# Optimizing pre-analytic sample handling for high throughput TCR sequencing in cutaneous T cell lymphoma

> **NIH NIH U01** · BRIGHAM AND WOMEN'S HOSPITAL · 2020 · $422,791

## Abstract

Summary/Abstract
High throughput sequencing of the rearranged T cell receptor genes (HTS) has transformed the diagnosis, care
and assessment of therapeutic responses in patients with cutaneous T cell lymphoma (CTCL) and this assay is
becoming the gold standard in CTCL clinical trials. HTS results are highly reproducible in frozen CTCL skin
biopsies but the formalin used to preserve skin biopsies in many clinical trials degrades DNA and affects HTS
measurements, potentially causing errors in patient diagnosis, assessment of responses and choices of therapy.
We seek to identify a single uniform tissue processing approach for small CTCL skin biopsies that will give
accurate and reproducible HTS results, support DNA, RNA and protein measurements, maintain excellent
histology, and preserve remaining tissue for future measurement of emerging biomarkers. In Aim 1, we identify
optimal tissue transport conditions and test non-cross-linking fixatives for their ability to support nucleic acid,
protein and histologic studies on small skin biopsies. Aim 2 studies the effects of storage time and temperature
on nucleic acid integrity, histologic performance and HTS readings, and tests two approaches to mitigate the
effects of DNA degradation on HTS measurements. Aim 3 provides real world testing of our optimized sample
handling procedures, using them to study skin biopsies obtained in the industry sponsored, randomized, placebo-
controlled phase III trial of topical resiquimod gel in CTCL. Our overall goals are to establish new best tissue
handling practices for future clinical trials and to establish corrections that allow accurate analyses of existing
specimens. HTS is now frequently used in many cancer types to measure tumor T cell numbers, diversity and
responses to immune therapies. The optimized tissue handling procedures we identify therefore have the
potential to be useful in many cancer types.

## Key facts

- **NIH application ID:** 10053369
- **Project number:** 1U01CA253190-01
- **Recipient organization:** BRIGHAM AND WOMEN'S HOSPITAL
- **Principal Investigator:** Rachael Ann Clark
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $422,791
- **Award type:** 1
- **Project period:** 2020-09-01 → 2025-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10053369

## Citation

> US National Institutes of Health, RePORTER application 10053369, Optimizing pre-analytic sample handling for high throughput TCR sequencing in cutaneous T cell lymphoma (1U01CA253190-01). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10053369. Licensed CC0.

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