Thursday, June 07, 2012 3:04:57 AM
Entire DNA of fetus revealed through risk-free testing
A lab technician cuts a DNA fragment under ultraviolet light.
(Wong Maye-e / Associated Press / June 6, 2012)
Researchers use blood from the mother and saliva from the father to determine a fetus' entire DNA sequence. If refined, the technique could provide a risk-free way to screen for genetic disorders.
By Rosie Mestel, Los Angeles Times
June 6, 2012, 5:44 p.m.
Scientists have pieced together the entire DNA sequence [i.e., genome] of an 18-week-old fetus without having to use any invasive tests that could result in a miscarriage — an advance that offers a glimpse of the future of prenatal testing.
Using blood drawn from the mother and a sample of saliva from the father, the researchers were able to scan the fetus' genome and determine whether it contained any of the myriad single-letter changes in the DNA code that can cause a genetic disorder. They could even pinpoint which mutations were inherited from Mom, which came from Dad, and which were brand-new.
If the technique is refined and the technology becomes inexpensive — as many experts anticipate — this type of prenatal testing could provide prospective parents with a simple, risk-free way to screen for a broad array of simple genetic disorders, according to the authors of a report [ http://stm.sciencemag.org/content/4/137/137ra76 ] in Thursday's edition of Science Translational Medicine.
The work is based on the fact that small fragments of fetal DNA circulate in the blood of pregnant women.
Several biotech companies are developing tests that capture those DNA fragments and screen them for signs of Down syndrome and other disorders that result from having an extra copy of an entire chromosome.
But that type of screening is far easier than searching for single-letter variations in individual genes, said senior author Jay Shendure, a geneticist at the University of Washington in Seattle.
An additional chromosome is "the equivalent of an extra chapter in a book," he said. "What we're trying to do is pick up a typo in a word."
To set about their task, Shendure's team started by sequencing the genome of an anonymous pregnant woman, using a complete sample of her DNA obtained from her blood cells. They also sequenced free-floating DNA fragments extracted from her blood plasma, repeating their work until they had decoded every part of the human genome 80 times.
That plasma contained a mix of 10% fetal DNA and 90% maternal DNA, all in tiny fragments. The scientists needed to be able to tell which pieces were from the mother and which belonged to the fetus.
To solve that problem, the scientists relied on the fact that genetic material is inherited in long strands of DNA, called chromosomes — and that tiny genetic variations on the same chromosome are usually inherited together, in blocks known as haplotypes. If a given haplotype was present in the fetus as well as in the mother, it would be detected in the plasma in extra amounts.
The scientists also sequenced the father's DNA, which was extracted from saliva. This allowed the team to figure out whether genetic variations in the fetus that didn't match the mother were inherited from the father or were new mutations. On average, about 50 new mutations show up in a fetus.
The scientists checked their results against a blood sample taken from the baby's umbilical cord after birth. Their calculations were more than 98% correct, they found, and they had detected 39 out of the 44 new mutations. None of those mutations had known medical consequences, the researchers said.
This approach could be used to devise a single test to screen for the 3,000 known disorders that are caused by mistakes in single genes. Individually, they are rare, but together they affect about 1% of births.
Technology like this could lead to more widespread screening of fetuses for genetic disorders that could benefit from early treatment, said Dr. Joe Leigh Simpson, senior vice president for research and global programs for the March of Dimes in White Plains, N.Y. It might even help doctors identify women at heightened risk for problems such as pre-term birth, he said.
rosie.mestel@latimes.com
*
Also
Biologists construct self-assembling tiles of DNA
http://www.latimes.com/news/science/la-sci-dna-shapes-20120602,0,182781.story
Detecting cancers -- from tiny bits of tumor DNA in blood
http://www.latimes.com/health/boostershots/la-heb-detecting-cancers-dna-blood--20120530,0,3112263.story
Turning DNA into a hard drive
http://www.latimes.com/news/science/la-sci-synthetic-biology-q-a-20120526,0,4569181.story
*
Copyright © 2012, Los Angeles Times
http://www.latimes.com/news/science/la-sci-fetal-genome-sequence-20120607,0,7625263.story [with comments]
===
Babies could be tested for 3,500 genetic faults
An ultrasound scan of a human foetus
Photo: ALAMY
Scientists could soon be able to routinely screen unborn babies for thousands of genetic conditions, raising concerns the breakthrough could lead to more abortions.
By Stephen Adams, Medical Correspondent
10:51PM BST 06 Jun 2012
A team has been able to predict the whole genetic code of a foetus by taking a blood sample from a woman who was 18 weeks pregnant, and a swab of saliva from the father.
They believe that, in time, the test will become widely available, enabling doctors to screen unborn babies for some 3,500 genetic disorders.
At the moment the only genetic disorder routinely tested for on the NHS is Down’s syndrome.
This is a large-scale genetic defect caused by having an extra copy of a bundle of DNA, called a chromosome.
Other such faults are sometimes tested for, but usually only when there is a risk of inheriting them from a parent.
By contrast, the scientists say their new test would identify far more conditions, caused by genetic errors.
However, they warned it raised “many ethical questions” because the results could be used as a basis for abortion.
These concerns were last night amplified by pro-life campaigners, who said widespread use of such a test would “inevitably lead to more abortions”.
The American scientists were able to map the baby’s genetic code principally from tiny traces free-floating DNA, which makes its way into the mother’s blood.
Blood sample DNA from the mother was also studied as well as DNA extracted from the father's saliva.
Fitting pieces of the genetic jigsaw together, scientists in the US were able to reconstruct the entire genetic code of an unborn baby boy.
They were then able to see what spontaneous genetic mutations had arisen.
Such natural mutations - called ‘de novo’ mutations - are responsible for the majority of genetic defects.
By checking their prediction of the baby’s genetic code with actual DNA taken after the birth, the team from the University of Washington in Seattle, found they were able to identify 39 of 44 such mutations in the child.
De novo mutations are thought to play a role in a number of complex conditions such as autism and schizophrenia.
The team also tested their approach on a woman who was earlier in her pregnancy than 18 weeks, and found it still worked.
Dr Jay Shendure, the lead scientist, said: "This work opens up the possibility that we will be able to scan the whole genome of the foetus for more than 3,000 single-gene disorders through a single, non-invasive test."
Jacob Kitzman, who worked on the project, added: “The improved resolution is like going from being able to see that two books are stuck together to being able to notice one word mis-spelled on a page.”
In future, a more refined and less costly version of the procedure could make pre-natal genetic testing far more comprehensive than it is now, the scientists say.
The research is reported in the journal Science Translational Medicine.
The scientists said the test would be a considerable improvement on current techniques, which involve inserting a probe into the womb to take fluid from the foetal sac or placental samples. This can be dangerous for both mother and child.
Such existing methods only enable doctors to check for a relatively small number of genetic disorders.
These include Down's syndrome and cystic fibrosis - which are both large-scale genetic defects - as well as muscular dystrophy and spina bifada, which can have hereditary elements.
As well as testing for thousands of genetic defects, the scientists said their test could give a wealth of information on the baby’s future health.
However, they warned: “The less tangible implication of incorporating this level of information into pre-natal decision-making raises many ethical questions that must be considered carefully within the scientific community and on a societal level.
“As in other areas of clinical genetics, our capacity to generate data is outstripping our ability to interpret it in ways that are useful to physicians and patients.”
Josephine Quintavalle, founder of the Pro-Life Alliance, put it more baldly.
She said: “One always hopes, vainly, that in utero testing will be for the benefit of the unborn child.
“But, whilst this new test may not itself be invasive, given our past track record, it is difficult to imagine that this new test will not lead to more abortions.”
© Copyright of Telegraph Media Group Limited 2012
http://www.telegraph.co.uk/health/healthnews/9315265/Babies-could-be-tested-for-3500-genetic-faults.html [with comments]
===
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A lab technician cuts a DNA fragment under ultraviolet light.
(Wong Maye-e / Associated Press / June 6, 2012)
Researchers use blood from the mother and saliva from the father to determine a fetus' entire DNA sequence. If refined, the technique could provide a risk-free way to screen for genetic disorders.
By Rosie Mestel, Los Angeles Times
June 6, 2012, 5:44 p.m.
Scientists have pieced together the entire DNA sequence [i.e., genome] of an 18-week-old fetus without having to use any invasive tests that could result in a miscarriage — an advance that offers a glimpse of the future of prenatal testing.
Using blood drawn from the mother and a sample of saliva from the father, the researchers were able to scan the fetus' genome and determine whether it contained any of the myriad single-letter changes in the DNA code that can cause a genetic disorder. They could even pinpoint which mutations were inherited from Mom, which came from Dad, and which were brand-new.
If the technique is refined and the technology becomes inexpensive — as many experts anticipate — this type of prenatal testing could provide prospective parents with a simple, risk-free way to screen for a broad array of simple genetic disorders, according to the authors of a report [ http://stm.sciencemag.org/content/4/137/137ra76 ] in Thursday's edition of Science Translational Medicine.
The work is based on the fact that small fragments of fetal DNA circulate in the blood of pregnant women.
Several biotech companies are developing tests that capture those DNA fragments and screen them for signs of Down syndrome and other disorders that result from having an extra copy of an entire chromosome.
But that type of screening is far easier than searching for single-letter variations in individual genes, said senior author Jay Shendure, a geneticist at the University of Washington in Seattle.
An additional chromosome is "the equivalent of an extra chapter in a book," he said. "What we're trying to do is pick up a typo in a word."
To set about their task, Shendure's team started by sequencing the genome of an anonymous pregnant woman, using a complete sample of her DNA obtained from her blood cells. They also sequenced free-floating DNA fragments extracted from her blood plasma, repeating their work until they had decoded every part of the human genome 80 times.
That plasma contained a mix of 10% fetal DNA and 90% maternal DNA, all in tiny fragments. The scientists needed to be able to tell which pieces were from the mother and which belonged to the fetus.
To solve that problem, the scientists relied on the fact that genetic material is inherited in long strands of DNA, called chromosomes — and that tiny genetic variations on the same chromosome are usually inherited together, in blocks known as haplotypes. If a given haplotype was present in the fetus as well as in the mother, it would be detected in the plasma in extra amounts.
The scientists also sequenced the father's DNA, which was extracted from saliva. This allowed the team to figure out whether genetic variations in the fetus that didn't match the mother were inherited from the father or were new mutations. On average, about 50 new mutations show up in a fetus.
The scientists checked their results against a blood sample taken from the baby's umbilical cord after birth. Their calculations were more than 98% correct, they found, and they had detected 39 out of the 44 new mutations. None of those mutations had known medical consequences, the researchers said.
This approach could be used to devise a single test to screen for the 3,000 known disorders that are caused by mistakes in single genes. Individually, they are rare, but together they affect about 1% of births.
Technology like this could lead to more widespread screening of fetuses for genetic disorders that could benefit from early treatment, said Dr. Joe Leigh Simpson, senior vice president for research and global programs for the March of Dimes in White Plains, N.Y. It might even help doctors identify women at heightened risk for problems such as pre-term birth, he said.
rosie.mestel@latimes.com
*
Also
Biologists construct self-assembling tiles of DNA
http://www.latimes.com/news/science/la-sci-dna-shapes-20120602,0,182781.story
Detecting cancers -- from tiny bits of tumor DNA in blood
http://www.latimes.com/health/boostershots/la-heb-detecting-cancers-dna-blood--20120530,0,3112263.story
Turning DNA into a hard drive
http://www.latimes.com/news/science/la-sci-synthetic-biology-q-a-20120526,0,4569181.story
*
Copyright © 2012, Los Angeles Times
http://www.latimes.com/news/science/la-sci-fetal-genome-sequence-20120607,0,7625263.story [with comments]
===
Babies could be tested for 3,500 genetic faults
An ultrasound scan of a human foetus
Photo: ALAMY
Scientists could soon be able to routinely screen unborn babies for thousands of genetic conditions, raising concerns the breakthrough could lead to more abortions.
By Stephen Adams, Medical Correspondent
10:51PM BST 06 Jun 2012
A team has been able to predict the whole genetic code of a foetus by taking a blood sample from a woman who was 18 weeks pregnant, and a swab of saliva from the father.
They believe that, in time, the test will become widely available, enabling doctors to screen unborn babies for some 3,500 genetic disorders.
At the moment the only genetic disorder routinely tested for on the NHS is Down’s syndrome.
This is a large-scale genetic defect caused by having an extra copy of a bundle of DNA, called a chromosome.
Other such faults are sometimes tested for, but usually only when there is a risk of inheriting them from a parent.
By contrast, the scientists say their new test would identify far more conditions, caused by genetic errors.
However, they warned it raised “many ethical questions” because the results could be used as a basis for abortion.
These concerns were last night amplified by pro-life campaigners, who said widespread use of such a test would “inevitably lead to more abortions”.
The American scientists were able to map the baby’s genetic code principally from tiny traces free-floating DNA, which makes its way into the mother’s blood.
Blood sample DNA from the mother was also studied as well as DNA extracted from the father's saliva.
Fitting pieces of the genetic jigsaw together, scientists in the US were able to reconstruct the entire genetic code of an unborn baby boy.
They were then able to see what spontaneous genetic mutations had arisen.
Such natural mutations - called ‘de novo’ mutations - are responsible for the majority of genetic defects.
By checking their prediction of the baby’s genetic code with actual DNA taken after the birth, the team from the University of Washington in Seattle, found they were able to identify 39 of 44 such mutations in the child.
De novo mutations are thought to play a role in a number of complex conditions such as autism and schizophrenia.
The team also tested their approach on a woman who was earlier in her pregnancy than 18 weeks, and found it still worked.
Dr Jay Shendure, the lead scientist, said: "This work opens up the possibility that we will be able to scan the whole genome of the foetus for more than 3,000 single-gene disorders through a single, non-invasive test."
Jacob Kitzman, who worked on the project, added: “The improved resolution is like going from being able to see that two books are stuck together to being able to notice one word mis-spelled on a page.”
In future, a more refined and less costly version of the procedure could make pre-natal genetic testing far more comprehensive than it is now, the scientists say.
The research is reported in the journal Science Translational Medicine.
The scientists said the test would be a considerable improvement on current techniques, which involve inserting a probe into the womb to take fluid from the foetal sac or placental samples. This can be dangerous for both mother and child.
Such existing methods only enable doctors to check for a relatively small number of genetic disorders.
These include Down's syndrome and cystic fibrosis - which are both large-scale genetic defects - as well as muscular dystrophy and spina bifada, which can have hereditary elements.
As well as testing for thousands of genetic defects, the scientists said their test could give a wealth of information on the baby’s future health.
However, they warned: “The less tangible implication of incorporating this level of information into pre-natal decision-making raises many ethical questions that must be considered carefully within the scientific community and on a societal level.
“As in other areas of clinical genetics, our capacity to generate data is outstripping our ability to interpret it in ways that are useful to physicians and patients.”
Josephine Quintavalle, founder of the Pro-Life Alliance, put it more baldly.
She said: “One always hopes, vainly, that in utero testing will be for the benefit of the unborn child.
“But, whilst this new test may not itself be invasive, given our past track record, it is difficult to imagine that this new test will not lead to more abortions.”
© Copyright of Telegraph Media Group Limited 2012
http://www.telegraph.co.uk/health/healthnews/9315265/Babies-could-be-tested-for-3500-genetic-faults.html [with comments]
===
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