Localization of a non‐melanoma skin cancer susceptibility region within the major histocompatibility complex by association analysis using microsatellite markers

Abstract

The major histocompatibility complex (MHC) is known to have a role in the development of non-melanoma skin cancer (NMSC), although the genes and mechanisms involved have yet to be determined. To identify the susceptibility locus for NMSC within the MHC, we used a collection of well-defined polymorphic microsatellite markers from the Human leucocyte antigen (HLA) region for an association analysis of 150 cases with NMSC and 200 healthy controls selected from the Busselton population in Western Australia. High-resolution mapping was undertaken using a total of 40 highly polymorphic markers located at regular intervals across the HLA region (3.6Mb). Polymerase chain reaction (PCR) analysis was initially performed on pooled DNA markers to detect those markers that showed different allele profiles. Statistically significant differences in allelic frequencies (differentiating alleles) were found between cases and controls at three polymorphic microsatellite loci within a 470-kb genomic susceptibility region ranging between 6 kb centromeric of the HLA-B gene and intron 5 of the DDR gene. Interestingly, this genome region corresponded completely with the psoriasis-susceptibility locus. The three differentiating alleles and another four markers outside the susceptibility region were then PCR tested by individual genotyping of cases and controls. The newly identified susceptibility locus for NMSC within the MHC was found to be significantly different between the cases and controls by comparisons of allele frequencies at the three differentiating loci estimated from DNA pools and then confirmed by individual genotyping. This is the first study using high density microsatellite markers to localize a NMSC susceptibility region within the human genome.

Polymorphic Alu insertions within the Major Histocompatibility Complex class I genomic region: a brief review

“…On the other hand, there was no significant association between the other POALINs and skin cancer except for possibly Aluy-MICB which was significant at close to the 0.05 level (data not shown). It is likely that the AluyTF and the microsatellites markers (Oka et al, 2003) when combined together would improve the correlation with skin cancer but this analysis has not yet been done.…”

“…1) using polymorphic microsatellite markers (Oka et al, 2003). It follows that one of the POALINs, AluyTF, might also be found to be significantly associated with skin cancer because its locus is close to the susceptibility locus.…”

Genome-wide association study of IgA nephropathy using 23 465 microsatellite markers in a Japanese population

“…14 The key factor in this methodology was the absolute equality of individual DNA quantities; therefore, we used a highly accurate quantitative procedure to construct a pooled DNA template for PCR amplification. DNA was extracted using the QIAamp DNA blood kit (QIAGEN, Valencia, CA, USA) with a standardized protocol to prevent variations in the quality of DNA.…”

Paternity Determination of Captive Bottlenose Dolphins (Tursiops truncatus) Using Microsatellite DNA Analysis

“…Microsatellite DNA analysis has become more widely used in recent times as a low-cost, rapid and accurate method of choice not only in humans for analysis of paternity [3,6] and disease susceptibility [4,7], but also for paternity and population studies in wild and captive animals [1,5,8,10].…”

“…Many modern aquariums and zoos no longer just maintain and display captured animals for public viewing and economic profit, but have also taken on the additional responsibilities of proper care and breeding programs for animals in captivity. The management by DNA analysis of individual animals and population groups within aquariums and zoos is now becoming an important tool for determination of the inherited variety, relationships and the kinship states between the individuals in populations under inbreeding pressure.Microsatellite DNA analysis has become more widely used in recent times as a low-cost, rapid and accurate method of choice not only in humans for analysis of paternity [3,6] and disease susceptibility [4,7], but also for paternity and population studies in wild and captive animals [1,5,8,10].Polymorphic microsatellites are variable and abundant tandem repeats of short sequences (2-6 bp) that are dispersed throughout most eukaryotic nuclear genomes and transmitted from one generation to the next by a simple and stable Mendelian inheritance [12]. Microsatellites are efficiently amplified using PCR techniques because of their relatively small sizes, which range within the limits of the standard amplification and detection methods.…”