Exponential growth of genomics | Dr. Vijay Chandru

most of us when we think about decisions

most of us when we think about decisions we have to make will go by averages

we have to make will go by averages

we have to make will go by averages right so I think you know when we when

right so I think you know when we when

right so I think you know when we when we hear the sound of hoofbeats what

we hear the sound of hoofbeats what

we hear the sound of hoofbeats what would you think of you would think of

would you think of you would think of

would you think of you would think of horses right but today we’re going to

horses right but today we’re going to

horses right but today we’re going to talk about situations where you think

talk about situations where you think

talk about situations where you think about zebras and not horses which is a

about zebras and not horses which is a

about zebras and not horses which is a much rarer phenomenon but you know it

much rarer phenomenon but you know it

much rarer phenomenon but you know it seems counterintuitive right it’s almost

seems counterintuitive right it’s almost

seems counterintuitive right it’s almost irrational to expect a miracle that

irrational to expect a miracle that

irrational to expect a miracle that you’ll hear hoofbeats and then suddenly

you’ll hear hoofbeats and then suddenly

you’ll hear hoofbeats and then suddenly a zebra shows up and not not horses

a zebra shows up and not not horses

a zebra shows up and not not horses right but let’s see why this is

right but let’s see why this is

right but let’s see why this is important

important

important the reason is we’re going to talk about

the reason is we’re going to talk about

the reason is we’re going to talk about cancer right now cancer is a of course a

cancer right now cancer is a of course a

cancer right now cancer is a of course a challenge today to humanity and many of

challenge today to humanity and many of

challenge today to humanity and many of us here in fact how many people in the

us here in fact how many people in the

us here in fact how many people in the audience actually have a family member

audience actually have a family member

audience actually have a family member or a friend or a friend’s parent or who

or a friend or a friend’s parent or who

or a friend or a friend’s parent or who have actually battled cancer have you so

have actually battled cancer have you so

have actually battled cancer have you so you see it’s I would say roughly about a

you see it’s I would say roughly about a

you see it’s I would say roughly about a third of the audience has has had that

third of the audience has has had that

third of the audience has has had that experience so it’s becoming really

experience so it’s becoming really

experience so it’s becoming really something that really affects everyone

something that really affects everyone

something that really affects everyone and now with cancer there are two

and now with cancer there are two

and now with cancer there are two aspects of technology that are that are

aspects of technology that are that are

aspects of technology that are that are actually starting to help us address

actually starting to help us address

actually starting to help us address cancer as an individual’s disease not

cancer as an individual’s disease not

cancer as an individual’s disease not necessarily only something that you use

necessarily only something that you use

necessarily only something that you use evidence-based or statistical decisions

evidence-based or statistical decisions

evidence-based or statistical decisions to treat right so so this is sometimes

to treat right so so this is sometimes

to treat right so so this is sometimes called the N of one phenomenon in

called the N of one phenomenon in

called the N of one phenomenon in medicine it’s also being called

medicine it’s also being called

medicine it’s also being called precision medicine and for cancer this

precision medicine and for cancer this

precision medicine and for cancer this is actually not that far away and so

is actually not that far away and so

is actually not that far away and so this is the idea

this is the idea

this is the idea want to converted it now what is

want to converted it now what is

want to converted it now what is actually causing this and I’m in an

actually causing this and I’m in an

actually causing this and I’m in an institute of technology and what I would

institute of technology and what I would

institute of technology and what I would like to point out is that the there are

like to point out is that the there are

like to point out is that the there are you are at a very interesting time right

you are at a very interesting time right

you are at a very interesting time right now because we have two technologies

now because we have two technologies

now because we have two technologies that have hit exponential scale right

that have hit exponential scale right

that have hit exponential scale right one is of course Moore’s law which which

one is of course Moore’s law which which

one is of course Moore’s law which which we know is you know an exponential law

we know is you know an exponential law

we know is you know an exponential law that has made electronics and computing

that has made electronics and computing

that has made electronics and computing and communications happen and the it’s

and communications happen and the it’s

and communications happen and the it’s shown here on a log linear scale so it’s

shown here on a log linear scale so it’s

shown here on a log linear scale so it’s actually an exponential law but it is

actually an exponential law but it is

actually an exponential law but it is what has driven in some ways the fourth

what has driven in some ways the fourth

what has driven in some ways the fourth Industrial Revolution right and we’re

Industrial Revolution right and we’re

Industrial Revolution right and we’re all affected by it we carry around a

all affected by it we carry around a

all affected by it we carry around a smartphone today which has pretty much a

smartphone today which has pretty much a

smartphone today which has pretty much a very powerful computer in it and that’s

very powerful computer in it and that’s

very powerful computer in it and that’s all possible because of Moore’s law well

all possible because of Moore’s law well

all possible because of Moore’s law well it turns out that there’s another law

it turns out that there’s another law

it turns out that there’s another law it’s that is also accelerating and that

it’s that is also accelerating and that

it’s that is also accelerating and that is called flat Lee’s law and flat leaves

is called flat Lee’s law and flat leaves

is called flat Lee’s law and flat leaves law is about being able to read DNA

law is about being able to read DNA

law is about being able to read DNA sequences in great detail and at

sequences in great detail and at

sequences in great detail and at reasonable cost right and if you see the

reasonable cost right and if you see the

reasonable cost right and if you see the curve there actually flattens law is

curve there actually flattens law is

curve there actually flattens law is drawing propping faster than Moore’s Law

drawing propping faster than Moore’s Law

drawing propping faster than Moore’s Law in the last maybe ten years and this is

in the last maybe ten years and this is

in the last maybe ten years and this is called next-generation sequencing and

called next-generation sequencing and

called next-generation sequencing and it’s actually moving roughly at the

it’s actually moving roughly at the

it’s actually moving roughly at the square of Moore’s law you see the

square of Moore’s law you see the

square of Moore’s law you see the timeline during which information

timeline during which information

timeline during which information technology has taken off is roughly the

technology has taken off is roughly the

technology has taken off is roughly the timeline during which the field of

timeline during which the field of

timeline during which the field of genomics has also developed so around

genomics has also developed so around

genomics has also developed so around the time that the first computers were

the time that the first computers were

the time that the first computers were being conceived you also had that the

being conceived you also had that the

being conceived you also had that the double helix structure of DNA solved by

double helix structure of DNA solved by

double helix structure of DNA solved by Watson and Crick and then you know

Watson and Crick and then you know

Watson and Crick and then you know industrialization in information

industrialization in information

industrialization in information technology have

technology have

technology have a little bit earlier but by about the

a little bit earlier but by about the

a little bit earlier but by about the mid-80s instruments for being able to

mid-80s instruments for being able to

mid-80s instruments for being able to sequence and read off genome data

sequence and read off genome data

sequence and read off genome data started becoming available if you look

started becoming available if you look

started becoming available if you look at the progress in in electronics in you

at the progress in in electronics in you

at the progress in in electronics in you know 1958 I guess the the first company

know 1958 I guess the the first company

know 1958 I guess the the first company that that made semiconductors was set up

that that made semiconductors was set up

that that made semiconductors was set up similarly for genomics it started in

similarly for genomics it started in

similarly for genomics it started in 1985 or so so it’s not a genomic started

1985 or so so it’s not a genomic started

1985 or so so it’s not a genomic started off a little bit later but by about 2006

off a little bit later but by about 2006

off a little bit later but by about 2006 you know we had reached what we call the

you know we had reached what we call the

you know we had reached what we call the second half of the chessboard you know

second half of the chessboard you know

second half of the chessboard you know the story about the chessboard right put

the story about the chessboard right put

the story about the chessboard right put one grain of rice on the first square

one grain of rice on the first square

one grain of rice on the first square double it on the second doublet again on

double it on the second doublet again on

double it on the second doublet again on the third and so forth so when you get

the third and so forth so when you get

the third and so forth so when you get halfway through the chessboard you reach

halfway through the chessboard you reach

halfway through the chessboard you reach about four billion now that means that

about four billion now that means that

about four billion now that means that the technology has improved four billion

the technology has improved four billion

the technology has improved four billion times right and that’s very substantial

times right and that’s very substantial

times right and that’s very substantial so once you get past that into that

so once you get past that into that

so once you get past that into that second half of the chessboard you see

second half of the chessboard you see

second half of the chessboard you see really miraculous use of technology and

really miraculous use of technology and

really miraculous use of technology and that’s what we’re experiencing today

that’s what we’re experiencing today

that’s what we’re experiencing today whether it’s autonomous vehicles or

whether it’s autonomous vehicles or

whether it’s autonomous vehicles or artificial intelligence systems and all

artificial intelligence systems and all

artificial intelligence systems and all kinds of impact of you know the the

kinds of impact of you know the the

kinds of impact of you know the the second half of the Moore’s Law impact in

second half of the Moore’s Law impact in

second half of the Moore’s Law impact in in technology now what what has happened

in technology now what what has happened

in technology now what what has happened in genomics is that it went along with

in genomics is that it went along with

in genomics is that it went along with Moore’s law for a while but then it

Moore’s law for a while but then it

Moore’s law for a while but then it accelerated even faster

accelerated even faster

accelerated even faster so it so happens that this year in 2017

so it so happens that this year in 2017

so it so happens that this year in 2017 we have entered the second half of

we have entered the second half of

we have entered the second half of genomics as well so what does this

genomics as well so what does this

genomics as well so what does this actually mean this means that it’s

actually mean this means that it’s

actually mean this means that it’s getting cheaper faster and better to be

getting cheaper faster and better to be

getting cheaper faster and better to be able to read the DNA of of an individual

able to read the DNA of of an individual

able to read the DNA of of an individual and be able to make certain decisions

and be able to make certain decisions

and be able to make certain decisions based on that and that’s what

based on that and that’s what

based on that and that’s what this whole thing with precision medicine

this whole thing with precision medicine

this whole thing with precision medicine and cancer is about right so ah there we

and cancer is about right so ah there we

and cancer is about right so ah there we go so what is this DNA this DNA is

go so what is this DNA this DNA is

go so what is this DNA this DNA is essentially a book that we have

essentially a book that we have

essentially a book that we have trillions of copies of right and it’s in

trillions of copies of right and it’s in

trillions of copies of right and it’s in the DNA of that you’re born with and

the DNA of that you’re born with and

the DNA of that you’re born with and that’s actually a book which is written

that’s actually a book which is written

that’s actually a book which is written in an alphabet of just four letters ACGT

in an alphabet of just four letters ACGT

in an alphabet of just four letters ACGT and it it’s a fairly long book in the

and it it’s a fairly long book in the

and it it’s a fairly long book in the sense that it’s three billion letters

sense that it’s three billion letters

sense that it’s three billion letters long right and we all have this it’s you

long right and we all have this it’s you

long right and we all have this it’s you know I think most of you have had some

know I think most of you have had some

know I think most of you have had some introductory biology so I won’t belabor

introductory biology so I won’t belabor

introductory biology so I won’t belabor this now what did the human genome

this now what did the human genome

this now what did the human genome project achieve it gave us the first

project achieve it gave us the first

project achieve it gave us the first reference genome of of a human being now

reference genome of of a human being now

reference genome of of a human being now so if the black band there is the

so if the black band there is the

so if the black band there is the reference genome now when I take an

reference genome now when I take an

reference genome now when I take an individual patients DNA and start

individual patients DNA and start

individual patients DNA and start sequencing it I’ll sequence it in small

sequencing it I’ll sequence it in small

sequencing it I’ll sequence it in small bits right and those are called reads

bits right and those are called reads

bits right and those are called reads now I can do a string matching and put

now I can do a string matching and put

now I can do a string matching and put that read against the reference genome

that read against the reference genome

that read against the reference genome and I know where it where it actually

and I know where it where it actually

and I know where it where it actually fits right but if you just do one copy

fits right but if you just do one copy

fits right but if you just do one copy of the DNA you’re likely to make errors

of the DNA you’re likely to make errors

of the DNA you’re likely to make errors so what we do is actually put many many

so what we do is actually put many many

so what we do is actually put many many copies of DNA cut it up into B’s pieces

copies of DNA cut it up into B’s pieces

copies of DNA cut it up into B’s pieces sequence those pieces and then assemble

sequence those pieces and then assemble

sequence those pieces and then assemble them so that’s a big computational

them so that’s a big computational

them so that’s a big computational challenge but it can be done right and

challenge but it can be done right and

challenge but it can be done right and so for cancer patients for example you

so for cancer patients for example you

so for cancer patients for example you take about a thousand copies of the DNA

take about a thousand copies of the DNA

take about a thousand copies of the DNA from the tumor and you will actually

from the tumor and you will actually

from the tumor and you will actually sequence those and put those thousand

sequence those and put those thousand

sequence those and put those thousand copies in fragments in reads as as you

copies in fragments in reads as as you

copies in fragments in reads as as you see in the picture there now you can

see in the picture there now you can

see in the picture there now you can actually look down a specific position

actually look down a specific position

actually look down a specific position in there

in there

in there friends genome and see if the same

friends genome and see if the same

friends genome and see if the same pattern is in all the reads and you see

pattern is in all the reads and you see

pattern is in all the reads and you see here there is there is a I think it’s an

here there is there is a I think it’s an

here there is there is a I think it’s an a which is replaced by a T right that’s

a which is replaced by a T right that’s

a which is replaced by a T right that’s called a single nucleotide polymorphism

called a single nucleotide polymorphism

called a single nucleotide polymorphism so it’s actually something so the the

so it’s actually something so the the

so it’s actually something so the the the easier way to call it is a snip it’s

the easier way to call it is a snip it’s

the easier way to call it is a snip it’s a snip right and these the snip actually

a snip right and these the snip actually

a snip right and these the snip actually is such that it is from in some sense

is such that it is from in some sense

is such that it is from in some sense from the the both copies of the of the

from the the both copies of the of the

from the the both copies of the of the DNA which means that it came from both

DNA which means that it came from both

DNA which means that it came from both parents right you can also have snips

parents right you can also have snips

parents right you can also have snips which are heterozygous that is it comes

which are heterozygous that is it comes

which are heterozygous that is it comes from only one parent right if it comes

from only one parent right if it comes

from only one parent right if it comes from both friends you call it homozygous

from both friends you call it homozygous

from both friends you call it homozygous if it’s from only one parent equal it

if it’s from only one parent equal it

if it’s from only one parent equal it heterozygous right and then you can

heterozygous right and then you can

heterozygous right and then you can start collecting and looking at all of

start collecting and looking at all of

start collecting and looking at all of these snips right now for each human

these snips right now for each human

these snips right now for each human being there are you know lots and lots

being there are you know lots and lots

being there are you know lots and lots of snips that that arise in the genome

of snips that that arise in the genome

of snips that that arise in the genome but only one of them or maybe a few of

but only one of them or maybe a few of

but only one of them or maybe a few of them together are causing problems

them together are causing problems

them together are causing problems causing a disease or some so you have to

causing a disease or some so you have to

causing a disease or some so you have to be able to sort it all out so we won’t

be able to sort it all out so we won’t

be able to sort it all out so we won’t get into the details of how you sort it

get into the details of how you sort it

get into the details of how you sort it all that but but let’s let’s look about

all that but but let’s let’s look about

all that but but let’s let’s look about look at how this is starting to help

look at how this is starting to help

look at how this is starting to help people right and so this is the famous

people right and so this is the famous

people right and so this is the famous story of a Ling young boy called

story of a Ling young boy called

story of a Ling young boy called Nicholas Volker who was in some sense

Nicholas Volker who was in some sense

Nicholas Volker who was in some sense the poster you know child of genomic

the poster you know child of genomic

the poster you know child of genomic medicine because you know he was having

medicine because you know he was having

medicine because you know he was having lots of problems with essentially with

lots of problems with essentially with

lots of problems with essentially with digestion and I had to have many many

digestion and I had to have many many

digestion and I had to have many many surgeries and at some point the doctors

surgeries and at some point the doctors

surgeries and at some point the doctors suspected that there was some problem

suspected that there was some problem

suspected that there was some problem with his immune system but to confirm it

with his immune system but to confirm it

with his immune system but to confirm it they sequenced his DNA and they actually

they sequenced his DNA and they actually

they sequenced his DNA and they actually found the culprit gene

found the culprit gene

found the culprit gene and they found that mutations which had

and they found that mutations which had

and they found that mutations which had caused the immunodeficiency at which

caused the immunodeficiency at which

caused the immunodeficiency at which point they were able to get him a bone

point they were able to get him a bone

point they were able to get him a bone marrow transplant and and this was about

marrow transplant and and this was about

marrow transplant and and this was about maybe eight years ago so so this boy is

maybe eight years ago so so this boy is

maybe eight years ago so so this boy is now healthy he is going to school then

now healthy he is going to school then

now healthy he is going to school then and so on so so they you know the the

and so on so so they you know the the

and so on so so they you know the the story of how this boy was you know

story of how this boy was you know

story of how this boy was you know diagnosed and then recovered is was

diagnosed and then recovered is was

diagnosed and then recovered is was written up as a book and it won the

written up as a book and it won the

written up as a book and it won the Pulitzer Prize

Pulitzer Prize

Pulitzer Prize the next story of course many of you are

the next story of course many of you are

the next story of course many of you are familiar with because this happened just

familiar with because this happened just

familiar with because this happened just a couple of years ago Angelina Jolie

a couple of years ago Angelina Jolie

a couple of years ago Angelina Jolie actually discovered that she has

actually discovered that she has

actually discovered that she has inherited some terrible genetic factors

inherited some terrible genetic factors

inherited some terrible genetic factors for breast and ovarian cancer from her

for breast and ovarian cancer from her

for breast and ovarian cancer from her mother and and she had two family

mother and and she had two family

mother and and she had two family members a mother and her aunt affected

members a mother and her aunt affected

members a mother and her aunt affected and and therefore took some bold

and and therefore took some bold

and and therefore took some bold decisions on elective surgeries to

decisions on elective surgeries to

decisions on elective surgeries to improve her chances of not getting

improve her chances of not getting

improve her chances of not getting cancer went in later age right so it’s

cancer went in later age right so it’s

cancer went in later age right so it’s an example of again you know where

an example of again you know where

an example of again you know where individualized medicine or you know I

individualized medicine or you know I

individualized medicine or you know I said the zebra right comes into play

said the zebra right comes into play

said the zebra right comes into play because in her case she had ovarian

because in her case she had ovarian

because in her case she had ovarian cancer which then later on there was a

cancer which then later on there was a

cancer which then later on there was a relapse in breast cancer and and then we

relapse in breast cancer and and then we

relapse in breast cancer and and then we analyzed her DNA a tumor DNA and we know

analyzed her DNA a tumor DNA and we know

analyzed her DNA a tumor DNA and we know not a tumor DNA but her the germline DNA

not a tumor DNA but her the germline DNA

not a tumor DNA but her the germline DNA the DNA she was born with and found that

the DNA she was born with and found that

the DNA she was born with and found that there was an inherited factor which

there was an inherited factor which

there was an inherited factor which which then led to treatment all of this

which then led to treatment all of this

which then led to treatment all of this type of diagnosis today is possible in

type of diagnosis today is possible in

type of diagnosis today is possible in India it’s done by this company called

India it’s done by this company called

India it’s done by this company called strand which which a bunch of us started

strand which which a bunch of us started

strand which which a bunch of us started and we have a platform called strand

and we have a platform called strand

and we have a platform called strand Ramanujan that actually helps with with

Ramanujan that actually helps with with

Ramanujan that actually helps with with this diagnosis if you want to read about

this diagnosis if you want to read about

this diagnosis if you want to read about more zebras stories there’s a book

Exponential growth of genomics | Dr. Vijay Chandru | TEDxCMRIT

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