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Daca-Roszak P, Fiedorowicz J, Jankowski M, Ciesielka M, Teresiński G, Lipska-Zietkiewicz B, Zietkiewicz E, Grzybowski T, Skonieczna K. The effect of library preparation protocol on the efficiency of heteroplasmy detection in mitochondrial DNA using two massively parallel sequencing Illumina systems. J Appl Genet 2024; 65:559-563. [PMID: 38110828 PMCID: PMC11310223 DOI: 10.1007/s13353-023-00821-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
Abstract
Massively parallel sequencing (MPS) technology has become the gold standard in mitochondrial DNA research due to its high sensitivity in detecting mtDNA heteroplasmy, a prognostic marker in various medical applications. Various MPS technologies and platforms used for mtDNA analysis exist. Obtaining reliable and sensitive results requires deep and uniform coverage of the entire mtDNA sequence, which is heavily influenced by the choice of library preparation method and sequencing platform. Here, we present a comparison of the sequencing coverage and the ability to heteroplasmy detection using two library preparation protocols (Nextera XT DNA Library Preparation Kit and Nextera DNA Flex Library Preparation Kit) and two different (MiSeq FGx and ISeq 100) Illumina MPS platforms. Our study indicates that the Nextera DNA Flex Library protocol provides a more balanced coverage along the mitogenome and a reliable heteroplasmy detection with both MiSeq and iSeq Illumina MPS systems.
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Affiliation(s)
| | - Joanna Fiedorowicz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
- Department of Animal Physiology, Biochemistry and Biostructure, Poznan University of Life Science, Poznan, Poland
| | - Maciej Jankowski
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Marzanna Ciesielka
- Chair and Department of Forensic Medicine, Medical University of Lublin, Lublin, Poland
| | - Grzegorz Teresiński
- Chair and Department of Forensic Medicine, Medical University of Lublin, Lublin, Poland
| | - Beata Lipska-Zietkiewicz
- Centre for Rare Diseases, Medical University of Gdansk, Gdansk, Poland; Clinical Genetics Unit, Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Ewa Zietkiewicz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Faculty of Medicine, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Katarzyna Skonieczna
- Department of Forensic Medicine, Faculty of Medicine, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland.
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2
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Skonieczna K, Grzybowski T. Capability of the iSeq 100 sequencing system from Illumina to detect low-level substitutions in the human mitochondrial genome. Forensic Sci Int Genet 2023; 66:102912. [PMID: 37451073 DOI: 10.1016/j.fsigen.2023.102912] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/22/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
The significance of mtDNA heteroplasmy in forensic and medical genetics has increased recently because massively parallel sequencing (MPS) technologies enable more accurate and precise detection of minority nucleotide variants. Recent reports have shown that detection of low-level substitutions may depend on library preparation or sequencing protocol, and can vary for different MPS platforms. The MiSeq (Illumina) and Ion S5 (Thermo Fisher Scientific) are mainly used for heteroplasmy detection, but no data are available regarding the iSeq 100, an Illumina platform of the smallest throughput. Notably, unlike the other systems, the machine utilizes sequencing by synthesis one-channel chemistry to determine DNA sequences. Thus, it is important to verify the capability of the iSeq 100 system to determine mitochondrial haplotypes and detect heteroplasmic substitutions. In this study, previously determined entire mitochondrial genomes were sequenced with the iSeq 100 system. Each mitogenome was sequenced twice, giving approximately 2000x and 10,000x coverage. All homoplasmic mutations and minority variants above the 19 % level detected with the iSeq 100 system were also observed after dideoxy sequencing. Moreover, all heteroplasmic substitutions above the 2 % level were consistently detected with SBS one-channel chemistry. However, detection of low-level mtDNA variants may require additional, confirmatory experiments. In summary, the iSeq 100 system enables reproducible and accurate sequencing of human mitochondrial genomes. Detection of mtDNA minority variants depends on the laboratory protocol and sequencing platform used, but homoplasmic mutations and heteroplasmy above the 2 % level can be correctly detected with the iSeq 100 system.
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Affiliation(s)
- Katarzyna Skonieczna
- Department of Forensic Medicine, Faculty of Medicine, Ludwik Rydygier Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz, Poland.
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Faculty of Medicine, Ludwik Rydygier Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz, Poland
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3
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Peng D, Geng J, Yang J, Liu J, Wang N, Wu R, Sun H. Whole Mitochondrial Genome Detection and Analysis of Two- to Four-Generation Maternal Pedigrees Using a New Massively Parallel Sequencing Panel. Genes (Basel) 2023; 14:genes14040912. [PMID: 37107670 PMCID: PMC10137955 DOI: 10.3390/genes14040912] [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: 03/16/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is an effective genetic marker in forensic practice, especially for aged bones and hair shafts. Detection of the whole mitochondrial genome (mtGenome) using traditional Sanger-type sequencing is laborious and time-consuming. Additionally, its ability to distinguish point heteroplasmy (PHP) and length heteroplasmy (LHP) is limited. The application of massively parallel sequencing in mtDNA detection helps researchers to study the mtGenome in-depth. The ForenSeq mtDNA Whole Genome Kit, which contains a total of 245 short amplicons, is one of the multiplex library preparation kits for the mtGenome. We used this system to detect the mtGenome in the blood samples and hair shafts of thirty-three individuals from eight two-generation pedigrees, one three-generation pedigree, and one four-generation pedigree. High-quality sequencing results were obtained. Ten unique mtGenome haplotypes were observed in the mothers from the ten pedigrees. A total of 26 PHPs were observed using the interpretation threshold of 6%. Eleven types of LHPs in six regions were evaluated in detail. When considering homoplasmic variants only, consistent mtGenome haplotypes were observed between the twice-sequenced libraries and between the blood and hair shafts from the same individual and among maternal relatives in the pedigrees. Four inherited PHPs were observed, and the remainder were de novo/disappearing PHPs in the pedigrees. Our results demonstrate the effective capability of the ForenSeq mtDNA Whole Genome Kit to generate the complete mtGenome in blood and hair shafts, as well as the complexity of mtDNA haplotype comparisons between different types of maternal relatives when heteroplasmy is considered.
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Affiliation(s)
- Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiaojiao Geng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiajun Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
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4
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Gendron EM, Sevigny JL, Byiringiro I, Thomas WK, Powers TO, Porazinska DL. Nematode mitochondrial metagenomics: A new tool for biodiversity analysis. Mol Ecol Resour 2023. [PMID: 36727264 DOI: 10.1111/1755-0998.13761] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/26/2023] [Accepted: 01/31/2023] [Indexed: 02/03/2023]
Abstract
DNA barcoding approaches have greatly increased our understanding of biodiversity on the planet, and metabarcoding is widely used for classifying members of the phylum Nematoda. However, loci typically utilized in metabarcoding studies are often unable to resolve closely related species or are unable to recover all taxa present in a sample due to inadequate PCR primer binding. Mitochondrial metagenomics (mtMG) is an alternative approach utilizing shotgun sequencing of total DNA to recover the mitochondrial genomes of all species present in samples. However, this approach requires a comprehensive reference database for identification and currently available mitochondrial sequences for nematodes are highly dominated by sequences from the order Rhabditida, and excludes many clades entirely. Here, we analysed the efficacy of mtMG for the recovery of nematode taxa and the generation of mitochondrial genomes. We first developed a curated reference database of nematode mitochondrial sequences and expanded it with 40 newly sequenced taxa. We then tested the mito-metagenomics approach using a series of nematode mock communities consisting of morphologically identified nematode species representing various feeding traits, life stages, and phylogenetic relationships. We were able to identify all but two species through the de novo assembly of COX1 genes. We were also able to recover additional mitochondrial protein coding genes (PCGs) for 23 of the 24 detected species including a full array of 12 PCGs from five of the species. We conclude that mtMG offers a potential for the effective recovery of nematode biodiversity but remains limited by the breadth of the reference database.
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Affiliation(s)
- Eli M Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Joseph L Sevigny
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA.,Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Innocent Byiringiro
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, USA
| | - W Kelley Thomas
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA.,Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Thomas O Powers
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, USA
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
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5
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Skonieczna K, Ciesielka M, Teresiński G, Grzybowski T. Low-level point heteroplasmy detection in human mitogenomes amplified with different polymerases and sequenced on MiSeq FGx platform. ARCHIVES OF FORENSIC MEDICINE AND CRIMINOLOGY 2023; 73:131-138. [PMID: 38186038 DOI: 10.4467/16891716amsik.23.011.18686] [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] [Indexed: 01/09/2024] Open
Abstract
Introduction Massively parallel sequencing of mitogenomes usually requires prior amplification. The PCR step may influence the quality of the data obtained, especially when low-level heteroplasmy detection is applied. Aim The aim of this study was to compare the reliability of two different DNA polymerases in detecting homoplasmic and heteroplasmic substitutions in human mitogenomes. Material and methods Mitogenomes of five samples were amplified with Long PCR Enzyme Mix from Fermentas or TaKaRa LA Taq DNA Polymerase from TaKaRa. Then, NexteraTM XT DNA libraries were sequenced on MiSeq FGx platform (Illumina). mtDNA substitutions were called for alternative variants above the 1% level. Results All homoplasmic substitutions detected in amplicons generated with polymerases studied here and sequenced on MiSeq FGx system were consistently identified as homoplasmies with alternative sequencing methods. TaKaRa LA Taq DNA Polymerase was found to be less accurate in low-level heteroplasmy detection than Long PCR Enzyme Mix enzyme as more false negative and false positive results were observed for minority variants called above the 1% level. Nevertheless, both PCR systems studied can be successfully used to detect authentic mtDNA substitutions, for which minority variants exceed the 3.61% level assuming at least 10,000x coverage and sequencing Nextera XT DNA libraries on MiSeq FGx machine. Conclusions The accuracy and sensitivity of point heteroplasmy detection with the MiSeq FGx instrument varies on polymerase used for mtDNA amplification. Therefore, it is recommended to validate the laboratory protocols used for mtDNA substitution detection prior to their implementation for the forensic or medical genetics purposes.
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Affiliation(s)
- Katarzyna Skonieczna
- Department of Forensic Medicine, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | | | - Grzegorz Teresiński
- Department of Forensic Medicine, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Tomasz Grzybowski
- Department of Forensic Medicine, The Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
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6
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Argopistes sexvittatus and Argopistes capensis (Chrysomelidae: Alticini): Mitogenomics and Phylogeny of Two Flea Beetles Affecting Olive Trees. Genes (Basel) 2022; 13:genes13122195. [PMID: 36553462 PMCID: PMC9777630 DOI: 10.3390/genes13122195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/06/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022] Open
Abstract
The genus Argopistes (Chrysomelidae: Alticini) is the only group of flea beetles specialized in plant hosts in the family Oleaceae. In southern Africa, Argopistes are often found feeding on African Wild Olive (Olea europaea subsp. cuspidata) and European cultivated olive (O. e. subsp. europaea), and heavy infestations can be devastating to mature trees and compromise the development of young trees. Despite their negative agricultural impact, African Argopistes are an understudied group for which no genetic data were available. We assessed the species diversity of olive flea beetles in the Western Cape province of South Africa, the largest olive-producing region in sub-Saharan Africa, by collecting adult specimens on wild and cultivated olive trees between 2015 and 2017. Argopistes sexvittatus Bryant, 1922 (n = 289) dominated at all sampling sites, and Argopistes capensis Bryant, 1944 (n = 2) was found only once. Argopistes oleae Bryant, 1922, a third species previously reported in the region, was not found. The complete mitogenomes of one A. capensis and two A. sexvittatus (striped and black morphotypes) individuals were sequenced for phylogenetic reconstruction in the context of other 64 species. The two olive flea beetle species form a monophyletic clade with other Argopistes, supporting the hypothesis that the exclusive feeding habit on Oleaceae is an evolutionary adaptation in this genus.
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7
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Ribarska T, Bjørnstad PM, Sundaram AYM, Gilfillan GD. Optimization of enzymatic fragmentation is crucial to maximize genome coverage: a comparison of library preparation methods for Illumina sequencing. BMC Genomics 2022; 23:92. [PMID: 35105301 PMCID: PMC8805253 DOI: 10.1186/s12864-022-08316-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/17/2022] [Indexed: 11/10/2022] Open
Abstract
Background Novel commercial kits for whole genome library preparation for next-generation sequencing on Illumina platforms promise shorter workflows, lower inputs and cost savings. Time savings are achieved by employing enzymatic DNA fragmentation and by combining end-repair and tailing reactions. Fewer cleanup steps also allow greater DNA input flexibility (1 ng-1 μg), PCR-free options from 100 ng DNA, and lower price as compared to the well-established sonication and tagmentation-based DNA library preparation kits. Results We compared the performance of four enzymatic fragmentation-based DNA library preparation kits (from New England Biolabs, Roche, Swift Biosciences and Quantabio) to a tagmentation-based kit (Illumina) using low input DNA amounts (10 ng) and PCR-free reactions with 100 ng DNA. With four technical replicates of each input amount and kit, we compared the kits’ fragmentation sequence-bias as well as performance parameters such as sequence coverage and the clinically relevant detection of single nucleotide and indel variants. While all kits produced high quality sequence data and demonstrated similar performance, several enzymatic fragmentation methods produced library insert sizes which deviated from those intended. Libraries with longer insert lengths performed better in terms of coverage, SNV and indel detection. Lower performance of shorter-insert libraries could be explained by loss of sequence coverage to overlapping paired-end reads, exacerbated by the preferential sequencing of shorter fragments on Illumina sequencers. We also observed that libraries prepared with minimal or no PCR performed best with regard to indel detection. Conclusions The enzymatic fragmentation-based DNA library preparation kits from NEB, Roche, Swift and Quantabio are good alternatives to the tagmentation based Nextera DNA flex kit from Illumina, offering reproducible results using flexible DNA inputs, quick workflows and lower prices. Libraries with insert DNA fragments longer than the cumulative sum of both read lengths avoid read overlap, thus produce more informative data that leads to strongly improved genome coverage and consequently also increased sensitivity and precision of SNP and indel detection. In order to best utilize such enzymatic fragmentation reagents, researchers should be prepared to invest time to optimize fragmentation conditions for their particular samples. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08316-y.
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Affiliation(s)
- Teodora Ribarska
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Kirkeveien 166, 0450, Oslo, Norway
| | - Pål Marius Bjørnstad
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Kirkeveien 166, 0450, Oslo, Norway
| | - Arvind Y M Sundaram
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Kirkeveien 166, 0450, Oslo, Norway
| | - Gregor D Gilfillan
- Department Medical Genetics, Oslo University Hospital and University of Oslo, Kirkeveien 166, 0450, Oslo, Norway.
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8
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Li X, Shi X, Gong Y, Guo W, Liu Y, Peng C, Xu Y. Selective Chemical Labeling and Sequencing of 5-Hydroxymethylcytosine in DNA at Single-Base Resolution. Front Genet 2021; 12:749211. [PMID: 34868220 PMCID: PMC8635956 DOI: 10.3389/fgene.2021.749211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/08/2021] [Indexed: 11/24/2022] Open
Abstract
5-Hydroxymethylcytosine (5hmC), the oxidative product of 5-methylcytosine (5mC) catalyzed by ten-eleven translocation enzymes, plays an important role in many biological processes as an epigenetic mediator. Prior studies have shown that 5hmC can be selectively labeled with chemically modified glucose moieties and enriched using click chemistry with biotin affinity approaches. Besides, DNA deaminases of the AID/APOBEC family can discriminate modified 5hmC bases from cytosine (C) or 5mC. Herein, we developed a method based on embryonic stem cell (ESC) whole-genome analysis, which could enrich 5hmC-containing DNA by selective chemical labeling and locate 5hmC sites at single-base resolution with enzyme-based deamination. The combination experimental design is an extension of previous methods, and we hope that this cost-effective single-base resolution 5hmC sequencing method could be used to promote the mechanism and diagnosis research of 5hmC.
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Affiliation(s)
- Xiaogang Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Xinxin Shi
- Gastrointestinal Surgery Department of the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yin Gong
- School of Electronics Engineering and Computer Science, Peking University, Beijing, China
| | - Wenting Guo
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yuanrui Liu
- Characteristic Medical Center of the Chinese People’s Armed Police Force, Tianjin, China
| | - Chunwei Peng
- Gastrointestinal Surgery Department of the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yingchun Xu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
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9
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Hlaka V, Guilbert É, Smit SJ, van Noort S, Allsopp E, Langley J, van Asch B. Species Diversity and Phylogenetic Relationships of Olive Lace Bugs (Hemiptera: Tingidae) Found in South Africa. INSECTS 2021; 12:830. [PMID: 34564270 PMCID: PMC8466438 DOI: 10.3390/insects12090830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/04/2021] [Accepted: 09/09/2021] [Indexed: 11/16/2022]
Abstract
Olive lace bugs (Hemiptera: Tingidae) are small sap-sucking insects that feed on wild and cultivated Olea europaea. The diversity of olive lace bug species in South Africa, the most important olive producer on the continent, has been incompletely surveyed. Adult specimens were collected in the Western Cape province for morphological and DNA-based species identification, and sequencing of complete mitogenomes. Cysteochila lineata, Plerochila australis, Neoplerochila paliatseasi and Neoplerochila sp. were found at 12 sites. Intra- and interspecific genetic divergences and phylogenetic clustering in 30 species in 18 genera of Tingidae using new and publicly available DNA barcodes showed high levels of congruity between taxonomic and genetic data. The phylogenetic position of the four species found in South Africa was inferred using new and available mitogenomes of Tingidae. Notably, olive lace bugs formed a cluster of closely related species. However, Cysteochila was non-monophyletic as C. lineata was recovered as a sister species to P. australis whereas Cysteochila chiniana, the other representative of the genus, was grouped with Trachypeplus jacobsoni and Tingis cardui in a different cluster. This result suggests that feeding on O. europaea may have a common origin in Tingidae and warrants future research on potential evolutionary adaptations of olive lace bugs to this plant host.
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Affiliation(s)
- Vaylen Hlaka
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (V.H.); (J.L.)
| | - Éric Guilbert
- Muséum National d’Histoire Naturelle, UMR 7179, CP50, 45 Rue Buffon, 75005 Paris, France;
| | - Samuel Jacobus Smit
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK;
| | - Simon van Noort
- Research and Exhibitions Department, Iziko South African Museum, P.O. Box 61, Cape Town 8000, South Africa;
- Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town 7700, South Africa
| | - Elleunorah Allsopp
- Agricultural Research Council, Infruitec-Nietvoorbij, Private Bag X5026, Stellenbosch 7599, South Africa;
| | - Jethro Langley
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (V.H.); (J.L.)
| | - Barbara van Asch
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (V.H.); (J.L.)
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10
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Groot J, Zhou Y, Marshall E, Cullen P, Carlile T, Lin D, Xu CF, Crisafulli J, Sun C, Casey F, Zhang B, Alves C. Benchmarking and optimization of a high-throughput sequencing based method for transgene sequence variant analysis in biotherapeutic cell line development. Biotechnol J 2021; 16:e2000548. [PMID: 34018310 DOI: 10.1002/biot.202000548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 12/13/2022]
Abstract
In recent years, High-Throughput Sequencing (HTS) based methods to detect mutations in biotherapeutic transgene products have become a key quality step deployed during the development of manufacturing cell line clones. Previously we reported on a higher throughput, rapid mutation detection method based on amplicon sequencing (targeting transgene RNA) and detailed its implementation to facilitate cell line clone selection. By gaining experience with our assay in a diverse set of cell line development programs, we improved the computational analysis as well as experimental protocols. Here we report on these improvements as well as on a comprehensive benchmarking of our assay. We evaluated assay performance by mixing amplicon samples of a verified mutated antibody clone with a non-mutated antibody clone to generate spike-in mutations from ∼60% down to ∼0.3% frequencies. We subsequently tested the effect of 16 different sample and HTS library preparation protocols on the assay's ability to quantify mutations and on the occurrence of false-positive background error mutations (artifacts). Our evaluation confirmed assay robustness, established a high confidence limit of detection of ∼0.6%, and identified protocols that reduce error levels thereby significantly reducing a source of false positives that bottlenecked the identification of low-level true mutations.
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Affiliation(s)
- Joost Groot
- Genome Technologies and Computational Sciences, Biogen, Cambridge, Massachusetts, USA.,Inzen Therapeutics, Cambridge, Massachusetts, USA
| | - Yizhou Zhou
- Protein Development, Biogen, Cambridge, Massachusetts, USA
| | - Eric Marshall
- Genome Technologies and Computational Sciences, Biogen, Cambridge, Massachusetts, USA
| | - Patrick Cullen
- Genome Technologies and Computational Sciences, Biogen, Cambridge, Massachusetts, USA
| | - Thomas Carlile
- Genome Technologies and Computational Sciences, Biogen, Cambridge, Massachusetts, USA
| | - Dongdong Lin
- Genome Technologies and Computational Sciences, Biogen, Cambridge, Massachusetts, USA
| | - Chong-Feng Xu
- Analytical Development, Biogen, Cambridge, Massachusetts, USA
| | | | - Chao Sun
- Genome Technologies and Computational Sciences, Biogen, Cambridge, Massachusetts, USA
| | - Fergal Casey
- Genome Technologies and Computational Sciences, Biogen, Cambridge, Massachusetts, USA
| | - Baohong Zhang
- Genome Technologies and Computational Sciences, Biogen, Cambridge, Massachusetts, USA
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11
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Holt CL, Stephens KM, Walichiewicz P, Fleming KD, Forouzmand E, Wu SF. Human Mitochondrial Control Region and mtGenome: Design and Forensic Validation of NGS Multiplexes, Sequencing and Analytical Software. Genes (Basel) 2021; 12:genes12040599. [PMID: 33921728 PMCID: PMC8073089 DOI: 10.3390/genes12040599] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023] Open
Abstract
Forensic mitochondrial DNA (mtDNA) analysis conducted using next-generation sequencing (NGS), also known as massively parallel sequencing (MPS), as compared to Sanger-type sequencing brings modern advantages, such as deep coverage per base (herein referred to as read depth per base pair (bp)), simultaneous sequencing of multiple samples (libraries) and increased operational efficiencies. This report describes the design and developmental validation, according to forensic quality assurance standards, of end-to-end workflows for two multiplexes, comprised of ForenSeq mtDNA control region and mtDNA whole-genome kits the MiSeq FGxTM instrument and ForenSeq universal analysis software (UAS) 2.0/2.1. Polymerase chain reaction (PCR) enrichment and a tiled amplicon approach target small, overlapping amplicons (60–150 bp and 60–209 bp for the control region and mtGenome, respectively). The system provides convenient access to data files that can be used outside of the UAS if desired. Studies assessed a range of environmental and situational variables, including but not limited to buccal samples, rootless hairs, dental and skeletal remains, concordance of control region typing between the two multiplexes and as compared to orthogonal data, assorted sensitivity studies, two-person DNA mixtures and PCR-based performance testing. Limitations of the system and implementation considerations are discussed. Data indicated that the two mtDNA multiplexes, MiSeq FGx and ForenSeq software, meet or exceed forensic DNA quality assurance (QA) guidelines with robust, reproducible performance on samples of various quantities and qualities.
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Gorden EM, Sturk-Andreaggi K, Marshall C. Capture enrichment and massively parallel sequencing for human identification. Forensic Sci Int Genet 2021; 53:102496. [PMID: 33770700 DOI: 10.1016/j.fsigen.2021.102496] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 01/07/2023]
Abstract
In the past decade, hybridization capture has gained attention within the forensic field for its possible use in human identification. One of the primary benefits to capture enrichment is its applicability to degraded DNA fragments that, due to their reduced size, are not amenable to traditional PCR enrichment techniques. Hybridization capture is typically introduced after genomic library preparation of extracted DNA templates for the subsequent enrichment of mitochondrial DNA or single nucleotide polymorphisms within the nuclear genome. The enriched molecules are then subjected to massively parallel sequencing (MPS) for sensitive and high-throughput DNA sequence generation. Bioinformatic analysis of capture product removes PCR duplicates that were introduced during the laboratory workflow in order to characterize the original DNA template molecules. In the case of aged and degraded skeletal remains, the fraction of endogenous human DNA may be very low; therefore low-coverage sequence analysis may be required. This review contains an overview of current capture methodologies and the primary literature on hybridization capture as evaluated for forensic applications.
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Affiliation(s)
- Erin M Gorden
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE, USA; SNA International LLC, Alexandria, VA, USA
| | - Kimberly Sturk-Andreaggi
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE, USA; SNA International LLC, Alexandria, VA, USA; Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Charla Marshall
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Dover, DE, USA; SNA International LLC, Alexandria, VA, USA; Forensic Science Program, The Pennsylvania State University, State College, PA, USA.
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13
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Assessment of Illumina® Human mtDNA Genome assay: workflow evaluation with development of analysis and interpretation guidelines. Int J Legal Med 2021; 135:1161-1178. [PMID: 33511452 DOI: 10.1007/s00414-021-02508-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/08/2021] [Indexed: 01/27/2023]
Abstract
Mitochondrial DNA (mtDNA) is a small but significant part of the human genome, whose applicability potential has gradually increased with the advent of massively parallel sequencing (MPS) technology. Knowledge of the particular workflow, equipment, and reagents used, along with extensive usage of negative controls to monitor all preparation steps constitute the prerequisites for confident reporting of results. In this study, we performed an assessment of Illumina® Human mtDNA Genome assay on MiSeq FGx™ instrument. Through analysis of several types of negative controls, as well as mtDNA positive controls, we established thresholds for data analysis and interpretation, consisting of several components: minimum read depth (220 reads), minimum quality score (41), percentage of minor allele sufficient for analysis (3.0%), percentage of minor allele sufficient for interpretation (6.0%), and percentage of major allele sufficient for homoplasmic variant call (97.0%). Based on these criteria, we defined internal guidelines for analysis and interpretation of mtDNA results obtained by MPS. Our study shows that the whole mtDNA assay on MiSeq FGx™ produces repeatable and reproducible results, independent of the analyst, which are also concordant with Sanger-type sequencing results for mtDNA control region, as well as with MPS results produced by NextSeq®. Overall, established thresholds and interpretation guidelines were successfully applied for the sequencing of complete mitochondrial genomes from high-quality samples. The underlying principles and proposed methodology on the definition of internal laboratory guidelines for analysis and interpretation of MPS results may be applicable to similar MPS workflows, e.g. targeting good-quality samples in forensic genetics and molecular diagnostics.
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Taylor CR, Kiesler KM, Sturk-Andreaggi K, Ring JD, Parson W, Schanfield M, Vallone PM, Marshall C. Platinum-Quality Mitogenome Haplotypes from United States Populations. Genes (Basel) 2020; 11:genes11111290. [PMID: 33138247 PMCID: PMC7716222 DOI: 10.3390/genes11111290] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022] Open
Abstract
A total of 1327 platinum-quality mitochondrial DNA haplotypes from United States (U.S.) populations were generated using a robust, semi-automated next-generation sequencing (NGS) workflow with rigorous quality control (QC). The laboratory workflow involved long-range PCR to minimize the co-amplification of nuclear mitochondrial DNA segments (NUMTs), PCR-free library preparation to reduce amplification bias, and high-coverage Illumina MiSeq sequencing to produce an average per-sample read depth of 1000 × for low-frequency (5%) variant detection. Point heteroplasmies below 10% frequency were confirmed through replicate amplification, and length heteroplasmy was quantitatively assessed using a custom read count analysis tool. Data analysis involved a redundant, dual-analyst review to minimize errors in haplotype reporting with additional QC checks performed by EMPOP. Applying these methods, eight sample sets were processed from five U.S. metapopulations (African American, Caucasian, Hispanic, Asian American, and Native American) corresponding to self-reported identity at the time of sample collection. Population analyses (e.g., haplotype frequencies, random match probabilities, and genetic distance estimates) were performed to evaluate the eight datasets, with over 95% of haplotypes unique per dataset. The platinum-quality mitogenome haplotypes presented in this study will enable forensic statistical calculations and thereby support the usage of mitogenome sequencing in forensic laboratories.
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Affiliation(s)
- Cassandra R. Taylor
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19002, USA; (C.R.T.); (K.S.-A.); (J.D.R.)
- SNA International, LLC; Alexandria, VA 22314, USA
| | - Kevin M. Kiesler
- National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA; (K.M.K.); (P.M.V.)
| | - Kimberly Sturk-Andreaggi
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19002, USA; (C.R.T.); (K.S.-A.); (J.D.R.)
- SNA International, LLC; Alexandria, VA 22314, USA
| | - Joseph D. Ring
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19002, USA; (C.R.T.); (K.S.-A.); (J.D.R.)
- SNA International, LLC; Alexandria, VA 22314, USA
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck 6020, Austria;
- Forensic Science Program, The Pennsylvania State University, State College, PA 16801, USA
| | - Moses Schanfield
- Department of Forensic Sciences, The George Washington University, Washington, DC 20007, USA;
| | - Peter M. Vallone
- National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA; (K.M.K.); (P.M.V.)
| | - Charla Marshall
- Armed Forces Medical Examiner System’s Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, DE 19002, USA; (C.R.T.); (K.S.-A.); (J.D.R.)
- SNA International, LLC; Alexandria, VA 22314, USA
- Forensic Science Program, The Pennsylvania State University, State College, PA 16801, USA
- Correspondence: ; Tel.: +1-302-346-8519
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Gregory T, Ngankeu A, Orwick S, Kautto EA, Woyach JA, Byrd JC, Blachly JS. Characterization and mitigation of fragmentation enzyme-induced dual stranded artifacts. NAR Genom Bioinform 2020; 2:lqaa070. [PMID: 33043294 PMCID: PMC7531576 DOI: 10.1093/nargab/lqaa070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 07/27/2020] [Accepted: 09/22/2020] [Indexed: 12/30/2022] Open
Abstract
High-throughput short-read sequencing relies on fragmented DNA for optimal sampling of input nucleic acid. Several vendors now offer proprietary enzyme cocktails as a cheaper and more streamlined method of fragmentation when compared to acoustic shearing. We have discovered that these enzymes induce the formation of library molecules containing regions of nearby DNA from opposite strands. Sequencing reads derived from these molecules can lead to artifact-derived variant calls appearing at variant allele frequencies <5%. We present Fragmentation Artifact Detection and Elimination (FADE), software to remove these artifacts from mapped reads and mitigate artifact-related effects on downstream analysis. We find that the artifacts principally affect downstream analyses that are sensitive to a 1-3% artifact bias in the sequencing reads, such as targeted resequencing and rare variant discovery.
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Affiliation(s)
- Thomas Gregory
- Division of Hematology, Ohio State University, Columbus, OH 43210, USA
| | | | - Shelley Orwick
- Division of Hematology, Ohio State University, Columbus, OH 43210, USA
| | - Esko A Kautto
- Division of Hematology, Ohio State University, Columbus, OH 43210, USA
| | - Jennifer A Woyach
- Division of Hematology, Ohio State University, Columbus, OH 43210, USA
| | - John C Byrd
- Division of Hematology, Ohio State University, Columbus, OH 43210, USA
| | - James S Blachly
- Division of Hematology, Ohio State University, Columbus, OH 43210, USA
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Gorden EM, Sturk-Andreaggi K, Warnke-Sommer J, Hazelwood A, Barritt-Ross S, Marshall C. Next generation sequencing of STR artifacts produced from historical bone samples. Forensic Sci Int Genet 2020; 49:102397. [PMID: 33017798 DOI: 10.1016/j.fsigen.2020.102397] [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: 06/11/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 11/17/2022]
Abstract
STR artifacts are commonly observed in electrophoretic data and can complicate interpretation of the profiles produced. Even when a consensus approach is applied, reproducible artifacts have the potential to convolute the analysis. DNA obtained from historical bone samples is often heavily degraded and damaged, requiring the use of more sensitive procedures to increase allele recovery. Additionally, skeletal remains exposed to environmental conditions may be afflicted with microbial DNA contamination that cross-reacts with the primers during short tandem repeat (STR) multiplex amplification. STR artifacts manifested as a result of these circumstances can be sourced and characterized using new sequencing technologies to potentially ease the analysis burden. For this study, PCR product from 17 low-quality bone samples exhibiting reproducible autosomal and Y-chromosomal STR (Y-STR) artifacts in capillary electrophoresis (CE) data were sequenced with next generation sequencing (NGS). Sequenced reads were bioinformatically sorted using STRait Razor to determine the authenticity of alleles and confirm the profile generated by CE. Sequence data from the PCR products and a subset of the associated extracts were further analyzed with Kaiju to classify the microbial species present and identify potential sources of artifact peaks. A suspected Y-STR artifact was similar in sequence to Pseudomonas sp. BAY1663, a species ubiquitously found in soil. Regions of homology were observed between the Pseudomonas genome and the presumed primer binding locations for Y-STRs included in the AmpFlSTR Y-Filer STR kit. Characterization of such supposed artifact peaks may aid in interpretation of CE data and ultimately lead to increased confidence in the reported results.
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Affiliation(s)
- Erin M Gorden
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Delaware, USA; SNA International, Contractor Supporting the AFMES-AFDIL and the DPAA, Alexandria, Virginia, USA
| | - Kimberly Sturk-Andreaggi
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Delaware, USA; SNA International, Contractor Supporting the AFMES-AFDIL and the DPAA, Alexandria, Virginia, USA
| | - Julia Warnke-Sommer
- SNA International, Contractor Supporting the AFMES-AFDIL and the DPAA, Alexandria, Virginia, USA; Defense Personnel Accounting Agency (DPAA), Offutt Air Force Base, Nebraska, USA
| | - Amy Hazelwood
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Delaware, USA; SNA International, Contractor Supporting the AFMES-AFDIL and the DPAA, Alexandria, Virginia, USA
| | - Suzanne Barritt-Ross
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Delaware, USA
| | - Charla Marshall
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), Dover Air Force Base, Delaware, USA; SNA International, Contractor Supporting the AFMES-AFDIL and the DPAA, Alexandria, Virginia, USA.
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17
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González-Castellano I, Pons J, González-Ortegón E, Martínez-Lage A. Mitogenome phylogenetics in the genus Palaemon (Crustacea: Decapoda) sheds light on species crypticism in the rockpool shrimp P. elegans. PLoS One 2020; 15:e0237037. [PMID: 32810189 PMCID: PMC7444591 DOI: 10.1371/journal.pone.0237037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/17/2020] [Indexed: 12/24/2022] Open
Abstract
The genus Palaemon comprises worldwide marine and freshwater shrimps and prawns, and some of them are ecologically or commercially important species. Palaemon is not currently a monophyletic group, so phylogenetics and systematics are constantly changing. Species crypticism has been pointed out in several Palaemon species, being the clearest evidence in the European rockpool shrimp P. elegans. Here we sequenced and described seven European Palaemon mitochondrial genomes. The mitochondrial protein-coding genes were used, along with those of three other Palaemon species, to perform mitogenome phylogenetic analyses to clarify the evolutionary relationships within the genus, and particularly to shed light on the cryptic species found within P. elegans. The Messinian Salinity Crisis (5.3-5.9 Ma, late Miocene) was proposed to be the origin of this cryptic species and it was used as aged constraint for calibration analysis. We provide the largest and the first time-calibrated mitogenome phylogeny of the genus Palaemon and mitogenome substitution rate was estimated (1.59% per million years) in Decapoda for the first time. Our results highlighted the need for future systematics changes in Palaemon and crypticism in P. elegans was confirmed. Mitochondrial genome and cox1 (1.41%) substitution rate estimates matched those published elsewhere, arguing that the Messinian Salinity Crisis was a plausible event driving the split between P. elegans and its cryptic species. Molecular dating suggested that Pleistocene glaciations were likely involved in the differentiation between the Atlantic and Mediterranean populations of P. elegans. On the contrary, the divergence between the Atlantic and Mediterranean populations of the common littoral shrimp P. serratus was greater and dated to be much older (4.5-12.3 Ma, Plio-Miocene), so we considered that they could represent two separated species. Therefore, species crypticism in the genus Palaemon seems to be a common phenomenon.
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Affiliation(s)
- Inés González-Castellano
- Departamento de Biología and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, A Coruña, Spain
| | - Joan Pons
- Instituto Mediterráneo de Estudios Avanzados (IMEDEA), Consejo Superior de Investigaciones Científicas (CSIC) and Universitat de les Illes Balears, Esporles, Spain
| | - Enrique González-Ortegón
- Instituto de Ciencias Marinas de Andalucía (ICMAN), Consejo Superior de Investigaciones Científicas (CSIC), Puerto Real, Spain
| | - Andrés Martínez-Lage
- Departamento de Biología and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, A Coruña, Spain
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18
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A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features. Nat Commun 2020; 11:3609. [PMID: 32681090 PMCID: PMC7367866 DOI: 10.1038/s41467-020-17445-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 06/22/2020] [Indexed: 11/08/2022] Open
Abstract
Standard units of measurement are required for the quantitative description of nature; however, few standard units have been established for genomics to date. Here, we have developed a synthetic DNA ladder that defines a quantitative standard unit that can measure DNA sequence abundance within a next-generation sequencing library. The ladder can be spiked into a DNA sample, and act as an internal scale that measures quantitative genetics features. Unlike previous spike-ins, the ladder is encoded within a single molecule, and can be equivalently and independently synthesized by different laboratories. We show how the ladder can measure diverse quantitative features, including human genetic variation and microbial abundance, and also estimate uncertainty due to technical variation and improve normalization between libraries. This ladder provides an independent quantitative unit that can be used with any organism, application or technology, thereby providing a common metric by which genomes can be measured.
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19
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Marine RL, Magaña LC, Castro CJ, Zhao K, Montmayeur AM, Schmidt A, Diez-Valcarce M, Ng TFF, Vinjé J, Burns CC, Nix WA, Rota PA, Oberste MS. Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses. J Virol Methods 2020; 280:113865. [PMID: 32302601 PMCID: PMC9119587 DOI: 10.1016/j.jviromet.2020.113865] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/04/2020] [Accepted: 04/06/2020] [Indexed: 02/06/2023]
Abstract
Next-generation sequencing is a powerful tool for virological surveillance. While Illumina® and Ion Torrent® sequencing platforms are used extensively for generating viral RNA genome sequences, there is limited data comparing different platforms. The Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5 platforms were evaluated using a panel of sixteen specimens containing picornaviruses and human caliciviruses (noroviruses and sapoviruses). The specimens were processed, using combinations of three library preparation and five sequencing kits, to assess the quality and completeness of assembled viral genomes, and an estimation of cost per sample to generate the data was calculated. The choice of library preparation kit and sequencing platform was found to impact the breadth of genome coverage and accuracy of consensus viral genomes. The Ion Torrent S5 510 chip runs produced more reads at a lower cost per sample than the highest output Ion Torrent PGM 318 chip run, and generated the highest proportion of reads for enterovirus D68 samples. However, indels at homopolymer regions impacted the accuracy of consensus genome sequences. For lower throughput sequencing runs (i.e., Ion Torrent 510 and Illumina MiSeq Nano V2), the cost per sample was lower on the MiSeq platform, whereas with higher throughput runs (Ion Torrent 530 and Illumina MiSeq V2) there is less of a difference in the cost per sample between the two sequencing platforms ($5.47-$10.25 more per sample for an Ion Torrent 530 chip run when multiplexing 24 samples). These findings suggest that the Ion Torrent S5 and Illumina MiSeq platforms are both viable options for genomic sequencing of RNA viruses, each with specific advantages and tradeoffs.
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Affiliation(s)
- Rachel L Marine
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Laura C Magaña
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Christina J Castro
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Kun Zhao
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Marta Diez-Valcarce
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Terry Fei Fan Ng
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Cara C Burns
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - W Allan Nix
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Paul A Rota
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - M Steven Oberste
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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20
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Zakaria MR, Lam MQ, Chen SJ, Abdul Karim MH, Tokiman L, Yahya A, Shamsir MS, Chong CS. Genome sequence data of Mangrovimonas sp. strain CR14 isolated from mangrove forest at Tanjung Piai National Park, Malaysia. Data Brief 2020; 30:105658. [PMID: 32426431 PMCID: PMC7225383 DOI: 10.1016/j.dib.2020.105658] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/23/2020] [Accepted: 04/28/2020] [Indexed: 12/20/2022] Open
Abstract
Mangrovimonas sp. strain CR14 is a halophilic bacterium affiliated with family Flavobacteriaceae which was successfully isolated from mangrove soil samples obtained from Tanjung Piai National Park, Johor. The whole genome of strain CR14 was sequenced on an Illumina HiSeq 2500 platform (2 × 150 bp paired end). Herein, we report the genome sequence of Mangrovimonas sp. strain CR14 in which its assembled genome consisted 20 contigs with a total size of 3,590,195 bp, 3209 coding sequences, and an average 36.08% G + C content. Genome annotation and gene mining revealed that this bacterium demonstrated proteolytic activity which could be potentially applied in detergent industry. This whole-genome shotgun data of Mangrovimonas sp. strain CR14 has been deposited at DDBJ/ENA/GenBank under the accession JAAFZY000000000. The version described in this paper is version JAAFZY010000000.
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Affiliation(s)
| | - Ming Quan Lam
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Sye Jinn Chen
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | | | - Lili Tokiman
- Johor National Parks Corporation, Kota Iskandar, 79575 Iskandar Puteri, Johor, Malaysia
| | - Adibah Yahya
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, 84600 Muar, Johor, Malaysia
| | - Chun Shiong Chong
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
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21
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Sturk-Andreaggi K, Parson W, Allen M, Marshall C. Impact of the sequencing method on the detection and interpretation of mitochondrial DNA length heteroplasmy. Forensic Sci Int Genet 2020; 44:102205. [DOI: 10.1016/j.fsigen.2019.102205] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 11/09/2019] [Accepted: 11/09/2019] [Indexed: 02/04/2023]
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22
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Marshall C, Sturk-Andreaggi K, Ring JD, Taylor CR, Barritt-Ross S, Parson W, McMahon TP. Advancing mitochondrial genome data interpretation in missing persons casework. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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23
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Young JM, Higgins D, Austin JJ. Hybridization Enrichment to Improve Forensic Mitochondrial DNA Analysis of Highly Degraded Human Remains. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00450] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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24
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Yokoi A, Villar-Prados A, Oliphint PA, Zhang J, Song X, De Hoff P, Morey R, Liu J, Roszik J, Clise-Dwyer K, Burks JK, O’Halloran TJ, Laurent LC, Sood AK. Mechanisms of nuclear content loading to exosomes. SCIENCE ADVANCES 2019; 5:eaax8849. [PMID: 31799396 PMCID: PMC6867874 DOI: 10.1126/sciadv.aax8849] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/24/2019] [Indexed: 05/20/2023]
Abstract
Exosome cargoes are highly varied and include proteins, small RNAs, and genomic DNA (gDNA). The presence of gDNA suggests that different intracellular compartments contribute to exosome loading, resulting in distinct exosome subpopulations. However, the loading of gDNA and other nuclear contents into exosomes (nExo) remains poorly understood. Here, we identify the relationship between cancer cell micronuclei (MN), which are markers of genomic instability, and nExo formation. Imaging flow cytometry analyses reveal that 10% of exosomes derived from cancer cells and <1% of exosomes derived from blood and ascites from patients with ovarian cancer carry nuclear contents. Treatment with genotoxic drugs resulted in increased MN and nExos both in vitro and in vivo. We observed that multivesicular body precursors and exosomal markers, such as the tetraspanins, directly interact with MN. Collectively, this work provides new insights related to nExos, which have implications for cancer biomarker development.
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Affiliation(s)
- Akira Yokoi
- Department of Gynecologic Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alejandro Villar-Prados
- Department of Gynecologic Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Paul Allen Oliphint
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xingzhi Song
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peter De Hoff
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Robert Morey
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Jinsong Liu
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason Roszik
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Karen Clise-Dwyer
- Section of Transplant Immunology, Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared K. Burks
- Department of Leukemia and Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Theresa J. O’Halloran
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Anil K. Sood
- Department of Gynecologic Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Interference and Non-Coding RNA, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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25
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Resolving mitochondrial haplogroups B2 and B4 with next-generation mitogenome sequencing to distinguish Native American from Asian haplotypes. Forensic Sci Int Genet 2019; 43:102143. [DOI: 10.1016/j.fsigen.2019.102143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/31/2019] [Accepted: 08/12/2019] [Indexed: 12/18/2022]
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Edson SM, Roberts M. Determination of materials present in skeletonized human remains and the associated DNA: Development of a GC/MS protocol. Forensic Sci Int Synerg 2019; 1:170-184. [PMID: 32411970 PMCID: PMC7219129 DOI: 10.1016/j.fsisyn.2019.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 08/07/2019] [Accepted: 08/09/2019] [Indexed: 11/24/2022]
Abstract
DNA testing of skeletonized human remains is considered to be challenging, especially when the remains have been exposed to inhibitory materials during decomposition. Inhibitors affect the processing of DNA, either by preventing efficient extraction or interfering with down-stream PCR-based processes. Limited studies have been performed on real-world samples that have been exposed to such inhibitors. This paper presents the development of a gas chromatography/mass spectrometry (GC/MS) protocol for the evaluation of materials present in skeletonized human remains recovered from the field, as well as the DNA extracted from the same materials. Twenty-one bone samples and seventeen DNA extracts were evaluated across three solvents and multiple GC/MS parameters to determine the optimal conditions for the recovery of trace materials present. The aim of this work is to provide a technique that can determine the presence of inhibitors prior to DNA extraction, allowing analysts to optimize removal of inhibitory materials.
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Affiliation(s)
- Suni M. Edson
- Flinders University, College of Science and Engineering, Adelaide, South Australia, Australia
- Armed Forces DNA Identification Laboratory, Armed Forces Medical Examiner System, 115 Purple Heart Drive, Dover AFB, DE, 19902, USA
| | - Marcel Roberts
- John Jay College of Criminal Justice, 524 W 59 St., New York, NY, 10019, USA
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27
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Edson SM. Getting Ahead: Extraction of DNA from Skeletonized Cranial Material and Teeth. J Forensic Sci 2019; 64:1646-1657. [DOI: 10.1111/1556-4029.14123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/15/2019] [Accepted: 06/20/2019] [Indexed: 01/10/2023]
Affiliation(s)
- Suni M. Edson
- Armed Forces DNA Identification Laboratory Armed Forces Medical Examiner System 115 Purple Heart Drive Dover AFB DE 19902
- College of Science and Engineering Flinders University Adelaide South Australia Australia
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28
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Ring JD, Sturk-Andreaggi K, Alyse Peck M, Marshall C. Bioinformatic removal of NUMT-associated variants in mitotiling next-generation sequencing data from whole blood samples. Electrophoresis 2018; 39:2785-2797. [DOI: 10.1002/elps.201800135] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/16/2018] [Accepted: 08/16/2018] [Indexed: 11/05/2022]
Affiliation(s)
- Joseph David Ring
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL); DE United States
- ARP Sciences, LLC; Rockville MD United States
| | - Kimberly Sturk-Andreaggi
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL); DE United States
- ARP Sciences, LLC; Rockville MD United States
| | - Michelle Alyse Peck
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL); DE United States
- ARP Sciences, LLC; Rockville MD United States
| | - Charla Marshall
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL); DE United States
- ARP Sciences, LLC; Rockville MD United States
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29
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Kavlick MF. Development of a triplex mtDNA qPCR assay to assess quantification, degradation, inhibition, and amplification target copy numbers. Mitochondrion 2018; 46:41-50. [PMID: 30261278 DOI: 10.1016/j.mito.2018.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/11/2018] [Accepted: 09/18/2018] [Indexed: 01/11/2023]
Abstract
A hybrid absolute/relative qPCR assay which provides information regarding the condition of mitochondrial DNA (mtDNA) in a DNA sample is described. MtDNA concentration (copy number/μL) is determined via absolute quantification using a standard curve of a synthetic duplex DNA previously described (Kavlick et al., 2011). The state of mtDNA degradation is determined via the relative quantification of a mtDNA target found within the 16 s rRNA gene which is 3× longer than that of the short target in the former duplex assay, using the delta, delta Ct (ΔΔCt) method. The presence or absence of PCR inhibitors in the sample is qualitatively determined using a custom internal positive control (IPC) system which targets a unique and non-naturally occurring duplex DNA sequence. This IPC effectively detected inhibition by humic acid, tannic acid, melanin, and EDTA. All three assay components utilize sensitive and specific hydrolysis probes. The utility of ΔΔCt method was demonstrated in a series of experiments involving laboratory-fragmented DNA. Also described is a method for estimating copy number of any mtDNA target longer than the two targets amplified. The described triplex assay works well for intact and for fragmented or degraded mtDNA and therefore may be useful in forensic and ancient DNA disciplines as well as in biomedical research or practice.
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Affiliation(s)
- Mark F Kavlick
- Counterterrorism and Forensic Science Research Unit, Laboratory Division, Federal Bureau of Investigation, 2501 Investigation Parkway, Quantico, VA 22135, United States.
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30
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Snider A, Nilsson M, Dupal M, Toloue M, Tripathi A. A Microfluidics Workflow for Sample Preparation for Next-Generation DNA Sequencing. SLAS Technol 2018; 24:196-208. [PMID: 30142015 DOI: 10.1177/2472630318796133] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Next-generation sequencing technology requires amplified, short DNA fragments with known end sequences. Samples must undergo processing steps, including extraction and purification of genomic DNA (gDNA), fragmentation, end repair, adapter ligation, and amplification, to prepare a sequencing library. The process of sample preparation requires careful control of temperature and buffer conditions, as well as the stringent removal of contaminants. As a result, library preparation methods are often plagued by sample loss, long protocol times, numerous manual steps, and high cost. We attempt to understand and optimize each step of sample preparation on a microfluidic platform using magnetic bead motion through channels containing immiscible phases. Our platform integrates all steps associated with library preparation with no buffer exchanges and utilizes just 30-60 µL of reagents. Our chip shows a sixfold improvement in yield compared with an affinity spin column when capturing gDNA from samples of ~50 ± 4 MCF-7 cells. Finally, we show whole-genome shotgun sequencing results from 660 pg of human gDNA, in which >93 ± 1% of reads map to a reference genome at or above 99.9% confidence, matching a commercially available sample preparation kit optimized for low-cell-count samples.
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Affiliation(s)
- Adam Snider
- 1 Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | | | | | | | - Anubhav Tripathi
- 1 Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
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31
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Peck MA, Sturk-Andreaggi K, Thomas JT, Oliver RS, Barritt-Ross S, Marshall C. Developmental validation of a Nextera XT mitogenome Illumina MiSeq sequencing method for high-quality samples. Forensic Sci Int Genet 2018; 34:25-36. [PMID: 29413633 DOI: 10.1016/j.fsigen.2018.01.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 12/21/2017] [Accepted: 01/12/2018] [Indexed: 12/15/2022]
Abstract
Generating mitochondrial genome (mitogenome) data from reference samples in a rapid and efficient manner is critical to harnessing the greater power of discrimination of the entire mitochondrial DNA (mtDNA) marker. The method of long-range target enrichment, Nextera XT library preparation, and Illumina sequencing on the MiSeq is a well-established technique for generating mitogenome data from high-quality samples. To this end, a validation was conducted for this mitogenome method processing up to 24 samples simultaneously along with analysis in the CLC Genomics Workbench and utilizing the AQME (AFDIL-QIAGEN mtDNA Expert) tool to generate forensic profiles. This validation followed the Federal Bureau of Investigation's Quality Assurance Standards (QAS) for forensic DNA testing laboratories and the Scientific Working Group on DNA Analysis Methods (SWGDAM) validation guidelines. The evaluation of control DNA, non-probative samples, blank controls, mixtures, and nonhuman samples demonstrated the validity of this method. Specifically, the sensitivity was established at ≥25 pg of nuclear DNA input for accurate mitogenome profile generation. Unreproducible low-level variants were observed in samples with low amplicon yields. Further, variant quality was shown to be a useful metric for identifying sequencing error and crosstalk. Success of this method was demonstrated with a variety of reference sample substrates and extract types. These studies further demonstrate the advantages of using NGS techniques by highlighting the quantitative nature of heteroplasmy detection. The results presented herein from more than 175 samples processed in ten sequencing runs, show this mitogenome sequencing method and analysis strategy to be valid for the generation of reference data.
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Affiliation(s)
- Michelle A Peck
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), 115 Purple Heart Drive, Dover AFB, DE, 19902, United States; ARP Sciences, LLC, Contractor Supporting the Armed Forces Medical Examiner System, 9210 Corporate Boulevard, Suite 120, Rockville, MD, 20850, United States
| | - Kimberly Sturk-Andreaggi
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), 115 Purple Heart Drive, Dover AFB, DE, 19902, United States; ARP Sciences, LLC, Contractor Supporting the Armed Forces Medical Examiner System, 9210 Corporate Boulevard, Suite 120, Rockville, MD, 20850, United States
| | - Jacqueline T Thomas
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), 115 Purple Heart Drive, Dover AFB, DE, 19902, United States; ARP Sciences, LLC, Contractor Supporting the Armed Forces Medical Examiner System, 9210 Corporate Boulevard, Suite 120, Rockville, MD, 20850, United States
| | - Robert S Oliver
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), 115 Purple Heart Drive, Dover AFB, DE, 19902, United States; ARP Sciences, LLC, Contractor Supporting the Armed Forces Medical Examiner System, 9210 Corporate Boulevard, Suite 120, Rockville, MD, 20850, United States
| | - Suzanne Barritt-Ross
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), 115 Purple Heart Drive, Dover AFB, DE, 19902, United States; ARP Sciences, LLC, Contractor Supporting the Armed Forces Medical Examiner System, 9210 Corporate Boulevard, Suite 120, Rockville, MD, 20850, United States
| | - Charla Marshall
- Armed Forces Medical Examiner System's Armed Forces DNA Identification Laboratory (AFMES-AFDIL), 115 Purple Heart Drive, Dover AFB, DE, 19902, United States; ARP Sciences, LLC, Contractor Supporting the Armed Forces Medical Examiner System, 9210 Corporate Boulevard, Suite 120, Rockville, MD, 20850, United States.
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Sturk-Andreaggi K, Peck MA, Boysen C, Dekker P, McMahon TP, Marshall CK. AQME: A forensic mitochondrial DNA analysis tool for next-generation sequencing data. Forensic Sci Int Genet 2017; 31:189-197. [DOI: 10.1016/j.fsigen.2017.09.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/21/2017] [Accepted: 09/16/2017] [Indexed: 12/20/2022]
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