Intron sequence analysis method for detection of adjacent and remote locus alleles as haplotypes

A method for producing RFLP patterns for an HLA locus of an individual comprising the steps of:

• a. amplifying HLA DNA from said individual with a primer pair specific for said HLA locus under conditions suitable to produce an amplified DNA sequence, said primers being located in intervening sequence I and in intervening sequence III when said HLA locus is a Class I locus and in intervening sequence I and in intervening sequence II when said locus is a Class II locus;
• b. producing a digest by combining said amplified DNA sequence with at least one endonuclease that cleaves said amplified DNA sequence to yield a set of fragments having distinctive fragment lengths;
• and
• c. producing RFLP patterns from said digest.

A method for determining whether DNA in a sample is from a particular individual comprising the steps of:

• a. amplifying DNA from said individual and DNA from said sample with a primer pair specific for an HLA locus under suitable conditions to produce an amplified DNA sequence from said individual and from said sample, said primers being located in intervening sequences I and III for an HLA Class I locus and in intervening sequences I and II for a Class II locus;
• b. combining said amplified DNA sequence from said individual and said amplified sample DNA from said sample with at least one endonuclease that cleaves said amplified DNA sequence into a plurality of cleaved sequences of sufficiently different lengths to distinguish between alleles of said HLA locus for a period of time sufficient for digestion of said amplified DNA to produce a digest;
• and
• c. comparing restriction fragment length polymorphic patterns produced by said digest from said individual and from said sample.

A method for determining whether an individual is the father of a child comprising the steps of:

• a. amplifying DNA from said individual, DNA from said child and DNA from said child's mother with a pair of primers specific for an HLA locus under suitable conditions to produce amplified DNA sequences, said primers being located in intervening sequences I and III for an HLA Class I locus and in intervening sequences I and II for a Class II locus;
• b. combining said amplified DNA sequence from said individual and said amplified sample DNA from said child with at least one endonuclease that cleaves said amplified DNA sequence into a plurality of cleaved sequences of sufficiently different lengths to distinguish between alleles of said HLA locus to produce a digest;
• and
• c. comparing restriction fragment length polymorphic patterns produced by said digest from said individual, from said child's mother and from said child.