|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jan 01, 2019 |
Title |
Genome-wide linkage analysis in Spanish melanoma-prone families [Round2] |
Organism |
Homo sapiens |
Experiment type |
Genome variation profiling by SNP array SNP genotyping by SNP array
|
Summary |
The main genetic factors for familial melanoma remain unknown in more than 75% of families. CDKN2A is mutated in around 20% of melanoma-prone families. Other high-risk melanoma susceptibility genes explain less than 3% of families studied to date. We performed the first genome-wide linkage analysis in CDKN2A-negative Spanish melanoma-prone families to identify novel melanoma susceptibility loci. We included 68 individuals from 2, 3 and 6 families with 2, 3 and at least 4 melanoma cases. We detected a locus with significant linkage evidence at 11q14.1-q14.3, with a maximum het-TLOD of 3.449 (rs12285365:A>G), using evidence from multiple pedigrees. The genes contained by the subregion with the strongest linkage evidence were: DLG2, PRSS23, FZD4 and TMEM135. We also detected several regions with suggestive linkage evidence (TLOD>1.9) (1q, 6p, 7p, 11q, 12p, 13q) including the region previously detected in melanoma-prone families from Sweden at 3q29. The family specific analysis revealed three loci with suggestive linkage evidence for family #1: 1q31.1-q32.1 (max. TLOD 2.447), 6p24.3-p22.3 (max. TLOD 2.409) and 11q13.3-q21 (max. TLOD 2.654). Future next generation sequencing studies of these regions may allow the identification of new melanoma susceptibility genetic factors.
|
|
|
Overall design |
The study included 29 melanoma cases and 39 non-affected individuals belonging to 11 Spanish melanoma prone families. Genome-wide genotyping was performed using the HumanOmni2.5 SNP array platform (Illumina).
|
|
|
Contributor(s) |
Potrony M, Puig-Butille JA, Farnham JM, Giménez-Xavier P, Badenas C, Tell-Martí G, Aguilera P, Carrera C, Malvehy J, Teerlink CC, Puig S |
Citation(s) |
29706638 |
Submission date |
Jan 15, 2018 |
Last update date |
Nov 02, 2020 |
Contact name |
joan anton Puig Butille |
E-mail(s) |
jantonpuig@gmail.com
|
Organization name |
Hospital Clínic
|
Street address |
Villarroel 170
|
City |
Barcelona |
ZIP/Postal code |
08036 |
Country |
Spain |
|
|
Platforms (1) |
GPL18952 |
Illumina HumanOmni2.5-8v1.1 beadchip |
|
Samples (15)
|
|
This SubSeries is part of SuperSeries: |
GSE109208 |
Genome-wide linkage analysis in Spanish melanoma-prone families |
|
Relations |
BioProject |
PRJNA430108 |
Supplementary file |
Size |
Download |
File type/resource |
GSE109207_RAW.tar |
792.3 Mb |
(http)(custom) |
TAR (of IDAT) |
GSE109207_Round2MatrixProcessed.txt.gz |
626.2 Mb |
(ftp)(http) |
TXT |
GSE109207_Round2MatrixSignalIntensities.txt.gz |
463.8 Mb |
(ftp)(http) |
TXT |
Processed data are available on Series record |
|
|
|
|
|