A Verifiable Conformance Relationship between Smart Card Applets and B security Models

International audienceWe propose a formal framework based on the B method, that supports the development of secured smart card applications. Accordingly to the Common Criteria methodology, we start from a formal definition and modelling of security policies, as access control policies. At the end of the development process, smart card applications are implemented in a standardized way, based on both the life cycle of smart card applets and the APDU protocol. In this paper, we define a conformance relationship that aims at establishing how smart card applications can be related to security requirement models. This embraces both the notions of security conformance as well as traceability allowing to relate basic events appearing at the level of applications with abstract security policies. This approach has been developed in the RNTL POS´E project1, involving a smart card issuer, Gemalto

Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples

<div><p>Next-generation sequencing (NGS) studies are becoming routinely used for the detection of novel and clinically actionable DNA variants at a pangenomic scale. Such analyses are now used in the clinical practice to enable precision medicine. Formalin-fixed paraffin-embedded (FFPE) tissues are still one of the most abundant source of cancer clinical specimen, unfortunately this method of preparation is known to degrade DNA and therefore compromise subsequent analysis. Some studies have reported that variant detection can be performed on FFPE samples sequenced with NGS techniques, but few or none have done an in-depth coverage analysis and compared the influence of different state-of-the-art FFPE DNA extraction kits on the quality of the variant calling. Here, we generated 42 human whole-exome sequencing data sets from fresh-frozen (FF) and FFPE samples. These samples include normal and tumor tissues from two different organs (liver and colon), that we extracted with three different FFPE extraction kits (QIAamp DNA FFPE Tissue kit and GeneRead DNA FFPE kit from Qiagen, Maxwell^™ RSC DNA FFPE Kit from Promega). We determined the rate of concordance of called variants between matched FF and FFPE samples on all common variants (representing at least 86% of the total number of variants for SNVs). The concordance rate is very high between all matched FF / FFPE pairs, with equivalent values for the three kits we analyzed. On the other hand, when looking at the difference between the total number of variants in FF and FFPE, we find a significant variation for the three different FFPE DNA extraction kits. Coverage analysis shows that FFPE samples have less good indicators than FF samples, yet the coverage quality remains above accepted thresholds. We detect limited but statistically significant variations in coverage indicator values between the three FFPE extraction kits. Globally, the GeneRead and QIAamp kits have better variant calling and coverage indicators than the Maxwell kit on the samples used in this study, although this kit performs better on some indicators and has advantages in terms of practical usage. Taken together, our results confirm the potential of FFPE samples analysis for clinical genomic studies, but also indicate that the choice of a FFPE DNA extraction kit should be done with careful testing and analysis beforehand in order to maximize the accuracy of the results.</p></div

Percentage of reads mapping outside target regions.

<p>A: FF and FFPE samples. B: FFPE samples grouped by extraction method.</p

Rate of SNVs C.G > T.A substitution in FF and FFPE samples.

<p>A: FF and FFPE samples. B: FFPE samples grouped by extraction method.</p

Percentage of duplicated reads for FF and FFPE samples.

<p>A: FF and FFPE samples. B: FFPE samples grouped by extraction method.</p

Difference in number of variants between FF and FFPE samples for all matched FF/FFPE pairs.

<p>A: SNVs. B: INDELs.</p

Single nucleotide variants (SNVs) analysis between FF and FFPE sample pairs.

<p>NFF: Number of SNV in FF samples, NFFPE: number of SNV in FFPE samples, NPos: number of common positions between FF and FFPE samples, Nco: number of concordant positions, Ndi: number of discordant positions, P: concordance rate (Nco/NPos * 100).</p

Insertion-deletion events (INDELs) analysis between FF and FFPE sample pairs.

<p>NFF: Number of INDELs in FF samples, NFFPE: number of INDELs in FFPE samples, NPos: number of common positions between FF and FFPE samples, Nco: number of concordant positions, Ndi: number of discordant positions, P: percentage of concordance Nco/NPos.</p

DNA fragment length values for FF and FFPE samples.

<p>A: FF and FFPE samples. B: FFPE samples grouped by extraction method.</p

Percentage of positions having a coverage greater then or equal to 30X.

<p>A: FF and FFPE samples. B: FFPE samples grouped by extraction method.</p