Next Generation Sequencing

The Next Generation Sequencing (NGS) facility at ACTREC has a HiSeq 1500 from Illumina and an Ion Torrent Personal Genome Machine from Thermofisher. The machines were used by in house scientists as well as those from BARC and IISER, Pune during 2017.

Transcriptome analysis was carried out on the Hiseq 1500 to understand the expression of genes in oral cancer cell lines, in human samples exposed to low dose radiation, and in medullary thyroid cancer.

Exome sequencing was carried out to profile mutations in individuals exposed to radiation, for de novo sequencing of an insect exome, and to find differences in the penetrance and disease aggression of germline mutations in inherited cancers. After DNA/ RNA sample quality checks, exome and transcriptome libraries for 55 samples were prepared in house and sequenced on the HiSeq 1500. Good quality data was obtained and downstream bioinformatics analysis was done with open resource tools by the users.

Ion Torrent PGM libraries for targeted resequencing of BRCA1 and BRCA2 genes were prepared in 108 cases of hereditary breast and ovarian cancer syndrome. Pathogenic mutations were identified in 45 families.