Introduction Facilitated by recent technological advances, numerous human genomes are being sequenced, cataloging an unprecedented amount of genetic variants (GVs) 1 . A major challenge exists in identifying and interpreting potentially functional GVs. Disease-associated GVs ofte…
Mutations and Copy Number Alterations in IDH Wild-Type Glioblastomas Are Shaped by Different Oncogenic Mechanisms - PMC Skip to main content Official websites use .gov A .gov website belongs to an official government organization in the United States. Secure .gov websites use HTT…
Kaiser and Semple Genome Biology (2018) 19:101 https://doi.org/10.1186/s13059-018-1483-4 RESEARCH Open Access Chromatin loop anchors are associated with genome instability in cancer and recombination hotspots in the germline Vera B. Kaiser* and Colin A. Semple Abstract Background…
Study participants The use of human participants (IRB-4237) and human-derived induced pluripotent stem cells (SCRO-568) in this study has been approved by the Stanford Research Compliance Office. The UKBB received ethical approval from the North West—Haydock Research Ethics Commi…
Abstract We tested and clinically validated a targeted next-generation sequencing (NGS) mutation panel using 80 formalin-fixed, paraffin-embedded (FFPE) tumor samples. Forty non-small cell lung carcinoma (NSCLC), 30 melanoma, and 30 gastrointestinal (12 colonic, 10 gastric, and 8…
Abstract Background Whole exome sequencing is increasingly used for the clinical evaluation of genetic disease, yet the variation of coverage and sensitivity over medically relevant parts of the genome remains poorly understood. Several sequencing-based assays continue to provide…
Abstract Context Chronic kidney disease (CKD) causes multiple interrelated disturbances in mineral metabolism. Genetic studies in the general population have identified common genetic variants associated with circulating phosphate, calcium, parathyroid hormone (PTH), and fibrobla…
Experimental methods Sample collection All the enrolled patients were consented to an institutional biospecimen banking protocol and MSK-IMPACT testing 53 , and all analyses were performed per a biospecimen research protocol. All protocols were approved by the Institutional Revie…
Haplotyping of human chromosomes is a prerequisite for cataloguing the full repertoire of genetic variation. We present a microfluidics-based linked-read sequencing technology that can phase and haplotype germline and cancer genomes using nanograms of input DNA. This high-through…
Carbohydrate Polymers 87 (2012) 1124–1130 Contents lists available at SciVerse ScienceDirect Carbohydrate Polymers journal homepage: www.elsevier.com/locate/carbpol Quantitative determination of cellulose dissolved in 1-ethyl-3-methylimidazolium acetate using partial least square…
Abstract Pulmonary arterial hypertension is a complication of methamphetamine use (METH-PAH), but the pathogenic mechanisms are unknown. Given that cytochrome P450 2D6 (CYP2D6) and carboxylesterase 1 (CES1) are involved in metabolism of METH and other amphetamine-like compounds, …
Abstract Cancer is generally thought to be caused by expansion of a single mutant cell 1 . However, analyses of early colorectal cancer lesions indicate that tumours may instead originate from several genetically distinct cell populations 2 , 3 . Detecting polyclonal tumour initi…
Analysis of SNVs in spatially and temporally distinct neuroblastoma samples reveals extensive intratumour heterogeneity To analyse neuroblastoma heterogeneity within the tumour tissue and across the course of disease in individual patients, we performed genomic and transcriptomic…
Abstract Copy number alteration (CNA) is a major contributor to genome instability, a hallmark of cancer. Here, we studied genomic alterations in single primary tumor cells and circulating tumor cells (CTCs) from the same patient. Single-nucleotide variants (SNVs) in single cells…
Classification of M. tuberculosis L1 Among 1174 successfully sequenced M. tuberculosis isolates, 480 were initially identified by LSP as belonging to the Indo-Oceanic family and had the 330 SNPs, previously reported to be specific to L1 27 (Supplementary Table S1 ). The following…