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Background  There is a shortage of data on the accuracy of statistical methods for the prediction of N-acetyltransferase 2 ( NAT2 ) haplotypes in the mixed ancestry population of the Western Cape.    Objective  This study aimed to identify the  NAT2  haplotypes and assess the accuracy of PHASE version 2.1.1 in assigning  NAT2  haplotypes to a mixed ancestry population from the Western Cape.    Methods  This study was conducted between 2013 and 2016. The  NAT2  gene was amplified and sequenced from the DNA of 100 self-identified mixed ancestry participants. Haplotyping was performed by molecular and computational techniques. Agreement was assessed between the two techniques.    Results  Haplotypes were assigned to 93 samples, of which 67 (72%) were ambiguous. Haplotype prediction by PHASE demonstrated 94.6% agreement (kappa 0.94,  p  < 0.001) with those assigned using molecular techniques. Five haplotype combinations (from 10 chromosomes) were incorrectly predicted, four of which were flagged as uncertain by the PHASE software. Only one resulted in the assignment of an incorrect acetylation phenotype (intermediate to slow), although the software flagged this for further analysis. The most common haplotypes were  NAT2 *4 (28%) followed by  NAT2 *5B (27.4%),  NAT2 *6A (21.5%) and  NAT2 *12A (7.5%). Four rare single nucleotide variants (c.589C>T, c.622T>C, c.809T>C and c.387C>T) were detected.    Conclusion  PHASE accurately predicted the phenotype in 92 of 93 samples (99%) from genotypic data in our mixed ancestry sample population, and is therefore a suitable alternative to molecular methods to individualise isoniazid therapy in this high burden tuberculosis setting.

Validation of PHASE for deriving N-acetyltransferase 2 haplotypes in the Western Cape mixed ancestry population