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Genetic Linkage

WTF? Did the rise of agriculture—and soft foods—give us the ability to drop F bombs?

We don't usually pay attention to how we position our teeth when biting into a tough steak or ripping soft kernels off a cob of corn. But a team of linguists has just reported in Science on their "biomechanical simulations of different human orofacial structures" to test the hypothesis that changes in dentition that accompanied a switch from a hunter-gatherer lifestyle to an agricultural one may have, perhaps accidentally, brought about the ability to pronounce "f" and "v" sounds.


These utterances that require the upper teeth to extend over the lower lip are called "labiodental sounds." They're harder to make than just extending the upper lip over the lower to produce "m," "w," and "p" sounds, which are common in many languages.


To continue reading go to Genetic Literacy Project, where this post first appeared.




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How DNA Ancestry Testing is Like the Wheel of Fortune: Filling in the Blanks

I'm a curious hybrid, a geneticist and an "NPE" – "not parent expected" – individual. My few posts about it, such as here and here, were from January, when I thought I had only one half-sibling. The discovery of others, some of whom know they were donor-conceived (DC), more or less confirms half of my origin.


So I wondered, on what percentage of a human genome's 3.2 billion DNA bases do the consumer DNA ancestry companies base these deductions that can shatter lives?


Do some tube-spitters and cheek-swabbers assume entire genomes are compared? No, not for $100, just yet. Others might not know what SNPs are, the  single-DNA-base markers that align in haplotypes on chromosomes and are used to match people, the algorithms trained on known relationships. With millions of people taking ancestry tests, the associations used in the matches are quite robust.


But I thought I'd do a small calculation to clarify what's probed when you plop your genetic essence into the mail, and how it represents an individual.



To continue reading go to my DNA Science blog at Public Library of Science.




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Roan’s Story and Fragile X Syndrome

For 2019's Rare Disease Day, DNA Science honors those who have fragile X syndrome (FXS). It isn't among the rarest of the rare, yet when health care providers can't assemble the diagnostic puzzle pieces that parents are practically yelling at them, the statistics don't matter and the diagnostic odyssey lengthens. Because fragile X is an "expanding repeat" disorder, it lies beneath the radar of standard chromosome and single-gene tests.


The Orphan Drug Act of 1983 in the US defined a rare disease as affecting fewer than 200,000 people. "Orphan" initially referred to pharma's disinterest in developing drugs with minuscule markets, but was deemed non-PC and became "rare" somewhere along the way. In the European Union, the definition is fewer than 1 in 2,000 people, which is pretty close to the US number. The disinterest in seeking treatments for ultrarare conditions has evolved into doing so, but with sky-high price tags.


A few weeks ago I heard from Desiree Moffitt, who uses my human genetics textbook to teach an online course. She kindly offered to share her family's story about life with a child who has fragile X syndrome. "Usually the face of disability is a very happy, quirky family. While we are happy and also quirky, our story isn't as fun," she emailed me. First, some background on fragile X.


To continue reading go to my DNA Science blog at PLOS, where this post first appeared.


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Newborns and Genome Sequencing: Do We Sacrifice Privacy in the Name of Health?

The day is coming when every newborn will have her or his genome sequenced, providing a personal health database for life. But will this ability to stay ahead of sickness compromise genetic privacy?


Initial findings of the ongoing BabySeq pilot project reported in January 2019 in The American Journal of Human Genetics demonstrate the power of genomics in predicting and preventing illness.


The National Institutes of Health unveiled BabySeq in 2013 with a news release, "NIH Seeks Proposals to Study Genomic Sequencing in Newborn Period." Using "genomic" instead of "genome" allows wiggle room to count kids who've had only their exomes sequenced, the 2 percent or so of the genome that encodes proteins – the parts most often implicated in disease. (The consumer DNA testing companies use far less information, typically a smattering of 750,000 or so SNP markers across the genome.)


The BabySeq "initiative will help us better understand how we can appropriately use this information to improve health and prevent disease in infants and children," said Eric Green, director of the National Human Genome Research Institute at the beginning.


The project is off to a great start. But if history provides a lesson, routine newborn genomic sequencing won't come without a fight, or at least objections.


To continue reading go to Genetic Literacy Project, where this post first appeared.

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People need a better understanding of how CRISPR works, researchers say



Google "CRISPR" and headlines touting "designer babies," "human rights," and "bioethics" are more likely to come up than descriptions of how researchers are actually using the powerful new technology.


Initial public outcry over a novel medical technology isn't anything new: vaccines, transfusions, transplants, recombinant DNA, in vitro fertilization, preimplantation genetic diagnosis, GMOs, gene therapy – the list is long.


But genome editing, using tools such as CRISPR, seems to have struck a public nerve in a more profound way, largely because of the reported rush to tinkering with human fertilized ova, fertilized ova, an intervention that would alter the genomes of future generations.


But what does the public really understand about "clustered regularly interspaced short palindromic repeats," aka CRISPR? It's fairly complicated to follow the details – the choreography of DNA, RNA and proteins; nuances of repeated and unique DNA sequences; details of recombination and DNA repair. But a PhD certainly isn't necessary to ponder the consequences of the ability to modify the human germline – the DNA that's passed on to future generations.


A carefully designed and tested questionnaire


In a paper in the January 2019 issue of Human Gene Therapy, Alex Hewitt, of the Menzies Institute for Medical Research at the University of Tasmania, a professor of ophthalmology who also has a PhD, and colleagues probed the reasons behind public perception of human gene editing


To continue reading, go to Genetic Literacy Project, where this post first appeared.





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Baboon Genomes Offer Clues to the Past and Future of Humanity

"Once upon a time, in a cave in the Altai Mountains of southern Siberia, different types of ancient peoples were having sex," I wrote last year in "The Cave Where It Happened: the Daughter of a Neanderthal Mom and a Denisovan Dad."


That long-ago admixture, plus other episodes, is why some of us have echoes of Neanderthal and Denisovan genomes in our DNA today. It's why some people learn from consumer genetic testing that 4% of their ancestors were Neanderthal. (Not the oft-claimed 3 or 4% of a genome, given that we share 98% of our genomes with chimpanzees.)


A new paper in Science Advances from the Baboon Genome Analysis Consortium provides a compelling possible view of our own prehistory, exploring genetic relationships among the six living species of genus Papio, the baboon. The animals maintain the traits that we say make them distinct species, differing in shape, size, and behavior, yet when members of different species meet, in geographical "hybrid zones," sometimes they indeed swap genes.


Have sex, that is.


To continue reading go to DNA Science, my weekly blog for Public Library of Science, where this post first appeared.


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Measles and an Outbreak of Science Illiteracy

On January 22, the World Health Organization declared anti-vaxxers a "Top Threat to Global Health in 2019." The agency specified "vaccine hesitancy" as the "reluctance or refusal to vaccinate despite the availability." It's the first time that vaccines have made the agency's list of the top ten biggest threats to global health.


Might it be time for President Trump to stop tweeting about the long-defunct link between vaccines and autism?


An Almost-Vanquished Childhood Disease


I had the measles when I was four, with its characteristic fever and spots, for an entire month. My sister got a vaccine. She shrieked at the two shots, but she became a teacher so I think in retrospect she'd agree it was worth it.


Before the measles vaccine became available in 1963, epidemics in the US cycled every 2 or 3 years, with 3 to 4 million cases a year, and on average 450 deaths. Before that time, half or more of an elementary school classroom could be vacant as the highly contagious disease swept through. Nearly everyone had had measles by age 15.


Measles was eliminated from the U.S. in 2000. But now it's back. This week the CDC reports outbreaks in 10 states, with 101 cases already for 2019. And it's only February.


To continue reading go to DNA Science, my weekly blog at Public Library of Science, where this post first appeared.

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300th Post at DNA Science Today

This is my 300th blog post for DNA Science. I'm so grateful to Public Library of Science for enabling me to comment so freely on all matters of genetics and genomics.


This week I look back on the crazy diversity of topics over the past year or so, and end with the posts that garnered the most attention, both good and bad. Two posts actually led to death threats.


I began DNA Science in September 2012, soon after my book The Forever Fix: Gene Therapy and the Boy who Saved It, was published. Luxturna, the blindness gene therapy that the book was about, received FDA approval at the end of 2017. And so the tag cloud focuses on gene therapy and diseases. But there's so much more, including my recent fascination with genetic genealogy, upon discovering half a dozen half-siblings.


The rest of the post links to the most popular and most controversial entries over the past 3 years. To continue reading go to DNA Science.




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A New Memoir about Donor Conception Confronts Genetic Determinism

In her just-released memoir "Inheritance: A Memoir of Genealogy, Paternity, and Love," Dani Shapiro tells of discovering that she was donor-conceived. The subtext of her compelling story is to confront genetic determinism: the idea that we are our genes.


Dani found her biological father (BF) just 36 hours after receiving surprising results from consumer DNA testing. My story, still unfolding, is much more typical, as I wrote last week.


In a few ways Dani's experience was opposite mine, although our journeys both began with Dani's trajectory, somewhat atypical, was to find first that her half-sister wasn't her half-sister; that she had a new first cousin who would turn out to provide a crucial clue; and that she was only half Ashkenazi Jewish.


(This post became outdated days after I wrote it, when another half-sister contacted me. There are, at last count, 5 or 6 of us!)


To continue reading go to DNA Science, where this post first appeared.


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I’m a Geneticist. A DNA Test Uncovered a Half-sister and Sparked Painful Questions

In her new book, "Inheritance: A Memoir of Genealogy, Paternity, and Love," Genealogy, Paternity, and Love," author Dani Shapiro is speaking for tens of thousands of us who are discovering that we are "NPE." Not Parent Expected.


Dani learned that the man who raised her and who she thought was her father was not so, biologically speaking, thanks to a DNA ancestry test.


My own discovery is so overwhelming that I can't talk about it much, even though my new half-sister has possibly saved my life by adding to my known family's cancer history, affecting a recent medical decision. So thank you Dani. Here's a short version of my story, as many of us face the deluge of new cousins coming in from the holiday wave of DNA tests.


Initially ignored


The first email came September 8, 2018:


"AncestryDNA says we're close family, maybe first cousins. My maiden name is Penny Krause. Sound familiar? I grew up in Brooklyn."



To continue reading go to Genetic Literacy Project, where this post first appeared.



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