Illumina Case Study: Dr. Avrum Spira

RNA-Seq Studies Identify Biomarkers for Early
Detection of Pulmonary Diseases
Dr. Avrum Spira explains how the HiSeq® 2000 system and RNA-Seq are enabling
new biological insights into pulmonary diseases.
Introduction
Dr. Avrum Spira, a pulmonary and critical care physician at Boston University
Medical Center (BUMC), is Chief of the Division of Computational Biomedicine in
the Department of Medicine at Boston University. In early 2000, Dr. Spira started
a lab with the goal of applying whole-genome gene expression platforms toclinical samples in an effort to develop biomarkers that could lead to potential
diagnosis and treatment of pulmonary disorders. Today, Spira’s lab uses theIllumina HiSeq 2000 system and RNA-Seq to discover molecular biomarkers
that may provide opportunities for early detection of pulmonary diseases.
“I initially focused on lung cancer,” says Dr. Spira, “we almost never detect it atan early stage. Using new genomic platforms, we hoped to develop molecularmarkers that could identify risk, and possibly help diagnose the disease at anearly stage.” After successful discovery of biomarkers that aid in early detection oflung cancer, Dr. Spira’s lab turned their efforts to other smoking-related diseases,
specifically chronic obstructive pulmonary disease, also known as emphysema.
“We are expanding our studies to other diseases beyond the lung, pushinginto translational areas where genomic technologies can be applied to clinicalAvrum Spira, M.D., is an associate professor of
medicine, pathology, and bioinformatics at Boston
University Medical School and a pulmonologist atBoston Medical Center.

samples, in clinical settings,” explains Dr. Spira. “We’re trying to use genomic
markers to help predict who might respond to given treatments, and toidentify potential new disease treatments and therapeutic targets.”

Increased Throughput and Depth of Coverage
Drives Discovery“We chose the HiSeq system for our studies because of its throughput anddepth of coverage,” states Dr. Spira. “We can run a greater number of samples
in a single lane, in a shorter period of time. The HiSeq has outperformed ourexpectations and is changing the way we use sequencers. The scalability anddepth of coverage of the HiSeq is enabling more efficient studies and, ultimately,
helping us identify new biomarkers that can potentially impact patient care.”Spira adds, “we believe Illumina’s RNA-Seq method offers the best technology
for unbiased discovery of disease-related transcript expression. For a numberof our projects, we switched from microarrays to primarily a sequencingbased platform because RNA-Seq provides us with a more comprehensive
approach to profiling the transcriptome across a broader dynamic range.”“The clear advantage of RNA sequencing is that it allows us to identify
transcript alterations and splicing events that may not be detectable ona microarray,” says Dr. Spira. In a recent publication, his lab has gone

“We’re starting projects that
we may not have otherwise
taken on...next-generation
sequencing with the HiSeq
allows an unprecedented
view of the transcriptome
in lung disease.”

back to bronchial airway samples originally analyzed by microarray andre-analyzed gene expression with Illumina sequencing. “The RNA-Seq
platform identified many of the changes that the microarray platform found,

Summary
Overview

plus a number of new changes,” says Dr. Spira. “There were transcriptomic

Avrum Spira, M.D., at Boston University Medicalalterations that the microarray either didn’t measure or didn’t pick up as

Center is developing biomarkers to help identify

changing, that the sequencer does. We can identify additional, potentiallyand diagnose pulmonary diseases at an early

valuable biomarkers with the Illumina next-generation sequencing platform.”and potentially curable stage.

Illumina Technology is Enabling New Projects

Challenge

Dr. Spira is starting three new projects for RNA-Seq and the HiSeq 2000. In

Existing genomic technologies have a narrow

the first study that is part of the NHLBI’s Lung Genomics Research Consortium(LGRC), Dr. Spira’s lab will analyze 400 diseased lung tissues using RNASeq. “We’re starting projects that we may not have otherwise taken on. This

dynamic range, limiting their ability to measure
low-abundant genes and detect splicing events.
This impacts the information needed to makestudy is being done explicitly because next-generation sequencing with thenovel discoveries about disease pathogenesis.

HiSeq allows an unprecedented view of the transcriptome in lung disease,”

Solution

he says. “These tissues have been run on microarrays, so the idea is to findnew biologically relevant transcriptomic alterations that reveal more about thepathogenesis of these diseases.”
In a second study funded by the NCI’s Early Detection Research Network

Dr. Spira is using RNA-Seq on the HiSeq
2000 system to identify novel biomarkers for
pulmonary diseases.

(EDRN), Dr. Spira is using the HiSeq system to develop microRNA-basedBenefits

biomarkers for the early detection of lung cancer. “There are microarrays

Illumina technology empowers a comprehensive

for measuring human microRNAs, but we don’t know how many are in theview of RNA expression, with higher throughput

genome,” says Spira. “Sequencing provides a clear advantage, in that you

and increased dynamic range, enabling new

can measure the complete spectrum of small RNAs expressed in the tissue,

biological studies that can be done quickly anduncovering novel microRNAs that associate with disease.”cost effectively.

In a third study funded by the Department of Defense, Dr. Spira is sequencing
premalignant cells from patients at risk for lung cancer. “These are really small,valuable tissue samples,” says Dr. Spira. “We elected to pursue sequencing
using HiSeq as opposed to an array, because we want to get the mostcomprehensive profiling of these precious specimens that we can.”

Making Sequencing More Accessible
Dr. Spira offered his perspective on the impact that the HiSeq system will
have on future projects. “In the last couple of years, sequencing has become
far more accessible to the average researcher. The cost of running an RNA-Seq
experiment has dropped. We can increase the throughput and run more
samples, decreasing the cost per sample,” he says. With regard to data

“While the complexity ofRNA-Seq data analysis is
greater than a microarray,groups like ours and others
are developing tools andpipelines for data analysis,
making it easier to analyze
the data.”

analysis, Dr. Spira says, “While the complexity of RNA-Seq data analysis is
greater than a microarray, groups like ours and others are developing tools
and pipelines for data analysis, making it easier to analyze the data.”

Learn more about the HiSeq 2000 system andRNA-Seq Sample Prep Kits at www.illumina.com/hiseq.

Illumina • 1.800.809.4566 toll-free (U.S.) • +1.858.202.4566 tel • techsupport@illumina.com • www.illumina.com
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Pub. No. 770-2011-033 Current as of 06 February 2012