Development of a system to protect and concentrate large DNA for genome analysis

PROJECT SUMMARY/ABSTRACT Structural variation alters approximately 3.4 times more base pairs than point mutations within the human genome. Structural variations, such as amplification, deletion, inversions, or translocations, alter genes and non-genic regions in several different diseases, such as Huntington’s, Parkinson’s, Charcot-Marie-Tooth,

cancer, chromoplexia, and undiagnosed genetic diseases. Long molecule read lengths are beneficial for studying complex disease genetics. Many diseases involve multiple genetic variants and regulatory elements, and longer reads provide a more comprehensive view of the genomic regions associated with disease

susceptibility, enabling the identification of variants and potential disease mechanisms. A significant obstacle in the field is DNA length prior to sequencing and physical mapping. Longer molecules are necessary to span large variations, with enough unique information on each side to determine the size and genetic information

within the variation. Our long-term goal is to develop a system to protect and concentrate huge DNA molecules for physical mapping or sequencing systems to analyze genomes for structural variations. The overall objective of this application is to protect and concentrate whole S. cerevisiae and E. coli chromosomes. Once the system

is tested with S. cerevisiae and E. coli, this system will be used for more complex samples. Our central hypothesis is that sizeable DNA molecules can be protected in an inverted insert and concentrated in a 3D- printed device with an acrylamide roadblock. The rationale for this project is to create a method to protect and

concentrate huge DNA molecules since no available system currently exists. To accomplish this, we put forth the following specific aims: 1) Develop an inverted insert to protect DNA during cell lysis. 2) Develop a roadblock to concentrate chromosomal DNA. This project is innovative as it a) utilizes 3D printing to create a

device and allows rapid modifications to the device, b) uses a roadblock to slow down the progression of DNA so DNA can be concentrated in the solution, c) protects DNA inside the inverted insert during cell lysis, so the DNA remains full length, and d) develops a system to protect and concentrate large DNA molecules (200 kb -

5 Mb). The significance of this project is devising a system to concentrate large DNA molecules that can span large variations within a genome with enough unique information on either side of the variation to discern variations associated with different diseases, enhance sequencing efficiency, improve genome assembly, and

aid in phasing and haplotype reconstruction.