Maya Angelou quote

People may not remember exactly what you did, or what you said, but they will always remember how you made them feel.

People might doubt what you say, but will always believe what you do.

When someone shows you who they are, believe them the first time.

Irvin Yalom and his books

http://www.yalom.com/index.html

http://en.wikipedia.org/wiki/Irvin_D._Yalom

Existential therapy

http://en.wikipedia.org/wiki/Existential_psychotherapy

In the existential view, there is no such thing as psychological dysfunction or being ill. Every way of being is merely an expression of how one chooses to live one's life. However one may feel unable to come to terms with the anxiety of being alone in the world. If so an existential psychotherapist can assist one in accepting these feelings rather than trying to change them as if there is something wrong. Everyone has the freedom to choose how they are going to be in life, however this may go unexercised because making changes is difficult; it may appear easier and safer not to make decisions that you will be responsible for. Many people will remain unaware of alternative choices in life for various societal reasons.

Existential belief suggests that it is possible for people to face the anxieties of life head-on and embrace the human condition of aloneness, to revel in the freedom to choose and take full responsibility for their choices. They courageously take the helm of their lives and steer in whatever direction they choose; they have the courage to be. One does not need to arrest feelings of meaninglessness, but can choose new meanings for their lives. By building, by loving, and by creating one is able to live life as one's own adventure. One can accept one's own mortality and overcome fear of death. Though the French author Albert Camus denied the specific label of existentialist, in his novel, L'Etranger, his main character Meursault, ends the novel by doing just this. He accepts his mortality and rejects the constrictions of society he previously placed on himself, leaving him unencumbered and free to live his life with an unclouded mind

The existential psychotherapist is generally not concerned with the client's past; instead, the emphasis is on the choices to be made in the present and future. The counselor and the client may reflect upon how the client has answered life's questions in the past, but attention ultimately shifts to searching for a new and increased awareness in the present and enabling a new freedom and responsibility to act. The patient can then accept they are not special, and that their existence is simply coincidental, without destiny or fate. By accepting this, they can overcome their anxieties, and instead view life as moments, in which they are fundamentally free.

book: if you meet the buddha on the road, kill him

I love this book very very much. I highly recommend this book.

Sheldon Kopp, 70, Psychologist Who Wrote About Self-Esteem

Sheldon Bernard Kopp, a clinical psychologist and author of books designed to bolster the reader's self-esteem, died on Monday, his 70th birthday, at Georgetown University Hospital in Washington. He lived in nearby Silver Spring, Md.
The cause was cardiac arrhythmia and pneumonia, his family said.
Dr. Kopp, who practiced in Washington for 35 years, wrote 17 books. Much of his writing was meant to guide readers in finding importance in their lives.
A book that got much attention was ''If You Meet the Buddha on the Road, Kill Him,'' published in 1972. Like many of the others, it was issued by Science and Behavior Books. In the book, Dr. Kopp analyzed the ways in which people sought to recognize significance and value in themselves, rather than rely on gurus. The book remains available from Bantam's New Age imprint.
''Back to One: A Practical Guide for Psychotherapists'' (1977), ''Even a Stone Can Be a Teacher'' (1985) and ''Blues Ain't Nothing but a Good Soul Feeling Bad: Daily Steps to Spiritual Growth'' (1992) are also in print. His other titles include ''The Naked Therapist'' (1976) and ''An End to Innocence'' (1978).
Dr. Kopp was born in the Bronx and graduated from Brooklyn College in 1951. He received a master's in 1953 and a doctorate in 1960 from the New School for Social Research, then interned and worked in New Jersey institutions and agencies.
He was a clinical psychologist and acting department head at Trenton State Hospital before going to Washington in 1961. He was the chief clinical psychologist in the District of Columbia Adult Mental Health Clinic before going into private practice.
Dr. Kopp is survived by his wife of 46 years, Marjorie Ice Kopp; three sons, Jonathan, of Novato, Calif., David, of Atlantic City, and Nicholas, of Germantown, Md., and four grandchildren.

Sheldon Kopp and books

http://en.wikipedia.org/wiki/Sheldon_Kopp


Guru: Metaphors from a Psychotherapist. Science & Behavior Books. 1971. ISBN 0831400250.
If you meet the Buddha on the road, kill him! The pilgrimage of psychotherapy patients. Lowe & Brydon (Printers) Ltd. 1974. ISBN 0-85969-022-9.
The Hanged Man. Science & Behavior Books. 1974. ISBN 0831400366.
No Hidden Meanings: An Illustrated Eschatological Laundry List. photography by Claire Flanders. Science and Behavior Books. 1975. ISBN 0831400439.
Naked Therapist - A Canterbury Tales collection of embarrassing moments from more than a dozen eminent psychotherapists. EdITS. 1976. ISBN 0912736186.
Back to One: A Practical Guide for Psychotherapists. Science and Behavior Books. 1977. ISBN 0831400552.
This Side of Tragedy: Psychotherapy as Theater. Science and Behavior Books. 1977. ISBN 0831400501.
An End to Innocence: Facing Life without Illusions. Macmillan. 1978. ISBN 0025664700.
What Took You so Long: An Assortment of Life's Everyday Ironies. photography by Claire Flanders. Science & Behavior Books. 1979. ISBN 0831400560.
Mirror, Mask, and Shadow: The Risk and Rewards of Self-acceptance. Macmillan. 1980. ISBN 0025664603.
The Pickpocket and the Saint: Free Play of the Imagination. Bantam. 1983. ISBN 0553235648.
Even a stone can be a teacher. Putnam's Sons. 1985. ISBN 0-87477-341-5.
Here I am, Wasn't I! The Inevitable Disruption of Easy Times. Bantam Books. 1986. ISBN 0-553-25424-3.
Who Am I Really?. Tarcher. 1987. ISBN 0874774292.
Raise Your Right Hand against Fear: Extend the Other in Compassion. 1988. ISBN 0896381552.
Rock, Paper, Scissors: Understanding the Paradoxes of Personal Power and Taking Charge of Our Lives. CompCare Publications. 1989. ISBN 0896381935.
All God's Children Are Lost, but Only a Few Can Play the Piano: Finding a Life That Is Truly Your Own. Simon & Schuster. 1991. ISBN 013026881X.
Blues ain't nothing but a good soul feeling bad. with Bonnie B. Hesse. Simon & Schuster. 1992. ISBN 0-671-76838-7.

choice theory

http://en.wikipedia.org/wiki/Choice_theory

William Glasser and his books

http://en.wikipedia.org/wiki/William_Glasser

http://www.realitytherapy.org.uk/

http://www.wglasser.com/

How to Set Boundaries in a Work Relationship

• Identify the players in the relationship.In the situation of a work relationship you may want to identify the company as a major player in the relationship. There may be company policies or standards of practice you need to consider before setting boundaries.
• Decide what you want out of the relationship.Boundaries can be set up for a couple of different reasons. Many people view boundaries as negative. They can be used in a very positive way. You can set up boundaries with a coworker to help you both stay focused while working instead of chatting all day. Boundaries can also be set to stop or prevent unwanted behavior. You need to set clear and concise boundaries. "We need to set aside a half our of our day to chat and not email each other randomly outside of that time period." Instead of saying, "You know, we talk too much, we should really focus on our work." This step sets specific criteria for your boundary.
• Communicate your expectations.Make sure you tell at least the main person in your relationship specifically what your boundary is. Remember to make sure you are detailed and concise.
• Follow through.One of the biggest mistakes made after a boundary is set is the lack of follow through. If you and your coworker decide to set a boundary where you only email each other during a certain time period throughout the day you need to make sure to follow through. This can be difficult to do since there will most likely be many times you have thoughts pop up throughout the day that you would love to share with this person. Discipline is the key to setting and keeping a successful boundary.

How to Set a Boundary

• To have healthy relationships with those in our lives, from co-workers to friends to spouses, it is important to have the ability to set boundaries. Setting boundaries with people is a proactive step toward personal health. There are many ways to set boundaries. This is one way to set boundaries with someone.
• Identify what is important for you before you set a boundary. People have individual needs, desires, wants, etc., so it is important to honor your personal needs and values while setting boundaries. For the purpose of this article, let's use the example of theft: A roommate is stealing money from you, you are angry, and want to set a boundary.
• When you feel that you are comfortable set a time to talk with the person with whom you need to set a boundary. You don't necessarily need to schedule a meeting, however it's important to talk when it feels safe to talk. Begin a conversation calmly, then lead into what you need to say.
• To set a boundary, use this basic sentence structure also known as a script: "If you ______. " Fill in the blank with a very specific description of the person's behavior that you need to set a boundary around. Theft example: "If you continue taking change from my coin jar then ____.""I will ______." Fill in the blank with the action you'll take if the boundary is violated. Your action is based on values and needs. Theft example: "I will put a lock on the bedroom door." "I will add the amount you take to your portion of the rent.""If you continue _____." Fill in the blank with actions you'll take to make sure the boundary is followed. Sometimes it isn't necessary to state this, but it depends on the circumstances and how you want to handle the situation.Theft example: "If you continue taking money, I'll will ask you to move out."
• Follow through on the boundary that you are setting. You must be willing to have the follow through because without it, the boundary will be worthless. They are not worth setting if you aren't willing to enforce them. You can change the wording of the above, but remember to be very specific and keep to the point.

How to Build Healthy Boundaries

Relationships are a beautiful thing but they can also be challenging. I love a cartoon that reads as follow: "Relationships: a mess worth making." It very well illustrates how many times relationships can be messy or unhealthy. The main cause of unhealthy relationships? Unhealthy boundaries. When talking about relationships we are talking about psychological boundaries. The dictionary defines a boundary as "Something that indicates a border or limit." If we do not know what they are, we cannot respect others boundaries and cannot enforce our own.Like a house or a country has boundaries, people have boundaries too. The basic rule to keep in mind is simple. I end where you begin and you end where I begin.Depression, co-dependency, anxiety, and a many other conditions can improve by creating and respecting our and other's personal boundaries. Here some steps for you to follow:

• Learn to say "no". It is ok to do things for others but like anything else in balance. Try to keep your needs in perspective as well.
• Move step by step into intimacy. There are people that after 2 or 3 weeks of meeting someone feel they can totally trust the person and revealed the most intimate secrets right away. That can lead you to enmeshment or resentment if the other person does not do the same. A healthy relationship needs time. Pace yourself.
• Learn who you are and what you want. Laura Stack says, "setting limits is a way of defining who you are and what you're all about, what you will do and what you won't; what's acceptable to you and what's not". It is ok to negotiate needs and be there for other people. The limit? Not all the time and not when it goes against your core values.
• Be proactive. Feeling like a victim or a martyr is a sign of weak boundaries. Learn to deal with the consequences of your actions and decisions. And do not take as yours other's people responsibilities.
• Assert yourself. Communicate your needs clearly and directly. People aren't mind readers. At the same time, if you ask for your needs and other people do not respond you need to take more extreme actions such as end the connection or remove yourself from the situation.
• Remember all you can change is yourself. When you start thinking if such and such did or didn't do "blank" everything would be fine, you are switching to rescue mood and setting yourself for failure and frustration. Start thinking, what you can do for yourself to either get what you need or to let go of the idea of convincing or changing the other person.
• Become your own loving parent. Recognize and accept that your needs won't always be met. Teach yourself to react as an adult while at the same time talking to yourself with gentleness, humor, love, and respect. If you don't do it, nobody else will.

How to Enforce Boundaries

• Once you have established the boundary you need in a relationship for it to be healthy you need to be consistent. Consistency is the key for people who deal with boundaryless individuals in their life. Over time, they will see your consistency.
• Be firm with what you desire in having healthy, respectable relationships. This is the step that requires steadfast will. Family members or close friends may give you resistance when you try to stay steadfast against their unhealthy patterns of trying to pull you in hundreds of directions emotionally, physically, or mentally, but stay true to what you desire and what you are trying to establish them. A health boundary is not easily established especially if its been years since living within healthy scenarios.
• Try to be patient when dealing with those around you who do not understand that your trying to establish a better way of life. Stick to your beliefs and how you want to live your life now that you recognize healthy boundaries are essentia

direct-to-consumer genetic testing companies

http://www.dnapolicy.org/news.release.php?action=detail&pressrelease_id=137

Let Go BEFORE You Know What Will Fill The Space

Waiting until you know what you want to do, what an end result will be or how something will work out before you let go doesn’t work. You must take the leap BEFORE you know. The good news is, once you do, new opportunities, resources and mentors will present themselves to you almost instantly.

The bigger the space you create by letting go, the more you’ll step forward powerfully and confidently into greater success, energy and purpose with your business.

Beike Biotech

http://www.beikebiotech.com/

stem cell china

http://www.stemcellschina.com/

learn something

"The best thing for being sad," replied Merlin, beginning to puff and blow,is to learn something. That's the only thing that never fails. You may grow old and trembling in your anatomies, you may lie awake at night listening to the disorder of your veins, you may miss your only love, you may see the world about you devastated by evil lunatics, or know your honor trampled in the sewers of baser minds. There is only one thing for it then-to learn. Learn why the world wags and what wags it. That is the only thing which the mind can never exhaust, never alienate, never be tortured by, never fear or distrust, and never dream of regretting. Learning is the onlything for you."
T.H. White, The Once and Future King

truth & perception

There is no truth. There is only perception. ~Gustave Flaubert

Stephen Hawking on ALS

I am quite often asked: How do you feel about having ALS?

The answer is, not a lot. I try to lead as normal a life as possible, and not think about my condition, or regret the things it prevents me from doing, which are not that many.

It was a great shock to me to discover that I had motor neurone disease. I had never been very well co-ordinated physically as a child. I was not good at ball games, and my handwriting was the despair of my teachers. Maybe for this reason, I didn't care much for sport or physical activities.

But things seemed to change when I went to Oxford, at the age of 17. I took up coxing and rowing. I was not Boat Race standard, but I got by at the level of inter-College competition. In my third year at Oxford, however, I noticed that I seemed to be getting more clumsy, and I fell over once or twice for no apparent reason. But it was not until I was at Cambridge, in the following year, that my father noticed, and took me to the family doctor. He referred me to a specialist, and shortly after my 21st birthday, I went into hospital for tests. I was in for two weeks, during which I had a wide variety of tests. They took a muscle sample from my arm, stuck electrodes into me, and injected some radio opaque fluid into my spine, and watched it going up and down with x-rays, as they tilted the bed. After all that, they didn't tell me what I had, except that it was not multiple sclerosis, and that I was an a-typical case. I gathered, however, that they expected it to continue to get worse, and that there was nothing they could do, except give me vitamins. I could see that they didn't expect them to have much effect. I didn't feel like asking for more details, because they were obviously bad. The realisation that I had an incurable disease, that was likely to kill me in a few years, was a bit of a shock.

How could something like that happen to me? Why should I be cut off like this? However, while I had been in hospital, I had seen a boy I vaguely knew die of leukaemia, in the bed opposite me. It had not been a pretty sight. Clearly there were people who were worse off than me. At least my condition didn't make me feel sick.

Whenever I feel inclined to be sorry for myself I remember that boy. Not knowing what was going to happen to me, or how rapidly the disease would progress, I was at a loose end. The doctors told me to go back to Cambridge and carry on with the research I had just started in general relativity and cosmology. But I was not making much progress, because I didn't have much mathematical background. And, anyway, I might not live long enough to finish my PhD. I felt somewhat of a tragic character. I took to listening to Wagner, but reports in magazine articles that I drank heavily are an exaggeration. The trouble is once one article said it, other articles copied it, because it made a good story. People believe that anything that has appeared in print so many times must be true. My dreams at that time were rather disturbed.

Before my condition had been diagnosed, I had been very bored with life. There had not seemed to be anything worth doing. But shortly after I came out of hospital, I dreamt that I was going to be executed. I suddenly realised that there were a lot of worthwhile things I could do if I were reprieved. Another dream, that I had several times, was that I would sacrifice my life to save others. After all, if I were going to die anyway, it might as well do some good. But I didn't die. In fact, although there was a cloud hanging over my future, I found, to my surprise, that I was enjoying life in the present more than before. I began to make progress with my research, and I got engaged to a girl called Jane Wilde, whom I had met just about the time my condition was diagnosed. That engagement changed my life. It gave me something to live for. But it also meant that I had to get a job if we were to get married. I therefore applied for a research fellowship at Gonville and Caius (pronounced Keys) college, Cambridge. To my great surprise, I got a fellowship, and we got married a few months later. The fellowship at Caius took care of my immediate employment problem.

I was lucky to have chosen to work in theoretical physics, because that was one of the few areas in which my condition would not be a serious handicap. And I was fortunate that my scientific reputation increased, at the same time that my disability got worse. This meant that people were prepared to offer me a sequence of positions in which I only had to do research, without having to lecture. We were also fortunate in housing. When we were married, Jane was still an undergraduate at Westfield College in London, so she had to go up to London during the week. This meant that we had to find somewhere I could manage on my own, and which was central, because I could not walk far. I asked the College if they could help, but was told by the then Bursar: it is College policy not to help Fellows with housing. We therefore put our name down to rent one of a group of new flats that were being built in the market place. (Years later, I discovered that those flats were actually owned by the College, but they didn't tell me that.)

However, when we returned to Cambridge from a visit to America after the marriage, we found that the flats were not ready. As a great concession, the Bursar said we could have a room in a hostel for graduate students. He said, "We normally charge 12 shillings and 6 pence a night for this room. However, as there will be two of you in the room, we will charge 25 shillings." We stayed there only three nights. Then we found a small house about 100 yards from my university department. It belonged to another College, who had let it to one of its fellows. However he had moved out to a house he had bought in the suburbs. He sub-let the house to us for the remaining three months of his lease. During those three months, we found that another house in the same road was standing empty. A neighbour summoned the owner from Dorset, and told her that it was a scandal that her house should be empty, when young people were looking for accommodation. So she let the house to us. After we had lived there for a few years, we wanted to buy the house, and do it up. So we asked my College for a mortgage. However, the College did a survey, and decided it was not a good risk. In the end we got a mortgage from a building society, and my parents gave us the money to do it up. We lived there for another four years, but it became too difficult for me to manage the stairs. By this time, the College appreciated me rather more, and there was a different Bursar. They therefore offered us a ground floor flat in a house that they owned. This suited me very well, because it had large rooms and wide doors. It was sufficiently central that I could get to my University department, or the College, in my electric wheel chair. It was also nice for our three children, because it was surrounded by garden, which was looked after by the College gardeners. Up to 1974, I was able to feed myself, and get in and out of bed. Jane managed to help me, and bring up the children, without outside help. However, things were getting more difficult, so we took to having one of my research students living with us. In return for free accommodation, and a lot of my attention, they helped me get up and go to bed. In 1980, we changed to a system of community and private nurses, who came in for an hour or two in the morning and evening. This lasted until I caught pneumonia in 1985. I had to have a tracheotomy operation. After this, I had to have 24 hour nursing care. This was made possible by grants from several foundations. Before the operation, my speech had been getting more slurred, so that only a few people who knew me well, could understand me. But at least I could communicate. I wrote scientific papers by dictating to a secretary, and I gave seminars through an interpreter, who repeated my words more clearly. However, the tracheotomy operation removed my ability to speak altogether. For a time, the only way I could communicate was to spell out words letter by letter, by raising my eyebrows when someone pointed to the right letter on a spelling card. It is pretty difficult to carry on a conversation like that, let alone write a scientific paper. However, a computer expert in California, called Walt Woltosz, heard of my plight. He sent me a computer program he had written, called Equalizer. This allowed me to select words from a series of menus on the screen, by pressing a switch in my hand. The program could also be controlled by a switch, operated by head or eye movement. When I have built up what I want to say, I can send it to a speech synthesizer. At first, I just ran the Equalizer program on a desk top computer.However David Mason, of Cambridge Adaptive Communication, fitted a small portable computer and a speech synthesizer to my wheel chair. This system allowed me to communicate much better than I could before. I can manage up to 15 words a minute. I can either speak what I have written, or save it to disk. I can then print it out, or call it back and speak it sentence by sentence. Using this system, I have written a book, and dozens of scientific papers. I have also given many scientific and popular talks. They have all been well received. I think that is in a large part due to the quality of the speech synthesiser, which is made by Speech Plus. One's voice is very important.

If you have a slurred voice, people are likely to treat you as mentally deficient: Does he take sugar? This synthesiser is by far the best I have heard, because it varies the intonation, and doesn't speak like a Dalek. The only trouble is that it gives me an American accent. I have had motor neurone disease for practically all my adult life. Yet it has not prevented me from having a very attractive family, and being successful in my work. This is thanks to the help I have received from Jane, my children, and a large number of other people and organisations. I have been lucky, that my condition has progressed more slowly than is often the case. But it shows that one need not lose hope.

Disease Cause Is Pinpointed With Genome

http://www.nytimes.com/2010/03/11/health/research/11gene.html
By NICHOLAS WADEPublished: March 10, 2010
Two research teams have independently decoded the entire genome of patients to find the exact genetic cause of their diseases. The approach may offer a new start in the so far disappointing effort to identify the genetic roots of major killers like heart disease, diabetes and Alzheimer¡¦s.
Dr. James R. Lupski, a medical geneticist with a nerve disease, had his whole genome decoded.
An Inherited DiseaseIn the decade since the first full genetic code of a human was sequenced for some $500 million, less than a dozen genomes had been decoded, all of healthy people.
Geneticists said the new research showed it was now possible to sequence the entire genome of a patient at reasonable cost and with sufficient accuracy to be of practical use to medical researchers. One subject¡¦s genome cost just $50,000 to decode.
¡§We are finally about to turn the corner, and I suspect that in the next few years human genetics will finally begin to systematically deliver clinically meaningful findings,¡¨ said David B. Goldstein, a Duke University geneticist who has criticized the current approach to identifying genetic causes of common diseases.
Besides identifying disease genes, one team, in Seattle, was able to make the first direct estimate of the number of mutations, or changes in DNA, that are passed on from parent to child. They calculate that of the three billion units in the human genome, 60 per generation are changed by random mutation ¡X considerably less than previously thought.
The three diseases analyzed in the two reports, published online Wednesday, are caused by single, rare mutations in a gene.
In one case, Richard A. Gibbs of the Baylor College of Medicine sequenced the whole genome of his colleague Dr. James R. Lupski, a prominent medical geneticist who has a nerve disease, Charcot-Marie-Tooth neuropathy.
In the second, Leroy Hood and David J. Galas of the Institute for Systems Biology in Seattle have decoded the genomes of two children with two rare genetic diseases, and their parents.
More common diseases, like cancer, are thought to be caused by mutations in several genes, and finding the causes was the principal goal of the $3 billion human genome project. To that end, medical geneticists have invested heavily over the last eight years in an alluring shortcut.
But the shortcut was based on a premise that is turning out to be incorrect. Scientists thought the mutations that caused common diseases would themselves be common. So they first identified the common mutations in the human population in a $100 million project called the HapMap. Then they compared patients¡¦ genomes with those of healthy genomes. The comparisons relied on ingenious devices called SNP chips, which scan just a tiny portion of the genome. (SNP, pronounced ¡§snip,¡¨ stands for single nucleotide polymorphism.) These projects, called genome-wide association studies, each cost around $10 million or more.
The results of this costly international exercise have been disappointing. About 2,000 sites on the human genome have been statistically linked with various diseases, but in many cases the sites are not inside working genes, suggesting there may be some conceptual flaw in the statistics. And in most diseases the culprit DNA was linked to only a small portion of all the cases of the disease. It seemed that natural selection has weeded out any disease-causing mutation before it becomes common.
The finding implies that common diseases, surprisingly, are caused by rare, not common, mutations. In the last few months, researchers have begun to conclude that a new approach is needed, one based on decoding the entire genome of patients.
The new reports, though involving only single-gene diseases, suggest that the whole-genome approach can be developed into a way of exploring the roots of the common multigene diseases.
¡§We need a way of assessing rare variants better than the genomewide association studies can do, and whole-genome sequencing is the only way to do that,¡¨ Dr. Lupski said.
With 10 genomes of healthy humans sequenced, Dr. Gibbs, a specialist in DNA sequencing, decided it was time to decode the genome of someone with a genetic disease and asked his colleague Dr. Lupski to volunteer.
Mutations in any of 39 genes can cause Charcot-Marie-Tooth, a disease that impairs nerves to the hands and feet and causes muscle weakness.
Fifty thousand dollars later, Dr. Lupski turned out to have mutations in an obscure gene called SH3TC2. The copy of the gene he inherited from his father is mutated in one place, and the copy from his mother in a second.
Both his parents had one good copy of the gene in addition to the mutated one. A single good copy can generate enough, or nearly enough, of the gene¡¦s product for the nerves to work properly. Dr. Lupski¡¦s mother was free of the disease and his father had only mild symptoms.
In the genetic lottery that is human procreation, two of their eight children inherited good copies of SH3TC2 from each parent; two inherited the mother¡¦s mutation but the father¡¦s good copy and are free of the disease; and four siblings including Dr. Lupski inherited mutated copies from both parents. These four all have Charcot-Marie-Tooth disease. The results are reported in The New England Journal of Medicine.
In Seattle, Dr. Hood and Dr. Galas have also applied whole-genome sequencing to disease. They analyzed the genome of a family of four, in which the two children each have two single-gene diseases, called Miller syndrome and ciliary dyskinesia. With four related genomes available, the researchers could identify the causative genes. They also improved the accuracy of the sequencing because DNA changes that did not obey Mendel¡¦s rules of inheritance could be classed as errors in the decoding process.
The Seattle team believes whole-genome sequencing can be applied to the study of the common multigene diseases and plans to sequence more than 100 genomes next year, starting with multigenerational families.
The family whose genomes they report in Science were sequenced by a company with a new DNA sequencing method, Complete Genomics of Mountain View, Calif., at a cost of $25,000 each. Clifford Reid, the chief executive, said that the company was scaling up to sequence 500 genomes a month and that for large projects the price per genome would soon drop below $10,000. ¡§We are on our way to the $5,000 genome,¡¨ he said.
Dr. Reid said the HapMap and genomewide association studies were not a mistake but ¡§the best we could do at the time.¡¨ But they have not yet revolutionized medicine, ¡§which we are on the verge of doing,¡¨ he said.
Dr. Goldstein, of Duke University, said the whole-genome sequencing approach that was now possible should allow rapid progress. ¡§I think we are finally headed where we have long wanted to go,¡¨ he said.

Whole-Genome Sequencing in a Patient with Charcot¡VMarie¡VTooth Neuropathy

http://content.nejm.org/cgi/content/full/NEJMoa0908094
ABSTRACT
Background Whole-genome sequencing may revolutionize medical diagnostics through rapid identification of alleles that cause disease. However, even in cases with simple patterns of inheritance and unambiguous diagnoses, the relationship between disease phenotypes and their corresponding genetic changes can be complicated. Comprehensive diagnostic assays must therefore identify all possible DNA changes in each haplotype and determine which are responsible for the underlying disorder. The high number of rare, heterogeneous mutations present in all humans and the paucity of known functional variants in more than 90% of annotated genes make this challenge particularly difficult. Thus, the identification of the molecular basis of a genetic disease by means of whole-genome sequencing has remained elusive. We therefore aimed to assess the usefulness of human whole-genome sequencing for genetic diagnosis in a patient with Charcot¡VMarie¡VTooth disease.
Methods We identified a family with a recessive form of Charcot¡VMarie¡VTooth disease for which the genetic basis had not been identified. We sequenced the whole genome of the proband, identified all potential functional variants in genes likely to be related to the disease, and genotyped these variants in the affected family members.
Results We identified and validated compound, heterozygous, causative alleles in SH3TC2 (the SH3 domain and tetratricopeptide repeats 2 gene), involving two mutations, in the proband and in family members affected by Charcot¡VMarie¡VTooth disease. Separate subclinical phenotypes segregated independently with each of the two mutations; heterozygous mutations confer susceptibility to neuropathy, including the carpal tunnel syndrome.
Conclusions As shown in this study of a family with Charcot¡VMarie¡VTooth disease, whole-genome sequencing can identify clinically relevant variants and provide diagnostic information to inform the care of patients.
----------------------------------------------------------The practice of medical genetics requires gene-specific analyses of DNA sequences and mutations to definitively diagnose disease, provide prognostic information, and guide genetic counseling regarding the risk of recurrence. Studies of autosomal recessive traits such as cystic fibrosis1 and some dominant traits such as neurofibromatosis type 12 revealed the role of single "disease genes" in conveying traits. However, many phenotypes of mendelian diseases (see the Glossary) are genetically heterogeneous: causative mutations have been identified in more than 100 genes for deafness and retinitis pigmentosa, for instance. Moreover, specific mutations may confer phenotypes that segregate as dominant, recessive, or even digenic3 or triallelic4 traits. There is also ample evidence of modifying loci in mendelian disorders.5,6 Thus, even when there are simple patterns of inheritance in syndromes with a well-characterized pathologic course, the underlying mutational events, which need to be resolved for precise molecular diagnosis, within individual families may be complex. Charcot¡VMarie¡VTooth disease is an inherited peripheral neuropathy with two forms: a demyelinating form (type 1) affecting the glia-derived myelin and an axonal form (type 2) affecting the nerve axon. The two forms can be distinguished by means of electrophysiological or neuropathological studies. Charcot¡VMarie¡VTooth disease has been used as a model disease to describe genetic heterogeneity, posit the relation of hereditary pattern to clinical severity, and investigate the relative importance of principal and modifying genes in determining human diseases.7,8 Mutant alleles underlying Charcot¡VMarie¡VTooth disease can segregate in an autosomal dominant, recessive, or X-linked manner (Figure 1). Both single-base variants (single-nucleotide polymorphisms [SNPs]) and copy-number variants,10 at 39 separate loci, confer susceptibility to Charcot¡VMarie¡VTooth disease. Most of these susceptibility variants cause dominant forms of the disease, although mutations in genes at 14 of the loci cause recessive disease.
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Figure 1. Charcot¡VMarie¡VTooth (CMT) Disease Phenotypes, Their Genetic Forms of Inheritance, and Their Mapped Genes and Loci.CMT is divided in two major phenotypic types ¡X glial myelinopathy (CMT type 1) and neuronal axonopathy (CMT type 2) ¡X according to electrophysiological, clinical, and nerve-biopsy evaluations. Each type can be inherited in a dominant, recessive, or X-linked fashion. There are also autosomal dominant intermediate forms of CMT that can have features of both axonal and demyelinating neuropathies. Several genes have been associated with CMT disease to date, and other loci have been associated and mapped but their genes not yet identified. MPZ, GDAP1, and GJB1 are known to be associated with CMT type 1, but select mutations in these genes can also cause CMT type 2; NEFL is known to be associated with CMT type 2, but select mutations convey a CMT type 1 phenotype. Dominant intermediate forms of CMT have been reported to be associated with MPZ mutations. Specific recessive alleles related to CMT have also been reported for EGR2 and PMP22. Of the 31 genes in 39 known CMT loci, only 15 genes are currently available for clinical testing. Current evidence-based clinical guidelines for distal symmetric polyneuropathy recommend genetic testing consisting of screening for common mutations, including the CMT1A duplication copy-number variant and point mutations of the X-linked GJB1 gene.9
Adult-onset Charcot¡VMarie¡VTooth disease is highly variable in presentation but is characterized by distal symmetric polyneuropathy,9 with slowly progressive distal muscle weakness and atrophy (particularly peroneal muscular atrophy) resulting in foot dorsiflexor weakness, foot drop, and secondary steppage gait. Pes cavus (highly arched feet) or pes planus (flat feet) occurs in most patients.
We applied next-generation-sequencing methods to identify the cause of disease in a family with inherited neuropathy that had been previously screened, with negative results, for alterations of some common Charcot¡VMarie¡VTooth genes, including PMP22,11 MPZ, PRX, GDAP1, and EGR2.
Methods
Study Participants
The study family consisted of four affected siblings, four unaffected siblings, and an unaffected mother and father, all of whom provided written informed consent for participation in the study. The study was approved by the institutional review board at Baylor College of Medicine. The diagnosis of Charcot¡VMarie¡VTooth type 1 disease in the proband and the three affected siblings was based on the results of physical examination (distal muscle weakness and wasting, pes cavus, and absence of deep-tendon reflexes) and electrophysiological studies.
Neurophysiological Assessments
Neurophysiological studies consisted of a standard battery of nerve-conduction studies, including motor responses of the median, ulnar, tibial, and peroneal nerves with F-wave latencies; orthodromic median-, ulnar-, and sural-nerve sensory potentials; and bilateral tibial H-reflexes. When these studies revealed demyelinating features, tests of blink reflexes were generally performed. Limbs were warmed to a temperature of at least 32¢XC in all instances. Demyelination was judged to be present if conduction velocities were significantly slowed and the late-response latencies were substantially delayed. Median-nerve mononeuropathy at the wrist was judged to be present when there was prolonged motor terminal latency or slowed median-nerve sensory velocity with disproportionate slowing in the palm-to-wrist segment, or both. The four affected subjects, all of whom had diffuse slowing of conduction, were also thought to have a median-nerve mononeuropathy at the wrist, since the median-nerve motor terminal latency was much more prolonged than the ulnar-nerve motor terminal latency (14.9 vs. 8.1, 10.2 vs. 7.5, 11.6 vs. 6.2, and 9.2 vs. 6.2 msec) (Table 1).
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Table 1. Neurophysiological Findings in the Study Family.

DNA Sequence Analysis
DNA sequencing was performed with the use of the SOLiD (Sequencing by Oligonucleotide Ligation and Detection) system (Applied Biosystems), a next-generation-sequencing platform that involves ligation-based sequencing and a two-base encoding method in which four fluorescent dyes are used to tag various combinations of dinucleotides. Its accuracy in sequencing 50-base reads is estimated at approximately 99.94%.12 Multiple sequences can be read simultaneously, and when the sequence reads overlap, the overall accuracy increases further, reducing the risk of false positive determinations and the need for additional data validation. We determined bases from the primary sequencing data, using the standard SOLiD analysis software. (For details, see the Supplementary Appendix, available with the full text of this article at NEJM.org.)
Array-Based Comparative Genomic Hybridization
For array-based comparative genomic hybridization and analysis of the copy-number variants in the proband as compared with those in a male control, we used a 1-million-probe high-resolution oligonucleotide whole-genome array (Agilent), a 2.1-million-oligonucleotide whole-genome array (NimbleGen), and a 44,000-oligonucleotide array (Agilent) that was custom-designed to assay genes previously implicated in inherited neuropathy. Analysis of the copy-number variants was performed according to the manufacturer's instructions and software.
Bioinformatic Analysis of SNP Variants
Analysis of SNP variants and cross-referencing of them with the Human Gene Mutation Database (www.hgmd.cf.ac.uk), the Online Mendelian Inheritance in Man database (www.ncbi.nlm.nih.gov/omim), and the PolyPhen database (http://genetics.bwh.harvard.edu/pph/data, based on the National Center for Biotechnology Information [NCBI] dbSNP, build 126) were performed with the use of Perl scripts. Alignment of the orthologous SH3TC2 (SH3 domain and tetratricopeptide repeats 2) proteins was performed with the use of the ClustalW program and reference SH3TC2 proteins from the following organisms: human (accession number, NP_078853 [GenBank] ), chimpanzee (XP_527069), macaque (XP_001104761), dog (XP_546315), horse (XP_001501607), cow (XP_616288), mouse (NP_766216 [GenBank] ), rat (XP_225887), opossum (XP_001380773), and chicken (XP_424256).
Segregation Analysis
Exons 5 and 11 of the SH3TC2 gene were amplified by means of a polymerase-chain-reaction (PCR) assay and directly sequenced in all members of the study family. To verify the Arg954ter amino acid mutation (R954X), corresponding to a GA mutation in the genomic DNA in exon 11 of SH3TC2 on chromosome 5 at nucleotide 148,386,628, we also generated a 312-bp PCR fragment and incubated it with the restriction enzyme TaqI; the nucleotide mutation results in elimination of the restriction site for TaqI.
Results
Nerve-Conduction Studies
In addition to the Charcot¡VMarie¡VTooth type 1 phenotype that segregates as a recessive trait, we identified through electrophysiological means an axonal neuropathy in one parent and one grandparent of the proband. Further evidence of a subtle phenotype evidenced by, at a minimum, median-nerve mononeuropathy at the wrist was also observed among all the proband's grandparents and both parents but had an unclear pattern of inheritance. Its variable presentation (Table 1) included three neurophysiologically defined phenotypes: a normal phenotype with superimposed severe median-nerve mononeuropathy at the wrist, thought to be an incidental finding in an 80-year-old man who had been a carpenter for more than 50 years (Subject I-1), a mild median-nerve mononeuropathy at the wrist (the proband's maternal grandmother and mother [Subject II-1]), and a more severe median-nerve mononeuropathy at the wrist associated with evidence of a more widespread axonal polyneuropathy (Subjects I-2 and II-2). The latter phenotype is similar to that of patients with hereditary neuropathy with liability to pressure palsies (Online Mendelian Inheritance in Man number, 162500 [OMIM] ), a disorder pathologically characterized by patchy myelin abnormalities and attributed to haploinsufficiency of PMP22 (as a consequence of genomic deletion)13; duplication of PMP22 causes Charcot¡VMarie¡VTooth type 1A disease, the most common form.14
Genome Variation
The sequencing of DNA samples obtained from the proband produced a mappable yield of 89.6 Gb of sequence data, representing an average depth of coverage of approximately 30 times per base. The data from sequential machine runs consisted of 8.3 Gb of 35-bp fragment sequence reads (one run), 30.3 Gb of 25-bp mate-pair sequence reads (two runs), and 51.0 Gb of 50-bp mate-pair sequence reads (one run).
We identified the differences between the consensus sequence of the proband and the human genome reference sequence. These were used to produce a list of putative single-base DNA substitutions, small insertions, and deletions and potential changes in DNA copy number. This list of variants included 3,420,306 SNPs. A total of 2,255,102 of the SNPs were in extragenic regions and 1,165,204 SNPs were within gene regions, including introns, promoters, 3' and 5' untranslated regions, and splice sites (Table 2). Of the intragenic SNPs, 9069 were nonredundant SNPs predicted to result in nonsynonymous codon changes, and 121 of the 9069 were nonsense mutations. The approximately 3.4 million SNPs identified represent about 0.1% of the reference haploid human genome,15 and both the total number of SNPs and the number of novel SNPs are similar to those discovered in other diploid genome sequences for individual subjects (Table 3).12,16,17,18,19,20,21 Of the more than 3.4 million SNPs, 2,858,587 were present in public databases and 561,719 were novel (Table 3). Data on the sequence reads, quality, and mapping have been deposited in the NCBI Sequence Read Archive (www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?) (accession number, SRP001734); variant data have been deposited in the dbSNP database.
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Table 2. SNPs Identified through Whole-Genome Sequencing of DNA from the Proband.

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Table 3. Individual Human Genomes Sequenced to Date.

We used two approaches to identifying copy-number variation: array-based comparative genomic hybridization and mate-pair sequencing. We identified 234 copy-number variants ranging in size from 1690 bp to 1,627,813 bp. Of these 234 variants, 132 were confirmed by at least one other method (Table 1 in the Supplementary Appendix); 220 of the 234 (94%) overlap with reported regions of copy-number variants in the Database of Genomic Variants (http://projects.tcag.ca/variation). We found no copy-number variants affecting genes known to be involved in Charcot¡VMarie¡VTooth disease or other neuropathies.
We cross-referenced the nonsynonymous SNPs that we detected by using whole-genome sequencing with a database of previously observed mutations implicated in human disease (the Human Gene Mutation database) (Table 4, and Table 2 in the Supplementary Appendix). Of the 174 nonsynonymous database SNPs identified in the proband, 159 had a clear association with a heritable trait (i.e., the database entry was not annotated with a question mark). Of these, 21 (13%) were described as causing mendelian disease; 16 were heterozygous in the proband, a finding that is consistent with the expected load of autosomal recessive mutations. The other five SNPs might have been erroneously assigned as disease mutations, which would explain why four of them were homozygous in the proband and have been found to be homozygous in unaffected persons. It would also explain why the sequence for the proband, who did not have adrenoleukodystrophy, contained a SNP in ABCD1 previously described as a dominant mutation that causes the X-linked disorder adrenoleukodystrophy.22 An alternative to the interpretation that the five SNPs might have been erroneously assigned as disease mutations is that these alleles might have reduced penetrance.
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Table 4. Disease and Trait Associations of Nonsynonymous SNPs Identified in the Proband, According to the Human Gene Mutation Database.

We examined the putative mutations in 40 genes known to cause or be linked to neuropathic or related conditions (Table 3 in the Supplementary Appendix). This exercise led to closer examination of 3148 putative SNPs, including 54 coding SNPs. Of these 54, 2 were at the SH3TC2 locus ¡X 1 missense mutation (identified at 7.7 average depth coverage) and 1 nonsense mutation (identified at 29.9 average depth coverage) (Fig. 1 in the Supplementary Appendix). Mutations in this locus have previously been found to be associated with Charcot¡VMarie¡VTooth type 4C disease, described in families of eastern European, Turkish or Spanish Gypsy origin.23,24,25 The R954X nonsense mutation has previously been implicated in Charcot¡VMarie¡VTooth disease; the missense mutation (AG, occurring on chromosome 5 at nucleotide 148,402,474 and corresponding to the amino acid mutation Tyr169His [Y169H]) is novel.
Correlation between Genotype and Phenotype
Segregation analyses verified independent maternal and paternal origins of the mutations (Figure 2). The nonsense mutation (R954X) appeared in one parent of the proband and in two siblings who did not have Charcot¡VMarie¡VTooth type 1 disease. The missense mutation (Y169H) was found in one parent and one grandparent, neither of whom had Charcot¡VMarie¡VTooth disease. Only the proband (Subject III-4) and three of his siblings (Subjects III-2, III-6, and III-8) who had inherited both mutant alleles had the Charcot¡VMarie¡VTooth type 1 phenotype (Figure 2).
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Figure 2. Pedigree of the Study Family and Segregation and Conservation of SH3TC2 Mutations.Panel A shows the pedigree of the proband (arrow) and his family and their SH3TC2 genotypes: plus signs indicate the wild-type allele; Y169H indicates the AG mutation on chromosome 5 at nucleotide 148,402,474 and corresponding to the amino acid missense mutation Tyr169His, and R954X indicates the GA mutation in the genomic DNA in exon 11 of SH3TC2 on chromosome 5 at nucleotide 148,386,628, leading to the amino acid nonsense mutation Arg954ter. (Genomic coordinates for the mutations in the proband are based on the human genome reference sequence, build 36.2.) Squares indicate male subjects, and circles female subjects; slashes indicate deceased subjects. Subjects in generations I and II had three phenotypes. The paternal grandfather (Subject I-1) was studied 20 years ago, at 80 years of age, and had normal results, with the sole exception of a median-nerve mononeuropathy at the wrist, thought to be caused by his occupation as a carpenter. The paternal grandmother (Subject I-2, 77 years of age at the time of evaluation) and the father (Subject II-2) had evidence of a patchy axonal polyneuropathy, with definite median-nerve mononeuropathy at the wrist. The maternal grandmother (evaluated at 90 years of age; data not shown) and the mother (Subject II-1) had normal findings except for very mild median-nerve mononeuropathy at the wrist. Two of the proband's sisters (Subjects III-3 and III-7) had this same phenotype. Two members of this generation had completely normal findings (Subjects III-1 and III-5). The other four siblings had diffuse, disproportionate conduction slowing in the distal median nerve, without evidence of conduction block, findings that are suggestive of a superimposed median mononeuropathy at the wrist. Subjects III-2, III-4, III-6, and III-8 had Charcot¡VMarie¡VTooth type 1 (CMT1) disease. Panel B shows the results of TaqI restriction digestion of the SH3TC2 exon 11 polymerase-chain-reaction product on which the GA mutation, corresponding to the R954X allele, occurs. This mutation was present in the proband's mother and six of the eight siblings, as well as in the maternal grandmother (not shown). The mutation destroys the restriction site for TaqI; the wild type yields two small bands and the heterozygous mutant yields three bands, the upper of which is the uncut DNA. Panel C shows sequence alignment of the SH3TC2 protein among various species. The downward arrowhead indicates the location of the highly conserved Tyr169 amino acid that, in persons with the novel missense mutation Y169H, is changed to His. Sequences were obtained from the National Center for Biotechnology Information.
The subjects with the heterozygous missense mutation (Y169H) (Subjects I-2 and II-2) (Figure 2) also had the apparently dominant axonal neuropathy phenotype, as detected by electrophysiological studies. These findings of axonal neuropathy (Table 1) suggest a gain of function (i.e., a toxic effect) of this mutation. In contrast, the presumed loss-of-function nonsense variant (R954X) was associated with electrophysiological evidence of the carpal tunnel syndrome, regardless of whether it was the sole mutation present (i.e., heterozygous genotype) or was accompanied by the missense variant (Y169H) (i.e., compound heterozygous genotype) (Table 1 and Figure 2).
Discussion
We ascertained the molecular basis of an inherited disease by using next-generation-sequencing methods. We chose whole-genome sequencing over targeted, exon-capture approaches26,27 because we did not know whether the "causative" mutations would reside in known coding elements, and targeted approaches are ill suited to capturing copy-number variants. The heterogeneity of our sequence data is emblematic of the current rapid progress of sequencing technology: over the 6-month course of this study, sequence read lengths doubled (from 25 bp to 50 bp), the density of samples on the sequencing slide increased, and mapping technology improved. Overall, the sequence yield increased by a factor of three, with no appreciable increase in expense. This rapid pace of technological improvement makes it difficult to accurately determine the expense of repeating this experiment, but given that the expense of sequencing reagents for a single run on the SOLiD instrument was $25,000 in April 2009, we estimate that the entire effort would currently cost less than $50,000.
The whole-genome sequencing approach used in this proband enabled us to identify the cause of his disease as compound heterozygous mutations in the SH3TC2 gene and thus to delineate the specific biologic basis of disease in his family. The SH3TC2 protein contains both SH3 and TPR motifs; SH3 motifs mediate the assembly of protein complexes binding to proline-rich proteins, and TPR motifs are involved in protein¡Vprotein interactions.
The mouse orthologue of SH3TC2 is specifically expressed in Schwann cells, and the SH3TC2 protein localizes to the plasma membrane and to the perinuclear endocytic recycling compartment, which is consistent with a role in myelination or in axon¡Vglia interactions.28 Mice lacking Sh3tc2 have abnormal organization of the node of Ranvier.28 Consistent with a role of SH3TC2 in endocytic processes29 is the finding that SH3TC2 mutations result in disruption of the endocytic and membrane recycling pathways.30
We observed that both of the SH3TC2 mutations, when heterozygous, have phenotypic consequences that can be detected by electrophysiological means. The Y169H missense variant segregates with an axonal neuropathy, whereas the nonsense R954X mutation is associated with subclinical evidence of the carpal tunnel syndrome; therefore, haploinsufficiency of SH3TC2 may cause susceptibility to the carpal tunnel syndrome. This susceptibility may also result from mutations in other genes related to Charcot¡VMarie¡VTooth disease in addition to PMP22 and SH3TC2. Whole-genome sequencing of other members of the proband's family might help clarify whether the additional 69 SNPs at the SH3TC2 locus and 3146 SNPs at the other 39 neuropathy-associated gene loci examined (including many rare variants, 466 of which have not previously been described [Table 3 in the Supplementary Appendix]) can modify the highly penetrant Y169H and R954X mutations and thereby influence the neuropathy phenotype.
The whole-genome sequencing approach that we describe here contrasts with other diagnostic approaches. A clinical-testing panel that screens for a copy-number variant that commonly causes Charcot¡VMarie¡VTooth disease14 and nucleotide-sequence variants in 15 of the genes known to be mutated in patients with the disease can cost more than $15,000.31 Mutations in two or more genes related to Charcot¡VMarie¡VTooth disease have been described as causing a phenotype more severe than that of our proband or other patients affected by the disease.32,33,34 Such groups of mutations include a combination of two SNPs at the ACBD1 locus and a copy-number variant affecting PMP22, as well as the combination of a SNP and a copy-number variant at the same locus.35,36 There is also a report of mutations in two genes related to Charcot¡VMarie¡VTooth disease segregating in the same family as either a recessive trait or a sporadic trait, the latter of which was attributed to a de novo copy-number variant.37 Given this locus heterogeneity, with evidence of a mutational load that has clinical consequences, as well as the ease of use and accuracy of the whole-genome sequencing methods we applied, clinical and genetics experts struggling to explain poorly understood high-penetrance genetic diseases can now seriously consider this approach for illuminating the molecular causes of these diseases. The approach may ultimately contribute to the care of patients and families living with such diseases.
Our results suggest that haploinsufficiency of SH3TC2 confers predisposition to a mild polyneuropathy with particular susceptibility to the carpal tunnel syndrome. More generally, they demonstrate the diagnostic power of whole-genome sequencing in the context of genetically heterogeneous mendelian disease and inform efforts to decipher the genetic bases of complex traits. As new, rare alleles at other gene loci are implicated in conditions such as diabetes, obesity, heart disease, and cancer and as the patterns of interaction of the alleles with a patient's phenotype are delineated, genetic susceptibility to such diseases may become clearer. As a practical matter, the identification of rare, heterogeneous alleles by means of whole-genome sequencing may be the only way to definitively determine genetic contributions to the associated clinical phenotypes.
Glossary
Array-based comparative genomic hybridization: A hybridization method for detecting copy-number variations in DNA samples from a patient as compared with a control sample. The method provides higher resolution than cytogenetic methods but lower resolution than sequencing methods.
Average depth of coverage: The average number of times each base in the genome was sequenced, as a function of the distribution and number of sequence reads that map to the reference genome.
Coding single-nucleotide polymorphisms: Single DNA-base changes that occur in the coding regions of genes.
Copy-number variation: DNA changes that involve sequences of more than 100 bp, larger than single-nucleotide changes or microsatellites, and that vary in their number of copies among individual persons. These variants can be benign and polymorphic, but some can cause disease.
DNA template: An individual fragment of DNA that is available for sequencing.
Exon capture: Methods for isolating and sequencing gene exons, to the exclusion of the remainder of the genome. The DNA templates from exons are "captured" with the use of probes complementary to the targeted exon sequences. After capture, the targeted DNA is eluted and sequenced. The cost of exon capture can be 10 to 50% lower than that of whole-genome sequencing, although the method is insensitive to copy-number variations and mutations that are outside the targeted regions.
Fragment-sequence read: The contiguous nucleotide sequence from one end of a DNA template (as opposed to a mate-pair read).
Haploinsufficiency: The state that occurs when a diploid organism has only a single functional copy of a gene, which does not produce enough protein to support normal function.
Mapping: The computational process of identifying the specific region of a reference genome from which an individual sequenced DNA template originated.
Mappable yield: The number of bases generated by a DNA-sequencing instrument that can be mapped to the reference genome.
Mate-pair sequencing: A sequencing strategy that permits the inference of structural changes in a genome by sequencing at both the 5' and 3' ends of each DNA template (as opposed to the fragment-sequencing approach).
Mendelian disease: Human disease caused by mutations in a single gene.
Missense mutations: Single DNA-base changes that occur in the coding regions of genes and alter the resulting encoded amino acid sequence.
Next-generation sequencing: DNA-sequencing methods that involve chemical assays other than the traditional Sanger dideoxy-chain-termination method. Next-generation-sequencing methods produce much larger quantities of data at less expense, but the individual raw sequence reads that are generated from individual amplified DNA-template sequences are shorter and have lower quality.
Nonsense mutations: DNA-base changes that introduce termination codons in the coding sequences of genes, resulting in truncated proteins.
Sequence read: The sequence generated from a single DNA template.
Single-base error rate: The total number of mismatched bases found in mapped sequence reads from a sequencing run, divided by the mappable yield. This rate estimates the probability that any given mappable base is an error.
Two-base encoding: A method used in the SOLiD (Sequencing by Oligonucleotide Ligation and Detection) DNA-sequencing platform that represents a DNA sequence as a chain of overlapping dimers encoded as single-base "colors." This allows for sequencing of the 16 unique sequence dimers with the use of only four unique dye colors and provides a method for improving the overall accuracy of the sequence reads (reducing the single-base error rate).
Supported in part by grants from the National Human Genome Research Institute (5 U54 HG003273, to Dr. Gibbs) and the National Institute of Neurological Disorders and Stroke (R01 NS058529, to Dr. Lupski).
Disclosure forms provided by the authors are available with the full text of this article at NEJM.org.
We thank Kevin McKernan, Michael Rhodes, Francisco de la Vega, Quynh Doan, and Fiona Hyland for extensive discussion and support and Cristian Coarfa for structural-variation analysis and insights.

Sequencing of families' genomes offers insights into rare genetic diseases.

http://www.nature.com/news/2010/100310/full/news.2010.116.html

Janelle Weaver

By sequencing the genomes of three patients with rare genetic disorders, and comparing them with genetic information from unaffected family members, two studies have managed to narrow down the causes of the diseases.
Between them, the analyses bring the number of individuals who have had their full genomes sequenced from seven to twelve.
A team led by David Galas of the Institute for Systems Biology in Seattle, Washington, sequenced the genomes of a family of four in which the two children had extremely rare genetic disorders — Miller syndrome and primary ciliary dyskinesia1. Miller syndrome causes facial and limb abnormalities, and primary ciliary dyskinesia prevents hair-like structures in the respiratory tract from removing mucus.
By comparing the genomes of the children with those of the unaffected parents, the team was able to pinpoint the specific recombinations of parental genes that led to the diseases, and eliminate other parts of the genome that previous studies had associated with the disorders. The researchers conclude that just four genes underlie the two diseases.
Scientist studied
And in a second analysis, author James Lupski became a subject of his own study. A molecular geneticist at Baylor College of Medicine in Houston, Texas, Lupski has a rare variation of Charcot-Marie-Tooth disease, which causes a loss of muscle and nerve function in the limbs, hands and feet. Having come up with no firm results in previous screenings of Lupski's family, scientists had puzzled over the genetic cause of the disease. But by sequencing Lupski's entire genome and comparing it with snippets from his family members, Lupski's colleagues have identified new mutations associated with his disease2.
First, Lupski and his colleagues compared his genome to the human genome reference sequence to identify places where single bases of DNA had been substituted. Of the genes they identified that had these mutations, called SNPs, the team focused on one known as SH3TC2 because it had been linked to other types of Charcot-Marie-Tooth disease. Then they sequenced portions of this gene in family members with mild nerve impairment in their hands or feet. The team discovered two mutations in SH3TC2 that were associated with different forms of nerve impairment, including carpal tunnel syndrome.
"The fact that these studies are coming out at once tells you where the field is moving," says Eric Topol, who studies the genetic basis of human disease at the Scripps Research Institute in La Jolla, California. "It's exciting to see that there are lots of ways to go after what were undiagnosed molecular abnormalities using pinpoint-precision sequencing."
Keep it in the family
The family-based approach has also provided researchers with another way to estimate the rate at which parents pass mutations to their offspring. Galas and his colleagues estimate that each offspring will have 70 new mutations, less than half the number obtained with previous approaches. "It is really important to know this number because it represents the source of all genetic variation we have, for good or bad, for health or disease," says Joseph Nadeau, a human geneticist at Case Western Reserve University in Cleveland, Ohio.
Although whole-genome sequencing might be highly accurate and getting cheaper, it isn't yet within practical reach. Lupski and colleagues, for instance, estimate that their study cost around US$50,000. Less complete forms of sequencing can provide similar information about the genetic underpinnings of diseases such as Miller syndrome and primary ciliary dyskinesia. Last year, scientists used a less intensive method to identify the role of DHODH and DNAH5 in these diseases3.
Ultimately, scientists may realize they don't have to sequence the whole genome, Topol says. "Another way may be cheaper and equally effective; we just don't know yet."

Aimee Mullins and her 12 pairs of legs

http://www.ted.com/index.php/talks/aimee_mullins_prosthetic_aesthetics.html

Carla Bruni Interview (Part 1)

http://www.youtube.com/watch?v=IRaUTQQ2bTo&NR=1

Her interesting response to the question ---- is she an adulteress?
I think it is not about good or bad, right or wrong. In every moment, people make decisions. Due to the decisions people make, they will get the results from the decisions. The cause and effect...........
nothing lasts, but decisions................. I find this short sentence in the beginning of one book. This sentence is very shocking for me.

National Center on Birth Defects and Developmental Disabilities

http://www.cdc.gov/ncbddd/AboutUs/index.html