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From: "Lowe DNA" <>
Subject: Definition of Haplotype
Date: Wed, 9 Jun 2004 13:44:22 -0500
In-Reply-To: <LAEMICGGMBKIADLLMIJEKENJDDAA.terry@bartonsite.org>


I was browsing this site and ran across this "patented" definition of
haplotype at...

http://www.simonsjunkdna.com/Full%20Article.htm

The Patent definition of Haplotype is: "As used herein, "haplotype" is a
region of genomic DNA on a chromosome which is bounded by recombination
sites such that genetic [coding] loci within a haplotypic region are usually
inherited as a unit. However, occasionally genetic rearrangements may occur
within a haplotype. Thus, the term haplotype is an operational term that
refers to the occurrence on a chromosome of linked [coding] loci". (NB - my
insertion of [coding] is to qualify the term 'locus' according to the Patent
's definition). Each of the coding loci within the haplotype are
represented as a single allele, so a haplotype is taken to mean the
combination of alleles at two or more linked loci on a single chromosome.

Subsequently, non-HLA geneticists have adopted the term 'haplotype' to apply
to combinations of SNPs at two or more linked single nucleotide polymorphic
loci, including non-coding loci. By this usage, the shortest 'haplotype' is
any pairwise combination of two adjacent nucleotides at contiguous
polymorphic loci. If the two single nucleotide polymorphic (SNP) loci are
separated by a distance that allows amplification of the sequence length
then the amplified sequence of any of the four combinations of the
di-nucleotide loci has also been termed a 'haplotype'. Ruano and Kidd (33)
employ the terms 'locus' and 'haplotype' in these ways when they termed the
amplicons generated by primers at two non-coding polymorphic (single
nucleotide) loci as 'haplotypes'. Multiple SNPs occurring in non-coding
DNA, particularly in intergenic sequences, are now employed for genome-wide
gene discovery by LD (Allele association) mapping, involving the assignment
of 'haplotypes'. Definitions of 'locus' and 'haplotype' in the patents
differ from these usages.

When two or more SNPs are identified at a coding locus, it has become common
practice to term combinations of those SNPs, inferred or observed, as
'haplotypes'. Sequence variations at coding loci define alleles. Not all
alleles at a coding locus are specified by a single SNP (i.e. an
allele-specific SNP). More usually, as best exemplified by HLA genes,
alleles are defined by unique combinations of SNPs distributed over coding
elements of the locus. Maximum statistical power for detection of
gene-trait associations can be expected to require assignment of coding
locus variation as locus alleles. Thus, for investigation of coding loci
for their role in disease / function, priority should be given to defining
the locus alleles present in a population, rather than to group two or more
SNPs together as so-called 'haplotypes'.

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