An apparent KIR2DS2-negative KIR2DL2-positive genotype discloses the novel allele KIR2DS2*00104

Alleles and intron polymorphism of KIR3DL1 shown by combination of allele group-specific primers and sequencing

Allelic polymorphism of killer immunoglobulin-like receptor (KIR) genes may affect receptor expression as well as function. We used a combination of allele group-specific primers and DNA sequencing techniques to verify our KIR genotyping primers in polymerase chain reaction and identified three KIR3DL1 alleles. By sequencing some introns of 3DL1 in 18 genomic DNA samples, we found that a 4-bp insert in intron 1 of 3DL1*002 exists in multiple alleles, but that a 2-bp deletion in intron 7 is unique to 3DL1*01501 and that a 19-bp insert in intron 1 seems specific to the CEPH family 1416. Our data suggest that extensive KIR gene polymorphisms are ubiquitous as well as quite complex.

Facilitation of KIR genotyping by a PCR-SSP method that amplifies short DNA fragments

Detection of killer-cell immunoglobulin-like receptors (KIR) genes by polymerase chain reaction with sequence-specific primers (PCR-SSP) led in 1997 to the discovery that human genomes diverge largely in the KIR they encode. While only a few KIR genes are conserved in all humans, most individuals lack several those genes, which tend to associate in diverse haplotypic combinations. The PCR-SSP technique, updated to detect the more recently identified KIR genes and alleles, is still used widely to analyze the diversity of human populations, and to study the influence of KIR-gene variability on human health. Several published PCR-SSP methods for KIR genotyping, although simple and robust, have the drawback of relying on the amplification of DNA fragments spanning 0.5-2.0 kbp, which tends to fail in low-quality DNAs. Valuable collections of DNAs often include such poor quality samples, which lead to loss of data and resources. Even worse, undetected falsely negative or positive reactions may result in erroneous gene frequencies and in odd gene combinations. To address those problems, we have redesigned our previously published KIR genotyping method so that it produces short amplicons (less than 200 bp for most genes). This modification minimizes amplification failures, thus conferring greater consistency and reliability to KIR genotyping. In addition, the new PCR-SSP method detects recently described alleles of several KIR genes, and allows for discrimination between the major structural variants of KIR2DS4 and KIR3DP1 without increasing the number of reactions.