Cancer Genomics Laboratory
The Cancer Genomics Laboratory is dedicated to pushing the boundaries of genomics research and delivering critical insights to advance cancer diagnostics and therapy. Our professional team works diligently with our researchers on an individual basis to personalize data tailored to their specific research needs.
The Cancer Genomics Laboratory (CGL) is a service-oriented lab that provides comprehensive suite of transformative services designed to illuminate the genetic underpinnings of cancer with unprecedented clarity. We offer services to researchers and clinicians at MD Anderson Cancer Center and external institutions throughout the United States and globally.
Aligning with MD Anderson¡¯s mission to integrate research and patient care in eliminating cancer, CGL methodologies are in compliance with the up-to-date quality standards, with the potential to translate pre-clinical applications to diagnostic laboratories upon CLIA validation.
CGL proudly provides a range of state-of-the-art services that constitute the cornerstone of our genomics expertise, such as Illumina Next-Generation Sequencing, Single Cell Analysis and Spatial Transcriptomics. These techniques are 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 a 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 appropriate platform (WEX, WGS) coverage and increase your coverage to increase the platform sensitivity.
- 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 to ensure the data shows exclusively somatic aberrations.
- Note: The Cancer Genomics Laboratory 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 Cancer Genomics Laboratory 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 the Cancer Genomics Laboratory (CGL) workflow from project planning to data delivery:
- Select one of our services. (Researchers can reach out to our team for platform selections and service recommendations.)
- Fill and submit the sample intake form (SIF) to cgl@mdanderson.org and the CGL lab coordinator.
- After reviewing the SIF, CGL team will arrange with you the samples¡¯ delivery.
- After assessing the sample quality and quantity, CGL team will send the QC report, including CGL sequencing recommendations, to the investigator.
- Based on the samples¡¯ quality report and sequencing recommendations, the investigator will choose the samples that will be progressed to NGS sequencing.
- Approved samples will be sequenced, and once completed, bioinformatics¡¯ analysis must be performed to obtain a report containing variant information.
- Sequencing QC metrics will be shared with the investigator.
- Sequencing results will be posted into a dedicated on the cluster and can be accessible by the investigator.
Accepted Sample Types, Quantities and Submission
Accepted Sample Types and Quantity
The Cancer Genomics Laboratory (CGL) accepts a wide range of samples types, primarily human samples, along with Xenograft samples from commonly used MD Anderson Xenograft mouse species.
Accepted Sample Types/recommended volumes
Sample Type |
Recommended Volume |
|---|---|
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 3 microliters (check "Nucleic Acid Amounts for NGS" table for more details) |
Extracted RNA |
200 ng/ at least 3 microliters (check "Nucleic Acid Amounts for NGS" table for more details) |
Extracted cfDNA |
200 ng/ at least 3 microliters (check "Nucleic Acid Amounts for NGS" table for more details) |
Note:
- Extracted DNA must be eluted into low TE buffer (1x Low TE: 10 mM Tris-HCl (pH8.0) + 0.1 mM EDTA), not exceeding 52 microliters total volume.
- Extracted RNA must be eluted into nuclease free water, not exceeding 30 microliters total volume.
Sample Submission Forms
Please choose the appropriate form to download and fill out:
Sample Submission/Delivery
Samples can be delivered in person by your team or via courier to the Zayed building, Z4.2024. If someone from the investigator¡¯s group is delivering the samples in person, they will need to contact cgl@mdanderson.org in advance and schedule an appointment for sample delivery review (typically 15 to 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, CGL reserves the right to return the samples to the investigator for correction. Please ensure that the samples are adequately 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).
Nucleic Acid (DNA/RNA) Extractions and Quality
Extractions
The Cancer Genomics Laboratory (CGL) provides DNA and RNA extraction services for up to 50 specimens per project. For projects with more than 50 specimens, they can be extracted in the Biospecimen Extraction Resource Facility (BER).
Quality
All received specimens that the Cancer Genomics Laboratory (CGL) extracts or already extracted will undergo standard QC, which includes TapeStation/Bioanalyzer quality assessment and PicoGreen quantification for DNA and RNA.
All samples that are re-submitted to CGL (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. This figure 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.
RNA
RNA samples with poor quality (seen in 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 (seen in 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 (seen in 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.
Sample Quality Control (QC) Report for PI Approval
The Cancer Genomics Laboratory (CGL) will provide investigators with a quality control (QC) report that summarizes the quantity and quality of samples, as well as provides 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.
This table shows the DNA input range for each platform. The higher the DNA input, the higher the library complexity will be, which translates in better sequencing data. Please add 25 ng to the quantities below for submission to complete QC, which is required for all samples.
Nucleic Acid Amounts for NGS
| Platforms | A1: Optimal Quantity (ng) |
A2: Sub Optimal Quantity (ng)* |
A3: Not sufficient Quantity (ng) |
Volume (?L) |
|---|---|---|---|---|
CGP, STP and LTP |
¡Ý 200 |
50-199 |
<50 |
55 |
WEX |
¡Ý 200 |
50-199 |
<50 |
55 |
WGS |
¡Ý 500 |
200 -499 |
< 200 |
55 |
RNAseq Capture |
¡Ý 150 |
50 -149 |
< 50 |
55 |
Total RNASeq |
¡Ý 300 |
50 -299 |
< 50 |
55 |
RNAseq-RiboZero |
¡Ý 300 |
50 -299 |
< 50 |
55 |
*Any samples that qualify as: ¡°acceptable, suboptimal¡± and ¡°low input¡± and all FFPE might not reach the aimed coverage. Those samples can be repeated at the investigator¡¯s cost.
Vocabulary for Quality: Nucleic Acid Quality Categories for NGS
| Nucleic Acid | Q1: Optimal Quality |
Q2: Sub Optimal Quality |
Q3: Indeterminate Quality |
|---|---|---|---|
DNA |
80-90% of the DNA is a high molecular weight (MW) |
Major peak at high MW but also a lower MW smear, or Major peak at low MW |
DIN <3 |
RNA |
2 rRNA peaks are sharp and visible |
rRNA peaks visible but many other bands also visible or rRNA peaks not visible, most of the bands in the left side of the gel |
RIN <3 or DV200 <30% |
Vocabulary for Final Recommendation: Final Sequencing Recommendation Logic
A1+Q1 |
Recommended |
A1+Q2 A2+Q1 A3+Q1 |
Recommended at Risk |
A3 and/or Q3 A3+Q2 |
Not Recommended |