Resources by Category: "Posters"

NGS libraries from cell-free DNA containing molecular tags prepared with ThruPLEX® technology improve ability to detect rare alleles

Matthew Carroll1, Dmitry Goryunov1, Konstantinos Charizanis1, Fang Sun1, Maria Dinkelmann1, Edward Jan1, Kamran Shazand1, Emmanuel Kamberov1, Shawn Quinn2, John Langmore1 1Rubicon Genomics, Inc. • Ann Arbor, MI • 2 Curio Genomics, Inc. Dexter, MI Liquid biopsies provide a non-invasive method to acquire the genetic information provided in cell-free DNA. Next Generation Sequencing enables access to… Read more »

High-Efficiency Detection of Low-Frequency Alleles in Cell-Free DNA

K. Shazand, J. Ning, E. Ranghini, A. Popkie, and J.P. Jerome The ability to detect rare alleles is key to the discovery and characterization of mutations in cancer research. These mutations are found at low frequencies, mainly because of tumor heterogeneity and tumor DNA dilution in the germline background. Cell-free DNA (cfDNA) in plasma provides… Read more »

Comparison of Sequencing Results of Commercially Available miRNA NGS Library Preparation Kits

M.J. Gonzalez-Plasky, A.M. McNulty, K. Charizanis, M. Carroll, E. Jan, K. Hecker, E. Kamberov miRNA sequencing (miRNA-Seq) is a useful tool for aiding researchers in the examination of miRNA expression patterns, the characterization of novel miRNAs, and for uncovering miRNA-disease associations. Since miRNAs are also unusually well-preserved in a range of specimens (e.g. urine, FFPE… Read more »

ThruPLEX™ Technology Repairs Damage and Amplifies Small Amounts of Biofluid DNA for NGS, Microarrays and PCR

M. Mastronardi, T. Tesmer, E. Kamberov, J. Langmore Biofluid Challenges: Biofluids, including plasma, serum, urine and CSF, contain valuable biomarkers that are used in research and diagnostics. These matrices present many challenges to traditional sample preparation methods. Biofluid DNA is fragmented (100-200 bp) and very dilute (e.g., 1-20 ng/mL of plasma). Additionally, the biomarker-containing DNA… Read more »

Comparison of Two New Methods to Increase the Sensitivity of Next Generation Sequencing for ChIP-seq, Methyl-seq and other Sonicated DNA Applications as well as for Short DNA in Non-Invasive Prenatal and Cancer Diagnostics

American Society of Human Genetics  2011 (Poster – PDF) E. Kamberov, J. Langmore, T. Tesmer1, M. Mastronardi, (Rubicon Genomics, Ann Arbor), M. Luo, M. Jeong, D. Sun, W. Lei, L. White, G. Darlington (Baylor College of Medicine, Houston) There is an increasing need to sequence picogram quantities of short DNA for diagnostics and research. For example, 1) maternal… Read more »

Next-Gen Sequencing of Single Human Cells for Detection of Copy Number Variations and Mutations

J. Langmore*, E. Kamberov*, T. Tesmer*, L. Patel**, and K. Pienta** *Rubicon Genomics, Ann Arbor, MI; ** Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109 Next-generation sequencing of single cells must be accurate, reproducible, rapid and inexpensive for use in research and diagnostics. This is difficult because conventional methods of DNA… Read more »

OmniPLEX® and ThruPLEX™ Technologies for Genome-Wide DNA Methylation Profiling using Microarrays, qPCR, and Illumina GA and HiSeq

T. Tesmer, M. Mastronardi, E. Kamberov, J. Langmore OmniPLEX is a patented technology to prepare high molecular weight or degraded DNA or RNA samples for PCR and microarray analyses using isothermal, quasi-random primed library synthesis and high-yield PCR amplification. OmniPLEX products can be adapted for next-generation sequencing analysis. OmniPLEX can be combined with methylation-sensitive restriction enzymes… 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 »

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 »