Page 74 - Annual report 2021-22

Annual Report 2021-22 |

Vinod Scaria

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Vinod Scaria works on genome informatics that includes mendelian genetic diseases, genetic
epidemiology of human diseases, pathogen genomics (SARS-CoV2), pharmacogenomics and non-
coding RNA biology.

In collaboration with Sridhar Sivasubbu, he developed the IndiGen app as part of the GenomeApp
project. The IndiGenome Card (GenomeApp) is a unique ID and barcode on a card which can be used
to access the genomic data interpretation on a cloud service over a mobile/web application. The
system enables relevance of interpretation of genetic variants and an easy method to access specific
genetic findings on clinical request. These could be for the primary indications (indications for the
diagnosis of the disease or genetic variants) or secondary indications (secondary indications could be
for modifier loci, pharmacogenomic variants, incidental findings etc.) which can provide insights into
the prognosis of the disease. The GenomeApp was developed, and pilot tested in Indian samples.

Over 1200 samples were collected through the clinical network. Following the genomic sequencing
and analysis, genetic screening assays for several genetic disorders were developed. These included
NGS and capillary sequencing based genetic screening assays. The goal was to couple the NGS genetic
screening assays and the GenomeCard for communicating the genomic evidence. The IndiGen App is
available on Google play store and has more than 1000+ downloads. The data on pharmacogenetic
variants have been widely accessed by the users of the app.

Under the INGEN-COV2 (Integrative Genomics of COVID-19), a collaborative project between IGIB and
CCMB, Vinod Scaria’s lab was involved in analyzing of the sequencing data of the SARS-CoV2 genomes
from samples collected at CSIR-IGIB. Of the 510 genomes sequenced, 319 were deposited in GISAID.
Longitudinal sampling from 79 COVID-19 positive mothers and infants born were enrolled in the study.
During this period, India also witnessed the challenging 2nd wave which was primarily over-
represented by the Delta variant. With increased ability of transmission, Delta variant also was
dominating the vaccination breakthroughs. Thus, during this period, SARS-CoV-2 genome sequencing
was performed to understand these aspects.

Another important focus area of his lab involves understanding idiopathic intellectual disability for
which next generation sequencing (NGS) is used. Intellectual Disability (ID) encompasses a broad class
of neurodevelopmental disorders that affects up to 2-3% of the population. Patients with ID are
screened in clinical settings utilizing karyotyping for known chromosomal syndromes like Down's
syndrome, chromosomal microarray (CMA) to detect submicroscopic aberrations across the genome,
or focused molecular testing for a suspected ID-causing single gene abnormality. With the growing
number of genetic causes of ID being discovered, targeted sequencing without specific clinical
indications is becoming more difficult. As a result, next-generation sequencing is becoming more
popular since it enables the identification of single-nucleotide alterations throughout the whole
genome or exome (WGS/WES). NGS based approaches offer the possibility to identify the genetic
cause for patients in which all previously available genetic tests, including karyotyping, specific gene
analysis, or microarray analysis do not reveal any causative abnormalities.