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Genomic Sciences and Precision Medicine Center (GSPMC)

Research

To discuss a custom project or to learn more about our research services, please contact GSPMCBusinessoffice@mcw.edu.

Programmatic areas of research of Genomic Sciences and Precision Medicine Center members:

  • Precision Medicine
  • Genetics and Genomics
     - Cancer
     - Complex disease (cardiovascular, renal)
     - Immunogenetics
     - Diabetes
     - Obesity
     - Transplantation
     - Metabolic function
  • Epigenetics
  • Physiological Genomics
  • Pharmacogenomics
  • Metabolomics
  • Microbiome/genetics
  • Bioinformatics
  • Biostatistics
  • Gene editing technologies
  • Mutation detection technologies
  • Sequencing, genotyping, expression profiling, biomarker development
  • Genetic Counseling

Test Types

all
Chromatin Immunoprecipitation (CHIP) Sequencing
Test Name
Chromatin Immunoprecipitation (ChIP) Sequencing

Test Information/Description
Analyze protein interactions with DNA and determine the sites on DNA where certain proteins or histone marks are bound.

Methodology
Cells are fixed in a way that crosslinks DNA sequences with proteins. The DNA is sheared to create small segments of DNA. Proteins are captured with antibodies and the DNA-protein complex is pulled down. The DNA and proteins are unlinked and resulting DNA undergoes library preparation for Illumina next generation sequencing. Matching input samples are required for all sample types submitted and act as a control level and coverage of total DNA isolated. Recommended coverage of 10-30 million reads per sample will depend on type of peaks expected from the protein pulldown.

Test Limitations
Specificity of antibody is necessary for clean capture of protein.

Specimen Type
Actively growing tissue culture cells or fixed cell pellet ** consultation available regarding method of fixation

Specimen Requirements
2-6 million cells per protein or histone mark desired to test.

Specimen Type
Tissue*** coming in the next year

Specimen Requirements
Flash frozen tissue, 50-200mg, depending on protein or histone mark desired to test.

Shipping Conditions
-80C, ultra frozen; overnight

Turnaround Time
6-8 weeks for histone marks; 8-10 weeks for other proteins
MicroRNA and miRNA Sequencing (Summer 2018)
Test Name
microRNA and miRNA Sequencing (Summer 2018)

Test Information/Description
Sample preparation will enrich for small RNA

Methodology
If total RNA is provided, input total RNA quality control with fragment analysis and quantification, library preparation (Captures small RNA with 3′ OH and 5′P modifications), Illumina sequencing. Recommended sequencing at 10 million reads per sample.

Test Limitations

Specimen Type
Total RNA, 1-1.5ug (at a concentration of at least 200ng/uL in nuclease free water); small RNA, 10-50ng (at a concentration of at least 2ng/uL in nuclease free water), quality and quantity of RNA will be verified in house prior to initiation of library preparation

Specimen Type and Requirements
Cells or fresh frozen tissue ** available with consultation; RNA extraction methods may be available for your cell or tissue type

Specimen Type
Completed library prep

Specimen Requirements
Sample numbers, adaptor sequence

Shipping Conditions
Dry ice (-80C), overnight

Turnaround Time
If RNA or completed library prep is provided, 4-6 weeks; RNA extraction and optimization may require additional 1-2 weeks
RNA-seq, Transcriptome
Test Name
RNA-seq, Transcriptome

Test Information/Description
Determination of the presence and quantity of RNA transcripts in relative levels between control and experimental samples.

Methodology
Stranded mRNA sequencing = input total RNA quality control with fragment analysis and quantification, library preparation (with polyA enrichment or ribosomal depletion to obtain the mRNA fraction), Illumina sequencing, 2x125bp reads (paired end). Recommended sequencing at 50 million reads per sample.

Test Limitations
polyA enrichment of RNA will eliminate lncRNA and miRNAs that do not have polyA tails

Specimen Type and Requirements
Isolated total RNA from 250ng to 1ug, quality and quantity of RNA will be verified in house prior to initiation of library preparation

Specimen Type and Requirements
Low input RNA (total RNA 10pg to 100ng) or low cell numbers (1000 to 10000 cells) *** coming in the next 6 months, cells cannot be stored in fixative

Specimen Type and Requirements
cells or fresh frozen tissue ** available with consultation; RNA extraction methods may be available for your cell or tissue type

Specimen Type and Requirements
FFPE ** available with consultation *** coming in the next year

Specimen Type
Completed library prep

Specimen Requirements
Sample numbers, adaptor sequence

Shipping Conditions
Dry ice (-80C), overnight

Turnaround Time
If RNA or completed library prep is provided, 4-6 weeks; RNA extraction and optimization will require additional 1-2 weeks.
Reduced Representation Bisulfide Sequencing (RRBS)
Test Name
Reduced Representation Bisulfide Sequencing (RRBS)

Test Information/Description
Sequence the methylation status of particular CpG rich regions of the genome.

Methodology
DNA Methylation Sequencing. DNA (150-300ng) will be digested at CpG motifs with MspI (10 Units, R0106L; New England Biolabs). Digested fragments will undergo end repair and A-tailing with Klenow fragment polymerase (5Units, M0212S; New England Biolabs) and overnight ligation with TruSeq adapters (Illumina) containing next generation barcode sequences. DNA cleanup and fragment size selection will be completed using Agencourt AMPure beads (Beckman Coulter) at 2x beads to sample volume. Samples then will be processed twice for bisulfite conversion using the EpiTect Bisulfite conversion kit (Qiagen). DNA up clean will be completed followed by relative abundance (SYBR green qPCR, Bio-Rad) and PCR amplification of the products performed (Pfu Turbo, Agilent). Libraries will be pooled in equimolar ratios and undergo size selection using 1.2x and 0.7x Agencourt AMPure beads to enrich for 150-500bp products. Final assessment and quantification of the RRBS libraries will be completed with qPCR, fluorescence measurements and Bioanalyzer 2100 DNA High Sensitivity Assay (Agilent). Next Generation Sequencing will be completed at the GSPMC Facility on the Illumina HiSeq 2500. Paired end, 125 base pair reads will be generated at 10-20 million reads per sample.

Test Limitations
Coverage is only a part of the genome

Specimen Type
Isolated DNA

Specimen Requirements
150-300ng

Specimen Type
Cells or fresh frozen tissue** available with consultation; DNA extraction methods may be available for your cell or tissue type

Specimen Requirements
150-300ng

Specimen Type
FFPE samples

Specimen Requirements
150-300ng of intact DNA **** size selection may be available to remove some fixation induced breaks

Shipping Conditions
-20C, frozen; overnight

Turnaround Time
6-8 weeks