23Mar / 2024

More genomes, more variation

The "All of Us Research Program" is an American effort to sequence one million genomes. The stated goal is to study human genetic variants and link them to genetic diseases. The study is complimentary to similar studies in Great Britain, Iceland, and Japan but the American team hopes to include more diversity in their study by recruiting people from different ethnic backgrounds.

All of Us published the results from almost 250,000 genome sequences in a recent issue of Nature (All of Us Research Program Investigators, 2024). They found one billion variants of which 275 million had not been seen before.

Recall that the UK study (UK Biobank) emphasized the importance of variation in determining whether a given region of DNA was functional or not. They noted that regions that were constrained (i.e. fewer variants) were likely under purifying selection whereas regions that accumulated variants were likely junk [Identifying functional DNA (and junk) by purifying selection]. Their results indicated that only about 10% of the genome was constrained and that's consistent with the view that 90% of our genome is junk. The American study did not address this issue so we don't know how it related to the junk DNA controversy.

Note that if 90% of our genome is junk then that represents 2.8 billion base pairs and the potential for more than 8 billion variants in the human population.¹ Some of these will be quite frequent in different groups just by chance but most of them will be quite rare. We'll have to wait and see how this all pans out when more genomes are sequenced. The idea of increasing the detection of unusual variants by sequencing more diverse populations is a good one but the real key is just more genome sequences.

One of the things you can do with this data is to cluster the variants according to the self-identified ethnic group of the participants and All of Us didn't hesitate to do this. They even identified the clusters as races, proving once again that there are clear genetic diffences between these groups, just as you would expect. Given the sensitive nature of this fact, you would also expect a lot of criticism on the internet and that's what happened.

1. I'm defining a "variant" as a difference from the reference genome sequence. I'm aware of the terminology issue but it's not important here. There will also be a large number of variants in the functional regions.
All of Us Research Program Investigators (2024) Genomic data in the All of Us Research Program. Nature 627:340. [doi: 10.1038/s41586-023-06957-x].

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18Oct / 2022

#PrepYourHealth for Power Outages

A young woman and boy make hand shadow puppets using a flashlight against a white wall.

October is Energy Awareness Month

Power outages (i.e., when the electrical power goes out unexpectedly) and precautionary power shutoffs are happening more often because of and to prevent emergencies. These emergencies include disasters, such as hurricanes and wildfires.

The U.S. Energy Information Administration (EIA) says, on average, U.S. electricity customers experienced just over 8 hours of electric power interruptions in 2020. That was the most since EIA began collecting electricity reliability data in 2013.(1)

The EIA further reported that customers in Alabama, Iowa, Connecticut, Oklahoma, and Louisiana experienced the most time with interrupted power in 2020. Severe weather was a factor in all these states.

Alabama experienced several hurricanes, including a direct hit from Hurricane Sally.
Tropical Storm Isaias left about 750,000 electricity customers in Connecticut without power. Some didn’t have power for over a week.
A derecho affected Iowa and other parts of the Midwest. It caused widespread power outages, damaged grid infrastructure, and forced the early retirement of Iowa’s only nuclear power plant.
An ice storm in October was to blame for widespread power outages across Oklahoma.
Louisiana experienced three hurricanes and two tropical storms.(1)

The impacts of power outages and power shutoffs are felt by everyone. Here are some ways you can prepare your health for a power outage.

Be Power Prepared

Be prepared to be without electricity during an emergency and, possibly, for several days after.

A power outage can affect people’s ability to use devices and the availability of refrigeration. This makes it especially important that people who rely on durable medical equipment and refrigerated medicines like insulin take steps to prepare. For example:

Identify emergency lighting, safe heating alternatives, and backup power sources for your mobile devices, appliances, and medical equipment.
Create an emergency power plan that includes model and serial numbers for your medical devices.
Read the user manual or contact the manufacturer to find out if your medical device is compatible with batteries or a generator.
Fully charge your cellphone, battery-powered medical devices, and backup power sources if you know a disaster, such as a hurricane, is coming.
If possible, buy manual alternatives for your electric devices that are portable, dependable, and durable. For example, a manual wheelchair, walker, or cane as a backup for an electric scooter.

Power outages can also put people at increased risk for post-disaster hazards, such as food and carbon monoxide poisoning.

The effects of emergencies, such as power outages, are experienced differently by different populations.

The places of our lives, including our neighborhoods and built environment, can influence our experience with emergencies.(2)

People who live in rural areas and places with an aging infrastructure may experience more frequent and longer-lasting power outages and face greater adversity because of it. They may also have limited access to the supplies they need to prepare for power outages.

Planning for Power Outages

People who use electricity- and battery-dependent assistive technology and medical devices must have an emergency power plan in case of a power outage.

Checklists are a way to break large jobs down into smaller chores. They can help you pack for a trip, grocery shop, and even prepare for emergencies.

The Americans with Disabilities Act (ADA) National Network’s emergency power planning checklist is for people who use electricity and battery-dependent assistive technology and medical devices. These include:

Breathing machines (e.g., respirators and ventilators).
Power wheelchairs and scooters.
Oxygen, suction, or home dialysis equipment.

The Food and Drug Administration’s “How to Prepare for and Handle Power Outages” guide for home medical device users is another useful planning resource. Use it to organize your medical device information, identify the supplies for the operation of your device, and know where to go or what to do during a power outage.

Health Care Preparedness

A power outage or shutoff can limit the operations of hospitals, outpatient clinics, pharmacies, and other patient-care facilities.

Healthcare facilities need electricity to care for patients, provide services, and “keep the lights on.” Since many facilities have resident populations, hygiene and feeding are also part of the electrical demand.

Resilience to power outages begins with the leadership at the facility. Here are some resources to help healthcare facilities plan for and respond to public health emergencies.

Additional resources to help healthcare systems and hospitals plan for public health emergencies are available on the CDC website.

Resources

References

Thanks in advance for your questions and comments on this Public Health Matters post. Please note that CDC does not give personal medical advice. If you are concerned you have a disease or condition, talk to your doctor.

Have a question for CDC? CDC-INFO (http://www.cdc.gov/cdc-info/index.html) offers live agents by phone and email to help you find the latest, reliable, and science-based health information on more than 750 health topics.

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29May / 2018

Hey journals, it is possible to quickly correct the record

Even when a paper is obviously flawed, it can take years for journals to take action. Some never do. But it doesn’t have to be that way. On April 27, a reader emailed the editors of two journals, noting that each had recently published a paper by the same group of authors that appeared strikingly … Continue reading

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16Oct / 2017

Preparing Your Medicine Cabinet for an Emergency: A Checklist

Closeup view of an eighty year old senior woman's hands as she sorts her prescription medicine.

If you read our blog on a regular basis you can probably recite the mantra “Make a kit. Have a plan. Be informed.” in your sleep. You are probably familiar with the important items you should keep in your emergency kit – water, food, a flashlight, and a battery-powered radio. What you may not think about is personalizing your kit for your unique medical needs or the needs of your family. Particularly, including prescription medications and other medical supplies in your emergency kit and plans.

As a pharmacist whose job is focused on emergency preparedness and response, I want to give you 10 pointers about how to prepare your medications for an emergency so you can decrease the risk of a life-threatening situation. infographic illustrating an emergency kit.

Make a list. Keep a list of all your medications and the dosages in your emergency kit. Make sure you have the phone numbers for your doctors and pharmacies.
Have your card. Keep your health insurance or prescription drug card with you at all times so your pharmacy benefits provider or health insurance plan can help you replace any medication that was lost or damaged in a disaster.
Keep a record. Make copies of your current prescriptions and keep them in your emergency kit and/or go bag. You can also scan and email yourself copies, or save them in the cloud. If you can’t reach your regular doctor or your usual pharmacy is not open, this written proof of your prescriptions make it much easier for another doctor to write you a refill.
Start a stockpile. During and after a disaster you may not be able to get your prescriptions refilled. Make sure you have at least 7 – 10 days of your medications and other medical supplies. Refill your prescription as soon as you are able so you can set aside a few extra days’ worth in your emergency kit to get you through a disaster.
Storage matters. Keep your medications in labeled, child-proof containers in a secure place that does not experience extreme temperature changes or humidity. Don’t forget to also include nonprescription medications you might need, including pain relievers, cold or allergy medications, and antacids.
Rotate the date. Don’t let the medications in your emergency supply kit expire. Check the dates at least twice every year.
Prioritize critical medicines. Certain medications are more important to your health and safety than others. Prioritize your medications, and make sure you plan to have the critical medications available during an emergency.
Communicate a plan. Talk to your doctor about what you should do in case you run out of a medication during an emergency. If you have a child who takes a prescription medication, talk to their daycare provider or school about a plan in case of an emergency.
Plan ahead. Make sure you know the shelf life and optimal storage temperature for your prescriptions, because some medications and supplies cannot be safely stored for long periods of time at room temperature. If you take a medication that needs to be refrigerated or requires electronic equipment plan ahead for temporary storage and administration in an emergency situation.
Check before using. Before using the medication in your emergency kit, check to make sure the look or smell hasn’t changed. If you are unsure about its safety, contact a pharmacist or healthcare provider before using.

Resources

Centers for Disease Control and Prevention: Gather Emergency Supplies
Express Scripts: Emergency Preparedness for Prescription Medications

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10Jan / 2017

Genomics and the Power of Public Health

On a bad day in the lab, we sometimes joke that if we really wanted to help save lives, we’d forget about molecular biology and go help people quit smoking. Relatively simple public health efforts – clean water, washing your hands before moving from one sick patient to another, basic vaccines – generally save many more lives that the cures that come out of the high tech stuff we do in the lab. Cancer immunotherapy may turn out to be a major advance in cancer treatment, but we’d reduce cancer even more if we could get everyone to quit smoking, lose weight, and stay physically active.

Genomics, whose near-term medical benefits have been the subject of a lot of hype, may turn out to be a high-tech, scientifically complex effort that actually does to have a big impact on people’s lives. As I discuss in my Pacific Standard column this week, part of that will be the long-term medical benefits that grow out of a better understanding of biology. But a more dramatic – and more near-term – impact may be how genomics changes public health. As some sort of genome analysis becomes a routine part of normal medical care, genetics will be integrated with other public health screenings (like testing your cholesterol), which, as two recent studies show, could have a big impact on avoiding preventable consequences of common diseases. Once exome sequencing is cheap enough, there could be a possible benefit of combining genomic screenings using existing medical knowledge – we don’t need to wait for distant future discoveries.

The takeaway is that policy and the infrastructure of the healthcare system, and not science, may soon be the rate-limiting step for realizing the medical benefits of genomics in some cases. Physicians, insurers, hospitals, and the health care system in general is utterly unprepared to handle the kinds of genomic data that could, in the near future, improve routine medical care.

Filed under: This Mortal Coil Tagged: genomics, medicine

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07Oct / 2016

Doctors’ political leanings

Based on data from researchers at Yale, the Upshot charts party registration by medical profession. Surgery and anesthesiology lean Republican, whereas psychiatry and infectious disease leans Democrat. As Margot Sanger-Katz notes, income between specialties likely plays a role. [Thanks, Bea]

Tags: medicine, politics, Upshot

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01Jun / 2016

Paper reports data from PET/CT scan, years before it arrived

Authors have retracted a study just three months after publishing it, upon realizing they made “several critical errors.” For one, the authors didn’t actually collect the data they claim to in the title of the paper, which reported on methods to screen patients for recurrence of lung cancer. The authors included data from positron emission tomography/computed tomography (PET/CT), […]

The post Paper reports data from PET/CT scan, years before it arrived appeared first on Retraction Watch.

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24Jan / 2016

What is in Traditional Chinese Medicines — a network analysis

I used to work for the New South Wales Institute of Technology, which in the late 1980s mutated into the University of Technology Sydney (UTS). During this process it acquired an organization called the College of Traditional Chinese Medicine. This group was placed in the Faculty of Science, for lack of anywhere else to put it.

These people had little contact with the rest of the faculty, and I don't recall ever meeting any of them. Indeed, their work was not really based on Western science. These days, the UTS College of Traditional Chinese Medicine offers a Bachelor of Health Science in Traditional Chinese Medicine, although they are most obvious in the UTS Chinese Herbal Medicine Clinic, which is also nominally still part of the Faculty of Science.

The presence of Traditional Chinese Medicine (TCM) in an Australian university setting is relevant to today's blog post, because Australia seems to be one of the few places to have shown any interest in connecting TCM and Western science. Indeed, there is also a Uniclinic of Traditional Chinese Medicine within the School of Science and Health at Western Sydney University. Most of the interest in studying TCMs has otherwise been confined to Asia (see Dennis Normile. 2003. The new face of Traditional Chinese Medicine. Science 299: 188-190).

Recently, a group of Australian researchers decided to have a look at the content of some of the TCMs available in their country:

Megan L. Coghlan, Garth Maker, Elly Crighton, James Haile, Dáithí C. Murray, Nicole E. White, Roger W. Byard, Matthew I. Bellgard, Ian Mullaney, Robert Trengove, Richard J.N. Allcock, Christine Nash, Claire Hoban, Kevin Jarrett, Ross Edwards, Ian F. Musgrave & Michael Bunce (2015) Combined DNA, toxicological and heavy metal analyses provides an auditing toolkit to improve pharmacovigilance of traditional Chinese medicine (TCM). Nature Scientific Reports 5: 17475.

Some of these TCMs (12 out of 26) are registered for use with the Therapeutic Goods Administration, which regulates their use within Australia, while the other TCMs are not (which technically means that they should not have been commercially available). However, there is little in the way of pharmacovigilance of herbal medicines anywhere in the world.

All of the products were comprehensively audited for their biological (via next generation DNA sequencing), toxicological (LC-MS analysis) and heavy metal (arsenic, cadmium and lead, via SF-ICP-MS analysis) contents. For the latter two analyses the amount of material detected was also quantified.

As usual, we can use a phylogenetic network to visualize these data, which I have done using a neighbor-net network on the presence-absence data. The result is shown in the figure. TCMs that are closely connected in the network are similar to each other based on their detected contents, and those that are further apart are progressively more different from each other. The registered products are highlighted in red.

There is wide variation among the products. The seven most divergent TCMs in the network are all unregistered, with the remaining seven being more similar to the registered TCMs. Only two TCMs (TCM10 and TCM17) have no discrepancies between the detected contents and what was declared (either to the regulatory agency, or to the consumer in the form of an ingredients list).

The authors summarize this situation:

Genetic analysis revealed that 50% of samples contained DNA of undeclared plant or animal taxa, including an endangered species of Panthera (snow leopard). In 50% of the TCMs, an undeclared pharmaceutical agent was detected including warfarin, dexamethasone, diclofenac, cyproheptadine and paracetamol. Mass spectrometry revealed heavy metals including arsenic, lead and cadmium, one with a level of arsenic >10 times the acceptable limit.

This study presents genetic, toxicological, and heavy metal data that should be of serious concern to regulatory agencies, medical professionals and the public who choose to adopt TCM as a treatment option. Of the 26 TCMs investigated, all but two can be classified as non-compliant on the grounds of DNA, toxicology and heavy metals, or a combination thereof. In total, 92% were deemed non-compliant with some medicines posing a serious health risk.

Such findings are not only of concern to the consumer, but also flag the need for detailed auditing of herbal preparations prior to evaluation in clinical trials.

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23Oct / 2015

Science for the People: Mandatory Vaccination

This week, we’re talking about disease prevention, public health, and whether or not some types of vaccinations should be mandatory. We’ll spend the hour in a panel discussion with Barry Bloom, Harvard University’s Distinguished Service Professor of the Department of Immunology and Infectious Diseases, University of Toronto public health ethicist Alison Thompson, pediatrician and University of Pennsylvania vaccinology professor Paul Offit, and Nicholas Little, Vice President and General Counsel at the Center for Inquiry.