This article nice frames the immaturity of the technology in the context of population health and prevention (vs. specific disease management), and even references the behaviour of evil corporations in its final paragraphs.<\/p>\n
<\/p>\n
Cost breakdown for Illumina\u2019s $1,000 genome:<\/p>\n
Reagent* cost per genome \u2014 $797<\/p>\n
Hardware price \u2014 $137**<\/p>\n
DNA extraction, sample prep and labor \u2014 $55-$65<\/p>\n
Total Price = $989-$999<\/p>\n
* Starting materials for chemical reactions<\/p>\n
** Assumes a four-year depreciation with 116 runs per year, per system. Each run can sequence 16 genomes.<\/p>\n
http:\/\/recode.net\/2014\/03\/25\/illuminas-ceo-on-the-promise-of-the-1000-genome-and-the-work-that-remains\/<\/span><\/p>\n March 25, 2014, 2:18 PM PDT<\/p>\n<\/div>\n By James Temple<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n Illumina seized the science world\u2019s attention at the outset of the year by\u00a0announcing it had achieved\u00a0the $1,000 genome, crossing a long-sought threshold expected to accelerate advances in research and personalized medicine.<\/p>\n The San Diego company unveiled the\u00a0HiSeqX Ten Sequencing System at the J.P. Morgan Healthcare Conference in January.<\/a>\u00a0It said\u00a0\u201cstate-of-the art optics and faster chemistry\u201d<\/a>\u00a0enabled a 10-fold increase in daily throughput over its earlier machines and\u00a0made possible the analysis of entire\u00a0human genomes for just under $1,000.<\/p>\n Plummeting\u00a0prices should\u00a0broaden\u00a0the applications and appeal of such tests, in turn enabling large-scale studies\u00a0that may\u00a0someday\u00a0lead to scientific\u00a0breakthroughs.<\/p>\n The new sequencers are making their way into the marketplace, with samples now running on a handful of systems\u00a0that have reached early customers,\u00a0Chief Executive Jay Flatley<\/a>\u00a0said in an interview with\u00a0Re\/code<\/strong>\u00a0last week. Illumina plans to begin \u201cshipping in volume\u201d during the second quarter, he said.<\/p>\n The Human Genome Project, the international effort\u00a0to map out the entire sequence of human DNA<\/a>\u00a0completed in 2003, cost $2.7 billion. Depending on whose metaphor you pick, the $1,000 price point for lab sequencing is akin to breaking the sound barrier or the four-minute mile \u2014 a psychological threshold where expectations and, in this case, economics change.<\/p>\n Specifically, a full genomic workup of a person\u2019s three billion DNA base pairs starts to look relatively affordable even for healthy patients. It offers orders of magnitude more information than the so-called SNPs test\u00a0provided by companies like 23andMe<\/a>\u00a0for $99 or so, which just looks at the approximately 10 million \u201csingle-nucleotide polymorphisms\u201d that are different in an individual.<\/p>\n With more data, scientists expect to gain greater insights into the relationship between genetic makeup\u00a0and observable\u00a0characteristics \u2014 including what genes are implicated in which diseases.\u00a0Among other things, it should improve our\u00a0understanding of the influences of DNA that doesn\u2019t directly code proteins (once but\u00a0no longer thought of as junk DNA<\/a>) and create\u00a0new research pathways<\/a>\u00a0for treatments and cures.<\/p>\n \u201cThe $1,000 genome has been the Holy Grail for scientific research for now over a decade,\u201d Flatley said. \u201cIt\u2019s enabled a whole new round of very large-scale discovery to get kicked off.\u201d<\/p>\n Cost breakdown for Illumina\u2019s $1,000 genome:<\/strong><\/p>\n Reagent* cost per genome \u2014 $797<\/strong><\/p>\n Hardware price \u2014 $137**<\/strong><\/p>\n DNA extraction, sample prep and labor \u2014 $55-$65<\/strong><\/p>\n Total Price = $989-$999<\/strong><\/p>\n * Starting materials for chemical reactions<\/strong><\/p>\n ** Assumes a four-year depreciation with 116 runs per year, per system. Each run can sequence 16 genomes.<\/strong><\/p>\n Source: Illumina<\/em><\/strong><\/p><\/blockquote>\n<\/div>\n Some have questioned the $1,000 claim, with\u00a0Nature noting<\/a>\u00a0research centers have to buy 10 systems for a minimum of $10 million \u2014 and that the math requires including machine depreciation and excluding the cost of lab overhead.<\/p>\n But Flatley defended the figure, saying it\u2019s impossible to add in\u00a0overhead since it will vary at every research facility.<\/p>\n \u201cOur math was totally transparent and it is exactly the math used by the (National Human Genome Research Institute<\/a>),\u201d he said. \u201cIt\u2019s a fully apples-to-apples comparison to how people have talked historically about the $1,000 genome.\u201d<\/p>\n He also questioned\u00a0the conclusions of a recent study published in the\u00a0Journal of the American Medical Association<\/a>, where researchers at Stanford University Medical Center compared results of adults who underwent next-generation whole genome sequencing by Illumina and Complete Genomics, the Mountain View, Calif., company\u00a0acquired last year by BGI<\/a>.<\/p>\n They found insertions or deletions of\u00a0DNA base pairs only concurred between 53 percent and 59 percent of the time. In addition, depending on the test, 10 percent to 19 percent of inherited disease genes were not sequenced to accepted standards.<\/p>\n \u201cThe use of [whole genome sequencing] was associated with incomplete coverage of inherited disease genes, low reproducibility of detection of genetic variation with the highest potential clinical effects, and uncertainty about clinically reportable findings,\u201d the researchers wrote.<\/p>\n Or as co-author Euan Ashley put it to me: \u201cThe test needs some tough love to get it to the point where it\u2019s clinical grade.\u201d<\/p>\n Flatley responded\u00a0that the sample size was small and that the sequencing platforms were several years old. But he did acknowledge they are still grappling with technology limitations.<\/p>\n \u201cWhat\u2019s hard is to determine whether there\u2019s a base inserted or deleted,\u201d he said. \u201cThat\u2019s abioinformatics<\/a>\u00a0problem, not a sequencing problem. That\u2019s a software issue that we and others and the whole world is trying to work on.\u201d<\/p>\n But, he stressed, that shortcoming doesn\u2019t undermine the value of what the tests\u00a0do<\/em>read\u00a0accurately.<\/p>\n \u201cThere are many, many, many things where it\u2019s clinically useful today,\u201d he said.<\/p>\n Flatley pointed to\u00a0several areas where we\u2019re already seeing real-world applications of improving sequencing technology, including cancer treatments targeted to the specific DNA of the tumor rather than the place where it shows up in the body. There are also blood tests under development that can sequence cancer cells, potentially avoiding the need for biopsies, including one from\u00a0Guardant Health<\/a>.<\/p>\n Another promising area is\u00a0noninvasive prenatal testing<\/a>, which allows expecting parents to screen for genetic defects such as Down syndrome through a blood draw rather than an amniocentesis procedure.<\/p>\n The technology\u00a0can delineate the DNA from the fetus circulating within the mother\u2019s bloodstream. It\u2019s\u00a0less invasive and dangerous than amniocentesis, which involves inserting a needle into the amniotic sac\u00a0and carries a\u00a0slight risk of miscarriage<\/a>. Because of that risk it\u2019s generally reserved for high-risk pregnancies, including for women 35 and older.<\/p>\n Illumina, which offers the blood screening\u00a0for out-of-pocket costs of around $1,500, recently funded a\u00a0study published in the New England Journal of Medicine<\/a>\u00a0that found the so-called cell-free fetal DNA tests produced more accurate results\u00a0than traditional tests for Down syndrome and Trisomy 18, a more life-threatening condition known as Edwards syndrome.<\/p>\n \u201cIt gives some earlier indicators to women in the average risk population if their babies have those problems,\u201d Flatley said. \u201cI think that it will broaden the overall market, and there are other tests that can be added over time.\u201d<\/p>\n But there are ethical issues that arise as prenatal genetic tests become more popular and revealing, including whether parents will one day terminate pregnancies based on intelligence, height, eye color, hair color or minor diseases.<\/p>\n For that reason,\u00a0Illumnia refuses to disclose those traits that are decipherable in the genome today.<\/p>\n But Flatley said they couldn\u2019t stop purchasers of its machines from doing so, nor competitors like BGI of China (for more on that issue see Michael Specter\u2019s\u00a0fascinating profile of the company<\/a>\u00a0in the New Yorker ). Flatley said there needs to be a public debate on these issues, and he expects that new laws will be put into place establishing commonsense boundaries in the months or years ahead.<\/p>\n \u201cThis isn\u2019t something we think we can arbitrate,\u201d he said. \u201cBut we won\u2019t be involved directly in delivering [results]\u00a0that would cross those ethical boundaries.\u201d<\/p>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":" This article nice frames the immaturity of the technology in the context of population health and prevention (vs. specific disease management), and even references the behaviour of evil corporations in its final paragraphs. Cost breakdown for Illumina\u2019s $1,000 genome: Reagent* cost per genome \u2014 $797 Hardware price \u2014 $137** DNA extraction, sample prep and … Continue reading Illumina’s $1000 genome<\/span> Illumina\u2019s CEO on the Promise of the $1,000 Genome \u2014 And the Work That Remains<\/h1>\n