# Project 1: Targeted sequencing and clinicopathology to evaluate primary melanoma molecular subtypes and outcomes

> **NIH NIH P01** · UNIVERSITY OF NEW MEXICO HEALTH SCIS CTR · 2020 · $96,699

## Abstract

Abstract
In this study, we will identify somatic tumor mutations, CNVs and a melanoma immune profile in relationship to
survival in order to identify patients with poor prognosis among AJCC TNM Stages IIA-IIIB and eventually
distinguish which patients may profit from adjuvant therapies and save lives. Our hypothesis is that primary
melanomas will have molecular and clinical features that will allow the prognostic stratification of melanoma
tumors among these patients. The current survival rate of individuals diagnosed at these stages ranges from
22 – 82%. There is little understanding of which patients will progress and which will not based on stage. The
ultimate intent of this project is to provide information to translate to the clinic to personalize care.
Currently, there is a dearth of studies in the melanoma field looking at epidemiology/genomic factors and
melanoma survival in order to identify, confirm and develop such biomarkers. We have brought together nine
cohorts of melanoma patients of 1,000 individuals and their tumors, half who have died from melanoma within
five years (median survival, 2.4 years) and half who have lived for at least five years (median follow up 8.5
years). Patients will be frequency matched for stage. Data will be randomly divided into a training set of 660
tumors and a validation set of 340 tumors, equally divided by poor and good prognosis. All patients have been
treated using standard-of-care surgery; they have adequate tumor tissue, germline DNA and clinical,
pathologic and demographic information recorded.
Project 1 will use targeted next generation sequencing of clinically actionable mutations and CNV’s in order to
develop subgroups of patients. Secondly, we will evaluate a melanoma immune profile, CD3/CD8/FOXP3
slides stained with immunofluorescence and PD1-PDL1 axis chromogenic staining, to compare to a strong
pathologic variable associated with survival, tumor infiltrating lymphoctyes (TILs). We will also evaluate ratios
of CD8:FOXP3 and CD8:PD-L1 as prognostic. The melanoma immune profile may be more quantitative and
reproducible than TIL score and we will determine this in this large study.
Finally, our strong multidisciplinary team of clinicians, biostatisticians, laboratory scientists and epidemiologists
will help to develop new strategies and new information to understand molecular factors associated with
prognosis in melanoma. Specifically, it will help to identify which individuals are likely to have a poor prognosis
and potentially identify these for new adjuvant therapy and closer surveillance.

## Key facts

- **NIH application ID:** 9938489
- **Project number:** 5P01CA206980-04
- **Recipient organization:** UNIVERSITY OF NEW MEXICO HEALTH SCIS CTR
- **Principal Investigator:** MARIANNE BERWICK
- **Activity code:** P01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $96,699
- **Award type:** 5
- **Project period:** — → —

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9938489

## Citation

> US National Institutes of Health, RePORTER application 9938489, Project 1: Targeted sequencing and clinicopathology to evaluate primary melanoma molecular subtypes and outcomes (5P01CA206980-04). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9938489. Licensed CC0.

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