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

Sex differences in oncogenic mutational processes

Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: 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

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

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

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

Effects of the lercanidipine - Enalapril combination vs. The corresponding monotherapies on home blood pressure in hypertension: Evidence from a large database

103siObjective: To compare a combination of a dihydropyridine calcium-channel blocker with an angiotensin converting enzyme inhibitor vs. monotherapy with one or the other drug and placebo for their effects on home blood pressure (HBP). Methods: After a 2-week placebo wash-out, patients with an elevated office blood pressure (BP) (diastolic 100–109 and systolic <180 mmHg) and HBP (diastolic 85 mmHg) were randomized double-blind to a 10-week treatment with placebo, lercanidipine, 10 or 20mg daily, enalapril, 10 or 20mg daily, or the four possible combinations. In addition to office BP, HBP was self-measured via a validated semiautomatic device twice in the morning and twice in the evening during the 7 days before randomization and at the end of treatment. Baseline and treatment HBP values were separately averaged for each day, morning, evening or the whole monitoring period, excluding the first day. Day-by-day HBP variability was defined as the SD or the variation coefficient of the daily BP averages. Results: Eight hundred and fifty-four patients with valid HBP recordings at baseline and at the end of treatment were analyzed (intention-to-treat population). From the baseline value (147.011.6 mmHg) systolic/diastolic HBP showed a small reduction (average baseline-adjusted change: –1.8/–1.6 mmHg) with placebo, a more marked significant fall with monotherapies (8.8/5.9 mmHg, P<0.001/<0.001 vs. placebo) and even more with combination treatment (11.6/7.6 mmHg, P<0.001/ <0.001 vs. placebo and P<0.01/<0.05 vs. monotherapy). A similar pattern was observed for each of the days of the BP self-monitoring period as well as for either morning or evening values, although the difference between mono and combination treatment appeared to be consistently significant for the morning values only. Dayby- day systolic BP-SD was unaffected by placebo and slightly reduced by drug treatments, with no, however, significant changes in SBP-variation coefficient. Baseline and end of treatment HBP values showed a limited correlation with office BP values, this being particularly the case for treatment-induced changes (correlation coefficients: 0.37 for systolic and 0.45 for diastolic BP). Conclusion: This large HBP database shows that the lercanidipine–enalapril combination lowers HBP more effectively than the corresponding monotherapies and placebo, and that this greater effect is consistent between days.reservedmixedMancia, Giuseppe; Omboni, Stefano; Chazova, Irina; Coca, Antonio; Girerd, Xavier; Haller, Hermann; Parati, Gianfranco; Pauletto, Paolo; Pupek-Musialik, Danuta; Svyshchenko, Yevgeniya; Boye, Alain; Charrier, Bruno; Couffin, Yvon; Marmor, Philippe; Marty, Jacques; Navarre, Jean Louis; Ansari, Anwar; Büttner, Claudia; Kropp, Maximilian; Mehling, Heidrun; Paschen, Christine; Schenkenberger, Isabelle; Schneider, Helmut; Sperling, Karsten; Stübler, Petra; Von Behren, Volker; Lembo, Giuseppe; Scanferla, Flavio; Sechi, Leonardo Alberto; Gębala, Andrzej; Hoffmann, Andrzej; Janik, Krzysztof; Klimza-Masłowska, Anna; Kaczmarek, Barbara; Koźminski, Piotr; Makowiecka-Cies̈la, Magdalena; Mordaka, Robert; Nowakowski, Tomasz; Pasternak, Dariusz; Skibińska, Elzbieta; Sulik, Piotr; Szpajer, Michał; Walczewska, Jolanta; Zaczek, Marcin; Zienciuk-Krajka, Agnieszka; Alexeeva, Nadezhda; Bokarev, Igor; Chazova, Iina; Conrady, Alexandra; Emelyanov, Alexander; Galustyan, Anna; Idrisova, Elena; Khasanov, Niyaz; Khokhlov, Alexander; Libov, Igor; Reshetko, Olga; Sokurenko, German; Stryuk, Raisa; Tereshchenko, Sergey; Trofimov, Vasily; Zrazhevsky, Konstantin; Carlos Calvo, S.; De Teresa, Luis; Ferre, Raimon; García, Juan; Gil, Apolonia; Gil, Blas; Montenegro, Jesús; Oliván, Josefina; Ortiz, Jacinto; Pascual, José María; Rivera, Antonio; De Quevedo, José Antonio Sainz; Zúñiga, Manuel; Martinez, Valentin; Pujol, Montserrat; Bazylevych, Andriy; Gyrina, Olga; Ignatenko, Grygoriy; Kazymyrko, Vitaly; Khomazyuk, Tetyana; Kononenko, Lyudmyla; Korzh, Oleksii; Kovalenko, Volodymyr; Kuryata, Oleksander; Kushnir, Mykola; Lishnevska, Viktoriia; Lymar, Iurii; Ostrovska, Lidiia; Popik, Galyna; Rudyk, Yuriy; Shershnyova, Oxana; Sierkova, Valentyna; Storozhuk, Borys; Tseluyko, Vira; Vatutin, Mykola; Vayda, Myroslava; Vizir, Vadym; Volkov, Volodymyr; Voloshyna, Olena; Yagensky, Andriy; Zhurba, Svitlana; Zorin, ValeriiMancia, Giuseppe; Omboni, Stefano; Chazova, Irina; Coca, Antonio; Girerd, Xavier; Haller, Hermann; Parati, Gianfranco; Pauletto, Paolo; Pupek Musialik, Danuta; Svyshchenko, Yevgeniya; Boye, Alain; Charrier, Bruno; Couffin, Yvon; Marmor, Philippe; Marty, Jacques; Navarre, Jean Louis; Ansari, Anwar; Büttner, Claudia; Kropp, Maximilian; Mehling, Heidrun; Paschen, Christine; Schenkenberger, Isabelle; Schneider, Helmut; Sperling, Karsten; Stübler, Petra; Von Behren, Volker; Lembo, Giuseppe; Scanferla, Flavio; Sechi, Leonardo Alberto; Gębala, Andrzej; Hoffmann, Andrzej; Janik, Krzysztof; Klimza Masłowska, Anna; Kaczmarek, Barbara; Koźminski, Piotr; Makowiecka Cies̈la, Magdalena; Mordaka, Robert; Nowakowski, Tomasz; Pasternak, Dariusz; Skibińska, Elzbieta; Sulik, Piotr; Szpajer, Michał; Walczewska, Jolanta; Zaczek, Marcin; Zienciuk Krajka, Agnieszka; Alexeeva, Nadezhda; Bokarev, Igor; Chazova, Iina; Conrady, Alexandra; Emelyanov, Alexander; Galustyan, Anna; Idrisova, Elena; Khasanov, Niyaz; Khokhlov, Alexander; Libov, Igor; Reshetko, Olga; Sokurenko, German; Stryuk, Raisa; Tereshchenko, Sergey; Trofimov, Vasily; Zrazhevsky, Konstantin; Carlos Calvo, S.; De Teresa, Luis; Ferre, Raimon; García, Juan; Gil, Apolonia; Gil, Blas; Montenegro, Jesús; Oliván, Josefina; Ortiz, Jacinto; Pascual, José María; Rivera, Antonio; De Quevedo, José Antonio Sainz; Zúñiga, Manuel; Martinez, Valentin; Pujol, Montserrat; Bazylevych, Andriy; Gyrina, Olga; Ignatenko, Grygoriy; Kazymyrko, Vitaly; Khomazyuk, Tetyana; Kononenko, Lyudmyla; Korzh, Oleksii; Kovalenko, Volodymyr; Kuryata, Oleksander; Kushnir, Mykola; Lishnevska, Viktoriia; Lymar, Iurii; Ostrovska, Lidiia; Popik, Galyna; Rudyk, Yuriy; Shershnyova, Oxana; Sierkova, Valentyna; Storozhuk, Borys; Tseluyko, Vira; Vatutin, Mykola; Vayda, Myroslava; Vizir, Vadym; Volkov, Volodymyr; Voloshyna, Olena; Yagensky, Andriy; Zhurba, Svitlana; Zorin, Valeri

Integrative pathway enrichment analysis of multivariate omics data

Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations

Author Correction: The landscape of viral associations in human cancers

author correctio