Coriell CNVs Track Settings
 
Coriell Cell Line Copy Number Variants   (All Phenotype and Literature tracks)

Display mode:   

Filter score range: min: max: (0 to 1000)

View table schema
Data last updated: 2013-01-03

Description

The Coriell Cell Line Copy Number Variants track displays copy-number variants (CNVs) in chromosomal aberration and inherited disorder cell lines in the NIGMS Human Genetic Cell Repository. The Repository, sponsored by the National Institute of General Medical Sciences, provides scientists around the world with resources for cell and genetic research. The samples include highly characterized cell lines and high quality DNA. NIGMS Repository samples represent a variety of disease states, chromosomal abnormalities, apparently healthy individuals and many distinct human populations.

Approximately 1000 samples from the Chromosomal Aberrations and Heritable Diseases collections of the NIGMS Repository were genotyped on the Affymetrix Genome-Wide Human SNP 6.0 Array and analyzed for CNVs at the Coriell Institute for Medical Research. Genotyping data for many of these samples is available through dbGaP.

The genotyped samples represent a diverse set of copy-number variants. The selection was weighted to over-sample commonly manifested types of aberrations. Karyotyping was performed on all NIGMS Repository cell lines that were submitted with reported chromosome abnormalities. When available, the ISCN description of the sample, based on G-banding and FISH analysis, is included in the phenotypic data. Karyotypes for these cells can be viewed in the online Repository catalog.

Field definitions for an item description:

  • CN State: Copy Number of the imbalance. Note that all CNVs with a copy number of 2 are colored neutral (black) and occur on the sex chromosomes, where a CN State of 2 should not be interpreted as normal, as it would be on an autosome.
  • Cell Type: Type of cell culture; one of the following: B Lymphocyte, Fibroblast, Amniotic fluid-derived cell line or Chorionic villus-derived cell line.
  • Description (Diagnosis): May be a medical diagnosis, such as "albinism" or a chromosomal phenotype, such as "translocation" or other description.
  • ISCN nomenclature: A description of the chromosomal karyotype in formal ISCN nomenclature.

CN State item coloring:

  • CN State 0 == score 0
  • CN State 1 == score 100
  • CN State 2 == score 200
  • CN State 3 == score 300
  • CN State 4 == score 400
Use the score filter limits on the configuration page to select desired CN States.

Credits

We thank Dorit Berlin and Zhenya Tang of the NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research for these data.

References

NCBI dbGaP: Genotyping NIGMS Chromosomal Aberration and Inherited Disorder Samples.
NIGMS Human Genetic Cell Repository online catalog at the Coriell Institute for Medical Research.