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| Status |
Public on Dec 31, 2018 |
| Title |
In vitro fertilization does not increase the incidence of de novo copy number alterations in fetal and placental lineages |
| Organism |
Homo sapiens |
| Experiment type |
SNP genotyping by SNP array
Genome variation profiling by SNP array
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| Summary |
Although chromosomal instability (CIN) is a common phenomenon
in cleavage-stage embryogenesis following in vitro
fertilization (IVF), its rate in naturally conceived human
embryos is unknown. CIN leads to mosaic embryos that contain
a combination of genetically normal and abnormal cells,
and is significantly higher in in vitro-produced preimplantation
embryos as compared to in vivo-conceived preimplantation
embryos. Even though embryos with CIN-derived
complex aneuploidies may arrest between the cleavage and
blastocyst stages of embryogenesis, a high number of
embryos containing abnormal cells can pass this strong selection
barrier. However, neither the prevalence nor extent of
CIN during prenatal development and at birth, following IVF
treatment, is well understood. Here we profiled the genomic
landscape of fetal and placental tissues postpartum from
both IVF- and naturally conceived children, to investigate the
prevalence and persistence of large genetic aberrations that
probably arose from IVF-related CIN. We demonstrate that
CIN is not preserved at later stages of prenatal development,
and that de novo numerical aberrations or large structural
DNA imbalances occur at similar rates in IVF- and naturally
conceived live-born neonates. Our findings affirm that human
IVF treatment has no detrimental effect on the chromosomal
constitution of fetal and placental lineages.
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| Overall design |
We applied haplarithmisis that allows scrutinizing the allelic architecture of human fetal and placental genomes in both IVF and naturally conceived newborns. Specifically, we employed single nucleotide polymorphism (SNP) genotypes of the entire genomes of father, mother, placenta and umbilical cord blood of 111 families, of which 62 and 49 quartets were from natural and IVF pregnancies, respectively. The naturally conceived pregnancies were further subdivided based on birthweight at delivery, with 16 families categorized as ‘appropriate birth weight for gestational age’ (AGA) and 10 families with ‘small birth weight for gestational age’ (SGA). We employed all DNA samples within a quartet to classify copy number variations (CNVs) found exclusively in a single sample or a few to all samples within a quartet.
The data is provided in quartest structure, including Father, Mother, cord blood and placenta.
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| Web link |
https://www.nature.com/articles/s41591-019-0620-2
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| Contributor(s) |
Zamani Esteki M, Viltrop T, Tšuiko O, Tiirats A, Koel M, Nõukas M, Žilina O, Teearu K, Marjonen H, Kahila H, Meekels J, Söderström-Anttila V, Suikkari A, Tiitinen A, Mägi R, Kõks S, Kaminen-Ahola N, Kurg A, Voet T, Vermeesch JR, Salumets A |
| Citation(s) |
31686035 |
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| Submission date |
Jan 10, 2017 |
| Last update date |
Nov 08, 2019 |
| Contact name |
Masoud Zamani Esteki |
| E-mail(s) |
masoud.zamaniesteki@mumc.nl
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| Phone |
+31 43 38 75306
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| Organization name |
Maastricht University Medical Center
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| Department |
Clinical Genetics
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| Lab |
Cellular Genomic Medicine
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| Street address |
P. Debyelaan 25
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| City |
Maastricht |
| State/province |
Limburg |
| ZIP/Postal code |
6229 HX |
| Country |
Netherlands |
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| Platforms (2) |
| GPL22819 |
Illumina Human PsychArray-24 v1.1 |
| GPL26750 |
Illumina Human PsychArray-24 v1.3 |
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| Samples (460)
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| Relations |
| BioProject |
PRJNA360684 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE93353_AllData_Batch1_V3_GSM2451742-to-GSM2451977.txt.gz |
762.2 Mb |
(ftp)(http) |
TXT |
| GSE93353_GtypeData_Batch2_GSM3154595_to_GSM3154822.txt.gz |
901.7 Mb |
(ftp)(http) |
TXT |
| GSE93353_NewBiopsies_PsychArray-24v1.1.txt.gz |
22.4 Mb |
(ftp)(http) |
TXT |
| GSE93353_NewBiopsies_PsychArray-24v1.3.txt.gz |
76.6 Mb |
(ftp)(http) |
TXT |
| GSE93353_RAW.tar |
3.8 Gb |
(http)(custom) |
TAR (of IDAT) |
| Processed data are available on Series record |
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