The ASML of DNA Sequencing 

Is there a Moore's Law for genome-sequencing?

What do you think of the size of economy, US vs China? Whose economy is bigger? I was surprised to find out that the US economy is probably less than half the size of Chinese economy. The sales of luxury cars in 2021: Benz: 758,863 sold in China, 276,102 in the US BMW: 846,237 sold in China, 336,644 in the US Audi: 701,289 sold in China, 196,038 in the US Porsche: 95,671 sold in China, 70,025 in the US EV: 2.8 million in China, 0.4 million in the US I looked into further, and there are lot of other evidences that prove China is bigger, has lot more money and resources than the US does.

Thank you for this clearly delineated and distinct sponsor read, much nicer than the fractional art investment thing in a recent video.

@@sbkarajan What does this have to do with the video? Just cos it mentioned one of their competitors is Chinese?

@Asianometry Please stop commending Nobel prizes, it's a scam as most prizes and awards

"Illumina-TIE" NVidia, Jensen Huang

Well done sir

Boy are we a nerdy, 😂😂

and the absolute worst of the worst in filing ridiculously offensive lawsuits combined 🥴

Ha ha ha ha... 😎

God I hate SNPs as they "stole" the acronym from my company's stock ticker which confuses google

What about the sci-fi sequencing where you use nano-machines and SEM to actually read tiny bits of DNA (without PCR amplification)? How's that going? A decade or two ago that was the "next big thing". Haven't kept up with the field since then.

@@raylopez99 that sound like nanopore technology (ONT). It’s going strong! They have a version (MinION) that about the size of an external SSD. Super neat for field works and environmental science folk. As a computational scientist, id say they have their problem with bias and lower accuracy than amplification methods, but they can be supplemented with short reads to build a robust and cheap sequencing

Everyone I work with simply refers to Illumina as NGS. Perhaps as consumers rather than developers of sequencing technology we’re too disconnected or lazy to bother making a distinction. Though it does speak to Illumina’s dominance in short reads. I agree that ‘next generation’ has been a comical misnomer for a decade at this point.

@@VuLamDang ONT's long read quality is better than you think. I routinely get quality scores comparable to illumina, every year they make huge strides on that, and now they have the advantage of being able to detect modified bases much better than any other method. If your experiments need long reads and nucleotide modifications, then ONT is really the only way to go.

Hi Thomas, greetings from JenOptik ;-) We'll send a bunch of new MNSQ & NSQ readheads out of the manufacturing to singapore tomorrow, make shure you'll sell them well. ;-)

Hope you enjoy those exorbitant stock options while the company is in severe distress!! I hope the owners stop paying so those who are corrupt leave or get FIRED!!!

Funnily, the HiSeq 2000 used readily available microscopes as the core body, they wrapped motorised parts around it. A lot of components are off-the-shelf systems integrated together. Despite the model being phased out and recycled, many parts are useful for optical builds to this very day. I pulled a couple apart and almost all the components have been reused at our institution. Recycling, done right!

Imagine you could use google:)

@@orangestapler8729 It really is master level. You can't show me a single teacher or professor researching and making a material like this for their studies let alone the delivery.

Same here.. I work as an IT consultant and support these in a genetics lab. The IT requirements for these is a monster.

why u using your name and address as your avatar if u no wanna dox?

@@timmata8143 Its ok. Its just some additional money you have to spend. But I remember the reaction of one of our colleagues in the IT department, when I requested some computing resources. He proudly offered me a VM with 16(!) Threads and up to 16 GB RAM. So I said: You did nothing wrong, everything is OK, but I need to talk to your boss. ;-) Right now we run two servers with a total of 1.75 TB RAM and 256 Threads. Do not get me started on storage. Sore topic.

Was Margarita Salas PCR discover ?... but He have a very good trips.

At the time when I used them, sequencing of homopolymers was a bit of an issue with the Oxford Nanopore MinION. Similar to the iontorrent. Back then the algorithms would sometimes miscount the number of nucleotides in this type of sequences.

@@johnsmith1926 I'm curious as well how conventional sequencing avoids misinterpreting long stretches of one nucleotide. Wouldn't synthesis proceed right through that sequence and the fluorescence not be able to distinguish it's length?

@@samrusoff from my understanding, the florescent molecule prevents further nucleotides from binding to the RNA strand being synthesised, meaning that for any given cycle, only one nucleotide can join to the end of a strand. The remaining reagent is cleared away, image of the clusters taken, then a buffer is pumped through the flowcell, destroying the florescent molecule before another set of reagents is pumped through to begin the next cycle.

@@johnsmith1926 Homopolymer basecalling remains a challenge, but not an insurmountable one. ONT has switched to nanopores with longer channels, so they read a longer stretch of nucleotides and can accurately basecall up to 10-20 bp homopolymers. And in the last year they’ve tweaked their flow cells so that for a large fraction (up to >50%) of the DNA molecules they read, they thread both strands of the duplex through; and by basecalling with information from both strands of the duplex they can get to Q30/99.9% accurate single molecule reads. This means that for applications where exact basecalling of long homopolymers matters, it should be possible to use a ‘polishing with dirt’ strategy, where you split and barcode a sample into two: one half that you prep and sequence regularly, and one half where you perform a super error-prone PCR (for instance, by spiking in mutagenic dPTP and 8-oxo-dGTP along with normal dNTPs; see Zaccolo et al) that gets you to 5-20% random mutations per base on each molecule. To call homopolymers, assemble the non-mutated sample reads as normal, then align the mutated reads to this ‘reference’ consensus. The random mutations in epPCRed reads break up the homopolymers with sequence variations that the basecaller can ‘see’ on each read, but that average out of the consensus. Haven’t seen anyone actually implement this yet, but no reason it shouldn’t work in principle!

What sources would you recommend to better understand ONT?

Let me guess. One of them is EcoRI?

@@johnsmith1926 Yep, Escherichia coli is the most popular bacteria in biological study.

Lucifer asa

😄 that's never gonna happen fool. Be realistic. It can come back to 100$ though.

@@nishant54 there is nothing in physical law preventing it from going arbitrarily low, FOOL

@@Muonium1 Everything preventing it from becoming near free fool.

That said, i would LOVE to see your take on Mass Spectrometry and Omics sciences! (Mostly proteomics... hehehehe)

To pick your interest, there is a Mass Spectrometer (more than one, actually) that measures mass-to-charge ratio within parts per million accuracy. One of wich "ignores the velocity distribution" of ions. (Im intentionally throwing words in the hopes you're like "omg what? That must be very cool!") Ahahahah

Lucifer Rise

#Luciferine

Not just them, the ISeq, MiniSeq and NextSeq 550 are manufactured there aswell. We send them a bunch of new readheads every week from jenoptik, germany. ^^

The founder of America's first German settlement, Franz Daniel Pastorius, got his law degree in your fine city.

Well, at least 3 of them with some soon to come followups ;-)

another instance of parents not listening to their kids. ah well.

I hope that you have told him what he turned down.

I heard about the technology in the end of 2008 and instantly decided to build my career on analyzing the vast amount of data these machines pump out. Today we're talking about up to 2 TB raw data per sequencing run. Was kind of difficult at first but I found my way into the industry. I was a molecular biologist at that time and it was one of these moments where I just knew that this was going to take of big and very soon, so I wanted to jump on board. Short time after that, I got my hands on 454 and Solexa sequencing data, fitting right into my PhD thesis. Right spot at the right time and keen senses, that's the ticket ;-) Whom am I kidding.. It was sheer luck. I was slacking off on a hacker conference when some guy from the Sanger institute in the UK gave a talk about his work.

Glad he didn't listen. ILMN stock price has dropped to almost 10 years ago's level.

@@jasonhu7995 illumina share price was ~80 in 2013. Its 214 as we speak. What are you smoking?

Technically, they didn't make as much as bought the dutch company Genalice, who made the fpga solution.

@@cptbenjaminwillard ahh, thank you for the correction.

Oh, turns out I was wrong! My apologies! Illumina bought Edico Genome's Dragen solution, which was a competitor to genalice. Genalice seems to have filed for bankruptcy in 2019.

Crispr allows you to selectively edit a genome - Illumina machines allow you to read and sequence. One is writing the other is reading, and the CRISPR tech is patented by another group so while they could potentially incorporate it in some future machine they would have to pay for the license to do that.

Crispr is something you do to genetically alter an organism, while genome sequencing is about reading the genetic information from an organism

Gene writing and editing requires NGS to determine if the editing has taken place and also to see if there are any off-target editing.

@@jinngeechia9715 verification could be done with a standard PCR most of the time or even a simple sanger sequence, I wouldn't see the point of doing a full sequence unless the process becomes excessively cheaper. I might be missing something though

@@cianrynne2140 for a simple experiment, you don't need NGS to verify edits. For really serious application of GWE, you need it. These ambitious GWE projects will always have deep pockets for NGS.

lol yep.. they all buy and sell each other. I've been working in lab IT for awhile now.. I have seen how they get bought and sold to each other.

HP ?