Oxford-Nanopore eBook - 4

From Bench to
Clinic: The
Potential of New
Sequencing Tools

s genome sequencing technology
advances, researchers are increasingly exploring emerging tools
for a host of potential clinical applications. Andrew Beggs of the University of
Birmingham is one of those pioneers. A
surgeon as well as a researcher in cancer
genetics, Beggs recently described several
applications of advanced sequencing technology that are widely used in research but
could, in the future, be applied in the clinic
as well.*
Organ and stem cell transplantation, for example, are life-saving treatments for a variety of illnesses, including cancers
and immune diseases. Approximately 140,000 solid organ
transplants are carried out around the globe each year, as well
as more than 50,000 stem cell transplants.
One of the critical steps in matching donor organs to patients
is accurate human leukocyte antigen (HLA) typing. The HLA

clinicalomics.com

Dr. Andrew Beggs describes
ultra-high resolution HLA
typing, CNV resolution on the
tiny Oxford Nanopore Flongle,
and WGS using the ultra-highthroughput PromethION
complex on chromosome 6 contains the most polymorphic
genes in the human genome. HLA class I and II genes define
specific adaptive immune responses and genetic variation in
these genes is associated with susceptibility to autoimmune
and infectious diseases. These genes also have a major role in
transplantation and immunology.
Currently, HLA genes are characterized using Sanger or
next-generation sequencing of a limited amplicon repertoire
or labeled oligonucleotides for allele-specific sequences. But
HLA typing is difficult for several reasons, including that the
locus is highly polymorphic and is co-dominantly inherited.
Plus, these sequencing techniques are expensive.
Beggs' lab has been testing nanopore-based HLA typing using
the portable MinION platform from Oxford Nanopore Technologies. This approach provides high resolution-4-field
(8-digit)-while exploiting the inherent advantages of
long reads. Compared to previous PCR assays, which used
96-well plates, Beggs says this is a "single-tube assay with a
150-minute turn-around."

The nanopore assay costs about $100, with just 60 ng
DNA required for the PCR reaction. Post-PCR, ligation
library preparation is performed (nanopore library prep kit
SQK-LSK109), 12-sample multiplexed sequencing is then

http://www.clinicalomics.com

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