X   Phy Chem Bio Med Soc
Reading P1 Multiplexing. Basic strategies for automation and scale-up include serial, parallel and multiplex. Inspired by optical fibers, molecular multiplexing methods and applications started with chemical analysis of DNA (including mC) in 1984. Multiplexing is not only applicable to reading, but also writing -- applied to combinatorial chemical synthesis since 1988, assembly of DNA (and libraires) from chips in 2004, and genome engineering in 2009. We have been involved in most of the NGS and nanopore methods (see list)

Cyclic Next Generation Sequencing (NGS). This arose from cycles of fluidics and imaging used in genomic sequencing in 1984. Then coupled to "in situ" polymerase colonies (polonies) in 1999.
DNA-Nanoball grid

Nanopore Sequencing 1988-1995. Note polymerase pore fusion in lower left and use of long labels on nucleotides in the middle.
Pore-Pol 1995

Nanopore Sequencing 2013. After 25 years the first commercial systems are appearing. The use of polymerases or helicases to control the polymer movement is widely used as are long modifications on nucleotides caoable of reaching into the pore.

Nanopore

Relevant Church Lab Publications:
2013 Highly multiplexed three-dimensional subcellular transcriptome sequencing in situ. Submitted
2012 Accurate whole genome sequencing and haplotyping from 10-20 human cells. Nature.
2004 Accurate Multiplex Gene Synthesis from Programmable DNA Chips. Nature.
1999 In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Research.
1998 Characterization of individual polymer molecules based on monomer-interface interactions. US # 5,795,782
1988 Multiplex DNA sequencing Science.
1984 Genomic Sequencing. PNAS.

Relevant companies:
Illumina, Complete Genomics, Oxford NanoPore Technologies, Noblegen Biosciences, Genia, NABsys, Genapsys.

B1 M1 S1
Writing P2 C2 B2 M2 S2
Arithmetic
P3 C3 B3 M3 S3