I ran across this Genome Medicine paper during the #SCOTUS  and  #BRCA  gene patent discussions back in June, but it’s been sitting in my “to read” pile since.  It’s a great resource if you’re curious about how much of the genome is covered by patents, because the answer is actually quite surprising.

Using bioinformatic methods, the authors look at the number of genes covered by patent claims.  Many patents claim even very short segments of a gene, like the 15bp segments in the Myriad BRCA patents.  But, as anyone who has tried to create nice specific PCR primers knows, most 15bp DNA sequences can be found in multiple places in the genome.  How many different places?  Drs. Rosenfeld and Mason are glad you asked.

The paper is open access so I recommend skimming through the whole thing.  But here are a few interesting tidbits.  The most broad claim in the BRCA patent (#5,747,282), the claim on any 15bp seqence from gene, actually also covers 689 (4%) other genes in the human genome.  That is, 689 other genes share identical 15bp stretches with BRCA1, and so they are actually covered by the patent as well.  How pervasive was this phenomenon of shared “15mers”?

• Every gene in the genome (they used the consensus CCDS) shares 15mers with another gene.  The lowest number of matching genes for a 15mer was 5.
• As stated above, BRCA1 matched 689 other genes.
• TTN, granted a very big gene, matched 7,688 (42%) other genes!
• If one considers all sequence, not just coding sequence, then 99.999% of 15mers in the human genome are repeated at least twice.
• 58 current gene patents cover each at least 10% of the bases of human genes
• The “top” patent was US7795422, which alone claims sequences matching 91.5% of all human genes
• And, in a discovery that underscores the absurdity of gene patenting, a patent for improving bovine traits (i.e. a patent on a cow gene) claims sequences matching 84% of human genes.

The authors conclude: These results demonstrated that short patent sequences are extremely non-specific and that a 15mer patent claim from one gene will always ‘cross-match’ and patent a portion of another gene as well.

It’s a great article so have a look:  http://genomemedicine.com/content/5/3/27

The plot below is titled: Total matches and average number of other genes patented plotted against k-mer size

The how, when and where of human genetic mutation is a complex and (to me, anyway) fascinating topic:

How: There are diverse and only partially understood molecular mechanisms by which DNA strands are altered, from a single base change up to complex rearrangements of entire chromosomes.

When: Mutations can occur at any time in life, from meiotic defects prior to fertilization all the way up to acquired mutations late in life.

Where: Mutations can be constitutional (in all your cells) or somatic (in just some of your cells). Constitutional changes are usually inherited from your parents, whilst somatic mutations are really the domain of cancer.

But you can also be mosaic for a mutation too, meaning that you have developed such that some of your cells contain a mutation while others do not.  So some of your tissues may be “mutant” while others will be “normal”, although what effect this has on phenotype is really all over the map.  Or, you can be a germline mosaic, which is a special situation where the mutation is generally confined to your germ cells (that make eggs/sperm).  For example, a mother has multiple sons with muscular dystrophy but testing her shows that she isn’t a carrier for the mutation.  Possibly her ovaries do carry the mutation, but her blood that was tested does not.  In practice, germline mosaicism is difficult to detect and it often keeps clinical geneticists from feeling certain about inherited disease.

All this is a very long-winded introduction to this recent paper on recurrent mutations in Noonan Syndrome.  Noonan Syndrome is an inherited disorder that affects about 1 in 2500 children worldwide – individuals have short stature, heart defects and characteristic physical features.

Mutations in genes of the RAS-MAPK pathway have been identified as the cause of this disorder.  In particular, a specific mutation in the gene PTPN11 has been seen in many affected individuals, and an association has been made between this mutation and increased paternal age.  In other words, the fathers of children who carry this mutation tend to be older.  But why is that?  The authors of this paper present data supporting a perhaps unexpected answer.  This particular mutation gives a selective growth advantage to their spermatocytes (sperm producing cells).  Natural selection. In your pants. It’s happening right now, guys.

Unlike women, as men age their germ cells continue to divide and during this time they can acquire new mutations resulting from errors during DNA replication.  If you’re 40 years old then your germ cells have gone through about 800 cell divisions (versus 23 for a woman), and each division carries the chance of creating a new mutation.  But since all spermatocytes have a roughly equal chance of producing the sperm that results in an offspring these mutations are generally diluted.  However, in the case of the PTPN11 mutation c.922A>G, the spermatocytes that acquire this mutation grow much better than the others and so they can out-produce their rivals.  This greatly increases the frequency of sperm carrying this same mutation, thus increasing the chances that offspring will inherit the change.  And while the mutation makes the spermatocytes grow better it causes Noonan Syndrome when carried as a constitutional mutation.

There is a whole lot more to the paper than this, but if nothing else it’s a great example of a neat when and where of human mutation.  Plus, it’s a reminder that selective growth advantage is important in biology in ways we often don’t appreciate.

Here’s the publication: https://www.sciencedirect.com/science/article/pii/S0002929713002140?np=y

Figure below shows the spatial distribution of mutation c.922A>G in the dissected testicles of healthy males.  (I think – I stopped reading the methods right around that point.)

When the authors of a report include “Highly Anticipated” in the title you know that either: 1) it is highly anticipated, or 2) they’re trying to get some attention.  In the case of the recent ACMG guidelines ACMG Recommendations for Reporting of Incidental Findings in Clinical Exome and Genome Sequencing Report (www.acmg.net) it’s both.  And what do these recommendations say?  For one thing, they say that if you get a sequencing test you can’t choose to not hear about anything bad that is discovered.

As most people are aware, recent advances in genome sequencing technologies have made it possible to sequence most or all of a patient’s genome for clinical diagnostic and predictive testing.  Here’s a couple of open-access reviews to get you up to speed on the details:

Genomics Reaches the Clinic: From Basic Discoveries to Clinical Impact
Teri A. Manolio and Eric D. Green
https://www.sciencedirect.com/science/article/pii/S0092867411010701

Next generation sequencing—implications for clinical practice
Eleanor Raffan and Robert K. Semple
http://bmb.oxfordjournals.org/content/99/1/53.full

So, now that we can do it, everyone is starting to concentrate on the next questions.  Should we do it and, if so, how and under what circumstances?  There are a number of big issues with this type of testing because it deals with genetics.  You can’t escape or change your DNA, your parents gave it to you and your kids will get half of it, and a myriad of privacy and legal issues.  Another concern is that during testing an unexpected discovery will be made: a so-called incidental finding.

Incidental findings have been an issue in other areas of medicine for some time: the phrase incidentaloma has been used in radiology to describe a tumour that is discovered during imaging for an unrelated condition (“my back hurts”, “OK let’s give you a chest x-ray”, “I’m sorry to say you have a lung tumour”).  In genetics they were not common because the testing was so targeted that it would usually only find what it was looking for.  (Incidental findings of non-paternity, consanguinity and sex-chromosome abnormalities are possible, among other things.)  But once we start sequencing entire exomes or genomes, it is increasingly likely that testing will discover medically-relevant changes in genes completely unrelated to the purpose of the test.

Incidental findings in research have been discussed for a few years now.  The concern there is that researchers will discover something in a patient’s genome but be unable to inform the patient, either due to legal and ethical restrictions or to sample anonymization.  See the following for an overview:

Disclosing pathogenic genetic variants to research participants: Quantifying an emerging ethical responsibility
Christopher A. Cassa, Sarah K. Savage, Patrick L. Taylor, Robert C. Green, Amy L. McGuire and Kenneth D. Mandl
http://genome.cshlp.org/content/22/3/421.full

In the clinical realm, the patient is known and there is a mechanism to inform the patient of genetic findings.  However, the patient might have had testing to see if they were a cystic fibrosis carrier, and perhaps the testing discovers that they carry a pathogenic BRCA1 variant.  Should they be informed that they are at high risk for developing breast or ovarian cancer?  Probably.  But they might not want to know.  And it means that their siblings, their children and other relatives should also be informed.  What if you’re testing a child and discover the same thing?  Should a child be told they carry a risk for an adult-onset disorder? (These are emphatically not even tested for currently).  There are a lot of scenarios but you can see the problem.  It’s potentially Pandora’s box and you don’t get to choose whether it’s opened.

These ACMG recommendations are brand new and everyone is taking some time to digest and consider them.  But they have some strong and possibly surprising rules for the labs doing the testing.  With the caveat that I’ve only given them a quick skim, here’s my quick interpretation of of the important bits:

1) Mutations found in a provided list of 56 genes (mostly cancer-associated) must be reported by the laboratory, regardless of the clinical indication (what the test is looking for).  If the labs generate the data they can’t mask or ignore it to avoid this requirement.
2) The clinician ordering the sequencing test is responsible for informing and consenting the patient about the possibility of these incidental findings.  About 1% of patients can expect to get one.
3) The patient can’t decline to have incidental findings returned – if they don’t want them their option is to not have the testing.  “Duty to warn” trumps “patient autonomy”.
4) These recommendations are still valid if the patient is a child.  “Parent’s right to know” trumps “child’s right to not know”.

The gene list has been carefully chosen to “prioritize[d] disorders where preventative measures and/or treatments were available and disorders in which individuals with pathogenic mutations might be asymptomatic for long periods of time.”  The stated assumption is that any reasonable person would want to know about these.  But that’s not a very nuanced position.

As I said, everyone is trying to think about what these might mean and how they’ll be implemented.  This is really big news in the medical genetics community and it has important implications for everyone.  Take a look at the link at the top (it’s not very technical) and think about it.  Everyone’s opinion is important.

What do you do if a bunch of young, uninhibited, disruptive elements are rampaging around the place, messing things up and getting into places they shouldn’t be?  You toss them in the pillory, that’s what.

The eukaryotic cell has learned this lesson well, at least with respect to the genome.  There are millions of copies of subversive retrotransposons in the genome and each would jump at the chance to move around, causing trouble in the process.

So, what’s a peace-and-order loving cell to do?  Wrap them tightly around a histone, cram everything into some dark and unloved corner of the nucleus and hope they’re never heard from again.  That’s what. Now they’re stuck in the jail that is heterochromatin.

They deserved it.

But, as even Darth Vadar discovered, repressive regimes can’t last forever.  And as the cell ages its ability to keep the transposons repressed slowly fades.  Complacency?  Weariness?  It’s hard to say.  But the result is predictable: transposons hopping amok, highjacking promoters and smashing into exons until the apoptotic end arrives.

[The paper is paywalled so instead I’m linking to the news-vertorial.]

http://news.brown.edu/pressreleases/2013/01/senescence

It may come as a surprise to many but Drosophila melanogaster, the common fruit vinegar fly, is almost as abundant in genetics labs as it is in your compost pail. And I’m not just talking about the lunch fridge. Drosophila has been an invaluable model organism for genetics and developmental biology research for over a century.

Its relatively tractable genome size (165 million base pairs) and importance in the research community led to its genome being sequenced early in the genomics era. The genomics company Celera famously accomplished this in 2000 as a warm-up to their human sequencing run. The assembled genome was a massively useful resource for the research community (including obscure grad students toiling in search of obscure genes).

At a later date (2007 perhaps?) an additional 11 species of Drosophila were sequenced. This set of 12 genomes has been useful for comparative analysis of these species, looking for differences in the genomes that have arisen since these species diverged. An interesting analysis from this dataset arrived inGenome Research earlier this week. [Paper link below – it’s Open Access!]

The authors looked at conservation of gene sequences between the genomes and noticed something unexpected. The DNA sequences of the genes are expected to be slightly different, with species more distantly-related having more differences, and this is what you see. The proteins that the genes encode, however, have to retain their function and so there are some limits on how much they can vary. So, what you would expect is that the protein-coding portions of the genes would display these constraints but the non-protein-coding portions of the genes would not. This is what is observed for most genes, but not all of them. In 283 genes, the sequence following the stop codon (where the protein should end) continued to show the functional constraints. This results suggests that in these genes the ribosome will sometimes disregard the stop codon and continue to add to the protein. And these additional sequences were conserved between species further suggesting that the extended proteins confer some sort of selective advantage.

On our morning walks to school I am always reminding my daughter that many drivers will see Stop signs but think they say “slow down a bit”. Now I’ll have to include ribosomes in my lectures too.

http://genome.cshlp.org/content/21/12/2096.full

In the animal kingdom the mother is generally the parent that provides the most care to the young.  Males are running around competing for access to females, and don’t really have the time to stuff worms in little beaks or wipe noses.  The argument goes that females devote more resources to growing the young and so it’s in their best interests to ensure that they survive.  Guys just need to sow their wild oats and by the way they really don’t appreciate all the criticism.

But in some species it’s the males that provide most care to the young.  Seahorses are a commonly-cited example of this.  So, what’s up with these guys that they’re willing to be Mr. Mom?

This paper (open-access at Nature Communications) provides data suggesting that it’s the male/female ratio skew in these species.  If there are more males than females then access to females is restricted.  Males benefit more by staying close to their mates and raising the young.  Notably, female polygamy is also increased in these situations since the males are busy and the females are in-demand.

Mammals appear to be somewhat immune to this phenomenon, since males can’t make the milk necessary to feed the young.  And in humans, the parenting skills of most males places a powerful negative selection on the evolution of this behavior.

http://www.nature.com/ncomms/journal/v4/n3/full/ncomms2600.html

I’m usually on Google+ (no, really).  But I’m thinking I should start filling space here too.  Everyone can use practice writing, right?