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Genome Med. 2011 Oct 10;3(10):65. doi: 10.1186/gm281.

Identification of cis-regulatory sequence variations in individual genome sequences.

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Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada.


Functional contributions of cis-regulatory sequence variations to human genetic disease are numerous. For instance, disrupting variations in a HNF4A transcription factor binding site upstream of the Factor IX gene contributes causally to hemophilia B Leyden. Although clinical genome sequence analysis currently focuses on the identification of protein-altering variation, the impact of cis-regulatory mutations can be similarly strong. New technologies are now enabling genome sequencing beyond exomes, revealing variation across the non-coding 98% of the genome responsible for developmental and physiological patterns of gene activity. The capacity to identify causal regulatory mutations is improving, but predicting functional changes in regulatory DNA sequences remains a great challenge. Here we explore the existing methods and software for prediction of functional variation situated in the cis-regulatory sequences governing gene transcription and RNA processing.

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