Post by Admin on Nov 22, 2019 19:13:35 GMT
HLA allele frequencies found in Kurd Iraq population: comparison with other Populations
The expected and observed allele frequency values for HLA-A, -B, -C, -DRB1 and -DQB1 shows that the population is in Hardy-Weinberg equilibrium. Table 3 depicts HLA allele frequencies found in the sampled population. Sixteen different HLA-A, twenty-seven different HLA-B and thirteen different HLA-C alleles were founds in class I. Only seven HLA-A alleles, nine HLA-B alleles and seven HLA-C alleles had frequencies higher than 4% (-A*01, -A*02, -A*03, -A*11, -A*24, -A*26, -A*32, -B*07, -B*08, -B*18, -B*35, -B*38, -B*41, -B*44, -B*51, -B*52, -C*04, -C*06, -C*07, -C*12, -C*15, -C*16 and -C*17). Twelve different HLA-DRB1 alleles and five different HLA-DQB1 alleles were found. Only eight HLA-DRB1 alleles and four HLA-DQB1 alleles had frequencies higher than 4% (-DRB1*01, -DRB1*03, -DRB1*04, -DRB1*07, -DRB1*11, -DRB1*13, -DRB1*14, -DRB1*15, -DQB1*02, -DQB1*03, -DQB1*05 and -DQB1*06).
Table 3. HLA-A, -B, -C, -DRB1, and -DQB1 allele frequencies in Iraq Kurds population.
DRB1 alleles were used to compare our three Kurd samples with other populations in NJ analysis. It was not possible to perform this study with HLA class I allele frequencies due to the lack of class I studies in many worldwide available populations (Table 2).
NJ relatedness dendrogram based on HLA-DRB1 analysis separates populations in two differentiated clusters: A and B (Fig 2). Cluster A groups North and South Mediterraneans (Europeans and Africans) and Middle East populations (included Iraq Kurds, Iran Kurds [13] and Georgia Kurds [5]). Cluster B includes Central and eastern Siberians and Oriental population: such Tuvinians [3], Todja, Tofalar, Ulchi, Negidal [31], Japanese [20], Kets, Evenks [34]. Cluster A1 contains Iraq Kurds and Georgia Kurds, which are placed together [5], Palestinians [41], Armenians [20], Iran Kurds [13], East Europe (Croatians) [21], Cretans [33], Macedonians [38], Near East (Lebanese) [21] and Non-Ashkenazi Jews [28] (Fig 2). Cluster A2 places together other Mediterraneans (Europeans and Africans such as Spaniards and Spanish Basques) [43], French [20], Berbers [30] and Moroccans [39] (Fig 2).
Fig 2. Neighbour-Joining dendrogram.
Neighbour-Joining (NJ) dendrogram constructed with HLA-DRB1 allele frequencies showing relatedness between Iraq Kurds and other World populations. Bootstrap values are 100%.
Correspondence analysis based on HLA-DRB1 allele frequencies (Fig 3) shows similar results to those of Fig 2. Two clusters are clearly defined according to first dimension that explains most of the variability among populations. The first one groups together Siberian and Oriental populations (left, Fig 3) and the second cluster comprises Europeans, Mediterraneans, Caucasus and Iranian populations; Iraq Kurds, Iran Kurds [13] and Georgia Kurds [5] are located relatively close together.
Fig 3. Correspondence analysis.
Correspondence analysis showing a global view of the relationship between Kurds and Mediterranean, Siberians and other World populations according to HLA-DRB1 (low resolutions) allele frequencies in three dimensions (bidimensional representation).
Plain genetic distances (DA) show that Iraq Kurds closest genetic distances are the following: Near East populations (Iran Kurds, Palestinians, FarsParsi, Georgia Kurds and Ashkenazi Jews), eastern Mediterranean populations (Armenians, Cretans and Macedonians), and Mediterranean populations (Sardinians, Spaniards, Algerians and Italians) (Results not shown).
The expected and observed allele frequency values for HLA-A, -B, -C, -DRB1 and -DQB1 shows that the population is in Hardy-Weinberg equilibrium. Table 3 depicts HLA allele frequencies found in the sampled population. Sixteen different HLA-A, twenty-seven different HLA-B and thirteen different HLA-C alleles were founds in class I. Only seven HLA-A alleles, nine HLA-B alleles and seven HLA-C alleles had frequencies higher than 4% (-A*01, -A*02, -A*03, -A*11, -A*24, -A*26, -A*32, -B*07, -B*08, -B*18, -B*35, -B*38, -B*41, -B*44, -B*51, -B*52, -C*04, -C*06, -C*07, -C*12, -C*15, -C*16 and -C*17). Twelve different HLA-DRB1 alleles and five different HLA-DQB1 alleles were found. Only eight HLA-DRB1 alleles and four HLA-DQB1 alleles had frequencies higher than 4% (-DRB1*01, -DRB1*03, -DRB1*04, -DRB1*07, -DRB1*11, -DRB1*13, -DRB1*14, -DRB1*15, -DQB1*02, -DQB1*03, -DQB1*05 and -DQB1*06).
Table 3. HLA-A, -B, -C, -DRB1, and -DQB1 allele frequencies in Iraq Kurds population.
DRB1 alleles were used to compare our three Kurd samples with other populations in NJ analysis. It was not possible to perform this study with HLA class I allele frequencies due to the lack of class I studies in many worldwide available populations (Table 2).
NJ relatedness dendrogram based on HLA-DRB1 analysis separates populations in two differentiated clusters: A and B (Fig 2). Cluster A groups North and South Mediterraneans (Europeans and Africans) and Middle East populations (included Iraq Kurds, Iran Kurds [13] and Georgia Kurds [5]). Cluster B includes Central and eastern Siberians and Oriental population: such Tuvinians [3], Todja, Tofalar, Ulchi, Negidal [31], Japanese [20], Kets, Evenks [34]. Cluster A1 contains Iraq Kurds and Georgia Kurds, which are placed together [5], Palestinians [41], Armenians [20], Iran Kurds [13], East Europe (Croatians) [21], Cretans [33], Macedonians [38], Near East (Lebanese) [21] and Non-Ashkenazi Jews [28] (Fig 2). Cluster A2 places together other Mediterraneans (Europeans and Africans such as Spaniards and Spanish Basques) [43], French [20], Berbers [30] and Moroccans [39] (Fig 2).
Fig 2. Neighbour-Joining dendrogram.
Neighbour-Joining (NJ) dendrogram constructed with HLA-DRB1 allele frequencies showing relatedness between Iraq Kurds and other World populations. Bootstrap values are 100%.
Correspondence analysis based on HLA-DRB1 allele frequencies (Fig 3) shows similar results to those of Fig 2. Two clusters are clearly defined according to first dimension that explains most of the variability among populations. The first one groups together Siberian and Oriental populations (left, Fig 3) and the second cluster comprises Europeans, Mediterraneans, Caucasus and Iranian populations; Iraq Kurds, Iran Kurds [13] and Georgia Kurds [5] are located relatively close together.
Fig 3. Correspondence analysis.
Correspondence analysis showing a global view of the relationship between Kurds and Mediterranean, Siberians and other World populations according to HLA-DRB1 (low resolutions) allele frequencies in three dimensions (bidimensional representation).
Plain genetic distances (DA) show that Iraq Kurds closest genetic distances are the following: Near East populations (Iran Kurds, Palestinians, FarsParsi, Georgia Kurds and Ashkenazi Jews), eastern Mediterranean populations (Armenians, Cretans and Macedonians), and Mediterranean populations (Sardinians, Spaniards, Algerians and Italians) (Results not shown).