Characterization Services


WiCell's Characterization Laboratory offers a suite of characterization services to help drive your research forward. Your lab can benefit from WiCell's rapid turn-around time, competitive pricing, and publication ready imaging.  Our offerings can range from one-sample requests to large-scope or multiple sample runs with high quality and dependable results every time.    

  

Characterization testing guidelines

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Assay

What it Detects

What it Doesn’t Detect

TATi

When to Use

Fluorescence In Situ Hybridization (FISH)

·       Genomic sequence of interest

-   Duplications or deletions >20 Kb

-   >2% mosaicism (for example:  cultures where >2 of 100 cells are trisomy 12)

-   Chromosomal location of genomic gains

-   Chromosome fusions (breakaparts)

·      Changes in regions other than the probe-specific sequence

 

10-15 days

·       To confirm findings and refine breakpoints detected by g-banded karyotyping

·       To confirm findings and localize genomic gains detected by SNP microarray

·       As a screen for microdeletions/duplications of known targets

G-Banded Karyotyping

·    Microscopic genomic abnormalities   (>5-10 Mb)

-   Inversions

-   Duplications/deletions

-   Balanced and unbalanced translocations

-   Aneuploidies

·    >10% mosaicism (for example:  cultures where >1 of 10 cells are trisomy 12)

·      Submicroscopic genomic abnormalities (<5 Mb)

·      <~10% culture mosaicism (for example:  cultures where 1 of 10 cells is trisomy 12)

7-10 days

(4-6 days expedited)

·       As a baseline genomic screen

-    At derivation of cell lines

-    At the start of experimental protocols

-    To assess and monitor genomic stability (for example: every 5-10 passages of cell culture)

-    At conclusion of experiments (prior to publication)

-    For cell line banking

·       When publication-quality karyotypes are needed

Mycoplasma Detection by PCR

·    96 species of mycoplasma contamination from stem cell cultures.

-   Sensitivity (5-100 CFU/ml)

 

·    This system does not allow for the amplification of DNA originating from other sources, such as bacteria.

 

5-7 days

·       To monitor the health of your cell line

·       To monitor for contamination in shared lab spaces

·       To assure that mycoplasma is not interfering with your experiments

·       To rule out mycoplasma as the culprit of chromosomal aberrations

Short Tandem Repeat Analysis (STR)

·       STR polymorphisms for 15 loci plus amelogenin (Promega® PowerPlex® 16)

·       Probability of matching identity to an existing STR profile

·      STR polymorphisms in areas other than those represented in Promega® PowerPlex® 16

 

10-20 days

·       To monitor identity of a cell line

·       To confirm relationship of iPS cells to their parent line

·       To establish an STR profile of a newly derived or reprogrammed cell line

·       To rule out culture cross-contamination

Single nucleotide polymorphism (SNP) Microarray



 

·       Submicroscopic genomic abnormalities   (>5-10 Mb)

·        Genomic gains and losses (>50 Kb)

-   Copy number variants

-   Duplications/deletions

-   Unbalanced translocations

-   Aneuploidies

·      Copy neutral Loss of Heterozygosity (LOH)  / Absence of Heterozygosity (AOH) (>5 Mb)

·       >~10% mosaicism (for example: cultures where >1 of 10 cells are trisomy 12

·      Balanced translocations
  - Robertsonian 

·      Balanced insertions

·      Inversions

·      <~10% culture mosaicism (for example:  cultures where 1 of 10 cells is trisomy 12)

·      Chromosomal position of genomic gains

 

14-21 days

·       As a baseline genomic screen

-    To detect submicroscopic (<5 Mb) abnormalities

-    To identify amplified or deleted genes of interest

-    To assess and monitor genomic stability (for example: every 5-10 passages of cell culture)

·       In conjunction with g-banded karyotyping

-    To define unbalanced translocation breakpoints

·       For research of genomic copy number change

-    To identify structural variation within populations or disease cohorts

-    To develop a cell line copy number variant profile

Spectral Karyotyping (SKY)

·       Microscopic genomic abnormalities   (>5-10 Mb)

-   Balanced and unbalanced translocations

-   Aneuploidies

·      Submicroscopic genomic abnormalities (<5 Mb)

·      Inversions

·      Duplications/deletions

14-21 days

 

·       As an adjunct to g-banded karyotyping

-    To define complex rearrangements

-    To identify marker chromosomes

·       When publication-quality spectral karyotypes are needed


 
 iTurn-around-times (TAT) provided are based on provision of sufficient mitotically active hES or iPS cultures grown in Matrigel/TeSR or MEF/hES media conditions.


“Before we began using WiCell’s cytogenetic services, we often waited weeks or even months to receive karyotype data. Experiments often were delayed and our lab staff was frustrated. The fast turnaround and high levels of communication from the WiCell Cytogenetic Lab has allowed karyotyping to become a routine quality control measure for us, not a bottleneck to research projects.”

— Jessica Antosiewicz-Bourget, lab manager for Dr. James Thomson, University of Wisconsin–Madison and Morgridge Institute for Research