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CS4880: Lecture 1: Girish Raguvir J, CS14B059 Due On: 28th January 2018

This lecture discussed the big data challenges in genomics and healthcare. Dr. Rohit Gupta from MedGenome discussed how determining DNA sequences is useful for diagnosis but produces extremely large amounts of data. Variant calling, which identifies differences in DNA sequences, poses challenges for data alignment and storage due to the large search space and volume of data. While finding causative variants is difficult, genomics research has great potential to cure diseases and is an important area for future work.

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49 views1 page

CS4880: Lecture 1: Girish Raguvir J, CS14B059 Due On: 28th January 2018

This lecture discussed the big data challenges in genomics and healthcare. Dr. Rohit Gupta from MedGenome discussed how determining DNA sequences is useful for diagnosis but produces extremely large amounts of data. Variant calling, which identifies differences in DNA sequences, poses challenges for data alignment and storage due to the large search space and volume of data. While finding causative variants is difficult, genomics research has great potential to cure diseases and is an important area for future work.

Uploaded by

Girish Raguvir
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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CS4880: Lecture 1

Girish Raguvir J, CS14B059


Due on: 28th January 2018

This lecture was given by Dr. Rohit Gupta on the topic "Big data challenges in
the field of genomics and healthcare". Dr. Rohit Gupta is the Chief Infor-
mation Officer at MedGenome, a testing and research lab which specializes in DNA
diagnostics and screening.

DNA sequencing is the process by which one determines the precise order of nu-
cleotides in a piece of DNA. Determination of the sequence is highly useful in diag-
nosis and curing of diseases. People are starting to realise it’s utility and some small
countries such as Faroe Islands are even going as far as attempting to sequence the
genes of their entire population. It’s believed to chart the way for future genomic
medicine.

However, the volume of data is often extremely large and handling such volumi-
nous data becomes a severe bottleneck. Big data challenges are predominant in
the field of genomics and healthcare. People face both storage and computational
challenges. Efficient software and hardware optimisations are needed.

Typical analysis pipeline starts with pre-processing, followed by variant identifica-


tion and then post-processing. Variant calling, an important problem in genomics,
is the process by which one identifies variants from sequence data. This also poses
another important problem of data alignment where two sequences have to be first
appropriately aligned before variant analysis can be done. Currently used algorithms
for data alignments involve suffix-tree based indexing, burrows-wheeler transforma-
tion etc.

There are 3.5 million possible variants in the human genome and often only a few
are causative. It’s like finding a needle in a haystack. Storage, computation and
analysis challenges are huge. But the problem that is being solved is extremely
important. Especially in India, where consanguineous marriages are prevalent, dis-
eases arising due to genetic issues are highly probable. Attempt at curing cancer or
finding vaccines through the study of genomics is also very promising.

The potential of this study is immense and much of it is still untapped. This field
has many open research problems and most of them have a direct impact on the
society. It’s a platform where academia and industry can come together to progress
towards a brighter future in the health of mankind.

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