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Genetic Linkage

DNA Day Has a New Meaning For Me This Year: I’m an NPE

"Not parent expected" – NPE – is a surprise that thousands of us have gotten as a result of consumer ancestry DNA testing. We discover that we are the offspring of a sperm donor, or sexual violence, or a long-ago fuzzy night at a party, a brief interval between partners, an affair, or a single experimental partner-swap long forgotten.

 

We find out that we aren't who we thought we were, at least in our genes. I know I'm the same person, of course, but something has changed.

 

DNA Day to me this year means that I share approximately 25% of the DNA signposts used to assess ancestry – some 700,000 or so data points that mark genetic diversity – with six half-siblings, and possibly more.

 

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

 

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Revived pig brains may unleash uncomfortable questions for how we define death

When Yale researchers announced that they'd kept pig brains quasi-functional for several hours after they'd been separated from the bodies, writers wrote, bioethicists weighed in on the fine line between life and death, and animal rights activists objected.

 

But I thought about the pilot episode of Star Trek.

 

Pigs have long been models in cardiovascular disease research, because their hearts and blood vessels are about the same size as ours. My favorite experimental pig, though, lent her liver.

 

Sweetie Pie had been genetically modified so that her cells were festooned with human proteins, preventing organ rejection. In 1997, when she was 15 weeks old, her detached but functioning liver kept 19-year-old Robert Pennington, suffering from acute liver failure and desperately needing a transplant, alive for 6.5 hours. The young man's blood was cleansed outside of his body through Sweetie Pie's living liver until a human one became available.

 

tz pigPigs mixing with humanity figure into sci-fi and even comedy. The 1960 Twilight Zone episode "Eye of the Beholder" visited a society in which people have pig faces, and the few with human faces are condemned to live out their lives out of sight in their own villages. And on Seinfeld, Kramer reported a pig man on the loose on the top floor of a hospital.

 

Introducing BrainEx

The title of the Nature paper says it all: "Restoration of brain circulation and cellular functions hours post-mortem."

 

 

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

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An Ultrarare Liver Disease, PFIC2: Trinity’s Story

Ultrarare genetic diseases often appear with a series of symptoms that might seem unconnected.

 

Trinity's troubles began right away: GERD (gastroesophageal reflux disease) so severe that she would frequently stop breathing. The first sign that something complicated was going on began at five months. "She started having bruises all over her body. These later grew and then within a day or two, turned into huge hematomas," Brooke recalled. The baby could barely sleep or eat and Brooke and her mother took shifts in providing the round-the-clock care.

 

Then the pruritis started, an intense, unremitting itching emanating from deep within the skin. Brooke had to dress the child in special mittened onesies to keep her from tearing her skin off. In adults, pruritus leads to thoughts of suicide.

 

Fortunately, diagnosis was relatively fast for the rare disease world. Trinity's local pediatrician sent her to the emergency room at Anne Arundel Medical Center, where they found highly abnormal clotting levels, indicating a liver problem. Then she was referred to Johns Hopkins Medical Center and finally to Cincinnati Children's Hospital. Liver function tests, scans, liver biopsy, and extensive genetic testing, plus consideration of the little girl's symptoms, led to her diagnosis at 7 months old: progressive familial intrahepatic cholestasis type 2 (PFIC2).

 

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

 

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NASA twins study highlights key risks for long-term space travel: Cosmic rays and microgravity

When NASA reported preliminary observations about the famous "twin astronaut" study a year ago, the media rushed in, reporting the effort with mind-boggling inaccuracy. The agency was quick to correct the confusion of gene mutations with changes in gene expression, promising a full paper once the findings were more fully scrutinized. Long-awaited, "The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight," appears in the April 11 issue of Science.

 

To recap, Scott Kelly (Space Twin) spent a year aboard the International Space Station (ISS) while his identical twin Mark (Earth Twin) stayed in Arizona. Both men are 50 years old. Mark, also an astronaut, is married to Gabrielle Giffords and is running for the Senate in 2020.

 

A data deluge

 

With last year's overreaction, it's understandable that announcement of the full paper to reporters ahead of publication set the stage for a news blitz. The four press releases, images and videos, a list of quotes from NASA scientists, phone news conferences from Science and NASA, a summary, web materials, and a short feature article in Science sent my hype-o-meter into overdrive.

 

Much of the news isn't news – Genetic Literacy Project covered it a year ago. Plus, many of the monitored biological functions didn't change much in space or did so only transiently.

 

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

 

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Taking a bad trip and why marijuana edibles may be a prescription for psychosis

As drugstore chains embrace products with traces of CBD, two recent reports in prominent medical journals point out the dangers of the other familiar component of cannabis, THC.

 

An article in Lancet Psychiatry strengthens the link of THC to psychosis, and one in Annals of Internal Medicine chronicles people ending up in the emergency departments of hospitals after indulging in edibles. The news media picked up the edible-ED story, the psychosis one not so much.

 

From 2012 through 2016, the University of Colorado Hospital saw a more than 3-fold increase in cannabis-associated ED visits. Edibles, which became available there in 2014, were disproportionately represented in those visits – 10.7 percent due to edibles, despite making up only 0.32 percent of total cannabis sales.

 

I can relate.

 

A short, strange trip

 

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

 

 

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Genetic uncertainty: When research participants should be told that their test results have changed

"Do you mind if we take one more sample?" asked the endocrinologist who had already stuck six needles into the bulge in my neck that would turn out to be thyroid cancer. "It's for a research study."

 

"On what?"

 

"Something called p53."

 

That's a tumor suppressor, a gene that lies at the crux of cancers triggered by environmental factors, like the 5 years of unprotected dental x-rays I'd had as a kid.

 

"I know what that is and hope I don't have a mutation. When will I get the results?"

 

"I'm afraid you won't. That's part of the protocol." My sample would be de-identified.

 

I forgot about it. Years later, I had genetic testing again, this time for breast cancer, from a blood sample sent to Invitae, a clinical testing lab. They applied their 80-gene cancer panel and threw in probes for another two dozen genes they were developing.

 

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

 

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Milkweed Bug Genome Revealed

I'll admit that I have long admired the beauty of the large milkweed bug Oncopeltus fasciatus, without knowing anything about it. So I was pleased to read of the recent publication of its genome sequence, an effort undertaken by 83 researchers working as 27 teams in 10 nations. The findings are reported in Genome Biology.

 

Most of the 100+ insect species that have had their genomes sequenced are homometabolous, which means that they develop through several stages of larvae, metamorphose, and then burst from their cocoons looking completely different. (See "The Making of a Mutant" for a scintillating view of fruit fly larvae living in goop in a milk bottle.) Flies, beetles, wasps, and butterflies are among the homometabolous.

 

In contrast, milkweed bugs are hemimetabolous. The species of this group are less well represented among the sequenced, although they are more numerous. The juvenile stages of milkweed bugs are tiny, flightless versions of the adults, called nymphs, that have more orange.

 

The hemimetabolous insects have trademark mouthparts that pierce and suck, and include agricultural pests and vectors of human disease, like the kissing bugs that deliver Trypanosoma cruzi, the cause of Chagas' disease. A more familiar hemimetabolous insect is the bed bug Cimex lectularius.

 

The milkweed bug, so-named because it eats the bitter seeds of the milkweed plant Asclepias syriaca, joins many other insects and their arthropod cousins in having their genetic selves laid bare as part of the i5k project. The international consortium is sequencing the genomes of 5,000 arthropod species.

 

So far partial or complete genomes have been unveiled for, in alphabetical order, ants, aphids, bedbugs, bees, beetles, borers, cockroaches, crabs, crayfish, fleas, flies, lice, locusts, mealybugs, midges, mites, mosquitoes, pillbugs, psyllids, scorpions, shrimp, spiders, stinkbugs, ticks, wasps, weevils, worms, the delightful-sounding snowberry maggot and meadow spittlebug, and a pretty butterfly called a Glanville fritillary.

 

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

 

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Cataracts and Amyloid Beta: Early Marker and New Drug Target?

 

I've just had cataract surgeries, so I wasn't thrilled to find a new report in the Proceedings of the National Academy of Sciences comparing the protein glitch behind them to the one behind Alzheimer's. Fortunately the similarity is only in how the proteins fold.

 

The amyloid beta buildup of cataracts could be an early marker that might eventually allow drug treatment to replace surgery. Too late for me, but that could be great news for the more than 18 million people worldwide  blinded by cataracts because they can't get surgery.

 

Cataracts develop as proteins coalesce in the lens, triggering spreading of patches of blurriness. They are the leading cause of blindness globally and affect half of people over age 50. My fellow PLOS blogger Hilda Bastian recently recounted the compelling story of the origin of cataract surgery.

 

A human lens is fascinating, in terms of biochemistry, cell biology, and evolution.

 

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

 

 

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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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