A Lack of an "Original" SOLiD Paper--why?

[SamCurt]

When I tried to prepare a presentation for NGS, I was surprised to find there's no such thing as an "original" paper for SOLiD.

Usually, there must be a proof-of-concept paper published first, then papers that came out of the platform's beta testers. This is how I have observed with other providers.

People often quote George Church's paper on the Polonator as the original proof-of-concept of SOLiD, but I disagree. The Polonator could have been a proof-of-concept for Complete Genomics, but IMO, sequential ligation, double interrogation, and colour space, all major features of SOLiD, were never discussed by the Church Lab.

How can ABI (or Agencourt Personal Genomics) get away with starting a platform's paper trail with a stem-cell paper?

[pmiguel]

It is because there is no requirement that investigators base their discoveries only on completely disclosed methodologies. Arguably there should be. But like any other field of human endeavor, science is rife with contradictory ideologies.

Ostensibly, your publication of a result requires you to disclose your methods. But if you threw your samples into a black box instrumentation system and results emerged, frequently that will be sufficient disclosure on your part.

--
Phillip

[Chipper]

I think the first SOLiD human genome paper could be regarded as the "original" methods paper since it describes 2BE, emulsions, ligation sequencing etc. http://genome.cshlp.org/content/19/9/1527/suppl/DC1

[SamCurt]

I think the first SOLiD human genome paper could be regarded as the "original" methods paper since it describes 2BE, emulsions, ligation sequencing etc. http://genome.cshlp.org/content/19/9/1527/suppl/DC1

By the time SOLiD v1 has been released for more than a year. Also, this does not explain why most scientist still consider the Polonator paper as the "original" SOLiD paper...

[SeqAA]

1. you do not need a technology paper.
2. it's actually quite rare
3. it's also difficult to get published.

[epistatic]

Valouev, A. et al. 2008. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 18: 1051–1063.

Cloonan N, et al. 2008. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5:613–619.

McKernan KJ, et al. 2009. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Research 19 (9): 1527–1541.