To assess the performance of the Oxford Nanopore Technologies MinION sequencing platform, cDNAs from the External RNA Controls Consortium (ERCC) RNA Spike-In mix were sequenced. This mix mimics mammalian mRNA species and consists of 92 polyadenylated transcripts with known concentration. cDNA libraries were generated using a template switching protocol to facilitate the direct comparison between different sequencing platforms. The MinION performance was assessed for its ability to sequence the cDNAs directly with good accuracy in terms of abundance and full length. The abundance of the ERCC cDNA molecules sequenced by MinION agreed with their expected concentration. No length or GC content bias was observed. The majority of cDNAs were sequenced as full length. Additionally, a complex cDNA population derived from a human HEK-293 cell line was sequenced on an Illumina HiSeq 2500, PacBio RS II and ONT MinION platforms. We observed that there was a good agreement in the measured cDNA abundance between PacBio RS II and ONT MinION (rpearson = 0.82, isoforms with length more than 700bp) and between Illumina HiSeq 2500 and ONT MinION (rpearson = 0.75). This indicates that the ONT MinION can sequence quantitatively both long and short full length cDNA molecules.

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Therapies targeting epidermal growth factor receptor (EGFR) have variable and unpredictable responses in breast cancer. Screening triple-negative breast cancer (TNBC) patient-derived xenografts (PDXs), we identify a subset responsive to EGFR inhibition by gefitinib, which displays heterogeneous expression of wild-type EGFR. Deep single-cell RNA sequencing of 3,500 cells from an exceptional responder identified subpopulations displaying distinct biological features, where elevated EGFR expression was significantly enriched in a mesenchymal/stem-like cellular cluster. Sorted EGFR subpopulations exhibited enhanced stem-like features, including ALDH activity, sphere-forming efficiency, and tumorigenic and metastatic potential. EGFR cells gave rise to EGFR and EGFR cells in primary and metastatic tumors, demonstrating an EGFR-dependent expansion and hierarchical state transition. Similar tumorigenic EGFR subpopulations were identified in independent PDXs, where heterogeneous EGFR expression correlated with gefitinib sensitivity. This provides new understanding for an EGFR-dependent hierarchy in TNBC and for patient stratification for therapeutic intervention.

To assess the performance of the Oxford Nanopore Technologies MinION sequencing platform, cDNAs from the External RNA Controls Consortium (ERCC) RNA Spike-In mix were sequenced. This mix mimics mammalian mRNA species and consists of 92 polyadenylated transcripts with known concentration. cDNA libraries were generated using a template switching protocol to facilitate the direct comparison between different sequencing platforms. The MinION performance was assessed for its ability to sequence the cDNAs directly with good accuracy in terms of abundance and full length Transcriptome sequencing using short read technologies (Illumina HiSeq 2500 1 , Ion Proton 2 ) provides valuable information on transcript abundance, rare transcripts and variable transcription start or end sites. Nevertheless, inferring alternatively spliced isoforms of genes from short read data through statistical assignment of the most probable combination of exons is still computationally challenging and not very accurate 3 . Uneven read coverage 4 , complex splicing 5 and potential sequencing bias 6 complicates even more the task. The PacBio RS II 7 zero-mode waveguide (ZMW) long-read sequencing technology has proven capable of characterizing the transcriptome in its native, full-length form unravelling novel gene isoforms not previously observed in RNA-seq experiments 8 . Recently, another long-read DNA sequencing technology based on nanopore sequencing (MinION) was introduced from Oxford Nanopore Technologies Ltd (ONT) 9 . Similar to PacBio RS II, the ONT MinION has been shown that can resolve the exon structure of mRNA molecules transcribed from genes with a large variety of isoforms 10 . Here, we assessed the ONT MinION performance for its ability to sequence the cDNAs with good accuracy in terms of cDNA abundance, sequence identity and in full length. To evaluate the performance of the ONT MinION platform, the cDNA of a commercially available defined set of 92 polyadenylated transcripts, that mimic mRNA species (ERCC RNA Spike-In mix), was sequenced with the Illumina HiSeq 2500 or MiSeq instruments, the PacBio RS II platform and the ONT MinION. Additionally, a complex cDNA population from a HEK-293 cell line was sequenced in the same sequencing platforms and the agreement in the cDNA abundance of the different transcript isoforms across the three platforms was assessed. The results indicate that the ONT MinION platform

We report changes in the genomic landscape in the development of head and neck squamous cell carcinomas HNSCC from potentially premalignant lesions (PPOLS) to malignancy and lymph node metastases. Likely pathological mutations predominantly involved a relatively small set of genes reported previously ( TP53 , KMT2D , CDKN2A , PIK3CA , NOTCH1 and FAT1 ) but also other predicted cancer drivers ( MGA , PABPC3 , NR4A2 , NCOR1 and MACF1 ). Notably, all these mutations arise early and are present in PPOLs. The most frequent genetic changes, which follow acquisition of immortality and loss of senescence, are of consistent somatic copy number alterations (SCNAs) involving chromosomal regions enriched for genes in known and previously unreported cancer-related pathways. We mapped the evolution of SCNAs in HNSCC progression. One of the earliest SCNAs involved deletions of CSMD1 (8p23.2). CSMD1 deletions or promoter hypermethylation were present in all of the immortal PPOLs and occurred at high frequency in the immortal HNSCC cell lines. Modulation of CSMD1 in cell lines revealed significant suppression of proliferation and invasion by forced expression, and significant stimulation of invasion by knockdown of expression. Known cancer drivers NOTCH1 , PPP6C , RAC1 , EIF4G1 , PIK3CA showed significant increase in frequency of SCNA in transition from PPOLs to HNSCC that correlated with their expression. In the later stages of progression, HNSCC with and without nodal metastases showed some clear differences including high copy number gains of CCND1 , hsa-miR-548k and TP63 in the metastases group.