DNA testing – Part 3 – Follow-up

June 5, 2017 at 10:27 pm | Posted in Health, History, Online services, Science | 1 Comment
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I’ve written before on DNA testing. In the first article in 2015, I compared the 4 prominent services for personal DNA testing. I chose 23andme. I then reported the broader results. Now I have some updates to that discussion.

It’s turned out the Y chromosome has had a lot more mutation than the maternal line so they had to update the haplogroup naming conventions last year. The original paternal haplogroup name is no longer current and the tree more complex. In my case, the guys wandered further too.

A few terms for the major testing:
Autosomal is the 22 pairs of chromosomes in the cells nucleus, excluding the pair of sex chromosomes. It’s the broad overview and allows you to match to other family members, etc.

Y-DNA is the Y or male sex chromosome. It traces your male line back: fathers, fathers, father, etc. You need to be a male or have a male member of the family tested for this one.

mtDNA – mitochondrial DNA comes from the mitochondria. It is passed down from mothers to both sons and daughters. It traces the mothers line back: mothers, mothers, mothers, etc.

Haplogroup – those that share a common ancestor based on haplotypes, groups of genes inherited from a single parent. We all have a paternal and maternal haplogroup. Haplogroups can be viewed in a tree structure of sequential mutations.

They can trace these 2 lines back roughly 100,000 years now for well-tested populations.

23andMe
Skip forward 2 years and 23andMe has finally upgraded my data to their new site format as promised. For a while, they were offering health results only to Canada and the UK due to US restrictions on “diagnosis.” With the site redesign, they’ve removed a lot of the more detailed health analysis and focus now on general markers like lactose intolerance, sleep depth, and so forth. Gone are more diagnostic things like Celiac and Parkinson’s markers.

Reporting is more centralized and distributed to tabs to support smaller screens. It surprised me to discover printing the reports (for me to PDF) gave a more complete view.

A new report on the Maternal line (haplogroups) goes back as far as the National Geographic’s “Deep Ancestry” report (below) although the second has slightly more detail.

The paternal haplogroup name was updated but there’s a gap between the tree map in the paternal section and the specific haplogroup named. As I discovered on FTDNA below, it’s also less specific.

Genographic
Meantime, I had also decided to take advantage of a sale on National Geographic’s Genographic Project. I wanted to support their work, and it offers more of a deep ancestry approach.

Here a deviation has taken place. Family Tree DNA used to do all their testing, allowing you to load your DNA test results into FTDNA (below) afterwards for free. However, for US customers, Helix is now doing their testing. They’re using a newer system that is not compatible with FTDNA. If you get the Helix test (white box, spit not swab), you can’t download the genome after either.

But as I’m Canadian, I still got the black, cheek swab kit to send to FTDNA in Texas.

My first impression of the Genographic results wasn’t positive – they didn’t notify me when the results were up. And the first presented report is “Genius” matches. It displayed famous people (not geniuses) who had some unmentioned genetic match. Essentially a pointless report.

The Regional Ancestry report had quite different percents from 23andMe but I suspect was less accurate due to the much smaller testing population.

What I did enjoy was the Deep Ancestry reports. This showed the maternal and paternal lines over thousands of years, migrating across vast distances as the ages changed.

There is also a Hominin report for the percent of Neanderthal DNA. This varied substantially from the 23andMe result as well.

Another disappointment was printing. The reports didn’t print well and the official printable report that summarized much of the above was missing all the maps even though the reports refer to them. I had to use screen captures for the maps and assemble them with the reports myself.

Given that 23andMe now includes very similar reports and has a great deal more other ones, it’s certainly preferable. It’s possible the Helix testing for Americans offers more reports or detail but that’s unclear. I suspect 23andMe would still be superior.

Family Tree DNA
Because I got the old Genographic kit, I could transfer the results to Family Tree DNA for free. This allowed downloading the Genome file and offered a few basic reports.

One of note though was the Y-DNA haplotree. This went much further than 23andMe, offering a Haplogroup that was 15 steps more detailed. And there they offered a further test (at a cost) to take it a few steps further.

From this, I discovered the links between the 23andMe paternal map and their designation of my haplogroup plus further steps that FTDNA named.

One of the bigger differences with FTDNA is their a la carte approach to ordering tests. You send in or transfer one sample and then pay just for the tests you want when you want them. Where the others above include autosomal, mtDNA, and Y-DNA, FTDNA lets you choose. Y-DNA is of no use for women, for example, as they don’t have the Y chromosome.

You can also choose the degree of testing for the mt and Y reports. If you’re a male and test all 3 at the basic level, it will cost you more than these others. But for serious researchers, there is a level of detail available you don’t see in the one-size services.

The site has many “projects” where members discuss details of their research. The one’s I looked at required the Y67 test to join as they were specific to certain haplogroups.

FTDNA offered me a significant autosomal discount, so I ordered the Family Finder test to connect with a few relatives on the system. This gave me the Matches section and Chromosome browser, similar to what 23andMe has. The Origins reports where too general to be of much use. They did not match known family regions either.

Also note they’re using the oldest technology now.

Conclusions
I’d still recommend 23andMe for the overview. Their reports are broader and bring a more complete perspective. They use newer tech and have a larger customer base which increases accuracy and matches.

Family Tree DNA is superior if you want to explore genealogy in greater detail. They have more detailed test options but use older tech and are more expensive. Just understanding the value of their options requires a serious exploration.

National Geographic Genographic Project loses much of it’s advantage as others begin to include deep ancestry reporting. With their migration to the newer tech, it can’t be uploaded to FTDNA nor the genome downloaded for other services.

Ancestry also includes a DNA testing service but this would only be helpful if you use their services already. The family tree building software is sophisticated but is an ongoing expense.

From some of the commentary I’ve read on-line, serious researchers use several of the services for different features and to connect with different populations. As the number tested grows, the detail levels will increase. Added features will make going back in and taking a look around again useful, even for the casually curious.
David

Minimizing Cancer Risk

May 13, 2015 at 10:40 pm | Posted in Health, Science | 4 Comments
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Our bodies are naturally self-healing if we give them the right nutrition, activity, and environment. This doesn’t have to be perfect – just within reasonable ranges.

However, our modern lifestyle has lead to some poor habits that, over time, create imbalances in the body that gradually throw systems out of whack. That leads to a wide range of common illnesses, including Cancer. Yet, cancer itself is not actually an illness – it’s a symptom of an illness or imbalance that leads to an out-of-control healing (cell-replenishment) process, much as chronic inflammation leads to many other troubles.

If your immune system is in good shape, you won’t get cancer. The body will take care of naturally occurring problems, including malignant growth.

What is the largest influence on the risk of cancer? Lifestyle habits. Carcinogens have links to cancer but are a far smaller influence than lifestyle. And lifestyle is something you can control.

The World Cancer Research Fund International has been running an ongoing and continually updated meta-analysis of published papers on cancer research. They have reviewed over 9,000 studies of some 17 cancers.

Their recommendations to reduce the largest risk factors:

1) Loose Excess Weight and maintain a healthy weight (a BMI of 21) through a balanced diet and exercise.
2) Be Physically Active at least 30 minutes each day. As fitness improves, aim for 60 minutes. Limit sedentary activity, like being a couch potato.
3) Limit consumption of Energy-Dense Foods – these are foods high in fat and/or sugar and low in fibre. Avoid sugary drinks and limit fruit juices (some have more sugar than pop plus low fibre). Limit fast food and processed food. When foods are low in fibre, we don’t feel full and continue to eat, leading to weight gain. Not to mention that cancer lives solely on sugar. People who die from cancer effectively starve to death as the cancer consumes all the bodies energy. Energy-dense foods feed cancer.
4) Eat mostly foods of plant origin: vegetables, fruits, whole grains and pulses. Favour unprocessed cereals. These foods have lower energy density and higher fibre. They help fill us up and carry away toxins. They reduce cancer growth by reducing fuel.
5) Limit red meats and avoid processed meat.
6) Limit or avoid Alcoholic Drinks. Purple grape juice offers the same health benefits touted for red wine. But moderately as it’s also energy-dense.
7) Limit consumption of Salt (and salty foods and salt preserved foods). Check the labels on packaged and canned goods. Many have high amounts of sugar and/or salt, even “healthy” and organic foods. Also – avoid mouldy grains and legumes.
8) Don’t use dietary supplements to protect against cancer. Aim to meet your nutritional needs through diet.
9) Breastfeed – this protects both mother and child
10) Cancer survivors should also follow these guidelines: before, during and after treatment

Put simply – favour a whole foods, plant-based diet and get active. Again, this is research-based. Alcohol, sugary drinks, fat, and other energy-dense foods all produce sugars that feed cancer, add weight, and increase inflammation.

And of course, quit smoking. Whatever kind of plants you smoke.

This approach will also reduce inflammation, much as I noted prior. This means it will also help avoid high blood pressure, heart disease, and so much more. And it will improve not just your health but overall quality of life. And don’t forget to clean up inflammatory emotions. We have to take care of our emotional and mental health too or that will contribute to physical illness.

To your health and well being.
David

Some CHIP Science

April 13, 2015 at 11:57 am | Posted in Health, Psychology, Science | 9 Comments
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As I discussed prior, CHIP is one of the best researched lifestyle upgrade programs available. They lean on a lot of other research. Let’s see if I can explain the basics of the value proposition for health.

Essentially, the bodies immune system produces inflammation at an injury point while the healing is underway. But lifestyle factors like smoking, high fat or sugar in the diet, inactivity, excess alcohol, salt, obesity, poor sleep, and stress can all lead to chronic low-level inflammation. Similarly, the same lifestyle factors create more “oxidative stress”, an imbalance between damaging free radicals and the antioxidents that manage them. If free radicals get the upper hand, all sorts of problems can arise, including higher cancer risk.

We most notice inflammation in the joints when we have discomfort and pain. But one of the primary sites where chronic low-level inflammation develops is in blood vessels. Over time, this damages the vessel walls protection. LDL (“bad”) cholesterol influenced by free radicals becomes sticky and adheres at these points, causing narrowing of the arteries, atherosclerosis. That impedes the circulatory system and the distribution of oxygen and nutrients required by all areas.

The trick is – where that is occurring more is what leads to a chronic ailment in that area. The best known is of course coronary artery or heart disease. But in the brain, it’s senility or stroke. High blood pressure. Kidney disease. Hearing loss. And macular degeneration in the eyes.

The main point – “most chronic diseases have a common cause in chronic low-level inflammation linked to oxidative stress.” This is backed up by a lot of research.

For example, several long term studies, like the Adventist study and the China study, have demonstrated that every step closer to being a straight vegetarian you are, the lower your rate of chronic disease: by a 4 and 5 to one ratio to meat eaters. Meat eaters, for example, have a 5 times higher likelihood of developing high cholesterol (somewhat obviously). This means a 5 times higher likelihood of a lower quality of life. Spread that over multiple issues and you get the message.

CHIP feels these chronic diseases can be moderated and potentially corrected with diet, sufficient activity, emotional health and stress management. They hope to wean you off any related medications for symptoms.

I’ve been surprised how thorough they’re being. They want to really drive the points home. It’s completely your choice how far you want to take it on the diet and exercise scale. But they want you to understand the choices you’re making and their benefits.

And we’re not just talking a longer life but one of higher quality too.
David

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