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| Status |
Public on Apr 19, 2017 |
| Title |
MRPL53, a New Candidate Gene for Orofacial Clefting, Identified Using an eQTL Approach |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
SNP genotyping by SNP array
|
| Summary |
This SuperSeries is composed of the SubSeries listed below.
A valuable approach to understand how individual and population genetic differences can predispose to disease is to assess the impact of genetic variants on cellular functions (e.g., gene expression) of cell and tissue types related to pathological states. To understand the genetic basis of nonsyndromic cleft lip with or without cleft palate (NSCL/P) susceptibility, a complex and highly prevalent congenital malformation, we searched for genetic variants with a regulatory role in a disease-related tissue, the lip muscle (orbicularis oris muscle [OOM]), of affected individuals. From 46 OOM samples, which are frequently discarded during routine corrective surgeries on patients with orofacial clefts, we derived mesenchymal stem cells and correlated the individual genetic variants with gene expression from these cultured cells. Through this strategy, we detected significant cis-eQTLs (i.e., DNA variants affecting gene expression) and selected a few candidates to conduct an association study in a large Brazilian cohort (624 patients and 668 controls). This resulted in the discovery of a novel susceptibility locus for NSCL/P, rs1063588, the best eQTL for the MRPL53 gene, where evidence for association was mostly driven by the Native American ancestry component of our Brazilian sample. MRPL53 (2p13.1) encodes a 39S protein subunit of mitochondrial ribosomes and interacts with MYC, a transcription factor required for normal facial morphogenesis. Our study illustrates not only the importance of sampling admixed populations but also the relevance of measuring the functional effects of genetic variants over gene expression to dissect the complexity of disease phenotypes.
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| Overall design |
Refer to individual Series
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| Citation(s) |
29053389 |
| |
| Submission date |
Aug 18, 2016 |
| Last update date |
Jul 26, 2018 |
| Contact name |
Cibele Masotti |
| Organization name |
University of Sao Paulo
|
| Department |
Genetics and Evolutionary Biology
|
| Lab |
Human Development Genetics Lab
|
| Street address |
Rua do Matao, 277.
|
| City |
Sao Paulo |
| State/province |
São Paulo |
| ZIP/Postal code |
05508-090 |
| Country |
Brazil |
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| Platforms (3) |
| GPL3718 |
[Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array |
| GPL3720 |
[Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array |
| GPL6244 |
[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version] |
|
| Samples (138)
|
| GSM2283457 |
Patient F3404 |
| GSM2283458 |
Patient F3413 |
| GSM2283459 |
Patient F3427 |
| GSM2283460 |
Patient F3430 |
| GSM2283461 |
Patient F3434 |
| GSM2283462 |
Patient F3436 |
| GSM2283463 |
Patient F3439 |
| GSM2283464 |
Patient F3440 |
| GSM2283465 |
Patient F3458 |
| GSM2283466 |
Patient F3459 |
| GSM2283467 |
Patient F3462 |
| GSM2283468 |
Patient F3463 |
| GSM2283469 |
Patient F3468 |
| GSM2283470 |
Patient F3474 |
| GSM2283471 |
Patient F3476 |
| GSM2283472 |
Patient F3478 |
| GSM2283473 |
Patient F3479 |
| GSM2283474 |
Patient F3480 |
| GSM2283475 |
Patient F3484 |
| GSM2283476 |
Patient F3488 |
| GSM2283477 |
Patient F3491 |
| GSM2283478 |
Patient F3493 |
| GSM2283479 |
Patient F3496 |
| GSM2283480 |
Patient F3497 |
| GSM2283481 |
Patient F3507 |
| GSM2283482 |
Patient F4219 |
| GSM2283483 |
Patient F4257 |
| GSM2283484 |
Patient F4317 |
| GSM2283485 |
Patient F4437 |
| GSM2283486 |
Patient F5610 |
| GSM2283487 |
Patient F5614 |
| GSM2283488 |
Patient F5647 |
| GSM2283489 |
Patient F5662 |
| GSM2283490 |
Patient F5686 |
| GSM2283491 |
Control F5715 |
| GSM2283492 |
Control F5716 |
| GSM2283493 |
Patient F5959 |
| GSM2283494 |
Control F5992 |
| GSM2283495 |
Patient F6010 |
| GSM2283496 |
Patient F6023 |
| GSM2283497 |
Patient F6081 |
| GSM2283498 |
Patient F6130 |
| GSM2283499 |
Control F8000 |
| GSM2284834 |
F1403Nsp, Patient |
| GSM2284835 |
F3292Nsp, Patient |
| GSM2284836 |
F3324Nsp, Patient |
| GSM2284837 |
F3404Nsp, Patient |
| GSM2284838 |
F3413Nsp, Patient |
| GSM2284839 |
F3427Nsp, Patient |
| GSM2284840 |
F3430Nsp, Patient |
| GSM2284841 |
F3434Nsp, Patient |
| GSM2284842 |
F3436Nsp, Patient |
| GSM2284843 |
F3439Nsp, Patient |
| GSM2284844 |
F3440Nsp, Patient |
| GSM2284845 |
F3458Nsp, Patient |
| GSM2284846 |
F3459Nsp, Patient |
| GSM2284847 |
F3462Nsp, Patient |
| GSM2284848 |
F3463Nsp, Patient |
| GSM2284849 |
F3468Nsp, Patient |
| GSM2284850 |
F3474Nsp, Patient |
| GSM2284851 |
F3476Nsp, Patient |
| GSM2284852 |
F3478Nsp, Patient |
| GSM2284853 |
F3479Nsp, Patient |
| GSM2284854 |
F3480Nsp, Patient |
| GSM2284855 |
F3484Nsp, Patient |
| GSM2284856 |
F3488Nsp, Patient |
| GSM2284857 |
F3491Nsp, Patient |
| GSM2284858 |
F3493Nsp, Patient |
| GSM2284859 |
F3496Nsp, Patient |
| GSM2284860 |
F3497Nsp, Patient |
| GSM2284861 |
F3506Nsp, Patient |
| GSM2284862 |
F3507Nsp, Patient |
| GSM2284863 |
F4219Nsp, Patient |
| GSM2284864 |
F4257Nsp, Patient |
| GSM2284865 |
F4317Nsp, Patient |
| GSM2284866 |
F4437Nsp, Patient |
| GSM2284867 |
F5610Nsp, Patient |
| GSM2284868 |
F5614Nsp, Patient |
| GSM2284869 |
F5647Nsp, Patient |
| GSM2284870 |
F5662Nsp, Patient |
| GSM2284871 |
F5686Nsp, Patient |
| GSM2284872 |
F5715Nsp, Control |
| GSM2284873 |
F5716Nsp, Control |
| GSM2284874 |
F6010Nsp, Patient |
| GSM2284875 |
F6023Nsp, Patient |
| GSM2284876 |
F6081Nsp, Patient |
| GSM2284877 |
F6130Nsp, Patient |
| GSM2284878 |
F8000Nsp, Control |
| GSM2284879 |
F1403Sty, Patient |
| GSM2284880 |
F3292Sty, Patient |
| GSM2284881 |
F3324Sty, Patient |
| GSM2284882 |
F3404Sty, Patient |
| GSM2284883 |
F3413Sty, Patient |
| GSM2284884 |
F3427Sty, Patient |
| GSM2284885 |
F3430Sty, Patient |
| GSM2284886 |
F3434Sty, Patient |
| GSM2284887 |
F3436Sty, Patient |
| GSM2284888 |
F3439Sty, Patient |
| GSM2284889 |
F3440Sty, Patient |
| GSM2284890 |
F3458Sty, Patient |
| GSM2284891 |
F3459Sty, Patient |
| GSM2284892 |
F3462Sty, Patient |
| GSM2284893 |
F3463Sty, Patient |
| GSM2284894 |
F3468Sty, Patient |
| GSM2284895 |
F3474Sty, Patient |
| GSM2284896 |
F3476Sty, Patient |
| GSM2284897 |
F3478Sty, Patient |
| GSM2284898 |
F3479Sty, Patient |
| GSM2284899 |
F3480Sty, Patient |
| GSM2284900 |
F3484Sty, Patient |
| GSM2284901 |
F3488Sty, Patient |
| GSM2284902 |
F3491Sty, Patient |
| GSM2284903 |
F3493Sty, Patient |
| GSM2284904 |
F3496Sty, Patient |
| GSM2284905 |
F3497Sty, Patient |
| GSM2284906 |
F3506Sty, Patient |
| GSM2284907 |
F3507Sty, Patient |
| GSM2284908 |
F4219Sty, Patient |
| GSM2284909 |
F4257Sty, Patient |
| GSM2284910 |
F4317Sty, Patient |
| GSM2284911 |
F4437Sty, Patient |
| GSM2284912 |
F5610Sty, Patient |
| GSM2284913 |
F5614Sty, Patient |
| GSM2284914 |
F5647Sty, Patient |
| GSM2284915 |
F5662Sty, Patient |
| GSM2284916 |
F5686Sty, Patient |
| GSM2284917 |
F5715Sty, Control |
| GSM2284918 |
F5716Sty, Control |
| GSM2284919 |
F5959Sty, Patient |
| GSM2284920 |
F5992Sty, Control |
| GSM2284921 |
F6010Sty, Patient |
| GSM2284922 |
F6023Sty, Patient |
| GSM2284923 |
F6081Sty, Patient |
| GSM2284924 |
F6130Sty, Patient |
| GSM2284925 |
F8000Sty, Control |
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| This SuperSeries is composed of the following SubSeries: |
| GSE85748 |
MRPL53, a New Candidate Gene for Orofacial Clefting, Identified Using an eQTL Approach [expression array] |
| GSE85814 |
MRPL53, a New Candidate Gene for Orofacial Clefting, Identified Using an eQTL Approach [SNP array] |
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| Relations |
| BioProject |
PRJNA339466 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE85817_RAW.tar |
2.5 Gb |
(http)(custom) |
TAR (of CEL, CHP) |
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