Cancer Genomics

The Cancer Genomics Shared Resource (CGSR) provides comprehensive genomic services and many state-of-the-art technologies via the MCC Cytogenomics Shared Service and the University of Minnesota Genomics Center (UMGC).

Investigators are encouraged to utilize one or both of the resources, depending on goals of the project, whether the need is for classic cytogenetics or the newest molecular genetic sequencing assay.

Contact either facility for guidance on technology selection.

Services

Services

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.

Rates

Rates

Services and fiscal year 2018 rates*

Karyotyping Normal/Simple Abnormal: $447.53

Karyotyping Quick QC: $119.46

Fluorescent-In-Situ-Hybridization (FISH) using home-brew and commerical probes/Interphase, metaphase: $224.77

FISH homebrew DNA: $293.58

FISH homebrew DNA/BAC: $413.88

Microarray CGH 4x180K array: $380.22

MLPA: $41.39

Hourly rate: $62.31

Telomere Assay (including DNA extraction): $38.89

* Rates listed above apply to Masonic Cancer Center members. Please contact LeAnn Oseth (oseth003@umn.edu) or Paula Haffner (phaffner@umn.edu) for external rates.

Images

Images

G-banding followed by FISH identifies the integration site of a transposon plasmid probe to mouse chromosome band 6B3-6C2G-banding followed by FISH identifies the integration site of a transposon plasmid probe to mouse chromosome band 6B3-6C2

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

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

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

 

Video on services provided

University of Minnesota Genomics Center (UMGC)

Visit the UMGC page for services, updated rates, and contact information.

Staff

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

Director - UMGC
Kenny Beckman, Ph.D.
612-626-2985
kbeckman@umn.edu

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

Cytogenetic Technologist
Molly Lynch
612-626-3302
lynch199@umn.edu