Antibody (or immunoglobulin) structure is made up of two heavy-chains and two light-chains. These chains are held together by disulfide bonds. The arrangement or processes that put together different parts of this antibody molecule play important role in antibody diversity and production of different subclasses or classes of antibodies. The organization and processes take place during the development and differentiation of B cells. That is, the controlled gene expression during transcription and translation coupled with the rearrangements of immunoglobulin gene segments result in the generation of antibody repertoire during development and maturation of B cells.
During the development of B cells, the immunoglobulin gene undergoes sequences of rearrangements that lead to formation of the antibody repertoire. For example, in the lymphoid cell, a partial rearrangement of the heavy-chain gene occurs which is followed by complete rearrangement of heavy-chain gene. Here at this stage, Pre-B cell, mμ heavy chain and surrogate light chain are formed. The final rearrangement of the light chain gene generates immature B cell and mIgM. The process explained here occurs only in the absence of the antigen. The mature B cell formed as RNA processing changes leaves the bone marrow and is stimulated by the antigen then differentiated into IgM -secreted plasma cells. Also at first, the mature B cell expresses membrane-bound IgD and IgM. These two classes could switch to secretory IgD and IgM during the processing of mRNAs.
Finally, further class switching follows as the cell keep dividing and differentiating. For instance, IgM switches to IgG which switches to IgA that eventually switches to IgE
The multigene organization of immunoglobulin genes
From studies and predictions such as Dreyer and Bennett’s, it shows that the light chains and heavy chains are encoded by separate multigene families on different chromosomes. They are referred to as gene segments and are separated by non-coding regions. The rearrangement and organization of these gene segments during the maturation of B cells produce functional proteins.The entire process of rearrangement and organization of these gene segments is the vital source where our body immune system gets its capabilities to recognize and respond to variety of antigens.
Light chain multigene family
The light chain gene has three gene segments. These include: the light chain variable region (V), joining region (J), and constant region (C) gene segments. The variable region of light is therefore encoded by the rearrangement of VJ segments. The light chain can be either kappa,κ or lambda,λ. This process takes place at the level of mRNAs processing. Random rearrangements and recombinations of the gene segments at DNA level to form one kappa or lambda light chain occurs in an orderly fashion. As a result, “a functional variable region gene of a light chain contains two coding segments that are separated by a non-coding DNA sequence in unrearranged germ-line DNA” (Barbara et al., 2007). Interestingly, the immunoglobulin lambda light chain locus contains protein-coding genes that can be lost with its rearrangement. This is based on a physiological mechanism and is not pathogenetic for leukemias or lymphomas. However,the rearrangement of several lambda variable subgenes can activate expression of an overlapping miRNA gene, which has consequences for gene expression regulation.
Heavy-chain multigene family
Heavy chain contains similar gene segments such as VH, JH and CH, but also has another gene segment called D (diversity). Unlike the light chain multigene family, VDJ gene segments code for the variable region of the heavy chain. The rearrangement and reorganization of gene segments in this multigene family is more complex . The rearranging and joining of segments produced different end products because these are carried out by different RNA processes. The same reason is why the IgM and IgG are generates at the time.
The variable region rearrangements happen in an orderly sequence in the bone marrow. Usually, the assortment of these gene segments occurs at B cell maturation.
Light chain DNA
The kappa and lambda light chains undergo rearrangements of the V and J gene segments. In this process, a functional Vlambda can combine with four functional Jλ –Cλ combinations. On the other hands, Vk gene segments can join with either one of the Jk functional gene segments. The overall rearrangements result in a gene segment order from 5 prime to 3 prime end. These are a short leader (L) exon, a noncoding sequence (intron), a joined VJ segment, a second intron, and the constant region. There is a promoter upstream from each leader gene segment. The leader exon is important in the transcription of light chain by the RNA polymerase. To remain with coding sequence only, the introns are removed during RNA- processing and repairing. In summary,
Heavy chain DNA
The rearrangements of heavy-chains are different from the light chains because DNA undergoes rearrangements of V-D-J gene segments in the heavy chains. These reorganizations of gene segments produce gene sequence from 5 prime to 3 prime ends such as a short leader exon, an intron, a joined VDJ segment, a second intron and several gene segments. The final product of the rearrangement is transcribed when RNA polymerase
Mechanism of variable region rearrangements
It is understood that rearrangement occurs between specific sites on the DNA called recombination signal sequences (RSSs). The signal sequences are composed of a conserved palindromic heptamer and a conserved AT- rich nonamer. These signal sequences are separated by non-conserved spacers of 12 or 23 base pairs called one-turn and two-turn respectively. They are within the lambda chain, k-chain and The processes of rearrangement in these regions are catalyzed by two recombination-activating genes: RAG-1 and RAG-2 and other enzymes and proteins. The segments joined due to signals generated RSSs that flank each V, D, and J segments. Only genes flank by 12 -bp that join to the genes flank by 23-bp spacer during the rearrangements and combinations to maintain VL-JL and VH-DH-JH joining.
Generation of antibody diversity
Antibody diversity is produced by genetic rearrangement after shuffling and rejoining one of each of the various gene segments for the heavy and light chains. Due to mixing and random recombination of the gene segments errors can occur at the sites where gene segments join with each other. These errors are one of the sources of the antibody diversity that is commonly observed in both the light and heavy chains. Moreover, when B cells continue to proliferate, mutations accumulate at the variable regions through a process called somatic hypermutation. The high concentrations of these mutations at the variable region also produce high antibody diversity.
When the B cells get activated, class switching can occur. The class switching involves switch regions that made up of multiple copies of short repeatts(GAGCT and TGGGG). These switches occur at the level of rearrangements of the DNA because there is a looping event that chops off the constant regions for IgM and IgD and form the IgG mRNAs. Any continuous looping occurrence will produce IgE or IgA mRNAs.
In addition, cytokines are factors that have great effects on class switching of different classes of antibodies. Their interaction with B cells provides the appropriates signals needed for B cells differentiation and eventual class switching occurrence. For example, interleukin-4 induces the rearrangements of heavy chain immunoglobulin genes. That is IL- 4 induces the switching of Cμ to Cγ to Cκ.
They act through receptors, and are especially important in the immune system; cytokines modulate the balance between humoral and cell-based immune responses, and they regulate the maturation, growth, and responsiveness of particular cell populations. Some cytokines enhance or inhibit the action of other cytokines in complex ways.
They are different from hormones, which are also important cell signaling molecules, in that hormones circulate in less variable concentrations and hormones tend to be made by specific kinds of cells.
They are important in health and disease, specifically in host responses to infection, immune responses, inflammation, trauma, sepsis, cancer, and reproduction.
Researchers discovered that the genes that were the strongest linked to intelligence are ones involved in pathways that play a part in the regulation of the nervous system’s development and apoptosis (a normal form of cell death that is needed in development). The most significant SNP was found within FOXO3, a gene involved in insulin signalling that might trigger apoptosis. The strongest associated gene was CSE1L, a gene involved in apoptosis and cell proliferation.
Does this all mean that intelligence in humans depends on the molecular mechanisms that support the development and preservation of the nervous system throughout an person’s lifespan? It’s possible.
And is it possible to explain intelligence through genetics? This paper suggests it is. Nevertheless, it might be warranted to consider that intelligence is a very complex trait and even if genetics did play a role, environmental factors such as education, healthy living, access to higher education, exposure to stimulating circumstances or environments might play an equally or even stronger role in nurturing and shaping intelligence.
It is also worth considering that the meaning of “intelligence” rather falls within a grey area. There might be different types of intelligence or even intelligence might be interpreted differently: in which category would for example a genius physicist – unable to remember their way home (Albert Einstein) – fall? Selective intelligence? Mozart nearly failed his admission tests to Philharmonic Academy in Bologna because his genius was too wide and innovative to be assessed by rigid tests. Is that another form of selective intelligence? And if so, what’s the genetic basis of this kind of intelligence?
Studies like this are extremely interesting and they do show we are starting to scratch the surface of what the biological basis of intelligence really is.
What are they? FOXO proteins are a subgroup of the Forkhead family of transcription factors. This family is characterized by a conserved DNA-binding domain (the ‘Forkhead box’, or FOX) and comprises more than 100 members in humans, classified from FOXA to FOXR on the basis of sequence similarity. These proteins participate in very diverse functions: for example, FOXE3 is necessary for proper eye development, while FOXP2 plays a role in language acquisition. Members of class ‘O’ share the characteristic of being regulated by the insulin/PI3K/Akt signaling pathway. How did this family get named ‘Forkhead’? Forkhead, the founding member of the entire family (now classified as FOXA), was originally identified in Drosophila as a gene whose mutation resulted in ectopic head structures that looked like a fork.
Forkhead proteins are also sometimes referred to as ‘winged helix’ proteins because X-ray crystallography revealed that the DNA-binding domain features a 3D structure with three α-helices flanked by two characteristic loops that resemble butterfly wings.
How many FOXOs are there? In invertebrates, there is only one FOXO gene, termed daf-16 in the worm and dFOXO in the fly. In mammals, there are four FOXO genes, FOXO1, 3, 4, and 6. Hey, what about FOXO2 and FOXO5? FOXO2 is identical to FOXO3 (a.k.a. FOXO3a, as opposed to FOXO3b, a pseudogene). FOXO5 is the fish ortholog of FOXO3. FOX hunting…
FOXO genes were first identified in humans because three family members (1, 3, and 4) were found at chromosomal translocations in rhabdomyosarcomas and acute myeloid leukemias. Just after FOXO factors were identified in human tumor cells, the crucial role of DAF-16 in organismal longevity was discovered in worms.
DAF-16 activity was shown to be negatively regulated by the insulin/PI3K/Akt signaling pathway. Subsequent experiments in mammalian cells showed that mammalian FOXO proteins were directly phosphorylated and inhibited by Akt in response to insulin/ growth factor stimulation. Thus, FOXO factors are evolutionarily conserved mediators of insulin and growth factor signaling.
Why are they important? FOXO transcription factors are at the interface of crucial cellular processes, orchestrating programs of gene expression that regulate apoptosis, cell-cycle progression, and oxidativestress resistance (Figure 1). For example, FOXO factors can initiate apoptosis by activating transcription of FasL, the ligand for the Fas-dependent celldeath pathway, and by activating the pro-apoptotic Bcl-2 family member Bim. Alternatively, FOXO factors can promote cellcycle arrest; for example, FOXO factors upregulate the cell-cycle inhibitor p27kip1 to induce G1 arrest or GADD45 to induce G2 arrest.
FOXO factors are also involved in stress resistance via upregulation of catalase and MnSOD, two enzymes involved in the detoxification of reactive oxygen species. Additionally, FOXO factors facilitate the repair of damaged DNA by upregulating genes, such as GADD45 and DDB1. Other FOXO target genes have been shown to play a role in glucose metabolism, cellular differentiation, muscle atrophy, and even energy homeostasis.
Is there a connection between FOXO and cancer?
Because FOXO proteins were originally identified in human tumors, and because they play an important role in cell-cycle arrest, DNA repair, and apoptosis — cell functions that go awry in cancer — the FOXO family is thought to coordinate the balance between longevity and tumor suppression. Consistent with this idea, in certain breast cancers, FOXO3 is sequestered in the cytoplasm and inactivated. Expression of active forms of FOXO in tumor cells prevents tumor growth in vivo. Additionally, protein partners of FOXO, such as p53 and SMAD transcription factors, are tumor suppressors. Investigating the ensemble of FOXO protein partners will provide insight into the connection between aging and cancer.
Dr Mercola’s book ‘Fat for Fuel’ book is a revolutionary diet to combat cancer, boost brain power and increase your energy.
Dr Mercola’s story…
In 1995, my understanding of chronic disease took a quantum leap. I was introduced to Dr. Ron Rosedale and his breakthrough views on clinical metabolic biochemistry.
In a nutshell, Dr. Rosedale taught me that defective metabolic processes in your mitochondria, not your genetic makeup, cause cancer and nearly all other chronic diseases, including accelerated aging.
And what causes these faulty processes?
Insulin and leptin receptor resistance from too many net carbs and activation of the mTOR metabolic signaling pathway by too much protein.
Let me put this into more easily understood terms…
When you eat too many sugars and carbs without fiber, along with too much protein, you can ignite a cascade of metabolic events that includes:
Widespread inflammation and cellular damage, especially your mitochondria, or your cells’ power factories
Faster aging and a greater risk of all cancers from the activation of your body’s most important signaling pathway from eating excess protein
An increase in insulin resistance that can progress to prediabetes or Type 2 diabetes because your cells have lost their ability to respond to insulin effectively
Overeating due to the loss of control over your appetite and knowing when you’re “full”
An inability to lose weight because your body is holding on to fat instead of burning it for fuel
So how can you take what I’ve learned and put it to good use? That’s the idea behind my new book, Fat for Fuel – to help you take control over obesity and chronic disease, including advanced cancer.
Why Cancer Is One Of The Most Manageable Diseases We Know Of Today
“Once you realize what cancer is, that it’s a metabolic disease, you can take charge of those kinds of things. In other words, getting cancer is not God’s will. It’s not bad luck.”
— Thomas Seyfried, Ph.D.
I believe, along with many of the experts I interviewed for Fat for Fuel, more than 90 percent of cancer cases are either preventable or treatable.
That should be very welcome news to most people – even if you’re not currently fighting cancer or have a friend or family member who is.
But here’s something that I think should be even more reassuring…
Many people don’t realize that their chances of developing cancer are slim if their mitochondria are healthy and functional.
Researcher Dr. Peter Pederson from Johns Hopkins, recently made a fascinating discovery:
One characteristic that cancer cells share with one another is that they have a radically reduced number of fully functional mitochondria.
Maybe you remember learning about mitochondria in science class…
These tiny organelles, originally thought to have evolved from bacteria, exist in nearly all your cells. Most cells have several thousands of them, and can comprise up to 50 percent of your cells’ volume!
Your mitochondria are truly your body’s lifeline. They supply over 90 percent of your body’s energy needs by converting the food you eat and the air you breathe into usable energy.
Powerful Strategies For Repairing And Nurturing Your Mitochondria
As you age, your body produces fewer mitochondria, so that makes taking care of the ones you have all the more important.
When a significant percentage of your mitochondria stops functioning properly, your health can falter and leave you more vulnerable to cancer and other chronic diseases.
However, we now know there are powerful strategies that can repair and improve the health of your mitochondria.
What I believe to be the most valuable strategy for repairing your mitochondria is the main subject of my newest book: Fat for Fuel: A Revolutionary Diet to Combat Cancer, Boost Brain Power, and Increase Your Energy.
You see, everything you eat affects your mitochondria – positively or negatively.
When you make food choices that boost your mitochondrial health, you reduce the risk of damage to your cells’ genetic material or DNA that can lead to disease or cancer.
In Fat for Fuel, here’s just a sampling of what you will learn:
How to trigger powerful changes in your health in just a few days
How to avoid feeding cancer cells’ mitochondria while repairing your healthy mitochondria
How to starve out cancer cells (and not harm your healthy cells!)
How to permanently shed unwanted pounds and inchesfaster than you ever thought possible
How to feel sharper mentally and improve your memory just by changing how and when you eat
How to boost your physical stamina and endurance
How to eliminate excessive hunger pangs and food cravings
How to explain to your friends, family, and doctorexactly what you’re doing and get their unwavering support
How to monitor your progress and find the least expensive supplies
Beyond Ketogenic Diets: The Eating Program That Can Heal Your Mitochondria
“A truly revolutionary program. . . Fat for Fuel will change the way you think about nutrition and your health.”
— Leo Galland, M.D.
Author of The Allergy Solution
Let me be very clear… you don’t need to be sick, overweight, or have cancer, heart disease or Alzheimer’s to benefit from the information in Fat for Fuel.
This book is designed for anyone wishing to improve his or her health. There’s tremendous value in repairing and nurturing damaged mitochondria just to feel more energetic and to help live a long life free from disease.
However, the sicker you are or the older you are (because you now have fewer mitochondria), the more you stand to benefit from the strategies I present in Fat for Fuel.
My program, Mitochondrial Metabolic Therapy, or MMT, is a system of eating that aims to heal the root cause of chronic disease and aging – and your mitochondria themselves.
It does this by shifting your metabolism from burning glucose as your primary fuel to burning fat instead.
When you replace carbs with fat for fuel, potentially:
You optimize your mitochondrial function
You turn on your body’s ability to burn body fat
Your metabolism runs more efficiently
You enjoy long-lasting energy and stamina
Your brain functions more efficiently and you feel sharper mentally
Glucose is a “dirty” fuel, while fat burns much cleaner. So by replacing carbs with healthy fats, your cells’ mitochondria are less likely to suffer damage from free radicals that are caused by reactive oxygen species or ROS.
Since 90 percent or more of the total ROS in your body are produced within your mitochondria, these fragile components of your cells are continually under siege when there are excessive ROS. Some are needed for crucial cellular functions, but too many cause devastating damage.
Previously, it was thought excessive ROS could be addressed by taking antioxidants, but we now know that this was a flawed strategy and it is far better to prevent their production by eating an optimal fuel mixture.
MMT can help your cells’ mitochondria reach the “Goldilocks” zone for producing ROS — not too much and not too little, but just the “right” amounts for healthy cellular and mitochondrial function.
Why You Need Mitochondrial Metabolic Therapy (MMT)
What many people may not realize is that switching over to fat-burning is not an instantaneous “aha” moment. Nor is it a one-size-fits-all plan.
That may be why, if you’ve ever tried a ketogenic diet, you weren’t able to reach or remain in ketosis long enough to produce significant health effects.
My MMT program is a highly customizable, multi-step process that can take a few days or as long as a few months to become fully fat-adapted. Everyone is different.
Fat for Fuel walks you through the complete step-by-step process. You learn which foods and practices work best for you.
My goal is to help you get there smoothly and as easily as possible, identifying and removing potential challenges ahead of time that can derail you off course.
Here are some of the valuable insights you’ll gain from Fat for Fuel to help you succeed:
The 7 most common symptoms to expect while shifting to fat burning and simple ways to ward them off
How to use timing and spacing of meals to propel your results
The weight loss bonus that will hook you in your first few days on MMT
How to overcome emotional roadblocks that may arise before and during MMT
One simple way to tell if you’re exercising too much (or too little) while adjusting to fat burning
The 7 most common challenges people face when adopting a fat-burning eating plan and how to face them head on
How to customize MMT for you so you’ll want to continue it for life (although you’ll most likely be convinced that long-term is for you once you experience how much better you feel when eating this way!)
Why your brain loves ketones (Hint: it has to do with how easily they are whisked across your blood-brain barrier into your brain tissue)
Why it’s easier to lose weight on a ketogenic diet (and especially my MMT plan) and keep it off
The greatest tool I’ve found to help keep on track, pinpoint nutritional deficiencies in my diet – and to stay motivated
The effective and inexpensive long-term alternative to blood tests for monitoring ketones
My guidelines for long-term optimum fat-burning, including the ideal amount of protein to eat at any meal to avoid activating mTOR
The other side of eating that most people ignore, yet it’s equally important for your body to function at its best (it happens to be the oldest dietary intervention in the world!)
Why taking too many antioxidants can be dangerous and actually aid the survival of cancer cells
The popular cooking oils that can harm your cell membranes and threaten your mitochondrial health
Why it may be a big mistake to follow your conventional doctor’s advice about fat in your diet
Why MMT Is One Of The Most Powerful Strategies For Lasting Weight Loss And Much More…
“Beautifully lays out the history—and the myths—behind the high-carbohydrate, low-fat diet that has been at the root of so much illness and death in the last half-century.”
— Ron Rosedale, M.D.
As a healthy child, you had healthy metabolic flexibility. When you ate a limited amount of sugar and net carbs (carbs minus the fiber) and greater amounts of healthy fat, you were easily able to burn clean burning fats as your primary fuel.
After eating a high net-carb diet, your body loses its ability to switch effortlessly from glucose-burning to fat-burning. And, if you’re like the majority of adults, your health — especially your metabolic health — has suffered as a result.
One visual gauge of your current metabolic health is the amount of body fat you’re carrying, especially around your waistline. This is largely unhealthy visceral fat.
You need a certain amount of body fat to protect your organs, but too much puts you at higher risk for chronic diseases like cancer, diabetes and heart disease.
By making MMT part of your everyday life, you can regain that long-lost metabolic advantage. And that puts you squarely into control of your health – and weight – like no other step you could possibly take!
Similar to a ketogenic diet, MMT is a high-fat, low-carb, and moderate-protein eating plan. But unlike a ketogenic diet, it emphasizes on high-quality, unprocessed whole foods.
Since your body was designed to run more efficiently on fats than on carbs, when you successfully shift over to what’s called nutritional ketosis, you optimize your mitochondrial function and your body’s ability to burn body fat.
While fitting into your favorite skinny jeans is certainly a valuable side effect of MMT, my plan’s primary aim goes much deeper – to heal your metabolism at the cellular level and ward off the development of most common chronic diseases and premature aging, including:
Type 2 diabetes
Atherosclerosis and heart disease
And of course, that includes the core causes of obesity!
Please Don’t Confuse Paleo With My Advanced Version Of Ketogenic…
Paleo diets are one of the hottest eating trends today. Many people claim eating that way helps them feel more energetic. Others swear by them for weight loss.
But it’s not the same thing as MMT…
While there are many advantages to the Paleo diet – it’s certainly a big step above the typical American diet – it doesn’t initially control net carbs.
Paleo restricts grains, dairy, starches, and processed foods, but the diet allows some starchy vegetables, fruits, and sugars like honey and coconut sugar.
And it encourages protein from meat, seafood, and nuts and seeds – lots of it! Many people who follow the Paleo diet consume far too much protein.
Too much sugar and too much protein can make it impossible to maintain a state of ketosis, especially if you are new to nutritional ketosis.
Eating too much protein can also activate your body’s most important signaling pathway – mTOR, or the mammalian target of rapamycin – and boost your risk of cancer. Your mTOR pathway organizes all the nutrient sensors in your body to regulate metabolism, growth, cell differentiation, and cellular survival.
Researchers have discovered that low-protein diets extend lifespan in flies because they improve mitochondrial function and inhibit mTOR.
MMT or my version of the ketogenic diet provides very precise protein recommendations to help avoid activating mTOR and, at the same time, restore health to your mitochondria.
With the guidance I provide in Fat for Fuel, you’ll know how to determine the exact amount of protein that’s right for you!
Just As Important As What You Eat Is What You Don’t Eat
“Fat for Fuel . . . reveals truths the food industry won’t tell you about the food you eat and starts you on a path to radically transforming your health.”
— Mark Hyman, M.D.
#1 New York Times best-selling author of Eat Fat, Get Thin and
director of the Cleveland Clinic’s Center for Functional Medicine
Sometimes we get so wrapped up in what we should eat that it’s easy to forget the other side that’s equally important for your mitochondrial health. And that’s not eating.
Consider your early ancestors… They didn’t have ready access to food 24 hours a day, 7 days a week. Instead, they evolved to withstand extended periods without food. You and I are here today, so they obviously thrived.
Could your body perhaps be equipped to function optimally by not eating?
Fasting can rapidly accelerate your transition to fat-burning and immediately begin to improve metabolic pathways involved with many health challenges.
Think of it as a jump start to success… Starting MMT when you’re already adapted to burning fat through fasting makes your eating plan much easier to implement and stick with.
Fasting also provides numerous benefits in itself. When you fast, your:
Blood sugar stabilizes
Insulin levels fall and insulin resistance improves
Digestive tract gets to rest and repair its mucosal lining
Immune system participates in the regeneration of your body’s organs
Stem cells produce new white blood cells to boost immunity
Body produces ketones to fuel your brain and nervous system while preserving muscle mass
Metabolic rate increases to provide energy in the absence of food
Damaged cells are cleared out through a natural cleansing routine
Excess body fat is shed without the loss of lean body mass
Levels of pro-inflammatory cytokines and cancer-promoting hormones drop
Rate of aging slows as does the accumulation of cellular free radicals
Brain function is protected by higher levels of brain-derived neurotropic factor (BDNF) and other chemicals
Your Biggest Decision Likely Won’t Be If You’ll Fast, It’ll Be Which Fast Will You Choose?
I think you’ll agree that fasting provides an exceptional way to jump-start your mitochondria and become fat-adapted in as short a time as possible, and start reaping the many benefits of fat burning.
You can do a traditional 2- to 3-day water fast where you drink nothing but water plus minerals, or you can take your pick of at least 5 other types of fasts to make the transition to fat-burning even easier.
You’ll find detailed information about each type of fast in Fat for Fuel, including:
How to find the “right” fast for you
The fast that burns through your glycogen stores the quickest and pushes your body to start using fat for energy (You’ll want this one if you’ve just received a very serious diagnosis)
How to get the benefits of water fasting without the typical loss of energy
How to quickly shed your cravings for sweets and carbs while fasting
How to optimize your body’s repair and rejuvenation processes
How to use timing to reap many of the same benefits as long-term calorie restriction without the pain, suffering, and compliance challenges
How to know if fasting is safe for you (Especially if you have low blood pressure, thyroid disease, diabetes, cardiovascular disease, or are taking diuretics or blood pressure medications)
The fast where you’re still eating food (This may be a tougher approach!)
What you need to know about exercising while fasting
How to fast without upsetting your body’s circadian rhythm
A quick trick to help extend your fast while warding off your hunger without raising your blood sugar (Many will enjoy this taste treat!)
The 3-hour window when you never want to eat (To help optimize your mitochondrial function and prevent cellular damage and faster aging)
My favorite form of fasting – and the one I personally use (It’s the easiest to maintain once you’ve shifted over to fat-burning)
Is There Life After MMT?
As I show in Fat for Fuel, switching to burning fat as your primary fuel is a very powerful strategy for improving the health of your mitochondria, and in turn, your overall health.
But maybe you’re wondering, “Do I have to eat this way for the rest of my life?”
The short answer is, no you do not. In fact, I don’t want you to.
In Fat for Fuel, I help you determine how long is enough for you based on your genetic and mitochondrial differences, as well as any hormonal challenges you may have.
MMT is not intended to be a long-term deprivation diet. Once you regain the ability to burn fat as your primary fuel you’re ready to listen to your body and increase the flexibility in your diet.
By mimicking the eating pattern of many of our ancient ancestors, you can use what I call “feast-famine cycling,” a strategy that many in the body-building community have embraced to optimize their performance.
There are multiple ways to use this clever strategy and I review them all in Fat for Fuel. When done correctly, you’ll enjoy a greater variety of delicious, wholesome foods without harming your body’s newly regained ability to burn fat.
And I think you’ll agree… With greater variety and flexibility, it’s much easier to stick to a lifetime of healthy eating!
The Stealth Threat Facing Every Man And Postmenopausal Woman, Exposing You To Obesity, Cancer, Cognitive Decline, And Heart Disease
My MMT Program helps control the production of damaging ROS and secondary free radicals in three important ways. The first two are the foods you eat and when you eat them.
The third is such a serious threat to overall health that it absolutely astounds me that more doctors aren’t giving it the attention it deserves, including many holistic practitioners.
This threat targets every single man and postmenopausal woman, and it isn’t related to a reckless lifestyle or poor eating habits.
You could even be following my MMT eating plan and be at high risk for this health-wrecking threat!
I’m talking about iron.
Excess iron can lead to one of the most dangerous reactions in your body — the Fenton reaction — that decimates your mitochondrial DNA, proteins, and membranes and contributes to system-wide inflammation.
And all you may initially notice is some joint pain, fatigue, gut pain, memory fog, or an irregular heartbeat!
Even moderately elevated levels of iron can contribute to:
Obesity — Obese individuals are more likely to have high levels of iron in their bodies.
Cancer — Elevated levels of iron are found in patients with many types of cancer, including breast cancer, melanoma, pancreatic cancer, renal cell carcinoma, and Hodgkin’s lymphoma.
Alzheimer’s, Parkinson’s and ALS — High levels of iron in your brain tissue (which can easily happen as you age) can lead to cognitive impairment and inflammation.
Cardiovascular disease — Women’s risk of heart disease rises significantly after they either go through menopause or have a hysterectomy (and stop losing blood each month through menses).
Diabetes — Men with high iron stores were found to be 2.4 times as likely to develop Type 2 diabetes as men with lower levels.
The growth of pathogens — High iron levels facilitate the growth of disease-causing bacteria, fungi, and protozoa.
Osteoporosis — Too much iron in your body can damage your bones, but unfortunately, symptoms don’t typically appear until your levels are dangerously high.
What You Learn About Iron In Fat For Fuel Could Literally Save Your Life
Many doctors, including some Naturopathic physicians, aren’t doing the right test to give you the information you need about your iron levels.
Yet, they’ll insist they know best, and may even try to talk you out of the test you really need.
It’s much easier to manage your situation if you discover your high levels early, which is just one of the reasons why I’ve become so passionate about this topic.
Fat for Fuel is your guide to repairing and nourishing your mitochondria. But, you simply can’t optimize your mitochondrial health – or that of your entire body – if you have excess iron.
I’ve dedicated an entire chapter to the topic of excess iron, where you’ll learn:
The real test that you need to find out how high your levels truly are
The ideal range you want to maintain (it’s not what labs and most doctors consider “normal”)
The 7 things that increase your absorption of iron (it’s not only cast iron pans)
What to avoid eating or drinking with a steak to minimize your absorption of iron from red meat
The fastest way to lower excess iron levels (and what I do each month to help maintain safe low levels)
The 6 alternative strategies that can lower your absorption of iron as much as 95 percent
The 3 popular beverages that help protect you from the iron in foods
When never to take vitamin C or calcium supplements as they can increase your absorption of unwanted iron
The controversial strategy that provides the same iron level reduction as donating blood (it even provides up to a 75 percent lower rate of certain cancers), but it may not be for everyone
Your iron levels are so crucial, I’ve made getting them tested the right way a prerequisite before proceeding with my MMT plan!
10 Bonus Strategies To Boost Your Mitochondrial Health
Without question, my MMT diet is the most effective way to improve the health of your mitochondria. But it’s not the only way…
In Fat for Fuel, I outline 10 other powerful strategies for boosting mitochondrial health. At least half of them you can do at home without any special tools or equipment!
In this bonus chapter, I show you:
How to use photobiology to create energy to improve your mitochondrial function (first, make sure your cells have enough of this beneficial fatty acid)
The two-part strategy to gain a powerful synergy that could help reverse any health challenge
How to use light to deeply penetrate your tissues to deliver energy to your mitochondria for increased ATP production (it must be this certain hard-to-find wavelength!)
How to renew damaged proteins inside your cells, inside of allowing them to accumulate and form plaque deposits in your brain and vascular systems
The inexpensive tool to help protect your circadian rhythms and natural melatonin production to help you sleep better at night and help lower your cancer risk
The simple change you can make in your home to nearly duplicate the sun’s healthy, natural lighting for your eye health
What to do if you wake up before sunrise, especially during the darker months of winter (and continue to do it until the sun rises)
How to stimulate the production of new mitochondria and boost the destruction of diseased ones
The 20-second trick to double your body’s production of norepinephrine for improved focus and attention and to boost mood and alleviate pain
The four supplements to avoid if you have (or suspect) cancer as they can make cancer cells stronger and more resistant to anti-cancer treatment (this is a mistake many natural medicine practitioners make!)
The ancient healing method that’s been shown to be useful in treating pain conditions, depression, age-related mental decline, and Alzheimer’s (I use it every night to help quell free radicals and protect against EMFs)
Two ways to help your body increase levels of healthier “structured” water inside your cells and two simple ways to create it yourself from regular drinking water
Why My Book May Not Be For Everyone
Chances are if you’re still reading this, Fat for Fuel is exactly what you need to make significant strides in your health.
But I’ll be very blunt… Fat for Fuel isn’t for everyone.
If all you want are some smart but quick fixes, this is not the right book for you.
If you just want to upgrade your nutrition and improve your eating habits and overall health with small, simple tweaks to what you’re doing now, you may be better served by my last book Effortless Healing.
Effortless Healing walks you through nine powerful principles or steps that you can apply right away to your daily life to create healthy new habits and radically improved health.
Or you can go to Mercola.com and review the Nutritional Plan on the right side of the home page. Here you’ll find plenty of useful information, and if you sign up for my free newsletter, you’ll receive regular cutting edge health updates.
Fat for Fuel digs deeper – much deeper – into the very source of cancer, obesity, diabetes, mental decline and other chronic diseases that are affecting Westerners especially in epidemic numbers.
And it provides a real solution that works.
However, you’ll have to do more than just read the book… Getting the amazing benefits and results that my MMT plan offers takes a focused commitment and action.
Is Fat For Fuel For You?
“This book should be read by anyone interested in maintaining their health without toxic pharmaceuticals.”
— Thomas Seyfried, Ph.D.
Author of Cancer as a Metabolic Disease and professor of biology at Boston College
To help you decide if Fat for Fuel: A Revolutionary Diet to Combat Cancer, Boost Brain Power, and Increase Your Energy is right for you, take a moment and see if any of these statements resonate with you:
You have a serious health issue and need effective help now
You’re frustrated with your current health treatments and feel like there’s something missing in your care
You’d like to see a chronic condition ease up or disappear entirely (be sure to work with your health care provider as you may need to reduce or eliminate medications as your health improves!)
You want to lose weight (and keep it off) without sacrificing lean muscle mass
You’d like to get rid of your “brain fog” and enjoy greater mental clarity
You want to stay healthy and live independently for as long as possible
You’d like more sustained energy for everyday tasks and for the things you enjoy doing
You need to lower your fasting blood glucose levels, regain insulin receptor sensitivity and reduce inflammation throughout your body
You’ve dabbled with a low carb or ketogenic diet and would like to learn how to customize it for real results
You’re following a ketogenic, low carb or whole foods diet now and want to take it to the next level
You’d like to go through your day without feeling excessively hungry and craving sweets and carbs
You want to experience improved digestion, less bloating and reflux, and more regular bowel movements (a 2016 autism study confirms that you may notice significantly improved gut and microbiome health)
If you agree with just one of these statements, then I can assure you there is solid value waiting for you within the covers of Fat for Fuel.
Dr. Perlmutter Praises Fat For Fuel
Dr. David Perlmutter, board-certified neurologist and author of the #1 New York Times bestseller Grain Brain and The Grain Brain Whole Life Plan has provided his endorsement to Fat for Fuel. He states:
“…Fat for Fuel eloquently presents the leading edge of science, exploring how best to power your body. This is a life-changing text that not only provides a deep dive into why choosing fat as our primary fuel source powerfully correlates with health and disease resistance, but also delivers in terms of how the reader can easily bring about this fundamentally important change.”
Get Rewarded When You Take Action Now
Maybe you feel like you have time to wait before making profound changes to your health. Or maybe you don’t.
Either way, I believe in rewarding action.
The strategies I present in Fat for Fuel: A Revolutionary Diet to Combat Cancer, Boost Brain Power, and Increase Your Energy are just too important for your health and well-being to set aside and “wait until the timing feels right.”
You’re growing older each day. Your body is producing fewer mitochondria, so that puts you at a disadvantage right from the gate. Time really may not be on your side.
Acetylcholine/Choline Deficiency in Chronic Illness – The Hunt for the Missing Egg.
Those who lack choline are prone to mental illness, heart disease, fatty liver and/or hemorrhagic kidney necrosis and chronic illness as choline is oxidized to betaine which acts as an important methyl donor and osmolyte. With fatty liver, a person can be prone to diabetes and other chronic illness. Eggs are rich in choline. Choline is also found in a wide range of plant foods in small amounts. Eating a well-balanced vegan diet with plenty of whole foods should ensure you are getting enough choline. Soymilk, tofu, quinoa, and broccoli are particularly rich sources.
Eggs are an excellent source of choline and selenium, and a good source of high-quality protein, vitamin D, vitamin B12, phosphorus andriboflavin. In addition, eggs are rich in the essential amino acid leucine(one large egg provides 600 milligrams), which plays a unique role in stimulating muscle protein synthesis.
We hear a lot about vitamins and minerals such as B12, folate, magnesium, vitamin C, and so on, but there seems very little talk these days on the importance of dietary lecithin and choline. Are you consuming an adequate amount of acetylcholine, or other phospholipids? The odds are that you are not.
A little bit about choline
The human body produces choline by methylation of phosphatidylethanolamine (from dietary sources such as lecithin and others) to form phosphatidylcholine in the liver by the PEMT enzyme. Phosphatidylcholine may also be consumed in the diet or by supplementation. Choline is oxidized to betaine which acts as an important methyl donor and osmolyte.
For those wanting to see how this relates to the methylation cycle, below is a nice graphic (courtesy of Wikipedia).
It is well known that magnesium deficiency is widespread (57% of the population does not meet the U.S. RDA according to the USDA), but the numbers for choline deficiency are even more shocking.
According the National Health and Nutrition Examination Survey (NHANES) in 2003-2004, only about 10% of the population have an adequate intake of choline. This means about 90% of the population consumes a diet deficient in choline. Furthermore, those without an adequate intake of choline may not have symptoms.
Along with folate and B12 deficiency, inadequate consumption of choline can lead to high homocysteine and all the risks associated with hyperhomocysteinaemia, such as cardiovascular disease, neuropsychiatric illness (Alzheimer’s disease, schizophrenia) and osteoporosis. Inadequate choline intake can also lead to fatty liver or non-alcoholic fatty liver disease (NAFLD).
The most common symptoms of choline deficiency are fatty liver and/or hemorrhagic kidney necrosis. Consuming choline rich foods usually relieve these deficiency symptoms. Diagnosing fatty liver isn’t as simple as running ALT and AST since nearly 80% of people with fatty liver have normal levels of these enzymes according to a population study published in the journal Hepatology. In fact, in an experiment, 10 women were fed a diet low in choline. Nine developed fatty liver and only one had elevated liver enzymes.
Estrogen and Choline Deficiency
Given the connection between low lipids and choline deficiency, it would be tempting to think that as long as someone has enough cholesterol and TG that they will be protected from choline deficiency. Unfortunately this is not the case. Having adequate lipids does indeed help support healthy choline levels, but it does not guarantee a person will avoid choline deficiency. The truth is that choline deficiency can come from more than one source. Both sex hormone levels and genetic SNPs may lead to a choline deficiency by influencing the PEMT enzyme – the enzyme responsible for synthesis of choline inside the body. Recent research now confirms how hormones and genetic polymorphisms play a major role in choline deficiency.
The body can make choline only one way; that is by methylating a molecule of phosphatidylethanolamine (PE) into a molecule of phosphatidylcholine (PC). The body’s only method for accomplishing this is via the enzyme PEMT (phosphatidylethanolamine N-methyltransferase) which is found in the liver, brain, muscle, fat and other tissues.1,2 As with other well-known methylation enzymes like MTHFR and COMT, the PEMT enzyme can have genetic SNPs that slow it down. When this enzyme slows down the body cannot make choline in high amounts and choline deficiency is more likely. But there is more to the story of PEMT than just polymorphisms. In addition to being slowed by SNPs, PEMT is also dependent upon the hormone estrogen for activation. 1, 3 What this means is that the PEMT enzyme, the body’s only method of synthesizing choline, has not one but two Achilles heals. The PEMT pathway and how it relates to phosphatidylcholine production is shown in Figure 1.3 below.
Figure 1.3 – PEMT is shown as the rate-limiting reaction in the production of phosphatidylcholine inside the human body. Due to genetic and hormonal variances, most people have a PEMT enzyme working too slow and are susceptible to choline deficiency when there is not enough choline in the diet. ACoA – Acetyl-CoA; TG – Triglycerides; PE – phosphatidylethanolamine; PC – phosphatidylecholine; PEMT – phosphatidylethanolamine N-methyltransferase.
As mentioned above, the sex hormone estrogen is intimately linked with the production of choline. Women have a biological advantage here as the premenopausal female body has much higher levels of estrogen than does the male body. When a woman becomes pregnant this advantage is taken to an extreme, as pregnancy increases estrogen levels over 30 times normal.4 A successful pregnancy requires high amounts of nutrients delivered to the growing baby, esp. choline. Since the mother’s body is building a human being from scratch, there is an added burden on her biology to provide enough nutrition to her growing baby. Viewed from this perspective, the high estrogen levels during pregnancy can be seen to act like a biochemical insurance policy. Since the PEMT enzyme requires estrogen to function, pregnancy allows a woman to make extra choline for her developing child. Furthermore, the nervous system is the first system to form in utero and is a tissue that requires high levels of choline for proper development.5, 6 Choline plays such an important role in cell membranes, myelin sheaths, and nervous system tissue that the high estrogen levels during pregnancy help make sure the growing brain and nervous system is nourished. It is a genius system that assures the health and survival of the child.
Even though Nature has conferred an advantage to females by providing them with higher estrogen levels, esp. during pregnancy, this alone cannot protect against a lack of choline in the diet. All the estrogen in the world will not save a woman from choline deficiency if the gene responsible for producing choline is slowed down by a polymorphism. Genetic research has shown that the gene responsible for synthesizing choline, the PEMT gene, is susceptible to common polymorphisms which alter its function by slowing it down. In a recent study looking at a population in North Carolina, men and women of various ages were placed on a choline-deficient diet. They were followed closely for up to 42 days on a low choline diet consisting of less than 50mg choline per day. Throughout the study, the participants’ liver function was continuously assessed for any sign of fatty liver and damage. After eating a choline deficient diet for just six weeks, 63% of participants developed liver dysfunction and choline blood levels dropped 30% in every single participant, including premenopausal females.7 During this six week trial of low dietary choline the odds of developing liver dysfunction were 77% for men, 80% for postmenopausal women and just 44% for premenopausal women.7 Based on what has been discussed so far about estrogen and choline, it makes sense that men and postmenopausal women would be more susceptible to developing fatty liver since they don’t have high estrogen levels. And based on the fact that estrogen levels drive choline production, premenopausal women should have been protected from fatty liver since they make higher amounts of choline – but that was not the case.
With dietary choline restricted to just 50 mg/day, approximately half of the premenopausal group also suffered liver dysfunction, suggesting that a choline deficient diet can even harm women with higher estrogen levels. In addition, blood tests revealed that premenopausal female experienced a 30% loss of choline on a low choline diet right along with everyone else. Despite the fact that higher estrogen levels allow fertile women to make more choline, many were not able to make enough to avoid problems. A PEMT gene polymorphism is the only mechanism that can explain how women with high estrogen levels are still susceptible to choline deficiency when placed on a low choline diet.
Just like many individuals in the population, some of the premenopausal women inherited one or two copies of the PEMT gene which slows down the production of choline. This study showed that fatty liver occurred in 80% of the premenopausal women with two copies of PEMT and in 43% with only one copy of PEMT.8 What this means is that a premenopausal woman with two copies of the slowed PEMT gene has exactly the same risk of fatty liver as a postmenopausal woman. It is as if inheriting two copies of the PEMT gene effectively shuts off all estrogen-related choline production in the body. If a woman only has a single copy of the slowed PEMT gene, she will still have a roughly 50% chance of liver dysfunction on a low choline diet. Thus a single copy of the gene is only slightly better than two copies, as at least some estrogen-related choline production is preserved.
If having a PEMT gene can put one at risk for choline-related diseases like fatty liver, then it is important to know how common these genes are in population. We know that 74% of all women in the study had a SNP in the PEMT that made their PEMT enzyme unresponsive to estrogen.9 This means that only 26% of women can make enough choline on a low choline diet; and that ability depends on whether the woman is still fertile or has entered menopause. In this way genetics can take away the biological advantage that high estrogen levels usually offer to premenopausal females. Women with these PEMT genes will be at risk for choline deficiency and liver damage just like all men and post-menopausal women – two groups who don’t have enough estrogen to make choline regardless of their genes. Due to all the interference from the PEMT gene, dietary choline levels must be optimized for the vast majority of our population.
Summary of PEMT and Choline Deficiency:
In humans, choline is only made by the PEMT enzyme
Estrogen is required for the PEMT enzyme to activate and function normally
Men and postmenopausal women have an elevated risk of choline deficiency due to low estrogen levels.
The PEMT enzyme is commonly slowed down by polymorphisms, making it unresponsive to estrogen levels
74% of women have at least one copy of a slowed PEMT
Homozygous carriers of PEMT have much higher risk of choline deficiency
Men, postmenopausal women, and premenopausal women with PEMT SNPs need to increase choline intake in the diet to offset elevated risk of liver dysfunction
The take away here is that studies have recently shown that because of common genetic polymorphisms, choline deficiency is a widespread problem. Normally the hormone estrogen allows the body to make choline from scratch. However, genetic variation in the PEMT enzyme, estrogen levels and gender differences prevent most people from making adequate choline. Realistically then the only group in our population who is protected from choline deficiency are premenopausal females without a single copy of the slowed PEMT gene. Every single male, every single postmenopausal woman, and 74% of premenopausal woman all require daily intake of approx. 500 mg of choline to prevent fatty liver, organ damage, and the associated health problems.7 If the body is already depleted, then levels that simply prevent deficiency won’t be enough to replete the body. In these cases, higher daily doses of at least 1 gram or more are needed to replenish the tissues. Choline it seems must be absorbed from the diet in just about everyone except for the few young women who have a normal PEMT gene and can synthesize choline regardless of dietary intake.
1 Resseguie ME, da Costa KA, Galanko JA, et al. Aberrant estrogen regulation of PEMT results in choline deficiency-associated liver dysfunction. J Biol Chem. 2011 Jan 14;286(2):1649-58.
2 Tehlivets O. Homocysteine as a risk factor for atherosclerosis: is its conversion to s-adenosyl-L-homocysteine the key to deregulated lipid metabolism? J Lipids. 2011;2011:702853. Epub 2011 Aug 1.
3 Wallace JM, McCormack JM, McNulty H, et al. Choline supplementation and measures of choline and betaine status: a randomised, controlled trial in postmenopausal women. Br J Nutr. 2012 Oct;108(7):1264-71. Epub 2011 Dec 15.
4 Guyton AC, Hall JE. Textbook of Medical Physiology, 11th ed. Philadelphia, PA: Elsevier, 2006, p. 1033.
5 Sadler, TW. Medical Embryology, 10th ed. Baltimore, MD: Lippincott Williams & Wilkins, 2006, p. 86.
6 Steinfeld R, Grapp M, Kraetzner R, et al. Folate Receptor Alpha Defect Causes Cerebral Folate Transport Deficiency: A Treatable Neurodegenerative Disorder Associated with Disturbed Myelin Metabolism. Am J Hum Genet. 2009 September 11; 85(3): 354–363.
7 da Costa KA, Kozyreva OG, Song J, et al. Common genetic polymorphisms affect the human requirement for the nutrient choline. FASEB J. 2006 Jul;20(9):1336-44.
8 Fischer LM, da Costa KA, Kwock L, et al. Dietary choline requirements of women: effects of estrogen and genetic variation. Am J Clin Nutr. 2010 Nov;92(5):1113-9. Epub 2010 Sep 22.
9 Zeisel SH. Nutritional genomics: defining the dietary requirement and effects of choline. J N
When you are ready to have a better understanding of your human genome responsible for a majority of known disease-related variants that can help you and your doctor monitor and predict your health and be proactive with disease related challenges in the future to achieve a better health outcome, you may use this letter.
Disease prediction, senior care and health concierge
Exome sequencing provides a cost-effective alternative to whole genome sequencing as it targets only the protein coding region of the human genome responsible for a majority of known disease related variants. Whether you are conducting studies in rare Mendelian disorders, complex disease, cancer research, or human population studies, Novogene’s comprehensive human whole exome sequencing service provides a high-quality, affordable and convenient solution.
Novogene’s bioinformatics analysis includes data QC, mapping with reference genome, SNP/InDel, somatic SNP/InDel calling, statistics and annotation. Novogene utilizes internationally recognized software in bioinformatics analysis, e.g. BWA, SAMtools, GATK, etc.
In particular, Novogene bioinformatics pipeline includes annotation with the exome aggregation consortium (ExAC). ExAC dataset spans 60,706 unrelated individuals sequenced as part of various disease-specific and population genetic studies. This population scale database greatly facilitates research of disease pathogenesis.
The Novogene Advantage
Unsurpassed data quality: We guarantee a Q30 score ≥80%, exceeding Illumina’s official guarantee of ≥75%. See our data example.
State-of-the-art exome capture: Agilent SureSelect Human All Exome V6 (58 M) is used.
Accurate variant calling with longer read length up to 150 bp.
Extraordinary informatics expertise: Novogene uses its cutting-edge bioinformatics pipeline and internationally recognized best-in-class software to provide customers with “publication-ready data”.
Agilent SureSelect Human All Exon V6 Kit
180~280 bp insert DNA library
HiSeq platform, paired-end 150 bp
Data Quality Guarantee
We guarantee that ≥ 80% of bases have a sequencing quality score ≥ Q30, which exceeds Illumina’s official guarantee of ≥ 75%.
For fresh sample: ≥ 1.0 μg (a minimum of 200 ng can be accepted with risk)
For FFPE sample: ≥ 1.5 μg
DNA concentration: ≥ 20 ng/μl
DNA Volume: ≥ 10 μl
OD260/280 = 1.8 – 2.0 without degradation or RNA contamination
Within 22 working days after verification of sample quality (without data analysis)
Additional 5 working days for data analysis
Recommended Sequencing Depth
For Mendelian disorder/rare disease: effective sequencing depth above 50×
For tumor sample: effective sequencing depth above 100×
1. Variant filtering
2. Analysis under dominant/recessive model (Pedigree information is needed)
2.1 Analysis under dominant model
2.2 Analysis under recessive model
3. Functional annotation of candidate genes
4. Pathway enrichment analysis of candidate genes
5. Linkage analysis
6. Regions of homozygosity (ROH) analysis
1. Variant filtering
2. Analysis under dominant/recessive model (Pedigree information is needed)
2.1 Analysis under dominant model
2.2 Analysis under recessive model
3. Functional annotation of candidate genes
4. Pathway enrichment analysis of candidate genes
5. De novo mutation analysis (Trio/Quartet)
5.1 De novo SNP/InDel detection
5.2 Calculation of de novo mutation rates
6. Protein-protein interaction (PPI) analysis
7. Association analysis of candidate genes (at least 20 trios or case/control pairs)
Cancer (for tumor-normal pair samples)
1. Screening for predisposing genes
2. Mutation spectrum & mutation signature analyses
3. Screening for known driver genes
4. Analyses of tumor significantly mutated genes
5. Analysis of copy number variations (CNV)
5.1. Analysis of CNV distribution
5.2.Analysis of CNV recurrence
6. Fusion gene detection (for WGS porject only)
7. Purity & ploidy analyses of tumor samples
8. Tumor heterogeneity analyses
9. Tumor evolution analysis
10. Display of genomic variants with Circos
(Reuters Health) – Women whose breasts are composed mainly of dense glandular tissue rather than fat may have higher odds of developing breast cancer, a recent study suggests.
Researchers examined data on more than 18,000 women with breast malignancies and 184,000 women the same age without breast cancer. They found breast density appeared to be the biggest indicator of cancer risk, even more than other common risk factors like family history or waiting until after age 30 to have babies.
“Women with dense breasts have a roughly 2-fold higher breast cancer risk relative to women with non-dense breasts,” said lead study author Dr. Natalie Engmann of the University of California, San Francisco.
This is a problem because 60 percent of younger women have dense breasts and so do 40 percent of older women who have gone through menopause – and because dense breasts make tumors harder to detect on mammograms, Engmann said.
“Our findings suggest that because breast density is a strong, common risk factor that can be modified, reducing the number of women with dense breasts may prevent a substantial proportion of breast cancer cases,” Engmann added by email.
The results don’t mean that breast density would be the most meaningful risk factor for every woman, however. Rather, from an epidemiology standpoint they explain many cancer cases in the general population because so many women have dense breasts.
In the study, researchers examined data on women with four categories of breast density: almost entirely fat, mostly fat with some dense tissue, moderately dense and predominantly dense.
Then, they looked at several known breast cancer risk factors: women’s weight, family history of the disease, personal history of benign biopsy results, breast density and having a first baby after age 30.
About 39 percent of breast cancer cases before menopause and 26 percent of cases afterwards might be prevented if women in the two highest breast-density categories had less dense breast tissue, the study team calculated.
There isn’t much women can do to reduce breast density, the authors acknowledge. One drug, tamoxifen, reduces cancer risk and breast density but it has serious side effects and generally isn’t recommended to women unless they have a high risk of cancer.
Gaining weight tends to add fatty tissue to the breasts and lower density, but obesity is independently tied to an elevated risk of breast cancer in older women, the study also found.
In fact, roughly 23 percent of breast cancers in older women might be prevented if overweight or obese women shed enough pounds to achieve a healthy weight, the researchers also calculated.
Still, compared to breast density or obesity, some other common risk factors didn’t appear to explain as many cancer cases in the general population. Family history was linked to about 9 percent of cases for younger women and 8 percent in older women, for example, while delayed childbirth was tied to 9 percent of cases for younger women and 5 percent for older women.
One limitation of the study is that it didn’t look at certain risk factors like genetic mutations that can greatly increase the odds of breast cancer for individual women, the authors note.
Only 5 percent to 10 percent of breast cancers diagnosed in the U.S. are due to inherited gene mutations linked to breast cancer, according to the National Cancer Institute (NCI). Women with these mutations, however, are much more likely to develop cancer, and to have aggressive tumors that are hard to treat.
It’s unclear that women can do anything to reduce breast density, but it may make sense for them to consider screening alternatives to mammograms, said Dr. Christine Berg, a NCI researcher who wasn’t involved in the study.
“I think it makes more sense for a woman with dense breasts, particularly with other risk factors, to discuss with her doctor and the radiologist whether or not she would benefit from other types of screening such as MRI,” Berg said by email. “Breast tomosynthesis is an emerging technology which I think is better than standard mammography.”
Berg also recommended a calculator (here: http://bit.ly/2knIYuH) developed by the Breast Cancer Surveillance Consortium for women to assess their individual risk.