Two New Techniques Make Genome Sequencing Faster and Cheaper

Two new genome-sequencing techniques allow the genetic material of an organism to be read on a smaller scale than previously, allowing it to be done more quickly and cheaply.

    Both Harvard Medical School and Connecticut-based 454 Life Sciences Corp. developed sequencing techniques that move toward the National Human Genome Research Institute’s goal of human genome sequencing for $100,000 in the short term. NHGRI hopes the process will eventually be accomplished for $1,000. A human genome currently costs $10 million, according to the organization.

    “The NIH-NHGRI genome sequencing technology project is barely a year old and these two methods suddenly show that ‘incremental’ improvements are not the only game in town,” Harvard Medical School spokeswoman Judith Montminy said via email.

    Glenn Schulman, spokesman for 454 Life Sciences, explained that the ability to routinely sequence the human genome would allow researchers to understand how hundreds of genes function. This would increase scientists’ understanding of complex diseases.

    In a statement encouraging the $1,000 genome goal, Francis Collins, NHGRI director, said, “not only will these technologies substantially reduce the cost of sequencing a genome, but they will provide a quantum leap in the scope and scale of research aimed at uncovering the genomic contributions to common diseases, such as cancer, heart disease and diabetes.”

    Inexpensive sequencing would show the “true value of pharmacogenomics,” Shulman predicted. This would allow researchers to understand how people respond differently to different drugs.

    He also indicated that the technique could be used to help understand the HIV virus and predict how it resists certain drugs.

How It’s Done

The 454 technique begins by attaching single-stranded DNA fragments to silica-coated beads, with each bead containing only one fragment, Schulman explained. These are then amplified so that each bead contains multiple, identical fragments.

    The beads are placed on a special fiber-optic slide, according to Schulman. The slide is then inserted into 454’s sequencing machine. A solution containing one type of nucleotide, for example just adenine (A), is washed across the plate allowing it to pair with thymine (T) bases in the single stranded fragments on the bead. When the pairing occurs, it causes light to be released by activating luciferase, an enzyme involved in giving fireflies their characteristic glow.

    The 454 machine is able to tell the position and number of the base pairings by reading the light reactions, Schulman said. The slide is then washed with a second type of nucleotide and the process is repeated until the entire molecule is known.

    According to Schulman, this process can be used to re-sequence already mapped genomes or to assemble the sequence of an unknown genome, a process called de novo sequencing.

    The Harvard process is similar, according to Montminy. It also uses DNA fragments attached to beads. But the fragment is read by attaching nucleotides that are each marked by a different colored dye. The molecules are placed in a gel and a special microscope, common to many labs, is used to read the pattern of colors and know the sequence of nucleotides. This is compared to a known genome sequence.

    This is one of the main differences between the two techniques. According to Montminy, the Harvard technique can only be used to detect differences between the DNA of an individual and an already mapped genome. It can detect mutations but cannot sequence an unknown genome.

    Montminy said, however, that the Harvard technique is more accurate, 99.7 percent versus 96 percent. It is also less expensive, she said. The machine used to read the sequence in the 454 technique costs about $500,000. The microscope used by Harvard costs $140,000.

    But she did point out that 454’s technique is faster. Schulman added that the 454 method is also able to read a longer fragment of DNA.