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Quadros L, Ghosh K, Shetty S. A common G10430A mutation (Gly 60 Ser) in the factor IX gene describes the presence of moderate and mild hemophilia B in the majority of the Gujarati population. Ann Hematol 2007; 86:377-9. [PMID: 17308903 DOI: 10.1007/s00277-007-0250-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Accepted: 12/30/2006] [Indexed: 10/23/2022]
Abstract
Hemophilia B is an X-linked recessively inherited bleeding disorder afflicting humans across all socio-economic as well as racial groups. A wide range of mutations showing high heterogeneity has been reported in different populations. Thus, it has been difficult to adopt a cost-effective strategy for the genetic diagnosis of hemophilia B families. We report the presence of a common G10430A mutation in exon d of the factor IX gene, wherein the highly conserved Gly 60 residue of the first epidermal growth like domain was changed to Ser in 22 out of 22 moderately severe to mild hemophilia B patients originating from Gujarat. None of the eight Gujarati severe hemophilia B patients, 30 normal Gujarati men, and 20 moderately severe to mild hemophilia B patients belonging to other communities showed the presence of this mutation. This mutation occurred in the same haplotype background thereby suggesting a 'founder effect.' The direct detection of this G10430A mutation can be used for accurate carrier detection and prenatal diagnosis in mild to moderate factor-IX-deficient patients belonging to the Gujarat state of western India.
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Affiliation(s)
- Leera Quadros
- KEM Hospital, Institute of Immunohaematology ICMR, Parel, Mumbai, India
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2
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Borst A, Box ATA, Fluit AC. False-positive results and contamination in nucleic acid amplification assays: suggestions for a prevent and destroy strategy. Eur J Clin Microbiol Infect Dis 2004; 23:289-99. [PMID: 15015033 DOI: 10.1007/s10096-004-1100-1] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Contamination of samples with DNA is still a major problem in microbiology laboratories, despite the wide acceptance of PCR and other amplification techniques for the detection of frequently low amounts of target DNA. This review focuses on the implications of contamination in the diagnosis and research of infectious diseases, possible sources of contaminants, strategies for prevention and destruction, and quality control. Contamination of samples in diagnostic PCR can have far-reaching consequences for patients, as illustrated by several examples in this review. Furthermore, it appears that the (sometimes very unexpected) sources of contaminants are diverse (including water, reagents, disposables, sample carry over, and amplicon), and contaminants can also be introduced by unrelated activities in neighboring laboratories. Therefore, lack of communication between researchers using the same laboratory space can be considered a risk factor. Only a very limited number of multicenter quality control studies have been published so far, but these showed false-positive rates of 9-57%. The overall conclusion is that although nucleic acid amplification assays are basically useful both in research and in the clinic, their accuracy depends on awareness of risk factors and the proper use of procedures for the prevention of nucleic acid contamination. The discussion of prevention and destruction strategies included in this review may serve as a guide to help improve laboratory practices and reduce the number of false-positive amplification results.
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Affiliation(s)
- A Borst
- Eijkman-Winkler Center for Microbiology, Infectious Diseases and Inflammation, University Medical Center, PO Box 85500, 3508 GA Utrecht, The Netherlands
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3
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Ketterling RP, Drost JB, Scaringe WA, Liao DZ, Liu JZ, Kasper CK, Sommer SS. Reported in vivo splice-site mutations in the factor IX gene: severity of splicing defects and a hypothesis for predicting deleterious splice donor mutations. Hum Mutat 2000; 13:221-31. [PMID: 10090477 DOI: 10.1002/(sici)1098-1004(1999)13:3<221::aid-humu6>3.0.co;2-u] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Small consensus sequences have been defined for RNA splicing, but questions about splicing in humans remain unanswered. Analysis of germline mutations in the factor IX gene offers a highly advantageous system for studying the mutational process in humans. In a sample of 860 families with hemophilia B, 9% of independent mutations are likely to disrupt splicing as their primary mode of action. This includes 26 splicing mutations reported herein. When combined with the factor IX splice mutations reported by others, at least 104 independent mutations have been observed, 80 of which are single base substitutions within the splice donor and splice acceptor consensus sequences. After analysis of these mutations, the following inferences emerge: (1) the susceptibility of a splice donor sequence to deleterious mutation depends on the degree of similarity with the donor consensus sequence, suggesting a simple "5-6 hypothesis" for predicting deleterious vs. neutral mutations; (2) the great majority of mutations that disrupt the splice donor or splice acceptor sequences result in at least a 100-fold decrement in factor IX coagulant activity, indicating that the mutations at these sites generally function as an on/off switch; (3) mutations that create cryptic splice junctions or that shorten but do not interrupt the polypyrimidine tract in the splice acceptor sequence can reduce splicing by a variable amount; and (4) there are thousands of potential donor-acceptor consensus sequence combinations in the 38-kb factor IX gene region apparently not reduced by evolutionary selective pressure, presenting an apparent paradox; i.e., mutations in the donor and acceptor consensus sequences at intron/exon splice junctions can dramatically alter normal splicing, yet, appropriately spaced, good matches to the consensus sequences do not predispose to significant amounts of alternative splicing.
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Affiliation(s)
- R P Ketterling
- Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, Minnesota, USA
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4
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Giannelli F, Green PM, Sommer SS, Poon M, Ludwig M, Schwaab R, Reitsma PH, Goossens M, Yoshioka A, Figueiredo MS, Brownlee GG. Haemophilia B: database of point mutations and short additions and deletions--eighth edition. Nucleic Acids Res 1998; 26:265-8. [PMID: 9399849 PMCID: PMC147172 DOI: 10.1093/nar/26.1.265] [Citation(s) in RCA: 125] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The eighth edition of the haemophilia B database (http://www.umds.ac. uk/molgen/haemBdatabase.htm ) lists in an easily accessible form all known factor IX mutations due to small changes (base substitutions and short additions and/or deletions of <30 bp) identified in haemophilia B patients. The 1713 patient entries are ordered by the nucleotide number of their mutation. Where known, details are given on: factor IX activity, factor IX antigen in circulation, presence of inhibitor and origin of mutation. References to published mutations are given and the laboratories generating the data are indicated.
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Affiliation(s)
- F Giannelli
- Paediatric Research Unit, Guy's Tower, London Bridge, London SE1 9RT, UK
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5
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Giannelli F, Green PM, Sommer SS, Poon MC, Ludwig M, Schwaab R, Reitsma PH, Goossens M, Yoshioka A, Figueiredo MS, Brownlee GG. Haemophilia B: database of point mutations and short additions and deletions, 7th edition. Nucleic Acids Res 1997; 25:133-5. [PMID: 9016521 PMCID: PMC146360 DOI: 10.1093/nar/25.1.133] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The seventh edition of the haemophilia B database lists in easily accessible form all known factor IX mutations due to small changes (base substitutions and short additions and/or deletions of <30 bp) identified in haemophilia B patients. The 1535 patient entries are ordered by the nucleotide number of their mutation. Where known, details are given on: factor IX activity, factor IX antigen in circulation, presence of inhibitor and origin of mutation. References to published mutations are given and the laboratories generating the data are indicated.
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Affiliation(s)
- F Giannelli
- Paediatric Research Unit, Guy's Tower, London Bridge, London SE1 9RT, UK
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6
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Sommer SS, Ketterling RP. The factor IX gene as a model for analysis of human germline mutations: an update. Hum Mol Genet 1996; 5 Spec No:1505-14. [PMID: 8875257 DOI: 10.1093/hmg/5.supplement_1.1505] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The variation generated by germline mutation is essential for evolution, but individuals pay a steep price in the form of Mendelian disease and genetic predisposition to complex disease. Indeed, the health of a species is determined ultimately by the rate of germline mutation. Analysis of the factor IX gene in patients with hemophilia B has provided insights into the human germline mutational process. Herein, seven topics will be reviewed with emphasis on recent advances: (i) proposed mechanisms of deletions, inversions, and insertions; (ii) discordant sex ratios of mutation and associated age effects; (iii) somatic mosaicism; (iv) founder effects; (v) mutation rates; (vi) the factor IX gene as a germline mutagen test; and (vii) cancer as a possible mechanism for maintaining a constant rate of germline mutation.
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Affiliation(s)
- S S Sommer
- Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, MN 55905, USA
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7
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Giannelli F, Green PM, Sommer SS, Poon MC, Ludwig M, Schwaab R, Reitsma PH, Goossens M, Yoshioka A, Brownlee GG. Haemophilia B (sixth edition): a database of point mutations and short additions and deletions. Nucleic Acids Res 1996; 24:103-18. [PMID: 8594556 PMCID: PMC145614 DOI: 10.1093/nar/24.1.103] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The sixth edition of the haemophilia B database lists in easily accessible form all known factor IX mutations due to small changes (base substitutions and short additions and/or deletions of <30 bp) identified in haemophilia B patients. The 1380 patient entries are ordered by the nucleotide number of their mutation. Where known, details are given on factor IX activity, factor IX antigen in circulation and origin of mutation. References to published mutations are given and the laboratories generating the data are indicated.
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8
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Schwaab R, Oldenburg J, Schwaab U, Johnson DJ, Schmidt W, Olek K, Brackman HH, Tuddenham EG. Characterization of mutations within the factor VIII gene of 73 unrelated mild and moderate haemophiliacs. Br J Haematol 1995; 91:458-64. [PMID: 8547094 DOI: 10.1111/j.1365-2141.1995.tb05322.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
To screen for mutations within the factor VIII gene of 101 patients (85 unrelated), we used denaturing gradient gel electrophoresis (DGGE) after DNA amplification of target regions, including all coding regions except for the middle part (amino acid 757 to amino acid 1649) of the B domain. With this method, missense mutations were identified in 86% of unrelated patients. 41 different mutations were identified: 25 of them have not been described previously. Five of the genotypes are associated with CRM+ and 26 with CRMred status. Patients who are definitely related to each other showed no differences in DNA sequence. One patient showed two different base pair alterations, the first at amino acid 469 [ala(GCA-->gly(GGA)] and the second at position 473 [tyr(TAT)-->cys(TGT)]. One patient with an amino acid change at position 1689 [arg(CGC)-->his(CAC)] has developed an inhibitor against factor VIII.
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Affiliation(s)
- R Schwaab
- Institut für Experimentelle Hämatologie und Transfusionsmedizin, Bonn, Germany
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9
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Affiliation(s)
- P M Green
- Division of Medical and Molecular Genetics, United Medical School, Guy's Hospital, London, United Kingdom
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10
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Giannelli F, Green PM, Sommer SS, Lillicrap DP, Ludwig M, Schwaab R, Reitsma PH, Goossens M, Yoshioka A, Brownlee GG. Haemophilia B: database of point mutations and short additions and deletions, fifth edition, 1994. Nucleic Acids Res 1994; 22:3534-46. [PMID: 7937052 PMCID: PMC308314 DOI: 10.1093/nar/22.17.3534] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The fifth edition of the haemophilia B database lists in easily accessible form all known factor IX mutations due to small changes (base substitutions and short additions and/or deletions of < 30bp) identified in haemophilia B patients. The 1,142 patient entries are ordered by the nucleotide number of their mutation. Where known, details are given on: factor IX activity, factor IX antigen in circulation, and origin of mutation. References to published mutations are given and the laboratories generating the data are indicated.
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11
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Knobloch O, Zoll B, Zerres K, Brackmann HH, Olek K, Ludwig M. Recurrent mutations in the factor IX gene: founder effect or repeat de novo events. Investigation of the German haemophilia B population and review of de novo mutations. Hum Genet 1993; 92:40-8. [PMID: 8365725 DOI: 10.1007/bf00216143] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The investigation of 114 unrelated patients, representing about half the sample of the German haemophilia B population, enabled us to delineate the causative mutation in 103 (90.4%) haemophilic factor IX genes. Of these 103 cases 84 (81.6%) turned out to be unique molecular events, the remainder being repeats. Haplotype analysis revealed that the great majority, if not all, of these recurrent observations occurred independently. This conclusion is supported by our finding that three de novo mutations could be demonstrated at two sites of frequent mutation. A further 20 de novo events could be established in an unselected sample of 37 families with sporadic haemophilia B and 37 families with a history of the disease. Altogether, the germ line of origin could be determined in 21 of these 23 cases, thereby indicating a ratio of male to female mutation rates close to 2. On the basis of the data available, it is becoming clear that rearrangements in the factor IX gene (35.4% of de novo cases) are responsible for haemophilia B at a higher frequency than has been observed today (12.3%). More than two-thirds of the de novo cases cause the severe form of the disease, thereby reflecting the deficit of these haemophilic genes in the actual gene pool because of excess mortality in the past. In addition 40% (12/30) of the de novo single-base mutations were transitions at CpG dinucleotides. Compared with the expected at-random frequency, this observation indicates an 83-fold enhancement of mutation at CpG.
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Affiliation(s)
- O Knobloch
- Institut für Humangenetik, Göttingen, Germany
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12
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Bottema CD, Sommer SS. PCR amplification of specific alleles: rapid detection of known mutations and polymorphisms. Mutat Res 1993; 288:93-102. [PMID: 7686270 DOI: 10.1016/0027-5107(93)90211-w] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We review a method termed PCR Amplification of Specific Alleles (PASA), a generally applicable technique for the detection of known point mutations, small deletions and insertions, polymorphisms and other sequence variations. PASA is a modification of PCR that depends on the synthesis of a PCR oligonucleotide primer that precisely matches with one of the alleles but mismatches with the other. When the mismatch occurs near the 3' end of the PCR primer, amplification is inefficient. Therefore, preferential amplification of the perfectly matched allele is obtained. The method should be generally applicable as our results indicate that with proper optimization all possible alleles can be reliably distinguished. The ease and technical simplicity of PASA make genetic analyses more accessible. PASA can be also adapted to accommodate specific requirements and can be extended by incorporating other techniques. Moreover, PASA shows promise for population screening because the technique is rapid, highly reproducible, inexpensive, nonisotopic, and amendable to automation.
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Affiliation(s)
- C D Bottema
- Department of Biochemistry and Molecular Biology, Mayo Clinic Foundation, Rochester, MN 55905
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13
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Giannelli F, Green PM, High KA, Sommer S, Poon MC, Ludwig M, Schwaab R, Reitsma PH, Goossens M, Yoshioka A. Haemophilia B: database of point mutations and short additions and deletions--fourth edition, 1993. Nucleic Acids Res 1993; 21:3075-87. [PMID: 8392713 PMCID: PMC309734 DOI: 10.1093/nar/21.13.3075] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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14
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Bottema CD, Ketterling RP, Vielhaber E, Yoon HS, Gostout B, Jacobson DP, Shapiro A, Sommer SS. The pattern of spontaneous germ-line mutation: relative rates of mutation at or near CpG dinucleotides in the factor IX gene. Hum Genet 1993; 91:496-503. [PMID: 8314564 DOI: 10.1007/bf00217779] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Mutations at CpG dinucleotides were delineated in the factor IX gene of 38 hemophilia B patients. When transitions at CpG were considered with those previously reported by us and those compiled in the factor IX mutation database, the following patterns emerged. Many CpG sites were mutated with high frequency, while two CpG sites were infrequently mutated (R29-->Q and R116-->TGA). Of the 6 possible nonsense mutations and the 14 missense mutations that would produce a nonconservative change at conserved amino acids, all have been observed to cause hemophilia B except A-10-->T and R338-->Q. By contrast, none of the 6 missense changes at nonconserved amino acids have been observed to cause hemophilia B. At those CpG sites that are frequently mutated, the rate of transitions is estimated to be 20-fold higher than transitions at non-CpG sites. Point mutations in close proximity to CpG dinucleotides did not seem elevated.
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Affiliation(s)
- C D Bottema
- Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, MN 55905
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15
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Bottema CD, Sarkar G, Cassady JD, Ii S, Dutton CM, Sommer SS. Polymerase chain reaction amplification of specific alleles: a general method of detection of mutations, polymorphisms, and haplotypes. Methods Enzymol 1993; 218:388-402. [PMID: 8510541 DOI: 10.1016/0076-6879(93)18031-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- C D Bottema
- Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, Minnesota 55905
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16
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Giannelli F, Green PM, High KA, Sommer S, Lillicrap DP, Ludwig M, Olek K, Reitsma PH, Goossens M, Yoshioka A. Haemophilia B: database of point mutations and short additions and deletions--third edition, 1992. Nucleic Acids Res 1992; 20 Suppl:2027-63. [PMID: 1598234 PMCID: PMC333981 DOI: 10.1093/nar/20.suppl.2027] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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17
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Sarkar G, Yoon HS, Sommer SS. Screening for mutations by RNA single-strand conformation polymorphism (rSSCP): comparison with DNA-SSCP. Nucleic Acids Res 1992; 20:871-8. [PMID: 1371869 PMCID: PMC312031 DOI: 10.1093/nar/20.4.871] [Citation(s) in RCA: 116] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Single-strand conformation polymorphism (SSCP) is a simple method for detecting the presence of mutations in a segment of DNA, but the fraction of all mutations detected is unclear. We have evaluated SSCP for the detection of single-base mutations in the factor IX gene. Multiple conditions were examined including electrophoresis temperature, electrophoresis buffer concentration, acrylamide to bis-acrylamide ratio, and water-cooled versus fan-cooled gel apparatuses. Depending on conditions, 10-11 of 12 known mutations were detected in a 183 bp segment whereas only 11-14 of 22 known mutations were detected in a 307 bp segment. We hypothesized that single stranded RNA should have a larger repertoire of secondary structure because shorter hairpins form stable duplexes and the 2' hydroxyl group is available for sugar-base and sugar-sugar hydrogen bonds. By incorporating phage promoter sequences into PCR primers, RNA-SSCP (rSSCP) could be compared directly with standard DNA SSCP. rSSCP was generally superior to SSCP, especially for the 307 bp segment. In addition, the abundance of transcript produced as a result of rSSCP allows the rapid, nonradioactive detection of mutations by staining the gel with ethidium bromide. To gauge the utility of the method in a prospective manner, a blinded study was performed in which SSCP, rSSCP, and direct genomic sequencing were compared in 28 patients with hemophilia B. A total of 2.6 kb of factor IX genomic sequence was examined in nine regions ranging from 180 to 497 nucleotides of factor IX sequence. Sequence changes at 20 different sites were detected by direct genomic sequencing; 70% of these were detected by rSSCP while only 35% were detected by SSCP.
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Affiliation(s)
- G Sarkar
- Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, MN 55905
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18
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Picketts DJ, D'Souza C, Bridge PJ, Lillicrap D. An A to T transversion at position -5 of the factor IX promoter results in hemophilia B. Genomics 1992; 12:161-3. [PMID: 1733855 DOI: 10.1016/0888-7543(92)90421-n] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The molecular pathology that results in hemophilia B has been determined by many studies to be highly variable. Several point mutations have been identified in a 40-bp region within the Factor IX promoter. These include mutations at nucleotides -20, -6, +8, and +13. Here we report an A to T transversion at position -5 of the Factor IX gene. There is strong circumstantial evidence to support an important role for this region of the Factor IX promoter in the developmental regulation of the gene through the binding of specific transcription factors.
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Affiliation(s)
- D J Picketts
- Department of Pathology, Queen's University, Kingston, Ontario, Canada
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19
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Paynton C, Sarkar G, Sommer SS. Identification of mutations in two families with sporadic hemophilia A. Hum Genet 1991; 87:397-400. [PMID: 1908817 DOI: 10.1007/bf00197155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Direct sequencing of segments of the factor VIII gene in 30 hemophiliacs with sporadic disease (32+ kb of sequence in total) revealed two missense transitions: glutamate 1704 to lysine (E1704----K) in a patient with severe hemophilia A and proline 2300 to serine (P2300----S) in a patient with mild hemophilia. Both transitions are likely to be causative mutations because the amino acids affected were evolutionarily conserved. Haplotype and sequence analysis of the mother and grandparents of patient HA12 (E1704----K) indicate that the mutation arose in the grandfather who was 27 years old when his daughter was conceived. The origin of mutation in patient HA39 (P2300----S) could not be determined. As mutations that cause mild disease can be found in seemingly unrelated families, 96 unrelated hemophiliacs were screened rapidly for the P2300----S mutation with polymerase chain reaction (PCR) amplification of specific alleles (PASA). None of these patients had the mutation. PASA was also used to conveniently assess a polymorphic site in intron 7. The polymorphism is estimated to be informative in 13% of Korean females and in 23% of Western European females.
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Affiliation(s)
- C Paynton
- Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, MN 55905
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20
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Ketterling RP, Bottema CD, Phillips JA, Sommer SS. Evidence that descendants of three founders constitute about 25% of hemophilia B in the United States. Genomics 1991; 10:1093-6. [PMID: 1916816 DOI: 10.1016/0888-7543(91)90207-u] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In our sample of 160 consecutive Caucasian hemophiliacs, 14 (9%) had a G----A transition at bp 10,430 that substitutes serine for glycine 60 in the first EGF domain of the factor IX molecule. Each of these hemophiliacs had clinically mild disease. Haplotype data and familial pedigrees indicate that 12 of these hemophiliacs are likely to be related to a common ancestor. The 13th and 14th patients possess different haplotypes and thus represent independent origins of the mutation. In addition, we have screened these 160 hemophiliacs for the previously reported mutations resulting from founder effects at IIe397----Thr and Thr296----Met. Herein we report an additional nine hemophiliacs with the mutant Thr397 allele and five additional hemophiliacs with the mutant Met296 allele. Haplotype data for these 14 hemophiliacs support the original founder effect hypotheses for these mutations. In total, the above three mutations are found in 44 of the 160 seemingly unrelated Caucasian hemophiliacs (28%). The sample includes patients from all regions of the United States and Ontario, Canada. Descendants of these three founders comprise approximately two-thirds of the missense mutations found in our sample of Caucasian hemophiliacs with clinically mild disease.
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Affiliation(s)
- R P Ketterling
- Department of Biochemistry and Molecular Biology, Mayo Clinic/Foundation, Rochester, Minnesota 55905
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21
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Hamaguchi N, Charifson P, Pedersen L, Brayer G, Smith K, Stafford D. Expression and characterization of human factor IX. Factor IXthr-397 and factor IXval-397. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)98605-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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22
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Chen SH, Zhang M, Lovrien EW, Scott CR, Thompson AR. CG dinucleotide transitions in the factor IX gene account for about half of the point mutations in hemophilia B patients: a Seattle series. Hum Genet 1991; 87:177-82. [PMID: 2066105 DOI: 10.1007/bf00204177] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hemophilia B is due to multiple molecular defects in the factor IX gene. Over 80% of mutations are single base substitutions. By amplification and direct sequencing, 51 single base substitutions were found in the transcribed sequence of the factor IX genes of patients from 50 distinct families with hemophilia B. These include 30 mutations in 29 families not previously reported by us; of these, 12 are novel, i.e., not previously published in other series. Of the 51 substitutions in our overall series 23 (45%) occurred as C-to-T or G-to-A transitions at 11 sites within CG dinucleotides. It is estimated that CG transitions occur from one to two orders of magnitude more frequently than mutations in nucleotides that are not within a CG pair. More than one family had identical defects for 6 of the CG mutations. At 4 of these sites, most patients had different haplotypes compatible with distinct mutations. Non-CG-type mutations occurred throughout the coding regions with only one mutation in more than one family. The latter included 7 families with a 397 Ile-to-Thr defect that all share a rare haplotype, suggesting a common ancestor.
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Affiliation(s)
- S H Chen
- Department of Pediatrics, University of Washington, Seattle 98195
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Giannelli F, Green PM, High KA, Sommer S, Lillicrap DP, Ludwig M, Olek K, Reitsma PH, Goossens M, Yoshioka A. Haemophilia B: database of point mutations and short additions and deletions--second edition. Nucleic Acids Res 1991; 19 Suppl:2193-219. [PMID: 2041805 PMCID: PMC331353 DOI: 10.1093/nar/19.suppl.2193] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- F Giannelli
- Paediatric Research Unit, Guy's Tower, London, UK
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Kuppuswamy MN, Hoffmann JW, Kasper CK, Spitzer SG, Groce SL, Bajaj SP. Single nucleotide primer extension to detect genetic diseases: experimental application to hemophilia B (factor IX) and cystic fibrosis genes. Proc Natl Acad Sci U S A 1991; 88:1143-7. [PMID: 1671714 PMCID: PMC50973 DOI: 10.1073/pnas.88.4.1143] [Citation(s) in RCA: 121] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In this report, we describe an approach to detect the presence of abnormal alleles in those genetic diseases in which frequency of occurrence of the same mutation is high (e.g., cystic fibrosis and sickle cell disease), and in others in which multiple mutations cause the disease and the sequence variation in an affected member of a given family is known (e.g., hemophilia B). Initially, from each subject, the DNA fragment containing the putative mutation site is amplified by the polymerase chain reaction. For each fragment two reaction mixtures are then prepared. Each contains the amplified fragment, a primer (18-mer or longer) whose sequence is identical to the coding sequence of the normal gene immediately flanking the 5' end of the mutation site, and either an alpha-32P-labeled nucleotide corresponding to the normal coding sequence at the mutation site or an alpha-32P-labeled nucleotide corresponding to the mutant sequence. Single nucleotide primer extensions are then carried out and analyzed by denaturing polyacrylamide gel electrophoresis and autoradiography. As predicted by the Watson-Crick base-pair rule, in the wild type only the normal base, in an affected member only the mutant base, and in carriers both the normal and the mutant base are incorporated into the primer. Thus, an essential feature of the present methodology is that the base immediately 3' to the template-bound primer is one of those altered in the mutant, since in this way an extension of the primer by a single base will give an extended molecule characteristic of either the mutant or the wild type. The method is rapid and should be useful in carrier detection and prenatal diagnosis of every genetic disease with a known sequence variation.
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Affiliation(s)
- M N Kuppuswamy
- Department of Medicine, St. Louis University School of Medicine, MO 63104
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