Why did EFSA not reduce its ADI for aspartame or recommend its use should no longer be permitted?

On behalf of the European Food Safety Authority (EFSA), Kass and Lodi recently published a letter purporting to 'refute' our July 2019 analysis of EFSA's December 2013 assessment of the risks of aspartame. We had previously claimed inter alia that the EFSA panel had evaluated studies that had indicated that aspartame might be harmful far more sceptically than those that had not indicated harm. We reported that EFSA had deemed every one of 73 studies suggesting harm to have been unreliable. Kass and Lodi provided a tabulation with figures that differed from ours in every detail. This commentary shows that, while Kass and Lodi provided a response to our analysis, they have not come close to refuting it. Our analysis provided detailed characterisations of each of the studies and how the panel interpreted them, but Kass and Lodi provide no corresponding information at all. Kass and Lodi claim that EFSA deemed 21 of 35 studies that had indicated possible harm to have been reliable. But if that is so, we now ask: why did the EFSA panel not recommend that aspartame should be banned, or at least tightly restricted?

EFSA's toxicological assessment of aspartame: was it even-handedly trying to identify possible unreliable positives and unreliable negatives?

BACKGROUND: A detailed appraisal is provided of the most recent (December 2013) assessment of the safety and/or toxicity of the artificial sweetener aspartame by the European Food Safety Authority's Panel on Food Additives and Nutrient Sources Added to Food. That appraisal is prefaced with a contextualising chronological account drawn from a documentary archive of the key highlights of the antecedent scientific and policy debates concerning this sweetener from the early 1970s onwards. The appraisal focuses specifically on Section 3.2 of the panel's review, which is headed 'Toxicological data of aspartame'. METHODS: The methodology of the appraisal focusses on the extent to which the panel was symmetrically alert to possible false positives and false negatives, which in toxicological terms denote misleading indications of possible toxicity or misleading indications of safety. The methodology involved identifying and tabulating the prima facie indications of each of 154 empirical studies, and then comparing them with the way in which the panel chose to interpret the studies' findings, by focussing primarily on whether the panel deemed those studies to be reliable or unreliable. If the panel had been even-handed, the criteria for assessing reliability should have been the same for both putative positive and negative studies. RESULTS: Eighty-one studies were identified that prima facie did not indicate any possible harm, and of those the panel deemed 62 to be reliable and 19 as unreliable. Seventy-three studies were identified that prima facie did indicate possible harm; of those the panel deemed all 73 to be unreliable; none were deemed reliable. A qualitative comparative review of the criteria of appraisal invoked by the panel to judge the reliability of putative negative and positive studies is also provided. CONCLUSION: The quantitative result indicate that the panel's appraisal of the available studies was asymmetrically more alert to putative false positives than to possible false negatives. The qualitative analysis shows that very demanding criteria were used to judge putative positive studies, while far more lax and forgiving criteria were applied to putative negative studies. DISCUSSION: That quantitative and qualitative patterns are very problematic for a body supposed to prioritise the protection of public health. Given the shortcomings of EFSA's risk assessment of aspartame, and the shortcomings of all previous official toxicological risk assessments of aspartame, it would be premature to conclude that it is acceptably safe. They also imply that the manner in which EFSA panels operate needs to be scrutinised and reformed.

COSMIC: the Catalogue Of Somatic Mutations In Cancer.

COSMIC, the Catalogue Of Somatic Mutations In Cancer (https://cancer.sanger.ac.uk) is the most detailed and comprehensive resource for exploring the effect of somatic mutations in human cancer. The latest release, COSMIC v86 (August 2018), includes almost 6 million coding mutations across 1.4 million tumour samples, curated from over 26 000 publications. In addition to coding mutations, COSMIC covers all the genetic mechanisms by which somatic mutations promote cancer, including non-coding mutations, gene fusions, copy-number variants and drug-resistance mutations. COSMIC is primarily hand-curated, ensuring quality, accuracy and descriptive data capture. Building on our manual curation processes, we are introducing new initiatives that allow us to prioritize key genes and diseases, and to react more quickly and comprehensively to new findings in the literature. Alongside improvements to the public website and data-download systems, new functionality in COSMIC-3D allows exploration of mutations within three-dimensional protein structures, their protein structural and functional impacts, and implications for druggability. In parallel with COSMIC's deep and broad variant coverage, the Cancer Gene Census (CGC) describes a curated catalogue of genes driving every form of human cancer. Currently describing 719 genes, the CGC has recently introduced functional descriptions of how each gene drives disease, summarized into the 10 cancer Hallmarks.

COSMIC: somatic cancer genetics at high-resolution.

COSMIC, the Catalogue of Somatic Mutations in Cancer (http://cancer.sanger.ac.uk) is a high-resolution resource for exploring targets and trends in the genetics of human cancer. Currently the broadest database of mutations in cancer, the information in COSMIC is curated by expert scientists, primarily by scrutinizing large numbers of scientific publications. Over 4 million coding mutations are described in v78 (September 2016), combining genome-wide sequencing results from 28 366 tumours with complete manual curation of 23 489 individual publications focused on 186 key genes and 286 key fusion pairs across all cancers. Molecular profiling of large tumour numbers has also allowed the annotation of more than 13 million non-coding mutations, 18 029 gene fusions, 187 429 genome rearrangements, 1 271 436 abnormal copy number segments, 9 175 462 abnormal expression variants and 7 879 142 differentially methylated CpG dinucleotides. COSMIC now details the genetics of drug resistance, novel somatic gene mutations which allow a tumour to evade therapeutic cancer drugs. Focusing initially on highly characterized drugs and genes, COSMIC v78 contains wide resistance mutation profiles across 20 drugs, detailing the recurrence of 301 unique resistance alleles across 1934 drug-resistant tumours. All information from the COSMIC database is available freely on the COSMIC website.

COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer.

The catalogue of Somatic Mutations in Cancer (COSMIC) (http://www.sanger.ac.uk/cosmic/) is the largest public resource for information on somatically acquired mutations in human cancer and is available freely without restrictions. Currently (v43, August 2009), COSMIC contains details of 1.5-million experiments performed through 13,423 genes in almost 370,000 tumours, describing over 90,000 individual mutations. Data are gathered from two sources, publications in the scientific literature, (v43 contains 7797 curated articles) and the full output of the genome-wide screens from the Cancer Genome Project (CGP) at the Sanger Institute, UK. Most of the world's literature on point mutations in human cancer has now been curated into COSMIC and while this is continually updated, a greater emphasis on curating fusion gene mutations is driving the expansion of this information; over 2700 fusion gene mutations are now described. Whole-genome sequencing screens are now identifying large numbers of genomic rearrangements in cancer and COSMIC is now displaying details of these analyses also. Examination of COSMIC's data is primarily web-driven, focused on providing mutation range and frequency statistics based upon a choice of gene and/or cancer phenotype. Graphical views provide easily interpretable summaries of large quantities of data, and export functions can provide precise details of user-selected data.

Mutation analysis of EP300 in colon, breast and ovarian carcinomas.

The putative tumour suppressor gene EP300 is located on chromosome 22q13 which is a region showing frequent loss of heterozygosity (LOH) in colon, breast and ovarian cancers. We analysed 203 human breast, colon and ovarian primary tumours and cell lines for somatic mutations in EP300. LOH across the EP300 locus was detected in 38% of colon, 36% of breast, and 49% of ovarian primary tumours but no somatic mutations in EP300 were identified in any primary tumour. Analysis of 17 colon, 11 breast, and 11 ovarian cancer cell lines identified truncating mutations in 4 colon cancer cell lines (HCT116, HT29, LIM2405 and LIM2412). We confirmed the presence of a previously reported frameshift mutation in HCT116 at codon 1699 and identified a second frameshift mutation at codon 1468. Bi-allelic inactivation of EP300 was also detected in LIM2405 that harbours an insC mutation at codon 927 as well an insA mutation at codon 1468. An insA mutation at codon 1468 was identified in HT29 and a CGA>TGA mutation at codon 86 was identified in LIM2412. Both these lines were heterozygous across the EP300 locus and western blot analysis confirmed the presence of an apparently wild-type protein. Our study has established that genetic inactivation of EP300 is rare in primary colorectal, breast and ovarian cancers. In contrast, mutations are common among colorectal cancer cell lines with 4/17 harbouring homozygous or heterozygous mutations. The rarity of EP300 mutations among these tumour types that show a high frequency of LOH across 22q13 may indicate that another gene is the target of the loss. It is possible that bi-allelic inactivation of EP300 is not necessary and that haploinsufficiency is sufficient to promote tumorigenesis. Alternatively, silencing of EP300 may be achieved by epigenetic mechanisms such as promoter methylation.

A first-generation linkage disequilibrium map of human chromosome 22.

DNA sequence variants in specific genes or regions of the human genome are responsible for a variety of phenotypes such as disease risk or variable drug response. These variants can be investigated directly, or through their non-random associations with neighbouring markers (called linkage disequilibrium (LD)). Here we report measurement of LD along the complete sequence of human chromosome 22. Duplicate genotyping and analysis of 1,504 markers in Centre d'Etude du Polymorphisme Humain (CEPH) reference families at a median spacing of 15 kilobases (kb) reveals a highly variable pattern of LD along the chromosome, in which extensive regions of nearly complete LD up to 804 kb in length are interspersed with regions of little or no detectable LD. The LD patterns are replicated in a panel of unrelated UK Caucasians. There is a strong correlation between high LD and low recombination frequency in the extant genetic map, suggesting that historical and contemporary recombination rates are similar. This study demonstrates the feasibility of developing genome-wide maps of LD.