One of the important questions plaguing most women during their middle age is whether they should opt for menopausal hormone therapy to alleviate menopausal symptoms.
Many women in this delicate phase count fretfully the number of sleepless nights, the night sweats and hot flashes that interrupt their otherwise normal life.
The U.S Centers for Disease Control and Prevention analyzed a 2015 National Health Interview survey (NHIS) and found that over 56% of perimenopausal women failed to get sufficient sleep.
The dwindling levels of estrogen has been associated with the classic symptoms of menopause, which led people to believe that menopausal hormone therapy could lower the intensity of symptoms.
This made estrogen supplementation very popular during the late 1960s with the belief that it could make women ‘young forever’.
FDA approval for estrogen therapy for osteoporosis helped gain confidence of more women, with observational studies conducted in 1990s showing reductions in coronary heart disease and Alzheimer’s.
The first study that raised an alarm about the use of menopausal hormone therapy and breast cancer risk was the Women’s Health Initiative study. This study found that for every 10,000 person-years of use of menopausal hormone therapy (MHT) use, there were 8 more invasive breast cancers.
Estrogen is a female hormone which is mostly produced in the ovaries. During breast development, the DNA present in the cells is constantly copied before the development of new breast cells.
This delicate process could increase the risk of development of genetic abnormalities.
Estrogen plays an important role in breast tissue development and supplementation with this hormone during menopause, therefore, has been shown to be associated with an increased risk for breast cancer.
The results of the Women’s Health initiative study led to a considerable drop in the use of hormone therapy in the U.S.
The assumption was that women would use it for a short period of time with the risk of breast cancer being uniform.
However, a large study conducted by the Breast Cancer Association Consortium on perimenopausal women showed that specific genetic variants modified the effect of hormone therapy use on the risk of breast cancer.
The study included a large sample size and three loci present on the chromosomes 13, 14 and 16 were found to alter breast cancer risk on menopausal hormone therapy use.
Women who had more than 5 or 6 high risk variants were found to have an 86% increased risk for breast cancer on MHT use while there was no association with breast cancer risk on MHT use among women with fewer than 2 risk variants.
The results of the study should stress the importance of identifying genetic variants and weighing the relief of symptoms against the unhealthy legacy of taking these medications.
You can now find out if you carry the variants associated with Menopausal hormone therapy and breast cancer risk from Xcode’s Breast Cancer report by uploading your 23andMe or any other Ancestry DNA raw data.
You can read more about the Xcode Breast Cancer report here.
When 23andMe receives your saliva sample, it extracts cells (mostly cheek cells) from your saliva, then breaks down the cell and nucleus to get your DNA. Your DNA is then purified and multiplied several folds to make it easily detectable.
23andMe uses a “genotyping chip” to detect your DNA data. What part of your DNA is detected depends on which chip was used. 23andme has used different chips over the years. Think of it in terms of smart phones. Each year, new versions of chips are released with more and more functionality than the previous version. Similarly, the DNA chips are constantly upgraded and the latest “chip” is typically better than the previous version in terms of how much information it detects from your DNA.
In 2017, 23andMe migrated from the Illumina OmniExpress chip that was used across multiple ancestry DNA companies. The current 23andme v5 chip, the Global Screening Array (GSA) is a next-generation genotyping array for population-scale genetics, variant screening, pharmacogenomics studies, and precision medicine research. This version of the chip has around 650,000 SNPs suitable for both ancestry and health testing.
Keep in mind that 23andme includes a list of their own unique features to the standard GSA chip.
According to Illumina, the GSA covers a multi-ethnic, genome wide markers with curated clinical research variants and markers that serve as quality control for precision medicine research. The content has been selected for high imputation accuracy specifically to the minor allele frequencies above 1%. All the 26 1000 Genomes Project populations have been considered. The balance between the health and ancestry markers is evident in that, variants with established associations with diseases, pharmacogenomic relevance have been included. The content is curated based on ClinVar, National Human Genome Research Institute (NHGRI), PharmGKB, Exome Aggregation Consortium (ExAc Database). In-built quality control markers enable sample identification for applications in large scale genomics and screening, which is very useful for companies with a huge customer demand like 23andMe.
The Illumina Omniexpress chip, is the current chip version for other popular companies like Ancestry DNA and Family Tree DNA. However given the demand for third party re-analysis from companies like Xcode Life, and GSA’s compatibility with these tools, all other ancestry companies are likely to migrate to this version. While the OmniExpress chip was satisfactory for the European populations, it could not be applied to the other populations. The GSA is more inclusive of other world populations.
Because there are so few overlapping markers between the GSA and the OmniExpress this change will also present problems for companies and third-party websites that accept autosomal DNA transfers. A choice will need to be made as to whether to do comparisons using only the overlapping markers or whether to experiment with imputation. Xcode’s platform caters to all major genotyping platforms across the ancestry DNA testing companies.
Those of you who purchased the 23andMe kit after August 2017, will have reports based on Illumina’s latest v5 chip. Given that this chip is the most conducive with health-related traits, let’s take a look at a list of all traits that you can do from the raw data file:
| CHIP | NAME | NO. OF SNPs | Applications |
| 23andMe | Major categories | ||
| v1 | HumanHap550+ | 576,000 |
|
| v2 | HumanHap550+ | 597,000 | |
| v3 | HumanOmniExpress+ | 992,000 | |
| v4 | HTS iSelect HD | 611,000 | |
| v5* | Global Screening Array (GSA) | ~650,000 | |
| Ancestry DNA | |||
| v1 | OmniExpress Genotyping BeadChip | 701,400 | |
| v2* | OmniExpress Plus Genotyping BeadChip | 669,000 | |
| Family Tree DNA | |||
| - | OmniExpress microarray chip | 696,800** | |
| Living DNA | |||
| - | Global Screening Array (GSA) | ~650,000 | |
| MyHeritage | |||
| - | OmniExpress microarray chip | 696,800** | |
*current chip
**Only for autosomal and the X chromosome
A haplogroup is a global extension of your family. Depending on the sequence of genetic markers that they carry in their cells people can be grouped into specific ancestry DNA haplogroups. A group of individuals belonging to the same haplogroup can trace their roots back to a common ancestor. This usually also points to a specific geographical point since each haplogroup has a definite migratory pattern. If you want to know more about the science behind these ancestry DNA haplogroups, you can refer here
Besides their common geography and migratory pattern haplogroups are characterized by a de novo mutation. These mutations are carried and undergo vertical transmission through subsequent generations. When sufficient number of people carry this single base change in their DNA sequence they will together form a haplogroup. Needless to say that it takes thousands for sufficient individuals to carry the mutation (now called polymorphism) and form a haplogroup.
Haplogroups are not permanent. They have in the past phased-out and formed new ones. Though some of them have successfully sustained themselves to the present day. Nearly 50% of all Europeans have the haplogroup H. This means that they have all descended from a single person who had lived thousands of years back.
The head of the maternal or paternal haplogroup within whom the set of gene variation first occurred.
New haplogroups are formed when a gene mutation occurs in someone from a particular ancestral clan. However, it is not before many generations that enough people carry the mutation for it to spread, become prevalent to be considered as a haplogroup. Any haplogroups that start forming today will not be recognized as new ones for centuries, or even millennia. The haplogroups that form today will eventually be able to be traced back to the earliest known person to carry the mutation, just as today’s known haplogroups can be traced back to the earliest known person to carry it in the distant past.
Everyone inherits the DNA within a cell organelle called the mitochondria from the mother only. Hence maternal haplogroups are defined using variants in an individual’s mitochondrial DNA. Another interesting fact about the mitochondrial DNA is that it does not undergo the process of recombination with other types of DNA (like your nuclear DNA). This means it is inherited as it is with limited changes directly from you mother. Therefore individuals with the same maternal line will share the same maternal haplogroup. Each maternal haplogroup traces back to a single mutation at a specific location and time.
Y chromosome is found exclusively in males (with the exception of individuals with Klinefelter’s syndrome). The Y chromosome undergoes genetic recombination with the X chromosome at a specific region called the pseudoautosomal region. In other words, this region of the Y chromosome behaves like an autosome in spite of being a sex chromosome. However this a very small fraction. Around 95% of the Y chromosome remains unchanged across generations. This is used to trace your paternal ancestry. Though females do not have a Y chromosome, they would share the same paternal haplogroup with another male member of the direct line (e.g father, brother).
Breast Cancer Prognosis using your 23andme BRCA1 raw data
Breast cancer prognosis is good when the cancer is detected earlier than when it is detected during the later stages of the disease. According to WHO, Breast Cancer is the most common malignancy among women, both in the developed as well as in the developing nations. Though this type of cancer is known to have a good prognosis, there are variations in survival, which is indicative of a genetic basis.
There have been considerable strides in developing candidate gene testing for breast cancer over the past 10 years with variants primarily identified in breast cancer susceptibility genes, microenvironment of the tumour and in genes associated with drug metabolism. Genome wide association studies have permitted the identification of gene variants that are located in genes which have never been associated with cancer susceptibility. The common breast cancer variant markers, commonly SNPs are found in the new v5 23andme chip. Hence it is possible to use your 23andme BRCA1 raw data to learn more about breast cancer prognosis.
Genetic Testing for Breast Cancer Prognosis:
A study conducted on a Swedish family with affected first degree family showed a higher risk of mortality, indicative of a genetic basis. Women with breast cancer are found to have 60 to 80% higher risk of mortality when they have first degree relatives with poor prognosis than if they have relatives with good prognosis. The association with prognosis was more definitive when the cancer was detected at a young age. If you have already done an ancestry genetic report for your family all you have to do is upload the your raw data onto our tool to learn more about breast cancer prognosis.
The host genetic makeup, apart from familial inheritance, plays an important role in the molecular profiling of the cancer subtype. Such differences could lead to altered molecular behaviour, affecting the prognosis of the patient.
Genetic susceptibility to certain cancers
In the Swedish study, there existed a smaller gap in the age at which the cancer was detected between sisters when compared with the age of diagnosis of breast cancer in the mother, suggestive of a larger genetic aspect in determining prognosis.
There is increasing evidence from research studies that specific gene variants are associated with specific types of cancer, which is, in turn, influence the survival of the individual. For example, BRCA1 is associated with early onset breast cancer, which is also associated with poor prognosis.
The gene variants carried by an individual could influence
This can be identified using your 23andme BRCA1 raw data.
Role of genetic variant implicated in breast cancer prognosis
One of the genetic variants associated with prognosis has been shown to regulate the expression of SNCG (Synuclein gamma) gene. Studies have shown that an increased expression of synuclein gamma is associated with an increase in the motility of cancer cells, contributing to their survival. This gene has also been implicated in late stage metastasis in breast and ovarian cancer.
Another genetic variant associated with prognosis is present near a gene which codes for a specific proteasome component. There is an increase in proteasome activity among tumor cells, associated with an increase in cell growth.
The biological associations of these genetic variants along with their association with prognosis in population studies, make them candidate genes for prognosis analysis.
Identifying the genetic variants that you carry will help in developing treatment strategies to improve prognosis. One study showed that hormone replacement therapy was associated with prognosis, while another study found that the number of pregnancies and the age at pregnancy was also associated with prognosis. Response to chemotherapy is also associated with genetic variants carried and this information can also be used to for a personalized treatment plan.
You can now find out if you carry the variants associated with breast cancer prognosis from Xcode’s Breast Cancer report by uploading your 23andme BRCA1 raw data or any other ancestry DNA raw data. You can read more about the Xcode Breast Cancer report here.
The FDA gave the go-ahead to 23andme in April of last year to provide information about an individual’s personal health risks. Now for an additional $100 23andme health report are available for more than 10 conditions.
The newly approved 23andMe health report focus on specific genetic variants related to 10 diseases or conditions:
| Genetic Health Risk Report | Wellness Report | Trait Report | Carrier Status Report |
| BRCA1/BRCA2 (Selected Variants) Age-Related Macular Degeneration Alpha-1 Antitrypsin Deficiency Celiac Disease G6PD Deficiency Hereditary Hemochromatosis (HFE‑Related) Hereditary Thrombophilia Late-Onset Alzheimer's Disease Parkinson's Disease | Alcohol Flush Reaction Caffeine Consumption Deep Sleep Genetic Weight Lactose Intolerance Muscle Composition Saturated Fat and Weight Sleep Movement | Ability to Match Musical Pitch Asparagus Odor Detection Back Hair (available for men only) Bald Spot (available for men only) Bitter Taste Cheek Dimples Cilantro Taste Aversion Cleft Chin Earlobe Type Early Hair Loss (available for men only) Earwax Type Eye Color Fear of Heights Finger Length Ratio Freckles Hair Photobleaching (hair lightening from the sun) Hair Texture Hair Thickness Light or Dark Hair Misophonia (hatred of the sound of chewing) Mosquito Bite Frequency Newborn Hair Photic Sneeze Reflex Red Hair Skin Pigmentation Sweet vs. Salty Toe Length Ratio Unibrow Wake-Up Time Widow's Peak | ARSACS Agenesis of the Corpus Callosum with Peripheral Neuropathy Autosomal Recessive Polycystic Kidney Disease Beta Thalassemia and Related Hemoglobinopathies Bloom Syndrome Canavan Disease Congenital Disorder of Glycosylation Type 1a (PMM2-CDG) Cystic Fibrosis D-Bifunctional Protein Deficiency Dihydrolipoamide Dehydrogenase Deficiency Familial Dysautonomia Familial Hyperinsulinism (ABCC8-Related) Familial Mediterranean Fever Fanconi Anemia Group C GRACILE Syndrome Gaucher Disease Type 1 Glycogen Storage Disease Type Ia Glycogen Storage Disease Type Ib Hereditary Fructose Intolerance Herlitz Junctional Epidermolysis Bullosa (LAMB3-Related) Leigh Syndrome, French Canadian Type Limb-Girdle Muscular Dystrophy Type 2D Limb-Girdle Muscular Dystrophy Type 2E Limb-Girdle Muscular Dystrophy Type 2I MCAD Deficiency Maple Syrup Urine Disease Type 1B Mucolipidosis Type IV Neuronal Ceroid Lipofuscinosis (CLN5-Related) Neuronal Ceroid Lipofuscinosis (PPT1-Related) Niemann-Pick Disease Type A Nijmegen Breakage Syndrome Nonsyndromic Hearing Loss and Deafness, DFNB1 (GJB2-Related) Pendred Syndrome and DFNB4 Hearing Loss (SLC26A4-Related) Phenylketonuria and Related Disorders Primary Hyperoxaluria Type 2 Rhizomelic Chondrodysplasia Punctata Type 1 Salla Disease Sickle Cell Anemia Sjögren-Larsson Syndrome Tay-Sachs Disease Tyrosinemia Type I Usher Syndrome Type 1F Usher Syndrome Type 3A Zellweger Syndrome Spectrum (PEX1-Related) |
A few more conditions have been added under this category ever since like Glycogen storage diseases, Leigh’s syndrome, Bloom’s syndrome, Sickle cell anemia, Tay Sach disease, Phenylketonuria etc.
Other than disorders the 23andme health report also covers some heritable traits listed below:
| Type 2 diabetes Hypertension Cardiovascular disease Obesity Thrombosis Familial Hypercholesterolemia Beta Thalassemia Atrial fibrillation Cardiomyopathy Hypertriglyceridemia Cystic fibrosis Depression Epilepsy Psoriasis Rheumatoid arthritis Scoliosis | Chronic Obstructive Pulmonary Disease (COPD) Non-Alcoholic Fatty Liver disease Ulcerative Colitis Stroke Bone Mineral Density Osteoarthritis Anxiety Depression Gallstone disease Glaucoma Gout Hemochromatosis Anemia Multiple sclerosis Crohn’s disease | Osteoporosis Age-related Macular Degeneration Chronic Kidney Disease Asthma Vitiligo Migraine Alzheimer’s Disease Parkinson’s Disease Schizophrenia Bloom’s Syndrome Beta Thalassemia Hemophilia Glycogen storage disease Alopecia Areata Anorexia |
However there are many more companies and online tools today who provide you with health information and you definitely don’t need a $100. The raw data that you receive after you take the ancestry genetic test from 23andme is your true treasure. Uploading it onto third party sites like Promethease, Xcode Life, Nutrahacker, Genetic Genie will give you information that both you and your specialist will find useful.
In contrast let’s look at what you get for $99 at Xcode Life:
Understanding the functioning of your nutritional metabolism is a prerequisite to healthy living. The nutrition report will help you translate the results from your DNA test into actionable recommendations that are suited to your genetic nature. Upload your 23andme raw data establish unique nutrition goals, tailor a unique diet plan according to your genetic metabolism of macronutrients, requirements of micronutrients and food sensitivities.
Categories covered under Gene Nutrition:
| Tendency To Overeat Tendency To Prefer Fatty Foods Tendency To Prefer Sweets Tendency To Prefer Bitter Vegetables Tendency To Gain Weight Carbohydrate Intake And Weight Gain Tendency Saturated Fats, Intake And Weight Gain Tendency | Mono Unsaturated Fats Intake And Weight Gain Tendency PUFA Intake And Weight Gain Tendency Protein Intake And Weight Loss Tendency Fibre Intake And Weight Loss Tendency Tendency To Regain Weight Vitamin requirements Calcium Needs Choline Deficiency | Copper Needs Iron Needs Magnesium Needs Phosphate Needs Zinc Needs Antioxidant Needs Caffeine Metabolism Alcohol Metabolism Gluten Sensitivity Lactose Intolerance Salt Intake And Blood Pressure Sensitivity. |
Optimizing your fitness routine requires a deep understanding of your body type. Without proper knowledge about yourself, you are bound to engage in lots of wasted effort through trials and errors. Studies have shown that a significant part of the athletic ability is inherited, meaning, its coded in the genes. Hence, understand your genetics makes a big difference in optimizing your fitness regimen according to your genetic nature.
Categories covered under Gene Fitness:
| Endurance Power Aerobic capacity Heart Capacity Lung Capacity Handgrip strength Tendon strength | Ligament strength Exercise motivation Likelihood of injury Likelihood of fatigue HDL cholesterol level with exercise Insulin sensitivity with exercise Weight loss or weight gain with exercise |
More than 30% of the Indian population suffers from at least one allergic disease. Do not wait for a sudden reaction to an exposure to learn about your allergies. Know of your genetic sensitivities to the most common allergens and protect yourselves from the allergens. Allergens are everywhere and easily affect those who are genetically susceptible to allergies.
Categories covered under Gene Allergy:
| Cockroach Allergy Dust Mites Allergy Pets Allergy Egg Allergy Milk Allergy | Peanut Allergy Pollen Allergy Histamine intolerance Misophonia Motion sickness |
A comprehensive assessment comprising of an analysis of around 200 genes pertaining to hypertension, heart diseases, obesity and type 2 diabetes. All these conditions are genetically- and lifestyle-mediated, and can be prevented by making appropriate dietary and lifestyle modifications. An early predisposition warning will help you from developing these conditions.
NOTE: These reports are to be interpreted only by your physician.
Categories covered under Gene Health:
| Type 2 diabetes Hypertension Cardiovascular disease Obesity Thrombosis Familial Hypercholesterolemia Beta Thalassemia Atrial fibrillation Cardiomyopathy Hypertriglyceridemia Cystic fibrosis Depression Epilepsy Psoriasis Rheumatoid arthritis Scoliosis | Chronic Obstructive Pulmonary Disease (COPD) Non-Alcoholic Fatty Liver disease Ulcerative Colitis Stroke Bone Mineral Density Osteoarthritis Anxiety Depression Gallstone disease Glaucoma Gout Hemochromatosis Anemia Multiple sclerosis Crohn’s disease | Osteoporosis Age-related Macular Degeneration Chronic Kidney Disease Asthma Vitiligo Migraine Alzheimer’s Disease Parkinson’s Disease Schizophrenia Bloom’s Syndrome Beta Thalassemia Hemophilia Glycogen storage disease Alopecia Areata Anorexia |
A genetic report for personalised and proactive skin care. Your skin type is unique in terms of its tone, collagen content, aging profile, oxidation, glycation among various other factors. Understanding genetic aspects of your skin helps you nurture it in the correct way.
Categories covered under Gene Skin:
| Glycation protection Contact Dermatitis Atopic Dermatitis Generalized Psoriasis Rosacea Dry Skin Folate deficiency Vitamin Deficiency Skin Antioxidant capacity | Freckles/Ephelides Sun spots/Lentigines Tanning response Wrinkle and Collagen degradation Response to Cellulite Striae Distensae/ Stretch Marks Varicose Veins Response to UV Radiation (UVR). |
34% of all clinically significant drug interactions have a genetic basis. Get the right medications at the right dose. The precision medicine report helps you avoid unnecessary side-effects from medications that may not work for you.The Xcode Precision Medicine report covers more than 150 drugs under various categories like cardiology, neuropsychiatry, antidiabetics and pain-related drugs.
NOTE: These reports are to be interpreted by your physician ONLY.
An MTHFR status report is one of the many indicators for identifying the risk of developing cardiovascular disease, or the risk for neural tube defects and sensitivity to methotrexate. This report profiles more than 70 known genetic polymorphisms in the MTHFR gene and related genes.
This test could help individuals presenting with the following conditions:
| Coronary Artery Disease Elevated Homocysteine Bipolar Disorder Schizophrenia Peripheral Vascular Artery Disease Acute Myocardial Infarction | Depression Stroke Venous Thromboembolism Migraines History of Preeclampsia Neural Tube Defects Recurrent Miscarriages Autism Spectrum Disorders |
Summary: 23andme health report is tuned towards informing an individual about rare diseases and physical and other characteristics. In contrast, Xcode Life health reports are designed to inform the individual about common and preventable health conditions (and recommendations to prevent these), your unique nutritional metabolism and nutrient requirements, your genetic body type and the fitness regimen most suited to your genetics and much more. The focus of Xcode Life health reports is to empower the individual with information about their genetics that will help them live a healthy life.
Get the Xcode MegaPack ($99) for all the above reports and more!
