What is a Haplotype? What is a Haplogroup?

One of the ways geneticists and genealogists help to distinguish the deep origins of a person’s maternal and paternal ancestors who lived thousands of years ago is through the identification of their haplogroup and haplotype.

Basically, a haplogroup is roughly equivalent to a person’s nation of origin. A haplotype is a subset of a haplogroup and helps to further drill down the nation and region of a person’s origin. Because some haplotypes are more common in certain haplogroups, it is many times possible to predict what a person’s haplogroup is based on what their haplotype is.

Haplotype is actually short for “haploid genotype” and refers to the combination of genetic markers in multiple locations in a single chromosome. If two people match exactly on all of the markers they have had tested, they share the same haplotype and are related.

The degree of relatedness can be predicted based on the number of markers that have been tested. The more markers tested and compared, the better and more accurate the prediction.

Haplogroups to refer to the single nucleotide polymorphism mutations (SNPs) that determine the clade that a collection of haplotypes belong.

Man originated in Africa and has migrated throughout the world since that time. As that migration has taken place, man has changed and adapted to his surroundings over thousands of years.

For example, in places where there is limited sun, man’s skin has lightened. To better protect against the cold of northern regions, man’s build has become more stocky and insulated. These changes have created different genetic compositions.

For identification purposes, these different genetic compositions are known as haplogroups. Haplotypes are subsets of various haplogroups.

How Many Haplogroups and Haplotypes are there?

All Y-chromosomal haplogroups can trace their common lineage from a Y-chromosomal Adam who is the most recent patrineal ancestor of all people living today.

It is believed he lived about 236,000 years ago. He was not the only man living at that time, he simply was the only man with an unbroken male line of descent to the present day. He is known as the “most common recent ancestor” which is sometimes designated as MCRA.

From this common ancestor, it is possible to create a family tree of sorts of the human race known as a Phylogenetic tree of Y-DNA haplogroups. The human Y-chromosome accumulates about two mutations per generation. Y-DNA haplogroups share hundreds or even thousands of mutations that are unique to each haplogroup.

The International Society of Genetic Geneaology has created the following Phylogenetic tree of the Y-DNA haplogroups. Because of continuing research, the structure of the Y-DNA Haplogroup Tree changes quite often to keep updated with the latest developments in the field.

The tree is chronological in nature with the oldest haplogroups appearing at the top of the tree, and the most recently created haplogroups appearing at the bottom of the tree.

For example, Haplogroup A’s possible time of origin is estimated at 236,000 years ago. Haplogroup F is believed to have originated about 65,900 years ago in Eurasia. And Haplogroup R possibly originated about 31,900 years ago in Asia.

Within each of these broad haplogroups, there are sub-haplogroups with various designations as well that have developed through ongoing genetic mutations.

For example, Haplogroup R-M420 (R1a) is believed to have originated 22,800 years ago in Eurasia. Haplogroup E-M191 is thought to have originated about 7,400 years ago in East Africa while more recently, Haplogroup R1a-M458 originated out of Eastern Europe approximately 4,700 years ago.

In broad strokes, here are the major Haplogroup geographic locations:

• Haplogroup A is found mainly in Southern Africa and represents the oldest Y-chromosome haplogroup.
• Haplogroups BT and CT are found predominantly in Africa but separated by about 50,000 years or possible origin
• Haplogroup F is found predominantly in Eurasia starting about 65,900 years ago.
• Haplogroup E is found in East Africa or Asia. Haplogroup E1b1a is predominantly found among sub-Sahara African populations. Haplogroup E1b1b is predominantly found around the coast of the Mediterranean.
• Haplogroup G has found throughout in Europe, northern and western Asia, northern Africa, the Middle East and India.
• Haplogroup J and its subgroups are found primarily around the coast of the Mediterranean and the Middle East. J subgroups are often associated with Jewish populations.
• Haplogroup I and its subgroups are mostly found in northwestern Europe (Scandinavia) and central Europe and include ancestors of Viking heritage.
• Haplogroup N is found in northeastern Europe and especially in Finland.
• Haplogroup Q is primarily associated with Native American populations.
• Haplogroup R1a and its subgroups are predominantly found in eastern Europe and in western and central India and Asia. In eastern Europe, it is frequently associated with Slavic populations.
• Haplogroup R1b and its subgroups are predominantly found in western Europe and the British Isles. It is the most common haplogroup in Europe.

The following National Geographic map gives a visual representation of Y-DNA haplogroups and possible migration routes.

Mitochondrial DNA (mtDNA) is passed from a mother to a child. Only females pass along their mtDNA which means that when testing for mtDNA it can tell researchers about a person’s direct maternal lineage.

Both men and women get mtDNA from their mothers, so it is possible to test both sexes for mtDNA to determine their maternal geneaology.

Mutations do take place in mtDNA slowly over time. Over thousands of years, these mutations will build up distinguishable characteristics and as migration has taken place, it also allows researchers to test mtDNA to identify a person’s lineage.

Just as with y-DNA haplogroups, mtDNA haplogroups tend to be continent specific and region specific.

The mtDNA phylogenic tree is similar to the Y-DNA phylogenic tree, but with different naming conventions for the haplogroups.

The mtDNA migration map is also similar to the Y-DNA migration map as well.

What is a Haplotype Map (HapMap)?

About 2.4 million variants of DNA sequences called SNPs have been discovered in the human genome. There are millions more that exist. These variants can help researchers discover genes that are useful as they relate to health and disease if their haplotype structure along chromosomes is known.

Haplotypes maps are blocks of SNPs that are being developed thanks to technology that is now available to study the extent and patterns of human genetic variations on a large scale.

When haplotype maps are used, they help to contribute to an understanding of diseases, so that methods and treatments can be developed to combat these diseases.

Most people do not have single-gene disorders. Instead they develop common diseases such as heart disease, stroke, diabetes, cancers or psychiatric disorders that are affected by many genes and environmental factors. Scientists and researchers are continuing to study the genetic contribution to these diseases.

Some SNP alleles are the functional variants that contribute to the risk of getting a disease.

People with these SNP alleles have a higher risk for that disease than do individuals without that SNP allele. To find the regions with genes that contribute to a disease, the frequencies of many SNP alleles are compared in individuals with and without the disease.

When a region has SNP alleles that are more frequent in people with the disease than in those without the disease, those SNPs and their alleles are associated with the disease.

An international consortium coordinated by the National Institutes of Health is working to map the pattern of common haplotypes throughout the genome. The Haplotype Mapping (HapMap) group at the Broad Institute generates new data and is creating new analytic methods to study haplotype information.

The HapMap project's primary goal is to identify sets of SNPs, or tags, that can generate predictions for various increased incidences of certain conditions. As the number of tags grows, the number of SNPs that need to be studied goes down and this allows researchers to start to hone in on risk genes for diseases in a quicker and more cost-effective way.

When SNP data is created and then analyzed it generates tags to study and this is what creates the resulting HapMap which is used to identify risk genes that affect health, disease, and drug responses.

Testing for Haplotypes (DNA Tests). How can SNP Haplotypes be Determined?

Geneological DNA tests look at specific locations of a person’s genome. This verifies the ancestry and genealogical relationships that allow researchers to determine the ethnic mix of an individual.

Different testing companies use different baseline reference groups, so it’s possible that an ethnic mix might not match up and could actually be very contradictory among companies.

There are three types of DNA tests that can test for haplotypes:

Autosomal – This may result in a large amount of DNA matches that indicate a number of people that a tested person may be related to for both male and female lines. The drawback is that because there is a limited and random nature of which and how much DNA is inherited by each tested person, accurate conclusions can only be concluded from just a few generations back. They are used primarily in estimating a person’s ethnic mix.

Mitocondrial (mtDNA) and Y-DNA – These are more reliable but will produce fewer matches and can trace back in finding prehistoric relationships through ancient DNA. They can be verified through family registers along a strict female and male lineage and will assist in determining the migration paths of a person’s ancestors from thousands of years ago. Because Y-DNA is only passed from a father to a son, only men can take Y-DNA tests.

An SNP is a variation in a single nucleotide that occurs at a specific position in the genome. SNPs are present to some appreciable degree within a population and SNP halotypes can be determined by using tagged SNPs specific to identifying halotypes.

What is the Difference Between Genotype and Haplotype?

Your genotype is simply a categorical list of individual genes. It includes all of your unique DNA, all your SNPs and all the genes your inherited from your parents. Your genotype will show you if you have inherited a good, bad or ugly version of a given gene.

Taken by itself, a genotype is not useful in providing an individual with enough information that can be used to create an effective approach to treatments for diseases or conditions. For this to happen, an analysis must also be done of a person’s haplotype and phenotype.

A haplotype is a set of DNA variations that are usually inherited together. The alleles that make up a haplotype can be located on different parts of a single chromosome, but they are all inherited together.

These sets or haplotypes are located on one chromosome. The alleles making up a haplotype can be located in different places on the chromosome but they are inherited together.

Other people will have the exact same haplotype as you do, but no one will have your genotype unless they are an identical twin.

But to be able to fully treat a disease, it’s also important to look at the phenotype as well. The phenotype is what medical science uses to label the disease a patient may have, whether it is cancer, diabetes, heart disease and so forth.

Phenotype is more than just describing symptoms, it also takes into account of the genes that are inherited are impacted by diet, malnutrition, stress, toxins and other environmental and experiential impacts. Phenotype is important because it applies the practical application of what people experience in their lives and incorporates it with the concept of genetics.

Applying SNP Profiles to Drug Choices: What’s realistic?

Scientists and researchers have been studying the associations between genes and drug response for decades. As new avenues of technology and research have opened up, the intensity and scope of this study has accelerated.

Two areas in particular are drawing heightened attention.

Pharmacogenetics which is the study of genetic factors that influence a drug response, and pharmacogenomics which adopts large and wide scale genome level methods for research and analysis.

As the body of research and results from that research builds, it is becoming more possible to lower the risk of under dosing or over dosing patients on medications instead of just using clinical information alone.

SNP-based genetic profiles, once created, are allowing medical professionals to further define the risk of a patient’s response to certain drugs and to their susceptibility to contract various illnesses. This is leading to less trial and error, and a much more customized and effective delivery of personalized medicine.

It reduces the use of drugs and limits the exposure medicines that might not be effective or may even be toxic to a patient, based on their genetic make-up.

As the identification and characterization of larger numbers of SNPs continues, it is turning them into an even more effective tool to combat afflictions to the human condition.

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