Presence Of Rare Alleles Research Articles

Sampling properties of the heterozygote-excess estimator of the effective number of breeders

The effective number of breeders (N b) for a cohort of progeny can be estimated from an excess of heterozygotes that arises in progeny produced by finite numbers of parents. In principle, N b is a simple function of the standardized deviation (D) of the proportion of heterozygous progeny from its expectation under random mating. We explored the sampling properties of this D-estimator of N b through computer simulation. The accuracy of the D-estimator is remarkably robust to variation in numbers of alleles and loci and the presence of rare alleles, though precision can be low if, relative to a given N b, the sample of progeny or the cumulative number of independent alleles (n ci) sampled is too small. For N b up to 30 parents, acceptable accuracy is achieved with sample sizes of 200 or more progeny and 80 or more independent alleles; for N b of 50–100, a sample of 500–1,000 progeny and 450–900 independent alleles are required for similar accuracy and precision. Though the estimator is most applicable for the situation of random union of gametes (as may occur in some marine invertebrates or fish, for example), it works for other mating systems (monogamous or polygamous pairings, polygyny), when the effective number of breeders is small (N b ≤ 20). Simulations reveal small overestimation biases with smaller sample sizes, rare alleles, or highly polymorphic loci (≥10 alleles). Despite this bias, multiallelic loci are preferable to many loci with few alleles, which have larger sampling errors.

Feed-backs between genetic structure and perturbation-driven decline in seagrass (Posidonia oceanica) meadows

We explored the relationships between perturbation-driven population decline and genetic/genotypic structure in the clonal seagrass Posidonia oceanica, subject to intensive meadow regression around four Mediterranean fish-farms, using seven specific microsatellites. Two meadows were randomly sampled (40 shoots) within 1,600 m2 at each site: the “impacted” station, 5–200 m from fish cages, and the “control” station, around 1,000 m downstream further away (considered a proxy of the pre-impact genetic structure at the site). Clonal richness (R), Simpson genotypic diversity (D*) and clonal sub-range (CR) were highly variable among sites. Nevertheless, the maximum distance at which clonal dispersal was detected, indicated by CR, was higher at impacted stations than at the respective control station (paired t-test: P < 0.05, N = 4). The mean number of alleles (Â) and the presence of rare alleles ( r) decreased at impacted stations (paired t-test: P < 0.05, and P < 0.02, respectively, N = 4). At a given perturbation level (quantified by the organic and nutrient loads), shoot mortality at the impacted stations significantly decreased with CR at control stations (R 2 = 0.86, P < 0.05). Seagrass mortality also increased with  (R 2 = 0.81, P < 0.10), R (R 2 = 0.96, P < 0.05) and D* (R 2 = 0.99, P < 0.01) at the control stations, probably because of the negative correlation between those parameters and CR. Therefore, the effects of clonal size structure on meadow resistance could play an important role on meadow survival. Large genotypes of P. oceanica meadows thus seem to resist better to fish farm-derived impacts than little ones. Clonal integration, foraging advantage or other size-related fitness traits could account for this effect.

A method to bin alleles of genetic loci that maintains population heterogeneity

Fishery resources are often studied when individuals from multiple stocks are aggregated. For that reason, mixed-stock analysis (MSA), i.e., estimation of the stock composition of a mixture of individuals, is an important component of many research programs. Although many characteristics can be used in MSA, DNA loci, particularly microsatellites, have become extremely common. Microsatellite loci usually have a greater number of potential expressions, or alleles, than other marker types. A high degree of polymorphism can enhance the power of MSA, but allele proportions are estimated less precisely and rare alleles are absent or observed in very small numbers in typically sized samples. The reduced precision and presence of rare alleles can degrade the performance of some analytic methods. Although the effect can be reduced by binning alleles, which is common, an objective method of doing so has not been available previously. We present a method for binning alleles that reduces the number of rare alleles, largely preserves the genetic relationships observed among stocks, and modestly improves the performance of mixed-stock and individual-assignment analyses. The method is illustrated with data from Yukon River chum salmon (Oncorhynchus keta) and western Alaska Dolly Varden (Salvelinus malma).

Isozyme Similarity inAnopheles oswaldoiSensu Lato (Diptera: Culicidae) from the Amazon Region, Brazil

Isozyme electrophoresis studies were conduced on Anopheles oswaldoi sensu lato from three states in Amazonian (Brazil), including Acre, where this taxon has been incriminated as a potential human malaria vector. The 13 enzymes analyzed yielded a total of 20 loci. Of these, 10 were monomorphic in the three samples. Diagnostic loci were not found. The measures of genetic variability showed mean number of alleles per locus between 1.5 and 2.0, percentage of polymorphic loci of 40%, and mean heterozygosities from 0.031 to 0.062. The inbreeding coefficient F(IS) had a moderate mean value (0.109), which resulted from heterozygote genotype deficiencies and the presence of rare alleles in the homozygote state. Mean F(ST) value (0.0502) and genetic distance values (Nei's genetic similarity values of 0.994-0.997; Roger's genetic similarity values of 0.963-0.968) were very low among the three samples of An. oswaldoi s. l. Preliminary results of identifications of male genitalia indicated that An. oswaldoi s. s. Peryassú and Anopheles konderi Galvão & Damasceno of the An. oswaldoi complex coexist sympatrically in Sena Madureira, Acre, and São Miguel, Rondônia, whereas in the sample from Coari, Amazonas, only An. konderi was identified. The isozyme results do not suggest differences between these species, particularly in areas of sympatry.

Isozyme Similarity in Anopheles oswaldoi Sensu Lato (Diptera: Culicidae) from the Amazon Region, Brazil

Isozyme electrophoresis studies were conduced on Anopheles oswaldoi sensu lato from three states in Amazonian (Brazil), including Acre, where this taxon has been incriminated as a potential human malaria vector. The 13 enzymes analyzed yielded a total of 20 loci. Of these, 10 were monomorphic in the three samples. Diagnostic loci were not found. The measures of genetic variability showed mean number of alleles per locus between 1.5 and 2.0, percentage of polymorphic loci of 40%, and mean heterozygosities from 0.031 to 0.062. The inbreeding coefficient F(IS) had a moderate mean value (0.109), which resulted from heterozygote genotype deficiencies and the presence of rare alleles in the homozygote state. Mean F(ST) value (0.0502) and genetic distance values (Nei's genetic similarity values of 0.994-0.997; Roger's genetic similarity values of 0.963-0.968) were very low among the three samples of An. oswaldoi s. l. Preliminary results of identifications of male genitalia indicated that An. oswaldoi s. s. Peryassu and Anopheles konderi Galvao & Damasceno of the An. oswaldoi complex coexist sympatrically in Sena Madureira, Acre, and Sao Miguel, Rondonia, whereas in the sample from Coari, Amazonas, only An. konderi was identified. The isozyme results do not suggest differences between these species, particularly in areas of sympatry.

Interaction between Polymorphisms MTHFR C677T and MTRR A66G and Vitamin Levels in Pregnant Women.

In the homocysteine metabolic pathway, several key enzymes, including methylenetetrahydrofolate reductase (MTHFR) and methionine synthase reductase (MTRR), have been implicated in abnormal homocysteine accumulation in the presence of rare alleles. In previous study, we showed that lower maternal Cbl levels were associated with higher tHcy and lower S-adenosylmethionine/S-adenosylhomocysteine ratio in pregnant women and their neonates.The aim of this study is to investigate whether MTHFR and MTRR polymorphisms are involved in the risk for elevated total homocysteine (tHcy) and its interaction with low cobalamin (Cbl) or serum folate (SF) levels. Genotypes for polymorphisms MTHFR C677T and MTRR A66G were determined by PCR-FLRP. The serum levels of Cbl, SF and tHcy were determined in 377 pregnant women (37–42 weeks of gestational age), and cutoff values for Cbl and SF were considered the first quartile (low values). Four models of univariate logistic regression analyses were used (Table 1). Pregnant women with MTHFR 677T allele have high risk for elevated tHcy that is increased when 677T allele is associated with low Cbl. Increased risk for elevated tHcy is also met when MTRR 66G allele and low Cbl levels were associated. Women with low SF and common MTHFR and MTRR alleles have high risk for elevated tHcy, that is increased when in association with 677T allele or with 66G allele.Interaction between MTHFR C677T and MTRR A66G polymorphisms and vitamins levels in pregnant womenDependent variablesComparation levels (N)P valueOdd Ratios95% CItHcy>8.3μmol/LMTHFR 677CC genotype and Cbl> 115.8 pmol/L (ref) (136) a1.00MTHFR 677CC genotype and≤Cbl 115.8 pmol/L (45)0.2981.570.67 – 3.63MTHFR 677CT and 677TT genotypes and Cbl>115.8 pmol/L (145)0.0152.091.16 – 3.77MTHFR 677CT and 677TT genotypes and≤Cbl 115.8 pmol/L (48)0.0014.632.22 – 9.65tHcy>8.3μmol/LMTHFR 677CC genotype and SF > 10.9 nmol/L (ref) (148) b1.00MTHFR 677CC genotype and≤SF 10.9 nmol/L (33)0.0083.201.35 – 7.59MTHFR 677CT and 677TT genotypes and SF > 10.9 nmol/L (133)0.0351.951.05 – 3.61MTHFR 677CT and 677TT genotypes and≤SF 10.9 nmol/L (59)0.0016.623.31 – 13.26tHcy>8.3μmol/LMTRR 66AA genotype and Cbl> 115.8 pmol/L (ref) (96) c1.00MTRR 66AA genotype and ≤Cbl 115.8 pmol/L (23)0.2221.900.68 – 5.29MTRR 66AG and 66GG genotypes and Cbl>115.8 pmol/L (183)0.4181.290.70 – 2.39MTRR 66AG and 66GG genotypes and ≤Cbl 115.8 pmol/L (69)0.0132.461.21 – 5.01tHcy>8.3μmol/LMTRR 66AA genotype and SF > 10.9 nmol/L (ref) (92) d1.00MTRR 66AA genotype and ≤SF 10.9 nmol/L (27)0.0063.831.47 – 9.96MTRR 66AG and 66GG genotypes and SF > 10.9 nmol/L (186)0.3991.340.68 – 2.63MTRR 66AG and 66GG genotypes and≤SF 10.9 nmol/L (65)0.0014.782.26 – 10.10P for trend: (a) P<0.001; (b) P<0.001; (c) P=0.067; (d) P<0.001In conclusion, the interaction between MTHFR and MTRR polymorphisms and low folate and cobalamin serum levels may explain the increased risk for elevated tHcy found in pregnant women.

Genetic subdivision of Dagestan ethnic populations

Relationships between ethnic and genetic differentiation with respect to 54 microsatellites have been analyzed in five Daghestan ethnic groups. To detect the microsatellites, human chromosomes 3, 17, and 18 were screened with a step of 10 cM (Weber/CHLC 9.0 markers) at the Mammalian Genotyping Service (National Institute of Health, United States). Comparison of the polymorphism of these loci in Daghestan populations with average worldwide data has revealed generally low heterozygosity in Daghestan populations, which is accounted for by traditional endogamous and consanguineous marriages throughout the history of these populations. The inbreeding coefficient in Daghestan ethnic groups varies from 0.005 to 0.0134 and is close to the worldwide maximum known to date. For some DNA loci, significant differences between the offsprings of consanguineous and exogamous marriages with respect to allele sizes and their variance have been found. The Daghestan ethnic populations studied differ from one another in both the frequencies of common alleles and the presence of rare alleles that are unique for each ethnic group of Daghestan and have not been found in any other population in the world.

What can nuclear microsatellites tell us about maritime pine genetic resources conservation and provenance certification strategies?

Maritime pine (Pinus pinaster Ait.) is the first conifer used for reforestation in France and now covers 2.4 million ha of the Iberian Peninsula. In order to preserve the genetic resources of this economically and ecologically important species prior knowledge of the distribution of genetic diversity is needed. In this paper, a genetic diversity study was performed using nuclear simple sequence repeats (SSRs or microsatel- lites). Classical parameters of diversity (allelic richness and heterozygosity) and differentiation were estimated for 47 populations of P. pinaster. Most of the populations (40) were collected in France, six populations were also collected in the Iberian Peninsula and one Moroccan population was also included in the study. The population genetic parameters indicated that some populations should be a focus of conservation efforts (hig- her level of diversity, higher allelic richness and presence of rare alleles). A diagnostic test for sample origin was developed to distinguish Corsi- can from Landes populations. Pinus pinaster / nuclear microsatellites / genetic diversity / conservation / provenance identification

RareHRAS1 alleles are a risk factor for the development of brain tumors

The highly polymorphic HRAS1 minisatellite locus, located 1 kilobase downstream from the H-ras1 gene, has been associated with increased susceptibility to a variety of cancers. Microsatellite instability (MI), another molecular abnormality observed in human neoplasms, most likely reflects an increased mutation rate and also is thought to underlie cancer predisposition. The purpose of this study was to investigate the association between rare HRAS1 alleles and brain tumors and to correlate the HRAS1 allelotype with MI and clinicopathologic features. Ninety-four patients with primary brain tumors (52 gliomas, 32 meningiomas, and 10 schwannomas) and 109 healthy control individuals were studied. The size of HRAS1 alleles was determined by fluorescent detection in an automated DNA sequencer. The interspersion pattern was assessed by the minisatellite variant repeat-polymerase chain reaction technique. Twenty of 94 (21.28%) patients with brain tumors had at least one rare allele, compared with 13 of 109 (11.92%) in the control population (Fisher exact test; P = 0.0329). The presence of rare alleles was associated with an increased risk of brain tumors (odds ratio, 1.99; 95% confidence interval, 0.93-4.27). The overrepresentation of rare alleles in tumor patients mainly reflects the higher frequency observed in the glioma group (P = 0.0086). The authors did not detect association between the presence of rare HRAS1 alleles and MI in their series. No significant difference in the distribution of these alleles was found when tumors were compared according to other clinicopathologic variables. The presence of rare HRAS1 alleles is associated with an increased risk for the development of glial neoplasms (OR = 2.72; 95% CI, 1.17-6.32). The lack of association between rare HRAS1 polymorphisms and MI suggests that these two genetic factors are not likely to be expression of the same underlying defect.

Genetic variation and migration pathways of maritime pine (Pinus pinaster Ait) in the Iberian peninsula

The genetic variability and migration pathways of Pinus pinaster after glaciation in the Iberian peninsula was studied by means of 18 loci from 12 natural populations of the species. The analysis showed the existence of three groups of populations with different levels of diversity and patterns of recolonization. The southern Iberian group displays a high level of diversity, with a stepping-stone model of variation. The presence of rare alleles in this group and their position in the phylogenetic tree suggest the existence of refugia during glaciations in this zone. The eastern Iberian group also has high levels of diversity but is clearly separate from the first group based on their genetic distances. The Atlantic group displays a low level of diversity that could be interpreted as a rapid recolonization of the entire area by the Eastern group that has not yet developed to a divergence in this area. The southern Iberian range is indicated to be the dispersal centre of the species after the last glaciation.

Polymorphic expression of biotransformation enzymes in Barrett's oesophagus and oesophageal carcinomas

Background: Susceptibility to oesophageal cancer or Barrett's epithelium, with 30-125 fold increase for development of adenocarcinoma, of a particular individual may depend in part on the balance between phase I drug metabolizing (e.g. cytochrome P450 IA1; CYPIA1) and phase II detoxification enzymes (e.g. glutathione S-transferase; GST). Polymorphic variants in exon 7 (CYPIAIlNcol) and 3' flanking region (CYPIAIlMspl) of the CYPIA1 gene may lead to increased levels of bioactive compounds. In addition GSTM1 and GSTF1 null genotypes, resulting in complete absence of these GST isoforms and consequently resulting in deficient detoxification, were described. Aims: To study the frequency of polymorphic variants in the CYPIA1 gene in combination with GSTM1 and GSTF1 null genotypes in patients with squamous cell carcinoma (SCC, n=ll), adenocarcinoma (AC, n=23) or Barrett's epithelium (BE, n=56) in the oesophagus as compared to healthy blood donors (BD, n=207). Methods: DNA was extracted from whole blood and genetic polymorphisms were studied by polymerase chain reaction (PCR) based techniques. Chi square analysis was used for statistical evaluation. Results: CYPIAI/Ncol as well as CYPIAIlMspl rare alleles were more common in patients with SCC (each 38.5%) as compared to BD (Ncol 23.5%, Z2=4.07, p=0.04; Mspl 15.9%, ;~2=4.34, p=0.04). No differences in CYPIA1 polymorphic variants were found between the other populations. GSTM1 and GSTT1 null genotypes did not differ between the patient and control populations. Summary/conclusions: Presence of rare alleles in CYPIA1 exon 7 or the 3' flanking region, both leading to increased bioactivation of precarcinogens, may result in increased susceptibility to squamous cell carcinoma of the oesophagus.

Ha-ras rare alleles in breast cancer susceptibility.

Over the last several years, evidence has accumulated to support the idea that rare Ha-ras polymorphisms are associated with inherited susceptibility to certain human cancers. A recent epidemiologic study conducted at our institution found a significant association specifically with breast cancer, although the mechanism underlying this relationship remains unclear. We have proposed that rare Ha-ras alleles are markers of a genomic instability that predisposes to breast cancer. To address this hypothesis, we are investigating the relationship between the presence of rare alleles and another form of instability, gene amplification, and are developing new methodologies both to improve VNTR allele length detection and to characterize the internal repeat sequence variations of the various alleles. These studies should enable us to more clearly define the role of this region in cancer development by delineating VNTR structure and function and the mechanisms of rare allele generation. Ultimately, we hope to identify VNTR characteristics that will permit more accurate cancer risk assessment.

H-ras-1 restriction fragment length polymorphism in normal individuals and oral cancer patients in India.

Restriction fragment length polymorphism (RFLP) of the human H-ras-1 gene has been indicated as a marker for detection of individuals at high risk of cancer. We have investigated the association of RFLP at the H-ras-1 locus and susceptibility to oral cancer by Southern hybridization analysis in 77 primary oral tumors and 99 healthy donors. The frequency distribution of the BamHI fragments of H-ras-1 revealed homozygous or heterozygous alleles in the two subpopulations. The heterozygous genotype occurred more frequently in the normal subjects (53%) as compared to the cancer patients (36%). Four common alleles-C1 to C4, were noted predominantly in both groups, with rare alleles detected at a lower frequency. The common allele with 7.6 kb BamHI fragment was significantly higher in normals (10%) than in the tumor population (4%) (P < 0.05). However, a similar distribution of rare alleles in both groups indicated that the presence of rare alleles is not indicative of predisposition to oral cancer.