 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 24, 2024 |
| Title |
Identification of skewed X chromosome inactivation using exome and transcriptome sequencing in patients with suspected rare genetic disease |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: Evaluation of XCI status in a cohot of female patients with suspected rare genetic diseases using exome and RNA sequencing
Results: We developed a method for estimating X inactivation status, using exome and transcriptome sequencing data from 112 female samples. We built a reference model for evaluation of XCI in 135 females from the GTEx consortium. We tested and validated the model on 14 female individuals with different types of undiagnosed rare genetic disorders who were clinically tested for X-skew using the AR gene assay and compared results to our outlier-based analysis technique. In comparison to the AR clinical test for identification of X inactivation, our method was concordant with AR method in 9 samples, discordant in 3, and provided measures of X inactivation in 2 samples with uninformative clinical results. We applied this method on an additional 98 females presenting to the clinic with phenotypes consistent with different hereditary disorders without a known genetic diagnosis. Here we show the use of transcriptome sequencing data to provide an accurate and complete estimation of X-inactivation and skew status in female patients.
|
| |
|
| Overall design |
RNA from whole blood for all patients was extracted in a PAXgene Tube following manufacturer’s instructions (Qiagen). The miRNeasy Mini kit from Qiagen was used for isolation of RNA and 101 base pair paired libraries were prepared using capture probes from the TruSeq®RNA Access Library Prep Kit (Illumina). Samples were sequenced at Mayo Clinic Medical Genome Facility (MGF) using Illumina Hiseq 4000 generating on average greater than 100 million reads per sample.
|
| |
|
| Contributor(s) |
Klee E, Fadra N, Jenkinson G, Rogers LS, Chanana P, Cousin MA, Macke EL, Ferrer A, Vairo FE, Olson R, Oliver GR, Mulvihill LA |
| Citation(s) |
38627676 |
| Submission date |
Jun 09, 2023 |
| Last update date |
Apr 25, 2024 |
| Contact name |
Numrah Fadra |
| E-mail(s) |
Fadra.Numrah@mayo.edu
|
| Phone |
2039178890
|
| Organization name |
Mayo clinic
|
| Street address |
625 19th Street NW, Apt 405, 405, 405, 405
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55901 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
|
| Samples (112)
|
|
| Relations |
| BioProject |
PRJNA982123 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE234607_RAW.tar |
50.6 Mb |
(http)(custom) |
TAR (of CSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...