An integrated semiconductor device enabling non-optical genome sequencing

Abstract

The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip. The ion chip contains ion-sensitive, field-effect transistor-based sensors in perfect register with 1.2 million wells, which provide confinement and allow parallel, simultaneous detection of independent sequencing reactions. Use of the most widely used technology for constructing integrated circuits, the complementary metal-oxide semiconductor (CMOS) process, allows for low-cost, large-scale production and scaling of the device to higher densities and larger array sizes. We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome.DNA sequencing and, more recently, massively parallel DNA sequencing 1-4 has had a profound impact on research and medicine. The reductions in cost and time for generating DNA sequence have resulted in a range of new sequencing applications in cancer 5,6 , human genetics 7 , infectious diseases 8 and the study of personal genomes 9-11 , as well as in fields as diverse as ecology 12,13 and the study of ancient DNA 14,15 . Although de novo sequencing costs have dropped substantially, there is a desire to continue to drop the cost of sequencing at an exponential rate consistent with the semiconductor industry's Moore's Law 16 as well as to provide lower cost, faster and more portable devices. This has been operationalized by the desire to reach the $1,000 genome 17 .To date, DNA sequencing has been limited by its requirement for imaging technology, electromagnetic intermediates (either X-rays 18 , or light 19 ) and specialized nucleotides or other reagents 20 . To overcome these limitations and further democratize the practice of sequencing, a paradigm shift based on non-optical sequencing on newly developed integrated circuits was pursued. Owing to its scalability and its low power requirement, CMOS processes are dominant in modern integrated circuit manufacturing 21 . The ubiquitous nature of computers, digital cameras and mobile phones has been made possible by the low-cost production of integrated circuits in CMOS.Leveraging advances in the imaging field-which has produced large, fast arrays for photonic imaging 22 -we sought a suitable electronic sensor for the construction of an integrated circuit to detect the hydrogen ions that would be released by DNA polymerase 23 during sequencing by synthesis, as opposed to a sensor designed for the detection of photons. Although a variety ...

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