BACKGROUND: Sickle cell anemia is caused by a single type of mutation, a 
homozygous A→T substitution in the ß globin gene. Clinical severity is diverse, 
partially due to additional, disease-modifying genetic factors. We are studying 
one such modifier locus, HMIP (HBS1L-MYB intergenic polymorphism, chromosome 
6q23.3). Working with a genetically admixed patient population, we have 
encountered the necessity to generate haplotype signatures of genetic markers to 
label genomic fragments with distinct genealogical origin at this locus. With 
the goal to generate haplotype signatures from patients experimentally, we have 
investigated the suitability of an existing nanofluidic assay platform to 
perform phase alignment with single-nucleotide polymorphism alleles.
METHODOLOGY/PRINCIPAL FINDINGS: Patient DNA samples were loaded onto Fluidigm 
Digital Arrays and individual DNA molecules were assayed with allele-specific 
probes for SNP markers. Here we present data showing the utility of the 
nanofluidic approach, yielding haplotype data identical to those obtained with a 
family-based method. We then determined haplotype composition in a group of 
patients with sickle cell disease, including in those where a mathematical 
inference approach gave ambiguous or misleading results. Experimental phasing of 
genotypes across 3.8 kb for rs9399137, rs9402685, and rs11759553 created 
unequivocal haplotype signatures for each of the patients. In 68 patients, we 
found 8 copies of a haplotype signature ('C-C-T'), which is known to be 
prevalent in Europeans but to be absent in West African populations. We have 
confirmed the identity of our phased allele pairs by single-molecule sequencing 
and have demonstrated, in principle, that three-allele phasing (using three 
colors) is a potential extension to this method.
CONCLUSIONS/SIGNIFICANCE: Phased haplotypes yield more information than the 
individual marker genotypes. Procedures such as the one described here would 
therefore benefit genetic mapping and functional studies as well as diagnostic 
procedures where the identity or parental origin of short genetic fragments is 
of importance.