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The diversity of the HLA CLASS I introns reflects the ancestral relationships of the coding regions
Abstracts
55
2.4 #25
HLA DRB/DQBl HAPLOTYPES IN TWO LEBANESE VILLAGES ISOLATED BY GEOGRAPHY AND RELIGION. WH Wood III, WB Bias, B Cissell, NN Salti ' , and BJ Schmeckpeper, Johns Hopkins University, Baltimore, MD and lAmerican University of Beirut, Beirut, Lebanon. Samples were obtained from 200 people (SO husband/wife pairs and 2 of their children) from each of two isolated villages within the same ethnic group for a study of the diversity of HLA alleles and haplotypes. The Lebanese villages sampled were Kafar Zubian (KZ), a Maronite Christian village isolated for at least 400 years, and Yohmor (YH), a Shia Muslim village isolated for 300 or more years. DNA from each sample was typed by PCR/SSOP, and the HLA DRBl, DRB3, DRB4, DRBS, and DQBl allele frequencies were determined. For village KZ, 89 parents were typed; 24 DRBI alleles and 11 DQBl alleles were found. The S most frequent DRBI alleles were *1104, *0403, *0102, *03011 and *1101. Four of these were found on the most frequent DR/DQ haplotypes and only on these haplotypes: DRB1*1104/DRB3*0202/DQB1*0301 (f=0.20); DRB1*0102/DQB1*OSOl (0.10), DRB1*03011/DRB3*0202/DQB1*02XX (0.09) and DRB1*1101/DRB3*0202/ DQBl*0301 (0.09). The other frequent DRBI allele, DRBl*0403, was found on two haplotypes: DRB1*0403/DRB4*0103/DQB1*0302 (0.04) and DRBl*0403/ DRB4*0103/DQB1*030S (O.OS). For village YH 80 parents were typed; 21 DRBI and 13 DQBl alleles were found. The most frequent DRB1 alleles were *0701, *1101, *1104, *0402 and *03011. The most frequent haplotypes were DRB1*1101/DRB3*0202/DQB1*0301 (f=0.13), DRB1*1104/DRB3*0202/ DQB1*0301 (0.12), DRBl*03011/DRB3*0202/DQBl*02XX (0.07) and DRB1*0402/DRB4*0103/DQB1*0302 (0.06). The DRBl*0701 allele was found on 6 haplotypes, with 2 of these being equally common: DRB1*0701/DRB4*01011/DQBl*02XX and DRB1*0701/DRB4*0103/DQB1*02XX. The populations of the two villages differ in the alleles present. The DRB1*03011, *1101 and *1104 haplotypes are conserved in both groups. Both have an unusual DRB1*040S/DRB4*0103/DQB1*02XX haplotype. The YH group has three unusual DR7 haplotypes: DRB1*0701/DRB4*01011/DQB1*03032; DRB1*0701/DRB4*01011/DQBl*0302; and DRB1*0701/DRB4*0103/DQB1*0302.
2.4 #26
THE DIVERSITY OF THE HLA CLASS I INTRONS REFLECTS THE ANCESTRAL RELATIONSHIPS OF THE CODING REGIONS. Rainer Blasczyk and .lenny Wehling, Humboldt-University, Virchow-Klinikum, Bloodbank, Berlin, Germany The sequence database ofHLA class I genes is mainly derived from mRNA analysis. Little is known about the complete genomic sequence of the different class I alleles. We have determined the sequence of the I st through 3rd intron of the majority of HLA-A and B alleles in 48 well defined cell lines and 195 peR typed clinical samples. The few published sequences emerged to contain substantial errors. The introns turned out to be highly polymorphic. Besides extensive homologies, numerous locus- and group-specific sites could be identified. The most intriguing finding was, that most of the polymorphic motifs were related to ancestral families. These sequence motifs are extremely beneficial for setting up peR based typing systems. In particular, sequencing based typing strategies will benefit from intron-restricted priming for amplification and sequencing by enabling complete analysing of the polymorphic exons. The determination of cis/trans linkages of sequence motifs will be substantially facilitated. Apart from the advantages for setting up peR based typing systems, the intron sequences are useful for evolutionary studies delivering more insights in the genetic relationships between different alleles and the mechanisms involved in the development of the diversity of HLA. Moreover, the variability of the introns may provide a structural basis for the identification of regulatory elements acting on the level of transcription.
55
2.4 #25
HLA DRB/DQBl HAPLOTYPES IN TWO LEBANESE VILLAGES ISOLATED BY GEOGRAPHY AND RELIGION. WH Wood III, WB Bias, B Cissell, NN Salti ' , and BJ Schmeckpeper, Johns Hopkins University, Baltimore, MD and lAmerican University of Beirut, Beirut, Lebanon. Samples were obtained from 200 people (SO husband/wife pairs and 2 of their children) from each of two isolated villages within the same ethnic group for a study of the diversity of HLA alleles and haplotypes. The Lebanese villages sampled were Kafar Zubian (KZ), a Maronite Christian village isolated for at least 400 years, and Yohmor (YH), a Shia Muslim village isolated for 300 or more years. DNA from each sample was typed by PCR/SSOP, and the HLA DRBl, DRB3, DRB4, DRBS, and DQBl allele frequencies were determined. For village KZ, 89 parents were typed; 24 DRBI alleles and 11 DQBl alleles were found. The S most frequent DRBI alleles were *1104, *0403, *0102, *03011 and *1101. Four of these were found on the most frequent DR/DQ haplotypes and only on these haplotypes: DRB1*1104/DRB3*0202/DQB1*0301 (f=0.20); DRB1*0102/DQB1*OSOl (0.10), DRB1*03011/DRB3*0202/DQB1*02XX (0.09) and DRB1*1101/DRB3*0202/ DQBl*0301 (0.09). The other frequent DRBI allele, DRBl*0403, was found on two haplotypes: DRB1*0403/DRB4*0103/DQB1*0302 (0.04) and DRBl*0403/ DRB4*0103/DQB1*030S (O.OS). For village YH 80 parents were typed; 21 DRBI and 13 DQBl alleles were found. The most frequent DRB1 alleles were *0701, *1101, *1104, *0402 and *03011. The most frequent haplotypes were DRB1*1101/DRB3*0202/DQB1*0301 (f=0.13), DRB1*1104/DRB3*0202/ DQB1*0301 (0.12), DRBl*03011/DRB3*0202/DQBl*02XX (0.07) and DRB1*0402/DRB4*0103/DQB1*0302 (0.06). The DRBl*0701 allele was found on 6 haplotypes, with 2 of these being equally common: DRB1*0701/DRB4*01011/DQBl*02XX and DRB1*0701/DRB4*0103/DQB1*02XX. The populations of the two villages differ in the alleles present. The DRB1*03011, *1101 and *1104 haplotypes are conserved in both groups. Both have an unusual DRB1*040S/DRB4*0103/DQB1*02XX haplotype. The YH group has three unusual DR7 haplotypes: DRB1*0701/DRB4*01011/DQB1*03032; DRB1*0701/DRB4*01011/DQBl*0302; and DRB1*0701/DRB4*0103/DQB1*0302.
2.4 #26
THE DIVERSITY OF THE HLA CLASS I INTRONS REFLECTS THE ANCESTRAL RELATIONSHIPS OF THE CODING REGIONS. Rainer Blasczyk and .lenny Wehling, Humboldt-University, Virchow-Klinikum, Bloodbank, Berlin, Germany The sequence database ofHLA class I genes is mainly derived from mRNA analysis. Little is known about the complete genomic sequence of the different class I alleles. We have determined the sequence of the I st through 3rd intron of the majority of HLA-A and B alleles in 48 well defined cell lines and 195 peR typed clinical samples. The few published sequences emerged to contain substantial errors. The introns turned out to be highly polymorphic. Besides extensive homologies, numerous locus- and group-specific sites could be identified. The most intriguing finding was, that most of the polymorphic motifs were related to ancestral families. These sequence motifs are extremely beneficial for setting up peR based typing systems. In particular, sequencing based typing strategies will benefit from intron-restricted priming for amplification and sequencing by enabling complete analysing of the polymorphic exons. The determination of cis/trans linkages of sequence motifs will be substantially facilitated. Apart from the advantages for setting up peR based typing systems, the intron sequences are useful for evolutionary studies delivering more insights in the genetic relationships between different alleles and the mechanisms involved in the development of the diversity of HLA. Moreover, the variability of the introns may provide a structural basis for the identification of regulatory elements acting on the level of transcription.