High prevalence of unusual KRAS, NRAS, and BRAF mutations in POLE-hypermutated colorectal cancers.

Exonucleasic domain POLE (edPOLE) mutations, which are responsible for a hypermutated tumor phenotype, occur in 1-2% of colorectal cancer (CRC) cases. These alterations represent an emerging biomarker for response to immune checkpoint blockade. This study aimed to assess the molecular characteristics of edPOLE-mutated tumors to facilitate patient screening. Based on opensource data analysis, we compared the prevalence of edPOLE mutations in a control group of unselected CRC patients (n = 222) vs a group enriched for unusual BRAF/RAS mutations (n = 198). Tumor mutational burden (TMB) and immune infiltrate of tumors harboring edPOLE mutations were then analyzed. In total, 420 CRC patients were analyzed: 11 edPOLE-mutated tumors were identified, most frequently in microsatellite (MMR)-proficient young (< 70 years) male patients, with left-sided tumors harboring noncodon 12 KRAS mutation. The prevalence of edPOLE-mutated tumors in the control vs the experimental screening group was, respectively, 0.45% (n = 1) vs 5.0% (n = 10). Among the 11 edPOLE-mutated cases, two had a low TMB, three were hypermutated, and six were ultramutated. EdPOLE-mutated cases had a high CD8+ tumor-infiltrating lymphocyte (TIL) infiltration. These clinicopathological and molecular criteria may help to identify edPOLE mutations associated with a high TMB in CRC, and improve the selection of patients who could benefit from immunotherapy.

Improved Efficiency and Reliability of NGS Amplicon Sequencing Data Analysis for Genetic Diagnostic Procedures Using AGSA Software.

Screening for BRCA mutations in women with familial risk of breast or ovarian cancer is an ideal situation for high-throughput sequencing, providing large amounts of low cost data. However, 454, Roche, and Ion Torrent, Thermo Fisher, technologies produce homopolymer-associated indel errors, complicating their use in routine diagnostics. We developed software, named AGSA, which helps to detect false positive mutations in homopolymeric sequences. Seventy-two familial breast cancer cases were analysed in parallel by amplicon 454 pyrosequencing and Sanger dideoxy sequencing for genetic variations of the BRCA genes. All 565 variants detected by dideoxy sequencing were also detected by pyrosequencing. Furthermore, pyrosequencing detected 42 variants that were missed with Sanger technique. Six amplicons contained homopolymer tracts in the coding sequence that were systematically misread by the software supplied by Roche. Read data plotted as histograms by AGSA software aided the analysis considerably and allowed validation of the majority of homopolymers. As an optimisation, additional 250 patients were analysed using microfluidic amplification of regions of interest (Access Array Fluidigm) of the BRCA genes, followed by 454 sequencing and AGSA analysis. AGSA complements a complete line of high-throughput diagnostic sequence analysis, reducing time and costs while increasing reliability, notably for homopolymer tracts.

DNA repair genes implicated in triple negative familial non-BRCA1/2 breast cancer predisposition.

Among breast cancers, 10 to 15% of cases would be due to hereditary risk. In these familial cases, mutations in BRCA1 and BRCA2 are found in only 15% to 20%, meaning that new susceptibility genes remain to be found. Triple-negative breast cancers represent 15% of all breast cancers, and are generally aggressive tumours without targeted therapies available. Our hypothesis is that some patients with triple negative breast cancer could share a genetic susceptibility different from other types of breast cancers. We screened 36 candidate genes, using pyrosequencing, in all the 50 triple negative breast cancer patients with familial history of cancer but no BRCA1 or BRCA2 mutation of a population of 3000 families who had consulted for a familial breast cancer between 2005 and 2013. Any mutations were also sequenced in available relatives of cases. Protein expression and loss of heterozygosity were explored in tumours. Seven deleterious mutations in 6 different genes (RAD51D, MRE11A, CHEK2, MLH1, MSH6, PALB2) were observed in one patient each, except the RAD51D mutation found in two cases. Loss of heterozygosity in the tumour was found for 2 of the 7 mutations. Protein expression was absent in tumour tissue for 5 mutations. Taking into consideration a specific subtype of tumour has revealed susceptibility genes, most of them in the homologous recombination DNA repair pathway. This may provide new possibilities for targeted therapies, along with better screening and care of patients.

Chest CT scan screening for lung cancer in asbestos occupational exposure: a systematic review and meta-analysis.

OBJECTIVE: Lung cancer is the most frequent malignant asbestos-related pathology and remains the most fatal cancer of industrialized countries. In heavy smokers, early detection of lung cancer with chest CT scan leads to a 20% mortality reduction. However, the use of CT scan screening for early detection of lung cancer in asbestos-exposed workers requires further investigation. This study aimed to determine whether CT scan screening in asbestos-exposed workers is effective in detecting asymptomatic lung cancer using a systematic review and meta-analysis. METHODS: We reviewed all cohort studies involving chest CT scan screening in former asbestos-exposed workers. The search strategy used the following keywords: "asbestos," "lung cancer," "screening," and "occupation*" or "work." Databases were PubMed, Cochrane Library, Science Direct, and Embase. RESULTS: Seven studies matched our inclusion criteria. Baseline screening detected 49 asymptomatic lung cancers among 5,074 asbestos-exposed workers. Of the 49 reported lung cancers, at least 18 were in the earliest stage (stage I), accessible to complete removal surgery. The prevalence of all lung cancers detected by CT scan screening in asbestos-exposed workers was 1.1% (95% CI, 0.6%-1.8%). CONCLUSIONS: CT scan screening in asbestos-exposed workers is effective in detecting asymptomatic lung cancer. Detection of lung cancer in asbestos-exposed workers using CT scanning is at least equal to the prevalence in heavy smokers (1%; 95% CI, 0.09%-1.1%) and also shared a similar proportion of stage I diagnoses. Screening asbestos-exposed workers could reduce mortality in proportions previously observed among heavy smokers and, thus, should not be neglected, particularly for individuals combining both exposures.