ArticleHuman genetics2010
A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.
Article in Human genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it, 31 citations in OpenAlex.
- Pooled it
- Comparative Transcriptomes of Canine and Human Prostate Cancers Identify Mediators of Castration Resistance.Veterinary and comparative oncology · 2024Article
- Functional roles of antisense enhancer RNA for promoting prostate cancer progression.Theranostics · 2021Article
- microRNA-205 and microRNA-338-3p Reduces Cell Apoptosis in Prostate Carcinoma Tissue and LNCaP Prostate Carcinoma Cells by Directly Targeting the B-Cell Lymphoma 2 (Bcl-2) Gene.Medical science monitor : international medical journal of experimental and clinical research · 2019Article
- Prostate Cancer Risk-Associated Single-Nucleotide Polymorphism Affects Prostate-Specific Antigen Glycosylation and Its Function.Clinical chemistry · 2019Article
- Characterization of the Glycosylation Site of Human PSA Prompted by Missense Mutation using LC-MS/MS.Journal of proteome research · 2015Article
- The PLCO Biorepository: Creating, Maintaining, and Administering a Unique Biospecimen Resource.Reviews on recent clinical trials · 2015Review
- Controlling the local false discovery rate in the adaptive Lasso.Biostatistics (Oxford, England) · 2013Article
- A resequence analysis of genomic loci on chromosomes 1q32.1, 5p15.33, and 13q22.1 associated with pancreatic cancer risk.Pancreas · 2013Article
- Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2011Article
- Current status of genome-wide association studies in cancer.Human genetics · 2011Review
- Fine mapping the KLK3 locus on chromosome 19q13.33 associated with prostate cancer susceptibility and PSA levels.Human genetics · 2011Article
- Phred-Phrap package to analyses tools: a pipeline to facilitate population genetics re-sequencing studies.Investigative genetics · 2011Article
- Genome-wide association studies in cancer--current and future directions.Carcinogenesis · 2010Article
- Admixture Mapping Links RACGAP1 Regulation to Prostate Cancer in African Americans.Cancer genomics & proteomicsArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
27 authors at 8 institutions in 4 countries.
Funding
Abstract
Single nucleotide polymorphisms (SNPs) in the KLK3 gene on chromosome 19q13.33 are associated with serum prostate-specific antigen (PSA) levels. Recent genome wide association studies of prostate cancer have yielded conflicting results for association of the same SNPs with prostate cancer risk. Since the KLK3 gene encodes the PSA protein that forms the basis for a widely used screening test for prostate cancer, it is critical to fully characterize genetic variation in this region and assess its relationship with the risk of prostate cancer. We have conducted a next-generation sequence analysis in 78 individuals of European ancestry to characterize common (minor allele frequency, MAF >1%) genetic variation in a 56 kb region on chromosome 19q13.33 centered on the KLK3 gene (chr19:56,019,829-56,076,043 bps). We identified 555 polymorphic loci in the process including 116 novel SNPs and 182 novel insertion/deletion polymorphisms (indels). Based on tagging analysis, 144 loci are necessary to tag the region at an r (2) threshold of 0.8 and MAF of 1% or higher, while 86 loci are required to tag the region at an r (2) threshold of 0.8 and MAF >5%. Our sequence data augments coverage by 35 and 78% as compared to variants in dbSNP and HapMap, respectively. We observed six non-synonymous amino acid or frame shift changes in the KLK3 gene and three changes in each of the neighboring genes, KLK15 and KLK2. Our study has generated a detailed map of common genetic variation in the genomic region surrounding the KLK3 gene, which should be useful for fine-mapping the association signal as well as determining the contribution of this locus to prostate cancer risk and/or regulation of PSA expression.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.