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Oncogenomics Shared Resource Facility (OG SRF)

Director: Kurt B. Hodges, MD, MBA Kurt.Hodges@uky.edu

  • Mission Statement

    The overall mission of the Oncogenomics Shared Resource Facility (OG SRF) laboratory is to accelerate the clinical genomics, precision medicine and genomic research interests at the Markey Cancer Center (MCC) by providing cutting-edge genomic technology services.

    Functioning as one component of the larger UK HealthCare Genomics Core, the OG SRF provides state-of-the-art technologies specifically adapted to needs of MCC investigators to facilitate ge­nomics into the translational pathway from basic research to clinical and population-based studies. The OG SRF plays a critical role in Markey’s directions for research and delivery of precision medicine. 

    The Genomics Core Laboratory, a College of American Pathologists-accredited facility, was established in 2015 as part of UK HealthCare, Department of Pathology and Laboratory Medicine and MCC's Genomics initiative. The facility occupies about 4,500 square feet within the UK HealthCare Clinical Laboratories. 

    You can browse our pages here to learn about our team, find our location and other vital information. For more, visit the Genomics Core Laboratory webpage.

  • Services

    We provide investigators access to a wide range of genomic services, including the following:

    Next-Generation Sequencing

    DNA Sequencing

    • Whole genome sequencing
    • Human and other organism
    • We prepare NGS libraries
    • Targeted resequencing
      • Amplicon sequencing and small gene panels
      • Investigators provide the probes/amplicons/libraries
    • Whole exome sequencing
      • We prepare the libraries
      • Agilent Clinical Research Exome
      • Roche Nimblegen MedExome
      • Illumina Rapid Exome

    RNA Sequencing

    • Whole transcriptome sequencing (RNA-seq)
      • We prepare NGS libraries/investigators can also prepare libraries
    • Targeted RNA-sequencing
      • Investigators provide the NGS libraries
    • Methylation sequencing
      • Whole genome methylation sequencing
      • Investigators can provide NGS libraries
    • Chip-sequencing
      • NGS library preparation & sequencing only
      • Investigators perform IP and provides the captured fragments

    Sanger Sequencing

    • Tier I – Sequencing only
      • Investigators perform PCR, sequencing reaction and cleanup
    • Tier II – Clean up and sequencing 
      • Investigator perform PCR and sequencing reaction
    • Tier III – Sanger sequencing reaction, cleanup and sequencing
      • Investigator perform PCR

    Fragment Analysis

    • Client performs reactions and fragment analysis on the ABI 3730

    Gene Expression Microarray

    • All standard arrays
    • miRNA array
    • Custom arrays

    Other Services

    • NanoString
    • Real-time-PCR
    • Bioanalysis
    • Covaris ultrasonication for ChIP-sequencing
  • Acknowledgement

    Investigators are required to acknowledge the Markey Cancer Center Oncogenomics Shared Resource Facility (OG SRF) in any publications that result from the use of the MCC OG SRF. For your convenience, you are welcome to use the following statement: The research was supported by the Oncogenomics Shared Resource Facility of the University of Kentucky Markey Cancer Center (P30CA177558).  

  • Faculty and Staff

    Director: Kurt B. Hodges, MD, MBA

    Kurt Hodges

    Associate Professor, Pathology and Laboratory Medicine 
    Director, Oncogenomics Shared Resource Facility, Markey Cancer Center 
    Phone: 859-218-5813 
    Email: Kurt.Hodges@uky.edu
    View physician profile


    Vijaya Sivaraj, PhD, MBA

     

    Manager, UK HealthCare Genomics Core Laboratory and Oncogenomics Shared Resource Facility, Markey Cancer Center 
    Phone: 859-218-5832 
    Email: Vijaya.Sivaraj@uky.edu


    Jennifer Stocks-Candelaria, BS, BA, MB (ASCP)CM

    Jennifer Stocks-Candeleria

    Chief Laboratory Technologist
    Oncogenomics Shared Resource Facility, Markey Cancer Center
    Email: Jennifer.Stocks-Candelaria@uky.edu

  • Cost Structure

    Price Schedule For MiSeq & Next Gen Libraries Related Services.

    Name of Service Description UK Price   MCC Member Price* 
    RES MISEQ RUN 2X250 V2 NANO MiSeq Run - Nano 250X 2 Flowcell. Run Only, QPCR may be required before run.  $900.00 $675.00
    RES MISEQ RUN 2X150 V2 MiSeq Run -150X2 Flowcell. Run Only, QPCR may be required before run.  $1205.03  $903.77
    RES MISEQ RUN 2X250 V2 MiSeq Run - 250X2 Flowcell. Run Only, QPCR may be required before run.  $1,285.11  $963.83
    RES MISEQ RUN 2X300 V3 MiSeq Run - 300X2 Flowcell. Run Only, QPCR may be required before run  $1,664.71  $1,248.53
    RES NEXTERA LIBRARY PREP ** MiSeq Nextera Library Preparation. Client provides DNA  $250.00  $187.50
    RES NEXTERA XT LIBRARY PREP ** MiSeq Nextera XT Library Preparation. Client provides DNA  $256.00  $192.00
    RES Q PCR FOR NGS LIBRARY QPCR for NGS  $35.00  $26.25
    RES DNA QUANT BY QUBIT DNA Quantitation by Qubit Per Sample  $2.08  $1.56
    RES RNA QUANT BY QUBIT RNA Quantitation by Qubit Per Sample.  $4.27  $3.20
    RES TRUSEQ PCR-FREE LIBRY PREP ** MiSeq TruSeq DNA PCR free Library Preparation  $255.00  $191.25
    RES TRUSEQ NANO LIBRARY PREP** MiSeq TruSeq DNA Library Preparation  $325.00  $243.75
    RES TRUSEQ RNA LIBRARY PREP ** MiSeq TruSeq RNA Library Preparation  $310.79  $233.09
    RES CANCER GENE PANEL Library preparation of custom 198-gene cancer panel using Agilent SureSelect XT kit and automation. Compatible with Illumina HiSeq Next Generation Sequencing. (Please contact for details regarding genes of interest, number of samples, and sequencing depth of coverage needed).  $559.60  $419.70
    RES AMPLICON DNASEQNEXTERA INDICES Amplicon DNA Seqencing using Nextera Indices. Client generates the 16S amplicons, using primers which incorporate the Illumina adaptor sequence, an 8 nucletides index sequence and the gene specific primer. The amplicons are sequenced on the Miseq plaform using 2x250 base reads.  $44.67  $33.50
    RES STR HUMAN CELL LINE AUTHENTICATION Uses the Promega PowerPlex 16 HS system in combination with the ABI 3130xl Genetic Analyzer to perform fragment analysis on client-supplied DNA.  Sixteen short tandem repeat sites are fragmented and assessed and  ABI Gene Mapper is used to generate fragment analysis plots for each STR. Both .fsa files and fragment analysis plots are provided to client for their use in ID or authentication of their human cell lines.  $63.25  $47.44
    RES SONICATION SINGLE SAMPLE Covaris Sonication - To shear / process one sample  $32.00  $24.00
    RES SONICATION ADDITOAL SAMPLE Covaris Sonication additional sample will include the base price of a single sample every additional sample cost.  $7.50  $5.63
    RES TAPE STATION RNA Tapestation RNA analysis Per Sample  $17.84  $13.38
    RES TAPE HIGHSENSITIV DNA 1000 Tapestation High Sensitivity DNA analysis Per Sample  $16.34  $12.26
    RES TAPES HIGH SENSITIVITY RNA Tapestation High Sensitivity RNA analysis Per Sample  $18.49  $13.87
    RES TAPESTATION GENOMIC DNA  Tapestation Genomic DNA analysis Per Sample  $16.39  $12.29
    RES TAP STATION DNA 1000 Tapestation DNA 1000 analysis Per Sample  $15.03  $11.27

    Note 1: ** Library Preparation includes ONLY Bio-Anlaysis and Qubit Cost and NOT the QPCR cost of $35.

    *Member price includes 25% subsidy.

    Non-UK clients pay list price plus 10%.

    Price Schedule for Sanger Sequencing Related Services

    Name of Service Description UK Price  MCC Member Price*  Notes 
    RES SANGER SEQUENCING TIER 1.1 Sequencing (Run) Only, 1-16 Samples $3.40 $2.55 Per Sample
    RES SANGER SEQUENCING TIER 1.2 Sequencing (Run) Only, 17-96 Samples  $50.00 $37.50 Flat Price / Plate
    RES SANGER SEQUENCIN TIER 2.1 Reaction Cleanup and Sequencing, 1-16 Samples $4.22 $3.17 Per Sample
    RES SANGER SEQUENCIN TIER 2.3 Reaction Cleanup and Sequencing, 17-96 samples  $55.00 $41.25 Flat Price / Plate
    RES SANGER SEQUENCIN TIER 3.1 Sequencing Reaction Setup, Cleanup and Sequencing, 1-20 Samples $9.94 $7.46 Per Sample
    RES SANGER SEQUENCING TIER 3.3 Sequencing Reaction Setup, Cleanup and Sequencing, 21-60 Samples $162.83 $122.12 Flat Price for all Units
    RES SANGER SEQUENCING TIER 3.4 Sequencing Reaction Setup, Cleanup and Sequencing, 61-94 Samples $195.00 $146.25 Flat Price/ Plate
    RES SANGER SEQUENCING TIER 3.5 Same as Tier 3.3 + Additional primer $162.83 $122.12 1 primer is included in $162.83
    RES SANGER SEQUENCING TIER 3.6 Same as Tier 3.4 + Additional primer $195 $146.25 1 primer is included in $195
    RES ADDITIONAL PRIMER Each additional primer for sequencing over one / plate is one unit $6.00 $4.50 Per Primer
    RES PCR PURIFICATION WELLPLATE PCR Purification of a wellplate (94): Magnetic Bead $149.46 $112.10 Per Plate
    RES PCR PURIFICATION PCR Product Purification: Magnetic Bead Prep $1.59 $1.19 Per Sample
    RES ENZYMATIC PCR PURIFICATION PCR Product Purification: Enzymatic Clean up  $3.31 $2.48 Per Sample
    RES FRAGMENT ANALYSIS PLATE Fragment analysis on the ABI 3730 (Client performs reactions) $86.01 $64.51 Per Plate

    *Member price includes 25% subsidy.

    Non-UK clients pay list price plus 10%.

    Price Schedule for HiSeq Related Services

    Name of Service Description UK Price    MCC Member Price* 
      High Output Run Mode    
    RES HOP FULL FLOW CELL SR 100 HiSeq High Output Run with a 100 bp Single Read Full Flowcell $9,200.00 $6,900.00
    RES HOP 1 LANE SR 100 HiSeq High Output Run with a 100 bp Single Read  1 Lane  $1,150.00 $862.50
    RES HOP FULL FLOW CELL PE 50 HiSeq High Output Run with a 50 bp Paired End Read Full Flowcell $11,261.00 $8,445.75
    RES HOP 1 LANE PE 50 HiSeq High Output Run with a 50 bp Paired End Read  1 Lane  $1,493.96 $1,120.47
    RES HOP FULL FLOW CELL PE 100 HiSeq High Output Run with a 100 bp Paired End Read Full Flowcell $16,396.26 $12,297.20
    RES HOP 1 LANE PE 100 HiSeq High Output Run with a 100 bp Paired End Read  1 Lane  $2,107.46 $1,580.60
    RES HOP FULL FLOW CELL PE 125 HiSeq High Output Run with a 125 bp Paired End Read Full Flowcell $16,396.26 $12,297.20
    RES HOP 1 LANE PE 125 HiSeq High Output Run with a 125 bp Paired End Read  1 Lane  $2,107.46 $1,580.60
    RES HOP FULL FLOW CELL SR 50 HiSeq High Output Run with a 50 bp Single Read Full Flowcell $7,000.00 $5,250.00
    RES HOP 1 LANE SR 50 HiSeq High Output Run with a 50 bp Single Read 1 Lane  $971.96 $728.97
      Rapid Run Mode     
    RES HISEQ RR FULL FLWC SR 50  HiSeq Rapid Run with a 50 bp Single Read Full Flowcell $1,650.00 $1,237.50
    RES SPLIT FLW CEL 2 LANES SR50 HiSeq Rapid Run with a 50 bp Single Read 2 lanes Split Flowcell $2,300.00 $1,725.00
    RES SPLIT FLOW CEL 1 LANE SR50 HiSeq Rapid Run with a 50 bp Single Read  1 lane Split Flowcell $1,150.00 $862.50
    RES HISEQ RR FUL FLWC SR 100 HiSeq Rapid Run with a 100 bp Single Read Full Flowcell $2,300.00 $1,725.00
    RES SPLIT FLW CEL 2LANES SR100 HiSeq Rapid Run with a 100 bp Single Read 2 lanes Split Flowcell $2,700.00 $2,025.00
    RES SPLIT FLW CEL 1 LANE SR100 HiSeq Rapid Run with a 100 bp Single Read  1 lane Split Flowcell $1,350.00 $1,012.50
    RES HiSEQ RR FULL FLOWCELL SR 200 HiSeq Rapid Run with a 200 bp Single Read  Full Flowcell $3,063.00 $2,297.25
    RES SPLIT FLW CEL 2LANES SR200 HiSeq Rapid Run with a 200 bp Single Read 2 lanes Split Flowcell $3,549.00 $2,661.75
    RES SPLIT FLW CEL 1 LANE SR200 HiSeq Rapid Run with a 200 bp Single Read  1 lane Split Flowcell $1,775.00 $1,331.25
    RES HISEQ RR FULL FLWCEL PE50 HiSeq Rapid Run with a 50 bp Paired End Read Length in Full Flowcell $3,115.00 $2,336.25
    RES SPLIT FLW CEL 2LANES PE50 HiSeq Rapid Run with a 50 bp Paired End Read 2 lanes Split Flowcell $3,601.00 $2,700.75
    RES SPLIT FLOW CEL 1 LANE PE50 HiSeq Rapid Run with a 50 bp Paired End Read Length in 1 lane Split Flowcell $1,801.00 $1,350.75
    RES HISEQ RR FUL FLWCELL PE100 HiSeq Rapid Run with a 100 bp Paired End Read  Full Flowcell $4,009.00 $3,006.75
    RES SPLIT FLW CEL 2LANES PE100 HiSeq Rapid Run with a 100 bp Paired End Read  2 lanes Split Flowcell $4,495.00 $3,371.25
    RES SPLIT FLW CEL 1 LANE PE100 HiSeq Rapid Run with a 100 bp Paired End Read 1 lane Split Flowcell $2,300.00 $1,725.00
    RES HISEQ RR FUL FLWCEL PE250 HiSeq Rapid Run with a 250 bp Paired End Read Full Flowcell $6,364.30 $4,773.23
    RES SPLIT FLW CEL 2LANES PE250 HiSeq Rapid Run with a 250 bp Paired End Read 2 lanes Split Flowcell $6,960.23 $5,220.17
    RES SPLIT FLW CEL 1 LANE PE250 HiSeq Rapid Run with a 250 bp Paired End Read 1 lans Split Flowcell $3,513.22 $2,634.92
    RES MISELLANEOUS CDM For our high expensive MiSeq & Hi Seq Split. Contact Genomics Core Manager Variable  

    *Member price includes 25% subsidy.

    Non-UK clients pay list price plus 10%.

    Price Schedule for MicroArray Related Services

    Name of Service Description UK Price   MCC Member Price* 
    RES BIOANALYSIS DNA-1000 Agilent Bioanalyzer DNA 1000, 1-12 samples,   sizing 25-1000 bp, concentration range 0.1-50 ng/ul, require 1-2ul of DNA sample  $44.02  $33.02
    RES BIOANALYSIS DNA-HS Agilent Bioanlayzer DNA High Sensitivity, 1-11 samples, sizing 50-7000bp, concentration range 5-500 pg/ul, require 1-2ul of DNA sample  $64.97  $48.73
    RES BIOANALYSIS NANODROP Concentration of DNA/RNA samples using Nanodrop Spectrometer, requires 1-2ul of sample  $5.15  $3.86
    RES BIOANALYSIS RNA-NANO Agilent Bioanalyzer RNA 6000 RNA Nano kit, 1-12 samples, concentration range 25-500 ng/ul, requires 1-2ul of RNA sample  $42.31  $31.73
    RES BIOANALYSIS RNA-PICO Agilent Bioanalyzer RNA Pico kit, 1-11 samples, concentration range 50-5000 pg/ul, requires 1-2ul of RNA sample  $45.17  $33.88
    RES MI-RNA PROCESSING miRNA processing for Nanostring nCounter, 12 samples, contact laboratory for concentration requirements  $155.00  $116.25
    RES RNA PROCESSING RNA processing for Nanostring nCounter system, 12 samples, contact laboratory for concentration requirements  $85.00  $63.75
    RES HT ARRAY/PICO WT PROTOCOL Affymetrix HTA array plus Pico WT processing  $609.85  $457.39
    RES GENE ARRAY/PICO WT PROTCOL Affymetrix Gene array plus  Pico  WT processing  $556.00  $417.00
    RES EXTRA GENE ARRAY Affymetrix Gene array only  $225.00  $168.75
    RES EXTRA HT ARRAY Affymetrix HTA array only  $299.00  $224.25
    RES MIRNA PROCESS & ARRAY Affymetrix miRNA array plus processing  $375.00  $281.25
    RES MIRNA PROCESSONLY Affymetrix miRNA processing only  $190.96  $143.22
    RES 3'IVT PROCESSING Affymetrix 3' IVT processing only  $290.00  $217.50
    RES WT PROCCESSING Affymetrix WT processing only  $294.00  $220.50
    RES PICO-WT PROCESSING Affymetrix Pico WT processing only  $331.00  $248.25
    RES BOVINE  GENE 1.0 ST ARRAY Affymetrix Bovine Gene 1.0 array plus processing  $525.00  $393.75
    RES C.ELEGANS GENE 1.0 ST ARRY Affymetrix C. Elegans Gene 1.0 array plus processing  $525.00  $393.75
    RES HUMAN GENE 1.0 ST ARRAY Affymetrix Human Gene 1.0 ST array plus processing  $525.00  $393.75
    RES HUMAN GENE 2.0 ST ARRAY Affymetrix Human Gene 2.0 ST array plus processing  $525.00  $393.75
    RES MOUSE GENE 1.0 ST ARRAY Affymetrix Mouse Gene 1.0 ST array plus processing  $525.00  $393.75
    RES MOUSE GENE 2.0 ST ARRAY Affymetrix Mouse Gene 2.0 ST array plus processing  $525.00  $393.75
    RES RAT GENE 1.0 ST ARRAY Affymetrix Rat Gene 1.0 ST array plus processing  $525.00  $393.75
    RES RAT GENE 2.0 ST ARRAY Affymetrix Rat Gene 2.0 ST array plus processing  $525.00  $393.75
    RES HUMAN HTA 2.0 ARRAY Affymetrix Human HTA 2.0 array plus processing  $599.00  $449.25
    RES MOUSE MTA 1.0 ARRAY Affymetrix Mouse MTA 1.0 array plus processing  $599.00  $449.25
    RES RAT MTA 1.0 ARRAY Affymetrix Rat RTA 1.0 array plus processing  $599.00  $449.25

    *Member price includes 25% subsidy.

    Non-UK clients pay list price plus 10%.