Alu polymorphism within the MICB gene and association with HLA-B alleles

Kulski, Jerzy K.; Dunn, David S.; Hui, Jennie; Martínez, Patricia; Romphruk, Amornrat; Leelayuwat, Chanvit; Tay, Guan K.; Oka, Akira; Inoko, Hidetoshi

doi:10.1007/s00251-002-0481-5

Cited by 12 publications

(39 citation statements)

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“…Recently, we identified five unique POALINs spanning approximately 1.8 Mbs within the class I region of the Major Histocompatibility Complex (MHC) on the short arm of chromosome 6 (Kulski et al, , 2002aDunn et al, 2002Dunn et al, , 2003b) that had not been previously described in an analysis of more than 4000 recently integrated AluYa5 and Yb8 family members ). The MHC is one of the most polymorphic regions of the human genome.…”

Section: Poalins and The Major Histocompatibility Complex (Mhc)mentioning

confidence: 99%

“…Since very little was known or understood about POALINs within the MHC genomic region, we undertook to identify some of the members of the AluYb8/AluYa5 subfamily and to study their frequency of distribution and genetic characteristics in different populations. As a result of our comparative genomic analyses, we have identified the insertion sites for five POALINs distributed within the MHC class I region and reported on their genetic characteristics (Kulski et al, , 2002aDunn et al, 2002Dunn et al, , 2003b. This brief review outlines the locations of the insertions and sequence features of the five MHC POALINs, as well as their single site and haplotype frequencies in different geographic populations, and their association with different HLA class I genes and disease.…”

Section: Poalins and The Major Histocompatibility Complex (Mhc)mentioning

confidence: 99%

“…Our method of identification of POALINs was dependent on the availability of a number of different MHC genomic sequences for comparative analysis (Kulski et al, , 2002aDunn et al, 2002Dunn et al, , 2003b using the information derived from RepeatMasker or Censor, dot plotting and multiple alignments . RepeatMasker (http://repeatmasker.genome.washington.edu/cgi-bin/RepeatMasker) and Censor (http://www.girinst.org/Censor_Server_Data_Entry_ Forms.html) are two independently developed web servers available for public use to identify the presence of interspersed repeats in a genomic sequence (Jurka et al, 1996).…”

Section: Identification Of Poalins Within the Mhc Class I Regionmentioning

confidence: 99%

“…Table 1 shows the primer sets and sequences that were used in PCR to detect the MHC POALINs, and their product sizes. The conditions for PCR were described previously (Kulski et al, , 2002aDunn et al, 2002Dunn et al, , 2003b. The PCR methods for the detection of the five MHC POALINs were first tested and optimised in celllines and in some of the Australian European, Thai and Japanese DNA samples.…”

Section: Detection Of Mhc Poalins By Pcrmentioning

confidence: 99%

“…The PCR methods for the detection of the five MHC POALINs were first tested and optimised in celllines and in some of the Australian European, Thai and Japanese DNA samples. PCRs were carried out using standard procedures with a positive and negative control and a heterozygote and homozygote control sample as previously described (Kulski et al, , 2002a. DNA samples produced the expected reactions with the designed primer sets.…”

Section: Detection Of Mhc Poalins By Pcrmentioning

confidence: 99%

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

Kulski¹,

Dunn²

2005

Cytogenet Genome Res

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Most polymorphic Alu insertions (POALINs) belong to a subgroup of the Alu multicopy retrotransposon family of short interspersed nucleotide elements (SINEs) that are categorized as AluYb8 and AluYa5. The number of AluYb8/AluYa5 members (∼4,492 copies) is significantly less than the ∼one million fixed Alu copies per human genome. We have studied the presence of POALINs within the Major Histocompatibility Complex (MHC) class I region on the short arm of chromosome 6 (6p21.3) because this region has a high gene density, many genes with immune system functions, large sequence variations and diversity, duplications and redundancy, and a strong association with more than 100 different diseases. Since little is known about POALINs within the MHC genomic region, we undertook to identify some of the members of the AluYb8/AluYa5 subfamily and to study their frequency of distribution and genetic characteristics in different populations. As a result of our comparative genomic analyses, we identified the insertion sites for five POALINs distributed within the MHC class I region. This brief review outlines the locations of the insertions and sequence features of the five MHC POALINs, their single site and haplotype frequencies in different geographic populations, and their association with different HLA class I genes and disease. We show that the MHC POALINs have a potential value as lineage and linkage markers for the study of human population genetics, disease associations, genomic diversity and evolution.

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Section: Poalins and The Major Histocompatibility Complex (Mhc)mentioning

confidence: 99%

Section: Poalins and The Major Histocompatibility Complex (Mhc)mentioning

confidence: 99%

Section: Identification Of Poalins Within the Mhc Class I Regionmentioning

confidence: 99%

Section: Detection Of Mhc Poalins By Pcrmentioning

confidence: 99%

Section: Detection Of Mhc Poalins By Pcrmentioning

confidence: 99%

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

Kulski¹,

Dunn²

2005

Cytogenet Genome Res

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Dimorphic Alu element located between the TFIIH and CDSN genes within the major histocompatibility complex

2003

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Most Alu members of the large SINE family are fixed within the human genome but some younger mobile members are dimorphic, that is, they are either present or absent in the genome. Four different dimorphic Alu insertions have been identified and characterized previously within the class I region of the major histocompatibility complex (MHC). Here we report on (i) the identification and characterization of a new dimorphic Alu insertion, AluyTF, located between the transcription factor II H (TFIIH) and corneodesmosin (CDSN) genes within a region of the MHC that is telomeric of the human leukocyte antigen type B (HLA-B) locus and centromeric of the HLA-A locus, (ii) the haplotypic relationships between the AluyTF dimorphism and the HLA-A and -B loci within a panel of 48 IHW cell-lines representing at least 36 different HLA class I haplotypes, (iii) the AluyTF genotype, allele and haplotype frequencies present in the Australian caucasian and Japanese populations, and (iv) the frequency of association between the AluTF dimorphisms and HLA-A and -B alleles in 108 Australian caucasians and 99 Japanese. The AluyTF insertion was present at 27% in the IHW cell lines, and the gene frequency was 0.107 and 0.083 in the Australian caucasian and Japanese population, respectively. The Alu haplotype frequencies constructed from four different dimorphic Alu loci including AluyTF within the MHC were not significantly different (p > 0.05) between the two populations. There were no significant associations between the Alu insertion and either the HLA-A or -B alleles except for a moderately strong association with HLA-A29 in the Australians (71.7%). This polymorphic AluyTF element, along with the four other previously described polymorphic Alu elements within the class I region of the MHC, will be useful lineage and linkage markers in human population studies and for elucidating the evolution of HLA class I haplotypes.

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MICA, MICB, and MHC Beta Block Matching in Bone Marrow Transplantation: Relevance to Transplantation Outcome

et al. 2006

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Alu polymorphism within the MICB gene and association with HLA-B alleles

Cited by 12 publications

References 0 publications

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

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

Dimorphic Alu element located between the TFIIH and CDSN genes within the major histocompatibility complex

MICA, MICB, and MHC Beta Block Matching in Bone Marrow Transplantation: Relevance to Transplantation Outcome

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