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this week on a special edition of to the contrary, we take an indepth look at dna sequencing and how it's helping children with rare dna sequencing and how it's helping children with rare diseases. [♪] >> hello i'm bonnie erbe welcome to to the contrary a discussion of news and social trends from diverse perspectives. this week we show you how advances in dna sequencing are helping scientists find cures for rare diseases especially rare childhood diseases. dr. james lupski is a man with a mission as a pediatrician at baylor

college of medicine in houston, dr. lupski has devoted much of his medical career to researching and treating children with rare diseases. >> the patients that i mainly see in the clinic are children and families in which a genetic disease will be evident for children often we will also be referred when there is either some kind of a development delay, when the child is not developing like one would expect. this could include speech delay, motor delay, other forms of delay. >> for parents, the first hurdle is diagnosis. which is difficult, because rare diseases are harder to diagnose. the second hurdle is treatment. few exist because drug companies devote scarce research resources to producing drugs for more common diseases. that so they can sell the drugs to a larger market and make back the large costs of

research and development. the same is true of government research grants, but for different reasons. the government wants most urgently to find cures for diseases affecting the largest numbers of citizens. dr. lupski knows all too well about the syndrome as he and several of his family members suffer from the rare neurological disorder known as sara manzano-diaz. charcot-marie tooth. to date there's no cure. >> basically what it is is it is a disorder of the peripheral nerve and that is like the wire that takes the signal from the brain and send it is out to the muscles and all the things in the preferry that you need to sense your environment and act on your environment. >> classified as a rare disease cmt affects 1-2500 people in the u.s. generally speaking a disease as rare if it afflicts fewer than 200,000 people.

many of these diseases are genetic. but in truth, there's nothing rare about rare diseases. >> conditions like for instance, hearing loss or deafness, there's many genes that can -- in which mutation can lead to hearing impairment. but in one specific family an individual single gene will be responsible. so in the mixture of the phenotype of how many people can have hearing impairment it's not as rare as people think it is. the same goes for conditions like developmental delay or even birth defects. 2-3% of all children are born with a major birth defect no matter where you do the studies around the world and that is a significant% of the population. they have different kinds of birth defects and the individual birth defect might be considered a rare defect like the general

heart defect or kidney defect. but actually there is many children that are born with birth defects. >> here in the u.s. there are more than 7,000 rare diseases affecting 25 million children and adults. studying the dna of those battling a disease could be the first step in finding a cure. sequencing technology gives doctors and researchers a detailed description of the chemical building blocks in any given sample of a patient's dna. the particular sequence or order of the building blocks tells them important genetic information about the patient. changes in that sequence also known as mutations, can cause disease. in the future, scientists hope to develop drugs that compensate for those mutations. right now, dna sequencing technology allows dr. lupski to identify and expand knowledge about gene mutations present in his patients. offering clues on why and

how a disease has taken over a child's body. >> the way i feel about when i see a patient or a family is, i want to treat them the same way. what i would want to know. tonight seems to me, every family wants to know what is this, and why did it happen, and what is the chances it's going to happen again. and this is important to their family planning issues. and we try our pest best to provide them to the answers to each one of the questions. one thing we've learned tremendously from dna sequencing is that many mutations can occur as new events. so it's never been passed in the family. it's happened for the first time in this individual patient. so if i get back to the questions that all parents want to know, what is this? why did it happen? and what is the chance of it happening again? often, one dna sequencing test can answer all those

questions for the family. >> in dr. lupski's case, state are the after the dna sequencing technology has helped narrow down the mutations that may create his type of cmt. in charcot-marie tooth as we knew that the condition could be inherited either as an recesssive trait as it is in my family, or it can be inherited as a dominant trait where it passes from one generation to the next and to the next. >> dr. lupski invisions a day when more doctors and research hospitals regularly use dna sequencing. rapidly developing technology is already driving down the cost and time needed to sequence gene samples. >> by its very nature medicine tends to be conservative. i think back when i was in medical school, and cat scans were just introduced into some of clinical practice many physicians

would still do a skull series, when a person had head trauma. which most of the time those x-rays were useless compared to what you could visualize with individual cat scans but in the beginning they were more expensive technologies they took time and the physicians were not used to how to interpret the data. i think we'll see some of that with dna sequencing. they become more familiar with it and more doctors are ordering dna sequencing tests even non-geneticists when they find in their specialty they can diagnose the different conditions when the gene is found by ordering the tests. but this will take time to transition. >> it will also take time to incorporate the latest research into clinical medicine. scientists have sequenced the whole human genome. that is a person's entire,g hairedtary blueprint.

in 2003, the national genometes of health project a 13 year long program to identify and map the some 25,000 genes in human dna found in our 24 chromosomes. >> in the research laboratory right now, what is being done is a sequencing the entire genome at once. and this has only been done an less than a dozen people at this point. but we see in the future that this will probably be done in the clinic in patients when you're having difficulty to try to understand their disease process you will try to see what is the genetic hand of cards they have been dealt by sequencing their whole genome. >> as it stands today, dna sequencing technology does have its limitationsism often we are able to make that secure decisionsies and

give prognostic information and even recurrence risk estimates for the family members. but we cannot predict severity of disease. from sequence information. and it certainly by no means leads to a cure for the disease. >> not yet at least. but dr. lupski has high hopes that some day dna sequencing will be able to do just that. >> i don't have a crystal ball so i cannot look into the future. let's say that i'm a lot more optimistic and hopeful than i was five or 10 years ago. that in my lifetime, we will see some major cures happening before because we understood the disease at the basic molecular level and we got there by finding the genes involved. and seeing exactly how

genetic variation leads to these disease processes. >> now, we examine the rapidly developing technology behind dna sequencing, and how it may soon make its way into our everyday lives. it's all in your genes. just ask dr. richard gibbs. as director of the human genome sequencing center at baylor college of medicine in houston of dr. gibbs spends his days investigating the way genes impact our health. >> the fundamental concept is that genetics is a big determinant of your future. and that whatever ails you or finishes you, will have a large genetic component. and for the most part right now we are focused on those obvious examples. we have disease in the family. but the fact is that every common disorder has some contribution from genetics. that we want to understand that and bring advances and

cure and diagnostics that are based on that understanding. >> which is why dna sequencing is so important. it's only been in existence for a few decades but dna sequencing has given doctors and researchers immeasurable amounts of data on the human body. >> dna sequence something a chemistry it means that you take the dna out of blood or whatever tissue that you can get and you treat it in a way with special chemicals and special processes and then you put it in a machine that somehow stretches out the dna and looks at every single base position and figures out what the sequences are. the dna is made up of four particular elements that we call the dna bases. and you know, two of them appear with each other and the four give us a code that is our genetic code our blueprint. so figuring out the order of those four in the three billion phases that you get

from your mother other father is dna sequencing. >> the baylor human genome sequencing center was one of five major labs to take part in the nih sponsored human genome project where scientists worked for more than 10 years to identify those three billion bases of human dna. today, dr. gibbs and a team of researchers are using state-of-the-art machines such as the solid 3 sequencing system to sequence the same amount of dna in just a matter of weeks. >> this is an actual dna sequencing machine. it's very different to the sequencing machines that we used to sequence the human genome. those older man machines could do 100 samples in three hours. this machine does 200 million samples in two weeks. it's dramatically different. the machine is loaded with individual tiny beads that are each loaded with an individual dna molecule that

is amplified and coded around the bead and all intersect together and there are chemical reactions performed on the surface. >> the science is making its way into medical and pediatric care. there are more than a thousand dna based gene tests available to infants and adults. newborn genetic screening can identify disorders present in a child and eliminate or reduce symptoms that might otherwise cause a lifetime of disability. one rare genetic disorder known as maple syrup urine disease or msud prevents the body from breaking down three amino acids. toxic levels of these amino acids in the blood cause severe mental retardation. left untreated most people die in the first two years of life. and now, newborns who test positive for msud start treatment immediately without any impact on

lifespan or intelligence. >> it's been a hard, slow road to get dna and the information from it integrated into people's health much less their lives. the technology has this way of not impacting lives until some moment. when things take off. and they are indeed transformative. >> whole genome sequencing is likely to open up more doors of discovery. and dr. gibbs thinks we are close to seeing the price for genome sequencing go down from several thousand to a few hundred dollars. that will make it accessible to almost everyone. and more widely available to predict rare pediatric diseases. >> it will be on your children's social networking accounts on the computer. they will have something about their dna history and they will share them with other people. it will be when you go to restaurants and they will say, these are your dna

sequences confer allergy food problems or preferences? it will be all in the different aspects of your life. >> with such easily available personal information problems can arise. >> all of these projects invoke big questions about our privacy and the fact is that these genetic data whether it be the genes that you inherited or the genes that are involved in cancer or the genes that are involved in the microiome that the organisms involved in the microbiome we think if people learned about that information in the context of employment or insurance that that could be damaging to us. so we have now fortunately, a robust set of discussions and new legislations and many other processes in place to deal with genetic privacy. >> the genetic information non-discrimination act enacted two years ago protects americans from discrimination in health insurance or employment based on genetic information. it is a much-needed law.

as the development of sequencing technology has exceeded the imagination of even the most optimistic scientists. >> if you look at the history of the internet of the personal computers or the history of telecommunication or the history of transport, no one at the beginning predicted what the impact of the technology would be. what the world would look like with the technologies fully integrated and how fast the transition would be once things really took off. so we believe that dna and the knowledge of dna sequence is just entering that transformative moment. >> now, we meet the beery family as they share their story of heartbreak and hope. today, twins alexis and noah beery are typical energetic and athletic 13-year-olds but their lives have not always been this way. the 8th grader recall a day when the most basic activity was a struggle. >> before we would wobble,

and we wouldn't be able to talk. we would just we couldn't do anything. we couldn't learn. >> i'd see other kids doing all this stuff doing sports and climbing and sliding down slides. you know, that was pretty much my biggest dream. >> shortly after birth, twins alexis and for what cried incessantly. doctors called it colic and retta beery sensed something else was off. >> when they were 9 months old we knew that something was wrong with their development. they were so floppy when they were 9 months old. when you would hold them they would flop back they had no muscle tone whatsoever. >> in the months and years that followed alexis and noah's condition deteriorated. the beery family went from one medical specialist to another. but none could offer a definitive diagnosis for their twins. >> not knowing what is going on, having the doctors grab

us and putting needles inside of us. and when we were younger we had no clue what was going on. >> i just remember feeling overwhelmed that our babies were going through so many things. it was really disheartening. >> the twins were diagnosed as having cerebral palsy. >> we had something now that we could grab hold of and move forward with. and we knew that cerebral palsy was not a progressive disorder. what you have is what you have it doesn't get worse. >> things did get worse. >> one or the other would be throwing up or alexis would be higher functioning in the morning and then she would be falling down and hurting herself. >> literally by 10:30, 11:00 in the morning she could no longer walk or no longer sit up and this is at age five-and-a-half. she could no longer swallow food. she lost 20% of her body weight. >> retta kept researching

the symptoms and possible treatments. she found an article that changed everything. >> i came across an article that was titled deft diagnosis, the segawa's dystonia mimics cerebral palsy. and i read about the case study of this girl who had very similar symptomses alexis. and the article was centered around a neurologist out of the university of michigan named dr. john fink. and as i read the article, i knew everything in me knew that this was what alexis had. i had no doubt. >> alexis was diagnosed with segawa's dystonia. a rare neurological movement disorder often mistaken for cerebral palsy. alexis took her first dose of what the beery's call the miracle drug sinemet in april of 2002. >> we gave her a quarter of this small pill that first

night and it was the first night that she had slept in her life through the night. so we didn't know what that meant. the next morning we woke up and she woke up and of the was good. we gave her another of a quarter of a pill after speaking with the dr. that morning and she walked out to the rental car on her own, for the first time in her life she was able to get into a car on her own. pulled a seatbelt down for the first time in her life on her own and this is age five-and-a-half. and we knew everything in us knew we were witnessing a miracle that everything was changing. >> because alexis and noah's symptoms differed slightly, doctors believed noah's cerebral palsy diagnosis was accurate but the beery's began to think otherwise. >> we pushed to start him on the medication. we had a clear reason to believe that the medication would stop his throwing up which did not make medical sense whatsoever. and dr. fink agreed for a

month's trial period of the medication for noah and it stopped his throwing up after almost six years of throwing up everyday of his life. >> life changed immediately. >> we could now do the normal things that other families often time take for granted like going out for dinner together as a family after four months on the medication, i got them into soccer, noah and alexis were both on a sketball team early on right after they started on the medication. alexis was in dancing gymnastics. they were able to do things that we never thought were possible. >> the beery's struggle is not as uncommon as one might think. nicole boys founder and -- nicole boice founder of the rare disease network hears stories similar to that of the beery family daily. >> i get calls and letters everyday from different parents and there are common themes common things that all of these families share. a they feel isolated and alone.

b, they have had trouble finding a diagnosis or they've had trouble finding the right caregivers. the necessary information that they need. nicole boice founded the children's rare disease network after watching a close friend struggle after the birth of a child. >> the whole entire process you know, the lack of diagnosis, the stress it was their first child, emotionally, physically, financially, socially, just the whole process seemed broken by just felt like there's got to be something that i can help with. >> but nicole boice believes the advent of low cost dna sequencing will help parents discovery of disease and diagnosis. >> what dna sequencing brings to these families is the potential of uncovering what the child has much more quickly. what it provides this community is unprecedented.

and it's what we've been waiting for. >> we spent five-and-a-half years searching for what in essence is a simple problem to solve. and it's in those five-and-a-half years is a parent that there would have been nothing that you would not have given to make them more comfortable to get them to where they are today. in sequencing, having had the ability to identify this problem early on, right after birth, would have been phenomenal. >> today, alexis and noah are healthy and function normally. with the help of sinemet which they take three times a day. >> got accustomed to it. it's a regular thing we do. >> now we're at the part in our life where we are just you know, we are normal kids now. >> we hope you enjoyed this special edition of to the contrary. join us on the web for to the contrary extra and whether your views are in agreement or to the contrary, please join us next time.

funding for to the contrary provided by... >> while other luxury carmakers are still building their first hybrids, lexus hybrids have traveled 5.5 billion miles. imagine where we'll go next. >> reporter: the life technologies foundation is proud to support to the contrary on pbs. we seek to advance science

education and further society's understanding of the life sciences including the impact of ginomics on the practice of medicine. >> and by sam's club. committed to small business and the spirit of the entrepreneur and proud to support pbs's to the contrary with bonnie erbe. and additional funding provided by... for videotapes of to the contrary, please contact...