PMC:5985360 / 16168-18912 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/5985360","sourcedb":"PMC","sourceid":"5985360","source_url":"https://www.ncbi.nlm.nih.gov/pmc/5985360","text":"To improve cross-classification with the Senegal and Benin haplotypes, we identified 27 markers with r2≥0.2. These markers extended across 725.3 kb, which is still less than the average distance between phasing errors. On the basis of these markers, we identified 59 unique haplotypes, of which 18 carried the sickle allele at rs334. A 19th sickle haplotype was observed once in the ACB sample, and a 20th sickle haplotype was observed once in the Baganda sample (Table 4). V˜2 between these 27 markers and rs334 was 0.728 (Figure 1C). The most common haplotype carried the ancestral allele at all 28 sites and accounted for 68.5% of all haplotypes in the continental Africans. Globally, the ancestral haplotype had a frequency of 91.9%, was the most frequent haplotype in all 26 samples in the 1000 Genomes Project, and was the only haplotype in 15 of those samples, including all ten samples from East Asia and Europe. 13 of the sickle haplotypes in the Baganda, the one in the Zulu, and all four in the Qatari were identical to HAP1, the haplotype most commonly designated CAR (Table 4). Additionally, the four Qatari carriers had (1) \u003e7.8% autosomal African ancestry, (2) an African mitochondrial haplogroup, or (3) an African Y chromosome haplogroup. The three most common haplotypes (HAP1, HAP16, and HAP20) correlated primarily with the CAR, Benin, and Senegal haplotypes, respectively (Table 4).\nTable 4 Distribution of Sickle Haplotypes under a Sequence-Based Classification Scheme Using 27 Markers\nName Haplotypea Arabian/Indian Benin Cameroon CAR Senegal Atypical\nAncestor 0000000000000000000000000010 NA NA NA NA NA NA\nHAP1 0000000000000000000010000010 1 0 2 37 0 1\nHAP2 0000000000000000000010110010 0 4 0 0 0 0\nHAP3 0000000000000000000010110101 0 0 0 0 1 0\nHAP4 0000000000000000001110110101 0 2 0 0 0 0\nHAP5 0000000000000000111110110101 0 5 0 0 0 0\nHAP6 0000000000000001100011001010 0 0 0 0 3 0\nHAP7 0000000100000100111110110101 0 1 0 0 0 0\nHAP8 0000000100000100111110110110 0 0 0 0 1 0\nHAP9 0000111011111011100011001010 0 0 0 0 1 0\nHAP10 0001000000000000000010000010 0 0 0 1 0 0\nHAP11 0001000100000100111110110101 0 2 0 0 1 0\nHAP12 0011000100000100101110000010 0 0 0 0 1 0\nHAP13 0011000100000100111110000010 0 1 0 0 0 1\nHAP14 0011000100000100111110110010 0 0 0 0 1 0\nHAP15 0011000100000100111110110100 0 2 0 0 1 0\nHAP16 0011000100000100111110110101 0 23 0 0 7 0\nHAP17 0011000100000100111110110110 0 6 0 0 5 0\nHAP18 0011000100000100111110110111 0 1 0 0 0 0\nHAP19 1100111011111011100010000010 0 0 0 0 3 1\nHAP20 1100111011111011100011001010 0 0 0 0 36 0\na 0 indicates the reference allele, and 1 indicates the alternate allele according to the coding scheme in the 1000 Genomes Project VCF files. The sickle site rs334 is 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