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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

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arrayMap 2014: an updated cancer genome resource.

Haoyang Cai¹, Saumya Gupta², Prisni Rath³

¹Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland Swiss Institute of Bioinformatics, 8057 Zurich, Switzerland Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China haoyang.cai@gmail.com.

Nucleic Acids Research

|November 28, 2014

Summary

This summary is machine-generated.

The arrayMap database now offers over 64,000 cancer genomic datasets for public access. This updated resource enhances data mining for somatic copy number aberrations (CNA) across human malignancies.

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Area of Science:

Oncogenomics
Cancer Genomics
Bioinformatics

Background:

Somatic copy number aberrations (CNA) are common in cancer genomes.
arrayMap is a public resource for oncogenomic array data and CNA profiles.
The 2014 edition expands content and data mining capabilities.

Purpose of the Study:

To present the 2014 edition of arrayMap, an enhanced resource for cancer genomic data.
To provide access to over 64,000 pre-processed array datasets covering numerous human malignancies.
To improve data mining support and visualization tools for cancer genomic research.

Main Methods:

Assembled and integrated over 64,000 genomic array datasets from public repositories and additional sources.
Applied custom processing pipelines for data integration and CNA profile generation.
Upgraded online tools for flexible array data visualization and processing of user-provided datasets.
Mapped data to multiple human reference genome editions (UCSC hg18, GRCh37).

Main Results:

The 2014 arrayMap release contains over 64,000 genomic datasets representing approximately 250 tumor diagnoses.
Enhanced data integration with multiple human reference genome versions.
Improved online tools for data visualization and processing of non-public data.
Freely downloadable tumor CNA data is available to promote data mining.

Conclusions:

The updated arrayMap resource significantly enhances the study of somatic copy number aberrations in cancer.
Provides a comprehensive and accessible platform for cancer genomic data mining and exploration.
Facilitates research into complex genomic events like chromothripsis-like patterns.