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Genetic Linkage

The Wuhan Coronavirus Inspires a Look Back at the Discovery of Viruses

I'm astonished at the speed with which geneticists and epidemiologists are zeroing in on the Wuhan coronavirus.


Nomenclature is still up in the air. The first name, "2019-nCoV" for "novel coronavirus first seen in 2019," is descriptive but not easy to remember. "Wu Flu" isn't correct – it's not a flu virus, nor is "Wuhan SARS" quite right because the new pathogen's genome isn't exactly like that of SARS.


I'll call it the Wuhan coronavirus until the World Health Organization decides on a name. WHO avoids places in disease names to avoid stigma, although I don't see the Rocky  Mountains suffering from lack of visitors due to the spotted fever that takes it's name (which isn't viral, but still).


Two Weeks to a Genome Sequence


Awareness of the new infectious disease began as 2019 drew to a close.


"On December 30th, China reported an outbreak of respiratory disease in Wuhan City, a major transportation hub about 700 miles south of Beijing with a population of more than 11 million people," Nancy Messonnier, director of CDC's National Center for Immunization and Respiratory Diseases, said at a press briefing January 17. A chart from the Wuhan Municipal Health Commission that shows the rapid uptick in cases means that you don't have to have seen the final scene in Rise of the Planet of the Apes, showing a virus ricocheting around the globe, to know where things are headed.


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

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How fertile are you? ‘Ovarian reserve’ DTC tests that count your eggs offer mixture of control and misinformation

The direct to consumer testing market comes in many flavors these days, with companies like 23andMe dominating headlines with their genetic/ancestry tests targeting folks eager to learn more about themselves. Also joining the fray are tests designed to help women — in theory, at least — assess fertility by counting the number of eggs left in their ovaries.


Sounds like a great idea. Just one problem: egg counts may not be such a great indicator of fertility, according to the American College of Obstetricians and Gynecologists.


Still, that doesn't mean these tests have no value. A new study suggests they can empower women. And that's especially true for those who do not fit into the binary gender categories that health insurers may require for covering clinical versions of the test that cost ten times as much.



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

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Will 2020 see the debut of promising gene therapy for hemophilia A? It’s up to the FDA.

The clotting disorder hemophilia A may become the third gene therapy that the US Food and Drug Administration approves, joining treatments for a form of retinal blindness in 2017, and spinal muscular atrophy in 2019.


Biomarin Pharmaceutical Inc. has submitted a biologics license application to FDA and documentation of clinical trial results to the European Medicines Agency, with reviews slated to begin early this year at both organizations.


An article in the January 2 New England Journal of Medicine from a UK research team presents the findings of a phase 3 analysis of continuing success of a phase 1/2 trial (instead of a new phase 3 trial). The hemophilia gene therapy – called valoctocogene roxaparvovec for now – can mean a one-time infusion that replaces the more than 100-150 infusions of clotting factor a patient takes each year, and can also alleviate the painful joint bleeding that is the hallmark of the disease.


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

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Novels ‘All About Evie’ and ‘The Family Upstairs’ illustrate how DNA tests can reveal ‘dark secrets’, from rape to unknown siblings

I recently read two works of fiction, "All About Evie" and "The Family Upstairs," that touch on the issue of defining family. The plots inadvertently echo current concerns over the possible fallout from unexpected consumer DNA ancestry testing results.


Each book is a multi-generational saga blooming with secrets and surprises. But one novel uses DNA testing to reveal relationships and the other doesn't.


My unplanned reading of one after the other served as a metaphor of sorts for the fallout from receiving a DNA surprise. The ending of the book based on the DNA test was abrupt and seemed contrived, much as discovering an insta-family can be. The ending of the book that slowly uncovered secrets as relatives recognized each other and connected was satisfying and rang true.


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

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How Breast Cancer Reunited Six High School Friends

Four of the six of us from my high school inner circle have had breast cancer over the past two years. And that has me wondering.


Did a shared environmental exposure, stamped onto our shared Ashkenazi Jewish heritage, during that critical period in our lives set the stage for cancer decades later? The timing and cancer subtypes suggest to me, the biologist in the group, that the answer could be yes. But I'm flummoxed.


An Illustrious High School


The long walk to James Madison High School began every weekday morning with me. I'd pick up my neighbor Amy, then Randy two blocks over, then across the street and a few steps to Wendy. We'd turn right onto Quentin Road to meet Tobie, then dip into East 18th Street, to get Bess in her rambling Victorian that was to the rest of us, from smaller homes and apartments, a mansion. It was the epicenter of the best parties.


We began tenth grade at Madison shortly after Woodstock and graduated as the class of 1972. Famous alumni include Carole King, Bernie Sanders, Chuck Schumer, Ruth Bader Ginsburg, Judge Judy Scheindlin, Martin Landau, and Chris Rock (See "How One 'Ordinary' Brooklyn High School Produced Six Nobel Laureates, a Supreme Court Justice, and Three Senators." )


To read more, go to DNA Science, where this post first appeared. 

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Will New Knowledge of Gender Identity Genomics Counter Discrimination?

If legislation being developed by State Rep. Ginny Ehrhart, (R-Powder Springs, Georgia) goes forward, a physician who provides surgery or hormones to assist a transgender individual age 18 or under in transitioning will be committing a felony. This treatment addresses gender dysphoria, which is the significant distress or inability to function when the gender assigned at birth (natal male or female) doesn't match the gender that a person feels.


Representative Ehrhart's press release introducing the "Vulnerable Child Protection Act" emphasizes that the proposed measures do not apply to adults. Her words are harsh: "This is about children who are being abused by adults. The sterilization and castration of children has no place in a civilized society." She got the idea, according to media reports, from the case in Texas of a 7-year-old whose mother supports the child's claiming to be female and the father opposes it. Sen. Ted Cruz called the child "a pawn in a left-wing political agenda." Because gender dysphoria isn't even diagnosed until puberty, the mutilation scenario seems an exaggeration.


The practice that Rep. Ehrhart refers to is more eloquently and accurately known as "gender affirming therapy," and includes hormone suppression that is already used to treat other conditions. At the Texas child's age, it might just mean allowing her to wear what she wants as a team of medical specialists evaluates the case. Several health organizations have published guidelines on therapy; here's one.

If the language in the press release is an indication of the coming legislation, then the rhetoric implies that gender dysphoria and even transgender identity do not exist.


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

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‘CRISPR this, CRISPR that’: Is our fascination with the popular gene-editing tool distracting us from the potential of gene-silencing RNAi technology?

CRISPR, it seems, is everywhere.


Google "crisper" and "Did you mean crispr?" shoots back.


The film Rampage brought a giant, CRISPRed wolf, ape and gator. In real life a year ago, renegade researcher He Jiankui announced CRISPRing human twins at fertilization and then vanished, an unpublished manuscript just now surfacing at MIT Tech Review. He's now in jail.


CRISPR is the subject of Netflix's Unnatural Selection and the upcoming documentary Human Nature.


CRISPR this, CRISPR that.


But drugs based on CRISPR are just entering clinical trials. Nevertheless, NPR breathlessly announces its "exclusive access" to the story of Victoria Gray, a woman receiving cells CRISPRed outside her body and then infused to treat her sickle cell disease. One patient, at the start of a trial.


Yet on November 20, the FDA approved the second drug based on RNA interference (RNAi) technology. I didn't see much mainstream media coverage.


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

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FDA Approvals in 2019 Reflect Eclectic Ways to Treat Genetic Disease

It was a good year for new treatments for genetic diseases! Of the 44 FDA approvals of new drugs, 8 were for 6 single-gene diseases: DMD, beta thalassemia, cystic fibrosis, a form of amyloidosis, and two each for sickle cell disease and porphyria.


The eight approvals showcase the diverse therapeutic strategies that are finally leaping from clinical trial to clinical reality. That's important. DNA, RNA, and protein-based treatments face an especially high bar because of the perceived permanence of a correction at these levels  of genetic information.


Slowing of disease progression or improvement in one or two symptoms are signs of success, but it might take time for some molecular corrections to translate into fading symptoms. That's why the multi-pronged strategies are critical.


If a gene therapy isn't leading to rapid or obvious improvement in a child with a brain or muscle disease, then perhaps RNAi, antisense therapy, or enzyme replacement therapy will. Better yet, instead of testing the technologies in tandem, do it in parallel.


I hope that this past year's progress isn't lost in the hype over gene editing in general, and CRISPR in particular. The media sometimes paints an unrealistic portrait of looming miracle cures and breakthroughs, which I analyzed last week here. New medical treatments are based on science, and that takes time – typically, three decades.


Here's a look at a handful of new treatments for genetic diseases approved in 2019, and how they work.


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

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5,700-Year-Old Lola, Her Genome Sequenced from Gum, Joins Other Named Forebears

About 5,700 years ago in southern Denmark, a woman enjoyed a meal of hazelnuts and duck, then chewed gum made from the boiled, tar-like gunk of birch bark. Pieces of DNA extracted from the ancient gum and overlapped to reconstruct her genome reveal that she had dark brown hair, dark skin, and blue eyes.


Her discoverers named her Lola, perhaps in honor of the eponymous Kinks song: "I asked her her name and in a dark brown voice she said, 'Lola.'"


Researchers from the University of Denmark and elsewhere published the findings in Nature Communications


Lola lived on the island of Lolland, east of Rødbyhavn in southern Denmark, where today an 11-mile-long tunnel is being dug to link to the German island of Fehrmarn. Archaeologists from the Museum Lolland-Falster are at the site, the largest from the Stone Age in Denmark. It's called Syltholm, and Lola, technically, the "syltholm individual."


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

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