Genome sequencing to map population diversity

posted Jul 26, 2019, 2:13 AM by Vinod Scaria   [ updated Jul 26, 2019, 2:14 AM ]

Jacob Koshy | The Hindu NEW DELHI, APRIL 19, 2019 00:11 IST

CSIR effort set to probe gene-disease link

In an indigenous genetic mapping effort, nearly 1,000 rural youth from the length and breadth of India will have their genomes sequenced by the Council of Scientific and Industrial Research (CSIR). The project aims at educating a generation of students on the “usefulness” of genomics.

Globally, many countries have undertaken genome sequencing of a sample of their citizens to determine unique genetic traits, susceptibility (and resilience) to disease. This is the first time that such a large sample of Indians will be recruited for a detailed study.

The project is an adjunct to a much larger government-led programme, still in the works, to sequence at least 10,000 Indian genomes.

Typically, those recruited as part of genome-sample collections are representative of the country’s population diversity. In this case, the bulk of them will be college students, both men and women, and pursuing degrees in the life sciences or biology.

“This will not be an exercise to merely collect samples from people,” said Vinod Scaria, a scientist at the Institute of Genomics and Integrative Biology (IGIB), a CSIR laboratory.

“We will be reaching out to a lot of collegians, educating them about genomics and putting a system in place that allows them to access information revealed by their genome,” he said. Because genomics is largely confined to a rich urban demographic in India, this exercise, according to Dr. Scaria, would make such information ubiquitous even to villages. “Just as CT scans are now known across the country, we hope to do the same for genomes,” he said.

5-year-old ‘butterfly’ boy at PGI for treatment

posted Apr 13, 2018, 10:29 PM by Vinod Scaria   [ updated Apr 13, 2018, 10:29 PM ]

Shimona Kanwar| TNN | Updated: Apr 12, 2018, 11:13 IST

CHANDIGARH: A five-year-old suffering from dystrophic Epidermolysis Bullosa (EB), a painful and rare genetic skin disease, is being treated in PGI. Kids with EB are often referred to as ‘butterfly children’.
The kid has a new genetic alteration, which caused the rare skin disease. A collaborative research between the Institute of Genomics and Integrative Biology (IGIB), New Delhi, and PGI has been able to uncover some novel variants in India causing EB. Consequently, molecular diagnosis and prenatal screening have recently helped one such case to terminate the pregnancy as the feotus was found to have a genetic mutation for the rare genetic condition, which makes the skin extremely fragile, almost like a butterfly’s wing. The ‘butterfly kids’ are prone to blisters.

In the area of genetic skin diseases, IGIB has been collaborating with the department of dermatology, PGI, and has been able to solve a number of cases of such diseases with molecular diagnosis. PGI has 40 families affected by this rare skin disease.

In this rare condition, the skin becomes fragile and breaks down in case of any minor pressure or trauma. EB is caused due to mutations, which affect the proteins involved in the architecture and anchoring of the skin layers. The disease has multiple levels of severity (less to moderately severe i.e. dystrophic). People with severe form EB can ultimately die.

“In the recent paper, we described the utility of genomics approach (whole exome sequencing). This approach makes it cost-effective, time-effective and efficient for clinical applications,” said Dr Vinod Scaria, senior scientist, IGIB.

The authors including Dr Rahul Mahajan and Dr Sanjeev Handa from the dermatology department, PGI, have described how this genomic approach could enable diagnosis, prognosis as well as prevention of the disease through appropriate prenatal testing, using the case example of two families.

“In case of both the families, the identification of the genetic variants confirmed clinical diagnosis. In the second family, the identification of novel variants also offered them a possibility to avail prenatal genetic testing,” said Dr Scaria.

Interpretation of a malady: how scientists zeroed in on one family's rare and crippling disease

posted Apr 21, 2017, 3:19 AM by Vinod Scaria   [ updated Apr 21, 2017, 11:03 PM ]

The poignant story of an Agra family, where six children have the Nalband mutation. Jacob Koshy reports on how a group of scientists linked it to a rare and crippling neurological disease

Read the full text here 

The year of Personal Genomics (The Hindu, Jan01,2017)

posted Jan 4, 2017, 6:47 AM by Vinod Scaria

The conversation around personal genomics amplified in 2016, as did the range of diagnostic options - by Jacob Koshy
Read Full-text here:

Qatar exome study: An advancement in precision medicine (Nature Middle East)

posted Sep 27, 2016, 12:02 AM by Vinod Scaria   [ updated Oct 4, 2016, 2:30 AM ]

By Louise Sarant 

Scientists look at Qataris' exome sequences to anticipate response to two common blood-thinners
The study, by a team from the Delhi-based CSIR Institute of Genomics and Integrative Biology, will be the first that tries to anticipate the reaction of a Qatari patient to a medication based on his or her genetic makeup. The study will appear in Pharmacogenomics
Scientists have used information from the whole-exome sequencing of 100 Qataris to create a comprehensive map of pharmacogenetic variants associated with two anticoagulants.

Should you take that genetic test ? Jacob Koshy (The Hindu May 15, 2016)

posted Jun 28, 2016, 2:48 AM by Vinod Scaria   [ updated Jun 28, 2016, 2:48 AM ]

Why Indians, SE Asian Malays respond differently to some drugs

posted Jun 14, 2016, 9:32 PM by Vinod Scaria

CSIR Young Scientist Award for Biological Sciences

posted Nov 11, 2012, 12:27 AM by Vinod Scaria   [ updated Jun 28, 2016, 2:46 AM ]

Click for High-Res Image

Detailed map of TB genome to help treatment

posted Apr 13, 2012, 1:58 AM by Vinod Scaria   [ updated Apr 13, 2012, 2:01 AM ]

Scientists from all over India have put together a visual map of the tuberculosis bacteria’s genome, a tool that will be freely available and could help researchers in their quest to develop a more accurate treatment for the disease. “The TB genome was sequenced in 1998, but more than 
half the genes in the genome did not have any function attached to them,” said Vinod Scaria, researcher at the Institute of Genomics and Integrative Biology in Delhi and one of the principal investigators for the Open Source Drug Discovery project. “We wanted to collect all the information in one place.” 

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