Microfluidic whole genome haplotyping
Haplotype information contributes to the understanding of the potential functional effects of variants in cis or in trans.
Haplotypes are more frequently resolved by inference through comparison with parental genotypes, or from population samples using statistical computational methods to determine linkage disequilibrium between markers.
Most of the knowledge of SNP association comes from the effort of the International HapMap Project, which has proved itself a powerful resource in the development of a publicly accessible database of human genetic variation.
Most current molecular biology methods use some form of MEMS, including microarray technology and next generation sequencing instruments.
In the first description of this technique, Fan et al. designed a custom-made program (MatLab) to control this process.
Once separated, the chromosomes are prepared for amplification by sequential addition and washout of trypsin, denaturation buffer and neutralization solution.
Whole genome haplotyping through microfluidics will increase the rate of discovery within the HapMap project, and provides an opportunity for corroboration and error detection within the existing database.
The amplification of each chromosome separately also provides a mechanism to potentially fill in some of the gaps that remain in the human reference genome.
[5] The scientific commons awaits further validation of this method and its efficacy in isolating and amplifying analyzable amounts of DNA.
Finally, since this entire process is based on amplification from a single cell, the accuracy of any genetic analysis is limited to the ability of commercially available platforms to produce sufficient amounts of unbiased and error free amplicon.
Like with the microfluidic technique, specialized amplification platforms are necessary to address the problem of a small initial DNA sample.
[6][7][8] Randomly partitioning a complete diploid fosmid library into various pools of equal size presents an alternative method for haplotype phasing.
In the proof of principle description of this technique[9] 115 pools were created containing ~5000 unique clones from the original fosmid library.
