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Genetic Linkage

A New Biological Aging Clock: Ribosomal DNA

Chronological aging is easy to track – birthdays. Biological aging can be obvious too – graying hair, sagging skin, and other inexorable signs of impending decrepitude. But measuring biological aging isn't as easy as noting the passage of time.

 

The best-studied measure of biological age is the shrinking of chromosome tips, or telomeres, that do so with each division of most types of cells. As soon as I posted "Telomere Testing: Science or Snake Oil?" here at DNA Science, my Facebook feed filled with ads from companies like this one, offering to enlighten me on the status of my chromosome tips.

 

The new biological ticker, the rDNA clock, makes its debut in the latest issue of Genome Research. Meng Wang and Bernardo Lemos, from the Harvard T.H. Chan School of Public Health, term rDNA a "universally applicable marker of aging." Their article also is a brilliant example of how science is done, with a series of hypotheses and experiments, countering the oft-bellowed mantra that one can "believe in" climate change, evolution, or cell structure.

 

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

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Are Eurocentric Genetic Databases Hampering Health Care?

A commentary published today in the journal Cell offers evidence of a stunning imbalance in the population groups that participate in genetic and genomic research, which can underlie some health care inequities. A glance at the pie chart below, which represents many genome-wide association studies (GWAS), reveals a telling tipping in favor of participants of European ancestry – 78 percent. Asians account for just 10 percent, and Africans 2 percent.

 

A GWAS is a sweeping look at single sites (SNPs) among a genome's 3.2 billion bases that differ among people. It's used to trace traits and conditions caused by multiple genes plus environmental influences. Algorithms deduce the associations from SNP data from people who share ancestry as well as a trait or disease of interest. "Ancestry" means shared heritage, manifest as hunks of genomes, and not what a sociologist might call race based on appearance.

 

The Eurocentric nature of the pretty pie charts and polygons of consumer ancestry tests of course reflect the market. The skewed representation in company databases can lead to surprise, confusion, and disappointment, when a population simply isn't yet on the radar.

 

In clinical studies, the stakes are higher. The overrepresentation of European whites can lead to sub-optimal diagnoses and therapeutic choices for people in other population groups. That's what prompted the commentary in Cell, "The Missing Diversity in Human Genetic Studies," from Giorgio Sirugo and Sarah Tishkoff from the University of Pennsylvania and Scott Williams of Case Western Reserve University. Citing examples from the long-studied single-gene conditions and others, they compellingly convey the importance of considering genetic ancestry in health care.

 

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

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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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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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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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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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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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