What is a haplotype? What is a haplogroup? We explain (2023)

One of the ways geneticists and genealogists help distinguish the deep origins of a person's maternal and paternal ancestors who lived thousands of years ago is by identifying 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 further detail a person's nation and region of origin. Because some haplotypes are more common in certain haplogroups, it is often 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 at multiple locations on a single chromosome. If two people match exactly on all the markers they tested, they share the same haplotype and are related.

The degree of relationship can be predicted based on the number of markers that were tested. The more markers that are tested and compared, the better and more accurate the prediction will be.

Haplogroups to refer to the single nucleotide polymorphism (SNP) mutations that determine the clade to which a collection of haplotypes belongs.

Man originated in Africa and has migrated all over the world ever since. While this migration was taking place, man changed and adapted to his environment over thousands of years.

For example, in places where the sun is limited, a man's skin becomes lighter. To better protect themselves against the cold of the northern regions, man's build became squatter and more insulated. These changes 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-chromosome haplogroups can trace their common ancestry back to a Y-chromosome Adam, who is the most recent patriarchal ancestor of all people living today.

It is believed that he lived about 236,000 years ago. He was not the only man alive at the time, he was simply the only man with an unbroken line of male descent to this day. He is referred to as the "most common recent ancestor", which is sometimes referred to as MCRA.

From this common ancestor, it is possible to create a kind of family tree of the human race known as a Y-DNA haplogroup phylogenetic tree. 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.

International Society for Genetic Genealogycreated the following phylogenetic tree of Y-DNA haplogroups. Due to ongoing research, the structure of the Y-DNA haplogroup tree changes frequently enough to keep up 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, the possible time of origin of haplogroup A is estimated to be 236,000 years ago. Haplogroup F is believed to have originated around 65,900 years ago in Eurasia. And the R haplogroup possibly originated around 31,900 years ago in Asia.

Within each of these broad haplogroups, there are also subhaplogroups with various designations that have developed through ongoing genetic mutations.

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

Broadly speaking, here are the main geographic locations of the haplogroup:

• Haplogroup A is found mainly in southern Africa and represents the oldest Y-chromosome haplogroup.
• The BT and CT haplogroups are found predominantly in Africa, but separated by about 50,000 years or their possible origin.
• Haplogroup F has been found predominantly in Eurasia since about 65,900 years ago.
• Haplogroup E is found in East Africa or Asia. The E1b1a haplogroup is found predominantly among sub-Saharan African populations. The E1b1b haplogroup is found predominantly on the Mediterranean coast.
• Haplogroup G has been found in Europe, North and West Asia, North Africa, the Middle East, and India.
• The J haplogroup and its subgroups are found mainly on the coasts of the Mediterranean and the Middle East. J subgroups are often associated with Jewish populations.
• Haplogroup I and its subgroups are found primarily 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.
• The R1a haplogroup and its subgroups are found predominantly in Eastern Europe and in India and Western and Central Asia. In Eastern Europe, it is often associated with Slavic populations.
• The R1b haplogroup and its subgroups are found predominantly in Western Europe and the British Isles. It is the most common haplogroup in Europe.

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

Mitochondrial DNA (mtDNA) is passed from mother to child. Only women pass on their mtDNA, which means that analyzing mtDNA can tell researchers about a person's direct maternal lineage.

Both males and females obtain mtDNA from their mothers, so it is possible to perform mtDNA testing on both sexes to determine their maternal genealogy.

Mutations occur in mtDNA slowly over time. Over thousands of years, these mutations will create distinctive features, and as migration occurs, it also allows researchers to analyze mtDNA to identify a person's lineage.

Like y-DNA haplogroups, mtDNA haplogroups tend to be continent- and region-specific.

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

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

What is a haplotype map (HapMap)?

About 2.4 million DNA sequence variants called SNPs have been discovered in the human genome. There are millions more out there. These variants can help researchers discover useful genes in terms of health and disease, if the structure of the haplotype along the chromosomes is known.

Haplotype maps are blocks of SNPs that are being developed using technology already available to study the extent and patterns of large-scale human genetic variations.

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

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

any SNPallelesare the functional variants that contribute to the risk of contracting a disease.

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

When a region has alleles of SNPs that are more common 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 across the genome. The Broad Institute's Haplotype Mapping (HapMap) group is generating new data and developing new analytical methods to study haplotype information.

The main goal of the HapMap project is to identify sets of SNPs, or tags, that can generate predictions for various increased incidences of certain conditions. As the number of tags increases, the number of SNPs that need to be studied decreases, allowing researchers to begin refining disease risk genes more quickly and cost-effectively.

When SNP data is created and analysed, 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.

Haplotype test (DNA tests). How can SNP haplotypes be determined?

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

Different testing companies use different benchmark reference groups, so an ethnic mix may not match and, in fact, be very inconsistent between companies.

There are three types of DNA tests that can detect haplotypes:

autosomal– This can result in a large number of DNA matches indicating a number of people a tested person may be related to, for both male and female lines. The downside is that since there is a limited and random nature to what and how much DNA each person tested inherits, accurate conclusions can only be drawn from a few generations back. They are mainly used to estimate a person's ethnic mix.

Mitochondrial (mtDNA) and Y-DNA– These are more reliable but will produce fewer matches and can be traced by finding prehistoric relationships through ancient DNA. They can be verified through family records along a strict male and female lineage and will help determine the migration routes of a person's ancestors thousands of years ago. Since Y-DNA is only passed from father to son, only men can get Y-DNA tests.

A SNP is a variation of a single nucleotide that occurs at a specific position in the genome. SNPs are present to an appreciable degree within a population and SNP halotypes can be determined using specific tagged SNPs to identify halotypes.

What is the difference between genotype and haplotype?

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

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

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

These groups or haplotypes are found on one chromosome. EITHERallelesthose that form a haplotype may be located at different places on the chromosome, but are inherited together.

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

But in order to fully treat a disease, it is also important to look at the phenotype. The phenotype is what medical science uses to label the disease that a patient may have, be it cancer, diabetes, heart disease, etc.

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

Application of SNP profiles to drug choice: what is 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 receiving more attention.

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

As the body of research and the results of that research increase, it becomes more possible to reduce the risk of drug underdosing or overdosing in patients, rather than relying solely on clinical information.

SNP-based genetic profiles, once created, allow medical professionals to better define a patient's risk of response to certain medications and their susceptibility to various diseases. This leads to less trial and error and a much more personalized and effective delivery of personalized medications.

It reduces drug use and limits exposure to medications that may not be effective or even toxic to a patient based on their genetic makeup.

As more SNPs continue to be identified and characterized, they will become an even more effective tool in combating the woes of the human condition.

Distributed byEditor Froala