# Core C - Sequencing and Analysis.

> **NIH NIH P01** · WASHINGTON UNIVERSITY · 2022 · $845,750

## Abstract

PROJECT SUMMARY/ABSTRACT
The goal of Core C is to provide high-throughput production and analysis of AML genomic and epigenomic
sequence data for all four projects in this PPG. This includes sequencing, somatic and germline variant
detection and validation, and integration of many data types. This will be achieved by generating high-quality
DNA and RNA sequencing data and analyzing it using cutting-edge algorithms and techniques.
Specific Aim/Core Service 1: (Sequence Production)
Sequencing of samples in Core C will take place using the Illumina HiSeqX, 4000, and NovaSeq platforms.
The data produced in Core C will be comprehensive: whole genome, exome, and capture validation for DNA,
as well as error-corrected sequencing, single-cell RNA-seq, total and small RNA-seq, whole genome bisulfite
sequencing, and other custom epigenetic analyses. These data will be processed through state-of-the-art
genomic pipelines to produce primary results like sequence alignments and variant calls.
Specific Aim/Core Service 2: (Bioinformatic Analysis)
These pipelines provide a starting point for the detailed, novel, and iterative analyses which will take place in
Core C and are foundational for each project. Project 1 will require integrative analysis of genomic and
epigenomic (transcriptome, scRNA-Seq, WGBS) data to better define the events that drive initiation,
progression, and relapse in samples with and without DNMT3A mutations. In Project 2, we will leverage our
experience in immunogenomics to define minor histocompatibility antigens that mediate allo-transplant
response, and characterize the genetic and epigenetic changes that drive relapse in a mouse model of
transplantation. In Projects 3 and 4, we will utilize enhanced WGS, error-corrected sequencing, bulk RNA-seq,
scRNA-seq, and phased-read data to define the mechanisms that drive subclonal expansion and progression
from MDS to sAML (Project 3), or the specific effects of TP53 mutations on the development of aneuploid AML
(Project 4).
Answering the questions outlined in these projects requires deep integrative analysis that goes far beyond the
simple mutation counting that was a hallmark of previous genomic studies. This requires common
infrastructure, comprehensive databases, and extensive expertise that will be provided by tight integration
between project leadership and the scientists in Core C.

## Key facts

- **NIH application ID:** 10311215
- **Project number:** 5P01CA101937-18
- **Recipient organization:** WASHINGTON UNIVERSITY
- **Principal Investigator:** Christopher A Miller
- **Activity code:** P01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $845,750
- **Award type:** 5
- **Project period:** 2003-09-19 → 2023-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10311215

## Citation

> US National Institutes of Health, RePORTER application 10311215, Core C - Sequencing and Analysis. (5P01CA101937-18). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10311215. Licensed CC0.

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