Resources by Category: "FFPE"

Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles

Paloma Cejas, Lewyn Li, Nicholas K O’Neill, Melissa Duarte, Prakash Rao, Michaela Bowden, Chensheng W Zhou, Marta Mendiola, Emilio Burgos, Jaime Feliu, Juan Moreno-Rubio, Héctor Guadalajara7, Víctor Moreno, Damián García-Olmo, Joaquim Bellmunt, Stephanie Mullane, Michelle Hirsch, Christopher J Sweeney, Andrea Richardson, X Shirley Liu, Myles Brown, Ramesh A Shivdasani, & Henry W Long. Nat Med. 2016 April 25…. Read more »

NovaPlex™ for Amplification and Analysis of Nucleic Acids from Formalin-Fixed, Paraffin-Embedded Tissue

T. Tesmer, M. Mastronardi, E. Kamberov, J. Langmore The fixation of human tissues with formalin, and their subsequent embedding in paraffin, has been a routine method of collecting and preserving surgical specimens for many years. These formalin-fixed, paraffin-embedded (FFPE) tissues represent an extremely valuable resource for investigators interested in determining both the pattern of gene… Read more »

Methods to simplify template preparations and increase sensitivity of next-generation sequencing of short DNA and cDNA for non-invasive prenatal and cancer diagnostics as well as for FFPE-seq, ChIP-seq, and methyl-seq

J. Langmore, E. Kamberov, T. Tesmer, M. Mastronardi (Rubicon Genomics, Ann Arbor), M. Luo, M. Jeong, D. Sun, W. Lei, L. White, G. Darlington (Baylor College of Medicine, Houston) Small amounts of degraded and/or rare DNA are useful for prenatal and cancer diagnostic sequencing. Unfortunately, conventional NGS preps require ng or mg amounts of starting… Read more »

Two Methods for High-Throughput NGS Template Preparation for Small Clinical Samples Without Automation

J. Langmore, E. Kamberov, T. Tesmer, M. Mastronardi (Rubicon Genomics, Ann Arbor) Clinical samples are difficult to prepare for NGS, because of the small amounts of formalin-fixed tissue, plasma, urine, and single-cell DNA available from patients. Conventional whole genome amplification methods are too biased for NGS applications, and the existing NGS preparation kits require intermediate… Read more »

Experience with 2 methods to simplify NGS Preps of clinical samples, including FFPE tissue, plasma, immunoprecipitates and single cells

J. Langmore, E. Kamberov, T. Tesmer, M. Mastronardi (Rubicon Genomics, Ann Arbor) Formalin-fixed tissue, FNA, plasma, urine, CSF and other clinical samples were standardized for many scientific and practical reasons long before the value and limitations of genetic testing were known. These clinical samples are highly degraded, and the analytes present in limiting quantities (e.g.,… Read more »

Quantitative Quality Metrics for NGS Libraries from Clinical Samples

J. Langmore, E. Kamberov, T. Tesmer, J. Jessmon, M. Carey, I. King (Rubicon Genomics, Ann Arbor) Clinical samples are difficult to prepare for NGS, because they are often present in small amounts, are highly degraded, and are of small size. We have tried to characterize clinical samples, suggest the effects of those characteristics on NGS… Read more »