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“Omics” Technologies in Vaccine Research
Published in Mesut Karahan, Synthetic Peptide Vaccine Models, 2021
The genomic era is a revolution in vaccine development. It started with the shotgun sequencing technology producing the genome sequence of Haemophilus influenzae in 1995 by The Institute for Genomic Research (TIGR). Later, many technologies were developed for next-generation sequencing, such as massively parallel signature sequencing, polony sequencing, 454 pyrosequencing, reversible terminator sequencing, sequencing by oligonucleotide ligation detection (SOLiD), single-molecule real-time sequencing, ion torrent sequencing, or DNA nanoball sequencing (reviewed by Rajesh and Jaya 2017). Due to these advanced technologies, the number of published bacterial genomes increased considerably with 14,754 completed and 128,146 permanent draft genomes deposited in the Genomes Online Database (GOLD, https://gold.jgi.doe.gov) by June 2020. The organisms with completed genomes cover various bacterial pathogens, and they serve vaccine development to find out potential antigens (Serruto et al. 2009).
Precision medicine in ovarian carcinoma
Published in Debmalya Barh, Precision Medicine in Cancers and Non-Communicable Diseases, 2018
Shailendra Dwivedi, Purvi Purohit, Radhieka Misra, Jeewan Ram Vishnoi, Apul Goel, Puneet Pareek, Sanjay Khattri, Praveen Sharma, Sanjeev Misra, Kamlesh Kumar Pant
The massively parallel signature sequencing advanced by Lynx Therapeutics was the second or next-generation approach to DNA sequencing. The elementary Lynx Therapeutics platform was a microsphere (bead)-based system that discovers nucleotides in groups of four via an adapter ligation and adapter decoding strategy using reversible dye terminators (Mardis, 2008). Lynx Therapeutics (Hayward, California) merged with Solexa, which was later acquired by Illumina. This short-read sequencing technique is today incorporated into a fluidic flow cell design (HiSeq and Genome Analyzer systems, Illumina, San Diego, California) with eight individual lanes. The flow cell surface is established with capture oligonucleotide anchors, which hybridize the properly modified DNA segments of a sequencing library generated from a genomic DNA sample.
Melanoma Genomics—Techniques and Implications for Therapy
Published in Sanjiv S. Agarwala, Vernon K. Sondak, Melanoma, 2008
Adil I. Daud, Vernon K. Sondak, Ashani Weeraratna
The development of sequencing machines capable of handling large volumes of sequence information in a short amount of time has led to the large-scale sequencing of transcripts, or expressed sequence tags (ESTs), generated from random-primed complementary DNA (cDNA) libraries. Such effort has been pioneered by the Merck/Washington University (1) and is being extended by the Cancer Genome Anatomy Project (CGAP) (2). On their Web site (http://cgap.nci.nih.gov/), CGAP currently lists over one million ESTs from normal, premalignant, and malignant cells in its Tumor Gene Index (2). In an attempt to make the process of sequencing ESTs more efficient, massively parallel signature sequencing (MPSS) (3) and SAGE were developed (4). MPSS is a gene expression profiling method that sequences 16 to 20 base pair (bp) transcripts using a novel nongel-based signature-sequencing technique. MPSS can reliably generate an impressive two million tags from approximately 500 ng of messenger RNA (mRNA) (3). However, MPSS is a complex technique and is currently only available from Lynx Therapeutics Inc (Hayward, California, U.S.) (http://www.lynxgen.com).
Emerging drug targets for triple-negative breast cancer: a guided tour of the preclinical landscape
Published in Expert Opinion on Therapeutic Targets, 2022
Xuemei Xie, Jangsoon Lee, Toshiaki Iwase, Megumi Kai, Naoto T Ueno
One of the key challenges is the intratumoral heterogenicity of TNBC, whose TME is a complex entity composed of different stromal and immune cells and soluble factors. In the past decades, next-generation technology platforms and transcriptomic and computational screening methods have become a new standard for discovering novel targets for cancer treatment. However, most transcriptome analysis techniques, including the use of gene expression microarrays, serial analysis of gene expression, massively parallel signature sequencing, RNA sequencing (RNA-seq), and the detection flux of RNA seq, are based on data from the bulk cell population of a given tissue. Thus, these analyses may overlook genes that are differentially expressed by individual cells in the tissue. Indeed, different responses to treatment have been observed in clinics due to the extensive intratumoral heterogenicity of TNBC, namely, the existence of different gene expression patterns in different clusters of the same tumor [189–191]. Ideally, then, efforts to identify promising therapeutic targets in TNBC should produce results at the single-cell or single-tumor-component level.
Profile of women choosing the Harmony® Prenatal Test
Published in Expert Review of Molecular Diagnostics, 2018
Elisa Bevilacqua, Serena Resta, Andrew Carlin, Xin Kang, Teresa Cos Sanchez, Jérôme de Marchin, Jacques C. Jani
When it was shown that cfDNA fragments isolated in maternal blood could be used to detect fetal aneuploidy, several groups used this breakthrough to screen for T21, T18, and T13, using massively parallel DNA shotgun sequencing (MPSS) [28-32]. In order to address some limitations of MPSS, Ariosa Diagnostics developed a method called DANSR, which selectively evaluates specific genomic fragments from cfDNA. By enabling selective analysis of cfDNA, DANSR provides for more efficient use of sequencing in the detection of fetal aneuploidy [27], avoiding the large amounts of unused sequencing data generated by MPSS. Furthermore, DANSR allows for use of microarray technology for quantitation of cfDNA [33]. Using the FORTE algorithm (fetal-fraction optimized risk of trisomy evolution), Ariosa Diagnostics computed the probability of fetal trisomy in each subject [26] and demonstrated the efficacy of this assay and algorithm in the detection of fetal trisomies [8,26].