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Guidelines for human gene nomenclature (1997)
CURRENT LITERATURE
TRANSFUSION MEDICINE
REWEWS
Marion E. Reid, Sunny Dzik, and John J. Freedman, Abstract Editors
A Report on the International Nomenclature Workshop Held May 1997 at the Jackson Laboratory, Bar Harbor, Maine, U.S.A. Blake JA, Davisson MT, Eppig JT, etaL Genomics 45:464-468, 1997. The goals of the workshop were to meet members of nomenclature committees for a variety of organisms, to promote coordination between databases, and to further the development and use in different species of similar concepts in the nomenclature process. The report is dedicated to Phyllis McAlpine for her tireless efforts in human gene nomenclature. The meeting focused discussion on several emerging issues; namely: (1) To encourage stability in nomenclature, (2) to establish a single registry of gene symbols and names for as many species as possible, (3) to develop multiple classifications and controlled vocabularies, (4) to hold workshops and meetings that address comparative mapping and genomics and that include scientists and database specialists representing a wide range of organisms. Table 1 in the report lists 25 primary databases together with their World Wide Web addresses. Subsequent to the Workshop, ATCC agreed to establish a gene registry at their W W W site (http://www.atcc.org). The registry will be electronically populated from existing databases of various species and will include-gene/marker symbol, gene! marker name, species, authority (database source), and identifier (database accession number). The prototype became publicly available in September 1997.
Guidelines for Human Gene Nomenclature 119971. White JA, McA/pine PJ, Antonarakis S, et al. Genom ics 45:468-471, 1997, This article is a report of a meeting held in March 1997 in Toronto in association with HGM97 and with subsequent discussion with the cross-species International Workshop on Gene Nomenclature (see previous listing). The guidelines in this article should help to ensm'e that a gene symbol is unique and appropriate. In this article, a gene is defined as a DNA segment that contributes to phenotype/function. Information, guidance, and a submission form for approval of human gene symbols are on the Nomenclature Committee W W W page at URL http:// www.gene.ucl.ac.uk/nomenclature. General rules for gene nomenclature are given in the article under the following headings: Requirements for designation of gene symbol; gene symbols; gene names; and DNA segments. There are also recommendations for the construction of symbols, and Table 1 in the report lists the recommended abbreviations for 16 species.
Molecular Cloning and Characterization of DecayAccelerating Factor Deficiency in Cromer Blood Group Inab Phenotype. Wang L, Uchiwawa M, Tsuneyama K, et al. Blood 91:680-684, 1998. Cromer blood group antigens are carried on decay-accelerating factor (DAF; CD55). DAF is a protein attached to the red
226
blood cell membrane by a glycosylphosphatidylinositol linkage. The Cromer blood group system consists of seven highincidence antigens and three low-incidence antigens and a null phenotype known as the Inab phenotype. The molecular basis for the Inab phenotype in one individual has been determined (Lublin et al, Blood 84:1276-1282, 1994). A single-nucleotide substitution of G to A in codon 53 of exon 2 results in a change of a tryptophan codon to a stop codon, a gain of a BclI site, and explains the complete absence of surface DAF in this patient. Wang et al report results of their molecular analysis on the fourth proband (HA) with the Inab phenotype, Serological testing failed to detect the high-incidence Cromer antigens, Cr a, Tca, Dr a, IFC, and UMC and showed the presence of other GPI-linked proteins, namely, CD59 and those carrying Yt a, Gy ~, and JMH blood group antigens. Immunoblotting with a monoclonal anti-DAF showed a strong band in normal RBC membranes, but no band in RBC membranes prepared from H.A. Amplified DAF cDNA from H.A. digested with BclI and analyzed by PAGE showed that the molecular basis for the Inab phenotype in H.A. was different from that in the original proband. Ten cDNA clones for the entire DAF coding region from H.A.o were sequenced and compared with the normal DAF gene. A deletion of 26 nucleotides was noted that corresponded to bases 246 to 271 of the published DAF cDNA sequence (Medof et al, PNAS 84:2007, 1987) and was located at the 3' end of exon 2. This deletion caused a loss of a MbolI restriction site. The region of genomic DNA at the exon 2/intron 2 boundary region was cloned mad sequenced from base 1,531 to base 1,750 of the published DAF sequence (Ewulonu et al, PNAS 88:4675, 1991). A single nucleotide substitution of C 1579 to A, at the position 24 bp upstream from the 3' end of exon 2, was detected. This substitution activates a novel splice site and results in production of mRNA with a 26-bp deletion. This deletion introduces a frame shift and a premature stop codon immediately downstream of the deletion. This truncated protein of 238 amino acids would not have the carboxyl-terminal signal domain for GPIanchoring and, therefore, no DAF would be on the surface of the RBC membrane.
Haemolytic Disease of the Fetus and Newborn due to Anti-Fya and the Potential Clinical Value of Duffy Genotyping in Pregnancies at Risk. Goodrick M J, HadleyAG, Poole G. Transfus Med 7:301-304, 1997. The authors reviewed 68 pregnancies in which anti-Fy" had been detected. In these cases, the fetus was severely anemic, and two of them required intrauterine transfusions. The current guidelines recommend that pregnant women with anti-Fy a are monitored less rigorously than those with anti-D, -c, or -K. Based on the experience of the authors, they recommend that pregnancies in which anti-Fy a is detected at significant titers (greater than 64) should be closely monitored in a similar way to pregnancies in which other "significant" antibodies are present.
Transfusion Medicine Reviews,Vo112, No 3 (July), 1998: pp 226-232
TRANSFUSION MEDICINE
REWEWS
Marion E. Reid, Sunny Dzik, and John J. Freedman, Abstract Editors
A Report on the International Nomenclature Workshop Held May 1997 at the Jackson Laboratory, Bar Harbor, Maine, U.S.A. Blake JA, Davisson MT, Eppig JT, etaL Genomics 45:464-468, 1997. The goals of the workshop were to meet members of nomenclature committees for a variety of organisms, to promote coordination between databases, and to further the development and use in different species of similar concepts in the nomenclature process. The report is dedicated to Phyllis McAlpine for her tireless efforts in human gene nomenclature. The meeting focused discussion on several emerging issues; namely: (1) To encourage stability in nomenclature, (2) to establish a single registry of gene symbols and names for as many species as possible, (3) to develop multiple classifications and controlled vocabularies, (4) to hold workshops and meetings that address comparative mapping and genomics and that include scientists and database specialists representing a wide range of organisms. Table 1 in the report lists 25 primary databases together with their World Wide Web addresses. Subsequent to the Workshop, ATCC agreed to establish a gene registry at their W W W site (http://www.atcc.org). The registry will be electronically populated from existing databases of various species and will include-gene/marker symbol, gene! marker name, species, authority (database source), and identifier (database accession number). The prototype became publicly available in September 1997.
Guidelines for Human Gene Nomenclature 119971. White JA, McA/pine PJ, Antonarakis S, et al. Genom ics 45:468-471, 1997, This article is a report of a meeting held in March 1997 in Toronto in association with HGM97 and with subsequent discussion with the cross-species International Workshop on Gene Nomenclature (see previous listing). The guidelines in this article should help to ensm'e that a gene symbol is unique and appropriate. In this article, a gene is defined as a DNA segment that contributes to phenotype/function. Information, guidance, and a submission form for approval of human gene symbols are on the Nomenclature Committee W W W page at URL http:// www.gene.ucl.ac.uk/nomenclature. General rules for gene nomenclature are given in the article under the following headings: Requirements for designation of gene symbol; gene symbols; gene names; and DNA segments. There are also recommendations for the construction of symbols, and Table 1 in the report lists the recommended abbreviations for 16 species.
Molecular Cloning and Characterization of DecayAccelerating Factor Deficiency in Cromer Blood Group Inab Phenotype. Wang L, Uchiwawa M, Tsuneyama K, et al. Blood 91:680-684, 1998. Cromer blood group antigens are carried on decay-accelerating factor (DAF; CD55). DAF is a protein attached to the red
226
blood cell membrane by a glycosylphosphatidylinositol linkage. The Cromer blood group system consists of seven highincidence antigens and three low-incidence antigens and a null phenotype known as the Inab phenotype. The molecular basis for the Inab phenotype in one individual has been determined (Lublin et al, Blood 84:1276-1282, 1994). A single-nucleotide substitution of G to A in codon 53 of exon 2 results in a change of a tryptophan codon to a stop codon, a gain of a BclI site, and explains the complete absence of surface DAF in this patient. Wang et al report results of their molecular analysis on the fourth proband (HA) with the Inab phenotype, Serological testing failed to detect the high-incidence Cromer antigens, Cr a, Tca, Dr a, IFC, and UMC and showed the presence of other GPI-linked proteins, namely, CD59 and those carrying Yt a, Gy ~, and JMH blood group antigens. Immunoblotting with a monoclonal anti-DAF showed a strong band in normal RBC membranes, but no band in RBC membranes prepared from H.A. Amplified DAF cDNA from H.A. digested with BclI and analyzed by PAGE showed that the molecular basis for the Inab phenotype in H.A. was different from that in the original proband. Ten cDNA clones for the entire DAF coding region from H.A.o were sequenced and compared with the normal DAF gene. A deletion of 26 nucleotides was noted that corresponded to bases 246 to 271 of the published DAF cDNA sequence (Medof et al, PNAS 84:2007, 1987) and was located at the 3' end of exon 2. This deletion caused a loss of a MbolI restriction site. The region of genomic DNA at the exon 2/intron 2 boundary region was cloned mad sequenced from base 1,531 to base 1,750 of the published DAF sequence (Ewulonu et al, PNAS 88:4675, 1991). A single nucleotide substitution of C 1579 to A, at the position 24 bp upstream from the 3' end of exon 2, was detected. This substitution activates a novel splice site and results in production of mRNA with a 26-bp deletion. This deletion introduces a frame shift and a premature stop codon immediately downstream of the deletion. This truncated protein of 238 amino acids would not have the carboxyl-terminal signal domain for GPIanchoring and, therefore, no DAF would be on the surface of the RBC membrane.
Haemolytic Disease of the Fetus and Newborn due to Anti-Fya and the Potential Clinical Value of Duffy Genotyping in Pregnancies at Risk. Goodrick M J, HadleyAG, Poole G. Transfus Med 7:301-304, 1997. The authors reviewed 68 pregnancies in which anti-Fy" had been detected. In these cases, the fetus was severely anemic, and two of them required intrauterine transfusions. The current guidelines recommend that pregnant women with anti-Fy a are monitored less rigorously than those with anti-D, -c, or -K. Based on the experience of the authors, they recommend that pregnancies in which anti-Fy a is detected at significant titers (greater than 64) should be closely monitored in a similar way to pregnancies in which other "significant" antibodies are present.
Transfusion Medicine Reviews,Vo112, No 3 (July), 1998: pp 226-232