The Center for Cancer Genome Discovery (CCGD) provides DNA, RNA, and amplicon sequencing, as well as bioinformatics support and assistance in experimental design, new technology development, and help with challenging samples.
DNA can be sequenced on different scales. The most comprehensive data is reached by whole genome sequencing (WGS) and is able to discover most genomic aberrations. One can limit the sequencing space and reduce the complexity of analysis by limiting the sequence space to only the expressed portion of the genome and performing a whole exome sequencing (WES).
For most research questions and for most clinical applications, sequencing a subset of relevant genes by targeted sequencing is often sufficient. Targeted sequencing has the advantage of sequencing larger sample sizes with lower cost and easier data analysis.
Customize your baits
Design, mix, and match any genomic region in a custom baitset — targeted panels, exome+, translocations, promoters, enhancers. CCGD will take care of it.
Targeted sequencing and WES are accomplished by designing baits (or probes) complementary to the genes of interest, and subtracting those sequences from the DNA pool by hybridization and capture using the Agilent SureSelect platform. The current WES bait set used at CCGD is the Whole Exome_v5 Agilent SureSelect hybrid capture kit covering ~55Mb. Our hybrid selection libraries typically meet or exceed 80% of targets at 30x.
Our targeted panels are Oncopanel_version3 (OPv3), the Profile cancer panel (POPv2), or any custom gene panel specifically tailored for your research.
- Add or remove any genomic region to the whole exome
- Increase the power of the exome by adding intronic regions to detect rearrangements
- Add enhancers or promoters
- OPv3 is a new and improved targeted design that is capable of simultaneous detection of mutations, translocations, and copy-number variations in archival clinical tumor specimens.
- The bait set contains sequences complementary to exons of 559 genes and to 37 intronic regions frequently involved in rearrangements.
- In addition, baits were included that are complementary to common SNPs and for cancer risk factors determined by GWAS studies (www.genome.gov/gwastudies).
- POPv2 is the clinic gene panel as part of the Profile effort.
- This panel contains 309 genes and regions frequently involved in rearrangements in 35 genes.
Custom Bait Design
- Custom gene panels are often more affordable and can be tailored for your research.
- CCGD will take care of design and ordering.
DNA sequencing can provide information on:
- Somatic mutations and germline variants, including single nucleotide variants and small insertions and deletions
- Copy number variants, gene deletions/amplifications, and loss of heterozygosity
- Genomic rearrangements, including translocations, inversions, large deletions/insertions, and other complex rearrangements
- Sample identification and T/N matching via DNA fingerprinting
RNA sequencing – transcriptomics
RNA sequencing (RNAseq) is a transcriptome profiling approach that uses deep-sequencing technology. In conjunction with mutation detection it can functionally validate mutations identified by DNA sequencing by quantifying expression of the mutant allele or downstream genes in the pathway. Compared to expression microarrays, RNAseq is not limited to the microarray content, and therefore allows discovery of novel mutations and isoforms with greater accuracy. Similar to DNAseq, one can sequence the whole transcriptome or focus on specific genes using targeted RNAseq, and we can start from as little as 20ng total RNA extracted from fresh frozen or FFPE samples.
RNAseq can provide information on:
- Gene expression, including miRNA and non-coding RNA
- Allele-specific expression (preferential expression of mutant or WT transcript)
- Expression of splice variants
- Gene fusions
Amplicon-seq is a targeted approach enabling detection of genetic variants – including somatic mutations, SNPs, and small insertions and deletions – in a selected set of amplicons in a rapid and efficient manner. It allows sequencing of a large number of samples for specific genes or exons of particular interest rather than whole genomes. Amplicon-seq is ideal for very small gene panels (~10 genes) and for fast turnaround time.
Before starting a project, we will discuss the best sequencing strategies, experimental design, and analysis options with you. It is important that we understand the goals and scope of the project and that you appreciate the power and limitations of the technology and the expected outcome. CCGD will also organize follow-up meetings to transfer the data and discuss the results and conclusions. At that time, future experiments can be discussed, if needed.
CCGD's mission is to develop new and emerging technologies for exploring the cancer genome. CCGD will therefore partner with you to further develop your ideas or needs.
Assistance with challenging samples
CCGD has expertise in handling and extracting DNA from challenging formalin-fixed paraffin embedded tissue (FFPE) tissue. We have developed and optimized extraction protocols using Qiagen, QIAcube or the Covaris LE220 Focused-Ultrasonicator. For specimens needing pathology review, we collaborate closely with pathologists at Brigham and Women's Hospital.
CCGD has optimized protocols on both the Illumina HiSeq and MiSeq to process and sequence from as little as 50-200 ng of DNA from fresh frozen, blood, or FFPE tissue. CCGD's major strength is on smaller, focused projects consisting of challenging or unique samples.
Contact us to start collaborating