March 2019 digital v1

column
the cellview
Taking the lead
India can play a major role in world TB space by developing
supplementary technologies
DR RAJANI KANTH
VANGALA
The author is medical
scientist and former
director of SGRF,
Bangalore
The very fact that the sequencing
costs are coming down should make
multidrug-resistant Mycobacterium
tuberculosis (MDR-TB) more manageable.
However, that is not the case. Development
of novel technologies and a reduction
in costs and infrastructure barriers are
important to the reduction of disease burden
and better management. It is high time
that India embraces this fact and develops
research capabilities in two very important
aspects of tuberculosis diagnostics. The first
tool is a biospecimen/sputum collection
system, which will enable direct, wholegenome
sequencing, and the second is
building robust bioinformatics capabilities for
improved data analysis.
Historically, tuberculosis detection has
relied heavily on microscopy as the first-line
diagnosis, which often fails in the detection
of drug-resistant genotypes of the bacterium.
Traditional, culture-based diagnosis of TB
typically takes several weeks, owing to the
slow growth rate of M. tuberculosis. Some
technical advances have resulted in liquid
culture and an automated detection system
called mycobacteria growth indicator tube
(MGIT), which takes less than a fortnight
(Pfyffer et al., 1997). India, with increasing
infections of TB, can very much take the
lead in supplementing these technologies
by conducting large-scale, genome-wide
studies, in collaboration with companies or
research groups focusing on biospecimen
collection systems. Some of the tools
developed in this direction are SureSelelctXT
target enrichment, MolYsis Basic5 kit
(Molzym, Germany) and NucleoSpin Tissue-
Kit (Machery-Nagel, Duren, Germany).
Any NGS workflow will not be complete
without sequence data analysis, which
requires expertise in information technology
and clinical-data analytical capabilities -
both of which are already possessed by the
Indian scientific community, both commercial
and academic. In the past few years, there
has been an explosion of bioinformatics
platforms for both expert and non-expert
analysis and the interpretation of MTB
NGS data. The majority of existing tools
provide cloud-based WGS pipeline to start
processing from the raw sequence. There are
two important data consortiums, namely
ReseqTB and CRyPTIC, which have
accumulated large datasets and maintain
genomic and phenotypic data. New
advancements have resulted in several
WGS tools, of which Mykrobe predictor is
currently compatible with both Illumina and
Oxford Nanopore WGS data. However, there
is still a large gap in improving data quality
assessment (control parameters like base
score, quality score etc), which are presently
done by platforms like FastQC. There are
additional steps needed, like trimming and
combination of multiple sequencing files.
Easy-to-use, web-based tools, like Galaxy
Cloudman and Cloud Virtual Resources,
can facilitate user better outcomes. There
is also a need to work on providing more
computational space for data storage and
on developing a tailored analytical software
collection for customization. Another
important area where there is a large gap
is NGS data reporting, including sequence
variants (single nucleotide polymorphism –
SNPs), deletions, insertions and structural
variants.
These opportunities are some of the
important aspects that will need large-scale
collaborations for improved clinical research.
India can play a major role in emerging as a
leader in managing TB, not just here, but for
the world at large.
48 / FUTURE MEDICINE / March 2019