Christopher Capozziello for The New York Times

The inventor Jonathan Rothberg with a semiconductor chip used in the Ion Torrent machine.

By NICHOLAS WADE

Published: July 20, 2011

The inventor, Jonathan Rothberg of Ion Torrent Systems in Guilford, Conn., is one of several pursuing the goal of a $1,000 human genome, which he said he could reach by 2013 because his machine is rapidly being improved.

“Gordon Moore worked out all the tricks that gave us modern semiconductors, so he should be the first person to be sequenced on a semiconductor,” Dr. Rothberg said.

At $49,000, the new DNA decoding device is cheaper than its several rivals. Its promise rests on the potential of its novel technology to be improved faster than those of machines based on existing techniques.

Manufacturers are racing to bring DNA sequencing costs down to the point where a human genome can be decoded for $1,000, the sum at which enthusiasts say genome sequencing could become a routine part of medical practice.

But the sequencing of Dr. Moore’s genome also emphasizes how far technology has run ahead of the ability to interpret the information it generates.

Dr. Moore’s genome has a genetic variant that denotes a “56 percent chance of brown eyes,” one that indicates a “typical amount of freckling” and another that confers “moderately higher odds of smelling asparagus in one’s urine,” Dr. Rothberg and his colleagues reported Wednesday in the journal Nature. There are also two genetic variants in Dr. Moore’s genome said to be associated with “increased risk of mental retardation” — a risk evidently never realized. The clinical value of this genomic information would seem to be close to nil.

Dr. Rothberg said he agreed that few genes right now yield useful genetic information and that it will be a 10- to 15-year quest to really understand the human genome. For the moment his machine is specialized for analyzing much smaller amounts of information, like the handful of genes highly active in cancer.

The Ion Torrent machine requires only two hours to sequence DNA, although sample preparation takes longer. The first two genomes of the deadly E. coli bacteria that swept Europe in the spring were decoded on the company’s machines.

The earliest DNA sequencing method depended on radioactivity to mark the four different units that make up genetic material, but as the system was mechanized, engineers switched to fluorescent chemicals. The new device is the first commercial system to decode DNA directly on a semiconductor chip and to work by detecting a voltage change, rather than light.

About 1.2 million miniature wells are etched into the surface of the chip and filled with beads holding the DNA strands to be sequenced. A detector in the floor of the well senses the acidity of the solution in each well, which rises each time a new unit is added to the DNA strands on the bead. The cycle is repeated every few seconds until each unit in the DNA strand has been identified.

Several years ago, Dr. Rothberg invented another DNA sequencing machine, called the 454, which was used to sequence the genome of James Watson, the co-discoverer of the structure of DNA. Dr. Rothberg said he was describing how the machine had “read” Dr. Watson’s DNA to his young son Noah, who asked why he did not invent a machine to read minds.

Dr. Rothberg said he began his research with the idea of making a semiconductor chip that could detect an electrical signal moving across a slice of neural tissue. He then realized the device he had developed was more suited to sequencing DNA.

George Church, a genome technologist at the Harvard Medical School, said he estimated the cost to sequence Dr. Moore’s genome at $2 million. This is an improvement on the $5.7 million it cost in 2008 to sequence Dr. Watson’s genome on the 454 machine, but not nearly as good as the $3,700 spent by Complete Genomics to sequence Dr. Church’s genome and others in 2009.

Dr. Rothberg said he had already reduced the price of his chips to $99 from $250, and today could sequence Dr. Moore’s genome for around $200,000. Because of Moore’s Law — that the number of transistors placeable on a chip doubles about every two years — further reductions in the cost of the DNA sequencing chip are inevitable, Dr. Rothberg said.

Stephan Schuster, a genome biologist at Penn State, said his two Ion Torrent machines were “outstanding,” and enabled a project that would usually have taken two months to be completed in five days.

There is now “a race to the death as to who can sequence faster and cheaper, always with the goal of human resequencing in mind,” Dr. Schuster said.