What question did this study set out to answer?

To identify and define problematic genomic regions that produce anomalous, unstructured, or artificially elevated signals in high-throughput sequencing assays.

June 27, 2019Scientific ReportsOpen Access

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

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To identify and define problematic genomic regions that produce anomalous, unstructured, or artificially elevated signals in high-throughput sequencing assays.
Evaluated functional genomics datasets generated via next-generation sequencing across human, mouse, worm, and fly genomes.
Identified genomic regions displaying consistently anomalous signal profiles independent of specific cell lines or experimental conditions.
Defined the comprehensive ENCODE blacklist across human, mouse, nematode, and fruit fly reference genomes.
Characterized regions with non-specific, highly elevated background reads that distort sequencing results across diverse assay types.
Established the removal of blacklist regions as a critical quality control step for functional genomic data analysis.

Implication

Genomic study reveals anomalous high-signal sequencing regions across diverse organisms, highlighting an essential quality control filter for functional genomics.

Abstract

Functional genomics assays based on high-throughput sequencing greatly expand our ability to understand the genome. Here, we define the ENCODE blacklist- a comprehensive set of regions in the human, mouse, worm, and fly genomes that have anomalous, unstructured, or high signal in next-generation sequencing experiments independent of cell line or experiment. The removal of the ENCODE blacklist is an essential quality measure when analyzing functional genomics data.

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Cite This Study

Amemiya et al. (2019) studied this question.

synapsesocial.com/papers/69835b402ab7a8aa771d655f https://doi.org/10.1038/s41598-019-45839-z

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Implication

Genomic study reveals anomalous high-signal sequencing regions across diverse organisms, highlighting an essential quality control filter for functional genomics.

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

Key Points

Implication

Abstract

Discussion

Cite This Study

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

Key Points

Implication

Abstract

Discussion

Cite This Study

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