Building the foundation for genomics in precision medicine

Aronson, Samuel; Rehm, Heidi L.

doi:10.1038/nature15816

Cited by 412 publications

(266 citation statements)

References 53 publications

(51 reference statements)

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“…More effective infrastructure for data storage and sharing should be developed [81]. For integrative clustering, the methods should take more considerations on the increasing computational burden in future, such as memory requirement, parallel computing ability, and especially time cost.…”

Section: Discussionmentioning

confidence: 99%

Integrative clustering methods of multi‐omics data for molecule‐based cancer classifications

Wang

2016

Quant. Biol.

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One goal of precise oncology is to re-classify cancer based on molecular features rather than its tissue origin. Integrative clustering of large-scale multi-omics data is an important way for molecule-based cancer classification. The data heterogeneity and the complexity of inter-omics variations are two major challenges for the integrative clustering analysis. According to the different strategies to deal with these difficulties, we summarized the clustering methods as three major categories: direct integrative clustering, clustering of clusters and regulatory integrative clustering. A few practical considerations on data pre-processing, post-clustering analysis and pathway-based analysis are also discussed.

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Section: Discussionmentioning

confidence: 99%

Integrative clustering methods of multi‐omics data for molecule‐based cancer classifications

Wang

2016

Quant. Biol.

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“…The goal of the Alliance is to create data standards and strategies for storage and analysis of medically relevant genomic data, and to catalyze the creation of data sharing standards and methods to ensure worldwide interoperability of medical genomics data [30]. GA4GH includes institutions like EMBL-EBI that play a key role in facilitating the transfer of knowledge and expertise in data management and analysis of big data Anonymized data from the analyses of these projects can be made available for research use, either via controlled-access data repositories or open, public data repositories, depending on consent and data category.…”

Section: Data Storage and Sharingmentioning

confidence: 99%

A Review of Recent Advances in Translational Bioinformatics: Bridges from Biology to Medicine

Vamathevan¹,

Birney²

2017

Yearb Med Inform

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SummaryObjectives: To highlight and provide insights into key developments in translational bioinformatics between 2014 and 2016. Methods: This review describes some of the most influential bioinformatics papers and resources that have been published between 2014 and 2016 as well as the national genome sequencing initiatives that utilize these resources to routinely embed genomic medicine into healthcare. Also discussed are some applications of the secondary use of patient data followed by a comprehensive view of the open challenges and emergent technologies. Results: Although data generation can be performed routinely, analyses and data integration methods still require active research and standardization to improve streamlining of clinical interpretation. The secondary use of patient data has resulted in the development of novel algorithms and has enabled a refined understanding of cellular and phenotypic mechanisms. New data storage and data sharing approaches are required to enable diverse biomedical communities to contribute to genomic discovery. Conclusion: The translation of genomics data into actionable knowledge for use in healthcare is transforming the clinical landscape in an unprecedented way. Exciting and innovative models that bridge the gap between clinical and academic research are set to open up the field of translational bioinformatics for rapid growth in a digital era.

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“…Precision medicine classifies patients with the same disease further into finer subtypes based on their molecular biomarkers and offers them tailored therapies, with the hope of ensuring optimal benefits and concomitantly minimizing the risks, undesirable side effects and needless medical care [1,2]. The advancement of this concept has revolutionized the diagnosis and therapeutic management of diseases, especially made great strides in the field of oncology.…”

Section: Introductionmentioning

confidence: 99%

“…NSCLCs account for 80%-90% of newly diagnosed cases of lung cancers. However, the pathology of lung cancers is complex, and distinct genetic differences in patients cause different rates of responses to the same treatments, even if they share similar histological characteristics [2]. In 2004, the seminal discovery of activating epidermal growth factor receptor (EGFR) mutations that confer sensitivity to tyrosine kinase inhibitors (TKIs) in adenocarcinomas of NSCLCs heralded the beginning of the era of precision medicine that was based on the molecular diagnoses of NSCLCs [7,8].…”

Section: Introductionmentioning

confidence: 99%

Sample types applied for molecular diagnosis of therapeutic management of advanced non-small cell lung cancer in the precision medicine

Han

2017

Clinical Chemistry and Laboratory Medicine (CCLM)

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Abstract:In this era of precision medicine, molecular biology is becoming increasingly significant for the diagnosis and therapeutic management of non-small cell lung cancer. The specimen as the primary element of the whole testing flow is particularly important for maintaining the accuracy of gene alteration testing. Presently, the main sample types applied in routine diagnosis are tissue and cytology biopsies. Liquid biopsies are considered as the most promising alternatives when tissue and cytology samples are not available. Each sample type possesses its own strengths and weaknesses, pertaining to the disparity of sampling, preparation and preservation procedures, the heterogeneity of inter-or intratumors, the tumor cellularity (percentage and number of tumor cells) of specimens, etc., and none of them can individually be a "one size to fit all". Therefore, in this review, we summarized the strengths and weaknesses of different sample types that are widely used in clinical practice, offered solutions to reduce the negative impact of the samples and proposed an optimized strategy for choice of samples during the entire diagnostic course. We hope to provide valuable information to laboratories for choosing optimal clinical specimens to achieve comprehensive functional genomic landscapes and formulate individually tailored treatment plans for NSCLC patients that are in advanced stages.

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Building the foundation for genomics in precision medicine

Cited by 412 publications

References 53 publications

Integrative clustering methods of multi‐omics data for molecule‐based cancer classifications

Integrative clustering methods of multi‐omics data for molecule‐based cancer classifications

A Review of Recent Advances in Translational Bioinformatics: Bridges from Biology to Medicine

Sample types applied for molecular diagnosis of therapeutic management of advanced non-small cell lung cancer in the precision medicine

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