Scientists create device for ultra-accurate genome sequencing of single human cells

November 2, 2017, University of California - San Diego
Scientists create device for ultra-accurate genome sequencing of single human cells
Overview of experimental process using SISSOR technology. Single cell in suspension identified by imaging and captured, then chromosomal DNA molecules are separated into single-stranded form, which are then randomly distributed and partitioned in 24 MDA chambers and pushed into air-filled chamber and reaction solution. MDA reaction occurs after heat is applied to the device at 30 degrees C overnight, prior to collection and processing into bar-coded sequencing library. Credit: University of California - San Diego

An interdisciplinary team of researchers at the University of California San Diego has developed a technology for very accurate sequencing and haplotyping of genomes from single human cells. Their findings were published online in advance of the Proceedings of the National Academy of Sciences (PNAS) print edition.

"Accurate sequencing of single cells will enable the identification of mutations that cause cancer and genetic disease," said senior author Kun Zhang, a professor of bioengineering in the UC San Diego Jacobs School of Engineering. "At the same time, precise haplotyping will allow for the genotyping of haplotypes, combinations of different genes or alleles as a group from either parent."

Zhang's co-authors from the Department of Bioengineering include professor Xiaohua Huang and postdoctoral researcher and alumnus Wai Keung Chu (M.S., Ph.D. '11, '16), who is first author on the PNAS article. Collaborators on the research from the Department of Computer Science and Engineering (CSE) include professor Vineet Bafna, who is a bioinformatics expert in the Center for Microbiome Innovation and the CHO Systems Biology Center, both at UC San Diego, Ph.D. student Peter Edge, and CSE alumnus Vikas Bansal (Ph.D. '08), now a faculty-affiliate in CSE and professor of pediatrics in the UC San Diego School of Medicine. Adding to the project's interdisciplinary roots is Department of Electrical and Computer Engineering (ECE) alumnus Ho Suk Lee (M.S., Ph.D. '11, '15), now at Broadcom, who lent his expertise in microfluidic devices for single-cell analysis as well as years of working in the bioengineering labs of both professors Zhang and Huang.

Clinical applications of genome sequencing demand high accuracy in DNA sequencing. According to CSE's Bafna, until now, many applications were off-limits because current technologies were not accurate enough to be done at the level of the single human cell.

"Many individuals carry alleles that cause genetic disease or predispose them to cancer," said Bafna. "Each gene has two alleles, one from each parent. One of the alleles may contain disease-causing mutations. The carriers may be asymptomatic, but their offspring may show symptoms due to the combination of bad alleles or haplotypes from both parents."

Take the case of couples hoping to get pregnant via in-vitro fertilization (IVF). "For genetic diagnostics prior to IVF implantation, a human life is involved, so the utmost accuracy is required," explained bioengineering professor Xiaohua Huang. "With our technology, we can do highly accurate sequencing and haplotyping of the genome based on a single cell biopsied from early embryos."

In addition to IVF pre-implantation diagnostics and early cancer detection, other potential applications of the UC San Diego-developed technology include high-quality checking of genome-edited human cells for therapeutic purposes. "With the explosion in the use of CRISPR/Cas9 and other targeted genome-editing techniques, new treatments could be tweaked versions of the patient's own cells," said first author and bioengineering Ph.D. student Wai Keung Chu. "The technology makes it possible to use a single cell of the 'edited' gene and return results that would be as accurate as if we sequenced many cells."

The technology in question has two novel aspects: a microfluidic processor that allows for the manipulation of single cells and separate chromosomal strands into different chambers; and computational methods that exploit the strand information for haplotyping and error correction. The UC San Diego scientists have dubbed it "Single-Stranded Sequencing using micrOfluidic Reactors" (SISSOR).

"Essentially it enables the simultaneous sequencing of very long fragments of all four strands of the chromosomal DNA from both parents," explained CSE bioinformatics Ph.D. student Peter Edge, who works in Pediatrics professor Vikas Bansal's Genome Information Science lab. "This allows us to make comparisons and correct for errors."

The SISSOR technique also breaks what has been called the 'curse of polymerases', which introduce errors when making copies of DNA. Unfortunately, noted CSE's Bafna, "we cannot read genome information from single without polymerases, so we had to come up with a solution that gets rid of those errors."

Based on their findings, the PNAS paper's co-authors were able to demonstrate "the most accurate to date."

Senior author Kun Zhang says the interdisciplinary nature of the research collaboration was critical to finding a more precise way to sequence DNA from . "Our approach can simultaneously provide higher accuracy and longer haplotypes than other existing approaches," concluded Zhang. "This innovation required expertise that goes beyond what normally exists in a single department, and this case is a testament to UC San Diego's growing interdisciplinary research culture that allowed us to pull in collaborators from other departments who were critical to a technology whose payoff will hopefully be measured in lives saved – and perhaps more healthy children born via in-vitro fertilization."

Explore further: New technology illuminates microbes that can't be cultivated in a laboratory

More information: Wai Keung Chu et al. Ultraaccurate genome sequencing and haplotyping of single human cells, Proceedings of the National Academy of Sciences (2017). DOI: 10.1073/pnas.1707609114

Related Stories

Single-cell genome sequencing gets better

November 10, 2013

Researchers led by bioengineers at the University of California, San Diego have generated the most complete genome sequences from single E. coli cells and individual neurons from the human brain. The breakthrough comes from ...

Single-cell genome sequencing gets better (w/ Video)

January 16, 2014

(Phys.org) —Bioengineers at the Jacobs School have created a better way to sequence genomes from individual cells. The breakthrough, which relies on microwells just 12 nanoliters in volume (see image), is one of many recent ...

Recommended for you

Meteorite source in asteroid belt not a single debris field

February 17, 2019

A new study published online in Meteoritics and Planetary Science finds that our most common meteorites, those known as L chondrites, come from at least two different debris fields in the asteroid belt. The belt contains ...

Diagnosing 'art acne' in Georgia O'Keeffe's paintings

February 17, 2019

Even Georgia O'Keeffe noticed the pin-sized blisters bubbling on the surface of her paintings. For decades, conservationists and scholars assumed these tiny protrusions were grains of sand, kicked up from the New Mexico desert ...

Archaeologists discover Incan tomb in Peru

February 16, 2019

Peruvian archaeologists discovered an Incan tomb in the north of the country where an elite member of the pre-Columbian empire was buried, one of the investigators announced Friday.

Where is the universe hiding its missing mass?

February 15, 2019

Astronomers have spent decades looking for something that sounds like it would be hard to miss: about a third of the "normal" matter in the Universe. New results from NASA's Chandra X-ray Observatory may have helped them ...

What rising seas mean for local economies

February 15, 2019

Impacts from climate change are not always easy to see. But for many local businesses in coastal communities across the United States, the evidence is right outside their doors—or in their parking lots.

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.