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Rodriguez S, Al-Ghamdi OA, Guthrie PA, Shihab HA, McArdle W, Gaunt T, Alharbi KK, Day IN. Frequency of KLK3 gene deletions in the general population. Ann Clin Biochem 2016; 54:472-480. [PMID: 27555663 DOI: 10.1177/0004563216666999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background One of the kallikrein genes ( KLK3) encodes prostate-specific antigen, a key biomarker for prostate cancer. A number of factors, both genetic and non-genetic, determine variation of serum prostate-specific antigen concentrations in the population. We have recently found three KLK3 deletions in individuals with very low prostate-specific antigen concentrations, suggesting a link between abnormally reduced KLK3 expression and deletions of KLK3. Here, we aim to determine the frequency of kallikrein gene 3 deletions in the general population. Methods The frequency of KLK3 deletions in the general population was estimated from the 1958 Birth Cohort sample ( n = 3815) using amplification ratiometry control system. In silico analyses using PennCNV were carried out in the same cohort and in NBS-WTCCC2 in order to provide an independent estimation of the frequency of KLK3 deletions in the general population. Results Amplification ratiometry control system results from the 1958 cohort indicated a frequency of KLK3 deletions of 0.81% (3.98% following a less stringent calling criterion). From in silico analyses, we found that potential deletions harbouring the KLK3 gene occurred at rates of 2.13% (1958 Cohort, n = 2867) and 0.99% (NBS-WTCCC2, n = 2737), respectively. These results are in good agreement with our in vitro experiments. All deletions found were in heterozygosis. Conclusions We conclude that a number of individuals from the general population present KLK3 deletions in heterozygosis. Further studies are required in order to know if interpretation of low serum prostate-specific antigen concentrations in individuals with KLK3 deletions may offer false-negative assurances with consequences for prostate cancer screening, diagnosis and monitoring.
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Affiliation(s)
- Santiago Rodriguez
- 1 MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Osama A Al-Ghamdi
- 2 Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.,3 School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Philip Ai Guthrie
- 1 MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Hashem A Shihab
- 1 MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Wendy McArdle
- 3 School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Tom Gaunt
- 1 MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Khalid K Alharbi
- 2 Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ian Nm Day
- 3 School of Social and Community Medicine, University of Bristol, Bristol, UK
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Alharbi KK, Aldahmesh MA, Gaunt TR, Rassoulian H, Ai Guthrie P, Rodriguez S, Boustred CR, Spanakis E, Day INM. MeltMADGE for mutation scanning of specific genes in population studies. Nat Protoc 2010; 5:1800-12. [PMID: 21030955 DOI: 10.1038/nprot.2010.136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
MeltMADGE reconfigures the mutation scanning process of denaturing gradient gel electrophoresis so that the independent variable is time rather than space and the dependent (denaturing) variable is temperature rather than concentration of chemical denaturant. Use of a thermal ramp enables the use of a homogeneous gel and therefore of high-density arrays of wells such as those of microplate array diagonal gel electrophoresis (MADGE). In this configuration, electrophoresis of products on 10-12 96-well meltMADGE gels can be conducted in a 1- to 2-liter tank in a 1- to 2-h run, enabling the scanning of a target amplicon in over 1,000 subjects simultaneously. Gels are read by imaging the fluorescence of UV-excited ethidium bromide, giving a simple, economical system for identifying rarer sequence variants in target genes; it is suitable for large-scale case-control or population studies and other comparable applications. Different amplicons with similar melting characteristics can also be combined in the same run.
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Affiliation(s)
- Khalid K Alharbi
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
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Kurdyla TM, Guthrie PA, McDonald BA, Appel DN. RFLPs in mitochondrial and nuclear DNA indicate low levels of genetic diversity in the oak wilt pathogen Ceratocystis fagacearum. Curr Genet 1995; 27:373-8. [PMID: 7614561 DOI: 10.1007/bf00352107] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Genetic diversity in the oak wilt pathogen Ceratocystis fagacearum was assessed using restriction fragment length polymorphisms (RFLPs) of the mitochondrial DNA (mtDNA) and anonymous RFLP loci in the nuclear DNA (nuDNA). No genetic variation was detected in the mtDNA among 27 isolates sampled from a broad geographical area. Southern hybridization to 100 anonymous, random, nuDNA probes detected a low level of variation among nine of the isolates. Only 35 out of 437 probe-enzyme combinations detected RFLPs. Most of the RFLPs appeared to result from insertions and deletions of less than 200 bp. A composite multilocus haplotype based on hybridization to six anonymous probes could differentiate each of the nine isolates tested, suggesting that these probes may be useful for further studies of the population biology and epidemiology of this pathogen. Hypotheses are presented to account for the low level of genetic variation.
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Affiliation(s)
- T M Kurdyla
- Department of Plant Pathology and Microbiology, Texas A & M University, College Station 77843-2132, USA
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