Center for Applied Genomics
TypeGenomics Research Center
IndustryMedical Research
Founded2006
Headquarters
Philadelphia
,
United States
Area served
United States
Key people
Hakon Hakonarson, Director
Number of employees
89
ParentChildren's Hospital of Philadelphia
Websitehttp://www.caglab.org

The Center for Applied Genomics is a research center at the Children's Hospital of Philadelphia that focuses on genomics research and the utilization of basic research findings in the development of new medical treatments.

As one of the world's largest genetics research and analytical facilities, the Center for Applied Genomics has processed genetic samples from over 100,000 people due to its access to high-throughput genotyping technology.

The center is focused on detecting the genetic causes of prevalent childhood diseases including asthma, obesity, ADHD, autism, diabetes, inflammatory bowel disease, epilepsy, schizophrenia, and pediatric cancer, all of which are thought to potentially involve multiple, interacting genes within the body.

Projects

The Center for Applied Genomics is a Center for Emphasis at the Children's Hospital of Philadelphia

ADHD

In 2009, Center for Applied Genomics researchers identified copy number variants (CNVs) as a potential cause of the disorder. Although highly heritable, genetic correlates of attention deficit hyperactivity disorder (ADHD) have been difficult to pinpoint. The group found 222 CNVs that were more common in individuals with ADHD than in unrelated healthy individuals and published a paper on the findings.[1]

Asthma

In 2010, the center published a genome-wide association study of 3,377 children with asthma and 5,579 healthy children.[2] Researchers discovered a region on chromosome 17 and a previously unassociated region on chromosome 1 that strongly correlated with susceptibility to asthma.

Autism

In 2009, the Center conducted a genome-wide association study on a group of 780 families (3,101 individuals) with affected children, a second group of 1,204 affected individuals, and 6,491 controls, all of whom had European ancestry. By comparing genomics variations between the groups, researchers identified six genetic markers between two specific genes that confirmed susceptibility to ASDs.[3] In 2009, the Center published a second paper in the journal Nature that identified copy number variations (CNVs) as genetic features in autism based on the study of 859 autism cases and 1,409 healthy children of European ancestry.[4]

Cancer

In 2008, the Center group collaborated with the Maris Lab at the Children's Hospital of Pennsylvania to publish the first of three papers on the genetic causes of Neuroblastoma. They performed a genome-wide association study comparing the genomes of 1032 patients and 2043 controls. The researchers found a significant association between neuroblastoma and a region of chromosome 6.[5] In 2009, the Center performed another genome-wide association study that focused on a 397-person high-risk subset of the neuroblastoma group.[6] In 2009, the Center contributed another study identifying copy number variations (CNVs) as a potential cause of neuroblastoma.[7] The study was the first germline CNV study in any cancer.

In 2009, in collaboration with the Nathanson Lab at the University of Pennsylvania, the Center published the results of a genome-wide associated study that examined the genomes of 227 patients with testicular germ cell tumors and 919 controls.[8]

Crohn's Disease

In 2008, the Center proposed a strategy for examining the disorder by focusing on age-of-onset. To this end, they carried out a genome-wide association study of 1,011 individuals with pediatric-onset IBD and 4,250 matched controls.[9] In a subsequent paper, the Center applied pathway analysis to focus on multiple regions in the genome that may interact to cause Crohn's disease.[10]

In 2009, the center also published a genome-wide association study of inflammatory bowel diseases (Crohn's disease and ulcerative colitis) in 3,426 affected individuals and 11,963 genetically matched controls.[11]

Schizophrenia

In a genome-wide association study of 1,735 schizophrenic patients and 3,485 healthy adults.[12]

Type 1 Diabetes

In 2007, researchers performed a genome-wide association study in a large pediatric group that identified a previously unknown association between type 1 diabetes and a genetic variation on chromosome 16.[13]

Technology

The center is equipped with the Illumina BeadArray System and utilizes both the Infinium and GoldenGate analytical methods. The center's equipment includes multiple Tecan hardware systems and scanning instruments with integrative Laboratory Information Management System (LIMS). It uses several genotyping units from Affymetrix.

The center uses microarrays to perform whole-genome analysis – microarrays are slides consisting of thousands to millions of tiny probes. They allow researchers to screen an individual's genome for huge numbers of genetic markers called single nucleotide polymorphisms (SNPs).[14] At the center, researchers have examined over 100,000 individuals.

See also

References

  1. ↑ Elia J, Gai X, Xie HM, et al. (June 2010). "Rare structural variants found in attention-deficit hyperactivity disorder are preferentially associated with neurodevelopmental genes". Molecular Psychiatry. 15 (6): 637–46. doi:10.1038/mp.2009.57. PMC 2877197. PMID 19546859.
  2. ↑ Sleiman PM, Flory J, Imielinski M, et al. (January 2010). "Variants of DENND1B associated with asthma in children". The New England Journal of Medicine. 362 (1): 36–44. doi:10.1056/NEJMoa0901867. PMID 20032318.
  3. ↑ Wang K, Zhang H, Ma D, et al. (May 2009). "Common genetic variants on 5p14.1 associate with autism spectrum disorders". Nature. 459 (7246): 528–33. Bibcode:2009Natur.459..528W. doi:10.1038/nature07999. PMC 2943511. PMID 19404256.
  4. ↑ Glessner JT, Wang K, Cai G, et al. (May 2009). "Autism genome-wide copy number variation reveals ubiquitin and neuronal genes". Nature. 459 (7246): 569–73. Bibcode:2009Natur.459..569G. doi:10.1038/nature07953. PMC 2925224. PMID 19404257.
  5. ↑ Maris JM, Mosse YP, Bradfield JP, et al. (June 2008). "Chromosome 6p22 locus associated with clinically aggressive neuroblastoma". The New England Journal of Medicine. 358 (24): 2585–93. doi:10.1056/NEJMoa0708698. PMC 2742373. PMID 18463370.
  6. ↑ Capasso M, Devoto M, Hou C, et al. (June 2009). "Common variations in BARD1 influence susceptibility to high-risk neuroblastoma". Nature Genetics. 41 (6): 718–723. doi:10.1038/ng.374. PMC 2753610. PMID 19412175.
  7. ↑ Diskin SJ, Hou C, Glessner JT, et al. (June 2009). "Copy number variation at 1q21.1 associated with neuroblastoma". Nature. 459 (7249): 987–91. Bibcode:2009Natur.459..987D. doi:10.1038/nature08035. PMC 2755253. PMID 19536264.
  8. ↑ Kanetsky PA, Mitra N, Vardhanabhuti S, et al. (July 2009). "Common variation in KITLG and at 5q31.3 predisposes to testicular germ cell cancer". Nature Genetics. 41 (7): 811–5. doi:10.1038/ng.393. PMC 2865677. PMID 19483682.
  9. ↑ Kugathasan S, Baldassano RN, Bradfield JP, et al. (October 2008). "Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease". Nature Genetics. 40 (10): 1211–5. doi:10.1038/ng.203. PMC 2770437. PMID 18758464.
  10. ↑ Wang K, Zhang H, Kugathasan S, et al. (March 2009). "Diverse genome-wide association studies associate the IL12/IL23 pathway with Crohn Disease". American Journal of Human Genetics. 84 (3): 399–405. doi:10.1016/j.ajhg.2009.01.026. PMC 2668006. PMID 19249008.
  11. ↑ Imielinski M, Baldassano RN, Griffiths A, et al. (December 2009). "Common variants at five new loci associated with early-onset inflammatory bowel disease". Nature Genetics. 41 (12): 1335–40. doi:10.1038/ng.489. PMC 3267927. PMID 19915574.
  12. ↑ Glessner JT, Reilly MP, Kim CE, et al. (June 2010). "Strong synaptic transmission impact by copy number variations in schizophrenia". Proceedings of the National Academy of Sciences of the United States of America. 107 (23): 10584–9. Bibcode:2010PNAS..10710584G. doi:10.1073/pnas.1000274107. PMC 2890845. PMID 20489179.
  13. ↑ Grant SF, Hakonarson H, Schwartz S (April 2010). "Can the genetics of type 1 and type 2 diabetes shed light on the genetics of latent autoimmune diabetes in adults?". Endocrine Reviews. 31 (2): 183–93. doi:10.1210/er.2009-0029. PMID 20007922.
  14. ↑ "Single Nucleotide Polymorphisms". Dolan DNA Learning Center. Archived from the original on 2011-04-08. Retrieved 2010-11-23.

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