BackgroundComprehensive genomic sequencing (CGS) has the potential to revolutionize precision medicine for cancer patients across the globe. However, to date large-scale genomic sequencing of cancer patients has been limited to Western populations. In order to understand possible ethnic and geographic differences and to explore the broader application of CGS to other populations, we sequenced a panel of 415 important cancer genes to characterize clinically actionable genomic driver events in 201 Japanese patients with colorectal cancer (CRC).MethodsUsing next-generation sequencing methods, we examined all exons of 415 known cancer genes in Japanese CRC patients (n = 201) and evaluated for concordance among independent data obtained from US patients with CRC (n = 108) and from The Cancer Genome Atlas-CRC whole exome sequencing (WES) database (n = 224). Mutation data from non-hypermutated Japanese CRC patients were extracted and clustered by gene mutation patterns. Two different sets of genes from the 415-gene panel were used for clustering: 61 genes with frequent alteration in CRC and 26 genes that are clinically actionable in CRC.ResultsThe 415-gene panel is able to identify all of the critical mutations in tumor samples as well as WES, including identifying hypermutated tumors. Although the overall mutation spectrum of the Japanese patients is similar to that of the Western population, we found significant differences in the frequencies of mutations in ERBB2 and BRAF. We show that the 415-gene panel identifies a number of clinically actionable mutations in KRAS, NRAS, and BRAF that are not detected by hot-spot testing. We also discovered that 26% of cases have mutations in genes involved in DNA double-strand break repair pathway. Unsupervised clustering revealed that a panel of 26 genes can be used to classify the patients into eight different categories, each of which can optimally be treated with a particular combination therapy.ConclusionsUse of a panel of 415 genes can reliably identify all of the critical mutations in CRC patients and this information of CGS can be used to determine the most optimal treatment for patients of all ethnicities.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-016-0387-8) contains supplementary material, which is available to authorized users.

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2019) Histopathology 74, 908-916. https://doi.org/10.1111/his.13817 Utility of CD123 immunohistochemistry in differentiating lupus erythematosus from cutaneous T cell lymphomaAims: Histopathological overlap between lupus erythematosus and certain types of cutaneous T cell lymphoma (CTCL) is well documented. CD123 + plasmacytoid dendritic cells (PDCs) are typically increased in lupus erythematosus, but have not been well studied in CTCL. We aimed to compare CD123 immunostaining and histopathological features in these conditions. Methods and results: Skin biopsies of cutaneous lupus erythematosus (CLE, n = 18), lupus erythematosus panniculitis (LEP, n = 17), mycosis fungoides (MF, n = 25) and subcutaneous panniculitis-like T cell lymphoma (SPTCL, n = 9) were retrospectively reviewed and immunostained with CD123. Percentage, distribution and clustering of CD123 + cells were compared between CLE and MF and between LEP and SPTCL using v 2 and two-tailed t-tests. A higher percentage of CD123 + cells was observed in CLE than MF (P < 0.01), more frequently comprising ≥20% of the entire infiltrate (P < 0.01) and forming clusters (P < 0.01). Similarly, LEP showed a higher percentage of CD123 + cells than SPTCL (P = 0.01), more frequently comprising ≥20% of the infiltrate (P = 0.04) and forming clusters (P = 0.01). Basal vacuolar change or dyskeratosis was observed in all CLE cases and in 48% cases of MF cases (P = 0.05). Plasma cells were readily identified in 76% cases of LEP but in none of the SPTCL cases (P = 0.01). Adipocyte rimming by lymphocytes, hyaline fat necrosis and fibrinoid/grungy necrosis did not significantly differ between LEP and SPTCL. Dermal mucin also failed to distinguish between groups. Conclusions: CD123 immunostaining is helpful in differentiating CLE from MF and LEP from SPTCL, but should be interpreted in conjunction with clinicopathological features and other ancillary studies to ensure accurate diagnosis.

PURPOSE Vulvar squamous cell carcinoma (vSCC) encompasses two predominant variants: one associated with detectable high-risk strains of human papillomavirus (hrHPV) and a second form often occurring in the context of chronic dermatitis in postmenopausal women. Genomic assessment of a large-scale cohort of patients with aggressive vSCC may identify distinct mutational signatures. MATERIALS AND METHODS Tumor samples from a total of 280 patients with vSCC underwent hybridization capture with analysis of up to 406 cancer-related genes. Human papillomavirus (HPV) sequences were detected by de novo assembly of nonhuman sequencing reads and aligned to the RefSeq database. Immunohistochemistry for programmed death-ligand 1 (PD-L1) was assessed. RESULTS One hundred two of 280 vSCCs (36%) contained hrHPV sequences, predominantly HPV 16 (88%). The HPV-positive (HPV+) group was significantly younger (median age, 59 v 64 years; P = .001). Compared with HPV-negative (HPV–) vSCCs, HPV+ tumors showed more frequent pathogenic alterations in PIK3CA (31% v 16%; P = .004), PTEN (14% v 2%; P < .0001), EP300 (14% v 1%; P < .0001), STK11 (14% v 1%; P < .0001), AR (5% v 0%; P = .006), and FBXW7 (10% v 3%; P = .03). In contrast, HPV– vSCCs showed more alterations in TP53 (83% v 6%; P < .0001), TERTp (71% v 9%; P < .0001), CDKN2A (55% v 2%; P < .0001), CCND1 amplification (22% v 2%; P < .0001), FAT1 (25% v 4%; P < .0001), NOTCH1 (19% v 6%; P = .002), and EGFR amplification (11% v 0%; P < .0001), as well as a higher rate of 9p24.1 ( PDL1/PDL2) amplification (5% v 1%) and PD-L1 immunohistochemistry high-positive tumor staining (33% v 9%; P = .04). CONCLUSION Comprehensive molecular profiles of vSCC vary considerably with hrHPV status and may inform patient selection into clinical trials. Sixty-one percent of HPV+ vSCCs had a pathogenic alteration in the PI3K/mTOR pathway, whereas HPV– vSCCs showed alterations in TP53, TERTp, CDKN2A, CCND1, and EGFR, and biomarkers associated with responsiveness to immunotherapy.

Highlights KRAS mutation is a major driver in mesonephric and mesonephric-like carcinomas of cervical, endometrial or ovarian origin. ARID1A and PIK3CA mutations were also identified in endometrial and ovarian mesonephric-like carcinomas. Peripheral blood ctDNA liquid biopsy may detect mutations in recurrent and/or metastatic mesonephric carcinomas.