====================== Aging Variant Database ====================== :Abstract: We are constructing the most comprehensive database on genetic variants associated with longevity in humans. This project is a collaborative crowdsourced endeavor which will create a resource that is very valuable for deciphering the genetics of human Aging.
:Journal: Nucleic Acid Research :deadline: July 1. 2013
Aging has a genetic component which is estimated to be over 25%. Different individuals age with a different pace even if they have a similar lifestyle. The reason for this is that the genetic changes that differentiate an individual in specific genetic locations change the aging program or render an individual more resistant against damages and age-related diseases.
As the cost for genomic sequences falls the genetic markup underlying human longevity is becoming unraveled, there is a urgent need to utilize the knowledge on genetic variants that influence the speed of aging.
The simplest form of such variants are Single-Nucleotide Polymorphism (SNPs). Association to longevity can be identified either via high throughput Genome wide Association Studies (GWAS) or via focused candidate gene approaches.
This information is to increase the relevance about the functional modifications at the protein level in the SNP.
It is really important to have a idea why certain SNPs create a longevity effect, although this can not be done yet with all SNPs. SNPs some times change the promoter activity or protein function which can be used for functional networks algorithms. Some times they are just photogenic traces and the real criminal gene is surrounding there with other variants not detectable by SNP modifications.
It is important to know how a SNP affects protein function and activity and give some more relevance to the information. Functional assays are crucial for figuring out what longevity SNPs do and why they matter.
We designed a Boolean expression for paper identification. We use an inclusive policy which means positive as well as negative studies are included.
Articles were flagged as "curate" if they have valuable information for the database, "discard" if the are irrelevant", and "review" if they are relevant reviews. Reviews are not curated in any detail, but they are ranked on a subjective scale from 1to 5; where 1 means highly relevant.
Each genetic variant investigated in a study is a data record, which has defined polymorphism and a genomic location. If the polymorphism is within or next to a gene it is linked to the respective genetic factor. Further a record of a polmorphism has an informal description as well as association specific information such as the ethnicity, age of cases (mean) and shorter/longer-lived alleles. Further statistical data like number of cases/controls in the initial and replication studies, odds-ratio, p-value and whether it is significant are also included, if available. Moreover the utilized technology (e.g. PCR) and the type of study (GWAS, candidate gene). We strictly provide references to the primary information.
Where information is known about the functional impact of a longevity variant (e.g. APOE, CETP), this is also represented in the database.
For several longevity SNPs, no functional assays have been conducted yet, but then hopefully our database will help to identify the most well-replicated mystery SNPs, and let us prioritize them for functional follow-up.