Smaller, denser, smarter: improved Strand-seq library preparation, inversion genotyping, and phasing

Although DNA consists of two paired strands that run in opposite directions, conventional DNA sequencing ignores this directional information. But the direction of DNA can be used to distinguish different versions of genes (“alleles”) inherited from each of the parents, as well as to detect inversions—regions of DNA that are reversed in some individuals. In this thesis, I first describe an improved laboratory protocol for an existing directional DNA sequencing method, called Strand-seq. The key is that using volumes of reagents as small as one billionth of a liter makes the main chemical reaction more efficient. Second, I present a more reproducible and automated way to find inversions in directional DNA sequencing data. This new method is particularly useful for identifying small inversions that were previously difficult to detect. Third, I show how directional DNA sequencing from an individual can be used to determine which half of the DNA was inherited from the mother and which half was inherited from the father, without using any data from the parents. This new method requires incorporating information about variable chemical modifications of DNA called epigenetic marks. In future, the method may be used to identify which side of a patient’s family is at risk of an inherited disease when the patient’s parents are not available for genetic testing.

Dissertation: https://hdl.handle.net/11370/7168cd73-d672-4a9f-b1ff-334bd3757bd5