Author: Palmer, Duncan S.; Turner, Isaac; Fidler, Sarah; Frater, John; Goedhals, Dominique; Goulder, Philip; Huang, Kuan-Hsiang Gary; Oxenius, Annette; Phillips, Rodney; Shapiro, Roger; Vuuren, Cloete van; McLean, Angela R.; McVean, Gil
Title: Mapping the drivers of within-host pathogen evolution using massive data sets Document date: 2019_7_9
ID: 100r7w2n_106
Snippet: Throughout, HLA typing was restricted to two digits and HLA-A, B, and C alleles were analysed jointly. We truncated to two-digits in the interests of power: although the most common 4 digit HLAs could be considered separately, the majority are rare at 4 digit resolution in our data set (60.5% of 4-digit HLAs have a count of < 10, compared to 30.2% at 2-digit resolution). Moreover, 27.3% of the individuals were only typed at 2-digit resolution. Ho.....
Document: Throughout, HLA typing was restricted to two digits and HLA-A, B, and C alleles were analysed jointly. We truncated to two-digits in the interests of power: although the most common 4 digit HLAs could be considered separately, the majority are rare at 4 digit resolution in our data set (60.5% of 4-digit HLAs have a count of < 10, compared to 30.2% at 2-digit resolution). Moreover, 27.3% of the individuals were only typed at 2-digit resolution. However, this should be feasible in the future as sample sizes of viral sequence data with associated host HLA types increase.
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