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The SingHealth Exome Consortium (SEC)

About SEC

The SingHealth Exome Consortium (SEC) is an initiative started by PRISM to consolidate exomes from healthy individuals generated by investigators from SingHealth institutions and their affiliates. Over the last few years, various exome sequencing projects have taken place across SingHealth institutions, with most of them sequencing the exomes of healthy or normal individuals as controls. These exomes, kindly contributed by investigators from various institutions, have been re-analyzed and jointly-genotyped using the GATK (Genome Analysis Tool Kit) Best Practices Workflow. The latest version of the SEC dataset has variants from 1504 normal individuals. This dataset has been used for the following purposes:

  • To provide a matched population control in case-control cohort studies.

  • To filter local polymorphisms in cohort sequencing studies (these variants would be unique to the local population and not found in commonly-used databases such as ExAC and 1000 Genomes). Our collaborators have reported reductions of 30% - 40% in numbers of rare protein altering variants that need to be considered.

  • To estimate the burden of genetic disorders in the local population.

  • To improve interpretation of variant pathogenicity; variants classified as likely pathogenic by genetic testing companies (because they were rare or never seem in public databases) have been reclassified as probably benign due to high local frequency.

There are different levels of access to SEC data:

  • Beacon - The PRISM Beacon server can provide simple YES/NO answers to a query variant depending on whether it is present in the database. The Beacon server is publicly accessible with no authentication required.

  • Allele frequencies - Available upon request. Send us your VCF and we will annotate it with SEC allele frequencies. Get in touch with us for more details.

  • Genotypes - Requires formal research collaboration. Get in touch with us for more details. (

NOTE: The SEC dataset was generated using GATK v3.8 (Best Practices Workflow), using hs37d5 (hg19) as the reference genome.

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