Insertion Allele Frequency Research Articles

Deep amplicon sequencing reveals extensive allelic diversity in the erg11/CYP51 promoter and allows multi-population DMI fungicide resistance monitoring in the canola pathogen Leptosphaeria maculans

Continued use of fungicides provides a strong selection pressure towards strains with mutations to render these chemicals less effective. Previous research has shown that resistance to the demethylation inhibitor (DMI) fungicides, which target ergosterol synthesis, in the canola pathogen Leptosphaeria maculans has emerged in Australia and Europe. The change in fungicide sensitivity of individual isolates was found to be due to DNA insertions into the promoter of the erg11/CYP51 DMI target gene. Whether or not these were the only types of mutations and how prevalent they were in Australian populations was explored in the current study. New isolates with reduced DMI sensitivity were obtained from screens on DMI-treated plants, revealing eight independent insertions in the erg11 promoter. A novel deep amplicon sequencing approach applied to populations of ascospores fired from stubble identified an additional undetected insertion allele and quantified the frequencies of all known insertions, suggesting that, at least in the samples processed, the combined frequency of resistant alleles is between 0.0376% and 32.6%. Combined insertion allele frequencies positively correlated with population-level measures of in planta resistance to four different DMI treatments. Additionally, there was no evidence for erg11 coding mutations playing a role in conferring resistance in Australian populations. This research provides a key method for assessing fungicide resistance frequency in stubble-borne populations of plant pathogens and a baseline from which additional surveillance can be conducted in L. maculans. Whether or not the observed resistance allele frequencies are associated with loss of effective disease control in the field remains to be established.

Frequency and methylation status of selected retrotransposition competent L1 loci in amyotrophic lateral sclerosis

Long interspersed element-1 (LINE-1/L1) is the only autonomous transposable element in the human genome that currently mobilises in both germline and somatic tissues. Recent studies have identified correlations between altered retrotransposon expression and the fatal neurodegenerative disease amyotrophic lateral sclerosis (ALS) in a subset of patients. The risk of an individual developing ALS is dependent on an interaction of genetic variants and subsequent modifiers during life. These modifiers could include environmental factors, which can lead to epigenetic and genomic changes, such as somatic mutations, occurring in the neuronal cells that degenerate as the disease develops. There are more than 1 million L1 copies in the human genome today, but only 80–100 L1 loci in the reference genome are considered to be retrotransposition-competent (RC) and an even smaller number of these RC-L1s loci are highly active. We hypothesise that RC-L1s could affect normal cellular function through their mutagenic potential conferred by their ability to retrotranspose in neuronal cells and through DNA damage caused by the endonuclease activity of the L1-encoded ORF2 protein. To investigate whether either an increase in the genomic burden of RC-L1s or epigenetic changes to RC-L1s altering their expression, could play a role in disease development, we chose a set of seven well characterised genomic RC-L1 loci that were reported earlier to be highly active in a cellular L1 retrotransposition reporter assay or serve as major source elements for germline and/or somatic retrotransposition events. Analysis of the insertion allele frequency of five polymorphic RC-L1s, out of the set of seven, for their presence or absence, did not identify an increased number individually or when combined in individuals with the disease. However, we did identify reduced levels of methylation of RC-L1s in the motor cortex of those individuals with both familial and sporadic ALS compared to control brains. The changes to the regulation of the loci encompassing these RC-L1s demonstrated tissue specificity and could be related to the disease process.

Genetic Structural Differentiation Analyses of Intercontinental Populations and Ancestry Inference of the Chinese Hui Group Based on a Novel Developed Autosomal AIM-InDel Genotyping System.

In the present study, we investigated the genetic polymorphisms of 39 ancestry informative marker-insertion/deletion (AIM-InDel) loci in the Chinese Hui group using a previously self-developed panel, further clarified the genetic relationships between the Hui group and other reference populations, and assessed the ancestry inference efficiency of the AIM-InDel panel based on the worldwide population data from 1000 Genomes Phase 3. The results of the locus-specific informativeness (In) and pairwise fixation index (Fst) values, multidimensional scaling analysis, and success ratio of estimation with cross-validation showed that the novel panel could well reveal the genetic structural differentiations of the East Asian, European, African, and South Asian populations. Besides, the biogeographical ancestry origin inference both at the individual and population levels was conducted on the Chinese Hui group by principal component analysis and STRUCTURE analysis, and the results revealed that the Hui group had the East Asian origin, and the East Asian component ratio of Hui group was approximately 88.87%. Furthermore, the population genetic analyses among the Hui group and reference populations were performed based on the insertion allele frequency heat map, population pairwise Fst values and phylogenetic tree, and the results indicated that the Hui group was genetically closer to East Asian populations, especially two Chinese Han populations (CHS and CHB populations).

Forensic applicability of autosomal insertion/deletion loci in Chinese Daur ethnic group and genetic affinity evaluations between Daur group and reference populations.

In present study, we evaluated the genetic diversities of 30 insertion/deletion (InDel) loci and analyzed the genetic relationships between Daur and other comparison populations. In the studied Daur group, any two InDel loci showed no linkage disequilibrium, and all loci showed no deviations from exact tests of Hardy-Weinberg equilibrium. Insertion allele frequencies at 30 InDel loci ranged from 0.1459 (HLD39) to 0.8774 (HLD118). The observed heterozygosity and expected heterozygosity values were ranged from 0.1984 (HLD118) to 0.5564 (HLD6) and 0.2155 (HLD118) to 0.5000 (HLD92 and HLD6), respectively. The combined power of discrimination and power of exclusion values were 0.999999999993428 and 0.9878, respectively, which indicated that this panel of 30 InDels could be used for individual identifications in Daur group. Population genetic analyses including pairwise fixation index, STRUCTURE analysis, principal component analysis, genetic distance, multidimensional scaling analysis and phylogenetic analysis demonstrated that the Daur group had the closer genetic relationships with the groups from western China in comparison with other continental populations.

The HLA-G 14 bp allele frequency in different populations: A global meta-analysis

HLA-G gene encodes a non-classical molecule of major histocompatibility complex with important immunomodulatory properties, being expressed, primarily by cytotrophoblasts during pregnancy, or in pathological conditions (autoimmune diseases, cancer, transplants and viral infections). The insertion of 14 bp in HLA-G 3′UTR region has been related to reduced mRNA levels, consequently affecting the protein levels. Due to its importance for gene expression and in the context of several physiopathologic conditions, we assessed, by meta-analysis, the global distribution of the HLA-G 14 bp insertion allele frequency. We searched genetic association studies, published between 1997 and 2018, indexed in the PubMed, Science Direct and Google Scholar databases, using the descriptor: “HLA-G 14 bp”. All studies that presented allele counts in the healthy controls were included. We analyzed 20,755 individuals from 112 different populations of Africa, Asia, American and Europe. The global allelic frequency of HLA-G 14 bp insertion was 0.42 (95%CI = 0.41–0.44). When stratifying according to the continents, we observed the highest allelic frequency in the African continent (0.51) and the lowest in the European continent (0.41). Our meta-analysis demonstrates that HLA-G 14 bp insertion allele have a similar distribution around the world, indicating a possible action of balancing selection.

Forensic characteristics of Tibeto-Burman-speaking Tibetans revealed by 50 InDels

Insertion/deletion polymorphism (InDel) profiling has become a promising tool in forensic investigations and biogeographical ancestry inferences. Recently, the AGCU has designed an advanced InDel assay that allows co-amplification and fluorescent detection of the 47 autosomal InDels (A-InDels), 2 Y-chromosomal InDels (Y-InDels) and Amelogenin. In this study, 103 Tibeto-Burman-speaking Tibetan individuals were genotyped to investigate the effectiveness of this novel InDel kit. No significant deviation from Hardy-Weinberg equilibrium was observed at the 47 A-InDels after applying the Bonferroni correction. The allelic frequencies of insertion alleles at the 47 A-InDels ranged from 0.2087 to 0.7767, and the mean observed heterozygosity varied from 0.3010 to 0.5922. The combined power of discrimination reached 1–4.0688E-19, and the combined probability of exclusion was 0.9997. Overall, the observed results demonstrate that this novel InDel assay can be used as an efficient tool for individual identification and forensic paternity testing.

MHC class I polymorphic Alu insertion (POALIN) allele and haplotype frequencies in the Arabs of the United Arab Emirates and other world populations

Polymorphic Alu insertions (POALINs) are found throughout the human genome and have been used in various studies to infer geographic origin of human populations. The main aim of this study was to determine the allele and haplotype frequencies of five POALINs, AluHF, AluHG, AluHJ, AluTF and AluMICB, within the major histocompatibility complex (MHC) class I region of 95 UAE Arabs, and correlate their frequencies to those of the HLA-A, HLA-C and HLA-B class I allele lineages. Evolutionary relationships between the POALINs of the Arabs and those previously studied in populations of African, Asian and European descent were compared. At each of the five Alu loci (AluHF, AluHG, AluHJ, AluTF and AluMICB), Alu insertion was designated as Alu(locus)*02 and absence was Alu(locus)*01. The AluHG insertion (AluHG*02) had the highest frequency (0.332), followed by AluHF*02 (0.300), AluHJ*02 (0.263), AluMICB*02 (0.111) and AluTF*02 (0.058). Of the 270 Alu-HLA haplotypes pairs in the UAE Arabs, 110 had no Alu insertion, and 54 had an Alu insertion at >50% per haplotype. An Alu insertion >75% per haplotype was found between AluMICB*02 and HLA-B*14, HLA-B*22, HLA-B*44, HLA-B*55, HLA-B*57 and HLA-B*73, and with HLA-C*01 and HLA-C*18; AluHJ*02 with HLA-A*01, HLA-A*19, HLA-A*24 and HLA-A*32; AluHG*02 with HLA-A*02 and HLA-B*18; and AluHF*02 with HLA-A*10. The genotyped allele and haplotype frequencies of the MHC POALINs in UAE Arabs were compared with the results of 30 previously published Asian, European, American and African populations. Phylogenetic and multidimensional scaling (MDS) analysis of the relative MHC POALINs allele and haplotype frequencies revealed that the UAE Arabs have a similar lineage to Caucasians and the most distant genetic relationship to the Waorani native American population of Ecuador. The structure of both the phylogenetic tree and the MDS analysis supports the Out of Africa theory of human evolution. The nature of the clusters suggests the Arabian Middle East represents a crossroads from which human populations migrated towards Asia in the east and Europe to the north-west.

Distribution of angiotensin converting enzyme gene (insertion/deletion) polymorphism in Indian populations

The present study was carried out to understand the pattern of angiotensin-converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism (rs4646994) among five ethnic groups of Punjab (North-West India), and other culturally and linguistically different Indian population groups. A total of 1012 unrelated individuals belonging to Banias, Brahmins, Jat Sikhs, Khatris and Scheduled Castes were genotyped for Alu ACE gene I/D polymorphism. ID genotype was observed to have highest frequency among all the studied population groups except among Scheduled Castes. The frequency of insertion (I) allele was higher in all the studied groups as compared to the frequency of deletion (D) allele, except in Brahmins. Out of the 10 possible pairwise comparisons, four population combinations show remarkable difference. Furthermore, on comparing these five ethnic groups with other Indian populations, discrepancy was observed in the allele frequency distribution, which can be accounted for variations in sample size, study design, geographical location and diverse ethnic background.

Population Genetic Diversity and Clustering Analysis for Chinese Dongxiang Group With 30 Autosomal InDel Loci Simultaneously Analyzed.

In comparison with the most preferred genetic marker utilized in forensic science (STR), insertion/deletion analysis possesses further benefits, like absence of stutter peak, low mutation rate, and enabling mixed stain analysis. At present, a total of 169 unrelated healthy Dongxiang individuals dwelling in Dongxiang Autonomous county of Gansu province were recruited in our study to appraise the forensic usefulness of the panel including 30 autosomal diallelic genetic markers. The insertion allele frequencies were in the range of 0.1598 at HLD 111 to 0.8550 at HLD 118. The cumulative match of probability and the combined probability of exclusion were estimated based on independence of pairwise loci, with the values of 3.96 × 10-11 and 0.9886, respectively, which showed tremendous potential of this panel to be qualified for forensic personal identification in Chinese Dongxiang group. And it could also be used as a complementary tool for forensic parentage testing when combined with standard STR genetic markers. Furthermore, calculation of the DA distance and Fst values of pairwise populations, phylogenetic reconstruction, multidimensional scaling analysis, structure clustering analysis were also conducted to probe the genetic relationships between Dongxiang group and the other 30 reference populations. Results demonstrated that Dongxiang ethnic group might be genetically closer related with most Chinese populations involved in our study, especially Tibet groups, Xibe group, and several Han populations.

Evidence for positive selection on recent human transposable element insertions

Insertional activity of transposable elements (TEs) has had a major impact on the human genome; approximately one-half to two-thirds of the genome sequence is likely to be derived from TE insertions. Several families of human TEs – primarily Alu, L1 and SVA – continue to actively transpose, thereby generating insertional polymorphisms among individual genomes. The impact that TE insertions have on their human hosts' fitness, and accordingly the role that natural selection plays in shaping patterns of TE polymorphisms among populations, have yet to be systematically evaluated using whole genome sequence data. We present here a population genomic study of the effects of natural selection on human genetic variation that results from the recent activity of TEs. We developed a genome-wide scan for selection on human TE polymorphisms and applied it to a dataset of 14,384 locus-specific TE insertions characterized for 1511 individuals from 15 populations. Our TE selection scan looks for anomalously high population-specific TE insertion allele frequencies that are consistent with the action of positive (adaptive) selection. To control for the effects of demographic history, we compared the observed patterns of population-specific TE insertion allele frequencies to a neutral evolutionary model generated using time forward simulation of TE insertion allele frequencies among human population groups. This approach uncovered seven cases of polymorphic TE insertions that appear to have increased in frequency within specific human populations owing to the effects of positive selection. Five of the seven putatively selected TE insertions map to tissue-specific enhancers, and two cases correspond to expression quantitative trait loci that are associated with inter-individual gene regulatory differences. This study represents the first report of recent, local adaptation acting on polymorphic human TEs.

An age-of-allele test of neutrality for transposable element insertions.

How natural selection acts to limit the proliferation of transposable elements (TEs) in genomes has been of interest to evolutionary biologists for many years. To describe TE dynamics in populations, previous studies have used models of transposition–selection equilibrium that assume a constant rate of transposition. However, since TE invasions are known to happen in bursts through time, this assumption may not be reasonable. Here we propose a test of neutrality for TE insertions that does not rely on the assumption of a constant transposition rate. We consider the case of TE insertions that have been ascertained from a single haploid reference genome sequence. By conditioning on the age of an individual TE insertion allele (inferred by the number of unique substitutions that have occurred within the particular TE sequence since insertion), we determine the probability distribution of the insertion allele frequency in a population sample under neutrality. Taking models of varying population size into account, we then evaluate predictions of our model against allele frequency data from 190 retrotransposon insertions sampled from North American and African populations of Drosophila melanogaster. Using this nonequilibrium neutral model, we are able to explain ∼80% of the variance in TE insertion allele frequencies based on age alone. Controlling for both nonequilibrium dynamics of transposition and host demography, we provide evidence for negative selection acting against most TEs as well as for positive selection acting on a small subset of TEs. Our work establishes a new framework for the analysis of the evolutionary forces governing large insertion mutations like TEs, gene duplications, or other copy number variants.

PRNP gene variation in Pakistani cattle and buffaloes

Bovine spongiform encephalopathy (BSE) is a neurodegenerative prion protein misfolding disorder of cattle. BSE is of two types, classical BSE and atypical BSE which in turn is of two types, H-type BSE and L-type BSE. Both H-type BSE and L-type BSE are primarily sporadic prion disorders. However, one case of H-type BSE has recently been associated with E211K polymorphism in the prion protein gene (PRNP). Two polymorphisms in the bovine PRNP are also associated with susceptibility to classical BSE: a 23bp insertion/deletion (indel) in the PRNP promoter region and a 12bp indel in the first intron. No information regarding BSE susceptibility in Pakistani cattle is available. The present study aimed at achieving this information. A total of 236 cattle from 7 breeds and 281 buffaloes from 5 breeds were screened for E211K polymorphism and 23bp and 12bp indels employing triplex PCR. The E211K polymorphism was not detected in any of the animals studied. The 23bp insertion allele was underrepresented in studied cattle breeds while the 12bp insertion allele was overrepresented. Both 23bp and 12bp insertion alleles were overrepresented in studied buffalo breeds. Almost 90% of alleles were insertion alleles across all studied buffalo breeds. The average frequency of 23bp and 12bp insertion alleles across all studied cattle breeds was found to be 0.1822 and 0.9407, respectively. There were significant differences between Pakistani and worldwide cattle in terms of allele, genotype and haplotype frequencies of 23bp and 12bp indels. The higher observed frequency of 12bp insertion allele suggests that Pakistani cattle are relatively more resistant to classical BSE than European cattle. However, the key risk factor for classical BSE is the dietary exposure of cattle to contaminated feedstuffs.

Bovine spongiform encephalopathy associated insertion/deletion polymorphisms of the prion protein gene in the four beef cattle breeds from North China

Two insertion/deletion (indel) polymorphisms of the prion protein gene (PRNP), a 23-bp indel in the putative promoter region and a 12-bp indel within intron I, are associated with the susceptibility to bovine spongiform encephalopathy (BSE) in cattle. In the present study, the polymorphism frequencies of the two indels in four main beef cattle breeds (Hereford, Simmental, Black Angus, and Mongolian) from North China were studied. The results showed that the frequencies of deletion genotypes and alleles of 23- and 12-bp indels were lower, whereas the frequencies of insertion genotypes and alleles of the two indels were higher in Mongolian cattle than in the other three cattle breeds. In Mongolian cattle, the 23-bp insertion / 12-bp insertion was the major haplotype, whereas in Hereford, Simmental, and Black Angus cattle, the 23-bp deletion / 12-bp deletion was the major haplotype. These results demonstrated that Mongolian cattle could be more resistant to BSE, compared with the other three cattle breeds, because of its relatively low frequencies of deletion genotypes and alleles of 23- and 12-bp indel polymorphisms. Thus, this race could be important for selective breeding to improve resistance against BSE in this area.

ACE and LRPAP1 Insertion-Deletion Polymorphisms in a Northern Ivory Coast Population

The ACE and the LRPAP1 gene insertion-deletion polymorphisms were determined in 133 healthy individuals sampled from Ouangolodougou, a village located in northern Ivory Coast. No sex differences were found in ACE and LRPAP1 gene frequencies. The ACE insertion and deletion alleles had frequencies of 0.346 and 0.654, respectively. The ACE gene was not in Hardy-Weinberg equilibrium because of an excess of heterozygote genotypes and a deficiency of I/I genotypes compared to the expected values. Statistical analysis showed a significantly lower frequency of I/I genotypes in the Ivory Coast population compared to Sudan, Kenya, African Americans, and African Brazilians (p < 0.05), whereas no differences were found with respect to Somalia. Conversely, the frequencies of the insertion and deletion alleles in the Ivorian population did not differ from those of other African populations. The LRPAP1 insertion and deletion allele frequencies found in our study (0.192 and 0.808, respectively) did not differ significantly from the Czech and Spanish populations, the only two populations previously characterized for this polymorphism. However, the frequency of the I/I genotype was significantly lower than the frequencies observed in the European samples. Because of the limited information on the LRPAP1 gene polymorphism distribution in worldwide populations, it was not possible to draw any conclusion.

Effects of Angiotensin-Converting Enzyme Polymorphism on Aortic Elastic Parameters in Athletes

Background: Physiologic adaptations in an athlete’s heart include increased left and right ventricular chamber size, left ventricular wall thickness and mass. Angiotensin-converting enzyme (ACE) is a key enzyme in angiotensin II production causing cardiac hypertrophy. The cloning of the ACE gene has made it possible to identifya deletion (D)-insertion (I) polymorphism that appears to affect the level of serum ACE activity. Therefore, the ACE genes, which have been shown to be polymorphic, could be candidate genes for large-artery stiffness. Methods: 56 endurance athletes and 46 sedentary subjects were included in this study, and they underwent both complete echocardiographic examination, and analysis of ACE insertion (I) and deletion (D) allele frequencies in peripheral blood. The aortic diameter was recorded by M-mode echocardiography at a level 3 cm above the aortic valve. Aortic systolic diameter was measured at the time of full opening of the aortic valve, and diastolic diameter was measured at the peak of QRS. Aortic strain, stiffness index and distensibility were calculated. Results: Left ventricular mass index and left ventricular ejection fraction were significantly higher in athletes than controls (p < 0.001). The aortic distensibility index and strain were significantly greater in athletes compared with controls (respectively: 5.8 ± 2.7 vs. 4.7 ± 1.8 cm^–2 dyn^–1 10^–6, p = 0.017; 12.3 ± 2.4 vs. 9.3 ± 3.1, p < 0.001). The aortic stiffness index was significantly lower in athletes than in controls (4.8 ± 1.9 vs. 6.1 ± 2.1, p < 0.001). The aortic distensibility index and strain were statistically different in ACE DD vs. DI groups and DD vs. II groups of athletes. The aortic stiffness index was statistically different in ACE DD vs. II groups of athletes. Aortic parameters were similar according to ACE genotypes in controls. Conclusion: The results of this study indicate that aortic distensibility was increased by prolonged training in endurance athletes, particularly in those with the ACE II genotype. This effect represents an extracardiac adaptation to chronic prolonged training in athletes.

Angiotensin-converting enzyme polymorphism in healthy young subjects: relationship to left ventricular mass and functions

Objectives — Angiotensin-converting enzyme (ACE) is a key enzyme in the production of angiotensin II and thus may participate in the modulation of cardiac growth. The cloning of the ACE gene has made it possible to identify a deletion (D)-insertion (I) polymorphism that appears to affect the level of serum ACE activity.The aim of the study is to analyse the ACE gene I/D polymorphisms in healthy young subjects and to evaluate its relationship to left ventricular mass and functions.Methods — 38 women and 40 men (mean age 21.1 ± 1.7 and 21.4 ± 1.7 years) were studied. They underwent complete echocardiographic assessment and analysis of ACE insertion (I) and deletion (D) allele frequencies in peripheral blood by polymerase chain reaction. Thickness of interventricular septum (IVS) and posterior wall (LVPW) and left ventricular mass (LVM) and LVM index (LVMI) were measured by M-mode. Left ventricular ejection fraction (LVEF) was calculated by Simpson’s method.Results — There was no statistically significant difference among the DD, DI and II genotypes, concerning age, body mass index, heart rate, systolic and diastolic blood pressures.The thickness of IVS (9.5 mm), LVPW (9.0 mm), LVM (204.5 g) and LVMI (105.5 g/m2) in DD genotypes were higher than both DI (8.3 mm; 8.1 mm; 168.1 g; 90.9 g/m2) and II genotypes (8.2 mm; 7.0 mm; 141.7 g; 77.8 g/m2) in men, but not in women. LVEF among the 3 genotypes were not statistically different.Conclusion — Our findings suggest that left ventricular hypertrophy is partially determined by genetic disposition especially in men but not in women.

Polymorphism in the second intron of dopamine receptor D4 gene in humans and apes

The dopamine receptor D4 ( DRD4) has received increasing research attention in behavioral science, psychiatry, and psychopharmacology. However, the number of available genetic markers for primates is still insufficient. We identified a novel variation/polymorphism in the second intron of DRD4 in humans based on the survey of 210 Japanese: a 6 bp insertion (allele frequency: 0.002) and 8 bp deletion (0.024); however, 94 Hungarian Caucasians were found to be monomorphic. Polymorphisms of the homologous region were also found in a survey of 93 specimens from four species of great apes and 51 specimens from seven species of gibbons. The polymorphisms consist of both single nucleotide substitutions and variations in the number of tandem duplications of short GC-rich sequences. Because of usefulness of primates in behavioral science, this polymorphism may be a useful marker for association studies with behavioral traits in both humans and apes.

Effects of leptin receptor gene 3'-untranslated region polymorphism on metabolic profiles in young Japanese men.

We investigated the effects of leptin receptor gene 3'-untranslated region (3'-UTR) polymorphism on clinical and metabolic parameters in 221 young Japanese men aged 21 to 28 years. The polymerase chain reaction-restriction fragment length polymorphism method was used to identify a pentanucleotide (CTTTA) insertion in 3'-UTR of the leptin receptor gene. Body mass index, blood pressure, plasma glucose, insulin, leptin, total cholesterol, high-density lipoprotein (HDL)-cholesterol, low-density lipoprotein (LDL)-cholesterol, triglycerides, free fatty acids, uric acid, apolipoprotein A-I (apoA-I), and cholesteryl-ester transfer protein levels were measured. There was only 1 homozygote and 38 heterozygotes for the 3'-UTR insertion allele among the 221 subjects. The insertion allele frequency was 0.090. Plasma HDL-cholesterol and apoA-I levels were significantly lower (p = 0.015 and p = 0.032 by Mann-Whitney U test, respectively) in homozygous or heterozygous carriers of the insertion allele than in subjects homozygous for the normal allele. There were no differences in other parameters measured. Furthermore, when the subjects were divided into three groups according to HDL-cholesterol level, the percentage of insertion allele-positive subjects was significantly lower in the highest HDL-cholesterol group (chi(2) = 8.42, p = 0.015). These findings suggest that serum HDL-cholesterol and apoA-I levels are influenced by the leptin receptor gene 3'-UTR polymorphism in young Japanese men.

Allelic Heterogeneity in LINE-1 Retrotransposition Activity

De novo LINE-1 (long interspersed element-1, or L1) retrotransposition events are responsible for approximately 1/1,000 disease-causing mutations in humans. Previously, L1.2 was identified as the likely progenitor of a mutagenic insertion in the factor VIII gene in a patient with hemophilia A. It subsequently was shown to be one of a small number of active L1s in the human genome. Here, we demonstrate that L1.2 is present at an intermediate insertion allele frequency in worldwide human populations and that common alleles (L1.2A and L1.2B) exhibit an approximately 16-fold difference in their ability to retrotranspose in cultured human HeLa cells. Chimera analysis revealed that two amino acid substitutions (S1259L and I1220M) downstream of the conserved cysteine-rich motif in L1 open reading frame 2 are largely responsible for the observed reduction in L1.2A retrotransposition efficiency. Thus, common L1 alleles can vary widely in their retrotransposition potential. We propose that such allelic heterogeneity can influence the potential L1 mutational load present in an individual genome.

Dynamics of molecular genetic diversity in the East Midlands, UK: forensic and paternity implications

The objectives of this investigation were to establish the database of minisatellite (VNTRs), microsatellite (STRs), and ALU insertion allele frequencies for the regionally sub-divided populations of the East Midlands, which is suitable for population genetic and forensic investigations. The secondary objective was to determine if Caucasian subpopulation heterogeneity exits within the United Kingdom, within Europe and world Caucasian and racial populations at these loci. To evaluate the efficiency of these markers for forensic and paternity purposes in the East Midlands populations. Blood samples (600) were taken at random from the Caucasian East Midlands populations (five sub-populations). Using standard molecular genetic techniques, we analysed MS1, MS31, YNH24, MS43a VNTRs and HUMTH01, F13A, F13B, FES, LPL, VWA31 and CSF1PO STRs. Alu insertion polymorphisms studied included, ACE, TPA, PV92, D1, APO and FXIIIB. Overall efficiency of these loci for forensic and paternity work in the East Midlands populations is at a par with other Caucasian populations. Average value of PE is more than 0.999 and cumulative PM was 5.310 13 for UK populations with some regional and local variation. Significant heterogeneity chi-square values for MS43a, MS1 and YNH24 were found in a large number of FBI bins in UK Caucasian, European, world Caucasian and UK racial population comparisons. Overall comparisons provided interesting results suggesting caution should be exercised in the usage of pooled or general population databases for forensic and paternity investigations.