Scientific collaboration on a large scale has been a hallmark of genomics since the beginning of the field. NHGRI has been fortunate to be at the center of many large collaborative projects, such as the Human Genome Project (HGP). While the HGP represents one incredible milestone in the path to understanding human biology, it also resulted in new technologies and resources that are now foundational for many areas of biological research. This progression is nicely illustrated by an NIH-wide collaboration that has given researchers access to key genomic resources for the past 20 years - the Center for Inherited Disease Research (CIDR).
Emerging genomic technologies are not always available to all researchers, as instruments can be too expensive for small laboratories to purchase and only specialists might have the ability to perform appropriate data analyses. That such expertise was rare and hard to find was particularly apparent in the early days of the HGP, so in 1996, seven NIH Institutes and Centers (ICs) joined forces to establish CIDR, which aimed to gather the expertise and build the necessary infrastructure to provide large-scale genotyping services to investigators funded by those ICs.
The main goal of the CIDR service has been to fill the essential 'middle part' of the typical research path used for identifying disease genes. Investigators recruit study participants and collect their DNA. Then, a team of CIDR experts produces genome-wide genotype data for each sample, in essence determining the presence of specific genomic variants present in each DNA sample. After careful quality control, these data are returned to the original investigators. Under this model, the ICs benefit from CIDR's economies-of-scale and also share in the cost of evaluating new technologies. The investigators receive high-quality data, avoid having to keep up with technologic advances, and perhaps best of all, do not pay for the genotyping service (since the funding comes directly from the ICs).
CIDR also provides investigators with statistical expertise and analytical support. This includes playing a role in the design of the research projects, and later, the deposition of data into central databases.
At present, CIDR is one of the largest genotyping facilities in the world. The number of participating ICs has risen to 11. In the last five years, next-generation DNA sequencing was added to the menu of available technologies. Currently, Dr. Lawrence Brody of NHGRI manages the CIDR program under a contract with the McKusick-Nathans Institute of Genetic Medicine at the Johns Hopkins University. Dr. Kimberly Doheny directs the CIDR program for Johns Hopkins University.
The genotyping and DNA-sequencing approaches used by CIDR over the years nicely illustrate the evolution of genomic technologies. In the beginning, CIDR scientists used methods to detect several hundred microsatellite markers (i.e., stretches of DNA where short sequences are repeated). As the technology advanced, they began analyzing single-nucleotide polymorphisms (SNPs, pronounced "snips"). Most recently, CIDR is using next-generation DNA sequencing to conduct whole-genome and whole-exome sequencing. The former analyzes the entire genome, while the latter analyzes just the protein-coding regions.
The accomplishments of CIDR in its first 20 years are indeed impressive. To date, CIDR's work includes ~850 published papers, ~400 completed projects, ~900,000 analyzed samples, ~600 billion genotypes and 30 trillion bases of DNA sequence generated. Even more impressive is the increasing size of projects. Early projects often involved generating data for a small number of families. Taking advantage of the decreasing costs of genotyping and genome sequencing, CIDR generated data on over 100,000 people for a single study last year.
While NHGRI supports many valuable resource projects, CIDR is distinguished by its trans-NIH nature. The cooperative spirit of all the participating ICs has been instrumental to CIDR's success, as has the consistent focus on providing researchers access to the cutting-edge genomic tools for conducting their disease-oriented research. To access the CIDR website, see cidr.jhmi.edu.
Posted: June 7, 2016