With Singular Genomics announcing the new G4 system at the end of 2021, and Element Biosciences announcing the AVITI system in March 2022, here is a look at the existing state-of-the-art systems in a single graphic After spending some time in Los Angeles this week visiting a few existing and potential customers for Olink Proteomics, … Read more
NGHRI’s Dr. Adam Phillippy presents a remarkable dataset – the telomere-to-telomere assembly of a complete human X chromosome When the completion of the Human Genome Project was announced on June 6, 2002, President Bill Clinton said the following: We are here to celebrate the completion of the first survey of the entire human genome. Without … Read more
A Wellcome Trust supported effort, The Long Read Club seeks to resurrect a time-honored tradition: protocol development After a long 5 days away from home and work and the routines that surround it, attending AGBT (and likewise other major conferences) is a tremendous amount of work. I was teasing a division lead for a major … Read more
A commercial platform for droplet genomics Once upon a time Fluidigm had a single-system called the C1. Okay, it was back in September of 2013 that I wrote about it here; reading what I wrote way back then over five years ago there are newer and improved SMARTer cDNA kits (take a look at this … Read more
Yesterday’s Ion Torrent Proton PII™ and Illumina NextSeq 500™ post certainly got a reaction from several quarters, including detailed pricing information about the 1x75bp format for the high-throughput configuration on the consumables. Instead of making edits to the original here are some clarifying points, as it is clear that Illumina is making a break from … Read more
There has been a lot of publicity around the NextSeq 500 from Illumina, and it appears to have been designed to compete directly against Ion Torrent’s upcoming PII chip. Thanks to a visit to upstate New York last week, I met Dr. Sridar Chittur who told me how important it was to put current information out on this blog, and if I can put out the disclaimers up-front it would be very helpful for those thinking about what benchtop system to purchase over the next several months.
Today Ion Torrent launches a neat product based upon a highly multiplexed technology called AmpliSeq, called the Ion AmpliSeq Exome, covering >97% of the CCDS regions. But before getting into the details, a little context is in order.
Earlier this year at the February AGBT Conference, a person from QIAGEN came over to the Ion Torrent suite and asked me a few questions about the Ion Proton and in particular the upcoming Ion Chef unit. (The Ion Chef for those not familiar with it can replace the OneTouch 2 automated template preparation instrument with another one that will not only perform the emulsion PCR but also enrich the ion sphere particles, and load the chips as well.)
Every mother-to-be who has what is considered an ‘at-risk’ pregnancy is informed of the risks to the fetus of a genetic abnormality. ‘At-risk’ can involve a long list of medical conditions (diabetes or cancer for example) or poor health choices (illegal drug use or smoking). Yet a common cause of an at-risk pregnancy is age, having a child before the age of 17 or older than 35. In the US, no less than 750,000 are considered at-risk.
Immunology is a fascinating subject. Immense in its complexity, debilitating when the immune system malfunctions, our ability to fend off bacterial and viral infection, cancers of different types, and other foreign invaders is a remarkable biological capability.
The NIH estimates 24M Americans are affected with an autoimmune disorder, but that number rises to 50M when the definition is expanded from a list of 24 disorders to over 100 by the American Autoimmune Related Disease organization. It is the second highest form of chronic illness, arthritis being the most familiar to many.
This week a remarkable paper was published in Nature, called “Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells”. What makes it remarkable is the ability of this method to obtain rare variant phase information by changing the library preparation method. Until now to obtain completely phased individual genomes required a fair amount of laboratory manipulation.
Although the whole genome versus whole exome discussion was held previously, details around the methods of selecting out the whole exome have been not discussed (also called ‘targeted selection’), and the wide array of methods, costs, and effort required can be a rather complicated affair.