Project description:We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq), and pool matched low pass whole genome sequencing (WGS) of 12 treatment-naïve non-small cell lung cancer (NSCLC) primary tumors (PTs) and 31 treatment-naïve NSCLC brain metastases (BMs) . In total, we recovered 277,206 cell transcriptomes in 43 samples.
Project description:We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq), and pool matched low pass whole genome sequencing (WGS) of 12 treatment-naïve non-small cell lung cancer (NSCLC) primary tumors (PTs) and 31 treatment-naïve NSCLC brain metastases (BMs) . In total, we recovered 277,206 cell transcriptomes in 43 samples.
Project description:We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq), pool matched low pass whole genome sequencing (WGS) and single-cell spatial transcriptomics of 12 treatment-naïve non-small cell lung cancer (NSCLC) primary tumors (PTs) and 31 treatment-naïve NSCLC brain metastases (BMs) . In total, we recovered 277,206 cell transcriptomes in 43 samples. We performed matched spatial sequencing using SlideSeq2 on 14 snRNA-seq samples.
Project description:Background: Medulloblastoma (MB) is one of the most prevalent embryonal malignant brain tumors. Current classification organizes these tumors into four molecular groups (WNT-activated, SHH-activated and TP53-wild type, SHH-activated and TP53-mutant, and non-WNT/non-SHH). Recently, a comprehensive classification has been established, identifying numerous subgroups, some of which exhibit a poor prognosis. It is critical to establish effective subgrouping methods for accurate diagnosis and patient’s management that strikes a delicate balance between improving outcomes and minimizing the risk of comorbidities. Methods: We evaluated the ability of Nanopore sequencing to provide clinically relevant methylation and copy number profiles of MB. Nanopore sequencing was applied to an EPIC discovery cohort of frozen MB, benchmarked against the gold standard EPIC array, and validated further evaluated on an integrated diagnosis cohort of MB.
Project description:This is a single blind, case control, multicenter study jointly developed by Zhongshan Hospital of Fudan University, Shanghai Public Health Clinical Center, Shanghai Xuhui Central Hospital, Qingpu Branch of Zhongshan Hospital Affiliated to Fudan University, and Shanghai Singlera Genomics Company. The enrolled population will include positive group, precancerous lesions and healthy control group, which is expected to enroll 2,430 participants. The primary objective is to establish molecular testing methods for non-invasive screening and early diagnosis of digestive system cancers through ctDNA methylation and mutation, cfDNA and ctDNA fragment size, and end motif based model (for esophageal, gastric, colorectal cancer), and through ctDNA methylation detection, ctDNA low-pass WGS, miRNA7 and CTC detection and analysis technology based model (for hepatocellular carcinoma). The sensitivity and specificity of the models in cancer early detection will be evaluated.