61heterozygous SNPs into long haplotype blocks. This method also facilitates the
analysis of structural variation, for example, to anchor novel insertions to specifi c
locations and haplotypes.
The second method used a microfl uidic device capable of separating and ampli-
fying homologous copies of each chromosome from a single human metaphase cell
(Fan et al. 2011 ). SNP array analysis of amplifi ed DNA enabled complete whole-
genome, personal haplotyping of four individuals, including a HapMap trio with
European ancestry and an unrelated European individual. The phases of alleles were
determined at ∼99.8 % accuracy for up to ∼96 % of all assayed SNPs. Several prac-
tical applications were demonstrated including direct observation of recombination
events in a family trio, deterministic phasing of deletions in individuals and direct
measurement of the HLA haplotypes of an individual. This approach has potential
applications in personal genomics, single-cell genomics and statistical genetics.
A method has been described for rapid and cost-effective long-range haplotyping
(Kaper et al. 2013 ). Genomic DNA is diluted and distributed into multiple aliquots
such that each aliquot receives a fraction of a haploid copy. The DNA template in
each aliquot is amplifi ed by multiple displacement amplifi cation, converted into
barcoded sequencing libraries using Illumina’s Nextera technology, and sequenced
in multiplexed pools. To assess the performance of this method, two male genomic
DNA samples were combined at equal ratios, resulting in a sample with diploid X
chromosomes with known haplotypes. Pools of the multiplexed sequencing librar-
ies were subjected to targeted pull-down of a 1-Mb contiguous region of the
X-chromosome Duchenne muscular dystrophy (DMD) gene. The authors were able
to phase the DMD region into two contiguous haplotype blocks with a mean length
of 494 kb. The haplotypes showed 99 % agreement with the consensus base calls
made by sequencing the individual DNAs. They subsequently used the strategy to
haplotype two human genomes. Standard genomic sequencing to identify all het-
erozygous SNPs in the sample was combined with dilution-amplifi cation-based
sequencing data to resolve the phase of identifi ed heterozygous SNPs. Using this
procedure, they were able to phase >95 % of the heterozygous SNPs from the dip-
loid sequence data. The N50 for a Yoruba male DNA was 702 kb whereas the N50
for a European female DNA was 358 kb. Therefore, this strategy is suitable for
haplotyping of a set of targeted regions as well as of the entire genome. The method
can be used by any investigator with access to a NGS instrument.
Statistically aided, long-read haplotyping (SLRH) is a rapid, accurate method
that uses a statistical algorithm to take advantage of the partially phased information
contained in long genomic fragments analyzed by short-read sequencing (Kuleshov
et al. 2014 ). For a human sample, as little as 30 Gbp of additional sequencing data
are needed to phase genotypes identifi ed by 50× coverage WGS. Using SLRH, the
approach involved phasing 99 % of single-nucleotide variants in three human
genomes into long haplotype blocks 0.2–1 Mbp in length. The authors applied this
method to determine allele-specifi c methylation patterns in a human genome and
identify hundreds of differentially methylated regions that were previously
unknown. SLRH should facilitate population-scale haplotyping of human genomes.
Compared with existing dilution haplotyping methods, SLRH produces haplotypes
SNP Genotyping