ArticleAmerican journal of human genetics2004
Comparison of microsatellites versus single-nucleotide polymorphisms in a genome linkage screen for prostate cancer-susceptibility Loci.
Article in American journal of human genetics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 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
57 citing papers in PubMed, 1 synthesis or guideline pooled it, 136 citations in OpenAlex.
- Genetic studies of stuttering in a founder population.Journal of fluency disorders · 2007Pooled it
- An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern.BMC genomics · 2020Article
- Article
- DNA-based Determination of Ancestry in Cynomolgus Macaques (Journal of the American Association for Laboratory Animal Science : JAALAS · 2018Article
- Genetic diversity of Afrikaner cattle in southern Africa.Tropical animal health and production · 2018Article
- A genome-wide screen for acrophobia susceptibility loci in a Finnish isolate.Scientific reports · 2016Article
- Novel mutations in the inverted formin 2 gene of Chinese families contribute to focal segmental glomerulosclerosis.Kidney international · 2015Article
- The IL-33-ST2L pathway is associated with coronary artery disease in a Chinese Han population.American journal of human genetics · 2013Article
- The complexity of prostate cancer: genomic alterations and heterogeneity.Nature reviews. Urology · 2012Review
- Risk of nasopharyngeal carcinoma associated with polymorphic lactotransferrin haplotypes.Medical oncology (Northwood, London, England) · 2012Article
- Effect of CYP17 and PSA gene polymorphisms on prostate cancer risk and circulating PSA levels in the Slovak population.Molecular biology reports · 2012Article
- Chromosomes 4 and 8 implicated in a genome wide SNP linkage scan of 762 prostate cancer families collected by the ICPCG.The Prostate · 2012Article
- Article
- Genome-wide scan of granular corneal dystrophy, type II: confirmation of chromosome 5q31 and identification of new co-segregated loci on chromosome 3q26.3.Experimental & molecular medicine · 2011Article
- Linkage analysis of quantitative refraction and refractive errors in the Beaver Dam Eye Study.Investigative ophthalmology & visual science · 2011Article
- Genotyping errors in a calibrated DNA register: implications for identification of individuals.BMC genetics · 2011Article
- A pipeline for copy number variation detection based on principal component analysis.Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2011Article
- Integrated genomic analysis of sézary syndrome.Genetics research international · 2011Article
- Genome-wide linkage using the Social Responsiveness Scale in Utah autism pedigrees.Molecular autism · 2010Article
- A recessive gene for primary vesicoureteral reflux maps to chromosome 12p11-q13.Journal of the American Society of Nephrology : JASN · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 1 institution in 1 country.
Funding
Abstract
Prostate cancer is one of the most common cancers among men and has long been recognized to occur in familial clusters. Brothers and sons of affected men have a 2-3-fold increased risk of developing prostate cancer. However, identification of genetic susceptibility loci for prostate cancer has been extremely difficult. Although the suggestion of linkage has been reported for many chromosomes, the most promising regions have been difficult to replicate. In this study, we compare genome linkage scans using microsatellites with those using single-nucleotide polymorphisms (SNPs), performed in 467 men with prostate cancer from 167 families. For the microsatellites, the ABI Prism Linkage Mapping Set version 2, with 402 microsatellite markers, was used, and, for the SNPs, the Early Access Affymetrix Mapping 10K array was used. Our results show that the presence of linkage disequilibrium (LD) among SNPs can lead to inflated LOD scores, and this seems to be an artifact due to the assumption of linkage equilibrium that is required by the current genetic-linkage software. After excluding SNPs with high LD, we found a number of new LOD-score peaks with values of at least 2.0 that were not found by the microsatellite markers: chromosome 8, with a maximum model-free LOD score of 2.2; chromosome 2, with a LOD score of 2.1; chromosome 6, with a LOD score of 4.2; and chromosome 12, with a LOD score of 3.9. The LOD scores for chromosomes 6 and 12 are difficult to interpret, because they occurred only at the extreme ends of the chromosomes. The greatest gain provided by the SNP markers was a large increase in the linkage information content, with an average information content of 61% for the SNPs, versus an average of 41% for the microsatellite markers. The strengths and weaknesses of microsatellite versus SNP markers are illustrated by the results of our genome linkage scans.
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.