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Genotype, Phenotype and Haplotype


Genotype is an overloaded term that can mean one of two things:

  • Most commonly within the area of computational genomics, the term genotype refers to the particular alleles found at a given position or locus within the genome. For example, if position 7 on the theoretical chromosome in the figure below contains an A on one copy and a G on the other copy, this is said to be a genotype call of A/G at position 7.
  • Less commonly within the area of computational genomics, the term genotype will be used to reference an organism's complete set of genetic material, including all of the variants included therein.

Which definition is implied is largely based on the context of the conversation: if one is talking about a system-wide effect that is likely to be caused by the complicated interaction(s) between various parts of the organism's genetic code, then the second definition is more suited. Within computational genomics, we are often concerned with highly focal changes, hence the preference of the first definition above.


Throughout this guide, we'll assume the first definition for genotype unless otherwise specified.


An observed (often physical) trait that specific genes confer is known as a phenotype. When we see a person with blue eyes (a phenotype), we know that they carry a set of specific genetic sequences that makes that eye color possible (a genotype). In cancer, the features of the disease are the phenotype and the mutations and variants within the individual make up the genotype. In genomics, biologists seek to link genotypes to phenotypes to improve diagnoses and understand how cancer works. This phenomenon is known as a genotype-phenotype relationship.


Recall that each human genome is composed of pairs of chromosomes, one inherited from each parent. That means, with a few exceptions, nearly every gene has two copies. Often the two DNA sequences of that encoded gene differ. Each distinct copy is a haplotype for that gene. Together the two haplotypes make up the genotype, and the proteins they produce determine the phenotype. A variant is often detected in only one copy of the gene. If the variant causes a loss of function in an important gene, that one mutation may be insufficient to cause cancer but may create a predisposition to cancer later in life.

Figure showing the relationship between a genotype, a phenotype, and a haplotype