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

Abstract

The present invention provides a method for detection of at least one allele of a genetic locus and can be used to provide direct determination of the haplotype. The method comprises amplifying genomic DNA with a primer pair that spans an intron sequence and defines a DNA sequence in genetic linkage with an allele to be detected. The primer-defined DNA sequence contains a sufficient number of intron sequence nucleotides to characterize the allele. Genomic DNA is amplified to produce an amplified DNA sequence characteristic of the allele. The amplified DNA sequence is analyzed to detect the presence of a genetic variation in the amplified DNA sequence such as a change in the length of the sequence, gain or loss of a restriction site or substitution of a nucleotide. The variation is characteristic of the allele to be detected and can be used to detect remote alleles. Kits comprising one or more of the reagents used in the method are also described.

Description

[0001] This application is a Continuation In Part of U.S. application Ser. No. 07 / 465,863 (Attorney Docket No. 169.0011), filed Jan. 16, 1990, which application is a Continuation In Part of U.S. application Ser. No. 07 / 405,499 (Attorney Docket No. 169.0007), filed Sep. 11, 1989, which application is a Continuation In Part of U.S. application Ser. No. 07 / 398,217 (Attorney Docket No. 169.0003), filed Aug. 25, 1989, which applications are entitled IMPROVED HLA TYPING METHOD AND REAGENTS THEREFOR by Malcolm J. Simons. Each of those applications is incorporated herein by reference in its entirety.[0002] The present invention relates to a method for detection of alleles and haplotypes and reagents therefor.[0003] Due in part to a number of new analytical techniques, there has been a significant increase in knowledge about genetic information, particularly in humans. Allelic variants of genetic loci have been correlated to malignant and non-malignant monogenic and multigenic diseases. For ...

AI Technical Summary

Benefits of technology

[0068] Preferably, for each primer pair, the amplified DNA sequence defined by the primers includes at least 200 nucleotides, and more preferably at least 400 nucleotides, of an intervening sequence adjacent to the variable exon(s). Although the variable exon usually provides fewer variations in a given number of nucleotides than an adjacent intervening sequence, each of those variations provides allele-relevant information. Therefore, inclusion of the variable exon provides an advantage.

[0189] For analysis of MD, haplotypes on each side of the recombination hot spot are preferably determined. Primer pairs defining amplified DNA sequences are preferably located near, within about 1 to 10 Kbp of the hot spot on either side of the hot spot. In addition, due to the large size of the gene, primer pairs defining amplified DNA sequences are preferably located near each end of the gene sequence and most preferably also in an intermediate location on each side of the hot spot. In this way, haplotypes associated with the disease can be identified.

Problems solved by technology

However, individual-limited variation is uncommon.

However, occasionally, genetic rearrangements may occur within a haplotype.

Therefore, such regions do not contribute, or contribute only minimally, to the genetic variations present in the amplified DNA sequence.

Of course, the increased size of the amplified DNA sequence increases the chance of replication error, so addition of invariant regions provides some disadvantages.

However, those disadvantages are not as likely to affect an analysis based on the length of the sequence or the RFLP fragment patterns as one based on sequencing the amplification product.

Sequencing is the most time consuming and also the most revealing analytical method, since it detects any type of genetic variation in the amplified sequence.

Typically, the polymerase is not replenished when using a heat-stable polymerase.

However, the number of fragments must not be so large or so similar in size that a pattern that is not distinguishable from those of other haplotypes by the particular detection method is produced.

Patterns produced by simultaneous digestion by two or more enzymes will include more fragments than pooled products of separate digestions using those enzymes and will be more complex to analyze.

Inclusion of exons within the amplified DNA sequences does not provide as many genetic variations that enable distinction between alleles as an intron sequence of the same length, particularly for constant exons.

That alternative is generally considered unacceptable and is the cause of much concern in the scientific community.