Differences In Allele Distribution Research Articles

Using Genetics to Identify Intraspecific Conservation Units: a Critique of Current Methods

Genetic criteria have recently been proposed for identifying evolutionarily significant units (ESUs) and management units (MUs; Moritz 1994). Although this proposal has proved useful for focusing discussion about the intraspecific groupings of relevance to conservation, I am concerned that the criteria put forward have been accepted and applied without sufficient debate about their merit or limitations. My aim is to stimulate renewed debate on this subject by identifying some weaknesses in the proposed criteria. Although Moritz (1994) distinguished between the biological definitions of ESUs and MUs and the genetic criteria he proposed for recognizing such groups, many papers that cite his work erroneously refer to the recognition criteria as the definitions. An ESU is a group of organisms that has been isolated from other conspecific groups for a sufficient period of time to have undergone meaningful genetic divergence from those other groups (Ryder 1986). Moritz (1994) suggested that ESUs could be identified genetically as groups whose mtDNA lineages were reciprocally monophyletic, meaning that all lineages within each group share more-recent common ancestors than any lineage from one group shares with any lineage from the other group. In contrast, an MU is a group in which local population dynamics are determined primarily by birth and death rather than immigration and emigration (Moritz et al. 1995). Moritz (1994) suggested that MUs could be identified as populations with significant differences in allele distributions. An important point regarding both of these concepts is that they apply only when the populations under study are naturally divided into groups (Moritz et al. 1995). Of course, genetic study may also be of value in situations where populations are continuously distributed, but such populations cannot be subdivided into ESUs and MUs.

Differences in Allelic Distribution of Two Polymorphisms in the VHL-Associated Gene CUL2 in Pheochromocytoma Patients without Somatic CUL2 Mutations

Differences in Allelic Distribution of Two Polymorphisms in the VHL-Associated Gene CUL2 in Pheochromocytoma Patients without Somatic CUL2 Mutations

Association of an (A-C)n dinucleotide repeat polymorphic marker at the 5'-region of the aldose reductase gene with retinopathy but not with nephropathy or neuropathy in Japanese patients with Type 2 diabetes mellitus.

Recently an (A-C)n dinucleotide repeat polymorphic marker in the 5'-region of the ALR2 gene encoding aldose reductase was found to be associated with diabetic retinopathy in the Chinese population in Hong Kong, and with nephropathy and neuropathy in the British Caucasian population. The present study assessed the association between the polymorphism and microvascular complications in Japanese patients with Type 2 diabetes mellitus. DNA from 87 Japanese patients with Type 2 diabetes mellitus and 90 control subjects with normal glucose tolerance were typed for the polymorphic marker by polymerase chain reaction and direct sequencing. Six alleles, namely Z-12, Z-6, Z-4, Z-2, Z, and Z+2 were identified. There was no significant difference in allele distribution between diabetic patients and controls. The Z-2 allele frequency was significantly higher in subjects with diabetic retinopathy than those without retinopathy (0.35 vs. 0.20, P=0.039), suggesting that aldose reductase is involved in the development of diabetic retinopathy. In contrast, the microsatellite marker was not associated with diabetic nephropathy, peripheral or autonomic neuropathy. The discrepancy may be partly attributable to the low frequency of Z+2 allele in the Japanese subjects. The (A-C)n dinucleotide repeat polymorphism may be a useful genetic marker to screen for patients at high risk of retinopathy.

Differences in allelic distribution of two polymorphisms in the VHL-associated gene CUL2 in pheochromocytoma patients without somatic CUL2 mutations.

Although the two major familial forms of pheochromocytomas, multiple endocrine neoplasia type 2 and von-Hippel-Lindau disease (VHL), have been associated with mutations of the RET and VHL genes, respectively, the molecular pathogenesis of sporadic pheochromocytomas is largely unknown. Recently, a putative tumor suppressor gene has been identified, CUL2, whose product has been shown to interact with the VHL tumor suppressor. To examine whether CUL2 plays a role in pheochromocytoma pathogenesis, we analyzed a series of 26 distinct tumor samples for mutations in the whole coding region of this gene. There were no somatic pathogenic mutations in CUL2, except for 1 sporadic tumor that had a hemizygous gene deletion. We also found 3 novel polymorphisms in the gene. One of these variants, IVS5-6C/T, as well as another previously described one, c.2057G/A, were overrepresented among the pheochromocytoma patients compared to that in a control population (P < 0.005 and P < 0.01, respectively). Although our findings suggest that CUL2 does not play a major role in the pathogenesis of pheochromocytomas, it is still unknown whether epigenetic mechanisms are involved in its inactivation in VHL-associated tumors. Furthermore, the potential role for the overrepresented alleles in the pheochromocytoma group requires further investigation.

Allelic expression of p73 in human ovarian cancers

The p73 gene is structurally related to the tumor suppressor gene p53. The role of p73 in tumor development is still unclear and no data on ovarian cancer are so far available. For this reason we have analyzed, in a panel of ovarian cancers, the allelic distribution and expression of p73. Fifty-one samples from ovarian cancers and five human ovarian cancer cell lines growing in culture were analyzed. Allelic origin was analyzed by PCR after digestion with the restriction enzyme Sty I. Heterozygous, informative cases were selected for studies aimed at evaluating allelic expression of p73. We found an allelic distribution similar to that previously reported. LOH was found in two patients with ovarian cancer. In one case in which normal ovarian tissue was available biallelic expression of p73 was found. In comparisons of ovarian cancers and borderline tumors, no differences in allelic distribution and/or expression were found, suggesting that p73 does not play an important role in the pathogenesis and development of ovarian cancer.

Lack of association between genetic variations of apo A-I–C-III–A-IV gene cluster and myocardial infarction in a sample of European male: ECTIM study

The goal of the present study was to compare the allele frequency of four polymorphisms at the apo A-I C-III A-IV cluster gene locus—ApoA-I: XmnI and PstI; ApoC-III: SstI; ApoA-IV: XbaI—between male patients who had had a myocardial infarction ( n=614) and matched controls ( n=764). The association with a number of lipid lipoprotein, apolipoprotein and lipoprotein particle variables was also assessed. Patients and subjects were recruited in Belfast, Lille, Strasbourg and Toulouse in the framework of the ECTIM study. In the control group, the frequencies of the different polymorphic alleles were homogeneous among recruitment centres suggesting the absence of any European North to South gradient for these cluster polymorphisms. There was no evidence for a significant difference in allelic distribution between cases and controls suggesting that apo A-I, C-III, A-IV gene cluster polymorphisms do not explain MI survival in this sample of European men. There was no statistically significant association between apo A-I C-III A-IV cluster gene polymorphisms and lipid, lipoprotein, apolipoprotein, and lipoprotein particle levels. In conclusion, in the ECTIM study, the apo A-I, C-III, A-IV gene cluster polymorphism is associated with neither circulating plasma variables nor MI survival.

Molecular characterization of HLA class I in Colombians carrying HLA-A2: high allelic diversity and frequency of heterozygotes at the HLA-B locus.

Polymerase chain reaction using sequence-specific oligonucleotide probes (PCR-SSOP) typing was used to analyze HLA class I A, B and C alleles in three different Colombian populations. Fifty-nine samples were from Hispano-American Mestizos living in the urban areas of Cali (referred to here as Aso population). Forty-four and thirty samples were from the African Black populations of Zacarias (Zac) and Punta Soldado (PS), respectively. Samples were selected for expression of HLA-A2 by monoclonal antibody staining and allele-specific hybridization, and their HLA-A2 subtype distribution has been reported previously. Although only a limited number of samples was analyzed, the data suggest the existence of a remarkable degree of HLA class I polymorphism in the populations studied, with representatives of most serological classes. Despite their common African origin, the populations Zac and PS, both resident in malaria endemic regions, showed some striking differences in allelic distribution for all three class I loci. Furthermore, the samples from Aso and PS, but not Zac, showed a low percentage of blank alleles at the HLA-B locus (0 and 0.4%, respectively), suggesting the possibility of a heterozygote advantage for HLA-B alleles in Colombian populations.

Constitutional genetic variation at the human aromatase gene (Cyp19) and breast cancer risk.

The activity of the aromatase enzyme, which converts androgens into oestrogens and has a major role in regulating oestrogen levels in the breast, is thought to be a contributing factor in the development of breast cancer. We undertook this study to assess the role of constitutional genetic variation in the human aromatase gene (Cyp19) in the development of this disease. Our genotyping of 348 cases with breast cancer and 145 controls (all Caucasian women) for a published tetranucleotide repeat polymorphism at intron 4 of the Cyp19 gene revealed the presence of six common and two rare alleles. Contingency table analysis revealed a significant difference in allelic distribution between cases and controls (χ2 5df = 13.52, P = 0.019). The allele measuring 171 bp was over-represented in cases; of 14 individuals homozygous for this allele, 13 were cases. These individuals had a higher incidence of cancer in family members and an earlier age at diagnosis than other cases. In sequencing Cyp19's coding exons and regulatory regions, we discovered a perfect association between a silent polymorphism (G→A at Val80) and the high-risk genotype. Our conclusion is that constitutional genetic variation at the Cyp19 locus is associated with the risk of developing breast cancer, with the 171-bp allele serving as the high-risk allele. © 1999 Cancer Research Campaign

Microsatellite variation in the Australian dingo.

The dingo is thought to have arrived in Australia from Asia about 5,000 years ago. It is currently in danger because of interbreeding with domestic dogs. Several morphological, behavioral, and reproductive characteristics distinguish dingoes from domestic dog. Skull morphometrics are currently used to try to classify wild canids as pure dingo, dog, or hybrid. Molecular techniques based on diagnostic DNA differences between dogs and dingoes would make a much more reliable and practical test. A small number of markers (about 10) would allow detection of animals with domestic dog in their ancestry several generations back. We have typed 16 dingoes and 16 dogs of mixed breed for 14 microsatellites. The amount of variation in the Australian dingo is much less than in domestic dogs. The size distributions of microsatellites in the two groups usually overlap. The number of alleles in the dingo is much smaller in all cases. One dinucleotide repeat locus shows a size difference of 1 bp in allele classes between dog and dingo. This locus may be diagnostic for dog or dingo ancestry. The differences in distributions of alleles at other loci can also be used to classify animals using a likelihood method.

Single-nucleotide polymorphism in the human mu opioid receptor gene alters beta-endorphin binding and activity: possible implications for opiate addiction.

Opioid drugs play important roles in the clinical management of pain, as well as in the development and treatment of drug abuse. The mu opioid receptor is the primary site of action for the most commonly used opioids, including morphine, heroin, fentanyl, and methadone. By sequencing DNA from 113 former heroin addicts in methadone maintenance and 39 individuals with no history of drug or alcohol abuse or dependence, we have identified five different single-nucleotide polymorphisms (SNPs) in the coding region of the mu opioid receptor gene. The most prevalent SNP is a nucleotide substitution at position 118 (A118G), predicting an amino acid change at a putative N-glycosylation site. This SNP displays an allelic frequency of approximately 10% in our study population. Significant differences in allele distribution were observed among ethnic groups studied. The variant receptor resulting from the A118G SNP did not show altered binding affinities for most opioid peptides and alkaloids tested. However, the A118G variant receptor binds beta-endorphin, an endogenous opioid that activates the mu opioid receptor, approximately three times more tightly than the most common allelic form of the receptor. Furthermore, beta-endorphin is approximately three times more potent at the A118G variant receptor than at the most common allelic form in agonist-induced activation of G protein-coupled potassium channels. These results show that SNPs in the mu opioid receptor gene can alter binding and signal transduction in the resulting receptor and may have implications for normal physiology, therapeutics, and vulnerability to develop or protection from diverse diseases including the addictive diseases.

Genetic Profiles of Newly Inbred Dahl/Iwai Salt-Sensitive and Salt-Resistant Rats

Dahl-Iwai salt-sensitive (S) and salt-resistant (R) rat strains were established as inbred strains at Brookhaven National Laboratory, NY, and were introduced into Eisai Co., Ltd., Japan, and designated DIS/Eis and DIR/Eis. To examine whether there are different allele distributions among the substrains of inbred Dahl S and R rats, we determined biochemical and immunological alleles of DIS/Eis and DIR/Eis, and SS/Sea and SR/Sea, which were derived from SS/Jr and SR/Jr, which were developed by Rapp and Dene. Several differences of allele distribution were observed, indicating that the substrains have different genetic backgrounds. The phenotypic differences between the substrains, such as the severity of the hypertension induced, could be ascribed to the different genetic backgrounds.

Los genes TAP y EMP2 en el asma alérgica

Patients with mite-induced allergic asthma (AA) present strong IgE-response to mite allergens. Thus, immunogenetic study of this response could help in the understanding of allergic disease etiology. AA is a common disease in the Tropics, Blomia tropicalis and Dermatophagoides pteronyssinus being the principal causative agents. An association between HLA class II genes and IgE-response to mite allergens in AA patients from the prevalent ethnic mulatto group in Cartagena, a Caribbean city, has already been described (by these authors), the main vector being Blomia tropicalis. TAP and LMP genes play an important part in antigen processing but their possible role in AA pathogenesis has not been well-documented. In this study, the role of TAP and LMP2 polymorphism in the control of specific IgE-response to mite allergens has been evaluated in two groups, consisting of 96 unrelated asthmatic patients with IgE-response to mite allergens and 97 non-allergic controls belonging to the mulatto ethnic group. TAPl and TAP2 were typed by PCRISSO; LMP2 was typed by PCRIRFLP. Each alleles' frequency in AA patients and controls was: TAPO1 O1 : 52.6-56.2%; TAPO2011 : 35.9-34.9%; TAP*O301: 5.2-3.8%; TAP*0401: 6.3-4.7%; TAP2A: 31.5-30.5%; TAP2B: 44.3-46.6%; TAP2C: 16.5-1 8.0%; TAP 2H: 7.7-4.9%; LMP2*HI H: 6.7-1 0.4%; LMP2'RR: 42.7-44.8%; LMP2*RH: 50.6-44.8%. There was no significant statistical difference in allele distribution between the two groups studied. In addition, no linkage disequilibrium between the HLA DRBl allele and TAP and LMP2 genes was found. These findings suggest that TAP and LMP genes are not primarily involved in AA genetic susceptibility.

Multiple Allelic Variation in a Sodium Channel Gene from Populations of Australian Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) Detected via Temperature Gradient Gel Electrophoresis

Helicoverpa armigera, the cotton bollworm; is a significant pest of Australian field and vegetable crops and has a widespread incidence of resistance to pyrethroid insecticides. Naturally occurring variation in the para sodium channel gene was assayed in H. armigera. the polymerase chain reaction (PCR) was used to amplify part of the gene and temperature gradient gel electrophoresis (TGGE) used to detect differences in the melting properties of the amplified DNA fragments. A gene fragment of approximately 890 bp was characterised in a total of 66 individuals, comprising four sample groups: untreated controls and fenvalerate‐treated individuals from both the Namoi valley, NSW and the St. George irrigation area, Qld. At least sixteen alleles were detected for the 3′‐end, 250 bp, Hpall digest fragment of the amplified part of the gene. the Namoi and St. George allele distributions were significantly heterogeneous, making this locus a suitable marker for use, with others, in migratory studies among H. armigera populations. Since this gene is a candidate for pyrethroid resistance in the related American pest Heliothis virescens (F.) we looked for a difference in allele distributions between insecticide treated and untreated groups. No association between molecular variation in this gene and fenvalerate resistance was detected.

Dopamine D4 receptor gene polymorphisms: relation to ethnicity, no association with schizophrenia and response to clozapine in Israeli subjects

The dopamine D4 receptor (DRD4) is a candidate gene in the search for a genetic etiology of schizophrenia and for pharmacogenetic factors in the response to antipsychotic treatment. Previous work has not found linkage or association of a polymorphism in exon 3 of this gene with diagnosis of schizophrenia or response to clozapine. In this study we examined this association in Israeli schizophrenic subjects treated with clozapine, compared to ethnically matched controls. Another polymorphism of this gene, in exon 1, was also studied. Both polymorphisms showed no association with schizophrenia or treatment response. A significant difference in allelic distribution of DRD4 exon 3 polymorphism was found between Ashkenazi and non-Ashkenazi control subjects.

Genetic variation and evolutionary stability of the FMR1 CGG repeat in six closed human populations.

In an attempt to understand the allelic diversity and mutability of the human FMR1 CGG repeat, we have analyzed the AGG substructure of this locus within six genetically-closed populations (Mbuti pygmy, Baka pygmy, R. surui, Karitiana, Mayan, and Hutterite). Most alleles (61/92 or 66%) possessed two AGG interspersions occurring with a periodicity of one AGG every nine or ten CGG repeats, indicating that this pattern is highly conserved in all human populations. significant differences in allele distribution were observed among the populations for rare variants possessing fewer or more AGG interruptions than the canonical FMR1 CGG repeat sequence. Comparisons of expected heterozygosity of the FMR1 CGG repeat locus with 30 other microsatellite loci, demonstrated remarkably similar levels of polymorphism within each population, suggesting that most FMR1 CGG repeat alleles mutate at rates indistinguishable from other microsatellite loci. A single allele (1 out of 92) was identified with a large uninterrupted tract of pure repeats (42 pure CGG triplets). Retrospective pedigree analysis indicated that this allele had been transmitted unstably. Although such alleles mutate rapidly and likely represent evolving premutations, our analysis suggests that in spite of the estimated frequency of their occurrence, these unstable alleles do not significantly alter the expected heterozygosity of the FMR1 CGG repeat in the human population.

Linkage disequilibrium between four intragenic polymorphic microsatellites of the NF1 gene and its implications for genetic counselling.

Four intragenic polymorphic microsatellite markers, AAAT Alu repeat, IVS27AC28.4, ACI27.2, and IVS38GT53.0, located along a 65 kb DNA region of the NF1 gene, were used to genotype 64 Spanish families with neurofibromatosis type 1 (NF1). Linkage disequilirium between each pair of markers was evaluated. Three of these markers, AAAT Alu repeat, ACI27.2, and IVS38GT53.0, exhibit linkage disequilibrium between each other. Analysis of extended haplotypes provides further evidence of the disequilibrium within this region since only 11 haplotypes account for 52% of the total chromosomes. Because of linkage disequilibrium, the informativeness of marker combinations for genotyping of NF1 families is diminished. There was no difference in the overall distribution of alleles between affected and normal chromosomes. An at risk haplotype was not found, as expected for a disease with at least 50% of cases being sporadic.

Apolipoprotein B 3' hypervariable repeat genotype: association with plasma lipid concentration, coronary artery disease, and other restriction fragment polymorphisms

Apolipoprotein B gene 3' variable number tandem repeat (VNTR) and related regions were amplified by PCR and analyzed by agarose gel electrophoresis. Eighteen VNTR alleles (VNTR25, 26, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 58, 60) and 45 genotypes were observed in 477 Taiwanese subjects. The VNTR35 allele and genotype VNTR35/35 were observed most frequently in this population. The polymorphism information content was 0.62. Some minor alleles, such as VNTR25 and 60, were found only in coronary artery disease (CAD) and stroke patients in our sampling, and no statistically significant difference was observed in VNTR allelic frequency between control and CAD or stroke patients. Significant differences in allelic distribution of some VNTR alleles were observed between our normal Taiwanese population and a Caucasian group studied by others. VNTR43-47 and AluI+ (coding Ala591) restriction fragment length polymorphism (RFLP) as well as VNTR49-60 and EcoRI- (coding Lys4154) RFLP were found to be highly coinherited. No apparent association between the VNTR genotype and plasma lipid concentration was observed; however, for the same genotype, the CAD and stroke patients frequently showed higher lipoprotein(a) and lower HDL cholesterol concentrations than the control group.

An association in non-insulin-dependent diabetes mellitus subjects between susceptibility to retinopathy and tumor necrosis factor polymorphism

In IDDM an association between diabetic retinopathy and polymorphic markers of MHC has been described. However, these associations are complicated by a primary association between the MHC and IDDM. Because the pathogenesis of retinopathy is likely to be the same in IDDM and NIDDM, NIDDM subjects with retinopathy would be the ideal population to study for an association with MHC markers. The following South Indian subjects were therefore studied: unselected NIDDM ( n = 76), unselected IDDM ( n = 99), non-diabetic controls ( n = 96), NIDDM subjects with maculopathy (MAC), n = 55, NIDDM subjects with proliferative retinopathy (PR), n = 53, and without retinopathy (LTD), n = 46. DNA was amplified and studied using a microsatellite polymorphism located 3.5 kb upstream of TNF-β within the MHC class HI region on the short arm of chromosome 6. No differences in allelic distribution were observed between the random NIDDM subjects and controls ( p = 0.17). Differences in allelic distribution were found between unselected IDDM and controls ( p = 0.016) and between the NIDDM subjects with maculopathy and/or proliferative retinopathy and no retinopathy ( p = 0.006). This association could be accounted for by those patients with proliferative retinopathy (MAC vs LTD, p = 0.23; MAC vs PR, p = 0.07; and PR vs LTD, p = 0.002).

Detection and Analysis of the Human D4 Dopamine Receptor Gene (DRD4) Sequence Variant in the Japanese and Mongolian Population

A PCR-based Sma I restriction fragment length polymorphism (RFLP) in the human D4 dopamine receptor (DRD4) gene was investigated in 200 subjects each of Japanese and Mongolian populations. When compared to allele frequencies for Caucasians previously reported by Petronis et al., Japanese and Mongolian populations showed a decreased frequency of the allele which could not be digested with Sma I. The difference in allele distributions between these two ethnically defined populations (Japanese and Mongolians, and Caucasians) was statistically significant (p<0.05). This RFLP was suggested to be a racial difference between Asian and European populations. However, since the frequency of the non-digested allele was extremely low (1%) in the Asian populations, we cannot exclude the possibility that this allele represents a mutation. Sma I PCR-RFLP typing would not only be one of genetic markers, but might also be a specific marker for searching some neuropsychiatric abnormalities.

Analysis of the novel cyclin-dependent kinase 4 and 6 inhibitor gene p18 in lymphoma and leukemia cell lines

The genes for the CDK4/6-inhibitors p16 INK4A/MTS1 and p15 INK4B/MTS2 are frequently deleted in hematological malignancies. A new member of this family of CDK4/6 inhibitors is p18. In order to assess p18 growth-suppressor gene alterations in hematological neoplasms, we investigated 31 lymphoma and leukemia cell lines by PCR for both exons of this gene. No homozygous deletions were observed. Investigation of a new intragenic restriction fragment length polymorphism revealed no differences in allele distribution between the tumor cell lines and healthy volunteers. Our results suggest that homozygous deletion of the p18 gene does not play a major role in leukemogenesis or lymphomagenesis.