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Journal articles on the topic 'Next Generation Sequencin'

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Author: Grafiati

Published: 11 March 2023

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1

Barbosa, Cristina, Sofia Nogueira, Mário Gadanho, and Sandra Chaves. "Study on Commercial Spice and Herb Products Using Next-Generation Sequencing (NGS)." Journal of AOAC INTERNATIONAL 102, no. 2 (March 1, 2019): 369–75. http://dx.doi.org/10.5740/jaoacint.18-0407.

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Abstract Background: The use of deoxyribonucleic acid (DNA)-based testing methods is increasing in the food sector. DNA analyses can be a helpfultool for the analysis of many food products and can address some of the present concerns about adulteration and authenticity. Several analytical methods have been proposed to answer the specific topic of species composition in foods. Objective: The aim is to show that Next-generation sequencin(NGS) is a suitable tool for food analysis includingspices, herbs, seasoning, etc. Method: In the present study, we show how an internal NGSworkflow was setup and tested for species composition in real food seasoning samples. Results: Commercial samples of different spice and herb mixtures were analysed by our internal developed NGS workflow. The results obtained will be discussedbased on the labeling of the products relative tothetype of sample and species mixtures. Conclusions: Here we show that our internal NGS workflow can be successfully applied in complex commercial samples. Highlights: NGS can become a powerfull and reliable tool for authentication of spices and herbs products.

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C, Chinmayee, Amrita Nischal, and C. R. Manjunath Soumya K. N. "Next Generation Sequencing in Big Data." International Journal of Trend in Scientific Research and Development Volume-2, Issue-4 (June 30, 2018): 379–89. http://dx.doi.org/10.31142/ijtsrd12975.

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3

He, Jiahuan. "Next-Generation Sequencing on COVID-19 Pandemic." International Journal of Bioscience, Biochemistry and Bioinformatics 12, no. 2 (2022): 30–38. http://dx.doi.org/10.17706/ijbbb.2022.12.2.30-38.

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4

Vlk, D., and J. Řepková. "Application of next-generation sequencing in plant breeding." Czech Journal of Genetics and Plant Breeding 53, No. 3 (September 13, 2017): 89–96. http://dx.doi.org/10.17221/192/2016-cjgpb.

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In the past decade, next-generation sequencing (NGS) platforms have changed the impact of sequencing on our knowledge of crop genomes and gene regulation. These techniques are today acquiring a great potential in metagenomic and agrigenomic research while showing prospects for their utilization in plant breeding. We can now obtain new and beneficial information about gene regulation on the cellular as well as whole-plant level through RNA-sequencing and subsequent expression analyses of genes participating in plant defence reactions to pathogens and in abiotic stress tolerance. NGS has facilitated the development of methods to genotype very large numbers of single-nucleotide polymorphisms. Genotyping- by-sequencing and whole-genome resequencing can lead to the development of molecular markers suited to studies of genetic relationships among breeding materials, creation of detailed genetic mapping of targeted genes and genome-wide association studies. Plant genotyping can benefit plant breeding through selection of individuals resistant to climatic stress and to pathogens causing substantial losses in agriculture.

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Maver, Aleš, and Borut Peterlin. "Paediatria Croatica." Paediatria Croatica 57, no. 4 (December 20, 2013): 295–300. http://dx.doi.org/10.13112/pc.2013.1.

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6

Borodinov, A. G., V. V. Manoilov, I. V. Zarutsky, A. I. Petrov, and V. E. Kurochkin. "GENERATIONS OF DNA SEQUENCING METHODS (REVIEW)." NAUCHNOE PRIBOROSTROENIE 30, no. 4 (November 30, 2020): 3–20. http://dx.doi.org/10.18358/np-30-4-i320.

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Several decades have passed since the development of the revolutionary DNA sequencing method by Frederick Sanger and his colleagues. After the Human Genome Project, the time interval between sequencing technologies began to shrink, while the volume of scientific knowledge continued to grow exponentially. Following Sanger sequencing, considered as the first generation, new generations of DNA sequencing were consistently introduced into practice. Advances in next generation sequencing (NGS) technologies have contributed significantly to this trend by reducing costs and generating massive sequencing data. To date, there are three generations of sequencing technologies. Second generation se-quencing, which is currently the most commonly used NGS technology, consists of library preparation, amplification and sequencing steps, while in third generation sequencing, individual nucleic acids are sequenced directly to avoid bias and have higher throughput. The development of new generations of sequencing has made it possible to overcome the limitations of traditional DNA sequencing methods and has found application in a wide range of projects in molecular biology. On the other hand, with the development of next generation technologies, many technical problems arise that need to be deeply analyzed and solved. Each generation and sequencing platform, due to its methodological approach, has specific advantages and disadvantages that determine suitability for certain applications. Thus, the assessment of these characteristics, limitations and potential applications helps to shape the directions for further research on sequencing technologies.

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Mardis, Elaine, Timothy J. Ley, and Richard K. Wilson. "Sequencing Acute Myeloid Leukemia Genomes with “Next Generation” Technologies." Blood 112, no. 11 (November 16, 2008): sci—36—sci—36. http://dx.doi.org/10.1182/blood.v112.11.sci-36.sci-36.

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Abstract For most patients with a sporadic presentation of acute myeloid leukemia (AML), neither the initiating nor the progression mutations responsible for disease are known. Recent attempts to identify key mutations with directed sequencing approaches, or with array-based genomic studies, have had limited success, suggesting that unbiased whole genome sequencing approaches may be required to identify most of the mutations responsible for AML pathogenesis. Until recently, whole genome sequencing has been impractical due to the high cost of conventional capillary-based sequencing and the large numbers of enriched primary tumor cells required to yield the necessary genomic DNA for library preparation. “Next Generation” sequencing approaches have changed this landscape dramatically. Using the Solexa/Illumina platform, we have now sequenced the genomic DNA of highly enriched tumor cells and normal skin cells obtained from a carefully selected patient with a typical presentation of FAB M1 AML. We obtained 98.2 billion bases of sequences from the cytogenetically normal tumor cell genome (32.7 fold haploid coverage), and 41.8 billion bases of sequence from the normal skin genome (13.9 fold coverage). Using these data, we detected diploid sequence coverage of 91% of 46,320 heterozygous SNPs, defined in the tumor genome (by array-based genotyping), and 83% diploid coverage of the skin genome. Of 2,647,695 well-supported single nucleotide variants in the tumor genome, 2,588,486 (97.7%) were also detected in the patient’s skin genome, defining them as inherited. From the remaining variants, 8 have been fully validated as somatic mutations by conventional capillary sequencing using PCR-generated amplicons. We also detected somatic mutations in the FLT3 (ITD) and NPM1 genes (a classic NPMc mutation). Based on deep read-count data of the novel variants on a 454 sequencer, we hypothesize that all of the mutations are in virtually all of the tumor cells, and all were retained at relapse 11 months later, suggesting that a single dominant clone contained all of the mutations. None of the novel mutations has previously been detected in AML cases (and none were found in any of 187 additional AML cases studied here). A number of additional potential somatic mutations in regions lying near genes (but not altering coding sequences) are currently being validated and tested for recurrence in other AML samples. Whole genome sequencing of a second M1 AML genome is now underway. These results demonstrate the power of unbiased whole genome sequencing approaches to discover cancer-associated mutations in novel candidate genes.

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8

Kim, Minseok, Youlchang Baek, and Young Kyoon Oh. "Application of Next Generation Sequencing to Investigate Microbiome in the Livestock Sector." Journal of Animal Environmental Science 21, no. 3 (September 30, 2015): 93–98. http://dx.doi.org/10.11109/jaes.2015.21.3.93.

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Kim, Se Hee, Eun Young Nam, Kang-Hee Cho, Il Sheob Shin, Hyun Ran Kim, and Hae Seong Hwang. "Comparison of transcriptome analysis between red flash peach cultivar and white flash peach cultivar using next generation sequencing." Journal of Plant Biotechnology 39, no. 4 (December 31, 2012): 273–80. http://dx.doi.org/10.5010/jpb.2012.39.4.273.

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10

Zeeshan, Faiza, and Sadaf Razzak. "Next Generation Sequencing and its Role in Clinical Microbiology and Molecular Epidemiology." ANNALS of JINNAH SINDH MEDICAL UNIVERSITY 6, no. 1 (June 30, 2020): 31–32. http://dx.doi.org/10.46663/ajsmu.v6i1.31-32.

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11

Kumar, Kishore R., Mark J. Cowley, and Ryan L. Davis. "Next-Generation Sequencing and Emerging Technologies." Seminars in Thrombosis and Hemostasis 45, no. 07 (May 16, 2019): 661–73. http://dx.doi.org/10.1055/s-0039-1688446.

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AbstractGenetic sequencing technologies are evolving at a rapid pace with major implications for research and clinical practice. In this review, the authors provide an updated overview of next-generation sequencing (NGS) and emerging methodologies. NGS has tremendously improved sequencing output while being more time and cost-efficient in comparison to Sanger sequencing. The authors describe short-read sequencing approaches, such as sequencing by synthesis, ion semiconductor sequencing, and nanoball sequencing. Third-generation long-read sequencing now promises to overcome many of the limitations of short-read sequencing, such as the ability to reliably resolve repeat sequences and large genomic rearrangements. By combining complementary methods with massively parallel DNA sequencing, a greater insight into the biological context of disease mechanisms is now possible. Emerging methodologies, such as advances in nanopore technology, in situ nucleic acid sequencing, and microscopy-based sequencing, will continue the rapid evolution of this area. These new technologies hold many potential applications for hematological disorders, with the promise of precision and personalized medical care in the future.

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12

Burgess, Darren J. "Next-generation sequencing of the next generation." Nature Reviews Genetics 12, no. 2 (December 21, 2010): 78–79. http://dx.doi.org/10.1038/nrg2943.

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Hennekam, Raoul C. M., and Leslie G. Biesecker. "Next-generation sequencing demands next-generation phenotyping." Human Mutation 33, no. 5 (March 27, 2012): 884–86. http://dx.doi.org/10.1002/humu.22048.

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14

Bösl, Elsbeth, and Stefanie Samida. "Next generation sequencing." TATuP - Zeitschrift für Technikfolgenabschätzung in Theorie und Praxis 30, no. 2 (July 26, 2021): 10–52. http://dx.doi.org/10.14512/tatup.30.2.10.

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Next Generation Sequencing led to major knowledge gains in the molecular life sciences. But the new technology provides data that pose new challenges to both science and society. New fields of research are emerging and questions of identity on the basis of genetic analyses are being negotiated.

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15

Jain, AmitKumar, and Guruprasad Bhat. "Next generation sequencing." Indian Journal of Medical and Paediatric Oncology 41, no. 3 (2020): 381. http://dx.doi.org/10.4103/ijmpo.ijmpo_28_20.

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16

Patel, Snehal B., Wendy Kadi, Ann E. Walts, Alberto M. Marchevsky, Andy Pao, Angela Aguiluz, Tudor Mudalige, Zhenqui Liu, Nan Deng, and Jean Lopategui. "Next-Generation Sequencing." Journal of Molecular Diagnostics 19, no. 6 (November 2017): 870–80. http://dx.doi.org/10.1016/j.jmoldx.2017.07.006.

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17

HULICK, PETER. "Next-Generation Sequencing." Family Practice News 42, no. 9 (May 2012): 8. http://dx.doi.org/10.1016/s0300-7073(12)70394-8.

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18

HULICK, PETER. "Next-Generation Sequencing." Internal Medicine News 45, no. 6 (April 2012): 41. http://dx.doi.org/10.1016/s1097-8690(12)70305-0.

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19

Penttilä, S., T. Suominen, S. Lehtinen, M. Jokela, J. Palmio, and B. Udd. "NEXT GENERATION SEQUENCING." Neuromuscular Disorders 29 (October 2019): S152. http://dx.doi.org/10.1016/j.nmd.2019.06.406.

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20

Xiong, Momiao, Zhongming Zhao, Jonathan Arnold, and Fuli Yu. "Next-Generation Sequencing." Journal of Biomedicine and Biotechnology 2010 (2010): 1–2. http://dx.doi.org/10.1155/2010/370710.

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21

Hempel, M., T. B. Haack, S. Eck, and H. Prokisch. "„Next generation sequencing“." Monatsschrift Kinderheilkunde 159, no. 9 (September 2011): 827–33. http://dx.doi.org/10.1007/s00112-011-2446-y.

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22

Blow, Nathan. "DNA sequencing: generation next-next." Nature Methods 5, no. 3 (March 2008): 267–74. http://dx.doi.org/10.1038/nmeth0308-267.

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23

Carpentieri, Bruno. "Compression of Next-Generation Sequencing Data and of DNA Digital Files." Algorithms 13, no. 6 (June 24, 2020): 151. http://dx.doi.org/10.3390/a13060151.

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The increase in memory and in network traffic used and caused by new sequenced biological data has recently deeply grown. Genomic projects such as HapMap and 1000 Genomes have contributed to the very large rise of databases and network traffic related to genomic data and to the development of new efficient technologies. The large-scale sequencing of samples of DNA has brought new attention and produced new research, and thus the interest in the scientific community for genomic data has greatly increased. In a very short time, researchers have developed hardware tools, analysis software, algorithms, private databases, and infrastructures to support the research in genomics. In this paper, we analyze different approaches for compressing digital files generated by Next-Generation Sequencing tools containing nucleotide sequences, and we discuss and evaluate the compression performance of generic compression algorithms by confronting them with a specific system designed by Jones et al. specifically for genomic file compression: Quip. Moreover, we present a simple but effective technique for the compression of DNA sequences in which we only consider the relevant DNA data and experimentally evaluate its performances.

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24

Foley, A. Reghan, Sandra Donkervoort, and Carsten G. Bönnemann. "Next-generation sequencing still needs our generation's clinicians." Neurology Genetics 1, no. 2 (August 2015): e13. http://dx.doi.org/10.1212/nxg.0000000000000019.

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25

P.S, Kavyashree, Sweta Das, and Preetha Tilak. "Maple Syrup Urine Disease - Role of Next Generation Sequencing, A Newer Molecular Technique." Indian Journal of Genetics and Molecular Research 6, no. 2 (2017): 51–53. http://dx.doi.org/10.21088/ijgmr.2319.4782.6217.3.

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Стеценко, И. Ф., А. Ю. Красненко, У. С. Станоевич, А. А. Мещеряков, И. К. Воротников, О. С. Дружиловская, В. А. Белова, and А. В. Чуров. "Идентификация BRCA1/2-мутаций при раке молочной железы с применением технологии высокопроизводительного секвенирования." НАНОМЕДИЦИНА, no. 6 (December 24, 2018): 183–89. http://dx.doi.org/10.24075/vrgmu.2018.074.

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Рак молочной железы (РМЖ) является одной из наиболее распространенных форм солидных опухолей. Анализ особенностей патогенеза РМЖ на молекулярном уровне с применением современных методов генетического анализа и на разных стадиях заболевания позволяет получить новые данные для их дальнейшего применения в клинической практике. Молекулярное профилирование с применением технологий высокопроизводительного секвенирования все чаще применяют в качестве клинического теста при подборе таргетных препаратов для лечения пациентов с высокорезистентными к терапии опухолями при РМЖ. Целью работы было провести таргетное секвенирование генов BRCA1 и BRCA2 в составе панели онкогенов. Из 66 образцов ДНК пациентов с опухолями молочной железы, мутации BRCA1/2 обнаружены у 39 пацентов. Найдено 78 уникальных генетических вариантов, из них 30 мутаций в гене BRCA1 и 48 мутаций в гене BRCA2. Идентифицировано 33 мутации, оказывающие влияние на сайты посттрансляционной модификации белков (PMT-мутации).

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Fox, A., I. A. Adams, U. Hany, T. Hodges, S. M. D. Forde, L. E. Jackson, A. Skelton, and V. Barton. "The application of Next-Generation Sequencing for screening seeds for viruses and viroids." Seed Science and Technology 43, no. 3 (December 15, 2015): 531–35. http://dx.doi.org/10.15258/sst.2015.43.3.06.

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28

Mellmann, Alexander, Paal Skytt Andersen, Stefan Bletz, Alexander W. Friedrich, Thomas A. Kohl, Berit Lilje, Stefan Niemann, Karola Prior, John W. Rossen, and Dag Harmsen. "High Interlaboratory Reproducibility and Accuracy of Next-Generation-Sequencing-Based Bacterial Genotyping in a Ring Trial." Journal of Clinical Microbiology 55, no. 3 (January 4, 2017): 908–13. http://dx.doi.org/10.1128/jcm.02242-16.

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ABSTRACTToday, next-generation whole-genome sequencing (WGS) is increasingly used to determine the genetic relationships of bacteria on a nearly whole-genome level for infection control purposes and molecular surveillance. Here, we conducted a multicenter ring trial comprising five laboratories to determine the reproducibility and accuracy of WGS-based typing. The participating laboratories sequenced 20 blind-codedStaphylococcus aureusDNA samples using 250-bp paired-end chemistry for library preparation in a single sequencing run on an Illumina MiSeq sequencer. The run acceptance criteria were sequencing outputs >5.6 Gb and Q30 read quality scores of >75%. Subsequently, spa typing, multilocus sequence typing (MLST), ribosomal MLST, and core genome MLST (cgMLST) were performed by the participants. Moreover, discrepancies in cgMLST target sequences in comparisons with the included and also published sequence of the quality control strain ATCC 25923 were resolved using Sanger sequencing. All five laboratories fulfilled the run acceptance criteria in a single sequencing run without any repetition. Of the 400 total possible typing results, 394 of the reported spa types, sequence types (STs), ribosomal STs (rSTs), and cgMLST cluster types were correct and identical among all laboratories; only six typing results were missing. An analysis of cgMLST allelic profiles corroborated this high reproducibility; only 3 of 183,927 (0.0016%) cgMLST allele calls were wrong. Sanger sequencing confirmed all 12 discrepancies of the ring trial results in comparison with the published sequence of ATCC 25923. In summary, this ring trial demonstrated the high reproducibility and accuracy of current next-generation sequencing-based bacterial typing for molecular surveillance when done with nearly completely locked-down methods.

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Liu, Lin, Yinhu Li, Siliang Li, Ni Hu, Yimin He, Ray Pong, Danni Lin, Lihua Lu, and Maggie Law. "Comparison of Next-Generation Sequencing Systems." Journal of Biomedicine and Biotechnology 2012 (2012): 1–11. http://dx.doi.org/10.1155/2012/251364.

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With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities. NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world’s biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized.

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Chen, Peisong, Xuegao Yu, Hao Huang, Wentao Zeng, Xiaohong He, Min Liu, and Bin Huang. "Evaluation of Ion Torrent next-generation sequencing for thalassemia diagnosis." Journal of International Medical Research 48, no. 12 (December 2020): 030006052096777. http://dx.doi.org/10.1177/0300060520967778.

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Introduction To evaluate a next-generation sequencing (NGS) workflow in the screening and diagnosis of thalassemia. Methods In this prospective study, blood samples were obtained from people undergoing genetic screening for thalassemia at our centre in Guangzhou, China. Genomic DNA was polymerase chain reaction (PCR)-amplified and sequenced using the Ion Torrent system and results compared with traditional genetic analyses. Results Of the 359 subjects, 148 (41%) were confirmed to have thalassemia. Variant detection identified 35 different types including the most common. Identification of the mutational sites by NGS were consistent with those identified by Sanger sequencing and Gap-PCR. The sensitivity and specificities of the Ion Torrent NGS were 100%. In a separate test of 16 samples, results were consistent when repeated ten times. Conclusion Our NGS workflow based on the Ion Torrent sequencer was successful in the detection of large deletions and non-deletional defects in thalassemia with high accuracy and repeatability.

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Park, Kyungmin, Seung-Ho Lee, Jongwoo Kim, Jingyeong Lee, Geum-Young Lee, Seungchan Cho, Seung Ho Lee, et al. "Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea." Viruses 13, no. 5 (May 6, 2021): 847. http://dx.doi.org/10.3390/v13050847.

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Whole-genome sequencing of infectious agents enables the identification and characterization of emerging viruses. The MinION device is a portable sequencer that allows real-time sequencing in fields or hospitals. Hantaan orthohantavirus (Hantaan virus, HTNV), harbored by Apodemus agrarius, causes hemorrhagic fever with renal syndrome (HFRS) and poses a critical public health threat worldwide. In this study, we aimed to evaluate the feasibility of using nanopore sequencing for whole-genome sequencing of HTNV from samples having different viral copy numbers. Amplicon-based next-generation sequencing was performed in A. agrarius lung tissues collected from the Republic of Korea. Genomic sequences of HTNV were analyzed based on the viral RNA copy numbers. Amplicon-based nanopore sequencing provided nearly full-length genomic sequences of HTNV and showed sufficient read depth for phylogenetic analysis after 8 h of sequencing. The average identity of the HTNV genome sequences for the nanopore sequencer compared to those of generated from Illumina MiSeq revealed 99.8% (L and M segments) and 99.7% (S segment) identities, respectively. This study highlights the potential of the portable nanopore sequencer for rapid generation of accurate genomic sequences of HTNV for quicker decision making in point-of-care testing of HFRS patients during a hantavirus outbreak.

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AL-Obaidi, Omar Raheem Khalaf, Mohammed Ahmed Mustafa, and Rasha Abdul Adheem Yaseen. "Next-generation sequencing techniques." Science Archives 02, no. 01 (2021): 26–29. http://dx.doi.org/10.47587/sa.2021.2105.

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33

Shendure, Jay, and Hanlee Ji. "Next-generation DNA sequencing." Nature Biotechnology 26, no. 10 (October 2008): 1135–45. http://dx.doi.org/10.1038/nbt1486.

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Kolb, Bradford Alan, Valerie Lynn Baker, Angeline Beltsos, Selwyn Oskowitz, Kaylen M. Silverberg, and Andrew Anthony Toledo. "Next-Generation DNA Sequencing." Obstetrics & Gynecology 125 (May 2015): 92S. http://dx.doi.org/10.1097/01.aog.0000463186.97632.d2.

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Levy, Shawn E., and Braden E. Boone. "Next-Generation Sequencing Strategies." Cold Spring Harbor Perspectives in Medicine 9, no. 7 (October 15, 2018): a025791. http://dx.doi.org/10.1101/cshperspect.a025791.

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McCombie, W. Richard, John D. McPherson, and Elaine R. Mardis. "Next-Generation Sequencing Technologies." Cold Spring Harbor Perspectives in Medicine 9, no. 11 (November 26, 2018): a036798. http://dx.doi.org/10.1101/cshperspect.a036798.

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Tang, Lei. "Next-generation peptide sequencing." Nature Methods 15, no. 12 (November 30, 2018): 997. http://dx.doi.org/10.1038/s41592-018-0240-7.

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Mardis, Elaine R. "Next-Generation Sequencing Platforms." Annual Review of Analytical Chemistry 6, no. 1 (June 12, 2013): 287–303. http://dx.doi.org/10.1146/annurev-anchem-062012-092628.

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Wells, D., K. Kaur, E. Fragouli, and S. Munné. "I12 Next generation sequencing." Reproductive BioMedicine Online 26 (May 2013): S5. http://dx.doi.org/10.1016/s1472-6483(13)60018-8.

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Wistuba, Ignacio, and Xuefei Li. "MTE21.01 Next Generation Sequencing." Journal of Thoracic Oncology 12, no. 1 (January 2017): S172. http://dx.doi.org/10.1016/j.jtho.2016.11.153.

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Baker, Shawn C. "Next-Generation Sequencing Challenges." Genetic Engineering & Biotechnology News 37, no. 3 (February 2017): 1, 14–15, 17. http://dx.doi.org/10.1089/gen.37.03.01.

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Jarvie, Thomas. "Next generation sequencing technologies." Drug Discovery Today: Technologies 2, no. 3 (September 2005): 255–60. http://dx.doi.org/10.1016/j.ddtec.2005.08.003.

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Tsai, Chung-Jui. "Next-generation sequencing for next-generation breeding, and more." New Phytologist 198, no. 3 (April 12, 2013): 635–37. http://dx.doi.org/10.1111/nph.12245.

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Radovich, Milan, Ryan Frederick Porter, Madison Conces, Yaman Suleiman, Sunil S. Badve, Kenneth Kesler, Bryan P. Schneider, and Patrick J. Loehrer. "Next-generation sequencing of thymic malignancies." Journal of Clinical Oncology 30, no. 15_suppl (May 20, 2012): 7032. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.7032.

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7032 Background: Thymic malignancies are rare with ~500 cases in the US per year. Apart from standard chemotherapy, treatment options are limited. Further, the challenge of histologic subtyping of these tumors along with an inadequate understanding of the transcriptional biology is a hindrance to the development of targeted therapies. Methods: Thymic malignancies and normal tissues were obtained from the Indiana University Simon Cancer Center. The WHO subtypes of our samples include: (4) type A, (2) A/B, (1) B2, (5) B3, (1) C, and (3) normal tissues. RNA was sequenced on a Life Technologies SOLiD sequencer. For gene expression, reads were mapped to the genome using BioScope and outputs imported into Partek GS. In Partek, statistical comparison of gene expression as well as PCA & clustering analyses were performed. Results: Unsupervised hierarchical clustering of gene expression values revealed 100% concordance between gene expression clusters and WHO subtype. A subsequent unsupervised clustering of 705 pre-miRNAs also showed substantial concordance between clusters and subtype. By analyzing the dendrograms, A & A/B tumors were significantly different from B type tumors, as well as C and normal. A substantial differentiator was a large cluster of overexpression in A&A/B tumors that was nearly absent in the others on chr19q13.42 corresponding to the miR-515 cluster (43 miRNAs). When comparing A & A/B tumors vs. B type tumors, 1334 genes are differentially expressed (258 downregulated) (FDR<5%). 95/258 genes are predicted to be downregulated by the miR-515 cluster including several transcription factors and tumor suppressors. When looking at mutations, we detected no recurrent gene fusions, though we are detecting several point mutations and small insertion deletions. These are being followed up by exome sequencing. Conclusions: Analyses reveal that RNA-seq can be used to accurately subtype Thymic Malignancies and the development of an expression based diagnostic is feasible. Further, these data support that the main differentiator of thymomas may lie in the expression of a single miRNA cluster. In addition, several mutations in key pathways are implicated. Ongoing analyses include: alternative splicing, noncoding RNAs, viral analysis and exome sequencing.

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Саенко, В. В., and V. V. Saenko. "Дробно-устойчивая статистика экспрессии генов в экспериментальных данных секвенирования нового поколения." Mathematical Biology and Bioinformatics 11, no. 2 (November 25, 2016): 278–87. http://dx.doi.org/10.17537/2016.11.278.

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As has been shown, in the author's published articles, that the application of class of the fractional-stable laws to the genes expression results obtained by DNA-microarys leads to poor agreement between experimental and theoretical distributions. This difference can be explained by the imperfection of the technology of the gene expression determination. In this article the distributions of the gene expression obtained by Next Generation Sequence technology are investigated. In this technology the determination technique of the gene expression differs from the DNA-microarrays technology. This results to more qualitative results of an approximation. In particular, it is established that the probability density function of the gene expression has a form of shift-scale mixture of probability laws, where one of the components of the mixture is the fractional-stable distribution.

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Neafsey, Daniel E., and Brian J. Haas. "'Next-generation' sequencing becomes 'now-generation'." Genome Biology 12, no. 3 (2011): 303. http://dx.doi.org/10.1186/gb-2011-12-3-303.

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Shahid, Saba, Shariq Ahmed, Saima Siddiqui, Misha Sohail, and Tahir S. Shamsi. "Targeted Next Generation Sequencing for Myeloid Neoplasm in Pakistani Patients." Blood 132, Supplement 1 (November 29, 2018): 5137. http://dx.doi.org/10.1182/blood-2018-99-113766.

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Abstract Introduction: Myeloid malignancies are heterogenous diseases caused by excessive accumulation of apparently myeloid clone of cells. Genomic studies on myeloid malignancies in recent years have identified new genetic alterations with biological and clinical significance. In addition to cytogenetics and morphological examination these genetic mutation play an important role in diagnosis, prognosis and treatment of the patient. We assessed the frequency and clinicopathologic significance of 54 genes in myeloid neoplasm patients by using targeted next-generation sequencing. Methods: About 50 samples were collected from OPD at National Institute of Blood Diseases (NIBD), that consisting of 17 MDS, 18 AML and other myeloid neoplasms. They comprises of 33 males and 17 females with median age of 33 years (range: 5-69 years). The myeloid sequencing panel of 54 genes (complete coding exons of 15 genes and exonic hotspots of 39 genes) was sequenced. The panel total coverage was 141 kb in genomic sequence. TruSight myeloid sequencing (Illumina, CA) libraries were prepared and runs were performed on a MiSeq (Illumina) genome sequencer. The generated data were analyzed by on-instrument software or TruSeq Amplicon® and BaseSpace Apps®. Results: Overall 3092 variants were identified, after excluding intronic and synonymous variants, 380 missense variants were found in 50 patients. Around 38 mutations in 22 genes were identified in 23 out of 50 samples (46 %). The recurrent mutations found in RUNX1, ASXL1, GATA2 and CEPBA genes in our cohort. Conclusion: Most of the myeloid neoplasms are not easily manageable with limited treatment options. Therefore, targeted gene panel by next generation sequencing was an appropriate method for precise identification of mutations in myeloid neoplasms at our institution. Based on the obtained findings we will be able to design patient management plan with respect to individualize genetic mutations in the clinical setting. Disclosures No relevant conflicts of interest to declare.

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Tounsi, Wajnat A., Tracey E. Madgett, and Neil D. Avent. "Complete RHD next-generation sequencing: establishment of reference RHD alleles." Blood Advances 2, no. 20 (October 18, 2018): 2713–23. http://dx.doi.org/10.1182/bloodadvances.2018017871.

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Abstract The Rh blood group system (ISBT004) is the second most important blood group after ABO and is the most polymorphic one, with 55 antigens encoded by 2 genes, RHD and RHCE. This research uses next-generation sequencing (NGS) to sequence the complete RHD gene by amplifying the whole gene using overlapping long-range polymerase chain reaction (LR-PCR) amplicons. The aim was to study different RHD alleles present in the population to establish reference RHD allele sequences by using the analysis of intronic single-nucleotide polymorphisms (SNPs) and their correlation to a specific Rh haplotype. Genomic DNA samples (n = 69) from blood donors of different serologically predicted genotypes including R1R1 (DCe/DCe), R2R2 (DcE/DcE), R1R2 (DCe/DcE), R2RZ (DcE/DCE), R1r (DCe/dce), R2r (DcE/dce), and R0r (Dce/dce) were sequenced and data were then mapped to the human genome reference sequence hg38. We focused on the analysis of hemizygous samples, as these by definition will only have a single copy of RHD. For the 69 samples sequenced, different exonic SNPs were detected that correlate with known variants. Multiple intronic SNPs were found in all samples: 21 intronic SNPs were present in all samples indicating their specificity to the RHD*DAU0 (RHD*10.00) haplotype which the hg38 reference sequence encodes. Twenty-three intronic SNPs were found to be R2 haplotype specific, and 15 were linked to R1, R0, and RZ haplotypes. In conclusion, intronic SNPs may represent a novel diagnostic approach to investigate known and novel variants of the RHD and RHCE genes, while being a useful approach to establish reference RHD allele sequences.

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Panagiotis, Chatzinikolaou, Makris Christos, Dimitrios Vlachakis, and Sophia Kossida. "A Benchmark of Structural Variant Analysis Tools for Next Generation Sequencing Data." International Journal of Systems Biology and Biomedical Technologies 2, no. 4 (October 2013): 86–98. http://dx.doi.org/10.4018/ijsbbt.2013100106.

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In language of genetics and biochemistry, sequencing is the determination of an unbranched biopolymer's primary structure. A sequence is a symbolic linear depiction, result of sequencing. This sequence is a succinct summary of the most of the sequenced molecule's atomic-level structure. (Most known is DNA-sequencing, RNA-sequencing, Protein-sequencing and Next-Generation-sequencing)

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Tripathi, Pooja, Jyotsna Singh, Jonathan A. Lal, and Vijay Tripathi. "Next-Generation Sequencing: An Emerging Tool for Drug Designing." Current Pharmaceutical Design 25, no. 31 (November 14, 2019): 3350–57. http://dx.doi.org/10.2174/1381612825666190911155508.

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Background: With the outbreak of high throughput next-generation sequencing (NGS), the biological research of drug discovery has been directed towards the oncology and infectious disease therapeutic areas, with extensive use in biopharmaceutical development and vaccine production. Method: In this review, an effort was made to address the basic background of NGS technologies, potential applications of NGS in drug designing. Our purpose is also to provide a brief introduction of various Nextgeneration sequencing techniques. Discussions: The high-throughput methods execute Large-scale Unbiased Sequencing (LUS) which comprises of Massively Parallel Sequencing (MPS) or NGS technologies. The Next geneinvolved necessarily executes Largescale Unbiased Sequencing (LUS) which comprises of MPS or NGS technologies. These are related terms that describe a DNA sequencing technology which has revolutionized genomic research. Using NGS, an entire human genome can be sequenced within a single day. Conclusion: Analysis of NGS data unravels important clues in the quest for the treatment of various lifethreatening diseases and other related scientific problems related to human welfare.

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