Single Molecule Approaches to Genomic Analysis
T.S. Anantharaman (1), C. Cantor (2), V. Demidov (3), C.W. Dykes (6), J.
Gimzewski (4), B.B. Magee (5), P.T. Magee (5), M. Place (6), T. Rast (5), J.
Reed (4), M. Teitell (4), & B. Mishra (1)
(1) NYU, NY. (2) Sequenom, Inc., CA. (3) Boston U., MA, (4) UCLA, CA. (5) Univ.
Minnesota, MN. (6) OpGen, Inc., WI.
We explore various technological, mathematical and algorithmic questions, primarily
motivated by our wish to develop, an inexpensive technology to sequence a human size
genome of about 6 Gb, as it would include both haplotypes. To achieve this goal, it is
necessary to successfully integrate three different component technologies: (1) Optical
Mapping to create Ordered Restriction Maps with respect to one or more restriction
enzymes, (2) Hybridization of a pool of short nucleobase probes (PNA or LNA
oligomers) with Single Genome DNA molecules on a surface, and (3) Efficient
polynomial time algorithms to solve “localized versions” of the PSBH (Positional
Sequencing by Hybridization) problems over the whole genome. The design of such a
technology relies on a detailed probabilistic analysis, leading to an efficient exploitation
of a 0-1 law and its dependence on various parameters (optical sizing error, partial
digestion, haplotypic variations, false positives and negatives in hybridization rates,
errors in estimating probe hybridization locations, etc.), as has been previously achieved
by members of this team to design a robust optical mapping technology.
A key intermediate step is represented by the construction of a draft haplotype restriction
map of the fungal genome Candida Albicans (work-in-progress, in collaboration with
Opgen Inc., Wisconsin and Magee et al. of Univ. Minnesota), the first such assembly of a
single-molecule-based individual haplotype map.