Inclusive new tool makes genomic research better reflect world's
diversity
Expands reference point for 'normal' fromperson to thousands

Date:
March 10, 2022
Source:
University of Virginia Health System
Summary:
Scientists have developed a powerful, inclusive new tool for genomic
research that boosts efforts to develop more precise treatments
for many diseases by leveraging a better representation of the
genetic diversity of people around the world.



FULL STORY ========================================================================== Scientists have developed a powerful, inclusive new tool for genomic
research that boosts efforts to develop more precise treatments for many diseases by leveraging a better representation of the genetic diversity
of people around the world.


==========================================================================
The new tool will allow researchers to compare natural variations in
our genes against genome sequences collected from a diverse group of
people. Until now, scientists have compared these variations with a
"reference genome" primarily sequenced from a few volunteers (~70%
from one person) living near laboratories involved in the Human Genome
Project almost 20 years ago. This represented genomes from a small number
of people in a small number of countries.

The new software tool, called "Giraffe," enables the use of a reference
point that is far more diverse and inclusive. Instead of relying on a
single reference genome, Giraffe uses a "pangenome" that incorporates information about genome sequences from people around the world. This will
give scientists a much more global perspective and help them understand
why diseases often strike certain groups disproportionately.

"A major advantage of Giraffe is that it enables fast and sensitive
comparison of short-read human genome sequences to a pangenome, which is essential for the widespread use of reference graphs that reduce bias
in the human genome reference," said researcher Stephen S. Rich, PhD,
of the University of Virginia School of Medicine's Center for Public
Health Genomics. "Since the current effort in genomics is to move from
a European-Caucasian base to a global representation, Giraffe can better
define genetic variation in non-white populations and, as a result, have
a major impact on precision medicine and application to understanding
the genetic risk of disease." A Giraffe's-eye View Rich and UVA's
Aakrosh Ratan, PhD, were part of a team of scientists who developed
the new tool through the Trans-Omics for Precision Medicine (TOPMed)
program backed by the National Institutes of Health's National Heart,
Lung and Blood Institute.

Giraffe will make it easier for scientists to understand genetic variation
in different populations. Instead of the default point of comparison
being a single reference genome, it becomes more than 5,000 people from
many different backgrounds. That will help scientists better detect
important patterns in a global population approaching 8 billion. It will
also reduce unintentional biases in genomic data widely used by doctors
and scientists.

Giraffe will prove especially helpful when scientists are examining
larger, more complex stretches of our genetic code. It will make it
much easier for scientists to compare these large "structural variants,"
as the swathes are known. That will help scientists understand what the structural variants do and their role in diseases. That will, ultimately,
help guide the development of new treatments.

"Giraffe has made a great impact on the discovery of structural variants,
large and complicated regions in the human genome that could not be
resolved by standard, short-read sequencing," said Ratan, who, like Rich,
is part of the Center for Public Health Genomics and UVA's Department of
Public Health Sciences. "This is critical as structural variation has been shown to be important for the risk of autism and other neuropsychiatric disorders, as well as many cancers. Giraffe is especially useful for
detecting structural variation across diverse ethnic groups." There are
many other benefits as well, Rich added. "Giraffe has been shown to reduce bias, increase the speed of analysis, and improve discovery of large
blocks of variation in the human genome across diverse ancestries. This
single software tool increases inclusiveness and, hopefully, reduces
health disparities in genomic studies by enabling the use of a more
global pangenome reference."

========================================================================== Story Source: Materials provided by
University_of_Virginia_Health_System. Note: Content may be edited for
style and length.


========================================================================== Journal Reference:
1. Jouni Sire'n, Jean Monlong, Xian Chang, Adam M. Novak, Jordan
M. Eizenga,
Charles Markello, Jonas A. Sibbesen, Glenn Hickey, Pi-Chuan Chang,
Andrew Carroll, Namrata Gupta, Stacey Gabriel, Thomas W. Blackwell,
Aakrosh Ratan, Kent D. Taylor, Stephen S. Rich, Jerome I. Rotter,
David Haussler, Erik Garrison, Benedict Paten. Pangenomics
enables genotyping of known structural variants in 5202 diverse
genomes. Science, 2021; 374 (6574) DOI: 10.1126/science.abg8871 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/03/220310095942.htm

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