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Cancer Genomics Laboratory

The Cancer Genomics Laboratory (CGL) at the Institute for Personalized Cancer Therapy (IPCT) 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.

CGL 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.

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 below.
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 to data delivery:

Select one of the services listed below. (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. CGL typically sends data to be analyzed by 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 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.

Services

NEXT GENERATION SEQUENCING (NGS)
Whole Genome Sequencing
Whole Exome Sequencing
Cell Free DNA Sequencing
RNASeq, Capture method
Total RNASeq
TCRRNASeq
miRNAseq
Targeted Sequencing (Cancer Genomics Panel, Solid Tumor Panel & Liquid Tumor Panel)

SINGLE CELL ANALYIS
3' Single Cell RNASeq, Gene Expression
Single Cell RNASeq, Fixed Cells
5' Single Cell Immune Profiling
Single Cell Human BCR
Single Cell Human TCR
Single Cell Multiome
Single Cell ATAC V2

SPATIAL TRANSCRIPTOMICS
Visium CytAssist mini (6.5 mm)
Visium CytAssist max (11mm)

Prices

These tables include Cancer Genomics Laboratory (CGL) platforms and corresponding FY25 prices, effective September 1, 2024.

Targeted NGS

Service	Average Coverage	Cost/sample
Agilent_CGP_DNA_V1	1000x	$735
Agilent_CGP_RNA_V1	10,000 reads	$670
Takara TCRSeq a/b		$635

Whole Exome Sequencing (WES)

Service	Average Coverage	Cost/sample	Brief description
Agilent WES	200x	$885	This new Exon V8 provides comprehensive and most up-to-date coverage of protein coding regions from the most updated databases. It also covers the TERT promoter and hard-to-capture exons that are omitted by other exomes on the market.
Agilent WES	100x	$745

RNASeq

Service	Sample type	Average Coverage	Cost/sample	Brief description
RNASeq_Cap	Tumor RNA	70M reads	$850	Recommended for all new projects. Capture-based Agilent RNASeq v8.
Illumina Total_RNASeq	Tumor RNA	50M Reads	$800	Whole-transcriptome analysis with total RNA sequencing (RNA-Seq) detects coding plus multiple forms of noncoding RNA. Total RNA-Seq can accurately measure gene and transcript abundance, and identify known and novel features of the transcriptome.
Takara RNASeq_Ultra_Low	Tumor RNA	30M reads	$745	Whole-transcriptome analysis for ultra-low amounts of total RNA or directly from multiple intact cells (<1,000 cells). This platform can accommodate an input of 10 pg of total RNA.
Takara miRNA	Tumor miRNA	2.2M Reads	$785	For small RNASeq including micro RNA

Whole Genome Sequencing (WGS)

Service	Average Coverage	Cost/sample	Brief description
WGS	Up to 10x	$750	Agilent WGS
	Up to 30x	$1,365
	Up to 60x	$2,180

Single Cell Analysis

Service	Sample type	Average Coverage	Cost/sample	Brief description
3' Single Cell RNASeq, Gene Expression	Whole cells or Nuclei	5,000 cells, 25,000 reads/cell	$3675	The 3' Single Cell Assay from 10x Genomics is a powerful tool for transcriptomic analysis of individual cells. This assay provides a comprehensive view of gene expression in tens of thousands of individual cells, allowing researchers to identify rare cell types, discover new cell types, and analyze gene expression dynamics during development, disease progression, and drug response.
Single Cell RNASeq, Fixed Cells	Fixed Cells or Nuclei	5,000 cells, 25,000 reads/cell	$3755	The Fixed RNA Single Cell Assay from 10x Genomics enables an analysis of probe-targeted whole transcriptome at single cell/nuclei level from formalin-fixed, paraffin-embedded (FFPE) tissues. This assay allows researchers to analyze gene expression in archived tissue samples, which may have been previously inaccessible due to degradation of RNA.
5' Single Cell Immune Profiling	Sorted cells	5,000 cells, 25,000 reads/cell	$3700	The 5' V2 Immune Profiling Single Cell Assay from 10x Genomics is a specialized assay designed for the analysis of full-length V(D)J sequences at a single-cell level. This assay allows for the identification of immune cell types and the analysis of their gene expression patterns, including identifying T and/or B cell receptors and characterizing the immune response to disease.
Single Cell Human BCR				Add-ons; please contact CGL
Single Cell Human TCR				Add-ons; please contact CGL
Single Cell Multiome Gene Expression + ATAC	Nuclei Only	5,000 cells, 25,000 reads/cell	$5,775	Multiomic Gene Expression + ATAC Single Cell Assay enables simultaneous profiling of both 3' gene expression and chromatin accessibility at a single-cell level. The gene expression component of the assay uses barcoding technology to capture RNA transcripts from individual cells, while the ATAC (Assay for Transposase-Accessible Chromatin) component measures the accessibility of chromatin in the same cells.
Single Cell ATAC V2	Nuclei Only	5,000 cells, 25,000 reads/cell	$3,450	This platform can be used to analyze the epigenetic state of individual cells by measuring the accessibility of chromatin regions in the genome. The assay is based on the use of a transposase enzyme that cleaves open regions of chromatin, allowing the insertion of sequencing adapters. The sequencing adapters serve as primers for PCR amplification of the genomic DNA, which is then sequenced to identify the accessible chromatin regions.

Spatial Transcriptomics

Service	Sample type	Average Coverage	Cost/sample	Brief description
Visium CytAssist Mini (6.5 mm)	Tissue Slides or Tissue MicroArray	5,000 cells, 25,000 reads/cell	$2,650	This solution allows researchers to map gene expression in tissue samples, enabling them to study the spatial organization of cells within tissues and to identify cell types and subtypes. The solution includes a microfluidic chip, reagents and software for data analysis.
Visium CytAssist Max (11 mm)	Tissue Slides or Tissue MicroArray	5,000 cells, 25,000 reads/cell	$5,300
Visium HD			$4,835

Upon request or for project continuation

Service	Sample type	Average Coverage	Cost/sample	Brief description
Solid Tumor Panel (STP)	Tumor	up to 500x	$555	322 genes sequenced (all exons) and global copy number
Solid Tumor Panel (STP)	Normal	up to 100x	$470	322 genes sequenced (all exons) and global copy number
Liquid Tumor Panel (LTP)	Tumor	up to 500x	$555	303 genes sequenced (all exons) and global copy number
Liquid Tumor Panel (LTP)	Normal	up to 100x	$470	303 genes sequenced (all exons) and global copy number

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 quality control (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 particular 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 adequately 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 to 16 weeks

Accepted Sample Types, Quantities and Submission/Delivery

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 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

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).

Nucleic Acid (DNA/RNA) 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

Figure 1. (A) Tapestation evaluation of low DNA quality. Low quality genomic DNA samples will show smear pattern on the gel as shown in 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. (B) 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.

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

Figure 2. Evaluation of RNA quality by Bioanalyzer

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 (µL)
CGP, STP and LTP	≥ 200	50-199	<50	55
WEX	≥ 200	50-199	<50	55
WGS	≥ 500	200 -499	< 200	55
RNAseq Capture	≥ 150	50 -149	< 50	55
Total RNASeq	≥ 300	50 -299	< 50	55
RNAseq-RiboZero	≥ 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%

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,

Major peak at low MW

DIN <3

RNA

2 rRNA peaks are sharp and visible

rRNA peaks visible but many other bands also visible

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

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 Texas Medical Center 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 CGL@mdanderson.org. We can also accept a purchase order (PO) or wire transfer if paying by credit card is not possible.

Obtain MD Anderson institutional information to help you create your PO

Contact Information

Laboratory Personnel

Marcus Coyle
Laboratory Coordinator
Phone: 713-792-8198
Office: Z4.3002
Email: MDCoyle@mdanderson.org

Ping Song
Laboratory Coordinator
Phone: 713-792-6667
Office: Z4.3002
Email: PSong@mdanderson.org

Qingxiu Zhang
Sr. Research Scientist
Phone: 713-750-5764
Office: Z4.3002
Email: qinzhang@mdanderson.org

Mohammad M Mohammad, M.S., MSHA
Associate Director, Lab Operations
Phone: 713-745-8988
Office: Z4.3010
Email: MMMohammad@mdanderson.org

Address:
6565 MD Anderson Blvd.
Houston, TX 77030

Frequently Asked Questions (FAQs)

General

Who do I contact to set up a project with the CGL?
Please contact cgl@mdanderson.org

What kinds of specimens/samples can I submit and deliver to CGL?
You can find information on the types of specimens and samples that are accepted by the CGL above.

How do I extract DNA and/or RNA?
For projects with more than 50 samples and for Moonshots projects, DNA and RNA extractions must be done through the Biospecimen Extraction Resource Facility (BER). Projects with 50 samples or fewer may have DNA and RNA extracted within CGL. Specimen submission for extraction must specify on the CGL submission form whether to extract the specimen(s) for DNA or RNA.

Sample Submission

I don’t have access to CGL Data Portal. How do I get access?
Send an email to MMMohammad@mdanderson.org with the following information to request user account: Primary Investigator’s first and last name, and Primary Investigator’s MD Anderson username.

How do I submit samples to CGL?
Samples may be submitted to the CGL by contacting cgl@mdanderson.org. Please contact in advance of sample submission to ensure availability to receive and review your samples. A copy of the MD Anderson Submission Sheet can be downloaded here. For external projects, please use the Non-MD Anderson Submission Sheet here. Please see above for sample submission forms. For more information, look under Specimen and Sample Submission. You may hand deliver your samples or you can use the courier here at MD Anderson to deliver your samples to CGL.

What total amount, volume, quality, and buffer do I need for submitting DNA and/or RNA?
Please see our tables for minimum (determined by PicoGreen) amount, volume, and quality for processing. We typically request that stock samples of DNA and RNA be submitted, and we will return all remaining excess sample to the investigator. DNA and RNA quantities and concentrations determined by Nanodrop will typically be 2X-5X higher (and inaccurate) compared to the more accurate quantities and concentrations determined by PicoGreen. The CGL accepts both DNA and RNA samples in low TE buffer (1x Low TE: 10 mM Tris-HCl (pH8.0) + 0.1 mM EDTA).

How long is the turn-around time for sample QC?
Sample turnaround time is dependent upon queue length, as samples are run in the order they are received. If there are standard queues when samples are submitted, and there are ≤50 samples submitted, turnaround time per platform is provided here.

What is the shipping address for the CGL for sample submission?
IPCT Cancer Genomics Laboratory (CGL)
c/o Marcus Coyle
Zayed Z4.3010
M.D. Anderson Cancer Center
6565 M.D. Anderson Blvd.
Houston, TX 77030

Can I develop a custom experimental design?
We can develop custom experimental designs for the NGS platform. Please contact mmmohammad@mdanderson.org for more details.