The Johns Hopkins University

Duke University

Personal Genome Diagnostics, Inc.

Case Western Reserve University

Luis Diaz

Kenneth W Kinzler

Bert Vogelstein

Nickolas Papadopoulos

Drew M Pardoll

Suzanne L Topalian

Dung Le

Ralph Hruban

Victor E Velculescu

Yuchen Jiao

Darell D Bigner

Sanford D Markowitz

Yuxuan Wang

Hai Yan

Meng Li

Isaac A Kinde

Chetan Bettegowda

Rebecca J Leary

Frank Diehl

Nishant Agrawal

Simeon Springer

George J Netto

Theresa Zhang

James Robert White

Alan Meeker

Anirban Maitra

Jian Wu

Karin Sundfeldt

Bjorg Kristjansdottir

Mark Sausen

Bert Volgelstein

Nikolas Papadopoulos

Hanno Matthaei

Siân Jones

Samuel Vincent Angiuoli

Kerstin Schmidt

Nickolas Papadapoulos

Cancer immunology provides promising new avenues for cancer treatment but validation of potential neoantigens to target is costly and expensive. Analysis of MHC binding affinity, antigen processing, similarity to known antigens, predicted expression levels (as mRNA or proteins), self-similarity, and mutant allele frequency, provides screening method to identify and prioritize candidate neoantigens using sequencing data. Methods of the invention thereby save time and money by identifying the priority candidate neoantigens for further experimental validation.

Methods and systems for identification and prioritization of mutation-derived neoantigens

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

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

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

The recently developed liquid-based Papanicolaou (Pap) smear allows not only cytologic evaluation but also collection of DNA for detection of HPV, the causative agent of cervical cancer. We tested these samples to detect somatic mutations present in rare tumor cells that might accumulate in the cervix once shed from endometrial and ovarian cancers. A panel of commonly mutated genes in endometrial and ovarian cancers was assembled and used to identify mutations in all 46 endometrial or cervical cancer tissue samples. We were able also able to identify the same mutations in the DNA from liquid Pap smears in 100% of endometrial cancers (24 of 24) and in 41% of ovarian cancers (9 of 22). We developed a sequence-based method to query mutations in 12 genes in a single liquid Pap smear without prior knowledge of the tumor's genotype.

Papanicolaou test for ovarian and endometrial cancers

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Ellicott City, MD, United States of America

Luis Diaz