Landscape of genomic alterations in cervical carcinomas

Cervical cancer is responsible for 10-15% of cancer-related deaths in women worldwide. The aetiological role of infection with high-risk human papilloma viruses (HPVs) in cervical carcinomas is well established. Previous studies have also implicated somatic mutations in PIK3CA, PTEN, TP53, STK11 and KRAS as well as several copy-number alterations in the pathogenesis of cervical carcinomas. Here we report whole-exome sequencing analysis of 115 cervical carcinoma-normal paired samples, transcriptome sequencing of 79 cases and whole-genome sequencing of 14 tumour-normal pairs. Previously unknown somatic mutations in 79 primary squamous cell carcinomas include recurrent E322K substitutions in the MAPK1 gene (8%), inactivating mutations in the HLA-B gene (9%), and mutations in EP300 (16%), FBXW7 (15%), NFE2L2 (4%), TP53 (5%) and ERBB2 (6%). We also observe somatic ELF3 (13%) and CBFB (8%) mutations in 24 adenocarcinomas. Squamous cell carcinomas have higher frequencies of somatic nucleotide substitutions occurring at cytosines preceded by thymines (Tp*C sites) than adenocarcinomas. Gene expression levels at HPV integration sites were statistically significantly higher in tumours with HPV integration compared with expression of the same genes in tumours without viral integration at the same site. These data demonstrate several recurrent genomic alterations in cervical carcinomas that suggest new strategies to combat this disease.

Abstract 5135: Analysis of formalin-fixed paraffin-embedded (FFPE) samples

The availability of large numbers of formalin-fixed, paraffin-embedded (FFPE) tumor DNA samples, together with accurate and specific clinical annotations, can be a great resource for in-depth analysis of correlations of somatic and germline DNA alterations with clinical outcome. However, the effects of this tissue preservation technique on next-generation DNA sequencing technologies and downstream analyses are still being investigated. Furthermore, usually the archives of such FFPE samples do not include matched normal tissue, which complicates the process of identifying somatic alterations. We are in the process of analyzing lung adenocarcinoma, colorectal and prostate patient datasets, which contain both an FFPE and a fresh-frozen tumor together with a matched blood normal sample. The availability of both a frozen and an FFPE tumor sample enables us to compare the detected somatic point mutations and indels, taking into account the fact that these pairs are produced from different aliquots of DNA. This analysis includes calculating the power to detect variants in the FFPE sample given that they have been observed in the fresh frozen tumor, as well as the validation rate of clonal SNVs between the two samples. We are also developing a method for classification of SNVs as germline or somatic without a paired normal sample by taking advantage of the fact that most tumor samples contain a substantial fraction of normal cells. Because stromal contamination has a different effect on the allelic fraction of somatic vs. germline SNVs, we can apply algorithms to estimate tumor purity and absolute somatic copy numbers in order to distinguish the two types of events. We present preliminary results from these analyses.

Citation Format: Petar Stojanov, Scott L. Carter, Ivan Imaz Rosshandler, Andrey Sivachenko, Alberto Salido Guadarrama, Karla Vazquez, Sandra Romero Cordoba, Kristian Cibulskis, Carrie Sougnez, Douglas Voet, Gordon Saksena, Lee Lichtenstein, Lihua Zou, Scott Frazer, Chip Stewart, Rameen Beroukhim, Matthew Meyerson, Michael S. Lawrence, Gad Getz. Analysis of formalin-fixed paraffin-embedded (FFPE) samples. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5135. doi:10.1158/1538-7445.AM2013-5135

Abstract 4604: Landscape of human and viral genomic alterations in cervical carcinomas

Background: Cervical cancer is a major public health problem worldwide. The etiological role of human papilloma virus (HPV) infections in cervical cancer is well established. However, HPV infection is insufficient to account for the development of cervical cancers because only 2 % of women infected with HPV eventually develop invasive carcinomas. We have therefore initiated a large scale sequencing effort to provide comprehensive data on the global landscape of genomic aberrations and HPV variants that contribute to cervical cancer. Methods: We have carried out comprehensive whole exome sequencing analyses on 120 tumor-normal paired samples from Mexico and Norway. We also carried out transcriptome and whole genome sequencing analyses on a subset of the patients (81 and 14 individuals respectively). Results: The aggregate mutation rate across the dataset was 3.8 per megabase (Mb), with the most common mutations being C to T/G in the Tp*C dinucleotide context, at a rate of 15 mutations per Mb. In all, 18,037 mutations were found across the entire dataset, including 11,536 missense, 984 nonsense, 4691 silent, 231 splice site, 32 translation start site mutations, as well 443 deletions and 142 insertions. MutSig analyses to identify genes that were mutated at statistically significant frequencies across our dataset revealed 11 genes to be recurrently mutated with a false discovery rate of q<0.1 after correction for multiple hypothesis testing (and RNASeq-based evidence of robust gene expression). The most significantly mutated genes encode for members of the PIK3CA/PTEN and RAS/RAF/MAPK signaling pathways, as well as the major histocompatibility complex (MHC). We have also uncovered novel patterns of HPV transcript abundance and sites of recurrent HPV integration in cell cycle related genes. In addition, our whole genome sequencing data suggests that HPV-negative p53-mutant tumors harbor high frequencies of genomic rearrangements. Conclusion: The comprehensive catalogue of genomic alterations provided by this project reveals potential novel therapeutic targets in cervical carcinomas. Our data also sets the stage for improving diagnostic and preventive strategies, especially in resource-limited settings with the highest incidence of cervical cancer.

Citation Format: Akinyemi I. Ojesina, Lee Lichtenstein, Lauren Ambrogio, Kristian Cibulskis, Samuel Freeman, Chandra Sekhar Pedamallu, Bjørn Bertelsen, Ivan Imaz, Karla Vazquez, Alberto Salido Guadarrama, Victor Treviño, Sandra Romero-Cordoba, Fujiko Duke, Bethany Kaplan, Iram Rodriguez, Magali Espinosa Castilla, Katherine Woie, Line Bjorge, Elisabeth Wik, Mari K. Halle, Erling Høivik, Camilla Krakstad, Gabriela Gómez Macías, María de Lourdes Garza Rodríguez, Jorge Vazquez, Carlos Rodea, Adrian Cravioto, Maria L. Cortes, Heidi Greulich, Christopher P. Crum, Lars Akslen, Hugo Barrera Saldaña, Jorge Melendez-Zajgla, Gad Getz, Helga B. Salvesen, Matthew L. Meyerson. Landscape of human and viral genomic alterations in cervical carcinomas. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4604. doi:10.1158/1538-7445.AM2013-4604