Single cell sequencing in PGD and cancer treatment

Written by: Stephen Hsu

Primary Source: Information Processing

Note, the BGI Cognitive Genomics group with which I am associated is not involved in the work described below. Aneuploidy means an abnormal number of chromosomes within a cell, indicative of chromosomal abnormality. The most common type is Down Syndrome.

Single-cell Sequencing Makes Strides in the Clinic with Cancer and PGD First Applications (Genomeweb, October 02, 2013)

Single-cell sequencing is quickly entering the clinic with initial applications in cancer and pre-implantation genetic diagnosis and screening, researchers reported this week at the Beyond the Genome conference in San Francisco, Calif., which was sponsored by Genome Biology and Genome Medicine.

Within the field of pre-implantation genetic diagnosis and screening, BGI is already using single-cell sequencing to screen for aneuploidies prior to in vitro fertilization, and a team from Peking University is testing both single-cell transcriptome sequencing and single-cell whole genome sequencing for applications in IVF.

Meantime, a team from Harvard University has demonstrated through single-cell sequencing that circulating tumor cells from lung cancer patients show unique copy number variation profiles, while another group from Cold Spring Harbor Laboratory has tested single-cell sequencing methods in prostate cancer patients to monitor response to treatment and identify biomarkers and drug targets.

BGI’s Fei Gao said that BGI has been testing a method published earlier this year in PLoS One for detecting copy number variants from single-cell, low-pass, whole-genome sequencing on couples undergoing in vitro fertilization.

In August, the first IVF baby that was sequenced before implantation was born healthy, he said, and since then more than 20 healthy babies have been born healthy following pre-IVF single-cell sequencing to screen for aneuploidies and large copy number variants. [ Italics mine. ]

Gao said that the BGI team first tested several kits for whole-genome amplification including ones that used multiple displacement amplification, degenerate oligonucleotide primed PCR, and a technique known as MALBAC developed by Sunney Xie’s group at Harvard University. …

… Gao said the team analyzed the samples for chromosomal aneuploidies and large copy number variants, and showed that the results were concordant with microarrays.

Next, they conducted a study of 41 couples that were undergoing IVF either because they were carriers of chromosomal abnormalities or had already had repeated miscarriages.

From those 41 couples, the team biopsied and sequenced 150 blastocysts. While 71 were identified as euploid, 25 had chromosomal aberrations, 40 had imbalanced structural aberrations, and 14 had both chromosomal and structural aberrations.

The sequencing test enabled the physician to choose only euploid blastocysts for implantation, Gao said.

… Separately, a team from Peking University is testing single-cell whole-genome sequencing using Xie’s MALBAC technique, published in Science last year (IS 1/2/2013).

Fuchou Tang, an assistant professor at Peking University’s Biodynamic Optical Imaging Center, said this week that his group is testing the technique on the 1st and 2nd polar bodies — by-products of the IVF process from which chromosomal numbers in the female pronucleus can be deduced.

The advantage of sequencing the polar bodies, as opposed to cells from the blastomere, is that there is no risk in harming a potentially viable embryo.

Tang’s group has been collaborating with Xie’s group, who presented at this year’s Advances in Genome Biology and Technology meeting in Marco Island, Fla.

At the meeting, Xie said that in a pilot of six female donors, the technique could correctly infer embryo aneuploidy by sequencing to 0.1-fold depth (CSN 2/27/2013).

Since then, Tang’s group has demonstrated that sequencing depth can be as low as 0.03-fold to accurately call aneuploidies, and he is now testing the technique to call point mutations that cause Mendelian disease.

… Aside from IVF applications, researchers are looking to single-cell sequencing to aid in cancer prognostics, diagnostics, and disease monitoring. Harvard’s Xie has been using MALBAC to look at circulating tumor cells in lung cancer patients.

Circulating tumor cells are believed to be indicative of metastasis, which “accounts for 90 percent of cancer mortality,” Xie said. “We need single-cell techniques to tackle this problem,” particularly because cancer is so heterogeneous, and even more so after it metastasizes.

In a proof-of-concept study, Xie used MALBAC to do single-cell exome sequencing and in some cases whole-genome sequencing as well, of eight circulating tumor cells from one patient. He also sequenced the patients’ primary and metastatic tumor and compared the mutational profiles from each. …

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Stephen Hsu
Stephen Hsu is vice president for Research and Graduate Studies at Michigan State University. He also serves as scientific adviser to BGI (formerly Beijing Genomics Institute) and as a member of its Cognitive Genomics Lab. Hsu’s primary work has been in applications of quantum field theory, particularly to problems in quantum chromodynamics, dark energy, black holes, entropy bounds, and particle physics beyond the standard model. He has also made contributions to genomics and bioinformatics, the theory of modern finance, and in encryption and information security. Founder of two Silicon Valley companies—SafeWeb, a pioneer in SSL VPN (Secure Sockets Layer Virtual Private Networks) appliances, which was acquired by Symantec in 2003, and Robot Genius Inc., which developed anti-malware technologies—Hsu has given invited research seminars and colloquia at leading research universities and laboratories around the world.
Stephen Hsu

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