Masonic Cancer Center

A comprehensive cancer center designated by the National Cancer Institute

Cytogenomics

The University of Minnesota's Cytogenomics Laboratory provides investigators with a variety of cytogenetic and molecular cytogenetic services.

Investigators are encouraged to contact the cytogenomics laboratory or the director to discuss experimental design and development of related technologies as needed.

Video On Services Provided by the Cytogenomics Shared Resource

Cytogenomics Shared Resource Director
Betsy Hirsch, Ph.D.
612-273-4952
hirsc003@umn.edu

Cytogenomics Shared Resource Coordinator
LeAnn Oseth
Lab: 4-140 Moos Tower
612-626-3302
oseth003@umn.edu

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LeAnn Oseth in the lab.

High quality G-band karyotype analyses of human, mouse, rat and swine cell lines, embryonic stem (ES) cells, induced Pluripotent Stem (iPS) cells, blood, bone marrow or fresh tissue.

Fluorescence-in-situ-hybridization (FISH) studies performed on cell lines, fresh or paraffin-embedded tissue samples, including:

  • Generation of site-specific probes from genome resources BAC/PAC clones or investigator-provided DNA sequences
  • Use of commercially-available probes
  • Focused gene mapping of human or mouse genes using sequential G-banding and FISH and/or FISH and Spectral Karyotyping (SKY).
  • Metaphase and interphase FISH analyses to investigate the presence of, or monitor, a specific chromosomal or gene rearrangement, or XX/XY chimeras.

Spectral Karyotyping (SKY) multi-color FISH analyses for human, mouse and rat cell lines and tissues to identify structural chromosome abnormalities, and clarify tumor heterogeneity on a cell by cell basis

Genomic Microarrays for detection of Copy Number Variants and Copy Neutral changes.
This technology permits evaluation of tissues not amenable to conventional cytogenetics (solid tumors and mature nondividing tissues)

Human, mouse and rat arrays are available for detection of genome-wide copy number changes (e.g., gene duplication and deletions):

  • 4x180K, 2x400K and other array platforms
  • CUSTOM array platforms can be designed at no additional cost
  • Hybrid CGH+SNP and SNP microarrays

Mulitplex Ligation-Dependent Probe Assay (MLPA) analyses performed on DNA samples for detection of abnormal copy numbers and single gene aberrations. PCR primer probe sets for genetic syndromes, cancers and tumors are commercially available. MLPA can also be performed with Investigator designed primers or primers designed in collaboration with the Biomedical Genomics Center or MRC Holland.
 

Cytogenomics Core Laboratory

Core Director: Betsy Hirsch, Ph.D.
Core Coordinator: LeAnn Oseth, 626-3302, oseth003@umn.edu

G-Banded Karyotyping

  • Analysis and karyotype of Human cell lines, Normal / Simple Abnormal $515.99
  • Analysis and karyotype of Human cell lines, Abnormal $1,109.81
  • Analysis and karyotype of Mouse/Rat/Pig cell lines, Normal /S. Abnormal $446.34
  • Analysis and karyotype of Mouse/Rat/Pig cell lines, Abnormal $778.69
  • Chromosome breakage study and karyotyping of Human/Mouse $797.82
  • Extra screening $110.78

Flourescent-In-SITU-Hybridization (FISH)
**Details of analysis determined with investigator ,e.g. metaphase cells versus interphase cells, number of cells evaluated, etc.

  • FISH using BAC isolated and lab-prepared probe $541.12
    Includes ordering of BAC, DNA isolation, labeling of probe, and 2-3 hybridizations with analysis**
  • FISH using single probe provided by investigator $522.34
    Includes labeling of probe, hybridization and analysis**
  • FISH using commercial probes, Human or Mouse (limited) $377.92
    Includes interphase or metaphase cells examined**
  • Spectral Karyotyping (SKY) – Human, Mouse or Rat $664.51
    Includes 10 metaphase cells analyzed by SKY
     

Microscopy Comparative Genomic Hybridization (CGH)
Human, Mouse and Rat genome 60-mer oligonucleotide-based microarray CGH
(Agilent Technologies platform)

  • 4x180K Oligonucleotide microarray $723.90
    13 KB overall median probe spacing
  • 2x400K Oligonucleotide microarray $1,034.61
    5.3 KB overall median probe spacing
  • Custom arrays also available on request

MULTIPLEX LIGATION-DEPENDENT PROBE ASSAY (MLPA)

  • MLPA using COMMERCIAL or CUSTOM probesets available thru MRC Holland $111.42

Project costs can be determined on an individual basis to meet investigator needs.

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G-banding followed by FISH identifies the integration site of a transposon plasmid probe to mouse chromosome band 6B3-6C2

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Human bone marrow karyotype (Fanconi anemia): G-band karyotyping reveals a chromosome fragment resembling a portion of chromosome 3

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Spectral Karyotyping (SKY) or M-FISH (Multicolor FISH) confirms the G-band chromosomal fragment to be extra copy of a portion of chromosome 3

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View a larger image in a new window

Microarray comparative genomic hybridization (aCGH) identifies multiple gains (green) and losses (red) within this human DNA sample

 

 

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  • Last modified on February 10, 2014