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From Single Level Analysis to Multi-Omics Integrative Approaches: A Powerful Strategy towards the Precision Oncology
Published in Shaker A. Mousa, Raj Bawa, Gerald F. Audette, The Road from Nanomedicine to Precision Medicine, 2020
Maria Eugenia Gallo Cantafio, Katia Grillone, Daniele Caracciolo, Francesca Scionti, Mariamena Arbitrio, Vito Barbieri, Licia Pensabene, Pietro Hiram Guzzi, Maria Teresa Di Martino
Transcriptomic technologies allow for the production of information on the total transcripts of a genome or a specific cell by the use of two high-throughput methods: (i) microarrays, which allow the simultaneous detection and quantification of thousands of previously identified transcripts by hybridization of targets on high-density array containing complementary probes; (ii) RNA sequencing (RNA-Seq), which uses high-throughput massive parallel sequencing combined with computational methods to detect and quantify the complete set of RNA transcripts. Comparison of transcriptomes in different tissues, conditions, time points, or even at single cell level gives information on how genes are regulated and differentially expressed disclosing details about the biology of the system. Moreover, expression profiles can also help to infer the functions of previously unannotated genes. Thereby, the lowering of the technology costs and increased sensitivity allowed a large amount of studies. Many consortium efforts have produced transcriptomic data sets of (i) cancer cell lines, such as the Encyclopedia of DNA Elements (ENCODE) [46], the Cancer Cell Line Encyclopedia (CCLE) [47], and Genentech [48]; (ii) normal tissues, such as the Genotype-Tissue Expression (GTEx) project [49] and the Human Protein Atlas (HPA) [50]; and (iii) tumor tissues such as TCGA [51] and the Stand Up To Cancer-Prostate Cancer Foundation (SU2C-PCF) project [52]. RNA-seq has become the most robust and comprehensive transcriptome profiling technology, virtually replacing all expression microarrays. An example of the clinical utility of RNA-seq has been demonstrated by several studies disclosing a large number of new actionable genetic events [53] or the real-time management of pediatric tumors [54] as well as the characterization of metastatic tumors [55]. Moreover, the advance in RNA-Seq library preparation methods, resulted in enhanced sensitivity and effectiveness of single-cell in situ RNA-Seq also performed in fixed tissues [56].
A pilot study of exome sequencing in a diverse New Zealand cohort with undiagnosed disorders and cancer
Published in Journal of the Royal Society of New Zealand, 2018
Colina McKeown, Samantha Connors, Rachel Stapleton, Tim Morgan, Ian Hayes, Katherine Neas, Joanne Dixon, Kate Gibson, David M. Markie, Peter Tsai, Cherie Blenkiron, Sandra Fitzgerald, Paula Shields, Patrick Yap, Ben Lawrence, Cristin Print, Stephen P. Robertson
Diagnostic rates for genetic disorders have substantially improved over the last decade, first by the institution of chromosomal microarray analysis (CMA) which can detect sizeable deletions or duplications resulting in a diagnostic yield of 15%–20% compared to 5% using conventional karyotypic analysis (Yang et al. 2014; Chong et al. 2015; Valencia et al. 2015). Until recently, further sequential genetic testing required a strong hypothesis regarding a specific diagnosis and the gene involved (Shashi et al. 2014). With the advent of massively parallel sequencing (MPS), broader yet quicker and cheaper genetic testing has become possible, with its use rapidly increasing worldwide (de Ligt et al. 2012; Yang et al. 2014; Valencia et al. 2015; Wright et al. 2015; Monroe et al. 2016).
The interpretation of forensic DNA profiles: an historical perspective
Published in Journal of the Royal Society of New Zealand, 2020
Jo-Anne Bright, Hannah Kelly, Zane Kerr, Catherine McGovern, Duncan Taylor, John S. Buckleton
Another area of active development within the forensic community involves DNA typing using massively parallel sequencing (MPS), also referred to as next-generation sequencing (NGS). Unlike current methods which genotype a DNA sample by measuring the size of amplified DNA fragments, MPS determines the sequence(s) of the DNA present. Alleles that were indistinguishable by size using length-based analyses are now able to be resolved due to internal sequence differences. The addition of sequence information will further increase the discriminatory power of forensic DNA analysis. Commercial multiplex kits that type hundreds of markers are now available.