
- Silas Shumate
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Parma, Idaho, United States of America
| | - Maggie Haylett
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Parma, Idaho, United States of America
| | - Brenda Nelson
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Parma, Idaho, United States of America
| | - Nicole Young
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Parma, Idaho, United States of America
| | - Kurt Lamour
- Department of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Doug Walsh
- Department of Entomology, Washington State University, Prosser, Washington, United States of America
| | - Benjamin Bradford
- Department of Entomology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Justin Clements
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Parma, Idaho, United States of America
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Costa LC, Atha B, Hu X, Lamour K, Yang Y, O’Connell M, McFarland C, Foster JA, Hurtado-Gonzales OP. High-throughput detection of a large set of viruses and viroids of pome and stone fruit trees by multiplex PCR-based amplicon sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:1072768. [PMID: 36578329 PMCID: PMC9791224 DOI: 10.3389/fpls.2022.1072768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
A comprehensive diagnostic method of known plant viruses and viroids is necessary to provide an accurate phytosanitary status of fruit trees. However, most widely used detection methods have a small limit on either the number of targeted viruses/viroids or the number of samples to be evaluated at a time, hampering the ability to rapidly scale up the test capacity. Here we report that by combining the power of high multiplexing PCR (499 primer pairs) of small amplicons (120-135bp), targeting 27 viruses and 7 viroids of fruit trees, followed by a single high-throughput sequencing (HTS) run, we accurately diagnosed the viruses and viroids on as many as 123 pome and stone fruit tree samples. We compared the accuracy, sensitivity, and reproducibility of this approach and contrast it with other detection methods including HTS of total RNA (RNA-Seq) and individual RT-qPCR for every fruit tree virus or viroid under the study. We argue that this robust and high-throughput cost-effective diagnostic tool will enhance the viral/viroid knowledge of fruit trees while increasing the capacity for large scale diagnostics. This approach can also be adopted for the detection of multiple viruses and viroids in other crops.
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Affiliation(s)
- Larissa Carvalho Costa
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Benjamin Atha
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Xiaojun Hu
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
| | - Yu Yang
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Mary O’Connell
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Clint McFarland
- Plant Protection and Quarantine - Field Operations, Animal and Plant Health Inspection Service, United States Department of Agriculture, Raleigh, NC, United States
| | - Joseph A. Foster
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Oscar P. Hurtado-Gonzales
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
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7
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Development and application of multiplex targeted-sequencing approaches to identify Phytophthora species associated with root rot and wilting complex of red raspberry. PLoS One 2022; 17:e0275384. [PMID: 36417394 PMCID: PMC9683591 DOI: 10.1371/journal.pone.0275384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/15/2022] [Indexed: 11/26/2022] Open
Abstract
Phytophthora species are primary causal agents of raspberry root rot and wilting complex (RRWC), a disease complex that is of major concern to raspberry producers worldwide. Accurate identification of the causal agents is a first step for effective disease management. Advancements in molecular diagnostics can facilitate the detection of multiple pathogen species associated with this disease complex. We developed multiplex targeted-sequencing methods using degenerate primers for heat shock protein 90, elongation factor 1α and β-tubulin genes to identify Phytophthora species causing RRWC. One hundred and twenty-eight isolates recovered during 2018 to 2020 from diverse fields in major raspberry growing areas of British Columbia (BC) were sequenced and identified by comparing with known reference sequences of 142 Phytophthora species, 111 Pythium species, and nine Phytopythium species in the NCBI database. This multiplex targeted-sequencing method was highly specific and identified two species of Phytophthora associated with RRWC. These were P. rubi (85% of isolates) and P. gonapodyides (15% of isolates). Phytophthora rubi was predominantly isolated from the cultivars 'Chemainus' (51%), 'Rudi' (27%) and 'Meeker' (15%), whereas P. gonapodyides was predominately isolated from the moderately resistant cultivar 'Cascade Bounty'. Pathogenicity studies on intact plants and detached leaves confirmed that P. rubi and P. gonapodyides can cause symptoms of RRWC on raspberry, thus fulfilling Koch's postulates. To our knowledge, this is the first report of P. gonapodyides as a causal agent of RRWC on raspberry in BC. This study provides novel insights into the identification and species composition of Phytophthora associated with RRWC in raspberry production systems.
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de Jong TV, Kim P, Guryev V, Mulligan MK, Williams RW, Redei EE, Chen H. Whole genome sequencing of nearly isogenic WMI and WLI inbred rats identifies genes potentially involved in depression and stress reactivity. Sci Rep 2021; 11:14774. [PMID: 34285244 PMCID: PMC8292482 DOI: 10.1038/s41598-021-92993-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/17/2021] [Indexed: 02/06/2023] Open
Abstract
The WMI and WLI inbred rats were generated from the stress-prone, and not yet fully inbred, Wistar Kyoto (WKY) strain. These were selected using bi-directional selection for immobility in the forced swim test and were then sib-mated for over 38 generations. Despite the low level of genetic diversity among WKY progenitors, the WMI substrain is significantly more vulnerable to stress relative to the counter-selected WLI strain. Here we quantify numbers and classes of genomic sequence variants distinguishing these substrains with the long term goal of uncovering functional and behavioral polymorphism that modulate sensitivity to stress and depression-like phenotypes. DNA from WLI and WMI was sequenced using Illumina xTen, IonTorrent, and 10X Chromium linked-read platforms to obtain a combined coverage of ~ 100X for each strain. We identified 4,296 high quality homozygous SNPs and indels between the WMI and WLI. We detected high impact variants in genes previously implicated in depression (e.g. Gnat2), depression-like behavior (e.g. Prlr, Nlrp1a), other psychiatric disease (e.g. Pou6f2, Kdm5a, Reep3, Wdfy3), and responses to psychological stressors (e.g. Pigr). High coverage sequencing data confirm that the two substrains are nearly coisogenic. Nonetheless, the small number of sequence variants contributes to numerous well characterized differences including depression-like behavior, stress reactivity, and addiction related phenotypes. These selected substrains are an ideal resource for forward and reverse genetic studies using a reduced complexity cross.
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Affiliation(s)
| | - Panjun Kim
- University of Tennessee Health Science Center, Memphis, TN, USA
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, Groningen, The Netherlands
| | | | | | - Eva E Redei
- Northwestern University - Chicago, Chicago, IL, USA
| | - Hao Chen
- University of Tennessee Health Science Center, Memphis, TN, USA.
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9
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Schlum K, Lamour K, Tandy P, Emrich SJ, de Bortoli CP, Rao T, Viteri Dillon DM, Linares-Ramirez AM, Jurat-Fuentes JL. Genetic Screening to Identify Candidate Resistance Alleles to Cry1F Corn in Fall Armyworm Using Targeted Sequencing. INSECTS 2021; 12:insects12070618. [PMID: 34357278 PMCID: PMC8303720 DOI: 10.3390/insects12070618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Monitoring of resistance alleles is critical to the sustainability of transgenic crops producing insecticidal Cry proteins. Highly sensitive and cost-effective DNA-based methods are needed to improve current bioassay-based resistance screening. Our goal was to evaluate the use of targeted sequencing in detecting known and novel candidate resistance alleles to Cry proteins. As a model, we used field-collected fall armyworm (Spodoptera frugiperda) from Puerto Rico, the first location reporting continued practical field-evolved S. frugiperda resistance to corn producing the Cry1F insecticidal protein, and sequenced the SfABCC2 gene previously identified as critical to Cry1F toxicity. Targeted sequencing of SfABCC2 detected a previously reported Cry1F resistance allele and mutations originally identified in populations from Brazil. Importantly, targeted sequencing also identified nonsynonymous and frameshift mutations as novel candidate resistance alleles. These results advocate for the use of targeted sequencing in screening for resistance alleles to Cry proteins and support potential gene flow, including resistance alleles, between S. frugiperda from Brazil and the Caribbean. Abstract Evolution of practical resistance is the main threat to the sustainability of transgenic crops producing insecticidal proteins from Bacillus thuringiensis (Bt crops). Monitoring of resistance to Cry and Vip3A proteins produced by Bt crops is critical to mitigate the development of resistance. Currently, Cry/Vip3A resistance allele monitoring is based on bioassays with larvae from inbreeding field-collected moths. As an alternative, DNA-based monitoring tools should increase sensitivity and reduce overall costs compared to bioassay-based screening methods. Here, we evaluated targeted sequencing as a method allowing detection of known and novel candidate resistance alleles to Cry proteins. As a model, we sequenced a Cry1F receptor gene (SfABCC2) in fall armyworm (Spodoptera frugiperda) moths from Puerto Rico, a location reporting continued practical field resistance to Cry1F-producing corn. Targeted sequencing detected a previously reported Cry1F resistance allele (SfABCC2mut), in addition to a resistance allele originally described in S. frugiperda populations from Brazil. Moreover, targeted sequencing detected mutations in SfABCC2 as novel candidate resistance alleles. These results support further development of targeted sequencing for monitoring resistance to Bt crops and provide unexpected evidence for common resistance alleles in S. frugiperda from Brazil and Puerto Rico.
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Affiliation(s)
- Katrina Schlum
- Genome Science and Technology Graduate Program, University of Tennessee, Knoxville, TN 37996, USA; (K.S.); (K.L.); (S.J.E.)
| | - Kurt Lamour
- Genome Science and Technology Graduate Program, University of Tennessee, Knoxville, TN 37996, USA; (K.S.); (K.L.); (S.J.E.)
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (P.T.); (C.P.d.B.); (T.R.)
| | - Peter Tandy
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (P.T.); (C.P.d.B.); (T.R.)
| | - Scott J. Emrich
- Genome Science and Technology Graduate Program, University of Tennessee, Knoxville, TN 37996, USA; (K.S.); (K.L.); (S.J.E.)
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN 37996, USA
| | - Caroline Placidi de Bortoli
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (P.T.); (C.P.d.B.); (T.R.)
| | - Tejas Rao
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (P.T.); (C.P.d.B.); (T.R.)
| | - Diego M. Viteri Dillon
- Isabela Research Substation, Department of Agro-Environmental Sciences, University of Puerto Rico, Isabela, PR 00662, USA;
| | - Angela M. Linares-Ramirez
- Lajas Research Substation, Department of Agro-Environmental Sciences, University of Puerto Rico, Lajas, PR 00667, USA;
| | - Juan Luis Jurat-Fuentes
- Genome Science and Technology Graduate Program, University of Tennessee, Knoxville, TN 37996, USA; (K.S.); (K.L.); (S.J.E.)
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA; (P.T.); (C.P.d.B.); (T.R.)
- Correspondence: ; Tel.: +1-(865)-974-5931
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Clements J, Lamour K, Frost K, Dwyer J, Huseth A, Groves RL. Targeted RNA sequencing reveals differential patterns of transcript expression in geographically discrete, insecticide resistant populations of Leptinotarsa decemlineata. PEST MANAGEMENT SCIENCE 2021; 77:3436-3444. [PMID: 33817958 PMCID: PMC8252485 DOI: 10.1002/ps.6393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/23/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The Colorado potato beetle (Leptinotarsa decemlineata Say) is a major agricultural pest of commercial potatoes, partially due to its ability to rapidly develop resistance to multiple insecticide modes of action. Patterns of L. decemlineata insecticide resistance in the contiguous United States have been linked to geographic location and regional management practices. Several previous studies have classified enzymes that are overexpressed following L. decemlineata exposure to commercial pesticides, many of which have been linked to xenobiotic metabolism. Studies have further associated geographic disparities in resistance patterns to cross-resistance driven by fungicide exposure in the East Coast and Midwest. RESULTS In this study, our objective was to investigate transcript expression of 38 previously classified detoxification enzymes induced by imidacloprid (an insecticide) and chlorothalonil (a fungicide) within five discrete populations of L. decemlineata obtained from areas in the USA representing eastern, midwestern and western production regions. We found unique patterns of transcript expression in different geographic locations, including overexpression of transcripts related to insecticide metabolism within insecticide-resistant populations. CONCLUSION The results suggest the genetic response of these populations may be partially linked to geographic location and corresponding management practices. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Justin Clements
- Department of Entomology, Plant Pathology, and NematologyUniversity of IdahoParmaIDUSA
| | - Kurt Lamour
- Department of Genome Science and TechnologyUniversity of TennesseeKnoxvilleTNUSA
| | - Kenneth Frost
- Department of Botany and Plant PathologyOregon States UniversityCorvallisORUSA
| | - James Dwyer
- Cooperative ExtensionUniversity of MaineOronoMEUSA
| | - Anders Huseth
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
| | - Russell L Groves
- Department of EntomologyUniversity of Wisconsin‐MadisonMadisonWIUSA
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Samils B, Andersson B, Edin E, Elfstrand M, Rönneburg T, Bucur D, Hutton F, Heick TM, Hellin P, Kildea S. Development of a PacBio Long-Read Sequencing Assay for High Throughput Detection of Fungicide Resistance in Zymoseptoria tritici. Front Microbiol 2021; 12:692845. [PMID: 34234765 PMCID: PMC8256687 DOI: 10.3389/fmicb.2021.692845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/26/2021] [Indexed: 11/13/2022] Open
Abstract
Fungicide resistance has become a challenging problem in management of Septoria tritici blotch (STB), caused by Zymoseptoria tritici, the most destructive disease of winter wheat throughout western and northern Europe. To ensure the continued effectiveness of those fungicides currently used, it is essential to monitor the development and spread of such resistance in field populations of the pathogen. Since resistance to the key families of fungicides used for STB control (demethyalation inhibitors or azoles, succinate dehydrogenase inhibitors or SDHIs and Quinone outside Inhibitors or QoIs) is conferred through target-site mutations, the potential exists to monitor resistance through the molecular detection of alterations in the target site genes. As more efficient fungicides were developed and applied, the pathogen has continuously adapted through accumulating multiple target-site alterations. In order to accurately monitor these changes in field populations, it is therefore becoming increasingly important to completely sequence the targeted genes. Here we report the development of a PacBio assay that facilitates the multiplex amplification and long-read sequencing of the target gene(s) for the azole (CYP51), SDHI (Sdh B, C, and D), and QoI (cytochrome b) fungicides. The assay was developed and optimised using three Irish Z. tritici collections established in spring 2017, which capture the range of fungicide resistance present in modern European populations of Z. tritici. The sequences obtained through the PacBio assay were validated using traditional Sanger sequencing and in vitro sensitivity screenings. To further exploit the long-read and high throughput potential of PacBio sequencing, an additional nine housekeeping genes (act, BTUB, cal, cyp, EF1, GAPDH, hsp80-1, PKC, TFC1) were sequenced and used to provide comprehensive Z. tritici strain genotyping.
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Affiliation(s)
- Berit Samils
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Björn Andersson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Eva Edin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tilman Rönneburg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Diana Bucur
- TEAGASC, The Agriculture and Food Development Authority, Carlow, Ireland
| | - Fiona Hutton
- TEAGASC, The Agriculture and Food Development Authority, Carlow, Ireland
| | - Thies M. Heick
- Department of Agroecology, Aarhus University, Aarhus, Denmark
| | - Pierre Hellin
- Plant and Forest Health Unit, Walloon Agricultural Research Center, Gembloux, Belgium
| | - Steven Kildea
- TEAGASC, The Agriculture and Food Development Authority, Carlow, Ireland
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12
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Shaffer CM, Michener DC, Vlasava NB, Chotkowski H, Lamour K, Stainton D, Tzanetakis IE. The population structure of the secovirid lychnis mottle virus based on the RNA2 coding sequences. Virus Res 2021; 303:198468. [PMID: 34090963 DOI: 10.1016/j.virusres.2021.198468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 11/18/2022]
Abstract
Lychnis mottle virus (LycMoV), family Secoviridae, is one of several viruses recently detected in peony. Given the high prevalence of the virus in the more than 300 samples tested, the population structure of the virus was studied using 48 isolates representing at least 20 cultivars and collected from major producing and propagating states in the United States. The homogeneity of the United States population, based on data from the RNA2 coding region, along with phylogenetic analyses of all publicly available sequences point to the dissemination of the virus through propagation material rather that active vector-mediated transmission.
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Affiliation(s)
- Cullen M Shaffer
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - David C Michener
- University of Michigan Matthaei Botanical Gardens & Nichols Arboretum, Ann Arbor, MI 48105
| | | | | | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996
| | - Daisy Stainton
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701.
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13
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Mihelic R, Winter H, Powers JB, Das S, Lamour K, Campagna SR, Voy BH. Genes controlling polyunsaturated fatty acid synthesis are developmentally regulated in broiler chicks. Br Poult Sci 2020; 61:508-517. [PMID: 32316746 DOI: 10.1080/00071668.2020.1759788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
1. The objective of this study was to characterise the regulation of the pathways that synthesise long-chain polyunsaturated fatty acids (PUFA) on developing adipose deposits in broiler embryos and chicks. Subcutaneous adipose depots were harvested from embryos and embryonic d E13, E15 and E17. Subcutaneous, abdominal and crop (neck) adipose, as well as liver, were collected at 7 and 14 d post-hatch. 2. Targeted RNA sequencing was used to quantify expression of 6 elongation of very long-chain fatty acid (ELOVL) genes, two isoforms of stearoyl-CoA desaturase (SCD and SCD5), and three fatty acid desaturases (FADS1, FADS2, and FADS6) in each depot and in the liver. Expression levels of marker genes for fatty acid oxidation and adipogenesis (peroxisome proliferator-activated receptor gamma (PPARG)) were quantified. Fatty acid composition of subcutaneous adipose was analysed using gas chromatograph-mass spectrometry (GC/MS). 3. Genes in the PUFA synthetic pathway were differentially expressed across developmental ages and between depots. These include elongase and desaturase genes, that have not previously been characterised in chicken. Correlation analyses identified subsets of co-regulated genes and fatty acids and highlighted relationships that may influence adipose metabolism and development. 4. It was concluded that PUFA synthesis is an active and dynamically regulated pathway in developing adipose deposits in the broiler chick. These data highlighted potential novel roles for specific elongase and desaturase genes in adipose deposition and metabolism.
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Affiliation(s)
- R Mihelic
- Department of Animal Science, University of Tennessee , Knoxville, TN, USA
| | - H Winter
- Department of Animal Science, University of Tennessee , Knoxville, TN, USA
| | - J B Powers
- Department of Chemistry, University of Tennessee , Knoxville, TN, USA.,Biological and Small Molecule Mass Spectrometry Core, University of Tennessee , Knoxville, TN, USA
| | - S Das
- Department of Animal Science, University of Tennessee , Knoxville, TN, USA
| | - K Lamour
- Department of Entomology and Plant Pathology, University of Tennessee , Knoxville, TN, USA
| | - S R Campagna
- Department of Chemistry, University of Tennessee , Knoxville, TN, USA.,Biological and Small Molecule Mass Spectrometry Core, University of Tennessee , Knoxville, TN, USA
| | - B H Voy
- Department of Animal Science, University of Tennessee , Knoxville, TN, USA
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14
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Miao X, Li B, Shen Y, Yu H, Zhu G, Liang C, Fu X, Wang C, Li S, Zhang B. Development and Verification of an Economical Method of Custom Target Library Construction. ACS OMEGA 2020; 5:13087-13095. [PMID: 32548494 PMCID: PMC7288555 DOI: 10.1021/acsomega.0c01014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/21/2020] [Indexed: 05/13/2023]
Abstract
Although technological advances have greatly reduced the cost of DNA sequencing, sample preparation time and reagent costs remain the limiting factors for many studies. Based on low-cost targeted amplification, we developed an economical method for custom target library construction based on DNA nanoball (DNB) technology and two-step polymerase chain reaction (PCR). Here, we refer to this method as the two-step PCR, which was compared to traditional multiplex PCR methods in three aspects, data quality, efficiency, and specificity to humans. The results confirmed that two-step PCR reduces to finishing 128 sequencing libraries in only 2 h 24 min 59 s of the total PCR time and at a data utilization rate of 0.44 at a cost of approximately $1.70 per sample for targeted sequencing via the two-step PCR. The replacement of traditional multiplex PCR methods with this strategy makes the sample preparation process before sequencing relatively more cost-effective and further reduces the cost of next-generation sequencing (NGS). This method may also be free from the interference of other species and the limitations of sample type and DNA content. These findings reveal possibilities for broad applications of this approach in forensic research.
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Affiliation(s)
- Xinyao Miao
- School
of Forensic Sciences, Xi’an Jiaotong
University, 710049 Xi’an, P. R. China
| | - Bowen Li
- School
of Life Sciences, Sichuan University, 610207 Chengdu, P. R. China
| | - Yuesheng Shen
- School
of Life Sciences, Northwest University, 710069 Xi’an, P. R. China
| | - Huiyun Yu
- School
of Life Sciences, Northwest A&F University, 712100 Yangling, P. R. China
| | - Guoqiang Zhu
- Key
Laboratory of Bio-Resources and Eco-Environment of Ministry of Education,
College of Life Sciences, Sichuan University, 610065 Chengdu, P. R. China
| | - Chen Liang
- School of
Mechanical Engineering, Xi’an Jiaotong
University, 710049 Xi’an, P. R. China
| | - Xiao Fu
- The
Beijing Genomics Institute (BGI)—Tianjin, 301700 Tianjin, P. R. China
| | - Chu Wang
- School
of Life Sciences, Xiamen Medical College, 361023 Xiamen, P. R. China
| | - Shengbin Li
- School
of Forensic Sciences, Xi’an Jiaotong
University, 710049 Xi’an, P. R. China
| | - Bao Zhang
- School
of Forensic Sciences, Xi’an Jiaotong
University, 710049 Xi’an, P. R. China
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15
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Katsiani A, Stainton D, Lamour K, Tzanetakis IE. The population structure of Rose rosette virus in the USA. J Gen Virol 2020; 101:676-684. [PMID: 32375952 DOI: 10.1099/jgv.0.001418] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rose rosette virus (RRV) (genus Emaravirus) is the causal agent of the homonymous disease, the most destructive malady of roses in the USA. Although the importance of the disease is recognized, little sequence information and no full genomes are available for RRV, a multi-segmented RNA virus. To better understand the population structure of the virus we implemented a Hi-Plex PCR amplicon high-throughput sequencing approach to sequence all 7 segments and to quantify polymorphisms in 91 RRV isolates collected from 16 states in the USA. Analysis revealed insertion/deletion (indel) polymorphisms primarily in the 5' and 3' non-coding, but also within coding regions, including some resulting in changes of protein length. Phylogenetic analysis showed little geographical structuring, suggesting that topography does not have a strong influence on virus evolution. Overall, the virus populations were homogeneous, possibly because of regular movement of plants, the recent emergence of RRV and/or because the virus is under strong purification selection to preserve its integrity and biological functions.
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Affiliation(s)
- Asimina Katsiani
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville AR 72701, USA
| | - Daisy Stainton
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville AR 72701, USA
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville AR 72701, USA
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16
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Technological advances and computational approaches for alternative splicing analysis in single cells. Comput Struct Biotechnol J 2020; 18:332-343. [PMID: 32099593 PMCID: PMC7033300 DOI: 10.1016/j.csbj.2020.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 01/26/2020] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing of RNAs generates isoform diversity, resulting in different proteins that are necessary for maintaining cellular function and identity. The discovery of alternative splicing has been revolutionized by next-generation transcriptomic sequencing mainly using bulk RNA-sequencing, which has unravelled RNA splicing and mis-splicing of normal cells under steady-state and stress conditions. Single-cell RNA-sequencing studies have focused on gene-level expression analysis and revealed gene expression signatures distinguishable between different cellular types. Single-cell alternative splicing is an emerging area of research with the promise to reveal transcriptomic dynamics invisible to bulk- and gene-level analysis. In this review, we will discuss the technological advances for single-cell alternative splicing analysis, computational strategies for isoform detection and quantitation in single cells, and current applications of single-cell alternative splicing analysis and its potential future contributions to personalized medicine.
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17
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Kechin AA, Dymova MA, Tishkin AA, Grushin SP, Dashkovskiy PK, Filipenko ML. Targeted Sequencing for Studying Economically Useful Traits and Phylogenetic Diversity of Ancient Sheep. RUSS J GENET+ 2020. [DOI: 10.1134/s102279541912007x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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18
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Alburaki M, Karim S, Lamour K, Adamczyk J, Stewart SD. RNA-seq reveals disruption of gene regulation when honey bees are caged and deprived of hive conditions. ACTA ACUST UNITED AC 2019; 222:jeb.207761. [PMID: 31413101 DOI: 10.1242/jeb.207761] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/06/2019] [Indexed: 11/20/2022]
Abstract
In this study, we present phenotypic and genetic data characterizing the impact of imidacloprid and caging stress on honey bee Apis mellifera physiological responses and regulation of 45 genes using targeted-RNA seq. The term 'caging stress' characterizes the effects of depriving honey bees of all hive aspects and conditions. Two cohorts of 1 day old sister bees were subjected to different conditions. One cohort was caged and fed different imidacloprid-tainted sugar solutions and the second was marked and introduced back to its natal hive. Physiological bee parameters and diet behavior were monitored daily for caged bees over several weeks. Bee samples from both cohorts were sampled weekly for RNA sequencing and oxidative stress analyses. Imidacloprid induced significant protein damage and post-ingestive aversion responses in caged bees, leading to lower tainted syrup consumption and higher water intake compared with the controls. No differentially expressed genes were observed among caged bees in regards to imidacloprid treatment. However, significant upregulation in antioxidant genes was recorded in caged bees as compared with hive bees, with overwhelming downregulation in all gene categories in caged bees at week 4. We identified two sets of genes that were constantly regulated in caged bees, including Rsod with unknown function in insects that could potentially characterize caging stress in honey bees.
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Affiliation(s)
| | - Shahid Karim
- The University of Southern Mississippi, Department of Cell and Molecular Biology Sciences, Hattiesburg, MS 39406, USA
| | - Kurt Lamour
- The University of Tennessee, Entomology and Plant Pathology Department, Knoxville, TN 37996, USA
| | - John Adamczyk
- USDA-ARS Thad Cochran Horticulture Laboratory, Poplarville, MS 39470, USA
| | - Scott D Stewart
- The University of Tennessee, Department of Entomology and Plant Pathology, West Tennessee Research and Education Center, Jackson, TN 38301, USA
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19
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Hi-Plex2: a simple and robust approach to targeted sequencing-based genetic screening. Biotechniques 2019; 67:118-122. [PMID: 31267764 DOI: 10.2144/btn-2019-0026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We have previously reported Hi-Plex, a multiplex PCR methodology for building targeted DNA sequencing libraries that offers a low-cost protocol compatible with high-throughput processing. Here, we detail an improved protocol, Hi-Plex2, that more effectively enables the robust construction of small-to-medium panel-size libraries while maintaining low cost, simplicity and accuracy benefits of the Hi-Plex platform. Hi-Plex2 was applied to three panels, comprising 291, 740 and 1193 amplicons, targeting genes associated with risk for breast and/or colon cancer. We show substantial reduction of off-target amplification to enable library construction for small-to-medium-sized design panels not possible using the previous Hi-Plex chemistry.
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20
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Grolleman JE, de Voer RM, Elsayed FA, Nielsen M, Weren RDA, Palles C, Ligtenberg MJL, Vos JR, Ten Broeke SW, de Miranda NFCC, Kuiper RA, Kamping EJ, Jansen EAM, Vink-Börger ME, Popp I, Lang A, Spier I, Hüneburg R, James PA, Li N, Staninova M, Lindsay H, Cockburn D, Spasic-Boskovic O, Clendenning M, Sweet K, Capellá G, Sjursen W, Høberg-Vetti H, Jongmans MC, Neveling K, Geurts van Kessel A, Morreau H, Hes FJ, Sijmons RH, Schackert HK, Ruiz-Ponte C, Dymerska D, Lubinski J, Rivera B, Foulkes WD, Tomlinson IP, Valle L, Buchanan DD, Kenwrick S, Adlard J, Dimovski AJ, Campbell IG, Aretz S, Schindler D, van Wezel T, Hoogerbrugge N, Kuiper RP. Mutational Signature Analysis Reveals NTHL1 Deficiency to Cause a Multi-tumor Phenotype. Cancer Cell 2019; 35:256-266.e5. [PMID: 30753826 DOI: 10.1016/j.ccell.2018.12.011] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/17/2018] [Accepted: 12/26/2018] [Indexed: 01/01/2023]
Abstract
Biallelic germline mutations affecting NTHL1 predispose carriers to adenomatous polyposis and colorectal cancer, but the complete phenotype is unknown. We describe 29 individuals carrying biallelic germline NTHL1 mutations from 17 families, of which 26 developed one (n = 10) or multiple (n = 16) malignancies in 14 different tissues. An unexpected high breast cancer incidence was observed in female carriers (60%). Mutational signature analysis of 14 tumors from 7 organs revealed that NTHL1 deficiency underlies the main mutational process in all but one of the tumors (93%). These results reveal NTHL1 as a multi-tumor predisposition gene with a high lifetime risk for extracolonic cancers and a typical mutational signature observed across tumor types, which can assist in the recognition of this syndrome.
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Affiliation(s)
- Judith E Grolleman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Richarda M de Voer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
| | - Fadwa A Elsayed
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Robbert D A Weren
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Claire Palles
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Janet R Vos
- Department of Human Genetics, Radboud Institute for Health Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Sanne W Ten Broeke
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Renske A Kuiper
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Erik A M Jansen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - M Elisa Vink-Börger
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Isabell Popp
- Department of Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Alois Lang
- Vorarlberg Cancer Registry, Agency for Preventive and Social Medicine, Bregenz 6900, Austria
| | - Isabel Spier
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany
| | - Robert Hüneburg
- Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany; Department of Internal Medicine I, University of Bonn, 53127 Bonn, Germany
| | - Paul A James
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbournem, VIC 3000, Australia
| | - Na Li
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Marija Staninova
- Center for Biomolecular Pharmaceutical Analyzes, UKIM Faculty of Pharmacy, 1000 Skopje, Republic of Macedonia
| | - Helen Lindsay
- Leeds Genetics Laboratory, Leeds Teaching Hospitals NHS Trust, Leeds LS9 7TF, UK
| | - David Cockburn
- Leeds Genetics Laboratory, Leeds Teaching Hospitals NHS Trust, Leeds LS9 7TF, UK
| | | | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Kevin Sweet
- Division of Human Genetics, Ohio State University Medical Centre, Columbus, OH 43221, USA
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Wenche Sjursen
- Department of Medical Genetics, St Olavs University Hospital, 7030 Trondheim, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Hildegunn Høberg-Vetti
- Western Norway Familial Cancer Center, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Marjolijn C Jongmans
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Ad Geurts van Kessel
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Rolf H Sijmons
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Hans K Schackert
- Department of Surgical Research, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Clara Ruiz-Ponte
- Fundación Pública Galega de Medicina Xenómica (FPGMX)-SERGAS, Grupo de Medicina Xenómica-USC, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Galicia 15706, Spain
| | - Dagmara Dymerska
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Jan Lubinski
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Barbara Rivera
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 0G4, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Ian P Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Oxford National Institute for Health Research (NIHR) Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC 3010, Australia; Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC 3010, Australia
| | - Sue Kenwrick
- East Anglian Medical Genetics Service, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Julian Adlard
- Yorkshire Regional Genetics Service and University of Leeds, Leeds LS7 4SA, UK
| | - Aleksandar J Dimovski
- Center for Biomolecular Pharmaceutical Analyzes, UKIM Faculty of Pharmacy, 1000 Skopje, Republic of Macedonia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany
| | - Detlev Schindler
- Department of Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Roland P Kuiper
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584 CT Utrecht, The Netherlands.
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21
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Kechin A, Khrapov E, Boyarskikh U, Kel A, Filipenko M. BRCA-analyzer: Automatic workflow for processing NGS reads of BRCA1 and BRCA2 genes. Comput Biol Chem 2018; 77:297-306. [PMID: 30408727 DOI: 10.1016/j.compbiolchem.2018.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 09/14/2018] [Accepted: 10/22/2018] [Indexed: 12/20/2022]
Abstract
The use of targeted next-generation sequencing (NGS) provides great new opportunities for molecular and medical genetics. However, in order to take advantage of these opportunities, we need to have reliable tools for extracting the necessary information from the huge amount of data generated by NGS. Here we present our automatic multithreaded workflow for processing NGS data of BRCA1 and BRCA2 genes obtained with NGS technology named BRCA-analyzer. Optimizing it on the sequencing data of 899 samples from 693 patients, we were able to find the most reliable tools and adjust their parameters in such a way that all pathogenic variants found were confirmed by Sanger's sequencing. For 82 and 24 DNA samples from blood and formalin-fixed paraffin-embedded blocks, NGS libraries were prepared with GeneRead BRCA panel v2 (Qiagen). The reads obtained were processed with BRCA-analyzer and Qiagen GeneRead Data analysis workflow. In total 27 pathogenic variants were found and confirmed by Sanger's sequencing, with all of them determined with BRCA-analyzer. Qiagen GeneRead Data analysis discarded 5 true pathogenic variants due to their location in homopolymeric sequence stretches. For other 793 samples, libraries were prepared by the in-house method, and NGS data were analyzed by BRCA-analyzer in comparison to another free automatic amplicon NGS workflow Canary. From total 137 pathogenic variations, BRCA-analyzer found 135 and Canary 123. Mutations were missed by BRCA-analyzer due to the trimming primer sequences from reads before mapping to be fixed in the next version. On the freely available NGS data, we showed that BRCA-analyzer could also be used for hybrid capture gene panels, although it needs more extensive testing on such library preparation methods. Thus, BRCA-analyzer is an automatic workflow for processing NGS data of BRCA1/2 genes with variant filters adapted to amplicon-based targeted NGS data. BRCA-analyzer can be used to identify germline as well as somatic mutations. BRCA-analyzer is freely available at https://github.com/aakechin/BRCA-analyzer.
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Affiliation(s)
- Andrey Kechin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia.
| | - Evgeniy Khrapov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Uljana Boyarskikh
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Alexander Kel
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia; geneXplain GmbH, Wolfenbüttel, 38302, Germany; biosoft.ru, Novosibirsk, 630058, Russia
| | - Maxim Filipenko
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
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Pope BJ, Hammet F, Nguyen-Dumont T, Park DJ. Hi-Plex for Simple, Accurate, and Cost-Effective Amplicon-based Targeted DNA Sequencing. Methods Mol Biol 2018; 1712:53-70. [PMID: 29224068 DOI: 10.1007/978-1-4939-7514-3_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Hi-Plex is a suite of methods to enable simple, accurate, and cost-effective highly multiplex PCR-based targeted sequencing (Nguyen-Dumont et al., Biotechniques 58:33-36, 2015). At its core is the principle of using gene-specific primers (GSPs) to "seed" (or target) the reaction and universal primers to "drive" the majority of the reaction. In this manner, effects on amplification efficiencies across the target amplicons can, to a large extent, be restricted to early seeding cycles. Product sizes are defined within a relatively narrow range to enable high-specificity size selection, replication uniformity across target sites (including in the context of fragmented input DNA such as that derived from fixed tumor specimens (Nguyen-Dumont et al., Biotechniques 55:69-74, 2013; Nguyen-Dumont et al., Anal Biochem 470:48-51, 2015), and application of high-specificity genetic variant calling algorithms (Pope et al., Source Code Biol Med 9:3, 2014; Park et al., BMC Bioinformatics 17:165, 2016). Hi-Plex offers a streamlined workflow that is suitable for testing large numbers of specimens without the need for automation.
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Affiliation(s)
- Bernard J Pope
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Fleur Hammet
- Genomic Technologies Group, Genetic Epidemiology Laboratory, Department of Medicine, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Tu Nguyen-Dumont
- Genomic Technologies Group, Genetic Epidemiology Laboratory, Department of Medicine, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Daniel J Park
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia. .,Genomic Technologies Group, Genetic Epidemiology Laboratory, Department of Medicine, The University of Melbourne, Parkville, VIC, 3010, Australia.
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Kechin AA, Boyarskikh UA, Ermolenko NA, Tyulyandina AS, Lazareva DG, Avdalyan AM, Tyulyandin SA, Kushlinskii NE, Filipenko ML. Loss of Heterozygosity in BRCA1 and BRCA2 Genes in Patients with Ovarian Cancer and Probability of Its Use for Clinical Classification of Variations. Bull Exp Biol Med 2018; 165:94-100. [PMID: 29797126 DOI: 10.1007/s10517-018-4107-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Indexed: 11/25/2022]
Abstract
Changes (or variants) in BRCA1 and BRCA2 gene sequences can have different lengths and clinical significance: from single nucleotide variants (SNV) and short insertions/deletions (<50 bp) to extended deletions and duplications (so-called copy number variations, or CNV). According to their clinical significance, all variants can be divided into pathogenic, likely pathogenic, variants of uncertain significance, likely benign, and benign. Moreover, variants can be germinal (i.e. inherited from parents) and somatic (arising in the process of development of the organism). A specific somatic event is loss of heterozygosity (LOH), i.e. transition of one or many point and short variants from heterozygous to homozygous state. Such an event can be the key to the development of carcinogenesis for cells carrying a pathogenic variant, if we consider it within the framework of the Knudson's two-hit carcinogenesis theory. We studied the prevalence and nature of LOH in of ovarian cancer samples carrying or not carrying a pathogenic variant. To this end, a full coding sequence of BRCA1/2 genes was determined in 30 pairs of DNA samples isolated from blood cells and paraffinized histological blocks of patients on a MiSeq Illumina instrument. Analyss of the obtained reads revealed 9 pathogenic point and short variants (30% patients): 6 germinal (20%) and 3 somatic (10%), and 8 somatic CNV (3 deletions and 5 duplications of several or all exons of the BRCA1 gene). LOH was detected in 70% patients; among the carriers of pathogenic variants - in 83%. For pathogenic variants, the percentage of reads with the alternative allele increased more often than for benign variants located in another gene, or detected in other patients (67% vs. 44%). However, the difference was statistically insignificant, which can be due to insufficient number of patients. Only in 3 of 21 cases of LOH (14%), it can be attributed to CNV. In other cases, LOH is most likely determined by gene conversion, but further research is needed.
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Affiliation(s)
- A A Kechin
- Novosibirsk State University, Novosibirsk, Russia.
| | - U A Boyarskikh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N A Ermolenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A S Tyulyandina
- N. N. Blokhin National Medical Research Center of Oncology, the Ministry of Health of Russia, Moscow, Russia
| | - D G Lazareva
- Altai Territorial Cancer Control Center, Barnaul, Russia
| | - A M Avdalyan
- Altai Territorial Cancer Control Center, Barnaul, Russia
| | - S A Tyulyandin
- N. N. Blokhin National Medical Research Center of Oncology, the Ministry of Health of Russia, Moscow, Russia
| | - N E Kushlinskii
- N. N. Blokhin National Medical Research Center of Oncology, the Ministry of Health of Russia, Moscow, Russia
| | - M L Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
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Abstract
An apparently balanced t(2;3)(q37.3;q13.2) translocation that appears to segregate with renal cell carcinoma (RCC) has indicated potential areas to search for the elusive genetic basis of clear cell RCC. We applied Hi-Plex targeted sequencing to analyse germline DNA from 479 individuals affected with clear cell RCC for this breakpoint translocation and genetic variants in neighbouring genes on chromosome 2, ACKR3 and COPS8. While only synonymous variants were found in COPS8, one of the missense variants in ACKR3:c.892C>T, observed in 4/479 individuals screened (0.8%), was predicted likely to damage ACKR3 function. Identification of causal genes for RCC has potential clinical utility, where risk assessment and risk management can offer better outcomes, with surveillance for at-risk relatives and nephron sparing surgery through earlier intervention.
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Shrestha SK, Lamour K, Young-Kelly H. Genome sequences and SNP analyses of Corynespora cassiicola from cotton and soybean in the southeastern United States reveal limited diversity. PLoS One 2017; 12:e0184908. [PMID: 28910414 PMCID: PMC5599035 DOI: 10.1371/journal.pone.0184908] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 09/01/2017] [Indexed: 12/17/2022] Open
Abstract
Corynespora cassiicola attackes diverse agriculturally important plants, including soybean and cotton, in the US. It is a reemerge pathogen on cotton in southeastern US. Whole genome sequences of four cotton and one soybean isolate from Tennessee were used to develop single nucleotide polymorphism markers for cotton isolates. Cotton isolates had little diversity at the genome level and very little differentiation from the soybean isolate. Analysis of 75 isolates from cotton and soybean, using targeted-sequencing of 22 polymorphic SNP sites, revealed eight multi-locus genotypes and it appears a single clonal lineage predominates across the southeastern region. The cotton and soybean genome sequences were significantly different from the public reference genome derived from a rubber isolate and the utility of these novel resources will be discussed.
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Affiliation(s)
- Sandesh K. Shrestha
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, TN, United States of America
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, The University of Tennessee, Knoxville, TN, United States of America
| | - Heather Young-Kelly
- Department of Entomology and Plant Pathology, The University of Tennessee, Jackson, TN, United States of America
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Barchenger DW, Lamour KH, Sheu ZM, Shrestha S, Kumar S, Lin SW, Burlakoti R, Bosland PW. Intra- and Intergenomic variation of Ploidy and Clonality characterize Phytophthora capsici on Capsicum sp. in Taiwan. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1330-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Kechin A, Boyarskikh U, Kel A, Filipenko M. cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing. J Comput Biol 2017; 24:1138-1143. [PMID: 28715235 DOI: 10.1089/cmb.2017.0096] [Citation(s) in RCA: 540] [Impact Index Per Article: 77.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cutting of primers from reads is an important step of processing targeted amplicon-based next generation sequencing data. Existing tools are adapted for cutting of one or several primer/adapter sequences from reads and removing all of their occurrences. Also most of the existing tools use kmers and may cut only part of primers or primers with studied sequence of gene. Because of this, use of such programs leads to incorrect trimming, reduction of coverage, and increase in the number of false-positive and/or false-negative results. We have developed a new tool named cutPrimers for accurate cutting of any number of primers from reads. Using sequencing reads that were obtained during study of BRCA1/2 genes, we compared it with cutadapt, AlienTrimmer, and BBDuk. All of them trimmed reads in such a way that coverage of at least two amplicons decreased to unacceptable level (<30 reads) comparing with reads trimmed with cutPrimers. At the same time, Trimmomatic and AlienTrimmer cut all occurrences of primer sequences, so the length of the remaining reads was less than prospective.
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Affiliation(s)
- Andrey Kechin
- 1 Institute of Chemical Biology and Fundamental Medicine SB RAS , Novosibirsk, Russia .,2 Novosivirsk State University , Novosibirsk, Russia
| | - Uljana Boyarskikh
- 1 Institute of Chemical Biology and Fundamental Medicine SB RAS , Novosibirsk, Russia
| | - Alexander Kel
- 1 Institute of Chemical Biology and Fundamental Medicine SB RAS , Novosibirsk, Russia .,3 geneXplain GmbH, Wolfenbuettel, Germany .,4 biosoft.ru , Novosibirsk, Russia
| | - Maxim Filipenko
- 1 Institute of Chemical Biology and Fundamental Medicine SB RAS , Novosibirsk, Russia
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Shrestha SK, Cochran A, Mengistu A, Lamour K, Castro-Rocha A, Young-Kelly H. Genetic diversity, QoI fungicide resistance, and mating type distribution of Cercospora sojina-Implications for the disease dynamics of frogeye leaf spot on soybean. PLoS One 2017; 12:e0177220. [PMID: 28486517 PMCID: PMC5423647 DOI: 10.1371/journal.pone.0177220] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 04/24/2017] [Indexed: 11/19/2022] Open
Abstract
Frogeye leaf spot (FLS), caused by Cercospora sojina, causes significant damage to soybean in the U.S. One control strategy is the use of quinone outside inhibitor (QoI) fungicides. QoI resistant isolates were first reported in Tennessee (TN) in 2010. To investigate the disease dynamics of C. sojina, we collected 437 C. sojina isolates in 2015 from Jackson and Milan, TN and used 40 historical isolates collected from 2006-2009 from TN and ten additional states for comparison. A subset of 186 isolates, including historical isolates, were genotyped for 49 single nucleotide polymorphism (SNP) markers and the QoI resistance locus, revealing 35 unique genotypes. The genotypes clustered into three groups with two groups containing only sensitive isolates and the remaining group containing all resistant isolates and a dominant clonal lineage of 130 isolates. All 477 C. sojina isolates were genotyped for the QoI locus revealing 344 resistant and 133 sensitive isolates. All isolates collected prior to 2015 were QoI sensitive. Both mating type alleles (MAT1-1-1 and MAT1-2) were found in Jackson and Milan, TN and recovered from single lesions suggesting sexual recombination may play a role in the epidemiology of field populations. Analysis of C. sojina isolates using SNP markers proved useful to investigate population diversity and to elaborate on diversity as it relates to QoI resistance and mating type.
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Affiliation(s)
- Sandesh Kumar Shrestha
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Alicia Cochran
- Department of Entomology and Plant Pathology, University of Tennessee, Jackson, Tennessee, United States of America
| | - Alemu Mengistu
- United States Department of Agriculture, Agriculture Research Service, Jackson, Tennessee, United States of America
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Arturo Castro-Rocha
- Departamento de Ciencias Químico-Biológicas, Universidad Autónoma de Cd. Juárez, Chihuahua, Mexico
| | - Heather Young-Kelly
- Department of Entomology and Plant Pathology, University of Tennessee, Jackson, Tennessee, United States of America
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Park N, Vassiliou G. Design and Application of Multiplex PCR Seq for the Detection of Somatic Mutations Associated with Myeloid Malignancies. Methods Mol Biol 2017; 1633:87-99. [PMID: 28735482 DOI: 10.1007/978-1-4939-7142-8_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Targeted sequencing, in which only a selected set of genomic loci are sequenced, enables a much higher coverage of each target than what is obtained using whole genome or exome sequencing. Multiplex PCR offers a simple and affordable technique for specific capture of target regions and can be easily adapted to generate next-generation sequencing (NGS)-ready amplicons. Here we describe a multiplex PCR (MxPCR) approach for capturing 13 leukemia-associated mutation hotspots followed by MiSeq sequencing that enables robust detection of mutations with a variant allele fraction (VAF) as low as 0.8% (0.008) in blood DNA.
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Affiliation(s)
- Naomi Park
- DNA Pipelines Research and Development, Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | - George Vassiliou
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK.
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31
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Chen K, Zhou YX, Li K, Qi LX, Zhang QF, Wang MC, Xiao JH. A novel three-round multiplex PCR for SNP genotyping with next generation sequencing. Anal Bioanal Chem 2016; 408:4371-7. [PMID: 27113460 DOI: 10.1007/s00216-016-9536-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/27/2016] [Accepted: 03/31/2016] [Indexed: 11/28/2022]
Abstract
Owing to the high throughput and low cost, next generation sequencing has attracted much attention for SNP genotyping application for researchers. Here, we introduce a new method based on three-round multiplex PCR to precisely genotype SNPs with next generation sequencing. This method can as much as possible consume the equivalent amount of each pair of specific primers to largely eliminate the amplification discrepancy between different loci. After the PCR amplification, the products can be directly subjected to next generation sequencing platform. We simultaneously amplified 37 SNP loci of 757 samples and sequenced all amplicons on ion torrent PGM platform; 90.5 % of the target SNP loci were accurately genotyped (at least 15×) and 90.4 % amplicons had uniform coverage with a variation less than 50-fold. Ligase detection reaction (LDR) was performed to genotype the 19 SNP loci (as part of the 37 SNP loci) with 91 samples randomly selected from the 757 samples, and 99.5 % genotyping data were consistent with the next generation sequencing results. Our results demonstrate that three-round PCR coupled with next generation sequencing is an efficient and economical genotyping approach. Graphical Abstract The schematic diagram of three-round PCR.
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Affiliation(s)
- Ke Chen
- College of Environmental Science and Engineering, Donghua University, Shanghai, 05003365, China
| | - Yu-Xun Zhou
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China
| | - Kai Li
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China
| | - Li-Xin Qi
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China
| | - Qi-Fei Zhang
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China
| | - Mao-Chun Wang
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China
| | - Jun-Hua Xiao
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, 05003365, China.
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Klein JC, Lajoie MJ, Schwartz JJ, Strauch EM, Nelson J, Baker D, Shendure J. Multiplex pairwise assembly of array-derived DNA oligonucleotides. Nucleic Acids Res 2015; 44:e43. [PMID: 26553805 PMCID: PMC4797260 DOI: 10.1093/nar/gkv1177] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 10/22/2015] [Indexed: 01/16/2023] Open
Abstract
While the cost of DNA sequencing has dropped by five orders of magnitude in the past decade, DNA synthesis remains expensive for many applications. Although DNA microarrays have decreased the cost of oligonucleotide synthesis, the use of array-synthesized oligos in practice is limited by short synthesis lengths, high synthesis error rates, low yield and the challenges of assembling long constructs from complex pools. Toward addressing these issues, we developed a protocol for multiplex pairwise assembly of oligos from array-synthesized oligonucleotide pools. To evaluate the method, we attempted to assemble up to 2271 targets ranging in length from 192–252 bases using pairs of array-synthesized oligos. Within sets of complexity ranging from 131–250 targets, we observed error-free assemblies for 90.5% of all targets. When all 2271 targets were assembled in one reaction, we observed error-free constructs for 70.6%. While the assembly method intrinsically increased accuracy to a small degree, we further increased accuracy by using a high throughput ‘Dial-Out PCR’ protocol, which combines Illumina sequencing with an in-house set of unique PCR tags to selectively amplify perfect assemblies from complex synthetic pools. This approach has broad applicability to DNA assembly and high-throughput functional screens.
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Affiliation(s)
- Jason C Klein
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Marc J Lajoie
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jerrod J Schwartz
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Eva-Maria Strauch
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jorgen Nelson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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Hasmad HN, Lai KN, Wen WX, Park DJ, Nguyen-Dumont T, Kang PCE, Thirthagiri E, Ma'som M, Lim BK, Southey M, Woo YL, Teo SH. Evaluation of germline BRCA1 and BRCA2 mutations in a multi-ethnic Asian cohort of ovarian cancer patients. Gynecol Oncol 2015; 141:318-322. [PMID: 26541979 DOI: 10.1016/j.ygyno.2015.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/29/2015] [Accepted: 11/02/2015] [Indexed: 01/28/2023]
Abstract
OBJECTIVE Despite the discovery of breast and ovarian cancer predisposition genes BRCA1 and BRCA2 more than two decades ago, almost all the available data relate to women of European ancestry, with only a handful of studies in Asian populations. In this study, we determined the frequency of germline alterations in BRCA1 and BRCA2 in ovarian cancer patients from a multi-ethnic cross-sectional cohort of Asian ovarian cancer patients from Malaysia. METHODS From October 2008 to February 2015, we established a hospital-based cohort of ovarian cancer patients and the germline status of all 218 women with invasive epithelial ovarian cancer was tested using targeted amplification and sequencing of the intron-exon junctions and exonic sequences of BRCA1, BRCA2, PALB2 and TP53. RESULTS BRCA1 and BRCA2 mutations were found in 8% (17 cases) and 3% (7 cases) of the ovarian cancer patients, respectively. Mutation carriers were diagnosed at a similar age to non-carriers, but were more likely to be Indian, have serous ovarian cancer, and have more relatives with breast or ovarian cancer. Nonetheless, 42% (10/24) of mutation carriers did not have any family history of breast or ovarian cancer and offering genetic counselling and genetic testing only to women with family history would mean that 35% (6/17) of BRCA1 mutation carriers and 57% (4/7) of BRCA2 mutation carriers would not be offered genetic testing. CONCLUSIONS Our data suggest that, similar to Caucasians, a significant proportion of Asian ovarian cancer was attributed to germline mutations in BRCA1 and to a lesser extent in BRCA2.
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Affiliation(s)
| | - Kah Nyin Lai
- Cancer Research Malaysia, Subang Jaya, Malaysia.
| | | | - Daniel Jonathan Park
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Australia.
| | - Tú Nguyen-Dumont
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Australia.
| | | | | | - Mahirah Ma'som
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia.
| | - Boon Kiong Lim
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia.
| | - Melissa Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Australia.
| | - Yin Ling Woo
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia.
| | - Soo-Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Malaysia; Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia.
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McKerrell T, Park N, Moreno T, Grove CS, Ponstingl H, Stephens J, Crawley C, Craig J, Scott MA, Hodkinson C, Baxter J, Rad R, Forsyth DR, Quail MA, Zeggini E, Ouwehand W, Varela I, Vassiliou GS. Leukemia-associated somatic mutations drive distinct patterns of age-related clonal hemopoiesis. Cell Rep 2015; 10:1239-45. [PMID: 25732814 PMCID: PMC4542313 DOI: 10.1016/j.celrep.2015.02.005] [Citation(s) in RCA: 375] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 01/19/2015] [Accepted: 01/29/2015] [Indexed: 12/18/2022] Open
Abstract
Clonal hemopoiesis driven by leukemia-associated gene mutations can occur without evidence of a blood disorder. To investigate this phenomenon, we interrogated 15 mutation hot spots in blood DNA from 4,219 individuals using ultra-deep sequencing. Using only the hot spots studied, we identified clonal hemopoiesis in 0.8% of individuals under 60, rising to 19.5% of those ≥90 years, thus predicting that clonal hemopoiesis is much more prevalent than previously realized. DNMT3A-R882 mutations were most common and, although their prevalence increased with age, were found in individuals as young as 25 years. By contrast, mutations affecting spliceosome genes SF3B1 and SRSF2, closely associated with the myelodysplastic syndromes, were identified only in those aged >70 years, with several individuals harboring more than one such mutation. This indicates that spliceosome gene mutations drive clonal expansion under selection pressures particular to the aging hemopoietic system and explains the high incidence of clonal disorders associated with these mutations in advanced old age.
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Affiliation(s)
- Thomas McKerrell
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Naomi Park
- Sequencing Research Group, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Thaidy Moreno
- Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, 39011 Santander, Spain
| | - Carolyn S Grove
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Hannes Ponstingl
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Jonathan Stephens
- Department of Haematology, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK; NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | | | - Charles Crawley
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge CB2 0QQ, UK
| | - Jenny Craig
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge CB2 0QQ, UK
| | - Mike A Scott
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge CB2 0QQ, UK
| | - Clare Hodkinson
- Department of Haematology, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK; Cambridge Blood and Stem Cell Biobank, Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
| | - Joanna Baxter
- Department of Haematology, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK; Cambridge Blood and Stem Cell Biobank, Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
| | - Roland Rad
- Department of Medicine II, Klinikum Rechts der Isar, Technische Universität München, 81675 München, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Duncan R Forsyth
- Department of Medicine for the Elderly, Cambridge University Hospitals NHS Trust, Cambridge CB2 0QQ, UK
| | - Michael A Quail
- Sequencing Research Group, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | | | - Willem Ouwehand
- Department of Haematology, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK; NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK; Human Genetics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, 39011 Santander, Spain
| | - George S Vassiliou
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK; Department of Haematology, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK; Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge CB2 0QQ, UK.
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Nguyen-Dumont T, Mahmoodi M, Hammet F, Tran T, Tsimiklis H, Giles GG, Hopper JL, Southey MC, Park DJ. Hi-Plex targeted sequencing is effective using DNA derived from archival dried blood spots. Anal Biochem 2015; 470:48-51. [PMID: 25447460 PMCID: PMC4275364 DOI: 10.1016/j.ab.2014.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 11/28/2022]
Abstract
Many genetic epidemiology resources have collected dried blood spots (predominantly as Guthrie Cards) as an economical and efficient means of archiving sources of DNA, conferring great value to genetic screening methods that are compatible with this medium. We applied Hi-Plex to screen the breast cancer predisposition gene PALB2 in 93 Guthrie Card-derived DNA specimens previously characterized for PALB2 genetic variants via DNA derived from lymphoblastoid cell lines, whole blood, and buffy coat. Of the 93 archival Guthrie Card-derived DNAs, 92 (99%) were processed successfully and sequenced using approximately half of a MiSeq run. From these 92 DNAs, all 59 known variants were detected and no false-positive variant calls were yielded. Fully 98.13% of amplicons (5417/5520) were represented within 15-fold of the median coverage (2786 reads), and 99.98% of amplicons (5519/5520) were represented at a depth of 10 read-pairs or greater. With Hi-Plex, we show for the first time that a High-Plex amplicon-based massively parallel sequencing (MPS) system can be applied effectively to DNA prepared from dried blood spot archival specimens and, as such, can dramatically increase the scopes of both method and resource.
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Affiliation(s)
- T Nguyen-Dumont
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - M Mahmoodi
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - F Hammet
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - T Tran
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - H Tsimiklis
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - G G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
| | - J L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Parkville, Victoria 3010, Australia
| | - M C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - D J Park
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia.
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Nguyen-Dumont T, Hammet F, Mahmoodi M, Tsimiklis H, Teo ZL, Li R, Pope BJ, Terry MB, Buys SS, Daly M, Hopper JL, Winship I, Goldgar DE, Park DJ, Southey MC. Mutation screening of PALB2 in clinically ascertained families from the Breast Cancer Family Registry. Breast Cancer Res Treat 2015; 149:547-54. [PMID: 25575445 DOI: 10.1007/s10549-014-3260-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 12/22/2014] [Indexed: 11/28/2022]
Abstract
Loss-of-function mutations in PALB2 are associated with an increased risk of breast cancer, with recent data showing that female breast cancer risks for PALB2 mutation carriers are comparable in magnitude to those for BRCA2 mutation carriers. This study applied targeted massively parallel sequencing to characterize the mutation spectrum of PALB2 in probands attending breast cancer genetics clinics in the USA. The coding regions and proximal intron-exon junctions of PALB2 were screened in probands not known to carry a mutation in BRCA1 or BCRA2 from 1,250 families enrolled through familial cancer clinics by the Breast Cancer Family Registry. Mutation screening was performed using Hi-Plex, an amplicon-based targeted massively parallel sequencing platform. Screening of PALB2 was successful in 1,240/1,250 probands and identified nine women with protein-truncating mutations (three nonsense mutations and five frameshift mutations). Four of the 33 missense variants were predicted to be deleterious to protein function by in silico analysis using two different programs. Analysis of tumors from carriers of truncating mutations revealed that the majority were high histological grade, invasive ductal carcinomas. Young onset was apparent in most families, with 19 breast cancers under 50 years of age, including eight under the age of 40 years. Our data demonstrate the utility of Hi-Plex in the context of high-throughput testing for rare genetic mutations and provide additional timely information about the nature and prevalence of PALB2 mutations, to enhance risk assessment and risk management of women at high risk of cancer attending clinical genetic services.
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Affiliation(s)
- Tú Nguyen-Dumont
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia,
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Abridged adapter primers increase the target scope of Hi-Plex. Biotechniques 2015; 58:33-6. [PMID: 25605578 DOI: 10.2144/000114247] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 10/31/2014] [Indexed: 11/23/2022] Open
Abstract
Previously, we reported Hi-Plex, an amplicon-based method for targeted massively parallel sequencing capable of generating 60 amplicons simultaneously. In further experiments, however, we found our approach did not scale to higher amplicon numbers. Here, we report a modification to the original Hi-Plex protocol that includes the use of abridged adapter oligonucleotides as universal primers (bridge primers) in the initial PCR mixture. Full-length adapter primers (indexing primers) are included only during latter stages of thermal cycling with concomitant application of elevated annealing temperatures. Using this approach, we demonstrate the application of Hi-Plex across a broad range of amplicon numbers (16-plex, 62-plex, 250-plex, and 1003-plex) while preserving the low amount (25 ng) of input DNA required.
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Pope BJ, Nguyen-Dumont T, Hammet F, Park DJ. ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets. SOURCE CODE FOR BIOLOGY AND MEDICINE 2014; 9:3. [PMID: 24461215 PMCID: PMC3904415 DOI: 10.1186/1751-0473-9-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 01/08/2014] [Indexed: 01/03/2023]
Abstract
Background We recently described Hi-Plex, a highly multiplexed PCR-based target-enrichment system for massively parallel sequencing (MPS), which allows the uniform definition of library size so that subsequent paired-end sequencing can achieve complete overlap of read pairs. Variant calling from Hi-Plex-derived datasets can thus rely on the identification of variants appearing in both reads of read-pairs, permitting stringent filtering of sequencing chemistry-induced errors. These principles underly ROVER software (derived from Read Overlap PCR-MPS variant caller), which we have recently used to report the screening for genetic mutations in the breast cancer predisposition gene PALB2. Here, we describe the algorithms underlying ROVER and its usage. Results ROVER enables users to quickly and accurately identify genetic variants from PCR-targeted, overlapping paired-end MPS datasets. The open-source availability of the software and threshold tailorability enables broad access for a range of PCR-MPS users. Methods ROVER is implemented in Python and runs on all popular POSIX-like operating systems (Linux, OS X). The software accepts a tab-delimited text file listing the coordinates of the target-specific primers used for targeted enrichment based on a specified genome-build. It also accepts aligned sequence files resulting from mapping to the same genome-build. ROVER identifies the amplicon a given read-pair represents and removes the primer sequences by using the mapping co-ordinates and primer co-ordinates. It considers overlapping read-pairs with respect to primer-intervening sequence. Only when a variant is observed in both reads of a read-pair does the signal contribute to a tally of read-pairs containing or not containing the variant. A user-defined threshold informs the minimum number of, and proportion of, read-pairs a variant must be observed in for a ‘call’ to be made. ROVER also reports the depth of coverage across amplicons to facilitate the identification of any regions that may require further screening. Conclusions ROVER can facilitate rapid and accurate genetic variant calling for a broad range of PCR-MPS users.
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Affiliation(s)
| | | | | | - Daniel J Park
- Genetic Epidemiology Laboratory, Department of Pathology, Medical Building, The University of Melbourne, Melbourne, Victoria 3010, Australia.
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Nguyen-Dumont T, Teo ZL, Pope BJ, Hammet F, Mahmoodi M, Tsimiklis H, Sabbaghian N, Tischkowitz M, Foulkes WD, Giles GG, Hopper JL, Southey MC, Park DJ. Hi-Plex for high-throughput mutation screening: application to the breast cancer susceptibility gene PALB2. BMC Med Genomics 2013; 6:48. [PMID: 24206657 PMCID: PMC3829211 DOI: 10.1186/1755-8794-6-48] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/05/2013] [Indexed: 11/16/2022] Open
Abstract
Background Massively parallel sequencing (MPS) has revolutionised biomedical research and offers enormous capacity for clinical application. We previously reported Hi-Plex, a streamlined highly-multiplexed PCR-MPS approach, allowing a given library to be sequenced with both the Ion Torrent and TruSeq chemistries. Comparable sequencing efficiency was achieved using material derived from lymphoblastoid cell lines and formalin-fixed paraffin-embedded tumour. Methods Here, we report high-throughput application of Hi-Plex by performing blinded mutation screening of the coding regions of the breast cancer susceptibility gene PALB2 on a set of 95 blood-derived DNA samples that had previously been screened using Sanger sequencing and high-resolution melting curve analysis (n = 90), or genotyped by Taqman probe-based assays (n = 5). Hi-Plex libraries were prepared simultaneously using relatively inexpensive, readily available reagents in a simple half-day protocol followed by MPS on a single MiSeq run. Results We observed that 99.93% of amplicons were represented at ≥10X coverage. All 56 previously identified variant calls were detected and no false positive calls were assigned. Four additional variant calls were made and confirmed upon re-analysis of previous data or subsequent Sanger sequencing. Conclusions These results support Hi-Plex as a powerful approach for rapid, cost-effective and accurate high-throughput mutation screening. They further demonstrate that Hi-Plex methods are suitable for and can meet the demands of high-throughput genetic testing in research and clinical settings.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Daniel J Park
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia.
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Nguyen-Dumont T, Pope BJ, Hammet F, Mahmoodi M, Tsimiklis H, Southey MC, Park DJ. Cross-platform compatibility of Hi-Plex, a streamlined approach for targeted massively parallel sequencing. Anal Biochem 2013; 442:127-9. [PMID: 23933242 DOI: 10.1016/j.ab.2013.07.046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 07/31/2013] [Indexed: 12/11/2022]
Abstract
Although per-base sequencing costs have decreased during recent years, library preparation for targeted massively parallel sequencing remains constrained by high reagent cost, limited design flexibility, and protocol complexity. To address these limitations, we previously developed Hi-Plex, a polymerase chain reaction (PCR) massively parallel sequencing strategy for screening panels of genomic target regions. Here, we demonstrate that Hi-Plex applied with hybrid adapters can generate a library suitable for sequencing with both the Ion Torrent and the TruSeq chemistries and that adjusting primer concentrations improves coverage uniformity. These results expand Hi-Plex capabilities as an accurate, affordable, flexible, and rapid approach for various genetic screening applications.
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Affiliation(s)
- Tú Nguyen-Dumont
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Victoria 3010, Australia
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