Genetic factors are an important determinant of cancer risk;however, at present, only a small fraction of the genetic basis of cancer susceptibility is explained by known cancer susceptibility genes or genetic variants. It is widely believed that other rare variants exist but are yet to be discovered. While next-generation sequencing (NGS) has to date identified a plethora of putative rare variants, "filtering" of these variants by co-segregation or functional studies has remained a significant challenge. We propose to use NGS to discover novel variants associated with extreme phenotypes, specifically evaluating both germline and tumor genomes in individuals with rare double primary cancers, where an underlying genetic predisposition has been suggested in prior epidemiological studies. Hypothesis: We hypothesize that using unique groups of individuals with double primary neoplasms where germline (host) genetic factors have been implicated, will enable us to discover causal variants with higher probability due to enrichment for the extreme phenotype. Moreover, our approach of assessing both germline and tumor genomes from multiple primary cancers will be a powerful filter for the discovery of etiologic germline variants.
Specific Aims :
Aim 1 : Using an existing ascertainment of germline DNA from (1) patients with both renal cell carcinoma and non- Hodgkins lymphoma and (2) patients with both testicular germ cell tumor and melanoma, we will perform whole exome sequencing (WES) to discover novel rare cancer susceptibility variants in the constitutional genome.
Aim 2 : For the germline variants identified i Aim 1, we will further assess their potential role in cancer susceptibility by (1) evaluating matching tumor DNA for exploration of secondary somatic events by a combination of exome sequencing and SNP chip based copy number analysis and (2) analyzing the frequency of the identified genetic variants in existing germline DNA from large cohorts of patients with only one of the component cancers thereby distinguishing/filtering germline variants that may be specific to only one tumor type. Study Design: We will perform WES of germline DNA and using an analytical pipeline, developed by our lab for other sequencing projects, we will call and annotate the variants for frequency, and in silico predicted functional consequences.
In Aim -2, we will perform WES of the primary tumors and call variants to identify germline variants with a second somatic alteration at the genomic region of interest in the tumors. Recurring mutations, specifically those of high functional significance, will be assessed in larger control and single cancer cohorts to distinguish germline variants specific to only one tumor type and establish prevalence and risk estimates. Network analyses and burden test for the rare variants will be carried out to test for associations. Innovation/Impact: If successful, this approach to the study of cancer susceptibility may represent a more powerful method through which cancer predisposition could be studied in future research endeavors. Identification of genetic variants associated with an elevated risk of multiple primary cancers could provide clinically useful information for patients and at-risk family members in terms of cancer risk stratification, surveillance, and prevention of secondary cancers.

Public Health Relevance

The goal of this study is to identify specific genetic changes (mutations) that may place a cancer survivor at a high risk of developing certain types of second cancers. By identifying such genetic mutations, individuals, as well as their at-risk family members, may benefit from additional cancer prevention and screening approaches.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Exploratory/Developmental Grants (R21)
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Special Emphasis Panel (ZCA1-SRLB-J (M2))
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Nelson, Stefanie A
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Sloan-Kettering Institute for Cancer Research
New York
United States
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