DEAFNESS VARIATION DATABASE

Data sources

We collated all previously reported deafness-causing variants as described in Shearer AE, et al 2014. Annotation is based on data from the following sources:

1000 Genomes

Release
1000 Genomes Phase 3 Version 5a (2013-05-02)
Reference
Birney E, and Soranzo N. Human Genomics: The End of the Start for Population Sequencing. Nature 526, 52–53 (2015).

ClinVar

The DVD uses a special release of ClinVar provided by the MacArthur Lab for use in bioinformatics pipelines.
Release
2016 March 1 (provided by the MacArthur Lab)
Reference
Landrum MJ, et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res 44, D862–D868 (2016).

dbSNP

Release
Build 146
Reference
Sherry ST, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11.

ExAC

Release
Version 0.3.0
Reference
Exome Aggregation Consortium, et al. Analysis of Protein-Coding Genetic Variation in 60,706 Humans. bioRxiv, October 30, 2015, 030338. doi:10.1101/030338.

Exome Variant Server

Release
ESP6500SI-V2-SSA137
Reference
Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP), Seattle, WA

dbNSFP

Release
dbNSFP v3.0
References
Liu X, Jian X, and Boerwinkle E. 2011. dbNSFP: a lightweight database of human non-synonymous SNPs and their functional predictions. Human Mutat., 32, 894-899.

Liu X, Jian X, and Boerwinkle E. 2013. dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations. Human Mutat., 34, E2393-E2402.

Liu X, Wu C, Li C, and Boerwinkle E. 2013. dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Non-synonymous and Splice Site SNVs. Human Mutat., 37, 235-241.

OtoDB

Release
Version 1.0
Reference
Shearer AE, et al. Utilizing ethnic-specific differences in minor allele frequency to re-categorize reported pathogenic deafness variants. Am J Hum Genet 2014.