Open AccessComparison of the experimental methods in haplotype sequencing via next generation sequencing
Author(s) -
Tu Jing,
Lu Na,
Duan Mengqin,
Ju An,
Sun Xiao,
Lu Zuhong
Publication year - 2016
Publication title -
quantitative biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.707
H-Index - 15
eISSN - 2095-4697
pISSN - 2095-4689
DOI - 10.1007/s40484-016-0068-z
Subject(s) - haplotype , computer science , task (project management) , throughput , dna sequencing , computational biology , data mining , biology , genetics , engineering , telecommunications , dna , allele , systems engineering , wireless , gene
Although the diploid nature has been observed for over 50 years, phasing the diploid is still a laborious task. The speed and throughput of next generation sequencing have largely increased in the past decades. However, the short read‐length remains one of the biggest challenges of haplotype analysis. For instance, reads as short as 150 bp span no more than one variant in most cases. Numerous experimental technologies have been developed to overcome this challenge. Distance, complexity and accuracy of the linkages obtained are the main factors to evaluate the efficiency of whole genome haplotyping methods. Here, we review these experimental technologies, evaluating their efficiency in linkages obtaining and system complexity. The technologies are organized into four categories based on its strategy: (i) chromosomes separation, (ii) dilution pools, (iii) crosslinking and proximity ligation, (ix) long‐read technologies. Within each category, several subsections are listed to classify each technology. Innovative experimental strategies are expected to have high‐quality performance, low cost and be labor‐saving, which will be largely desired in the future.