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Monday, January 23, 2023

Read a short preview of What's in Your Genome

Check out this website, What's in Your Genome if you want to see a preview of my book (Preface, Prologue, part of Chapter 1).

The book will be released on May 16, 2023. We are currently working on the proofs prior to typesetting. You can preorder the hardcover version on Amazon.ca (Canada) for $39.95 (Cdn). I don't know when the electronic version will be available. You can also preorder on Amazon.co.uk for £26.99.

You can't yet preorder on Amazon.com and there's no information on that site about availability. I don't know about other Amazon sites.



11 comments :

Anonymous said...

Typo on the fist page of the prologue. I love the sentence, but what it says is, “The other one probably thought *they* those words were referring to him.”

Mikkel Rumraket Rasmussen said...

Good news Larry. I read the preview and I can't wait for the rest.

Jonathan Badger said...

Unfortunately you repeat the myth (promoted by Eric Lander, who as usual was being "economical with the truth" as he later did with his absurd ploy to imply that his Broad Institute were the real people behind CRISPR, which fortunately the Nobel committee didn't buy) when you claim that that the Celera genome could not be assembled without the public data. Lander claimed that shotgun sequencing (which was commonly used to assemble bacterial genomes at the time) was somehow incapable of assembling the human genome. This wasn't true then or now (when shotgun assembly is commonly used for that). I worked at JCVI with many ex-Celera employees who were involved with the assembly process and they assured me that the shotgun assembly worked as expected and in fact we used the Celera assembler at JCVI to assemble our stuff (at least until advances in sequencing required newer DeBruijn graph based solutions)

Note that this is a different issue about questioning Celera's business model. Yes, selling sequence didn't work as a business and was arguably bad for science as well.

SPARC said...

I doubt that it has ever been possible to assemble any mammalian genome by shotgun sequnecing withot prior knowledge derived from radiation hybrid maps, chromosome and cDNA libraries or the genome sequences of other species. If one ignored all Alu and other repetitive sequences in the human genome and ordered the reads containing exons by comparison with known mRNA sequences they might have obtained some kind of assembly but this surely wouldn't have resembled the publicalyy funded draft version. Even the later contained several gaps in the genes I was interested in.

Larry Moran said...

@anonymous

I ran a contest on Facebook to see who could find the typo.

Larry Moran said...

@Jonathan Badger

I wrote, "... the Celera researchers had chosen to use a good deal of IHGP data to complete their own assembly of small fragments into chromosome-sized DNA ..."

This issue was addressed in a paper by Myers, Sutton, Smith and Venter in March 2002. doi: 10.1073/pnas.092136699. They say,

"As described in table 2 of ref. 1, we combined our data with a uniformly spaced 2× shredding of 677,708 individual bactigs, contigs of bacterial artificial chromosomes (BAC) clones shotgun sequenced by the HGSC, not the genome assembly reported in ref. 2. The goal of including this sequence was to take advantage (with attribution) of the work of the HGSC to the extent that it would contribute additional sequence coverage."

They way I interpret that statement from Celera is that they used some of the IHGP data in their assembly and that's what I said.

You are arguing another point. You are countering the claim that Celera used the Ihgp ASSEMBLY and MAPPING data instead of assembling their own genome by a straightforward shotgun method. I did not make such a claim. Celera noted in their original paper on the draft sequence that they had created an assembly using the IHGP mapping data but they also created a separate assembly using only the shotgun method and that's the one they published. It's clear that they had the public partial assembly and mapping data "in house" and that aroused Lander's suspicions since he didn't trust that they had not used it.

I deliberately added the following sentence in order to make it clear that the Celera sequence was better than the IHGP sequence. "Ironically, the actual DNA sequences produced by Celera were probably just as good as those of the public project - possibly even a little bit better."


Larry Moran said...

@SPARC

Celera claims that later on it created a shotgun human genome sequence assembly using only their own data. They also claim that they created a mouse genome assembly using only the shotgun method without referring to any other data.

Their Drosophila sequence was the test case for shotgun sequencing and assembly. It wasn't a great sequence but it was a solid base for future improvements. It proved that a eukaryotic genome sequence could be produced using the shotgun method.

judmarc said...

Very much looking forward to electronic availability on Amazon.com! (Happy to send an email to the vast empire somewhere if you think it would help.)

Larry Moran said...

@judmarc

Do you want an electronic version of my book? May I ask why? I’ve always wanted hard copies of books that I use frequently for references and information.

judmarc said...

Regarding reference, I actually feel it is easier for me personally to find specific information in a book electronically rather than in hard copy. I also travel frequently and enjoy the convenience of having access to multiple books while doing so.

Anonymous said...

I prefer my Kindle when I travel simply for convenience. However, I have found that they don’t survive Germans sitting on them in a beer hall, or being soaked in beer in a beer garden. My current kindle’s ID is Ken’s 4th Kindle.