Background: This series contains brief reports on each of the "600 studies" held on the GENERA database, published at Bifortified.org, in the order in which they were listed on 18 Sept 2013. The general purpose is to counter the extraordinary claims that the entries on this list demonstrate the human food safety of GM crops. See the Introduction to this series [link].
Great Big List of Studies: Entry 16 – Arencibia et al 1998 [abstract link]
The full text pdf is behind a paywall. I will get it eventually and update this post.
The study belongs to the category of studies investigating the outcome on a plant genome of 'inserting one gene' using various techniques of genetic engineering. The techniques include the subsequent use of highly mutagenic tissue culture to produce a plant from a single transformed plant cell.
These are the studies that expose one of the Big Lies of the genetic engineering PR narrative, which says that a little bit of DNA is cut and pasted from organism to another, to produce a new protein, and that's all. These are the studies that expose the lie of 'precision'. Needless to say, this is not a study that demonstrates the human health and safety of commercial GM crops.
While I wait for the full text, this is how others have cited this study:
Latham, Wilson & Steinbrecher; The Mutational Consequences of Plant Transformation 
- "GENOME-WIDE MUTATIONS: The second class of mutations associated with plant transformation are genome-wide mutations. These are not necessarily genetically linked to the transgene insertion site but arise as a consequence of tissue culture, probably Agrobacterium infection and possibly particle bombardment and antibiotic use [3, 10, 47, 48]. There are 5 studies in which researchers have attempted to quantify mutations introduced throughout the plant genome during plant transformation. These researchers used DNA polymorphism analysis (based on RFLP, AFLP, and other PCR techniques) to sample and compare the genomic DNA of transformed plants with that of nontransformed control plants [49–53] [includes Arencibia et al 1998]. Their results are broadly consistent. They suggest that plant transformation procedures typically introduce many hundreds to thousands of genome-wide mutations into the DNA of transgenic plants. For example, Labra et al  estimated that the "genomic similarity value" of control plants was 100%, but only 96%–98% for the transgenic plants. In other words, very extensive genetic mutation had resulted from the plant transformation procedures. These studies suggest that most genome-wide mutations are caused by passage through tissue culture, which in plant transformation is used in a particularly mutagenic form ."
Latham, Wilson & Steinbrecher had made more expansive comments in a 2004 Technical Report, well worth the read [link]
- "The data discussed in Section 2.3 [included analysis of Arencibia et al 1998] indicate that plant transformation methods can induce mutations at many 100s to 1000s of different sites in the plant genome. These numbers are likely to be underestimates of the true number. This is due to the fact that all the analytical methods used (e.g. RFLP and RAMP) are able to detect only a subset of the possible mutations.
- "At present, there is no published study using such molecular techniques to look for genome-wide mutations in commercially approved transgenic lines or cultivars."
In 2008 Zolla et al  published an analysis of changes in Monsanto's commercial GM maize MON810 reporting that there were changes in the up or down-regulation of 43 proteins as a result of the insertion of a single GM gene, including these comments in respect of Arencibia et al 1998:
- "The former explanation agrees with what expected: while with A. tumefaciens, the insertion sites tend to have simpler structures, but with extensive chromosomal rearrangements, with the particle bombardment approach, the variability seems to
be associated with deletion and extensive scrambling of inserted and chromosomal DNA.22 The clearest evidence implicating A. tumefaciens infection as a mutagenic event comes from large-scale T-DNA tagging experiments,23,24 while it is not known yet whether particle bombardment results in chromosomal mutations, and those introduced at other random locations, commonly called genome wide mutations. In agreement with these observations, the experimental results reported by Arencibia et al.25 and by Bao et al.26 indicated that transgenic rice produced by A. tumefaciens treatment is characterized by fewer genomic changes than those produced with particle bombardment or cell electroporation. In this regard, so far only a handful of studies has provided detailed data on the chromosomal mutations resulting from particle bombardment insertion,27–30 but no large-scale study had been conducted on the transgene insertion patterns obtained with particle bombardment."
The fact that the plant engineers may not have really understood what they were doing was established back in the 1990's. With authors from the John Innes Centre this study was listed as part of a UK Aid Department for International Development project [link]. The final statement in the conclusions of this Project was
- "Results also suggest that current views in the mechanism of integration of transgenes in plants using Agrobacterium may be flawed."
 Latham, Wilson & Steinbrecher; The Mutational Consequences of Plant Transformation; Journal of Biomedicine and Biotechnology, Volume 2006, Article ID 25376, Pages 1–7; DOI 10.1155/JBB/2006/25376 [pdf link]
 Zolla et al; Proteomics as a Complementary Tool for Identifying Unintended Side Effects Occurring in Transgenic Maize Seeds As a Result of Genetic Modifications; J. Proteome Res., 2008, 7 (5), 1850-1861; DOI: 10.1021/pr0705082 [pdf link]