The Johns Hopkins University

Duke University

University of Utah Research Foundation

Cancer Institute

Morphotek, Inc.

Other

Imperial Chemical Industries Limited

Zeneca Limited

Genzyme Corporation

Biomed Valley Discoveries, Inc.

University of Texas System

State University of New York

Cancer Institute, Japanese Foundation for Cancer Research

Utrecht University

Pharmagenics, Inc.

Kenneth W Kinzler

Bert Vogelstein

Nickolas Papadopoulos

Victor E Velculescu

Luis Diaz

Hai Yan

Nicholas C Nicolaides

Isaac A Kinde

Raymond L White

Darell D Bigner

Shibin Zhou

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

Alexander Fred Markham

Hans Albertsen

Rakesh Anand

Geoff Joslyn

David E Hill

Mary Carlson

Philip John Hedge

Gregory J Riggins

Jimmy Cheng-Ho Lin

Marilee Burrell

Andrew Thliveris

Joanna Groden

Todd Waldman

Albert De La Chapelle

Yardena Samuels

Xiaosong Zhang

Christoph Lengauer

Yuxuan Wang

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

Saurabh Saha

Brad St Croix

Kornelia Polyak

Devin Dressman

Jin Jen

Jean-Francois Geschwind

Ian Cheong

Shanmugasundaram Ganapathy-Kanniappan

Michael I Sherman

Surojit Sur

Tobias Sjoblom

Tong-Chuan He

Simeon Springer

Phillip Buckhaults

Leigh Zawel

Laura D Wood

Thomas Barber

Diana Mandelker

Martin Gilbert Pomper

Wafik S El-Deiry

Andrew B Sparks

Scott E Kern

Catherine Anne Foss

Saeed R Khan

Anirban Maitra

Zachary James Reitman

Tian-li Wang

Patrick J Killela

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

Michael Goggins

Renyuan Bai

Manuel Medina Hidalgo

Erika Darrah

Verena Staedtke

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

TERT promoter mutations occur in both papillary and flat lesion bladder cancers, are the most frequent genetic alterations identified to date in noninvasive precursor lesions of the bladder, are detectable in urine, and appear to be strongly associated with bladder cancer recurrence. The TERT promoter mutations are useful urinary biomarker for both the early detection and monitoring of bladder neoplasia.

TERT promoter mutations in urothelial neoplasia

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Baltimore, MD, United States of America

Kenneth W Kinzler