Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

LA NECESIDAD DE MEDIADORES Y NEGOCIADORES EXPERTOS EN LAS COMISIONES DE LA VERDAD

Resumen: La finalidad de esta ponencia es destacar la importancia del establecimiento de comisiones de la verdad en nuestro país, fenómeno que está ocurriendo en diferentes países, con la finalidad de esclarecer hechos controvertidos, sobretodo de violaciones graves a los derechos humanos, principalmente sobre desaparición forzada de personas, que aunque algunos sucedieron hace muchos años, siguen impactando a nuestra sociedad; se aborda el derecho a la verdad como una obligación por parte del Estado Mexicano y como un derecho de victimas, familiares y sociedad de que se investiguen esos hechos controvertidos o en ocasiones que se niega que hayan sucedido, por parte del gobierno, consistentes en graves violaciones a los derechos humanos por parte de las autoridades; y se establece la necesidad de preparar a mediadores y negociadores expertos en las necesidades propias de esta clase de comisiones, que cuenten con cualidades y capacitación excepcional, que entiendan la justicia transicional, para que sean parte integrante de estas comisiones.Palabras clave: Comisiones de la verdad, Mediadores, Negociadores, Derecho a la Verdad, Justicia Transicional.

La Actualización de la Enseñanza del Derecho Respecto a la Reforma Legislativa sobre Justicia Ambiental.

Documento del Xl Congreso Internacional Retos y Expectativas de la Universidad (2011

La justicia restaurativa en el Derecho Internacional Público y su relación con la justicia transicional

Restorative justice is a philosophy and method for settling conflicts that have disturbed peace, in order to restore it through a process involving directly the victims, victimizer and community.Its application in daily conflicts with successful results has positioned it in the international arena and is now recommended in instruments of public international law to achieve the harmony lost by conflicts derived from facts considered crimes of public international law. A specific application is in the so-called transitional justice, as a method to restore peace without affecting the victims or favoring impunity, a process that Colombia is experiencing today.La justice réparatrice est une philosophie et une méthode pour régler les conflits qui ont troublé la paix, afin de la restaurer à travers un processus dans lequel les personnes impliquées interviennent directement: victime, agresseur et communauté. Son application dans les conflits quotidiens avec des résultats réussis l’a positionné au niveau international et est maintenant recommandé dans les instruments de droit international public pour réaliser l’harmonie perdue en raison des conflits découlant d’actes considérés comme des crimes de droit international public. Une application spécifique est dans la soi-disant justice transitionnelle, comme une méthode pour rétablir la paix sans affecter les victimes ou favoriser l’impunité, un processus que la Colombie connaît actuellement.La justicia restaurativa es una filosofía y un método para arreglar conflictos que han perturbado la paz, con el fin de restablecerla a través de un proceso en el que intervengan directamente los  nvolucrados: víctima, victimario y comunidad. Su aplicación en los conflictos cotidianos con resultados exitosos la ha posicionado en el ámbito internacional y ahora es recomendada en instrumentos de derecho internacional público para alcanzar la armonía perdida por conflictos derivados de hechos considerados delitos de derecho internacional público. Una aplicación específica es en la llamada justicia transicional, como un método para restablecer la paz sin afectar a las víctimas ni favorecer la impunidad, proceso que hoy está viviendo Colombia

Sex differences in oncogenic mutational processes

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Peer reviewe

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe