Schema for Coriell CNVs - Coriell Cell Line Copy Number Variants
  Database: hg19    Primary Table: coriellDelDup    Row Count: 957   Data last updated: 2013-01-04
Format description: Coriell Cell Line Deletions and Duplications
fieldexampleSQL type info description
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 61722int(10) unsigned range Start position in chromosome
chromEnd 228694int(10) unsigned range End position in chromosome
name GM01229varchar(255) values Short Name of item
score 100int(10) unsigned range score == (CN state * 100) -> (0,100,200,300,400)
strand +char(1) values + or -
thickStart 61722int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 228694int(10) unsigned range End of where display should be thick (stop codon)
itemRgb 11158528int(10) unsigned range color from CN state
CN_State 1enum('0', '1', '2', '3', '4') values CN State
cellType Fibroblastenum('B_Lymphocyte', 'Fibroblast', 'Amniotic_fluid_cell_line', 'Chorionic_villus_cell_line') values Cell Type
description TRANSLOCATED CHROMOSOMEvarchar(255) values Description (Diagnosis)
ISCN 46,XX,der(1)t(1;2)(p36;q32)patvarchar(255) values ISCN nomenclature

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEnditemRgbCN_StatecellTypedescriptionISCN
chr161722228694GM01229100+61722228694170,68,01FibroblastTRANSLOCATED CHROMOSOME46,XX,der(1)t(1;2)(p36;q32)pat
chr12286934773266GM23002100+2286934773266170,68,01B_LymphocyteCHROMOSOME 1P36 DELETION SYNDROME46,XX,del(1)(p36.3).ish del(1)(p36.3)(CEB108/T7-,SKI-,D1S3739+)
chr16254576332669GM22569100+6254576332669170,68,01B_LymphocyteCHROMOSOME 1P36 DELETION SYNDROME46,XX,del(1)(p36.3).ish del(1)(p36.3)(SKI-,D1S3739+)
chr16254572257863GM22977100+6254572257863170,68,01B_LymphocyteCHROMOSOME 1P36 DELETION SYNDROME46,XX.ish del(1)(p36.33)(CEB108/T7-,SKI-,D1S3739+)
chr17070866866626GM22976100+7070866866626170,68,01B_LymphocyteCHROMOSOME 1P36 DELETION SYNDROME47,XY,der(1)t(1;3)(p36.3;q26.3),+9.ish der(1)t(1;3)(p36.3;q26.3)(D3S4560+,CEB108/T7-,SKI-,D1S3739+)
chr17070863070322GM18827100+7070863070322170,68,01B_LymphocyteTRANSLOCATED CHROMOSOME46,XX,t(15;16)(q24.1;q24).ish t(15;16)(D15S936-,16qte148+;16qte148-,D15S936+)
chr17408565002713GM22995100+7408565002713170,68,01B_LymphocyteCHROMOSOME 1P36 DELETION SYNDROME46,XY,del(1)(p36.3).ish del(1)(p36.33)(CEB108/T7-,SKI-,D1S3739+)
chr17525655310980GM22991100+7525655310980170,68,01B_LymphocyteCHROMOSOME 1P36 DELETION SYNDROME46,XX.ish del(1)(p36.32)(CEB108/T7-,SKI-,D1S3739+)
chr1442575011002579GM50276100+442575011002579170,68,01B_LymphocyteCHROMOSOME DELETION46,XY,del(5)(p14p14)pat.ish del(5)(p14p14)(189N21+)
chr178322118067990GM50323300+783221180679900,68,1703B_LymphocyteISOCHROMOSOME47,XX,+i(18)(p11).ish i(18)(p11)(VIJ2yRM2102+,D18Z1+,VIJ2yRM2102+,wcp18+)

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Coriell CNVs (coriellDelDup) Track Description
 

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.