Clinical OMICS

MAR-APR 2018

Healthcare magazine for research scientists, labs, pathologists, hospitals, cancer centers, physicians and biopharma companies providing news articles, expert interviews and videos about molecular diagnostics in precision medicine

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www.clinicalomics.com March/April 2018 Clinical OMICs 43 On a cold winter 's day in February 1953, Francis Crick, with Jim Watson trailing behind him, burst into The Eagle pub in Cambridge at lunchtime and exclaimed: "We have discov- ered the secret of life!" Perhaps it's my cynical British nature, but I can easily imagine a local propping up the bar with his pint of bitter, glancing up from his newspaper and responding, "Oh do shut up Francis!" Regardless of how it was received, Crick's jubilation fits with the evidence. This anniversary—more specifically the formal publi- cation of the double helix model of DNA in April 1953 in Nature—is significant because 50 years later, it was used as the convenient reference point for the official declaration of the completion of the Human Genome Project (HGP), cour- tesy of an NIH press release. It was an open secret that the human genome had not been completely sequenced—even today, that's a difficult claim to make—but the golden jubi- lee was an anniversary too good to pass up. And so today, as we mark the 15th anniversary of the HGP, we also observe that the double helix turns 65— retire- ment age for some, but for this icon, it appears the fruits of the genomic revolution are only just beginning. It was about 15 years ago that the notion of "the $1,000 genome" was beginning to gain traction, thanks in large part to a public challenge laid down by Craig Venter and a wave of start-ups touting new sequencing technologies. As we now know, one of those—sequencing-by-synthesis (SBS)—developed by another (slightly less famous) Univer- sity of Cambridge tandem, Shankar Balasubramanian and David Klenerman, became the foundation of high-through- put, next-generation sequencing. The Cambridge chemists commercialized their technology in a British company, Sol- exa, which was acquired by Illumina in 2006 for some $650 million. It looked like a gamble at the time, but an absolute steal today. Over the past decade, Illumina has squeezed every ounce of performance from that SBS platform, with enhancements in chemistry, engineering, and software housed in instru- ments such as the top-of-the-line Novaseq finally delivering us to the $1,000 genome threshold. Illumina's CEO, Francis deSouza, has even declared that the $100 genome is not too far off. What will push that day more than anything is greater com- petition: for the past few years, Illumina has enjoyed a virtual monopoly in the sequencing market, although the long- read technology of Pacific Biosciences provides important advantages for de novo assembly and researchers in the plant genomics community. Back in the U.K., Oxford Nanopore has made impressive strides with its portable minION sequencer. Most of its recent success has come in the microbial field; but last January, University of Nottingham researchers reported in Nature Biotechnology the sequence of a complete human genome using the long reads (some up to and exceeding 1 million bases) of the nanopore platform. That probably won't concern Illumina too greatly for the time being: in February, Rady Children's Hospital geneticist Stephen Kingsmore claimed a new Guinness World Record for the time from clinical whole-genome sequence to a pos- itive diagnosis of less than 20 hours, which could in some cases be a lifesaver for critically ill new- borns. This pipeline features Illu- mina and a group of software and informatics collaborators. There is still so much we do not understand or appreciate about the human genome: the vagaries of epigenetics, the 3D structural organization of chromosomes, the regulatory framework of so-called "dark matter", the precise contribution of genetic elements in shaping risk to common diseases, and so on. Our ability to make a difference at the clinical level hinges not only on disruptive new sequencing and assay technologies but con- tinued advances at the most basic level into the secrets of the sequence. The double helix is entering its golden years. — Kevin Davies Golden Years for the Double Helix Kevin Davies, Executive Editor, The CRISPR Journal Jim Watson and co-authors celebrate the publication of "DNA: The Story of the Genetic Revolution."

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