Pharmacogenetic allele nomenclature: International workgroup recommendations for test result reporting.

This article provides nomenclature recommendations developed by an international workgroup to increase transparency and standardization of pharmacogenetic (PGx) result reporting. Presently, sequence variants identified by PGx tests are described using different nomenclature systems. In addition, PGx analysis may detect different sets of variants for each gene, which can affect interpretation of results. This practice has caused confusion and may thereby impede the adoption of clinical PGx testing. Standardization is critical to move PGx forward.

Short tandem repeat profiling provides an international reference standard for human cell lines.

Cross-contamination between cell lines is a longstanding and frequent cause of scientific misrepresentation. Estimates from national testing services indicate that up to 36% of cell lines are of a different origin or species to that claimed. To test a standard method of cell line authentication, 253 human cell lines from banks and research institutes worldwide were analyzed by short tandem repeat profiling. The short tandem repeat profile is a simple numerical code that is reproducible between laboratories, is inexpensive, and can provide an international reference standard for every cell line. If DNA profiling of cell lines is accepted and demanded internationally, scientific misrepresentation because of cross-contamination can be largely eliminated.

Regional mapping panels for human chromosomes 1, 2, and 7.

The NIGMS Human Genetic Cell Repository has assembled regional mapping panels for human chromosomes 1, 2, and 7 from human rodent somatic cell hybrids submitted to the collection by researchers from 14 different laboratories. All hybrids were characterized initially by the submitters and verified by the Repository. Each hybrid carries a stable defined human segment as a derivative or deletion chromosome. These panels define 8-10 intervals for each chromosome. The panel for chromosome 2 is a new resource. The panels for chromosomes 1 and 7 complement previously published panels. The Repository distributes these regional mapping panels as cell cultures or as DNA. Information about these panels as well as for panels for chromosomes 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 21, 22, 22, and X may be viewed in the NIGMS Repository electronic catalog (http://locus.umdnj.edu/nigms).

Regional mapping panels for chromosomes 3, 4, 5, 11, 15, 17, 18, and X.

The NIGMS Human Genetic Mutant Cell Repository collects and distributes well-characterized human/rodent somatic cell hybrid regional mapping panels for human chromosomes 3, 4, 5, 11, 15, 17, 18, and X. Each regional mapping panel consists of 4 to 11 hybrids that divide the chromosome into 5 to 11 intervals. These panels have been extensively characterized by the submitters and the NIGMS Repository.

NIGMS human/rodent somatic cell hybrid mapping panels 1 and 2.

The NIGMS Human Genetic Mutant Cell Repository is currently distributing two well-characterized human/rodent somatic cell hybrid mapping panels. Mapping Panel 1 consists of DNA isolated from 18 hybrid cell cultures retaining from 1 to 19 human chromosomes. Mapping Panel 2 contains DNA from hybrids retaining 1 or 2 human chromosomes. All but 2 of the hybrids retain a single intact human chromosome. Mapping Panel 2 is also available as cell cultures. These resources should prove valuable to the Human Genome Project initiative. This article describes the sources of the hybrid cell cultures and the procedures utilized to prepare and characterize the panels.

Characterization of a simian virus 40-transformed Fanconi anemia fibroblast cell line.

We have characterized a SV40-transformed human fibroblast cell line (GM6914) derived from a patient with Fanconi anemia (FA) in order to establish its usefulness for biochemical and genetic experiments, including DNA-mediated gene transfer. GM6914 cells have a growth rate similar to that of SV40-transformed normal human fibroblasts and an indefinite lifespan in culture. As has been established for other FA cell types, GM6914 cells have an increased sensitivity to DNA-crosslinking agents such as mitomycin C (MMC). The D10 for GM6914 cells is 8 times lower than for equivalent controls. GM6914 cells also have an elevated frequency of spontaneous chromosome aberrations and this frequency can be increased by MMC concentrations which show no effect on control cells. Genetic complementation studies with lymphoblasts derived from two affected sibs of the donor of GM6914 cells show that GM6914 belongs to FA complementation group A. In DNA-transfection studies using plasmid pRSVneo, colonies of GM6914 cells resistant to the drug G-418 were observed at frequencies ranging from 1.7 to 16 X 10(-4), values similar to those observed with several other SV40-transformed human cell lines. GM6914 should be a useful recipient cell line in experiments using DNA-mediated gene transfer to clone the normal allele of the gene which is defective in FA complementation group A. GM6914 would also be an excellent cell line for studies on mutagenesis, recombination and repair using plasmid vectors.

Characterization of a new human diploid cell line--IMR-91.

A human diploid fibroblast cell line has been established from the lung tissue of a male fetus. This has been characterized and frozen away in large quantity. A smaller quantity of fibroblastlike cells from skin has also been established, partially characterized, and placed in frozen storage from the same fetus. This project is in support of the National Institute on Aging research in general cell biology. The present lines designated IMR-91 lung and IMR-91 skin complement the previous human diploid fibroblast culture (IMR-90) established from a female fetus. The lack of random inactivation of one of the two X chromosomes in the present male line reduces the genetic heterogeneity inherent in the female line.

Induction of sister chromatid exchanges by transformation with simian virus 40.

The frequency of sister chromatid exchange (SCE) has been followed sequentially after the addition of SV40 to human diploid fibroblast cultures. The SCE frequency was nearly the same in uninfected controls and in infected cultures before they became tumor antigen positive. When cells exhibited tumor antigen, the SCE frequency increased over a wide range, and changes in chromosome number and structure were observed simultaneously. Cells with induced chromosome abnormalities without increased SCE's and the reverse present the possibility that the two phenomena have different viral mechanisms. This increase in SCE can be added to the previously demonstrated change in chromosome number and increase in chromosome breakage and rearrangement as indicators of genetic damage associated with viral transformation.

Characterization of a new human diploid cell strain, IMR-90.

A new human diploid fibroblast-like cell line has been established from lung tissue of a female fetus. This has been frozen away in large quantity and characterized for use in research and related purposes. This is the first of a planned series of human cell lines to be established, characterized, and banked in large quantity in support of the National Institute on Aging research and general cell biology.

Termination of deoxyribonucleic acid in Escherichia coli by 2',3'-dideoxyadenosine.

2',3'-Dideoxyadenosine was previously shown to be lethal to Escherichia coli and to inhibit deoxyribonucleic acid (DNA) synthesis irreversibly in this organism. It was also shown that triphosphate of this analogue terminates DNA chains in an in vitro system. Data presented here show that the nucleoside is relatively insensitive to E. coli adenosine deaminase and is converted intracellularly into the dideoxynucleotide, including the triphosphate. Thymine nucleotide pools were not reduced in inhibited bacteria, nor did preformed DNA break down. Some adenine was liberated from the dideoxyadenosine on incubation, and the latter was incorporated into ribonucleic acid. Nevertheless, about 4,000 molecules of the dideoxynucleoside were incorporated into DNA per cell. The dideoxynucleotide occurred in DNA chains in a terminal position, liberated selectively by venom phosphodiesterase. The possible nature of the lethal event is discussed.

The enzymatic termination of polydeoxynucleotides by 2',3'-dideoxyadenosine triphosphate.

The nucleoside 2',3'-dideoxyadenosine is lethal to E. coli and blocks DNA synthesis irreversibly. The hypothesis that a derived dideoxynucleoside triphosphate is incorporated terminally into the cellular DNA has been tested in an in vitro system. The triphosphate of dideoxyadenosine was synthesized and shown to inhibit the in vitro synthesis of DNA by purified E. coli DNA polymerase. The kinetics of inhibition of nucleotide incorporation and pyrophosphate exchange were studied. Early in synthesis the dideoxynucleotide is a competitive inhibitor of the enzyme. Subsequently, synthesis is almost completely arrested.Radioactive dideoxyadenosine triphosphate was prepared. The compound was shown to be incorporated enzymatically into dAT copolymer to the extent of about one molecule per molecule of template. It is released from such templates by DNA polymerase at less than 1 per cent of the rate of release of other natural nucleotides. The label is released by snake venom phosphodiesterase far more rapidly than total nucleotides. This nucleoside triphosphate has thus been shown to be a competitive inhibitor of DNA polymerase and a terminator of polydeoxynucleotide chains.