ID

45939

Description

Principal Investigator: Taylor Jensen, PhD, Sequenom Laboratories, San Diego, CA, USA MeSH: DNA Methylation,Prenatal Diagnosis,Epigenomics,Developmental Biology https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000846 *Background*: Circulating cell free (ccf) fetal DNA has enabled non-invasive prenatal fetal aneuploidy testing without direct discrimination of the genetically distinct maternal and fetal DNA. Current testing may be improved by specifically enriching the sample material for fetal DNA. DNA methylation may allow for such a separation of DNA and thus support additional clinical opportunities; however, this depends on knowledge of the methylomes of ccf DNA and its cellular contributors. *Results*: Whole genome bisulfite sequencing was performed on a set of unmatched samples including ccf DNA from 8 non-pregnant (NP) and 7 pregnant female donors and genomic DNA from 7 buffy coat and 5 placenta samples. We found CpG cytosines within longer fragments were more likely to be methylated, linking DNA methylation and fragment size in ccf DNA. Comparison of the methylomes of placenta and NP ccf DNA revealed many of the 51,259 identified differentially methylated regions (DMRs) were located in domains exhibiting consistent placenta hypomethylation across millions of consecutive bases, regions we termed placenta hypomethylated domains. DMRs identified when comparing placenta to NP ccf DNA were recapitulated in pregnant ccf DNA, confirming the ability to detect differential methylation in ccf DNA mixtures. *Conclusions*: We generated methylome maps for four sample types at single base resolution, identified a link between DNA methylation and fragment length in ccf DNA, identified DMRs between sample groups, and uncovered the presence of megabase-size placenta hypomethylated domains. Furthermore, we anticipate these results to provide a foundation to which future studies using discriminatory DNA methylation may be compared.

Link

dbGaP study=phs00084

Keywords

Versions (1)
  1. 09.03.24 09.03.24 - Madita Rudolph
Copyright Holder

Taylor Jensen, PhD, Sequenom Laboratories, San Diego, CA, USA

Uploaded on

9. März 2024

DOI

To request one please log in.

License

Creative Commons BY 4.0
Model comments :

You can comment on the data model here. Via the speech bubbles at the itemgroups and items you can add comments to those specificially.

Back to model comments
Itemgroup comments for :

Item comments for :

In order to download data models you must be logged in. Please log in or register for free.

dbGaP phs000846 Whole Genome Bisulfite Sequencing of ccf DNA and its Cellular Contributors

English

Eligibility Criteria

5 forms  
Inclusion and exclusion criteria
Description

Inclusion and exclusion criteria

Alias
UMLS CUI [1,1]
C1512693
UMLS CUI [1,2]
C0680251
Specimens analyzed for this study were collected under three separate IRB approved studies. Plasma was extracted from whole blood specimens from pregnant subjects collected under protocol SQNM-T21-106 (Compass IRB 00462). Subjects provided written informed consent and were 18 years of age or older and pregnant carrying a singleton fetus of 10 to 26 weeks gestational age inclusive. Plasma was extracted from whole blood specimens from non-pregnant female subjects collected under protocol SQNM-RND-103 (Aspire IRB T21106). Subjects provided written informed consent and were normal healthy volunteers 18 years of age or older confirmed not to be pregnant. Peripheral blood mononucleated cells (PBMCs or buffy coat) were extracted from whole blood specimens from pregnant subjects collected under protocol 1128724 (Western IRB 20111833). Placental tissue was collected from subjects under the same protocol (1128724). Subjects provided written informed consent and donated the whole blood and aborted material as an anatomical gift for the purposes of education, research, or for the advancement of medical science.
Description

Elig.phs000846.v1.p1.1

Data type

boolean

Alias
UMLS CUI [1,1]
C1706256
UMLS CUI [1,2]
C0001779
UMLS CUI [1,3]
C0032961
UMLS CUI [1,4]
C1313913
UMLS CUI [1,5]
C0017504
UMLS CUI [1,6]
C0021430
UMLS CUI [1,7]
C0200345
UMLS CUI [1,8]
C1321301
UMLS CUI [1,9]
C0032043
UMLS CUI [2,1]
C0009932
UMLS CUI [2,2]
C0001779
UMLS CUI [2,3]
C0086287
UMLS CUI [2,4]
C3898900
UMLS CUI [2,5]
C0232973
UMLS CUI [2,6]
C0021430
UMLS CUI [2,7]
C0200345
UMLS CUI [2,8]
C1321301
Back to the top of the page

Similar models

Eligibility Criteria

5 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
Inclusion and exclusion criteria
C1512693 (UMLS CUI [1,1])
C0680251 (UMLS CUI [1,2])
Elig.phs000846.v1.p1.1
Item
Specimens analyzed for this study were collected under three separate IRB approved studies. Plasma was extracted from whole blood specimens from pregnant subjects collected under protocol SQNM-T21-106 (Compass IRB 00462). Subjects provided written informed consent and were 18 years of age or older and pregnant carrying a singleton fetus of 10 to 26 weeks gestational age inclusive. Plasma was extracted from whole blood specimens from non-pregnant female subjects collected under protocol SQNM-RND-103 (Aspire IRB T21106). Subjects provided written informed consent and were normal healthy volunteers 18 years of age or older confirmed not to be pregnant. Peripheral blood mononucleated cells (PBMCs or buffy coat) were extracted from whole blood specimens from pregnant subjects collected under protocol 1128724 (Western IRB 20111833). Placental tissue was collected from subjects under the same protocol (1128724). Subjects provided written informed consent and donated the whole blood and aborted material as an anatomical gift for the purposes of education, research, or for the advancement of medical science.
boolean
C1706256 (UMLS CUI [1,1])
C0001779 (UMLS CUI [1,2])
C0032961 (UMLS CUI [1,3])
C1313913 (UMLS CUI [1,4])
C0017504 (UMLS CUI [1,5])
C0021430 (UMLS CUI [1,6])
C0200345 (UMLS CUI [1,7])
C1321301 (UMLS CUI [1,8])
C0032043 (UMLS CUI [1,9])
C0009932 (UMLS CUI [2,1])
C0001779 (UMLS CUI [2,2])
C0086287 (UMLS CUI [2,3])
C3898900 (UMLS CUI [2,4])
C0232973 (UMLS CUI [2,5])
C0021430 (UMLS CUI [2,6])
C0200345 (UMLS CUI [2,7])
C1321301 (UMLS CUI [2,8])
Back to the top of the page 

Contact

Please use this form for feedback, questions and suggestions for improvements.

Fields marked with * are required.

Help

Do you need help on how to use the search function? Please watch the corresponding tutorial video for more details and learn how to use the search function most efficiently.

Watch Tutorial