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PubMed2006

Correlations between heterozygosity and measures of genetic similarity: implications for understanding mate choice.

There is currently considerable interest in testing the effects of genetic compatibility and heterozygosity on animal mate preferences. Evidence for either effect is rapidly accumulating, although results are not always clear-cut. However, correlations between mating preferences and either genetic similarity or heterozygosity are usually tested independently, and the possibility that similarity and heterozygosity may be confounded has rarely been taken into account. Here we show that measures of genetic similarity (allele sharing, relatedness) may be correlated with heterozygosity, using data from 441 human individuals genotyped at major loci in the major histocompatibility complex, and 281 peafowl (Pavo cristatus) individuals genotyped at 13 microsatellite loci. We show that average levels of allele sharing and relatedness are each significantly associated with heterozygosity in both humans and peafowl, that these relationships are influenced by the level of polymorphism, and that these similarity measures may correlate with heterozygosity in qualitatively different ways. We discuss the implications of these inter-relationships for interpretation of mate choice studies. It has recently become apparent that mating preferences for 'good genes' and 'compatible genes' may introduce discordant choice amongst individuals, since the optimal mate for one trait may not be optimal for the other, and our results are consistent with this idea. The inter-relationship between these measures of genetic quality also carries implications for the way in which mate choice studies are designed and interpreted, and generates predictions that can be tested in future research.

Animals↗
PubMed1993

Research samples from families with genetic diseases: a proposed code of conduct.

Research on samples from families with genetic disease underlies many of the major advances that are occurring in medical genetics. But ethical and practical problems may arise when samples from relatives who are healthy but at risk are included in such studies. In particular, new molecular tests for specific gene mutations may result in the detection of a genetic defect in relatives who had neither expected this possibility nor given specific consent to such testing. Family members at risk should not be included in such studies unless strictly necessary, and in such cases specific consent should be obtained and information should be given about the implications of an abnormal result of a test. This is particularly important when stored samples from previous studies without such implications are being reused and is also relevant to the genetic testing of samples taken primarily for epidemiological studies of disorders when only a small proportion of cases is thought to be genetic in origin. There is a need for guidelines to protect both subjects and investigators in a field which is spreading rapidly and involving many clinical and laboratory research workers previously unfamiliar with genetic testing.

Anonymous Testing↗
PubMed1999

Genetic predictive testing for bowel cancer predisposition: the impact on the individual.

When considering the impact of a genetic diagnosis of hereditary predisposition to colon cancer, there are many similarities to other predictive genetic tests, but also many differences. The development and availability of such genetic diagnoses, and the concept of testing being linked to effective prevention, have advanced rapidly, opening up not only unique opportunities but also unique psychosocial situations for the affected families-and unusual ethical issues for the professional. Compared to a diagnosis of sporadic colorectal cancer for a patient, hereditary colorectal cancer requires an understanding of genetics, heredity, and the attendant mathematics of risk calculation, but, most importantly, there must be a belief that it is possible to remain healthy whilst having an increased risk. This paper outlines the possible impact of a genetic diagnosis of hereditary non-polyposis colorectal cancer (HNPCC) or familial adenomatous polyposis (FAP) on both the individual and the family and concludes that genetic testing should be accompanied by genetic counseling. Relevant ethical issues are also introduced, with the opinion presented suggesting that if primary considerations are always for the individual rather than the family or society, then unethical or eugenic decisions are likely to be avoided.

Adenomatous Polyposis Coli↗
PubMed2006

[Pharmacogenetic testing: utility in drug development and in routine clinical practice].

Pharmacogenetic tests can identify the role of genetic factors in the inter-individual variability of drug responsiveness. This variability can involve three systems, namely drug-metabolizing enzymes, transmembrane drug transporters, and drug effctor sites (receptors, enzymes, ion, channels, etc.). At present, pharmacogenetic testing is rarely used in clinical practice. A rapid survey of the four laboratories conducting such tests for Paris hospitals shows that about 750 tests were done during a 12-months period in 2004-2005, and that most focused on allelic variants of drug-metabolizing enzymes. Three other European laboratories perform between 25, and 7.000 tests per year. However, the number of pharmacogenetic tests is set to grow rapidely in the near future. The role of genetic factors in adverse drug reactions (ADR) has not yet been the subject of a systematic study. Drug-drug interactions that inhibit or induce certain enzyme activities are a major cause of adverse reactions, but they have not been exhaustively studied Pharmacogenetic and pharmacogenomic tools are increasingly used in the drug development process. This should result in the discovery of new therapeutic targets and in a better understanding of factors governing drug efficacy and tolerability. DNA samples are already collected systematically in many phase II and III clinical trials, and registration agencies such as the FDA are establishing guidelines for the submission of pharmacogenetic data on new drugs. These efforts, together with DNA samples collection during post-registration pharmacoepidemiological studies, should help to understand inter-individual variability in drug efficacy and tolerability. They may also result in the identification of new drug targets and will help to tailor therapy to the individual patient.

Clinical Medicine↗
PubMed2005

4,4'-methylenedianiline-induced hepatotoxicity is modified by N-acetyltransferase 2 (NAT2) acetylator polymorphism in the rat.

4,4'-Methylenedianiline (MDA) is widely used in the manufacturing of polyurethane foam, epoxy resins, and polymers. Exposure to MDA induces liver damage in humans and rats. MDA undergoes N-acetylation catalyzed by N-acetyltransferase 1 (NAT1) and 2 (NAT2) in the liver. Both human and rat NAT2 are polymorphic, and human NAT2 genetic polymorphism modifies the frequency and/or severity of drug and xenobiotic toxicity in human populations. Recombinant expression of rat Nats in Escherichia coli showed that MDA was acetylated by both recombinant rat Nat1 and Nat2 and was catalyzed at substantially higher rates by rapid acetylator Nat2 compared with slow acetylator Nat2. Rapid acetylator F344 rat liver cytosols catalyzed the N-acetylation of MDA at significantly higher rates than those from slow acetylator Wistar-Kyoto (WKY) inbred rats. To test the effect of NAT2 genetic polymorphism on hepatotoxicity from acute MDA exposure, we compared hepatotoxicity in rapid (F344) and slow (WKY) Nat2 acetylator inbred rats that were administered MDA. Based on the results of dose-response studies ranging up to 150 mg/kg MDA administered by intragastric gavage, the effect of a moderately hepatotoxic dose (37.5 mg/kg) was compared in rapid versus slow acetylator rats. Plasma alanine transaminase enzyme activities were approximately 5-fold higher (p < 0.05) in rapid versus slow acetylator rats after MDA treatment, and necrotizing hepatitis with portal damage consisting of bile ductular necrosis, portal expansion, and inflammation was clearly more prominent. These results suggest that acetylator phenotype is an important factor for susceptibility toward MDA hepatotoxicity.

Acetylation↗
PubMed1998

Comparison of the genetic diversity of wild and captive groups of Microcebus murinus using the random amplified polymorphic DNA method.

Continued survival of most animal species depends on population management and active protection. It is generally agreed that, in order to avoid extinction of endangered species, ex situ and in situ conservation must be developed in tandem. However, even though many recommendations have been put forward to promote the survival of captive populations, some rapidly become extinct due to loss of genetic diversity (drift effect). Genetic markers, such as random amplified polymorphic DNA (RAPD) markers, can be applied to rapid testing of many individuals. They also permit analysis of very small amounts of DNA, when small species such as mouse lemurs (Microcebus) are to be tested. Using RAPD markers, we compare genetic diversity in four captive groups of Microcebus murinus to that in a sample of 70 wild mouse lemurs. Following the principles of Mendelian inheritance, each amplified fragment of DNA may be considered as a 'locus' (or an amplifying site). The series of bands amplified by a particular primer in any individual is referred to as the individual's 'profile'. We tested 5 primers, or, in the above terms, we studied 98 different 'loci'. Results showed that the captive groups had lost genetic information with respect to the wild sample. Among the four captive groups, the loss of genetic diversity varied according to their number of founders and/or the management of their captive reproduction. Our study of polymorphism permitted us to establish tools for the genetic management of captive breeding, and for the determination of paternity which frequently give better results than behavioural studies; and simulation of introductions or departures of individuals in one very monomorphic group permitted estimation of future increases in its genetic diversity.

Amino Acid Sequence↗
PubMed2006

A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome.

The detection of footprints of natural selection in genetic polymorphism data is fundamental to understanding the genetic basis of adaptation, and has important implications for human health. The standard approach has been to reject neutrality in favor of selection if the pattern of variation at a candidate locus was significantly different from the predictions of the standard neutral model. The problem is that the standard neutral model assumes more than just neutrality, and it is almost always possible to explain the data using an alternative neutral model with more complex demography. Today's wealth of genomic polymorphism data, however, makes it possible to dispense with models altogether by simply comparing the pattern observed at a candidate locus to the genomic pattern, and rejecting neutrality if the pattern is extreme. Here, we utilize this approach on a truly genomic scale, comparing a candidate locus to thousands of alleles throughout the Arabidopsis thaliana genome. We demonstrate that selection has acted to increase the frequency of early-flowering alleles at the vernalization requirement locus FRIGIDA. Selection seems to have occurred during the last several thousand years, possibly in response to the spread of agriculture. We introduce a novel test statistic based on haplotype sharing that embraces the problem of population structure, and so should be widely applicable.

Alleles↗
PubMed2025

Long-term follow-up of children who received rapid genomic sequencing.

PURPOSE: To explore long-term trajectories of children who received rapid genome sequencing (RGS) in intensive care settings. METHODS: We examined the electronic health records of 67 critically ill pediatric patients who received RGS 6 to 8 years ago with a collective initial diagnostic yield of 46%. RESULTS: The median length of follow-up was 6.2 years (interquartile range 4.0-7.2 years). RGS-diagnosed patients had a longer average follow-up time compared with undiagnosed patients (5.9 years vs 4.8 years, P = .026) and more subspecialty appointments per follow-up year (9.4 vs 6.9, P = .036). Mortality during the follow-up period was 9%. Patients averaged 2.1 hospital readmissions per follow-up year and 28.1 hospitalized days per follow-up year. Forty-four patients (66%) had a documented new phenotype in the electronic health records during their follow-up period. Seven patients received clinician-driven reanalysis during the follow-up period, yielding 1 new diagnosis. Systematic reanalysis of RGS performed as part of this study identified 4 new candidate diagnoses. CONCLUSION: Pediatric patients who receive RGS during intensive care unit hospitalizations continue to be high health care utilizers in subsequent years, regardless of whether RGS identified a diagnosis. Additionally, two-thirds of this cohort had a documented phenotypic change over the follow-up period, indicating dynamic clinical evolution in the years after RGS.

Humans↗
PubMed2000

Pathogen analysis and genetic predisposition testing using microelectronic arrays and isothermal amplification.

BACKGROUND: A simple yet powerful tool for providing for rapid gene identification in the clinic would be the combination of isothermal gene amplification with electronic microchip analysis. This is a first report of such a union of these technologies. METHODS: The first assay demonstrates discrimination between four bacterial pathogens. For this, one portion of the bacterial 16S rRNA gene encompassing a microheterogeneous region was isothermally amplified using Strand Displacement Amplification (SDA). Type identification was then made by "sandwich" assay format either using selective electronic hybridization of amplicons to sequence-specific capture oligonucleotides and a universal, fluorescently labeled reporter oligonucleotide, or, alternatively, sequence-specific reporters and a universal capture oligonucleotide. The second assay tested for the presence or absence of the Factor V Leiden point mutation using DNA obtained from 18 patients in a blind assay. For this, allele-specific SDA was developed. Following amplification using a sense-biotinylated primer and either the corresponding antisense wild type or mutant primer, multiple patient amplicons were targeted to specified locations on the microarray and visualized using a fluorescently labeled reporter oligonucleotide. Positive signals were scored as greater than or equal to two times the background. RESULTS: Bacterial type-specific signals were between 3- to 10-fold greater than nonspecific in both assay formats. Using allele-specific SDA, 100% agreement was observed between PAGE analysis, microarray results, and clinical diagnosis in Factor V mutation analysis. CONCLUSIONS: We demonstrated two model clinical assays combining amplified materials and microelectronic arrays, one potentially suitable for pathogen screening and the other for a deleterious genetic mutation.

Bacteria↗
PubMed2003

Molecular genetic testing for prenatal diagnosis.

In the past few decades, enormous progress has been made in the field of prenatal molecular genetic testing. Based on the inheritance patterns of the disease and type of mutation, prenatal diagnosis is possible using direct or indirect methods of detection. Although direct mutation analysis is highly accurate, accuracy of indirect mutation analysis depends on the distance of the DNA marker to the disease locus. In the past decade, the discovery of new concepts--such as atypical inheritance patterns due to UPD and imprinting and triplet repeat disorders--have helped to increase understanding of the molecular basis of these unusual genetic disorders. Prenatal diagnosis using a single cell from a blastomere is rapidly becoming routine in clinical practice. Noninvasive procedures to obtain fetal DNA for molecular testing also are progressing very rapidly. With the completion of the genome project, resources now are available for developing new technologies, such as microarrays (DNA chips), for accurate, simultaneous, mutation detection. The next few decades hold the promise of many more advances in genetic testing, drug discovery, and therapy.

Adult↗
PubMed1992

Rapid DNA fingerprinting to control for specimen errors in HIV testing by the polymerase chain reaction.

Variable-number-tandem-repeats (VNTRs) are highly polymorphic and provide informative genetic markers for distinguishing between individuals. We have used PCR amplification of VNTR locus pMCT118 to identify mislabelled specimens submitted for HIV PCR testing. The method is rapid, can be applied to large numbers of samples and eliminates the need for radioactive probes. DNA samples (10 ng) are amplified for 25 cycles using fluorescence-labelled oligonucleotide primers (blue dye). An aliquot of the PCR product is then combined with an internal lane size standard (labelled with a red dye), electrophoresed through a 2% agarose gel on an automated fluorescence DNA fragment analyser and the size and quantity of the fragments determined automatically relative to the internal standard. Fifteen alleles, ranging in size from 398 tp 709 bp were readily identified in a random sampling of DNA from 63 unrelated HIV-infected patients. Fragment size was reproducible and corresponded to alleles containing from 16 to 35 repeats of a 16 bp unit. VNTR genotyping will prove useful for resolving discordant results due to specimen mix-up and ensuring that the correct samples have been analyzed.

Alleles↗
PubMed2002

Evolutionary rate heterogeneity in proteins with long disordered regions.

The dominant view in protein science is that a three-dimensional (3-D) structure is a prerequisite for protein function. In contrast to this dominant view, there are many counterexample proteins that fail to fold into a 3-D structure, or that have local regions that fail to fold, and yet carry out function. Protein without fixed 3-D structure is called intrinsically disordered. Motivated by anecdotal accounts of higher rates of sequence evolution in disordered protein than in ordered protein we are exploring the molecular evolution of disordered proteins. To test whether disordered protein evolves more rapidly than ordered protein, pairwise genetic distances were compared between the ordered and the disordered regions of 26 protein families having at least one member with a structurally characterized region of disorder of 30 or more consecutive residues. For five families, there were no significant differences in pairwise genetic distances between ordered and disordered sequences. The disordered region evolved significantly more rapidly than the ordered region for 19 of the 26 families. The functions of these disordered regions are diverse, including binding sites for protein, DNA, or RNA and also including flexible linkers. The functions of some of these regions are unknown. The disordered regions evolved significantly more slowly than the ordered regions for the two remaining families. The functions of these more slowly evolving disordered regions include sites for DNA binding. More work is needed to understand the underlying causes of the variability in the evolutionary rates of intrinsically ordered and disordered protein.

Amino Acid Sequence↗
PubMed2003

Quantitative assays for maedi-visna virus genetic sequences and mRNA's based on RT-PCR with real-time FRET measurements.

We developed robust, ultrasensitive, and accurate quantitative assays for maedi-visna virus (MVV) RNA and DNA genomic sequences and mRNA's expressed at various stages of lentiviral replication. Assay design was based on PCR with real-time fluorescence resonance energy transfer measurements. Specific assays were developed for gag-pol (genomic), tat, rev, env, and vif transcripts. Assay linearity ranged from 60 to 6 x 10(7) copies of target DNA. All assays were able to detect and measure corresponding mRNA's in MVV-infected FOS cells, whereas no signal was detected in mock-treated cells. In addition, RT-PCR based on amplification of gag sequences could be used to quantify RNA genomic sequences in supernatants from infected cells. These quantitative assays can be used to study the role of genetic elements in MVV infection and pathogenesis. They also allow rapid testing of lentiviral vectors and packaging systems based on MVV.

Animals↗
PubMedDate not supplied

Use of minisatellite DNA probes for determination of twin zygosity at birth.

Minisatellite DNA probes that detect highly polymorphic regions of the human genome were used to examine DNA from twelve sets of newborn twins. In the seven cases where the twins were known to be monozygotic or dizygotic, from sex observation or placental examination, the DNA result agreed with these findings. In the other five twin pairs and in two sets of triplets DNA analysis allowed rapid determination of zygosity. Minisatellite DNA probes provide a single genetic test that should allow positive determination of zygosity in all cases of multiple pregnancy.

DNA, Satellite↗
PubMed2003

The role of DNA testing in breast, ovarian, and colon cancers.

A proportion of cases of breast and colon cancers are caused by inherited mutations that confer a greatly increased susceptibility to malignancy. Certain clinical features may help distinguish patients with a genetic cause for their cancer from the larger number of patients with sporadic tumors. A thorough family medical history is also necessary to identify those at high risk for developing cancer. Many of the normal functions of these genes are understood, and mutation analysis for patients and their families is now available as a clinical service. Presymptomatic detection of mutations allows the patient to pursue preventive measures to reduce the probability of developing a malignancy. Evidence is now available that some prophylactic measures do reduce the incidence of cancer and reduce mortality in mutation carriers, and the standard of care is evolving rapidly. The essential elements necessary to provide accurate interpretations of molecular genetics test results to patients are described.

Breast Neoplasms↗
PubMed2003

Primer on medical genomics. Part VIII: Essentials of medical genetics for the practicing physician.

After the mapping and sequencing of the human genome, medical professionals from essentially all specialties turned their attention to investigating the role genes play in health and disease. Until recently, medical genetics was considered a specialty of minor practical relevance. This view has changed with the development of new diagnostic and therapeutic possibilities. It is now realized that genetic disease represents an important part of medical practice. Achievements in cancer genetics, in the field of prenatal diagnostics (including carrier testing for common recessive disorders), and in newborn screening for treatable metabolic disorders reinforce the rapidly expanding role of genetics in medicine. Diagnosing a genetic disorder not only allows for disease-specific management options but also has implications for the affected individual's entire family. A working understanding of the underlying concepts of genetic disease with regard to chromosome, single gene, mitochondrial, and multifactorial disorders is necessary for today's practicing physician. Routine clinical practice in virtually all medical specialties will soon require integration of these fundamental concepts for use in accurate diagnosis and ensuring appropriate referrals for patients with genetic disease and their families.

Chromosome Disorders↗
PubMed2003

Expressive genomic hybridisation: gene expression profiling at the cytogenetic level.

AIMS: To describe a cytogenetic technique suitable for the rapid assessment of global gene expression that is based on comparative genomic hybridisation (CGH), and to use it to understand the relation between genetic amplifications and gene expression. METHODS: Whereas traditional CGH uses DNA as test and reference in hybridisations, expressive genomic hybridisation (EGH) uses globally amplified mRNA as test and normal DNA as reference. EGH is a rapid and powerful tool for localising and studying global gene expression profiles and correlating them with loci of genetic amplifications using traditional CGH. RESULTS: EGH was used to correlate genetic amplifications detected by CGH with the expression profile of two independent cell lines-Colo320 and T47D. Although many amplifications resulted in overexpression, other amplifications were partially or completely silenced at the cytogenetic level. CONCLUSION: This technique will assist in the analysis of overexpressed genes within amplicons and could resolve a controversial issue in cancer cytogenetics; namely, the relation between genetic amplifications and overexpression.

Cell Line↗
PubMed1995

Presymptomatic testing for genetic diseases of later life. Pharmacoepidemiological considerations.

As the Human Genome Project gathers speed, new disease genes are rapidly being found. Important as these discoveries are, they are only the beginning of the process of characterising, diagnosing and treating genetic diseases. We now have the potential to predict the onset of many disorders before the appearance of clinical symptoms, even though treatment is not always available. In this review we have used a number of examples to illustrate various aspects of the presymptomatic diagnosis of genetic disease and, where possible, late-onset disorders have been chosen as examples. When treatment is available, the diagnosis of a disease before appearance of symptoms can greatly improve the prognosis. When treatment is not available, reasons to undergo presymptomatic testing may not be so obvious. However, appropriate lifestyle changes or medical surveillance can sometimes delay onset or decrease severity of a disorder. Even if no treatment is available, genetic testing and counselling for the patient and family members can provide useful information for future planning.

Aged↗