obsolete haplotype [GENO_0000915]

A haplotype is an allele that represents one of many possible versions of a ‘haplotype block’, which defines a region of genomic sequence that is typically ‘co-inherited’ across generations due to a lack of historically observed recombination within it. 1. The relationship between ‘haplotype’ and ‘haplotype block’ is analogous to the relationship between ‘gene allele’ and ‘gene’: a ‘gene allele’ is one of many possible instances of a ‘gene’, while a ‘haplotype’ is one of many possible instances of a ‘haplotype block’. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene). 2. Haplotypes typically contain more than one ‘genetically-linked’ loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of ‘haplotype’ is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur ‘in cis’ on the same chromosomal strand. GENO’s definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a ‘gene allele’ is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a ‘gene’ is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. 3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term ‘haplotype’ is most commonly used to describe the following scenarios of genetic linkage between ‘alleles’: a. The first is regions containing multiple linked ‘gene alleles’ - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. b. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of ‘haplotype’ is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur ‘in cis’ on the same chromosomal strand. c. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a ‘gene allele’ - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes. The GENO definition of ‘haplotype’ is broadly inclusive of these and any other scenarios where distinct ‘alleles’ of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations.
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Open obsolete haplotype in VFB

Term Information

  • ID: GENO_0000915
  • Name: obsolete haplotype
  • Definition: A haplotype is an allele that represents one of many possible versions of a ‘haplotype block’, which defines a region of genomic sequence that is typically ‘co-inherited’ across generations due to a lack of historically observed recombination within it.
  • Synonyms:
  • Type:
  • Comment: 1. The relationship between ‘haplotype’ and ‘haplotype block’ is analogous to the relationship between ‘gene allele’ and ‘gene’: a ‘gene allele’ is one of many possible instances of a ‘gene’, while a ‘haplotype’ is one of many possible instances of a ‘haplotype block’. In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene). 2. Haplotypes typically contain more than one ‘genetically-linked’ loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction. A common use of ‘haplotype’ is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur ‘in cis’ on the same chromosomal strand. GENO’s definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a ‘gene allele’ is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a ‘gene’ is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. 3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term ‘haplotype’ is most commonly used to describe the following scenarios of genetic linkage between ‘alleles’: a. The first is regions containing multiple linked ‘gene alleles’ - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome. b. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated). This use of ‘haplotype’ is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur ‘in cis’ on the same chromosomal strand. c. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene. In this case, the haplotype represents a ‘gene allele’ - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes. The GENO definition of ‘haplotype’ is broadly inclusive of these and any other scenarios where distinct ‘alleles’ of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations.

VFB Term Json

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            "label": "obsolete haplotype"
        },
        "description": [
            "A haplotype is an allele that represents one of many possible versions of a 'haplotype block', which defines a region of genomic sequence that is typically 'co-inherited' across generations due to a lack of historically observed recombination within it."
        ],
        "comment": [
            "1. The relationship between 'haplotype' and 'haplotype block' is analogous to the relationship between 'gene allele' and 'gene':  a 'gene allele' is one of many possible instances of a 'gene', while a 'haplotype' is one of many possible instances of a 'haplotype block'.  In this sense, a gene allele can be considered to be a haplotype whose extent is that of a gene (as it is generally true that there is a low probability of recombination within any given gene).\n\n2. Haplotypes typically contain more than one 'genetically-linked' loci where sequence alterations are known to exist, such that a set of alterations will be co-inherited together across many generations of reproduction.  A common use of 'haplotype' is in phasing of patient WGS or WES data, where this term refers to sequence containing two or more alterations that are beleived to occur 'in cis' on the same chromosomal strand.  \n\nGENO's definition is consistent with but more inclusive than this view, allowing for haplotypes with one or zero established alterations as long as there is a low probability of recombination within the region it spans (such that alterations found in cis are likely to remain in cis across successive generations). As a result, GENO considers any allele that spans an extent greater than that of a single sequence alteration to be a haplotype - as long as there is an expectation of low recombination frequency within the haplotype block occupied by the allele. For example, a 'gene allele' is a haplotype representing a particular version of a gene that contains one or more sequence alterations - as a 'gene' is a region of sequence with a low probability of recombination that is generally expeted to be inherited as a unit. \n\n3. As highlighted in https://en.wikipedia.org/wiki/Haplotype, the term 'haplotype' is most commonly used to describe the following scenarios of genetic linkage between 'alleles':\n\na. The first is regions containing multiple linked 'gene alleles' - i.e. specific versions of entire genes that are co-inherited because they reside in tightly linked clusters on a single chromosome.  \nb. The second is a region containing multiple linked single nucleotide polymorphisms (SNPs) that tend to occur together on a chromosomal strand (i.e. be statistically associated).  This use of 'haplotype' is commonly seen in phasing of patient WGS or WES data, to describe a state where two or more alterations that are believed to occur 'in cis' on the same chromosomal strand.  \nc. A third, which is related to the previous case, occurs when the extent of region containing linked SNPs is that of a single gene.  In this case, the haplotype represents a 'gene allele' - a version of an entire gene defined by the set of sequence alterations it contains. We may consider this a haplotype as most genes are small enough that there is little chance of recombination events moving cis alterations onto separate chromosomes.\n\nThe GENO definition of 'haplotype' is broadly inclusive of these and any other scenarios where distinct 'alleles' of any kind on the same chromosomal strand are genetically linked, and thus tend to be co-inherited across successive generations."
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