Category: Genomics
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On the real possibility of human differences
I have discussed the reality that many areas of psychology are susceptible enough to false positives that the ideological preferences of the researchers come to the fore. CBC Radio contacted me after that post, and I asked them to consider that in 1960 psychologists discussed the behavior of homosexuality as if it was a pathology.…
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How the worm turns the genic world
In the middle years of the last decade there were many papers which came out which reported many ‘hard’ selective sweeps reshaping the human genome. By this, I mean that you had a novel mutation arise against the genetic background, and positive selection rapidly increased the frequency of that mutation. Because of the power and…
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Genomes made real
Things we said today: But change is afoot. Numerous teams of clinicians and genomicists (including two at my own institution) have come together to sequence patients’ genomes and/or exomes to identify disease-causing mutations. Of course, doctors and researchers and genetic counselors are still bickering about when to sequence, whom to sequence, return of results, institutional…
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Personal genomics: more than fun & games
My main current interest in personal genomics right now is pure recreation. I don’t expect much utility out of it, because a lot of correlations between genes (SNPs, etc. ) and traits/diseases are rather weak. But there are some exceptions. Recently I was temporarily put on a prescription medication and I wanted to check if…
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How many human genomes have been sequenced?
That query doesn’t seem to have an easy answer on Google, so I’m trying to enter it here. A prominent genomicist asserted a ballpark figure of ~30,000 human genomes in the year 2011. Most of that is in the year 2011 itself. Also, in regards to the “$1,000 genome” question, it seems that some labs…
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The hunter-gatherers within us
Lesley-Ann Brandt One of the reasons that the HGDP populations are weighted toward indigenous groups is that there was the understanding that these populations may not be long for the world in their current form. But the Taino genome reconstruction illustrates that even if populations are no longer with us…they are still within us. With…
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Are most people “behaviorally modern”?
Paintings at Lascaux, Prof saxx Behavioral modernity: Behavioral modernity is a term used in anthropology, archeology and sociology to refer to a set of traits that distinguish present day humans and their recent ancestors from both living primates and other extinct hominid lineages. It is the point at which Homo sapiens began to demonstrate a…
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Ancient Roman DNA project
Dienekes already mentioned it, but readers might be curious about the Ancient Roman DNA Project. Here are the details: I’m asking for $6,000 for this project, which will cover the cost of testing DNA from the 20 immigrants to Rome I found in my previous project. Of course, I would love to test additional individuals…
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Men on the move, part n
Ancient DNA suggests the leading role played by men in the Neolithic dissemination: The impact of the Neolithic dispersal on the western European populations is subject to continuing debate. To trace and date genetic lineages potentially brought during this transition and so understand the origin of the gene pool of current populations, we studied DNA…
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Ancient DNA in the near future
I recently inquired if anyone was sequencing Cheddar Man. In case you don’t know, this individual died ~9,000 years ago in Britain, but the remains were well preserved enough that mtDNA was retrieved from him. He was of haplogroup U5, which is still present in the local region. Cheddar Man is also particularly interesting because…
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1000 Genomes Tutorial
I don’t have time for this, but I’m sure some readers do. 1000 Genomes has put a tutorial up. Breakdown: 1. Description of the 1000 Genomes Data, Gabor Marth pdf|pptx 2. How to access the Data, Paul Flicek pdf|pptx 3. Lessons in variant calling and genotyping, Hyun Min Kang pdf|pptx 4. Structural Variants, Ryan Mills pdf|pptx 5. Imputation in…
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1000 Genomes Tutorial
I don’t have time for this, but I’m sure some readers do. 1000 Genomes has put a tutorial up. Breakdown: 1. Description of the 1000 Genomes Data, Gabor Marth pdf|pptx 2. How to access the Data, Paul Flicek pdf|pptx 3. Lessons in variant calling and genotyping, Hyun Min Kang pdf|pptx 4. Structural Variants, Ryan Mills pdf|pptx 5. Imputation in…
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Ötzi, the dead sea scrolls of genomics?
Dienekes points me to the fact that Ewen Callaway has the dirt on what’s going on with Ötzi: To get a better grip on his ancestry and predisposition to disease, Albert Zink, head of the Institute for Mummies and the Iceman in Bolzano, and his team sequenced Ötzi’s 3 billion base pair nuclear genome from…
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The Ötzi embargo
Dienekes has some harsh words for the way some science is produced, focusing on the genome of Ötzi the Iceman as a case in point: Yesterday, I twitted in exasperation that Otzi’s genome, which must have been available in at least some sort of draft form since at least the beginning of this year, has been under…
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In the year 2015….
Recently I was having a discussion with some friends about getting the full genomes of everyone in my immediate family when the price point comes down to $1,000, just as I have had my immediately family genotyped. You can find some interesting stuff just from the genotype alone, which for current affordable platforms aims for…
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Why do we still vary?
I notice that last summer Karl Smith asked “Why Are There Short People?” His logic is pretty good, except for the fact that the fitness variation seems to be much starker in males than females (there is some evidence I’ve seen that shorter women can be more fertile, though that’s balanced by the fact that…
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Ötzi tidbits
The genome of Ötzi the Iceman is floating around somewhere, but for now we only have to go on what leaks out via the media. From National Geographic, Iceman Autopsy: The genetic results add both information and intrigue. From his genes, we now know that the Iceman had brown hair and brown eyes and that…
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The genetics of hair texture: a mystery
Lauryn Hill, Image credit: Lisa Lang I received an email today from a friend about speculation on the genetics of hair texture. More specifically, curly vs. straight hair. I know that there are a few SNPs which are correlated with straight vs. curly hair (23andMe has actually been involved in this), but the architecture hasn’t…
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Decency not by law alone
Rasmus Nielsen has a long response below to the issue of the getting some sort of consent from Aboriginals in the local region in regards to a specimen from a deceased individual. He has a full entry on this at the new weblog of his research group. As an aside, let me say that it…
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Sequencing everyone in the Faroe Islands
There was some speculation last week about which nation would have everyone sequenced first. We now have a contender, the Faroe Islands, a self-governing Danish dependency (they’re not part of the E.U.) is going to try and sequence most of the population of ~50,000 over the next five years: Around 100 people who are likely…