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IPCT Genomic Laboratory

The IPCT Genomic Laboratory (IPCT Lab) is a service-oriented lab that provides access to state-of-the-art Next-Generation Sequencing (NGS) services to researchers and clinicians at MD Anderson Cancer Center. We also collaborate with investigators from external institutions throughout the United States, and globally.

Our professional team is committed to helping principal investigators to solve highly diverse cancer research questions by providing a diverse portfolio of cutting-edge NGS technologies, specialized expertise, analytical advice and support. IPCT Lab is constantly striving to advance research productivity by reliably generating the highest quality data with rapid turnaround time, and competitive pricing by working with our clients on an individual basis to personalize data tailored to their specific research needs.

Aligning with MD Anderson’s mission to integrate research and patient care in eliminating cancer, IPCT-NGS methodologies follow the up-to-date quality standards, with the potential to translate pre-clinical applications in diagnostic laboratories upon CLIA-certified validation of the sequencing results.

IPCT Lab provides major NGS techniques such as targeted genes, whole exome, whole genome, RNAseq and various other custom-NGS platforms. Please contact Mohammad M. Mohammad, M.S., MSHA for more details on custom experimental design.

These techniques have been developed and optimized by our lab scientists to deliver the highest possible quality sequencing data from a wide variety of sample types such as peripheral blood, bone marrow, fresh frozen tissue and FFPE-derived tumor samples.

Planning Your Project

There are multiple factors to consider when planning an NGS sequencing project:

Determine your sample type.
Determine your sample size.
Specify the analyte type (DNA vs RNA vs cfDNA).
Select the sequencing methodology (WGS vs WEX vs targeted sequencing vs RNAseq) that will best answer your research questions.
Select the platform (WEX, WGS) coverage.
Batch samples efficiently based on the TAT information.
Are you going to use germline as normal controls? It is highly recommended to run normal germline samples in parallel with the corresponding tumor samples of the study. This is to ensure the data shows exclusively somatic aberrations.
- Note: IPCT can process tumor samples without normal controls for our targeted sequencing methodologies but we strongly advise you to provide a matched normal for whole exome experiments.

The IPCT Lab produces data primarily using the Illumina pipeline (targeted sequencing, whole exome, whole genome, and RNASeq). We recommend that investigators contact us directly for experimental design for non-standard Illumina sequencing projects.

Workflow

The following steps describe our research project workflow from sample receiving to data delivery:

Select one of the IPCT services listed in the table (IPCT can advise).
Fill and submit a sample submission form (linked below).
Collect and deliver samples to IPCT Lab coordinator.
After assessing the sample quality and quantity, IPCT will send the QC report to the investigator.
Based on the samples’ quality report, the investigator will choose the samples that will be progressed to NGS sequencing (IPCT can advise).
Approved samples will be sequenced. Once completed, bioinformatics’ analysis must be performed to obtain a report containing variant information. The IPCT Lab typically sends data to be analyzed by Dr. John (Jianhua) Zhang’s team. If the investigator has arranged alternative analysis, please let us know, and we can grant access to the data to the appropriate person(s).
Sequencing results will be posted into a folder accessible by the investigator.
A notification will be sent from IPCT to the investigator about the posted results.

Sample Submission Forms:

Please click on the links below to download and fill out the appropriate form:

Services & Fees

Download IPCT FY22 prices

Nucleic Acid (DNA/RNA) Extractions

Nucleic Acid (DNA/RNA) Extractions

IPCT Lab provides DNA and RNA Extraction services for up to 50 specimens per project. Projects with more than 50 specimens can be extracted in the Biospecimen Extraction Resource Facility (BER).

Nucleic Acid (DNA/RNA) quality

All received specimens that IPCT Lab extracts or already extracted will undergo standard quality control, which includes TapeStation/Bioanalyzer quality assessment and Picogreen quantification for DNA and RNA.

All samples that are re-submitted to the IPCT Lab (whether post-initial QC, or in cases where initial samples submitted have too little quantities to move forward without submitting more samples need to have the QC repeated to ensure that all subsequent sample processing is done accurately.)

DNA

The quality of DNA will directly influence several steps of the NGS sequencing workflow, from library preparation through mutation calls. The figure attached shows the difference between good-quality and poor-quality DNA on both TapeStation and Fragment Analyzer reports. The better the DNA we start with, the better the sequencing results will look. Poor-quality samples are processed at investigator’s risk.

Figure 1. Tapestation evaluation of low DNA quality. Low quality genomic DNA samples will show smear pattern on the gel as described in graph(A), column C1. If the band is overly faint and diffuse, there is likely to be a combination of low quantity and low quality of the sample. Tapestation evaluation of high DNA quality. Good quality genomic DNA samples will be high molecular weight, dark, and relatively tight bands. The broader the band, the more indication there is of degradation of useable DNA. If the band is centered on a lower molecular weight this also indicates degradation of DNA

Figure 2. Evaluation of RNA quality by Bioanalyzer. RNA samples with poor-quality (A) are characterized by low molecular weight, an excess number of bands on the gel, and short fragments. This is often reflected in a low RIN number, but RIN number is not perfectly correlated to RNA quality. RNA samples with moderate/acceptable quality (B) typically are not sharp peaks for size (sub-optimal) but have a range of sizes including large RNA fragments and evidence for high molecular weight components of the sample. They will also have the primary darkest band on the TapeStation gel at 1000bp or greater in size. RNA samples with good quality (C) for sequencing have higher molecular weight, fewer distinct bands, clear identification of ribosomal RNA fragments, and tight RNA fragment distributions that may be reflected in higher RIN numbers.

Platform Selection

Frequently Asked Questions

I have low quantity DNA or RNA samples (<150 ng of DNA or RNA available). What platforms are available for me?
If your samples are relatively high quality, you may want to run the low input STP Illumina platform, or speak to Mohammad M. Mohammad, M.S., MSHA about possible amplicon-based Illumina sequencing.

I want to make certain that I get data for a specific set of genes. Which platform is most appropriate?
Please find our gene lists here: Solid tumor Panel-STP (T200), and Liquid Tumor Panel-LTP (L300)

I’m running an experiment on cfDNA. Are there any standard assays or platforms that are appropriate?
The IPCT Lab can offer WEX, WGS, and Solid Tumor Panel for cfDNA testing.

Can I develop a custom experimental design?
We can develop custom experimental designs for the NGS platform. Please contact Mohammad M. Mohammad, M.S., MSHA for more details.

How do I find out about normal samples that the IPCT Lab may have banked (from Clearinghouse) that I may use in my project (limited availability)?
Please contact IPCT Lab via email: ipctlab@mdanderson.org and provide a list of the MRNs for which you seek normal DNA. If there is a sample available, we will inform you and provide information about a nominal fee for use of the banked DNA sample.

Payment

Inside MD Anderson: PeopleSoft Account/Chart field

Outside MD Anderson: Non-MD Anderson investigator-led projects may incur an additional 60% overhead charge. Any investigators who are participating in the CCSG TMC MOU are exempt from this 60% overhead charge. Our preferred method of payment is by credit card. You can complete the Credit Card Authorization Form and email it to ipctlab@mdanderson.org. We can also accept a PO (Purchase Order) or Wire Transfer if paying by credit card is not possible.

Obtain MD Anderson institutional information to help you create your PO

Turnaround Time

Projected timelines for completion of NextGen sequencing are affected by multiple factors. There are queues for each part of the sequencing pipeline from nucleic acid extraction and QC, library prep and capture to bioinformatics’ analysis. These queues are determined by the volume of samples that were submitted but have not yet been processed for any step of the pipeline.

Sequencing turnaround time starts after receiving the PI’s approval of the DNA/RNA QC results. We recommend that all investigators plan for foreseeable deadlines, and complicating factors that may include upcoming conferences, publication deadlines, grant submission deadlines and grant funding deadlines.

Platform turnaround time from platform approval to data receipt

DNA/RNA Extraction: Depends on the pipeline business but usually 10 business days
DNA/RNA QC: Depends on the pipeline business but usually 10 business days
Routine NGS-platforms: 12-16 weeks

The IPCT Lab accepts a wide range of sample types, primarily human samples, along with Xenograft samples from commonly used MD Anderson Xenograft mouse species. Accepted sample types, quantities and submission/delivery:

Accepted sample types/recommended volumes

FFPE (slides or Curls): 5-10 unstained slides (5 micron thickness)
Frozen Tissue: 10 mg
Peripheral Blood (PB): 3-5 mL
Bone Marrow (BM): 1-2 mL
Cell lines: >10,000 cells
Extracted DNA: 200 ng/ at least 3µL (check Table 4 for more details)
Extracted RNA: 200 ng/ at least 3µL (check Table 4 for more details)
Extracted cfDNA: 200 ng/ at least 3µL (check Table 4 for more details)

Note: Extracted nucleic acid (NA) must be eluted into low TE buffer (1x Low TE:  10 mM Tris-HCl (pH8.0) + 0.1 mM EDTA), not exceeding 52 µL total volume.

Sample Delivery

Samples can be delivered in person by your team or via courier to Zayed building, Z4.2024. If someone from the investigator’s group is delivering the samples in person, they will need to contact ipctlab@mdanderson.org in advance and schedule an appointment for sample delivery review (typically 15-30 minutes). This allows the lab coordinator to quickly correct any discrepancies between the submitted sample submission form and the samples being delivered.

If the investigator chooses to have the courier deliver samples, and if there are discrepancies between the sample submission form and the delivered samples, the IPCT Lab reserves the right to return the samples to the investigator for correction. Please ensure that the samples are protected from temperature variation regardless of the method of delivery. We strongly recommend submitting/delivering samples on either ice (for non-frozen DNA and FNA or FFPE slides) or dry ice (for RNA, and all currently frozen samples including DNA and tissue).

Quality Control

The IPCT Lab will provide investigators with a QC report that summarizes the quantity and quality of samples, as well as providing the actual measurements. Additionally, this report will give an overall sample QC evaluation that assesses both quantity and quality. Please see the tables below for assessments of quantity, quality, and overall QC assessment.

If you don’t have access to the IPCT Data Portal, email to Mohammad M. Mohammad, M.S., MSHA (MMMohammad@mdanderson.org) the following information to request a user account to the IPCT Data Portal:

Primary Investigator’s first and last name
Primary Investigator’s MD Anderson username

Resources

Precision Oncology Decision Support (PODS)

The PODS team provides clinical decision support to oncologists, facilitating matching the right drug to the right patient at the right time based on the patient’s tumor molecular profile.

Services and resources offered:

Patient-specific reports:

Interpretation of alterations’ functional impact and therapeutic actionability
Biomarker- and tumor type-matched therapies and clinical trials

OCTANE (Oncology Clinical Trial ANnotation Engine)  clinical trial search engine:

Search tool for finding clinical trials with emphasis on biomarker-matched options

Emailed clinical trial alerts:

Emailed alert to principal investigator and study teams of patients matching trial’s biomarker criteria
- Request service by emailing emailPCT@mdanderson.org
Proactive email alerts provided to physicians of available trial options for patients with tumors harboring specific actionable biomarkers

PersonalizedCancerTherapy.org

Publicly available website
For 32 actionable genes, provides:
- Description of alterations of known significance
- FDA-approved and investigational therapies
- Gene-matched clinical trials throughout the United States

Contact

Please send inquiries regarding IPCT Lab to ipctlab@mdanderson.org

Personnel Contact

Ping Song
Laboratory Coordinator
Phone: 713-563-6667
Address: 6565 MD Anderson Blvd.
Z4.3002
Houston, TX 77030
Email: PSong@mdanderson.org

Qingxiu Zhang
Sr. Research Scientist
Phone: 713-792-5764
Address:6565 MD Anderson Blvd.
Z4.3002
Houston, TX 77030
Email: qinzhang@mdanderson.org

Mohammad M. Mohammad, M.S., MSHA
Laboratory Manager
Phone: 713-745-8988
Address: 6565 MD Anderson Blvd.
Houston, TX 77030
Z4.3010
Email: MMMohammad@mdanderson.org