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.

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Grant Program Contact
Fernanda Rodriguez
UMN Genomics Center
Spatial Genomics Project Lead
612-624-6269
spatialomics@umn.edu

Calendar dates

Spatial Genomics request: https://forms.gle/LJmHcDNJ2GmeXvFb7

The Masonic Cancer Center is pleased to announce its Spatialomics Grant. This grant will provide up to $2,000 in reagents towards Spatial projects using the NanoString GeoMx or 10X Visium platforms.

These technologies enable spatially resolved profiling of RNA and protein targets, by combining tissue morphology visualization and molecular profiling. Depending on the technology, the user can choose between targeted panels to the whole transcriptome.

Applicants can submit a project by accessing the following link. Please provide a brief description of your project and indicate which platform you would like to use. Since MCC support will in most cases only cover a fraction of the project costs, we would like to ensure that PIs have other funds in place to complete the proposed experiments. For information on the technology and available panels go to NanoString or 10X Genomics, or contact Fernanda Rodriguez (mfrodrig@umn.edu or spatialomics@umn.edu).

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

Rates for fiscal year 2021

MCC Member Rate	MCC Non-Member Rate	External Rate
Karyotyping Normal/Simple Abnormal: $550.00	$877.03	$1,429.56
Karyotyping Quick QC: $158.00	$204.64	$333.56
Fluorescent-In-Situ-Hybridization (FISH) using home-brew and commerical probes/Interphase, metaphase: $279.80	$432.05	$704.24
FISH homebrew DNA: $386.48	$432.05	$920.92
FISH homebrew DNA/BAC: $514.12	$797.62	$1300.13
Hourly rate: $80.00	$136.43	$222.38
Telomere Assay (including DNA extraction): $69.69	$69.69	$113.59

Images

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

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

spectral karyotyping m fish — Spectral 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 — Microarray comparative genomic hybridization (aCGH) identifies multiple gains (green) and losses (red) within this human DNA sample