A new blood diagnostic test may offer hope for transplant recipients by analyzing cfDNA -
When the cells die, either by apoptosis or necrosis, DNA and other molecules present in these cells Don 't just disappear. They are found in the blood stream, where degraded bits and pieces can be extracted.
This DNA without cell (cfDNA) is degraded due to its exposure to enzymes in the blood, but is nevertheless a powerful tool for monitoring cancer, pregnancy and organ transplantation. A fairly recent breakthrough prenatal screening for conditions such as Down syndrome, like fragments of fetal cfDNA can be detected in the blood of the mother.
Now, borrowing a genomic technique used in the study of the ancient past, a Cornell graduate student came with a diagnostic tool that can open a window to the immediate future of the transplant recipient by analysis cfDNA.
Philip Burnham, a doctoral student in the lab of Iwijn Vlaminck, Robert N. Noyce assistant professor of life sciences and technology, proposed to use the preparation of the DNA library short strand for sequencing cfDNA in plasma of lung transplant recipients. A DNA library is a collection of DNA fragments were cloned into groups so that researchers can isolate desired fragments for the study.
The laboratory paper, "preparing the single-stranded DNA library discovers the origin and diversity of ultrashort DNA -free cells in plasma," was published online June 14 in Nature scientific reports. Burnham, a graduate student of third year physics and biomedical engineering, is the lead author for the work first published laboratory
The identification of the source of the cfDNA -. Some of them from the mitochondria, the energy producer in cells - can help determine if the transplanted organ is injured or rejected.
"mitochondrial donor sequences are different from those of the recipient, thus making this sequence analysis, you can tell them apart," Vlaminck said. "When cells are injured, they release mitochondrial DNA, and given that you can distinguish the patient's DNA donor, you can actually quantify the injury by these measures."
In 2012, the German anthropologist Matthias Meyer published an article on the study of denisovan - man there about 40,000 years -. and the use of a DNA bank of single-stranded preparation method to sequence the genome of Denisova hominid
nucleosomal DNA - the DNA found in cells - can be adapted for sequencing using double-stranded adapters DNA, but this is not an option for 40,000 years of genetic material. The collected DNA from old bones deteriorates and short strands -the same that many types of cfDNA.
"So Phil has decided to apply these concepts to the DNA in the blood," said De Vlaminck. "And when he did, we discovered a variety of short molecules DNA. "
the group took 40 samples from plasma cfDNA six double-lung transplant recipients and tested with both single-stranded and double-stranded library preparation. the single strand method was much more effective than the conventional method of double-stranded in identifying ultrashort cfDNA (shorter than 100 base pairs), which indicates that it would be better equipped for fetal surveillance and growth, as well.
Ideally, with this method, a transplant recipient could get an idea of how the new body responds with a simple blood test Currently, the only way to know is a biopsy -.. in some cases up to 10 of them in the first year, de Vlaminck said
"you could obviously afford to [a blood test] more often, and if it is more sensitive, the hope is that you can intervene early if problems arose, "he said.
the group hopes their methods will lead to more widespread use of cfDNA analysis, not only in the case of transplantation.
"At present, we are working in a nice model system - if we see the donor's DNA in lung transplant recipient
, then we know that it comes from the lung," said Burnham said. "But what we really push hard is the ability to start watching any tissue DNA derived without prior knowledge of what we are looking at and coupled with the ability to identify potential microbial pathogens cfDNA."
This method should also be effective for the detection of infections, which are a concern for transplant patients. immunosuppressive drugs reduce the risk of organ rejection, but leave a patient vulnerable to infection.
This DNA without cell (cfDNA) is degraded due to its exposure to enzymes in the blood, but is nevertheless a powerful tool for monitoring cancer, pregnancy and organ transplantation. A fairly recent breakthrough prenatal screening for conditions such as Down syndrome, like fragments of fetal cfDNA can be detected in the blood of the mother.
Now, borrowing a genomic technique used in the study of the ancient past, a Cornell graduate student came with a diagnostic tool that can open a window to the immediate future of the transplant recipient by analysis cfDNA.
Philip Burnham, a doctoral student in the lab of Iwijn Vlaminck, Robert N. Noyce assistant professor of life sciences and technology, proposed to use the preparation of the DNA library short strand for sequencing cfDNA in plasma of lung transplant recipients. A DNA library is a collection of DNA fragments were cloned into groups so that researchers can isolate desired fragments for the study.
The laboratory paper, "preparing the single-stranded DNA library discovers the origin and diversity of ultrashort DNA -free cells in plasma," was published online June 14 in Nature scientific reports. Burnham, a graduate student of third year physics and biomedical engineering, is the lead author for the work first published laboratory
The identification of the source of the cfDNA -. Some of them from the mitochondria, the energy producer in cells - can help determine if the transplanted organ is injured or rejected.
"mitochondrial donor sequences are different from those of the recipient, thus making this sequence analysis, you can tell them apart," Vlaminck said. "When cells are injured, they release mitochondrial DNA, and given that you can distinguish the patient's DNA donor, you can actually quantify the injury by these measures."
In 2012, the German anthropologist Matthias Meyer published an article on the study of denisovan - man there about 40,000 years -. and the use of a DNA bank of single-stranded preparation method to sequence the genome of Denisova hominid
nucleosomal DNA - the DNA found in cells - can be adapted for sequencing using double-stranded adapters DNA, but this is not an option for 40,000 years of genetic material. The collected DNA from old bones deteriorates and short strands -the same that many types of cfDNA.
"So Phil has decided to apply these concepts to the DNA in the blood," said De Vlaminck. "And when he did, we discovered a variety of short molecules DNA. "
the group took 40 samples from plasma cfDNA six double-lung transplant recipients and tested with both single-stranded and double-stranded library preparation. the single strand method was much more effective than the conventional method of double-stranded in identifying ultrashort cfDNA (shorter than 100 base pairs), which indicates that it would be better equipped for fetal surveillance and growth, as well.
Ideally, with this method, a transplant recipient could get an idea of how the new body responds with a simple blood test Currently, the only way to know is a biopsy -.. in some cases up to 10 of them in the first year, de Vlaminck said
"you could obviously afford to [a blood test] more often, and if it is more sensitive, the hope is that you can intervene early if problems arose, "he said.
the group hopes their methods will lead to more widespread use of cfDNA analysis, not only in the case of transplantation.
"At present, we are working in a nice model system - if we see the donor's DNA in lung transplant recipient
, then we know that it comes from the lung," said Burnham said. "But what we really push hard is the ability to start watching any tissue DNA derived without prior knowledge of what we are looking at and coupled with the ability to identify potential microbial pathogens cfDNA."
This method should also be effective for the detection of infections, which are a concern for transplant patients. immunosuppressive drugs reduce the risk of organ rejection, but leave a patient vulnerable to infection.
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