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454 Sequencing To Aid Transplant Matching

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Researchers at the Blood Center Linz in Austria are betting on second-generation sequencing technology to improve tissue matching between donors and bone marrow or stem-cell transplant patients.

The researchers, who acquired a 454 Genome Sequencer FLX in May, say they eventually want to develop a sequencing method for routine use in HLA typing, which they say would be one of the first applications of 454's technology in medical care.

Research groups elsewhere are working on similar methods using other approaches, among them microarrays or Sanger sequencing, but the main advantage of 454's platform is its speed and resolution, according to Christian Gabriel, medical director of the Blood Center Linz.

"It's not cheaper, but it will save time and we can get results with better and higher resolution that we could never get anywhere else," says Gabriel, whose center won a grant for a 454 system from the Austrian government last year. "Our idea is to [develop] this into some sort of method which we can use for patient care."

The human leukocyte antigen, or HLA, system is a region on chromosome 6 that encodes a large number of highly diverse genes, many of which have functions in the immune system. The six major antigens encoded by HLA genes are HLA-A, -B, -C, -DR, -DP, and -DQ.

HLA typing usually involves PCR-based assays, which can result in ambiguities. These can sometimes be solved by Sanger sequencing, though "you cannot discriminate between ambiguities where you have, let's say, overlapping SNPs," according to Gabriel.

That is when the researchers have to resort to family studies, which involve HLA-typing of several family members of a patient. "This is very, very time consuming," he says. "It takes approximately a month until you are through." The Linz researchers aim to use the 454 platform to develop a method that would eliminate the need for family studies.

— Julia Karow

Sequencing Notes

NHGRI announced the eight grants it has just funded through the $1,000 Genome program. These went to: Dan Branton and Jene Golovchenko at Harvard ($6.5 million over four years); Stephen Chou at Princeton ($920,000 over three years); Penn's Marija Drndic ($820,000 over three years); Stuart Lindsay at Arizona State ($370,000 for one year); Di Gao at the University of Pittsburgh ($370,000 over two years); Xiaohua Huang and Pavel Pevzner at UC San Diego ($2.5 million over four years); Predrag Krstiæ at Oak Ridge National Laboratory ($720,000 over two years); and Jiali Li at the University of Arkansas ($830,000 over three years). Much of the research revolves around nanopore-based approaches.

Datapoint

$4.6 million
Leerink Swann cut its 2008 revenue expectation for Helicos from $9.5 million to $4.6 million.

Funded Grants

$214,969/FY 2008
Molecular Tools for Genome Partitioning
Grantee: Jay Shendure, University of Washington
Began: Jul. 23, 2008; Ends: Jun. 30, 2010
This grant, from NHGRI, will allow Shendure to continue development of his genome partitioning technology "into broadly available methods that enable the selective and uniform amplification of complex, arbitrary subsets of a mammalian genome in a single reaction," the abstract says.

$46,826/FY 2008
Interrogating Genetic Interaction Networks via Next-Generation Sequencing
Grantee: Joseph Mellor, Harvard University
Began: Dec. 1, 2008
NHGRI has funded Mellor to use next-gen sequencing to "develop and apply a new approach termed 'barcode fusion genetics' on a pilot scale to study factors influencing DNA repair in yeast. This project would demonstrate feasibility for a technology that could produce a global genetic interaction map in a particular environmental condition by a single technician within a year," the abstract says.

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