Molecular Pathology

  • Hanina Hibshoosh, MD
    • Director
  • Sun Dajiang (Kevin)
    • Manager
  • Tao Su, PhD
    • Macromolecule Service Director

The Molecular Pathology Shared Resource (MPSR) facilitates tissue based, human and experimental, basic science and translational cancer research through three integrated services: Histology, Tumor banking and Macromolecule platform (next generation banking). The facility is directed by its founder, Hanina Hibshoosh, MD, and has 10 full-time employees including dedicated/certified histotechnologists, immunohistoochemistry experts, dedicated pathologist, PhD level molecular biologist as well as database experts. It has over three hundred distinct PIs utilizing its services. It is one of the largest and most robust facilities in NCI’s network.

All services are offered on a fee for service basis. Pricing information and online scheduling are available through iLab. For all service inquiries send e-mail to histologyservice@cumc.columbia.edu.


Services

Histology Service

The histology service offers routine and specialized histology services including grossing, embedding, tissue processing, sectioning and staining, whether routine H&E or specialized. It operates on frozen and FFPE tissue. It also offers tissue micro array construction service and expertise, and an experimental immunohistochemistry/ immunofluorescence service. Last year, it processed more than 13,000 blocks and an excess of 161,000 sections were generated. The service is known for its high quality, quick turn around time and dedicated personnel.

For all service inquiries send e-mail to histologyservice@cumc.columbia.edu MPSR main Tel: 1-212-305-1608

MPSR histology service location for drop off and pick up: Black Building 4-455
Hours: 09:00 - 17:00
(Drop-off: 09:00 - 12:00 & 13:30 - 16:00)
(Pick-up: 09:00 - 12:00 & 13:30 - 17:00)

Tumor bank

The tumor bank procures, bar codes, stores, annotates, processes, and distributes to investigators tumor and normal frozen tissue for research purposes. It operates under IRB approval, is HIPAA compliant, and is licensed by the New York State Department of Health, follows NCI best practices for biospecimen resources and is governed by a tissue utilization committee. The bank contains more than 19,000 tumor cases and collects approximately 1,800 cases per year. Its database (Freezerworks 3.1.08.1 multi-user version) utilizes caBIG compliant terminology and we are recipients of “Connecting with caBIG Award”. The bank distributes over 1,000 cases to investigators per year.

For all inquiries send e-mail to tissuebank@cumc.columbia.edu

In order to address the many challenges associated with traditional tumor banking's utility, and to reduce barriers to research, in the molecular era, we developed in 2002 the Molecular Platform (next generation banking).

Macromolecule Platform (next generation banking)

MPSR Macromolecule service director: Tao Su, PhD

For all inquiries send e-mail to: ts283@cumc.columbia.edu, tel 1-212-342-3468
Location: 3960 Broadway, Lasker Biomedical Research Building, Room 350A

The macromolecule platform is a research platform designed to facilitate, Columbia University wide and beyond, cancer research and foster collaboration by evaluating systematically the procured frozen tumors in our tumor bank. This is done by providing a set of thoroughly characterized frozen tumors and normal tissue, corresponding DNA/RNA (macromolecules extracted, quantified and assessed for quality, purity, diagnosis, size and stored), corresponding tissue micro-arrays, whole section banks of formalin fixed slides corresponding to cases, frozen tissue for Western blots/IHC, database (linked clinical/pathological and basic science characteristics) as well linkage to related cases (primary removed piece meal, recurrent and metastatic cases), professional services and expertise in tissue based analysis (extraction, storage, expression, and immuno and molecular genetic characterization).

All is offered in an “off the shelf” ready to use format. By keeping track of users projects and at times primary research results, it allows for leveraging the disparate research efforts of independent investigators. This creates a research “ecosystem” that fosters collaboration (intended and unintended prospectively and retrospectively). The bank relies on frozen (fn) and archival formalin fixed (fx) tumor and normal tissues collected at Columbia University Irving Medical Center. Furthermore, the bank utilizes a multidisciplinary approach to maximize value by integrating the work of Tao Su PhD and Xiaomei Wang in molecular biology/database maintenance/development, pathologists Hanina Hibshoosh MD, Director, and Aqeel Ahmed, MD, statistician.

Through its open, non-proprietary, multidisciplinary, large scale, “off the shelf,” highly characterized, robust, "macromolecule bank," discovery and collaboration are enabled and accelerated. Barriers to research are markedly reduced. This platform currently focuses on systematic evaluation of all tumors collected in our tumor bank corresponding to breast, prostate, bladder, and pancreas. The platform contains hundreds of tumors in each organ ready for biomarker analysis and correlation. It is next generation banking at its best and has already become the backbone of much of our organ based cancer research effort.

Molecular Biology Services

MPSR molecular biology service director: Tao Su, PhD

For all inquiries send e-mail to: ts283@cumc.columbia.edu, tel 1-212-342-3468
Location: 3960 Broadway, Lasker Biomedical Research Building, Room 350A

We also provide molecular biology services on a project-specific level to investigators operating on fresh/frozen or FFPE tissues or analytes prepared by our next generation biobanking service. These include:

  • High throughput RNA/DNA/protein extraction service: With our recently purchased Qiagen QIAsymphony SP allowing for 96 samples extraction/4 hours from fresh, frozen or FFPE tissue and blood.
  • Affymetrix/Agilent microarray labeling
  • Quantitation of macromolecules (RNA/DNA/protein) utilizing Agilent bioanalyzer, Qubit 2.0, and Nanodrop 8000 will provide researchers flexible, but accurate quantification and quality assessment.
  • Realtime PCR and RT-PCR service.

Lastly, during the past few years we introduced full cycle project management service, which allows researchers to send a cohort list (patients) and the facility will carry out and return biomarker analysis - managing the full cycle of pre-analyte retrieval, analyte isolation, biomarker analysis, reporting, and storage. As an example, following receipt of a cohort of patients and their controls we retrieve the corresponding H&E slides and blocks from the Department of Pathology, match them to frozen tissue, review H&E slides for desired lesions (usually a specific cancer type), make either TMA or slide banks (for IHC, 10X 10 micron slide bank for RNA or DNA extractions or protein), perform IHC/extract DNA/RNA/protein (for array based expression, RNAseq, copy number, methylation studies, RPPA), evaluate IHC, and report out results.


Location and Contacts

Histology Service

Black Building
650 West 168th Street, 4th Floor, Room 455
Hours: 09:00 - 17:00
(Drop-off: 09:00 - 12:00 & 13:30 - 16:00)
(Pick-up: 09:00 - 12:00 & 13:30 - 17:00)

Macromolecular Service

Lasker Biomedical Research Building
3960 Broadway, 3rd Floor, Room 350B (Entrance on 166th St.)
Contact: Tao Su 212-342-3468

Contacts

  • Hanina Hibshoosh MD
    • MPSR Director
  • Sun Dajiang (Kevin)
    • MPSR Manager

For all service inquiries send email to histologyservice@cumc.columbia.edu

  • MPSR main #: Tel 1-212-305-1608
  • MPSR histology service location for drop off and pick up: Black Building 4-455
  • MPSR Macromolecule service:
  • MPSR Tumor Bank:

Online Reservations and Policies

The Molecular Pathology Shared Resource uses the iLab Core Management System for service requests, billing, and policies. Before you can request services, you must log into iLab and be approved as a lab member.


User Fees

Histology Service

  • Histopathology
  • Tissue microarray (TMA) construction for immunohistochemical studies of human breast, prostate, kidney, and bladder cancers
  • Immunohistochemistry (IHC) for investigator-initiated projects
Service Number & Name HICCC Member Rate Columbia (Non-Member) Rate External Rate
001 Grossing - Tissue Preparation (Cassette)

$2.40

$3.60 $4.14
002 Processing & Embedding - Paraffin (Block)

$6.00

$9.00

$10.35

006 H&E Stain (Slide) $2.40 $3.60 $4.14
007 Serial Section - Regular Slide - Paraffin (Section)

$1.20

$1.80 $2.07
008 Serial Section - Charge Slide - Paraffin (Section) $1.50 $2.40 $2.76
009 Re-embedding - Paraffin (Block) $2.40 $3.60 $4.14
010 Special Stain (Slide) $12.00 $18.00 $20.70
011 Slides Box - 25 (Box) $4.80 $4.80 $4.80
011a Slides Box - 5 (Box) $1.00 $1.00 $1.00
012 Slides Box - 100 (Box) $6.00 $6.00 $6.00
013 Manual Processing & Embedding - Paraffin (Block) $24.00 $36.00 $41.40
014 Silver Stain (Slide) $24.00 $36.00 $41.40
015 Section in Tube (Tube) $7.20 $10.80 $12.42
016 Empty Cassette (Each)

$0.24

$0.36 $0.41
017a Frozen Section - 1-2 Sections per Block (Section) $6.00 $9.00

$10.35

017b Frozen Section - Additional Sections per Block (Section) $2.40 $3.60 $4.14
018 Make Frozen Block (Block) $6.00 $9.00 $10.35
019 Level Section (Section) $2.40 $3.60

$4.14

021 Special Handling (Hour) (See Details) $48.00 $72.00 $82.80
022 Tissue Array Block - Making Block (Block) $360.00 $540.00 $621.00
023 Tissue Array Block - Cutting (Section) $2.40 $3.60

$4.14

Immunohistochemistry Staining (IHC)

More than 10 years’ service has been provided on 900 distinct primary antibodies to 300+ members from 100+ labs. IHC could be performed on human or animal, frozen, or FFPE immunoblank slides, for chromogen or fluorescent protocol, either manually or on autostainer (20 slides at least). User should provide service requisition form, primary antibody, and immuneblanks.

Service Number & Name HICCC Member Rate Columbia (Non-Member) Rate External Rate
024 Staining - IHC Regular - Autostainer (Slide), 20 Slides Minimum $24.00 $36.00 $41.40
025 Staining - IHC Regular - Manual (Slide) $36.00 $54.00

$62.10

027 Staining - IHC Flourescent Double - Manual (Slide) $40.00

$55.00

$63.25
028 Staining - IHC Flourescent - Manual (Slide)

$24.00

$36.00 $41.40
029 TUNEL Apoptosis Detection Staining $52.00

$64.00

$73.60
030 Staining - IHC Regular Double - Manual (Slide) $44.00

$66.00

$75.90
031 Staining - IHC Flourescent Triple - Manual (Slide) $60.00 $80.00

$92.00

032 Staining - Antibody Test/Optimization, Per Slide

$54.00

$54.00 $62.10
033 Staining - 2100 Antigen Retriever. Per run

$30.00

$30.00 $34.50

Tumor Bank Service

  • Procurement and processing of normal and tumor tissue (all tumor types)
  • Storage of anonymized tissue samples (frozen and paraffin)
  • Distribution to investigators of frozen and paraffin tissue samples for research projects

Macromolecular Service

  • DNA/RNA extraction, processing, annotation
  • Storage of DNA/RNA/TMA paraffin
  • Distribution to investigators of DNA/RNA/TMA material for molecular biology studies
Service Number & Name HICCC Member Rate Columbia (Non-Member) Rate External Rate
501 Affymetrix 3' IVT cRNA Labeling, per labeling $150.00

$150.00

$172.50
502 Primer Synthesis, per primer $12.00 $12.00

$13.80

503 PCR Setup, per gene (2 pairs of primer design with quick PCR and agarose gel test.) $100.00 $100.00 $115
504 Reverse Transcription, per reaction $12.00 $12.00 $13.80
505 qPCR less than 48 wells, per well $3.60 $3.60 $4.14
506 qPCR 48 to 96 Wells, per well $2.40 $2.40 $2.76
507 qPCR 2nd plate and above, per well $1.80 $1.80 $2.07
508 Frozen DNA Extraction with RNase digestion, per sample $24.84 $24.84

$28.57

509 Frozen total RNA extraction with DNase digestion, per sample $24.84 $24.84 $28.57
510 FFPE DNA extraction, with RNase digestion, per sample $30.00 $30.00

$34.50

511 FFPE RNA extraction, with DNase digestion, per sample $30.00 $30.00 $34.50
512 Primer Test per pair (user provides)

$8.40

$8.40 $9.66
513 Agilent miRNA microarray one-color labeling, per labeling $125.00 $125.00 $143.75
514 Agilent gene expression microarray one-color labeling, per labeling

$125.00

$125.00 $143.75
515 Agilent gene expression microarray two-color labeling, per labeling $150.00 $150.00

$172.50

517 mBank handling fee, per hour

$50.00

$50.00

$57.50

518 Pathology review, per hour $99.90 $100.00 $115.00
520 Macrodissection from tissue slide, per case

$25.00

$25.00

$28.75

522 Affymetrix GeneChip WT Terminal labeling, per labeling

$200.00

$200.00

$230.00

523 NuGEN Ovation Pico WTA Amplification and Encore Biotin labeling, per labeling $180.00 $180.00 $207.00
524 NuGEN Ovation One-Direct Amplification and Encore Biotin labeling, per labeling

$210.00

$210.00 $241.50
525 Bioanalyzer test, rush service surcharge, per chip

$40.00

$50.00

$57.70

526 Qiagen Tissuelyser, up to 48 samples, per run

$25.00

$25.00

$28.75
527 5mm stainless steel bead for Qiagen Tissuelyser, per bead $1.00 $1.00 $1.15
528 QIAsymphony frozen DNA extraction with RNase digestion, per sample, 8 samples minimum $18.92 $19.00 $21.85
529 QIAsymphony frozen total RNA extraction with DNase digestion, per sample, 8 samples minimum

$18.00

$18.00

$20.70

530 QIAsymphony FFPE DNA or RNA extraction with RNase or DNase digestion, per sample, 8 samples minimum $20.00 $20.00 $23.00
532 Qubit assay, per sample, performed by core with $25 per 0.5 hour handling fee

$2.00

$2.00

$2.30

534 Nanodrop 8000 measurement, per sample, performed by core with $25 per 0.5 hour handling fee

$1.00

$1.00 $1.15
536 FFPE protein extraction, per sample $25.00 $25.00 $28.75

Leica SCN400 whole slide digital imaging (Slides Scanning - Brightfield only)

Auto bright field whole slide scanning system producing sharp images of up to 40x magnification with 100 seconds average scanning time for 20x magnification. Up to 384 slides could be loaded with autoloader per loading. Standard slide size (26x76 mm)

Service Number & Name HICCC Member Rate Columbia (Non-Member) Rate External Rate
201 Digital Imaging - Whole Slide Scanning on Leica SCN 400, Per Slide Per layer $3.00

$5.00

$5.75
202 Digital Imaging - Leica Unlimited DIH account and up to 100 scans storage, per year

$50.00

$80.00 $92.00

Bioanalyzer/Qubit

The facility provides Agilent Bioanalyzer 2100 and Lifetechnologies Qubit 2.0 analysis for DNA, RNA and protein quantitation and quality assessment. The facility will provide the chips and reagents.

Service Number & Name

HICCC Member Rate

Columbia (Non-Member) Rate External Rate
519 Bioanalyzer test, five or more samples, per sample

$10.00

$10.00 $11.50
525 Bioanalyzer test, one to four samples, per chip

$40.00

$40.00

$46.00
532 Qubit assay, per sample, performed by core with $25 per 0.5 hour handling fee $2.00 $2.00 $2.30
534 Nanodrop 8000 measurement, per sample, performed by core with $25 per 0.5 hour handling fee

$1.00

$1.00

$1.15

Independent Use of Equipment

In addition, users can schedule and use the following equipment themselves by scheduling a reservation in iLab:

Service HICCC Member Rate Columbia (Non-Member) Rate External Rate
IHC 2100 Antigen Retriever, per run (4 hours) $30.00 $30.00

$30.00

NanoDrop 8000, per hour $60.00 $60.00 $69.00
Nikon Microscope (Bright field/Fluorescent), per hour

$30.00

$40.00 $46.00
ABI QunatStudio 3 real-time PCR machine, per hour $7.99 $8.00

$9.20

Qubit 4.0, per hour $40.00 $40.00 $46.00
Tissuelyser II, per run $25.00 $25.00 $28.75
5mm stainless steel bead for Qiagen Tissuelyser, per bead $1.00 $1.00 $1.00
Patient-Specific Analyte Procurement

$120.05

$120.05 $138.06
Patient-Specific Analyte Procurement - hourly charge

$48.00

$48.00 $55.20