Monday, July 13, 2009

Sequencing Koreans

There are several complete1 sequences of human genomes. The standard reference sequence is the one published at NCBI as a result of the human genome project It is a composite sequence from several individuals.

There are four personal genomes available. Craig Ventor, Jim Watson, an African (Yoruban), and an individual from China. Last May the sequence of a Korean was published in Genome Research.
Ahn, S.M., Kim, T.H., Lee, S., Kim, D., Ghang, H., Kim, D.S., Kim, B.C., Kim, S.Y., Kim, W.Y., Kim, C., Park, D., Lee, Y.S., Kim, S., Reja, R., Jho, S., Kim, C.G., Cha, J.Y., Kim, K.H., Lee, B., Bhak, J., Kim, S.J. (2009) The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group. Genome Res. 2009 Jun 24. [Epub ahead of print] [PubMed] [doi: 10.1101/gr.092197.109],
Pay attention to the dates ... it's going to be important.

This paper was received by the journal on Feb. 3, 2009. It was accepted on May 22, 2009 and published online on May 26, 2009. The sequence was posted on a Korean website in December 2008 and it has been freely available since then.

Another Korean group published a paper In Nature last week.
Kim, J.I., Ju, Y.S., Park, H., Kim, S., Leek S., Yi, J.H., Mudge, J., Miller, N.A., Hong, D., Bell, C.J., Kim, H.S., Chung, I.S., Lee, W.C., Lee, J.S., Seo, S.H., Yun, J.Y., Woo, H.N., Lee, H., Suh, D., Lee, S., Kim, H.J., Yavartanoo, M., Kwak, M., Zheng, Y., Lee, M.K., Park, H., Kim, J.Y., Gokcumen, O., Mills, R.E., Zaranek, A.W., Thakuria, J., Wu, X., Kim, R.W., Huntley, J.J., Luo, S., Schroth, G.P., Wu, T.D., Kim, H., Yang, K.S., Park, W.Y., Kim, H., Church, G.M., Lee, C., Kingsmore, S.F., Seo, J.S. (2009) A highly annotated whole-genome sequence of a Korean individual. Nature July 8 [epub ahead of print] [PubMed] [doi: 10.1038/nature08211]
This paper was received by the journal on March 6, 2009. It was accepted on June 18, 2009 and published online on July 8, 2009.

Neither paper mentions the other. There is nothing in the Nature paper that acknowledges the prior publication of the complete genome of a Korean. (Normally in circumstances like this you would expect a note at the end of the paper.)

Were the authors of the Nature paper completely unaware of the other work and the availability of the sequence data? Probably not, since it's mentioned in the press release.
The announcement, however, is likely to fuel a dispute over who was the first to have completed a genome map in Korea. Professor Kim Seong-jin, director of the Lee Gil-ya Cancer and Diabetes Research Institute at Gachon University of Medicine and Science in Incheon, completed a genome map in December last year and published it in the international journal Genome Research.

Seo said, “Since the accuracy is inadequate, (Kim’s) map cannot be considered Korea’s first.”

Gachon professor Ahn Seong-min refuted Seo’s claim, however, saying, “Professor Kim’s genomes were analyzed 29 times and the map is no less accurate than Professor Seo’s.”
It's going to be very difficult for the authors of the second paper to defend their actions. It looks like they behaved unethically by completely ignoring their competitors in their publication and then making a feeble excuse in the press release.

I also think the authors of the first paper should have mentioned that another Korean genome was about to be published although they probably did not have access to the data.

It will be interesting to see how this plays out. My first thoughts are that Nature ought to take a stand and retract the paper. My second thoughts are that Korean science seems to be very competitive and the scientific standars in that country seem to be more "flexible" than elsewhere.

1. Published sequences don't include centromeric regions and other regions with large blocks of repetitive DNA.


  1. Not citing your competitors when their papers are 100% relevant to your report is shameful and despicable. It's dishonest and a breach of scientific ethic.

  2. There's nothing to cite. Both works are completely independent and may not have even known of each other. Also unknown from the dates given is whether the second work was resubmitted before or after the first paper appeared in eprint.

  3. I agree anon, larry keep in mind that scientific dishonesty is just part of the field, it happens, look at watson and crick, but life continues.

  4. There's nothing to cite. Both works are completely independent and may not have even known of each other.

    Absolute bullshit. Impossible. And whether they are completely independent or not is 100% irrelevant.

    1. Everyone knows the competition. Basically, worldwide. And science in S. Korea is a relatively small and a tight-knit community where, basically, everyone knows everyone.

    2. Before you publish, it is your obligation to find and cite everything that's directly relevant to your research or the understanding of thereof.
    WTF do you mean there is nothing to cite? The original paper was published way before the Nature paper. End of story.

    Oh, and HowTF is a genome sequence good enough for a Nature paper in 2009???
    These days, you can pay $50K to Illumina and ~$50K to two-three guys to annotate. Or at least that's my impression - someone please correct me if it is way off.

  5. anonymous says,

    look at watson and crick

    In spite of what you might have heard, Francis Crick did nothing dishonest and Watson's so-called "transgression" wasn't a big deal at the time.

    However, you are correct when you say that science is full of people who behave unethically.

    I presume you didn't mean that as an excuse?