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      The High-Throughput Analyses Era: Are We Ready for the Data Struggle?

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      1 , 2
      High-Throughput
      MDPI
      high-throughput analysis, next-generation sequencing, big data, -omic sciences, personalized medicine

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          Abstract

          Recent and rapid technological advances in molecular sciences have dramatically increased the ability to carry out high-throughput studies characterized by big data production. This, in turn, led to the consequent negative effect of highlighting the presence of a gap between data yield and their analysis. Indeed, big data management is becoming an increasingly important aspect of many fields of molecular research including the study of human diseases. Now, the challenge is to identify, within the huge amount of data obtained, that which is of clinical relevance. In this context, issues related to data interpretation, sharing and storage need to be assessed and standardized. Once this is achieved, the integration of data from different -omic approaches will improve the diagnosis, monitoring and therapy of diseases by allowing the identification of novel, potentially actionably biomarkers in view of personalized medicine.

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          Most cited references76

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          The impact of next-generation sequencing technology on genetics.

          If one accepts that the fundamental pursuit of genetics is to determine the genotypes that explain phenotypes, the meteoric increase of DNA sequence information applied toward that pursuit has nowhere to go but up. The recent introduction of instruments capable of producing millions of DNA sequence reads in a single run is rapidly changing the landscape of genetics, providing the ability to answer questions with heretofore unimaginable speed. These technologies will provide an inexpensive, genome-wide sequence readout as an endpoint to applications ranging from chromatin immunoprecipitation, mutation mapping and polymorphism discovery to noncoding RNA discovery. Here I survey next-generation sequencing technologies and consider how they can provide a more complete picture of how the genome shapes the organism.
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            High-throughput sequencing technologies.

            The human genome sequence has profoundly altered our understanding of biology, human diversity, and disease. The path from the first draft sequence to our nascent era of personal genomes and genomic medicine has been made possible only because of the extraordinary advancements in DNA sequencing technologies over the past 10 years. Here, we discuss commonly used high-throughput sequencing platforms, the growing array of sequencing assays developed around them, as well as the challenges facing current sequencing platforms and their clinical application. Copyright © 2015 Elsevier Inc. All rights reserved.
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              Methods of integrating data to uncover genotype-phenotype interactions.

              Recent technological advances have expanded the breadth of available omic data, from whole-genome sequencing data, to extensive transcriptomic, methylomic and metabolomic data. A key goal of analyses of these data is the identification of effective models that predict phenotypic traits and outcomes, elucidating important biomarkers and generating important insights into the genetic underpinnings of the heritability of complex traits. There is still a need for powerful and advanced analysis strategies to fully harness the utility of these comprehensive high-throughput data, identifying true associations and reducing the number of false associations. In this Review, we explore the emerging approaches for data integration - including meta-dimensional and multi-staged analyses - which aim to deepen our understanding of the role of genetics and genomics in complex outcomes. With the use and further development of these approaches, an improved understanding of the relationship between genomic variation and human phenotypes may be revealed.
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                Author and article information

                Journal
                High Throughput
                High Throughput
                high-throughput
                High-Throughput
                MDPI
                2571-5135
                02 March 2018
                March 2018
                : 7
                : 1
                : 8
                Affiliations
                [1 ]CEINGE-Biotecnologie Avanzate, via G. Salvatore 486, 80145 Naples, Italy; dargenio@ 123456ceinge.unina.it ; Tel.: +39-081-3737909
                [2 ]Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, via Pansini 5, 80131 Naples, Italy
                Author information
                https://orcid.org/0000-0001-9273-3698
                Article
                high-throughput-07-00008
                10.3390/ht7010008
                5876534
                29498666
                88ee8ae5-6d9e-4bb2-9898-c3f3b1296132
                © 2018 by the author.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 28 December 2017
                : 27 February 2018
                Categories
                Opinion

                high-throughput analysis,next-generation sequencing,big data,-omic sciences,personalized medicine

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