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A new method for non-invasive prenatal diagnosis of Down syndrome using MeDIP real time qPCR

View Article: PubMed Central - PubMed

ABSTRACT

During the last decade, the area of non-invasive prenatal diagnosis (NIPD) has rapidly evolved. Several methodological approaches have been presented and demonstrated a proof of concept for the NIPD of chromosomal aneuploidies. The two most promising methods are NIPD using next generation sequencing technologies and NIPD using Methylation DNA Immunoprecipitation (MeDIP) with real time qPCR. Both approaches have been validated with blind studies and have > 99% accuracy. NIPD using next generation sequencing is achieved by high throughput shotgun sequencing of DNA from plasma of maternal women followed by ratio comparisons of each chromosome sequence tag density over the median tag density of all autosomes (z-score analysis). The MeDIP real time qPCR method, which is described in this review in more detail, is based on the identification of differentially methylated regions (DMRs) and their use in discriminating normal from abnormal cases. More than 10,000 DMRs were identified for chromosomes 13, 18, 21, X and Y using high resolution oligo-arrays that can be potentially used for the NIPD of aneuploidies for chromosomes 13, 18, 21, X and Y. Both NIPD methods have several advantages and limitations and it is believed that they will soon be implemented in clinical practice. With the continuous advancements of genetic methodologies and technologies, we predict that within the next 10 years we will be able to provide NIPD for all common and rare genetic disorders where the molecular basis is known.

No MeSH data available.


Related in: MedlinePlus

Fetal specific DNA methylation ration permits NIPD of Down syndrome. DNA from peripheral blood of known normal and unknown pregnancies are first immunoprecipitated using the MeDIP protocol to enrich fetal DNA in regions (DMRs) that are known to be hypermethylated in the fetus and hypomethylated in the mother. Real time qPCR is used to quantify all DMRs on chromosome 21 and measures the fetal specific DNA methylation ratio between the test sample (Down syndrome in this figure) and a median of known normal samples. A D value is derived using the ratios from several DMRs and provides the final result of the test sample (Down syndrome in this figure). F: fetal, M: maternal, red dots: hypermethylated DNA, and black dots: hypomethylated DNA.
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f0010: Fetal specific DNA methylation ration permits NIPD of Down syndrome. DNA from peripheral blood of known normal and unknown pregnancies are first immunoprecipitated using the MeDIP protocol to enrich fetal DNA in regions (DMRs) that are known to be hypermethylated in the fetus and hypomethylated in the mother. Real time qPCR is used to quantify all DMRs on chromosome 21 and measures the fetal specific DNA methylation ratio between the test sample (Down syndrome in this figure) and a median of known normal samples. A D value is derived using the ratios from several DMRs and provides the final result of the test sample (Down syndrome in this figure). F: fetal, M: maternal, red dots: hypermethylated DNA, and black dots: hypomethylated DNA.

Mentions: In order to demonstrate that these DMRs can be used to identify fetal DNA in maternal peripheral blood and discriminate normal from Down syndrome cases, several samples of peripheral blood from normal as well as trisomy 21 pregnancies were tested and analyzed. Fig. 2 demonstrates the ratio value calculation of a Down syndrome or a normal case compared to the median value of normal control cases. These results, and statistical analysis of the ratio value differences between normal and abnormal cases, permitted the development of a new NIPD for trisomy 21 which is based on measuring and comparing fetal specific methylation ratios between unknown and known normal pregnancies (Fig. 2).


A new method for non-invasive prenatal diagnosis of Down syndrome using MeDIP real time qPCR
Fetal specific DNA methylation ration permits NIPD of Down syndrome. DNA from peripheral blood of known normal and unknown pregnancies are first immunoprecipitated using the MeDIP protocol to enrich fetal DNA in regions (DMRs) that are known to be hypermethylated in the fetus and hypomethylated in the mother. Real time qPCR is used to quantify all DMRs on chromosome 21 and measures the fetal specific DNA methylation ratio between the test sample (Down syndrome in this figure) and a median of known normal samples. A D value is derived using the ratios from several DMRs and provides the final result of the test sample (Down syndrome in this figure). F: fetal, M: maternal, red dots: hypermethylated DNA, and black dots: hypomethylated DNA.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5121212&req=5

f0010: Fetal specific DNA methylation ration permits NIPD of Down syndrome. DNA from peripheral blood of known normal and unknown pregnancies are first immunoprecipitated using the MeDIP protocol to enrich fetal DNA in regions (DMRs) that are known to be hypermethylated in the fetus and hypomethylated in the mother. Real time qPCR is used to quantify all DMRs on chromosome 21 and measures the fetal specific DNA methylation ratio between the test sample (Down syndrome in this figure) and a median of known normal samples. A D value is derived using the ratios from several DMRs and provides the final result of the test sample (Down syndrome in this figure). F: fetal, M: maternal, red dots: hypermethylated DNA, and black dots: hypomethylated DNA.
Mentions: In order to demonstrate that these DMRs can be used to identify fetal DNA in maternal peripheral blood and discriminate normal from Down syndrome cases, several samples of peripheral blood from normal as well as trisomy 21 pregnancies were tested and analyzed. Fig. 2 demonstrates the ratio value calculation of a Down syndrome or a normal case compared to the median value of normal control cases. These results, and statistical analysis of the ratio value differences between normal and abnormal cases, permitted the development of a new NIPD for trisomy 21 which is based on measuring and comparing fetal specific methylation ratios between unknown and known normal pregnancies (Fig. 2).

View Article: PubMed Central - PubMed

ABSTRACT

During the last decade, the area of non-invasive prenatal diagnosis (NIPD) has rapidly evolved. Several methodological approaches have been presented and demonstrated a proof of concept for the NIPD of chromosomal aneuploidies. The two most promising methods are NIPD using next generation sequencing technologies and NIPD using Methylation DNA Immunoprecipitation (MeDIP) with real time qPCR. Both approaches have been validated with blind studies and have > 99% accuracy. NIPD using next generation sequencing is achieved by high throughput shotgun sequencing of DNA from plasma of maternal women followed by ratio comparisons of each chromosome sequence tag density over the median tag density of all autosomes (z-score analysis). The MeDIP real time qPCR method, which is described in this review in more detail, is based on the identification of differentially methylated regions (DMRs) and their use in discriminating normal from abnormal cases. More than 10,000 DMRs were identified for chromosomes 13, 18, 21, X and Y using high resolution oligo-arrays that can be potentially used for the NIPD of aneuploidies for chromosomes 13, 18, 21, X and Y. Both NIPD methods have several advantages and limitations and it is believed that they will soon be implemented in clinical practice. With the continuous advancements of genetic methodologies and technologies, we predict that within the next 10 years we will be able to provide NIPD for all common and rare genetic disorders where the molecular basis is known.

No MeSH data available.


Related in: MedlinePlus