Tag: statistics

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Dueling BRCA Databases: What About the Patient?

The news release Monday morning grabbed my attention:

“Study finds wide gap in quality of BRCA1/2 variant
classification between Myriad Genetics and a common public database.”

Myriad Genetics had been exclusively providing tests, for
$3000+ a pop for full BRCA gene sequencing, for 17 years before the Supreme
Court invalidated key gene patents back in 2013. Since the ruling a dozen or so
competitors have been offering tests for much lower prices. Meanwhile, Myriad
has amassed a far deeper database than anyone else, having been in the business
so much longer. And it’s proprietary.

CLASSIFYING GENE VARIANTS

(NHGRI)

Public databases of variants of health-related genes have
been around for years too. The best known, ClinVar, collects and curates data
from the biomedical literature, expert panels, reports at meetings, testing
laboratories, and individual researchers, without access to Myriad’s database.
ClinVar uses several standard technical criteria to classify variants as
“pathogenic,” “benign,” or “of uncertain significance.” (“Likely pathogenic”
and “likely benign” were used more in the past.)

ClinVar lists 5400 variants just for BRCA1. The criteria
come from population statistics, how a particular mutation alters the encoded
protein, effects on the phenotype (symptoms), and other information.
Bioinformatics meets biochemistry to predict susceptibility. The BRCA1 protein
acts as a hub of sorts where many other proteins that control DNA repair
gather. DNA Science discussed the genes behind breast and ovarian cancers here.

As gene sequences accumulate in the databases and troops of
geneticists and genetic counselors annotate them, the proportion of pathogenic
and benign entries will increase as that of the unsettling “variants of
uncertain significance” — VUS — will decrease.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

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Law Changes and Slippery Slopes

Apparently, there was a TV programme in Australia the other day in which a there was a discussion of assisted dying.  It got reported in The Guardian, largely on the basis that an 81-year-old audience member kept calling Margaret Somerville “darling” and then got mildly sweary.  I’ve only seen those clips from the programme that are linked in the Graun‘s report, so I’m not going to comment on the tone of the debate in particular.  Rather, I’m interested in one of the responses to the programme, from Xavier Symons, writing in The Conversation.

Symons takes the opportunity to unpick the idea of a slippery slope argument – in this case, the claim that allowing some forms of assisted dying will commit us to allowing… well, that’s open-ended, but it’s sufficient to say that it’d be terrible.  We’d want to avoid terrible things; therefore, the argument goes, we shouldn’t allow any of it.  This is well-worn stuff in the seminar room, but it’s a mode of argument that refuses to die.  Quite correctly, Symons points out that

there is a need for empirical evidence or sound inferential reasoning to support the claim that event B will necessarily (or probably) follow on from event A.  Without this evidence, the argument is invalid. I can’t just claim, for example, that the legalisation of medicinal marijuana leads to the legalisation of ice – I need to show some empirical or logical connection between the two.

So far, so standard.  (I’d say “unsound” rather than “invalid”, because the validity of an argument doesn’t depend on its evidence – or, at least, not in the same way; but that’s a small matter.) 

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

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The Problem with Binary

by Sean Philpott-Jones, Chair, Bioethics Program of Clarkson University & Icahn School of Medicine at Mount Sinai

The Problem with Binary 

Throughout his raucous 2016 campaign, President Trump repeatedly claimed that he would be an ardent defender of the lesbian, gay, bisexual and transgender (LGBT) community. During the Republican National Convention, for instance, he proclaimed that, “As your president I will do everything in my power to protect LGBTQ citizens.” Despite this statement (which stood in stark contrast to the Republican Party’s virulently anti-LGBT political platform), and diverging from the public comments and actions when he was still a private citizen, since gaining the nomination and later the presidency, Donald Trump has largely kowtowed to the more homophobic wings of his party.

Although he has yet to repeal an Obama-era order protecting LGBT federal employees from workplace discrimination, for example, he has repeatedly expressed support for the First Amendment Defense Act. Modeled on the anti-LGBT legislation passed in Indiana when Vice-President Pence was governor of the Hoosier State, that Act would allow individuals, businesses, and healthcare providers to deny services to LGBT individuals based on their religious beliefs.

More recently, in spite of prior comments that “people should use the bathroom that they feel is appropriate,” Trump rescinded existing protections for transgender students. Previously, the federal government had issued guidelines that, while not legally binding, required public schools to allow transgender students to use bathrooms that corresponded with their gender identity rather than biological sex. Under the Obama administration, the Departments of Justice and Education had taken the position that existing regulations like Title IX, the federal law that prohibits sex discrimination in schools, also applied to discrimination based on gender identity.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

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The Problem with Binary March 10, 2017 Throughout his raucous 2016 campaign, President Trum…

by Sean Philpott-Jones, Chair, Bioethics Program of Clarkson University & Icahn School of Medicine at Mount Sinai

The Problem with Binary 

Throughout his raucous 2016 campaign, President Trump repeatedly claimed that he would be an ardent defender of the lesbian, gay, bisexual and transgender (LGBT) community. During the Republican National Convention, for instance, he proclaimed that, “As your president I will do everything in my power to protect LGBTQ citizens.” Despite this statement (which stood in stark contrast to the Republican Party’s virulently anti-LGBT political platform), and diverging from the public comments and actions when he was still a private citizen, since gaining the nomination and later the presidency, Donald Trump has largely kowtowed to the more homophobic wings of his party.

Although he has yet to repeal an Obama-era order protecting LGBT federal employees from workplace discrimination, for example, he has repeatedly expressed support for the First Amendment Defense Act. Modeled on the anti-LGBT legislation passed in Indiana when Vice-President Pence was governor of the Hoosier State, that Act would allow individuals, businesses, and healthcare providers to deny services to LGBT individuals based on their religious beliefs.

More recently, in spite of prior comments that “people should use the bathroom that they feel is appropriate,” Trump rescinded existing protections for transgender students. Previously, the federal government had issued guidelines that, while not legally binding, required public schools to allow transgender students to use bathrooms that corresponded with their gender identity rather than biological sex. Under the Obama administration, the Departments of Justice and Education had taken the position that existing regulations like Title IX, the federal law that prohibits sex discrimination in schools, also applied to discrimination based on gender identity.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

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How to Get Patients to Take More Control of Their Medical Decisions

March 9, 2017

(The Wall Street Journal) – Now researchers and health-care providers say they’re at last figuring out how to untie this doctor-knows-best knot and get patients to take charge of their own health. They’re designing decision aids, for instance, that walk patients through different options, translating complicated medical jargon and statistics about risk into simple language and visual aids. They’re offering patients full access to their own medical records, including their doctor’s notes about them. And they’re training doctors to help guide patients to make informed choices.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

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Medical Futility Blog Surpasses 2.5 Million Pageviews

Google provides the following statistics on this blog.  This does not include all those who read this blog’s content on WestlawNext or Bioethics.net.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

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Deadly U.S. Heroin Overdoses Quadrupled in Five Years

February 24, 2017

(Scientific American) – The number of deadly heroin overdoses in the United States more than quadrupled from 2010 to 2015, a federal agency said on Friday, as the price of the drug dropped and its potency increased. There were 12,989 overdose deaths involving heroin in 2015, according to the National Center for Health Statistics, compared with 3,036 such fatalities five years earlier. In 2010, heroin was involved in 8 percent of U.S. drug overdose deaths, a study by the Atlanta-based center said. By 2015, that proportion had jumped to 25 percent.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

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Controversial solution to self-harm

A child who self-harms must be one of the most agonising experiences a parent can have. But it is relatively common. A study in The Lancet a few years ago found that about 1 in 12 teenagers, mostly girls, engaged in self-harming behaviour, with the most common methods cutting or burning. Most of them stop as adults, but some continue. It is a phenomenon which still seems to baffle the medical profession, despite the abundance of statistics.

In this issue of BioEdge, we report on an interesting response to self-harm, at least for some patients – educate them to minimise the harm, but supply them with razors. Given that harm minimisation is a popular public policy approach in other areas, like drugs, this makes some sense. But I think that most people will regard it as quite confronting. What do you think?  

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

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Human-Pig Chimeras: The Potential and Concerns Of Hybrid Human-Animal Organs

One of the great advances in modern medicine has been the success of organ transplantation. Whilst complications still arise from its use, the refinement of drugs designed to reduce organ rejection alongside other improvements, mean that the procedure is often lifesaving.

As is frequently the case however, there is a caveat to this “wonder-cure”, namely, that far more people require organs than there are organs available. This global shortage has given rise to a host of complex ethical challenges. Several of these issues have already been explored here, including the implementation of ‘opt-in’ organ donation systems and the appropriateness of receiving organs on the basis of ability to pay1, 2, 3.

The development of chimeric human-pig embryos announced in the journal Cell last week may therefore be hailed as the much-needed answer to this problem of organ shortages. With over 120,000 people on the national transplant list in the US alone and 22 people on that list dying each day, any opportunity to increase the numbers of transplantable organs has an obvious appeal4. However, this development is far from a perfect solution.

Chimeric embryos are early life forms that are composed from 2 or more different sets of genetic material. In this case therefore, one set of genetic material is from a pig and the second from a human. These chimeras were initially made in the laboratory, before being transplanted into surrogate sows. In the study, only a fraction of the total embryos transplanted (just over 10%) showed successful development, surviving for 3-4 weeks5.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

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Snapshots of Life: Portrait of a Bacterial Biofilm

Credit: Scott Chimileski and Roberto Kolter, Harvard Medical School, Boston

In nature, there is strength in numbers. Sometimes, those numbers also have their own unique beauty. That’s the story behind this image showing an intricate colony of millions of the single-celled bacterium Pseudomonas aeruginosa, a common culprit in the more than 700,000 hospital-acquired infections estimated to occur annually in the United States. [1]. The bacteria have self-organized into a sticky, mat-like colony called a biofilm, which allows them to cooperate with each other, adapt to changes in their environment, and ensure their survival.

In this image, the Pseudomonas biofilm has grown in a laboratory dish to about the size of a dime. Together, the millions of independent bacterial cells have created a tough extracellular matrix of secreted proteins, polysaccharide sugars, and even DNA that holds the biofilm together, stained in red. The darkened areas at the center come from the bacteria’s natural pigments.

Scott Chimileski, a postdoc in Roberto Kolter’s lab at Harvard Medical School, Boston, created this image of a Pseudomonas biofilm—a winner in the Federation of American Societies for Experimental Biology’s 2016 BioArt competition—using a standard, professional DSLR camera. He used a macro lens to capture many close-up images of the bacterial colony that he later stitched together on a computer into one ultra-high resolution image. As a result, he’s able to zoom in on the image to examine fine details of the biofilm structure. He can also enlarge the image to print the bacterial colony at 100 times its actual size.

Chimileski specializes in finding new ways to image microbes and their macroscopic three-dimensional structures.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.