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High frequencies of human genetic diseases: founder effect with genetic drift or selection?

Rare genetic diseases have been reported with high frequency in some populations. The mechanisms which were proposed to explain most of these observations include founder effect, genetic drift or selective advantage. In recent years, many genes have been sequenced and mutations causing some of these disorders were characterized. According to the analysis of haplotypes and/or mutations, it may be possible to distinguish 3 groups of disorders frequent in isolated populations. In the first group, all the affected patients have only one frequent mutation, suggesting a founder effect with genetic drift. In the second group, more than one mutation is found among the patients; however, most of the patients are homozygotes for one frequent mutation which most probably originated from a common founder; the other patients are compound heterozygotes for the common mutation and a rare mutation. In the third group, more than one frequent mutation is found responsible for each disease. This may be due to a selective advantage which allows the expansion of each new mutation in the particular population or to multiple founder effect with genetic drift in smaller communities which thereafter mixed to form the larger population.

Canada↗

Dissemination of genetic risk information to relatives in the fragile X syndrome: guidelines for genetic counselors.

Fragile X Syndrome, which affects 1 in 1,250 males, is the most common inherited condition causing mental retardation. Although carrier detection for the fragile X syndrome utilizing DNA has now been simplified, genetic counseling and the process of informing at-risk family members remains complex. The purpose of this paper is to offer practical guidelines to health professionals providing genetic counseling to fragile X families in order to facilitate the dissemination of genetic risk information to relatives. This paper was developed from a workshop held at the 4th International Fragile X Conference. The guidelines presented here represent a beginning in the development of an approach to informing relatives in fragile X families about genetic risk, and the identification of mechanisms to reduce the burden to families.

Family↗

Re-screening serotonin receptors for genetic variants identifies population and molecular genetic complexity.

We have re-screened the genes for the 5-HT1A, 5-HT2A, 5-HT2C, and 5-HT7 serotonin receptors for genetic variants in a large African-American and Caucasian-American population sample. We have identified eight novel variants in these genes including four that are predicted to cause amino acid substitutions. These variants are additional candidates for association studies of behavioral disorders such as depression and schizophrenia as well as quantitative personality traits. We have also detected some, but not all, previously identified variants in these genes suggesting that many previously identified variants are unique to specific populations. The results of this study, and previous screens of serotonin receptors, demonstrate that the genes for serotonin receptors display marked population and molecular genetic complexity. These levels of complexity may have a substantial effect on genetic association studies of human behavioral variability related to these genes. We discuss the implications of these findings and propose methods to address complexity in genetic association studies.

Black or African American↗

The St. Lawrence Island Eskimos: genetic variation and genetic distance.

The Eskimos of St. Lawrence Island have been typed for genetic variation at 44 discrete genetic loci. Three private polymorphisms, at the 2,3-diphosphoglycerate mutase, peptidase B, and purine nucleoside phosphorylase loci, have been observed, which may be useful in future studies of genetic relationships between Eskimos and other circumpolar populations. Genetic distance analysis reveals a close relationship between the St. Lawrence Island Eskimos and other Eskimo populations and that the Eskimo populations form a distinct cluster from Amerindian populations. The St. Lawrence Island Eskimos appear to be more similar to Asiatic Eskimos than to other groups. Caucasian admixture in this population is estimated to be between 2 and 7%.

Alaska↗

Spread of phenotypic plasticity or genetic assimilation: the possible role of genetic constraints.

This paper considers possible outcomes of evolution in sexual diploid populations subjected to frequency-independent selection in favour of a phenotype which has appeared as a consequence of a change in environmental conditions. Depending on the details of genetic determination for the different development strategies ("plastic" or "canalized"), this situation results at least in either (i) the invasion of the population by "plastic" strategists, whose developmental plasticity was revealed by the environmental change, or (ii) the genetic assimilation of the new phenotype, or (iii) intermediate states in which only a certain proportion of individuals is genetically assimilated at equilibrium. Spread of plasticity during evolution in a series of distinct environments might, therefore, be hindered by genetic constraints.

Animals↗

Improving the efficiency of the genetic code by varying the codon length--the perfect genetic code.

The function of DNA is to specify protein sequences. The four-base "alphabet" used in nucleic acids is translated to the 20 base alphabet of proteins (plus a stop signal) via the genetic code. The code is neither overlapping nor punctuated, but has mRNA sequences read in successive triplet codons until reaching a stop codon. The true genetic code uses three bases for every amino acid. The efficiency of the genetic code can be significantly increased if the requirement for a fixed codon length is dropped so that the more common amino acids have shorter codon lengths and rare amino acids have longer codon lengths. More efficient codes can be derived using the Shannon-Fano and Huffman coding algorithms. The compression achieved using a Huffman code cannot be improved upon. I have used these algorithms to derive efficient codes for representing protein sequences using both two and four bases. The length of DNA required to specify the complete set of protein sequences could be significantly shorter if transcription used a variable codon length. The restriction to a fixed codon length of three bases means that it takes 42% more DNA than the minimum necessary, and the genetic code is 70% efficient. One can think of many reasons why this maximally efficient code has not evolved: there is very little redundancy so almost any mutation causes an amino acid change. Many mutations will be potentially lethal frame-shift mutations, if the mutation leads to a change in codon length. It would be more difficult for the machinery of transcription to cope with a variable codon length. Nevertheless, in the strict and narrow sense of coding for protein sequences using the minimum length of DNA possible, the Huffman code derived here is perfect.

Algorithms↗

Origins of gene, genetic code, protein and life: comprehensive view of life systems from a GNC-SNS primitive genetic code hypothesis.

We have investigated the origin of genes, the genetic code, proteins and life using six indices (hydropathy, alpha-helix, beta-sheet and beta-turn formabilities, acidic amino acid content and basic amino acid content) necessary for appropriate three-dimensional structure formation of globular proteins. From the analysis of microbial genes, we have concluded that newly-born genes are products of nonstop frames (NSF) on antisense strands of microbial GC-rich genes [GC-NSF(a)] and from SNS repeating sequences [(SNS)n] similar to the GC-NSF(a) (S and N mean G or C and either of four bases, respectively). We have also proposed that the universal genetic code used by most organisms on the earth presently could be derived from a GNC-SNS primitive genetic code. We have further presented the [GADV]-protein world hypothesis of the origin of life as well as a hypothesis of protein production, suggesting that proteins were originally produced by random peptide formation of amino acids restricted in specific amino acid compositions termed as GNC-, SNS- and GC-NSF(a)-0th order structures of proteins. The [GADV]-protein world hypothesis is primarily derived from the GNC-primitive genetic code hypothesis. It is also expected that basic properties of extant genes and proteins could be revealed by considerations based on the scenario with four stages.

Amino Acids↗

Genetic diversity and multilocus genetic structure in the relictual endemic herb Japonolirion osense (Petrosaviaceae).

Plant clonality may greatly reduce effective population size and influence management strategies of rare and endangered species. We examined genetic diversity and the extent of clonality in four populations of the monotypic herbaceous perennial Japonolirion osense, which is one of the most rare flowering plants in Japan. Allozyme analysis revealed moderate levels of genetic variation, and the proportion of polymorphic loci (P=66.7%) was higher than the value for species with similar life-history traits. With four polymorphic loci, 19 multilocus genotypes were observed among 433 aerial shoot samples and 10 (52%) were found only in single populations. The proportion of distinguishable genotypes (PD=0.10) and Simpson's index of diversity (D=0.52) also exhibited moderate levels of genotypic diversity compared to other clonal plants, with genotype frequencies at Hardy-Weinberg equilibrium. The distributions of genotypes were often localized and they were mostly found within a radius of 5 m. Spatial autocorrelation analysis showed that shoot samples located 4 m apart were expected to be genetically independent. The results suggest that the spatial extent of genets was relatively narrow and thus the clonality was not extensive.

Conservation of Natural Resources↗

Acceptance of and attitude toward genetic testing for hereditary nonpolyposis colorectal cancer: a comparison of participants and nonparticipants in genetic counseling.

PURPOSE: Data on the actual uptake of genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC) in a clinical sample is still inconclusive. The present study aimed to define the actual uptake of genetic counseling and testing offered to an unselected sample of 140 patients with colorectal cancer, fulfilling clinical criteria (Amsterdam or Bethesda) suggestive of HNPCC, and to identify demographic and psychosocial factors associated with the decision to participate in counseling. METHODS: Cross-sectional survey. Eligible subjects had been consecutively enrolled in a regional tumor registry between 1994 and 1998, and were invited to attend an information session for HNPCC at the time genetic testing for HNPCC became available. Participants and nonparticipants in the information session completed a short questionnaire. RESULTS: The actual uptake rate of the information session in this sample was 26 percent. Participants and nonparticipants were comparable with regard to clinical criteria suggestive of HNPCC, awareness of the potential hereditary predisposition, and previous history of cancer in the family. Some 60 percent of participants experienced pronounced distress related to their potential inheritance of the disorder, compared to 35 percent among nonparticipants. Distress reached a clinically significant level in 28 percent of participants. Restricted communication within the family was observed frequently. Irrespective of groups, a positive attitude toward obtaining a gene test result predominated. CONCLUSIONS: Results suggest that expressed intention and attitude toward genetic testing do not reliably predict actual uptake of counseling or testing. Thorough interdisciplinary counseling should be provided to every patient with clinical criteria suggestive of HNPCC. The considerable distress related to the hereditary disorder should be adequately addressed, as should be communication issues.

Adult↗

Genetic counseling for hereditary pancreatitis--the role of molecular genetics testing for the cationic trypsinogen gene, cystic fibrosis and serine protease inhibitor Kazal type 1.

The importance of pretest information, using an accredited DNA laboratory and interpreting the genotype on behalf of the patient and their physicians is emphasized. Care with predictive testing and the strong encouragement to involve a specialist genetic counseling service is made. A similar approach to genetic testing should be used when children are involved. Because of the incomplete pickup of PRSS1 mutations, particularly of a limited mutation panel of R122H and N291 (perhaps with A16V), a diagnosis of HP cannot be ruled out by molecular genetic testing alone. The A16V mutation has a reduced penetrance, and its contribution to pancreatitis remains unclear. The advice to patients with genetic forms of pancreatitis is a strong encouragement to avoid smoking, to avoid alcohol, and to remain in contact with clinical and research groups for their follow-up and screening trials for early pancreatic cancer. The remaining issues are of how wide to cast the net of investigation in patients with unexplained pancreatitis, particularly looking for mutations in the CFTR and lower penetrance genes such as PSTI/SPINK1.

Algorithms↗

A group theory analysis of the ambiguities in the genetic code: on the existence of a generalized genetic code.

It is known that in the transcription of genetic information there are ambiguities, i.e. the fact that a triplet codes for several aminoacids. This has generally been taken as due to errors in the transcription mechanisms. However, it has been postulated that instead of accidental miscoding, ambiguities are part of the expression of a generalized genetic code which depends on biological context. Group theory has been used to find the generalized genetic code. Here we present a new group theory approach which we think removes some weaknesses of previous works. The generalized genetic code presented here is different from that previously reported. We compare our results with experimental evidence and discuss the predictions presented.

Amino Acids↗

Cytokines in genetic susceptibility to multiple sclerosis: a candidate gene approach. French Multiple Sclerosis Genetics Group.

The immune system is involved in the pathophysiology of multiple sclerosis (MS) but the initiating antigen(s) is not yet identified. Since cytokines control both the intensity and the quality of the immune response they may be relevant candidates for the genetic susceptibility to MS. To analyze the contribution of type 1 and type 2 cytokine and cytokine receptor genes in the genetic susceptibility to MS, we have examined, in 116 French MS sibpairs, whether there is significant linkage between MS and 15 cytokine or cytokine receptor genes using 31 highly polymorphic genetic markers. The data were analyzed using the maximum likelihood score and the transmission disequilibrium approaches. None of the candidate genes tested was significantly linked to MS on the whole population. However, after stratification of the analysis on the basis of sharing (or not) of the HLA-DRB1*1501 allele, indication of linkage was found for the IL2-RB gene. These findings suggest that the IL2-RB locus contributes to the genetic susceptibility in a subgroup of MS patients.

Cytokines↗

Genetic diversity and genetic differentiation in Echinococcus granulosus (Batsch, 1786) from domestic and sylvatic hosts on the mainland of Australia.

Enzyme electrophoresis was used to examine genetic variation within and between populations of Echinococcus granulosus from domestic and sylvatic hosts in western and eastern Australia. Substantial genetic diversity was found within all populations. There was no evidence, however, of genetic differentiation between populations from different hosts or geographic areas. When isolates were grouped into previously described domestic or sylvatic strains on the basis of rostellar hook morphology, most (94%) of the genetic variation occurred within, rather than between strains. These results conflict with the currently accepted theory of separate domestic and sylvatic strains of E. granulosus on the mainland of Australia.

Alleles↗

Genetic variation in subdivided populations and conservation genetics.

The genetic differentiation of populations is usually studied by using the equilibrium theory of Wright's infinite island model. In practice, however, populations are not always in equilibrium, and the number of subpopulations is often very small. To get some insight into the dynamics of genetic differentiation of these populations, numerical computations are conducted about the expected gene diversities within and between subpopulations by using the finite island model. It is shown that the equilibrium values of gene diversities (HS and HT) and the coefficient of genetic differentiation (GST) depend on the pattern of population subdivision as well as on migration and that the GST value is always smaller than that for the infinite island model. When the number of migrants per subpopulation per generation is greater than 1, the equilibrium values of HS and HT are close to those for panmictic populations, as noted by previous authors. However, the values of HS, HT, and GST in transient populations depend on the pattern of population subdivision, and it may take a long time for them to reach the 95 per cent range of the equilibrium values. The implications of the results obtained for the conservation of genetic variability in small populations are discussed. It is argued that any single principle should not be imposed as a general guideline for the management of small populations.

Animals↗

Population genetic structure of the schistosome-vector snail Bulinus globosus: examining the role of genetic drift, migration and human activities.

Bulinus globosus, one of the intermediate hosts of the genus Schistosoma, is an hermaphrodite freshwater snail species. This species occupies different kinds of environments in Africa, which are generally subjected to large variations in water availability. The mating system of this species is outcrossing, although selfing has been suggested for one population. Here we investigate the genetic structure of populations of B. globosus in natural and human-modified environments from Niger and Ivory Coast using protein electrophoresis. Our goal is to analyse the respective role of the environment (genetic drift and gene flow), the mating system and human activities. Our results indicate a low intrapopulation polymorphism. A large differentiation among populations occurs on the scale of the whole study area whereas neighbouring populations can show little differentiation. These results point to the role of genetic drift and gene flow as the main factors shaping the genetic structure, with human activities playing a role occasionally.

Alleles↗

Digital genetics: unravelling the genetic basis of evolution.

Digital genetics, or the genetics of digital organisms, is a new field of research that has become possible as a result of the remarkable power of evolution experiments that use computers. Self-replicating strands of computer code that inhabit specially prepared computers can mutate, evolve and adapt to their environment. Digital organisms make it easy to conduct repeatable, controlled experiments, which have a perfect genetic 'fossil record'. This allows researchers to address fundamental questions about the genetic basis of the evolution of complexity, genome organization, robustness and evolvability, and to test the consequences of mutations, including their interaction and recombination, on the fate of populations and lineages.

Computational Biology↗

The non-standard genetic code of Candida spp.: an evolving genetic code or a novel mechanism for adaptation?

A number of yeasts of the genus Candida translate the standard leucine-CUG codon as serine. This unique genetic code change is the only known alteration to the universal genetic code in cytoplasmic mRNAs, of either eukaryotes or prokaryotes, which involves reassignment of a sense codon. Translation of CUG as serine in these species is mediated by a novel serine-tRNA (ser-tRNACAG), which uniquely has a guanosine at position 33, 5' to the anticodon, a position that is almost invariably occupied by a pyrimidine (uridine in general) in all other tRNAs. We propose that G-33 has two important functions: lowering the decoding efficiency of the ser-tRNACAG and preventing binding of the leucyl-tRNA synthetase. This implicates this nucleotide as a key player in the evolutionary reassignment of the CUG codon. In addition, the novel ser-tRNACAG has 1-methylguanosine (m1G-37) at position 37, 3' to the anticodon, which is characteristic of leucine, but not serine tRNAs. Remarkably, m1G-37 causes leucylation of the ser-tRNACAG both in vitro and in vivo, making the CUG codon an ambiguous codon: the polysemous codon. This indicates that some Candida species tolerate ambiguous decoding and suggests either that (i) the genetic code change has not yet been fully established and is evolving at different rates in different Candida species; or (ii) CUG ambiguity is advantageous and represents the final stage of the reassignment. We propose that such dual specificity indicates that reassignment of the CUG codon evolved through a mechanism that required codon ambiguity and that ambiguous decoding evolved to generate genetic diversity and allow for rapid adaptation to environmental challenges.

Adaptation, Physiological↗

A natural genetic code expansion cassette enables transmissible biosynthesis and genetic encoding of pyrrolysine.

Pyrrolysine has entered natural genetic codes by the translation of UAG, a canonical stop codon. UAG translation as pyrrolysine requires the pylT gene product, an amber-decoding tRNA(Pyl) that is aminoacylated with pyrrolysine by the pyrrolysyl-tRNA synthetase produced from the pylS gene. The pylTS genes form a gene cluster with pylBCD, whose functions have not been investigated. The pylTSBCD gene order is maintained not only in methanogenic Archaea but also in a distantly related Gram-positive Bacterium, indicating past horizontal gene transfer of all five genes. Here we show that lateral transfer of pylTSBCD introduces biosynthesis and genetic encoding of pyrrolysine into a naïve organism. PylS-based assays demonstrated that pyrrolysine was biosynthesized in Escherichia coli expressing pylBCD from Methanosarcina acetivorans. Production of pyrrolysine did not require tRNA(Pyl) or PylS. However, when pylTSBCD were coexpressed with mtmB1, encoding the methanogen monomethylamine methyltransferase, UAG was translated as pyrrolysine to produce recombinant monomethylamine methyltransferase. Expression of pylTSBCD also suppressed an amber codon introduced into the E. coli uidA gene. Strains lacking one of the pylBCD genes did not produce pyrrolysine or translate UAG as pyrrolysine. These results indicated that pylBCD gene products biosynthesize pyrrolysine using metabolites common to Bacteria and Archaea and, furthermore, that the pyl gene cluster represents a "genetic code expansion cassette," previously unprecedented in natural organisms, whose transfer allows an existing codon to be translated as a novel endogenously synthesized free amino acid. Analogous cassettes may have served similar functions for other amino acids during the evolutionary expansion of the canonical genetic code.

Amino Acid Sequence↗