rs12323459 (PTGER2-TXNDC16): Pediatric Glioma GWAS
Key takeaways
- rs12323459 sits in the genomic neighborhood of PTGER2 (prostaglandin E receptor 2) and TXNDC16
- A large GWAS of 4069 children with glioma and 8778 controls examined common variants across the whole genome
- The study's primary significant finding was at CDKN2B-AS1 on chromosome 9, not at the PTGER2-TXNDC16 locus
- No specific association for rs12323459 was reported in the available study text
- This study marked the first genome-wide significant common variant discovery in pediatric brain tumor research
Key takeaways
- rs12323459 sits in the genomic neighborhood of PTGER2 (prostaglandin E receptor 2) and TXNDC16 (thioredoxin domain containing 16)
- A large multi-ancestry GWAS (genome-wide association study) of 4069 children with glioma and 8778 controls examined common genetic variants across the entire genome
- The study's primary significant finding was at a different region, CDKN2B-AS1 at 9p21.3, not at the PTGER2-TXNDC16 locus
- No specific association for rs12323459 was reported in the provided study text
- This study marked the first genome-wide significant common variant discovery in pediatric brain tumor research
What the research says A multi-ancestry GWAS meta-analysis of 4069 children with glioma (a type of brain tumor) and 8778 cancer-free controls, drawn from populations in California and Scandinavia, examined common genetic variants across the entire genome to identify risk factors for pediatric brain tumors. The study identified CDKN2B-AS1 at chromosomal region 9p21.3 (near the tumor suppressor gene CDKN2B) as the first genome-wide significant common variant risk locus for childhood astrocytoma, the most frequent subtype of pediatric glioma. The provided study text does not include specific findings for rs12323459 in the PTGER2 (prostaglandin E receptor 2) and TXNDC16 (thioredoxin domain containing 16) region.
Reported associations
- Childhood astrocytoma: A variant at the CDKN2B-AS1 locus on chromosome 9 (rs573687, not rs12323459) was associated with childhood astrocytoma at genome-wide significance (odds ratio 1.27, 95% confidence interval 1.18-1.37, p = 6.97e-10), with the association driven primarily by low-grade cases (p = 3.82e-9). No specific association for rs12323459 was reported.
- Glioma overall: A second variant at the same locus (rs3731239) approached genome-wide significance for overall glioma (p = 5.41e-8). No specific association for rs12323459 was reported.
- High-grade glioma: No significant association was observed for high-grade tumors at the 9p21.3 locus. No findings for rs12323459 were reported in the provided text.
Evidence quality The source study is a well-powered, population-based GWAS meta-analysis with 4069 glioma cases and 8778 controls spanning six genetic ancestries, including European-American, African-American, Latino-American, and Scandinavian populations. The primary findings at the 9p21.3 locus were replicated in a separate independent case-control cohort and showed consistent, unidirectional effects across all six ancestries studied. A transcriptome-wide association study further linked risk variants to decreased brain tissue expression of CDKN2B (p = 8.09e-8), providing a functional basis for the main finding. The provided study text does not report associations specifically for rs12323459, making direct evidence quality assessment for this individual variant impossible from the available source material.
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What genes are near rs12323459?
rs12323459 is located in the genomic region near PTGER2 (prostaglandin E receptor 2) and TXNDC16 (thioredoxin domain containing 16).
Is rs12323459 linked to brain tumors or glioma?
The available study examined childhood glioma risk across the entire genome but did not report a specific association for rs12323459 in the provided text. The study's primary finding involved a different gene region on chromosome 9.
What is PTGER2?
PTGER2 stands for prostaglandin E receptor 2, a gene involved in prostaglandin signaling. Its specific role in relation to rs12323459 is not described in the available study text.
What did this childhood glioma GWAS find?
The study found that common variants near CDKN2B-AS1 on chromosome 9 were significantly associated with childhood astrocytoma (odds ratio 1.27), marking the first genome-wide significant common variant discovery in pediatric brain tumor genetics. The association was driven by low-grade astrocytoma and was consistent across six genetic ancestries.
How many children were included in this brain tumor genetics study?
The study included 4069 children with glioma and 8778 cancer-free controls from multiple genetic ancestries, including populations from California and Scandinavia.