The Johns Hopkins University

Duke University

University of Utah Research Foundation

Cancer Institute

Morphotek, Inc.

Other

Biomed Valley Discoveries, Inc.

Imperial Chemical Industries Limited

Zeneca Limited

Genzyme Corporation

University of Texas System

State University of New York

Cancer Institute, Japanese Foundation for Cancer Research

Case Western Reserve University

Eisai Inc.

Kenneth W Kinzler

Bert Vogelstein

Nickolas Papadopoulos

Victor E Velculescu

Luis Diaz

Hai Yan

Nicholas C Nicolaides

Shibin Zhou

Isaac A Kinde

Raymond L White

Darell D Bigner

Yusuke Nakamura

Luigi Grasso

Drew M Pardoll

Suzanne L Topalian

Sian Jones

Chetan Bettegowda

D Williams Parsons

Dung Le

Philip M Sass

Rebecca J Leary

Ralph Hruban

Hans Albertsen

Alexander Fred Markham

Rakesh Anand

David E Hill

Mary Carlson

Geoff Joslyn

Philip John Hedge

Gregory J Riggins

Jimmy Cheng-Ho Lin

Marilee Burrell

Joanna Groden

Andrew Thliveris

Todd Waldman

Albert De La Chapelle

Yardena Samuels

Xiaosong Zhang

Christoph Lengauer

Yuxuan Wang

Saurabh Saha

Chien-Tsun Kuan

Alberto Bardelli

Philipp Angenendt

Giovanni Parmigiani

Rachel Karchin

Yuchen Jiao

Lin Zhang

Frank Diehl

Meng Li

Long Dang

Jian Wu

Nishant Agrawal

Brad St Croix

Kornelia Polyak

Devin Dressman

Jin Jen

Jean-Francois Geschwind

Shanmugasundaram Ganapathy-Kanniappan

Michael I Sherman

Martin Gilbert Pomper

Wafik S El-Deiry

Andrew B Sparks

Catherine Anne Foss

Scott E Kern

Saeed R Khan

Craig A Rosen

Steven M Ruben

Mark D Adams

Ying-Fei Wei

Claire M Fraser

David Sidransky

William A Haseltine

Ewen F Kirkness

Robert D Fleischmann

Rebecca A Fuldner

Antony Rosen

Livia Angela Casciola-Rosen

Ian Cheong

Surojit Sur

Tobias Sjoblom

Simeon Springer

Tong-Chuan He

Phillip Buckhaults

Leigh Zawel

Laura D Wood

Thomas Barber

Diana Mandelker

Anirban Maitra

Zachary James Reitman

Joshua Cohen

Tian-li Wang

Michael Goggins

Renyuan Bai

Verena Staedtke

Manuel Medina Hidalgo

Erika Darrah

Provided herein are systems, kits, compositions and methods for sequencing library preparation and sequencing workflow (e.g., for the identification of mutations). In certain embodiments, provides herein systems and methods to identically barcode both strands of templates, and PCR-based enrichment of each strand that does not require hybridization capture.

Methods and materials for assessing nucleic acids

The present invention provides, inter alia, methods for treating or ameliorating an effect of a solid tumor present in a non-human animal. These methods include administering intratumorally to the non-human animal a unit dose of, preferablyNT, colony forming units (CFUs), which contains about 1×106-1×1010 CFUs suspended in a pharmaceutically acceptable carrier or solution. Methods for debulking a solid tumor present in a non-human animal, a method for microscopically precise excision of tumor cells in a non-human animal, methods for treating or ameliorating an effect of a solid tumor that has metastasized to one or more sites in a non-human animal, methods for ablating a solid tumor present in a non-human animal, unit doses of, preferablyNT, CFUs, and kits for treating or ameliorating an effect of a solid tumor present in a non-human animal are also provided.

C. novyi for the treatment of solid tumors in non-human animals

The presently disclosed subject matter provides methods and kits for treating solid tumors in a subject by using a combination of anti-CTLA-4 and/or anti-PD-1 antibodies with at least one member of the group consisting of a bacterium, bacterial product, and an immunoregulatory entity. In particular embodiments, the bacteria are toxin-depleted, anaerobic bacteria, such as-NT.

Use of bacteria, bacterial products, and other immunoregulatory entities in combination with anti-CTLA-4 and/or anti-PD-1 antibodies to treat solid tumor malignancies

Bottleneck Sequencing System (BotSeqS) is a next-generation sequencing method that simultaneously quantifies rare somatic point mutations across the mitochondrial and nuclear genomes. BotSeqS combines molecular barcoding with a simple dilution step immediately prior to library amplification. BotSeqS can be used to show age and tissue-dependent accumulations of rare mutations and demonstrate that somatic mutational burden in normal tissues can vary by several orders of magnitude, depending on biologic and environmental factors. BotSeqS has been used to show major differences between the mutational patterns of the mitochondrial and nuclear genomes in normal tissues. Lastly, BotSeqS has shown that the mutation spectra of normal tissues were different from each other, but similar to those of the cancers that arose in them.

Bottleneck sequencing

We queried DNA from saliva or plasma of 93 HNSCC patients, searching for somatic mutations or human papillomavirus genes, collectively referred to as tumor DNA. When both plasma and saliva were tested, tumor DNA was detected in 96% (95% CI, 84% to 99%) of 47 patients. The fractions of patients with detectable tumor DNA in early- and late-stage disease were 100% (n=10) and 95% (n=37), respectively. Saliva is preferentially enriched for tumor DNA from the oral cavity, whereas plasma is preferentially enriched for tumor DNA from the other sites. Tumor DNA in the saliva and plasma is a valuable biomarker for detection of HNSCC.

Head and neck squamous cell carcinoma assays

The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Though massively parallel sequencing instruments are in principle well-suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. One example of this approach, called 'Safe-SeqS' for (Safe-Sequencing System) includes (i) assignment of a unique identifier (UID) to each template molecule; (ii) amplification of each uniquely tagged template molecule to create UID-families; and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are truly mutant (“super-mutants”) if ≥95% of them contain the identical mutation. We illustrate the utility of this approach for determining the fidelity of a polymerase, the accuracy of oligonucleotides synthesized in vitro, and the prevalence of mutations in the nuclear and mitochondrial genomes of normal cells.

Safe sequencing system

Provided herein are methods and materials for detecting and/or treating subject (e.g. a human) having cancer. In some embodiments, methods and materials for identifying a subject as having cancer (e.g., a localized cancer) are provided in which the presence of member(s) of two or more classes of biomarkers are detected. In some embodiments, methods and materials for identifying a subject as having cancer (e.g. a localized cancer) are provided in which the presence of member(s) of at least one class of biomarkers and the presence of aneuploidy are detected. In some embodiments, methods described herein provide increased sensitivity and/or specificity in the detection of cancer in a subject (e.g. a human).

Methods and materials for assessing and treating cancer

Massively parallel sequencing of cell-free, maternal plasma DNA was recently demonstrated to be a safe and effective screening method for fetal chromosomal aneuploidies. Here, we report an improved sequencing method achieving significantly increased throughput and decreased cost by replacing laborious sequencing library preparation steps with PCR employing a single primer pair. Using this approach, samples containing as little as 4% trisomy 21 DNA could be readily distinguished from euploid samples.

Rapid aneuploidy detection

As cell-free DNA from brain and spinal cord tumors cannot usually be detected in the blood, we assessed the cerebrospinal fluid (CSF) that bathes the CNS for tumor DNA, here termed CSF-tDNA. The results suggest that CSF-tDNA could be useful for the management of patients with primary tumors of the brain or spinal cord.

Detection of tumor-derived DNA in cerebrospinal fluid

This document provides methods and materials for assessing a mammal having or suspected of having cancer and/or for treating a mammal having cancer. For example, molecules including one or more antigen-binding domains (e.g., a single-chain variable fragment (scFv)) that can bind to a modified peptide (e.g., a tumor antigen), as well as method for using such molecules, are provided.

MANAbodies and methods of using

The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Though massively parallel sequencing instruments are in principle well-suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. One example of this approach, called 'Safe-SeqS' for (Safe-Sequencing System) includes (i) assignment of a unique identifier (UID) to each template molecule; (ii) amplification of each uniquely tagged template molecule to create UID-families; and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are truly mutant ('super-mutants') if &#x2265;95% of them contain the identical mutation. We illustrate the utility of this approach for determining the fidelity of a polymerase, the accuracy of oligonucleotides synthesized in vitro, and the prevalence of mutations in the nuclear and mitochondrial genomes of normal cells.

Blockade of immune checkpoints such as cytotoxic T-lymphocyte antigen-4 (CTLA-4) and programmed death-1 (PD-1) shows promise in patients with cancer. Inhibitory antibodies directed at these receptors have been shown to break immune tolerance and promote anti-tumor immunity. These agents work particularly well in patients with a certain category of tumor. Such tumors may be particularly susceptible to treatment because of the multitude of neoantigens which they produce.

Checkpoint blockade and microsatellite instability

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Baltimore, MD, United States of America

Kenneth W Kinzler