biology


Matt Loose on "Read Until" or Adaptive Sequencing

Back before the world turned upside down, you know, all those years ago--early this February--a paper popped up on bioRxiv called, “Nanopore adaptive sequencing for mixed samples, whole exome capture and targeted panels." It’s an interesting paper.

In the paper, the authors, led by Matt Loose from the DeepSeq lab at the University of Nottingham, describe a method unique to nanopore sequencing where one can do "selective sequencing of single molecules in real time by individually reversing the voltage across specific nanopores.”

In other words, one can decide in the middle of sequencing a molecule that, nah . . . , this molecule bores me. I'll choose another.

Matt says Oxford Nanopore mentions the ability to do this back in 2014 in an aside. But he doesn’t fault us for just getting around to doing a podcast on it.

We do fault ourselves for just getting around to having Matt on the program. Hailing from the land of Robin Hood, it’s Matt Loose, Director of DeepSeq, previous record holder for sequencing the longest read, talking developmental biology, nanopore sequencing, and COG-UK, the UK’s collaborative effort to sequence the coronavirus.

All Sport Is Unfair, According to Geneticist. Is That True?

Yesterday a court ruled that the South African running sensation Caster Semenya must take medication to lower her level of testosterone to compete in certain women only running events such as the 400 and 800 meters.

Some are calling the ruling discrimination against a certain athlete or against transgener or intersex athletes.  Some say the ruling is necessary to keep the sport fair.  It’s a worthy debate.  

What I find particularly useful about the debate is what it tells us about how our colleagues in the science community are thinking.

September 2018 with Nathan and Laura: Studying the Same Genes and the Matt Fender Story

And here we were thinking it was a slow month!

We have two big stories today: first this philosophy of biology question about whether it’s a bad thing that we’ve been stuck circling the wagons ‘round the same ole genes. Is it just an economic question? Or is it that these are the most active genes, and so we need a meritocracy, as Nathan puts forth?

As if on time to answer this question, there’s a new project out this month to synthetically engineer 4,000 copies of a very studied gene, BRCA, which has Laura and other genetic counselors excited. As she explains, it will help with the problem of reducing variants of unknown significance.

And second, we discuss the fallout of Laura’s tour de force article in the New York Times and follow-up Beagle podcast about a young web developer, Matt Fender, who had a real scare with his 23andMe data. Theral says the story sounded an alarm at just the moment many of the field's KOLs are becoming relaxed about regulating DTC tests. Nathan says the story shows that the system is working.

May 2018 with Nathan and Laura: The Free Exome, California Database, and Mosaicism

Nathan Pearson and Laura Hercher are back for a look over a busy month of headlines.

May took us into the era of the free genome as Geisinger planted the genomic medicine flag on an even higher peak. And did you know California was keeping a genetic database for every baby born?

Meh. . . says Laura. Every state does it. Old news.

And mosaicism is old scientific news, says Nathan, but he likes the way Carl Zimmer brings it to light in a new book. Nathan and Laura then go above and beyond with their own elucidation.

It’s our final month-in-review before the break. Happy summertime!



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