page_title: Microfluidic whole genome haplotyping
section_title: Methods
hierarchical_section_title: Microfluidic whole genome haplotyping / Microfluidic direct deterministic phasing / Methods
caption_attribution_description: English: Microfluidics whole chromosome separation workflow
context_page_description: Microfluidic whole genome haplotyping is a technique for the physical separation of individual chromosomes from a metaphase cell followed by direct resolution of the haplotype for each allele.
context_section_description: A single metaphase cell is isolated from solution. The chromosomes are then released from the nucleus, and the cytoplasm is digested enzymatically.  Next, the chromosome suspension is directed towards multiple partitioning channels. The chromosomes are physically directed into the partitioning channels using a series of valves. 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. The DNA is then ready for further processing. Because of the small amount of DNA, amplification needs to be performed using kits specialized for very small initial DNA quantities. The amplified DNA is flushed out of the microfluidic device and solubilized by the addition of a buffer. The amplified DNA can now be analyzed by various methods.
  Once the chromosomes have been isolated and amplified any molecular haplotyping can be applied as long as the chromosomes remain distinct.  This could be accomplished by keeping them physically separated, or identifying each sample by genotyping.  Once each chromosome has been identified each pair of homologs can be assorted into one of two haploid genomes.
caption: Workflow of microfluidic whole genome chromosome isolation and amplification. Not at scale
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