Page 18 - Biennial Report 2018-20 Jun 2021

IndiGen: GENOMICS FOR PUBLIC HEALTH IN INDIA

India is a geographical entity that is home to an ethnically diverse set of people with distinct
patterns of descent and varying susceptibility to diseases. As part of a CSIR funded inter-
institutional collaboration between CSIR-IGIB and CSIR-CCMB, the Indigen project aims to carry
out, on a pilot scale (Phase I), sequencing of 1000 human genomes from India with the following
endpoints: (i) Demonstrate the capability to sequence human genomes and analyze them at
scale in defined timelines (six months). (ii) Develop the baseline genetic allele frequency to
enable development of technologies to implement carrier screening of individuals based on
genome sequences and prevent adverse events and enable optimal therapy through mining data
of clinically actionable pharmacogenetic variants. (iii) Identify and screen genetic mutations for
heritable cancers and mine genomes for actionable mutation specific therapies. The objective of
Indigen was to create baseline, India specific, genomic data so as to accelerate the
implementation of genomic testing in clinical settings and also engage the industry to develop
the ecosystem to start implementing genomic assays and interpretation in India.

Fresh sample collection from across India was initiated based on the Indian Genome Variation
grid map published previously by CSIR-IGIB. The plan was to collect about 30 to 100 samples
from each of the major populations in India. Over 25 sample collection camps were held across
India and volunteers were involved through the IndiGen website (https://indigen.igib.in/) and
social media also. In total over 1500 samples were collected across India.Whole Genome
Sequencing (WGS) of the participants was initiated after obtaining informed consent. The DNA
samples were subjected to library preparation and NGS sequencing on the Illumina
NovaSeq6000 sequencing platform. Whole Genome Sequencing for 1029 individuals has been
completed.

Analysis of the whole genome sequences was undertaken after appropriate quality check of the
data. Computational analysis protocols previously published from IGIB for population scale
whole genome datasets were applied. Genome scale analysis for identifying variants for
applications in carrier screening, pharmacogenomic, incidental findings and for mutation-
specific therapies in cancer were taken up as these have potential applications in clinical settings.
To involve key stakeholders in a collaborative and consultative approach and enable education,
awareness, and acceptance of genomic testing in healthcare, IGIB scientists have conducted or
actively participated in hands-on workshops, continuing medical education workshops, and
awareness campaigns. The IndiGenomes resource encompasses the genomic data from
over 1000 whole genome sequences sequenced from across India as part of the IndiGen
programme and represents diverse geographies and ethnicities. The resource provides
access to over 55 million genetic variants consisting of single nucleotide variants and
indels. The variants are systematically annotated with integration of clinically relevant
annotations as well as allele frequencies from global populations. The resource is
available at http://clingen.igib.res.in/indigen/.

17