StemCell Therapy

By Monica Heger

Researchers at BGI have published two papers in Cell outlining a single-cell exome sequencing technique that they demonstrated on cell lines, a previously sequenced genome, and cancer patient samples.

The papers show that single-cell analysis can provide a much finer-grained genetic characterization of heterogeneous tissues than bulk tissue sequencing and also point toward the use of the method in areas beyond cancer, such as stem cell research and preimplantation genetic diagnosis, according to the BGI researchers.

Moving forward, the team plans to improve the technique and use it to analyze single cells from different cancer types to study "metastasis, recurrence, and [tumors] before and after therapy," Luting Song, project manager at BGI and a co-author on the papers, told In Sequence in an e-mail.

Single-cell sequencing is thought to be especially useful in cancer samples because tumors are heterogeneous and bulk sequencing may miss rare clonal types. Additionally, sequencing individual cells could help study tumor evolution or be used to monitor relapse by sequencing circulating tumor cells in patients' blood.

However, sequencing single cells is tricky because it is difficult to capture the entire genome of a single cell and amplification strategies introduce bias. Nevertheless, a number of researchers and companies have been working on strategies to sequence single cells, including a team from Cold Spring Harbor Laboratory, which developed a strategy that uses degenerate oligonucleotide-primed PCR to amplify the genome (IS 5/18/2010), and Rubicon Genomics, which uses a technique called thermal cycle library formation that enables the creation of multiple copies of a library from one template strand (IS 3/22/2011).

The BGI team described its method in two papers published in Cell last week. In one, the researchers first validated the approach in two lymphoblastoid cell lines, and then performed single-cell exome sequencing on 90 cells from a patient with a myeloproliferative tumor.

In the second paper, the team demonstrated the single-cell exome sequencing method on 25 cells from a patient with clear cell renal cell carcinoma.

The BGI method relies on multiple displacement amplification, which uses the enzyme phi29 to amplify the DNA in a linear fashion. According to Song, compared to the degenerate oligonucleotide-primed PCR method, MDA generates larger amplicons on average 10 kilobases compared to 1 kilobase with DOP which "results in significantly higher genome recovery" and "allows greater resolution."

The greater resolution of MDA enables single-nucleotide variants to be called, while DOP can only reliably call copy number variations, Song added. The CSHL team that initially published the DOP method is now using it to analyze copy number variation from prostate cancer patients.

The rest is here:
BGI Demos Single-Cell Exome Sequencing Method on Tumor Cell Lines, Patient Samples

This entry was posted on March 7, 2012 at 2:00 pm and is filed under Stem Cell Negative. You can follow any responses to this entry through the RSS 2.0 feed. Both comments and pings are currently closed. |