The fundamental theorem of natural selection: the end of a story

The direction of research in population genetics theory is currently, and correctly, retrospective, that is directed toward the past. What events in the past have led to the presently observed genetic constitution of a population? This direction is inspired, first, by the large volumes of genomic data now available and, second, by the success of the classical prospective theory in validating the Darwinian theory in terms of Mendelian genetics. However, the prospective theory should not be forgotten, and in that theory, perhaps the most interesting and certainly the most controversial, is Fisher's so-called "Fundamental Theorem of Natural Selection." This article describes the history and the current status of that theorem.

Estimating the serological underrecognition of patients with weak or partial RHD variants

BACKGROUND

For patients with weak or discrepant RhD RBC phenotypes, RHD genotyping is employed to determine need for RhD-negative management. However, many RHD variants are type D-negative or D-positive. Serological recognition rates (RRs) of weak and partial RHD variants are poorly characterized.

STUDY DESIGN AND METHODS

Four US studies employing RHD genotyping for weak or discrepant RhD phenotypes provided data for race/ethnicity-specific serological recognition. Three studies used microplate, and 1 used gel and tube; 2 had anti-D data. We obtained White and Hispanic/Latino allele frequencies (AFs) of weak D types 1, 2, and 3 single-nucleotide variants (SNVs) from the Genome Aggregation Database (gnomAD, v4.0.0) and devised Hardy-Weinberg-based formulas to correct for gnomAD's overcount of hemizygous RHD SNVs as homozygous. We compiled common partial RHD AF from genotyped cohorts of US Black or sickle cell disease subjects. From variant AF, we calculated hemizygous-plus-homozygous genetic prevalences. Serological prevalence: genetic prevalence ratios yielded serological RRs.

RESULTS

Overall RRs of weak D types 1-3 were 17% (95% confidence interval 12%-24%) in Whites and 12% (5%-27%) in Hispanics/Latinos. For eight partial RHD variants in Blacks, overall RR was 11% (8%-14%). However, DAR RR was 80% (38%-156%). Compared to microplate, gel-tube recognition was higher for type 2 and DAU5 and lower for type 4.0. Anti-D was present in 6% of recognized partial RHD cases, but only in 0.7% of estimated total genetic cases.

DISCUSSION

Based on AF, >80% of patients with weak or partial RHD variants were unrecognized serologically. Although overall anti-D rates were low, better detection of partial RHD variants is desirable.

Molecular confirmation of alpha 1-antitrypsin deficiency in liver transplant setting: A province-wide experience

Background and Aim

Patients suspected of Alpha 1-Antitrypsin (A1AT) abnormality based on low serum concentration are routinely confirmed through polymerase chain reaction (PCR) testing of peripheral blood. Genotyping formalin-fixed paraffin-embedded (FFPE) tissue is a novel approach that could aid in detecting variant A1AT. We performed qPCR on FFPE liver explants with Periodic Acid Schiff after Diastase (PASD)- and A1AT-positive globules to confirm and estimate the frequency of A1AT deficiency in transplant cases.

Materials and Methods

Eighteen (12.68%) of 142 patients with end-stage liver disease showed PASD/A1AT positive globules. FFPE of the explants was tested through qPCR to detect S and Z alleles. A second age- and sex-matched control group consisting of five liver transplant patients with negative globules was included in the study.

Results

qPCR assay was successful with all the samples meeting QC parameters. All patients included in the study elucidated Z allele variants; 2 homozygous (11.1%) and 16 heterozygous (88.9%). The control group demonstrated normal wild-type MM allele.

Conclusion

Screening for A1AT deficiency using serum levels is not sufficiently sensitive to detect deficiency, especially in carriers. If A1AT testing was not performed preoperatively and the risk is high based on the PASD/A1AT-positive globules in the explants, then molecular testing of FFPE tissue can be a viable method for confirming the diagnosis.

Clinical spectrum and frequency of Charcot-Marie-Tooth disease in Italy: data from the national CMT registry

BACKGROUND

We report data from the Italian CMT Registry.

METHODS

The Italian CMT Registry is a dual registry where the patient registers, chooses a reference centre, where the attending clinician collects a minimal dataset of information and administers the CMT Examination/Neuropathy Score. Entered data are encrypted.

RESULTS

Overall, 1012 patients had registered (535 females) and 711 had received a genetic diagnosis. Demyelinating CMT (65.3%) was more common than axonal CMT2 (24.6%) and intermediate CMT (9.0%). The PMP22 duplication was the most frequent mutation (45.2%), followed by variants in GJB1 and MPZ (both ~10%) and MFN2 (3.3%) genes. We observed a relatively high mutation rate in some "rare" genes (HSPB1 1.6%, NEFL 1.5%, SH3TC2 1.5%) and the presence of multiple mutation clusters across Italy. CMT4A was the most disabling type, followed by CMT4C and CMT1E. Disease progression rate differed, depending on the CMT subtype. Foot deformities and walking difficulties were the main features. Shoe inserts and orthotic aids were used by almost one half of all patients. Scoliosis was present in 20% of patients, especially in CMT4C. Recessive forms had more frequently walking delay, walking support need and wheelchair use. Hip dysplasia occurred in early-onset CMT.

CONCLUSIONS

The Italian CMT Registry has proven to be a powerful data source to collect information about epidemiology and genetic distribution, clinical features and disease progression of CMT in Italy and is a useful tool for recruiting patients in forthcoming clinical trials.

Genetic background of idiopathic neurodevelopmental delay patients with significant brain deviation volume

BACKGROUND

Significant brain volume deviation is an essential phenotype in children with neurodevelopmental delay (NDD), but its genetic basis has not been fully characterized. This study attempted to analyze the genetic factors associated with significant whole-brain deviation volume (WBDV).

METHODS

We established a reference curve based on 4222 subjects ranging in age from the first postnatal day to 18 years. We recruited only NDD patients without acquired etiologies or positive genetic results. Cranial magnetic resonance imaging (MRI) and clinical exome sequencing (2742 genes) data were acquired. A genetic burden test was performed, and the results were compared between patients with and without significant WBDV. Literature review analyses and BrainSpan analysis based on the human brain developmental transcriptome were performed to detect the potential role of genetic risk factors in human brain development.

RESULTS

We recruited a total of 253 NDD patients. Among them, 26 had significantly decreased WBDV (<-2 standard deviations [SDs]), and 14 had significantly increased WBDV (>+2 SDs). NDD patients with significant WBDV had higher rates of motor development delay (49.8% [106/213] vs . 75.0% [30/40], P  = 0.003) than patients without significant WBDV. Genetic burden analyses found 30 genes with an increased allele frequency of rare variants in patients with significant WBDV. Analyses of the literature further demonstrated that these genes were not randomly identified: burden genes were more related to the brain development than background genes ( P  = 1.656e -9 ). In seven human brain regions related to motor development, we observed burden genes had higher expression before 37-week gestational age than postnatal stages. Functional analyses found that burden genes were enriched in embryonic brain development, with positive regulation of synaptic growth at the neuromuscular junction, positive regulation of deoxyribonucleic acid templated transcription, and response to hormone, and these genes were shown to be expressed in neural progenitors. Based on single cell sequencing analyses, we found TUBB2B gene had elevated expression levels in neural progenitor cells, interneuron, and excitatory neuron and SOX15 had high expression in interneuron and excitatory neuron.

CONCLUSION

Idiopathic NDD patients with significant brain volume changes detected by MRI had an increased prevalence of motor development delay, which could be explained by the genetic differences characterized herein.

Human serum albumin variants in China: a molecular epidemiological investigation and literature review

Background

Bisalbuminemia is a hereditary and/or acquired abnormality characterized by a double albumin (ALB) band on serum protein electrophoresis. However, there have been no epidemiological investigations of ALB variants in Chinese populations.

Methods

This retrospective study examined 71,963 unrelated subjects from five provinces in southern China. ALB variants were screened by cellulose acetate electrophoresis at pH 8.6 and ALB mutations were confirmed by polymerase chain reaction-DNA sequencing.

Results

The average incidence of inherited bisalbuminemia in the southern Chinese population was 0.0264% (19/71,963). Thirteen cases showed slow and six showed fast genetic variants on cellulose acetate electrophoresis. Four kinds of ALB variants were identified: proalbumin Lille (p.Arg23His), ALB Castel di Sangro (p.Lys560Glu), ALB Fukuoka-1 (p.Asp587Asn), and a novel ALB Wuxi (p.Lys562Glu). The gene frequency of ALB variants in the Wuxi region (0.126%, 13/10,297) was significantly higher than in other regions in southern China, and 90.9% (10/11) of cases of proalbumin Lille were also found in the Wuxi region.

Conclusions

This study provides the first report of the detailed prevalence and molecular characterization of ALB variants in southern China. Compared with other areas of China, Wuxi had a different pattern of ALB variants and a high prevalence of proalbumin Lille.

PCR-RFLP molecular confirmation of color dilution alopecia in dogs in Brazil

Color dilution alopecia (CDA) is a dermatopathy observed exclusively in animals having a diluted coat color. In dogs, color dilution occurs as a result of a single-nucleotide variation (SNV) c.-22G > A in the melanophilin gene. We standardized a PCR-restriction-fragment length polymorphism (PCR-RFLP) technique to identify this mutation and determine its frequency in dogs in Brazil. The standardized PCR-RFLP technique could efficiently identify the SNV c.-22G > A in the melanophilin gene, with mutated allele frequencies of 0.1, 0.1, and 0.0875 in Dachshund, Miniature Pinscher, and Yorkshire Terrier breeds, respectively, with no statistical difference among the breeds (p = 0.252). The mutation was identified in 2 homozygous Dachshund dogs with alopecia, confirming the clinical characteristic of CDA. The standardization of a simpler and more accessible molecular technique for recognition of the SNV c.-22G > A in the melanophilin gene allows identification of heterozygous (phenotypically normal) dogs that can be excluded from reproduction, to avoid the birth of dogs with diluted coat color and consequently CDA.

Prevalence of GJB2 gene mutations correlated to presence of clinical and environmental risk factors in the etiology of congenital sensorineural hearing loss of the Romanian population

Although etiologically heterogeneous at least 50% of all early on-set hearing losses have a genetic cause and of these, the large majority, 75-80% are most probably autosomal recessive and 70% are non-syndromic. The rest of the congenital hearing losses are determined by clinical and environmental factors such as ototoxic medication, prematurity, and complications at birth. During the last decade it became clear that 50-80% of all such afflictions result from mutations in a single gene, GJB2, which encodes the protein Connexin 26. In order to, at least partially clarify this problem, especially in an emerging country such as Romania, where the problem is not studied adequately, we developed a comprehensive study of genetic, clinical and environmental risk factors for congenital hearing loss. The two most common variations of this gene, 35delG and W24X in children with positive diagnosis of bilateral severe to profound sensorineural hearing loss were investigated. A cohort of 34 children (20 female and 14 male), ages between 2 and 10 (mean age 4.62 years), coming from 33 non-related families were evaluated. All cases were diagnosed with severe or profound bilateral congenital SNHL. A statistical comparison of genetic and environmental/clinical prevalence was also attempted since the presence of a genetic disorder cannot rule out the role of other documented risk factors in the etiology of SNHL. The results showed that, 29.4% of cases (10/34) were homozygotic for the 35delG mutation 35delG/35delG), also known as genotype Δ/Δ. 5.88% of cases (2/34) belong to the heterozygotic bi-genic group 35delG/W24X. The clinical factors with high statistical significance for SNHL in a non-genetic group have no significance for genetic SNHL patients. Thus, the present study confirms the relatively high prevalence of the 35delG and W24X mutations in cases of congenital non-syndromic severe of profound bilateral SNHL.

Genetic Analysis of Patients With Sickle Cell Anemia and Stroke Before 4 Years of Age Suggest an Important Role for Apoliprotein E

BACKGROUND

Ischemic stroke is a devastating complication affecting children with sickle cell anemia. Genetic factors are likely to be important in determining the risk of stroke but are poorly defined.

METHODS

We have studied a cohort of 19 children who had an overt ischemic stroke before 4 years of age. We predicted genetic determinants of stroke would be more prominent in this group. We performed whole exome sequencing on this cohort and applied 2 hypotheses to our variant filtering. First, we looked for strong, potentially mono- or oligogenic variants for ischemic stroke, and second, we considered that more common polygenic variants will be enriched in our cohort. Candidate variants emerging from both strategies were validated in a cohort of 283 patients with sickle cell anemia and known pediatric cerebrovascular outcomes. We used principal component analysis in this cohort to control for relatedness and population substructure.

RESULTS

Our primary finding was that the Apoliprotein E genotypes ε2/ε4 and ε4/ ε4, defined by the interplay of rs7412 and rs429358, were associated with increased stroke risk, with an odds ratio of 4.35 ([95% CI, 1.85-10.0] P=0.0011) for ischemic stroke in the validation cohort. We also found that rs2297518 in NOS (NO synthase) 2 (odds ratio, 2.25 [95% CI, 1.21-4.19]; P=0.014) and rs2230123 in signal transducer and activator of transcription (odds ratio, 2.60 [95% CI, 1.30-5.20]; P=0.009) both had increased odds ratios for ischemic stroke, although these two variants were below the threshold for statistical significance after correction for multiple testing.

CONCLUSIONS

These data identify new loci for future functional investigations into cerebrovascular disease in sickle cell anemia. Based on African population reference allele frequencies, the Apoliprotein E genotypes would be present in about 10% of children with sickle cell anemia and represent a genetic risk factor that is potentially modifiable by both dietary and pharmaceutical manipulation of its dyslipidemic effects.

Common, intermediate and well-documented HLA alleles in world populations: CIWD version 3.0.0

A catalog of common, intermediate and well-documented (CIWD) HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQB1 and -DPB1 alleles has been compiled from over 8 million individuals using data from 20 unrelated hematopoietic stem cell volunteer donor registries. Individuals are divided into seven geographic/ancestral/ethnic groups and data are summarized for each group and for the total population. P (two-field) and G group assignments are divided into one of four frequency categories: common (≥1 in 10 000), intermediate (≥1 in 100 000), well-documented (≥5 occurrences) or not-CIWD. Overall 26% of alleles in IPD-IMGT/HLA version 3.31.0 at P group resolution fall into the three CIWD categories. The two-field catalog includes 18% (n = 545) common, 17% (n = 513) intermediate, and 65% (n = 1997) well-documented alleles. Full-field allele frequency data are provided but are limited in value by the variations in resolution used by the registries. A recommended CIWD list is based on the most frequent category in the total or any of the seven geographic/ancestral/ethnic groups. Data are also provided so users can compile a catalog specific to the population groups that they serve. Comparisons are made to three previous CWD reports representing more limited population groups. This catalog, CIWD version 3.0.0, is a step closer to the collection of global HLA frequencies and to a clearer view of HLA diversity in the human population as a whole.

Potential Clinical Relevance of Differences in Allele Frequencies Found within Very Important Pharmacogenes between Hmong and East Asian Populations

OBJECTIVES

Implementing pharmacogenetics for very important pharmacogenes (VIPs) holds the promise of improving clinical outcomes through optimal medication selection and dosing. However, significant differences in the frequency of actionable variants in VIPs may exist within subpopulations of a given ancestral group. Furthermore, these differences can potentially impact drug selection and dosing. The purpose of this study was to ascertain allele frequencies for VIPs and to predict medication requirements using Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines in Hmong and compare with published data for East Asians.

METHODS

Using a community-based participatory action research approach, DNA collected from 194 Hmong adults living in the United States was analyzed for 22 genetic variants within eight VIPs (CYP2C9, CYP2C19, CYP4F2, DPYD, G6PD, SLCO1B1, TPMT, VKORC1). Allele frequencies for VIPs and predicted medication requirements using CPIC guidelines were compared between Hmong participants and East Asians.

RESULTS

Significant differences in allele frequencies between the Hmong and East Asians were found for 23% (5/22) of the CPIC-actionable variants tested. Allele frequencies for VIPs in Hmong versus East Asians were 16.6% versus 3.4% in CYP2C9*3A, 42.2% versus 29.0% for CYP2C19*2, 0.3% versus 8.3% in CYP2C19*3, 6.5% versus 22.1% in CYP4F2*3, and 3.6% versus 0.1% in SLCO1B1*5, respectively. These differences significantly influenced predicted medication usage recommendations in warfarin, simvastatin, and phenytoin between Hmong and East Asians.

CONCLUSIONS

Important differences in allele frequencies for key genetic variants influencing selection of medications and dosages were found between the Hmong and East Asians. The magnitude and nature of these differences can be expected to result in different medication recommendations for the Hmong relative to East Asians.

Chronic wasting disease associated with prion protein gene (PRNP) variation in Norwegian wild reindeer (Rangifer tarandus)

The emergence of CWD in Europe in 2016 and the first natural infection in wild reindeer warranted disease management. This led to the testing of 2424 hunted or culled reindeer during 2016–2018, from the infected subpopulation in the Nordfjella mountain range in Southern Norway. To identify any association between PRNP variation and CWD susceptibility, we characterized the open reading frame of the PRNP gene in 19 CWD positive reindeer and in 101 age category- and sex-matched CWD negative controls. Seven variant positions were identified: 6 single nucleotide variants (SNVs) and a 24 base pair (bp) deletion located between nucleotide position 238 and 272, encoding four instead of five octapeptide repeats. With a single exception, all variant positions but one were predicted to be non-synonymous. The synonymous SNV and the deletion are novel in reindeer. Various combinations of the non-synonymous variant positions resulted in the identification of five PRNP alleles (A-E) that structured into 14 genotypes. We identified an increased CWD risk in reindeer carrying two copies of the most common allele, A, coding for serine in position 225 (Ser225) and in those carrying allele A together with the 24 bp deletion.

Partitioning the Pleiotropy Between Coronary Artery Disease and Body Mass Index Reveals the Importance of Low Frequency Variants and Central Nervous System-Specific Functional Elements

BACKGROUND

The objective of this study is to investigate the extent and nature of pleiotropy between coronary artery disease (CAD) and body mass index (BMI).

METHODS

We examined the contribution of genome-wide single-nucleotide polymorphisms (minor allele frequency ≥0.01) to co-occurrence of CAD and BMI in a sample of genetically unrelated 8041 subjects (genetic resemblance ≤0.025) of European ancestry using mixed-linear-models. We further partitioned the estimated pleiotropy according to biological features to gain insight into the nature of pleiotropy between CAD and BMI.

RESULTS

We found significant (P<0.0001) positive genetic correlation between CAD and BMI (r_g =0.60). The estimated pleiotropy explained 68% of phenotypic correlation, and it was not proportionally distributed across the chromosomes; notably, chromosome 10 contributed more; whereas, chromosomes 11 and 14 contributed less to pleiotropy than expected given their chromosomal length. We noted that a large proportion (63%; P=0.002) of the pleiotropy is attributed to single-nucleotide polymorphisms with low allele frequency (minor allele frequency <0.05). Of note, pleiotropy was enriched among central nervous system genes and genes of metabolic pathways. Further analyses revealed that these effects are more pronounced in the proopiomelanocortin pathway and genes involved in carbohydrate metabolism. After genome-wide association study meta-analysis, only single-nucleotide polymorphisms downstream of the MC4R gene were found concordantly associated with (P<5×10^-8) BMI and CAD with lead single-nucleotide polymorphism being rs663129 (combined P=2.7×10^-65). Finally, partitioning the pleiotropy according to functional elements pointed to the importance of superenhancers and notably brain-specific superenhancers.

CONCLUSIONS

Genome-wide pleiotropy substantially contributes to co-occurrence of CAD and obesity, and it is highly enriched among low frequency variants and central nervous system-specific functional elements.

Creating and validating a warfarin pharmacogenetic dosing algorithm for Colombian patients

Purpose

Warfarin is an oral anticoagulant associated with adverse reaction to drugs due to wide inter- and intra-individual dosage variability. Warfarin dosage has been related to non-genetic and genetic factors. CYP2C9 and VKORC1 gene polymorphisms affect warfarin metabolism and dosage. Due to the central role of populations’ ethnical and genetic origin on warfarin dosage variability, novel algorithms for Latin American subgroups are necessary to establish safe anticoagulation therapy.

Patients and methods

We genotyped CYP2C9*2 (c.430C > T), CYP2C9*3 (c.1075A > C), CYP4F2 (c.1297G > A), and VKORC1 (−1639 G > A) polymorphisms in 152 Colombian patients who received warfarin. We evaluated the impact on the variability of patients’ warfarin dose requirements. Multiple linear regression analysis, using genetic and non-genetic variables, was used for creating an algorithm for optimal warfarin maintenance dose.

Results

Median weekly prescribed warfarin dosage was significantly lower in patients having the VKORC1-1639 AA genotype and poor CYP2C9*2/*2,*2/*3 metabolizers than their wild-type counterparts. We found a 2.3-fold increase in mean dose for normal sensitivity patients (wild-type VKORC1/CYP2C9 genotypes) compared to the other groups (moderate and high sensitivity); 31.5% of the patients in our study group had warfarin sensitivity-related genotypes. The estimated regression equation accounted for 44.4% of overall variability in regard to warfarin maintenance dose. The algorithm was validated, giving 45.9% correlation (R²=0.459).

Conclusion

Our results describe and validate the first algorithm for predicting warfarin maintenance in a Colombian mestizo population and have contributed toward the understanding of pharmacogenetics in a Latin American population subgroup.

Distribution of IFITM3 polymorphism (dbSNP: rs12252) in mestizo populations in four states of Mexico

Interferon‐inducible transmembrane protein 3 (IFITM3) participates in the defense against viral infections. This study identified and compared the frequency of the IFITM3 rs12252 polymorphism in 410 individuals in western Mexico. The western Mexican allelic frequencies (frequency of the “C” allele = 0.18) differ from some American, East Asian and European populations.

[Association between HLA-A and HLA-DRB1 allele polymorphisms and susceptibility to tuberculosis in southern Chinese population]

OBJECTIVE

To study the relationship between HLA allele frequencies in peripheral blood mononuclear cells (PBMCs) and the susceptibility to tuberculosis in southern Chinese population.

METHODS

The polymorphisms of HLA-A and HLA-DRB1 loci in the PBMCs were analyzed in 294 patients with active tuberculosis using polymerase chain reaction-sequence based typing (PCT-SBT). The allele frequencies in the patients were compared with the data from 644 control southern Chinese subjects obtained from the online database Allele Frequencies in Worldwide Population.

RESULTS

The frequencies of HLA-A^* 0101 and HLA-DRB1^*1454 alleles in the patient cohort with pulmonary tuberculosis were significantly higher than those in the control group (2.4% vs 0.6%, χ²=10.788, P=0.001, P_c=0.016; 7.5% vs 0%, χ²=69.850, P < 0.0001); the frequencies of HLA-DRB1^*1202 and HLA-DRB1^*1401 alleles were significantly lower in this patient cohort than in the control group (10.4% vs 16.1%, χ²=9.845, P=0.002, P_c=0.044; 0% vs 3.1%, χ²=18.520, P < 0.001).

CONCLUSIONS

The frequencies of HLA-A and HLA-DRB1 alleles are correlated with the susceptibility to active tuberculosis in this southern Chinese population. HLA-A^*0101, HLA-DRB1^*1454 and the other 3 alleles are likely susceptible genes to tuberculosis, while HLA-DRB1^*1202, HLA-DRB1^*1401 and the other 4 alleles can be protective genes in this population.

Human platelet antigens in Burmese, Karen and north-eastern Thais

OBJECTIVES

A comparative study of allele frequencies at HPA-1 to -6 and HPA-15 in Burmese and Karen populations as well as at HPA-15 in north-eastern Thais (NET) is presented.

BACKGROUND

Human platelet antigens (HPAs) are clinically important in several immune platelet disorders, including foetal and neonatal alloimmune thrombocytopenia (FNAIT), post-transfusion purpura (PTP) and platelet transfusion refractoriness (PTR). The knowledge of antigen frequencies in a population is essential for the evaluation of patients suffering from immune-mediated platelet disorders.

METHODS

A total of 285 unrelated, healthy Burmese, 242 Karen and 300 NET were recruited to this study. Genotype and allele frequencies of HPA-1 to -6 and HPA-15 were defined using polymerase chain reaction sequence-specific primers (PCR-SSP) RESULTS: No individuals homozygous for HPA-1bb, -2bb, -4bb, -5bb and -6bb were detected. HPA-1a, -2a, -4a, -5a and -6a were present in all samples of Burmese and Karen origin. HPA-1b, -2b, -4b, -5b and -6b were rare in these populations. The frequencies of HPA-3a/-3b were 60·4/39·6% in Burmese and 55·8/44·2% in Karen, respectively. Frequencies of HPA-15a/-15b were 57·2/42·8% in Burmese, 52·5/47·5% in Karen and 49·8/50·2% in NET.

CONCLUSIONS

The frequencies of HPA genotypes in our study indicates that HPA-1a, -2a, -4a, -5a and -6a are unlikely involved in FNAIT, PTP and PTR in Burmese and Karen populations. However, HPA-1b, -2b, -3a, -3b, -4b, -5b, -6b, -15a and -15b may likely stimulate alloantibodies in these populations.

Recognition of Y Fragment Deletion by Genotyping Graphs after Amplified by PowerPlex® 21 Detection Kit

OBJECTIVES

To recognize the possibility of Y fragment deletion of Amelogenin gene intuitively and simply according to the genotyping graphs.

METHODS

By calculating the ratio of total peak height of genotyping graphs, the statistics of equilibrium distribution between Amelogenin and D3S1358 loci, Amelogenin X-gene and Amelogenin Y-gene, and different alleles of D3S1358 loci from 1 968 individuals was analyzed after amplified by PowerPlex^® 21 detection kit.

RESULTS

Sum of peak height of Amelogenin X allele was not less than 60% that of D3S1358 loci alleles in 90.8% female samples, and sum of peak height of Amelogenin X allele was not higher than 70% that of D3S1358 loci alleles in 94.9% male samples.

CONCLUSIONS

The result of genotyping after amplified by PowerPlex^® 21 detection kit shows that the possibility of Y fragment deletion should be considered when only Amelogenin X-gene of Amelogenin is detected and the peak height of Amelogenin X-gene is not higher than 70% of the total peak height of D3S1358 loci.

Relationship between lipoprotein lipase gene polymorphism and hemorrhagic stroke in a Chinese population

OBJECTIVE

To investigate the relationship between lipoprotein lipase (LPL) gene polymorphism and cerebral hemorrhage in a Chinese population.

METHOD

This study was based on the case-control study, PCR-RELP and sequencing method were utilized for genotyping. LPL gene Hind III polymorphism was detected both in 300 patients with cerebral hemorrhage (CH group) and in 300 healthy control subjects (control group). Blood lipid level and blood glucose were detected at the same time.

RESULT

Our results showed that G allele frequency was significant lower in the CH group than that in the control group (OR=0.611; 95% CI: 0.427-0.876, P=0.001). We also found both GG (OR=0.543, 95% CI: 0.233-0.988; P=0.041) and TG (OR=0.609, 95% CI: 0.387-0.959, P=0.032) genotype were frequent in the control group than that in the CH group. TG level of the groups who carry TT genotype were much higher than that of the groups carrying TG+GG genotype (P<0.05). By means of adjusting age, hypertension and hyperglycemia, logistic multivariate regression analysis revealed that LPL Hind III G allele might be a protective factor (OR=0.601, 95% CI: 0.231-0.876; P=0.001) in the present study.

CONCLUSION

It is suggested that LPL Hind III G allelic mutation might be a protective factor against cerebral hemorrhage disease in Chinese population.

FCGR3B gene frequencies among ethnic Thai blood donors from a regional hospital in Eastern Thailand

The FCGR3B gene encodes three human neutrophil antigens which consist of HNA-1a, HNA-1b, and HNA-1c. These antigens are encoded by three alleles in the FCGR3B locus: FCGR3B*01, FCGR3B*02, and FCGR3B*03 alleles, respectively. The frequencies of FCGR3B alleles have been reported in different ethnic populations. This study compared the FCGR3B gene frequencies among 230 unrelated healthy Eastern Thai blood donors in Rayong hospital with the previously published studies. The polymerase chain reaction-sequence-specific primers method was performed to determine FCGR3B genotypes. The results showed that the allele frequencies of FCGR3B*01, FCGR3B*02, and FCGR3B*03 were 0.722, 0.274, and 0.009, respectively. The FCGR3B*01 and FCGR3B*02 frequencies found in the Eastern Thais were similar to the previous reports investigating in Northern Thais, Chinese Han, Taiwanese, and Japanese populations. Interestingly, our data showed statistically significant difference (P < 0.05) to Central Thais, Korean, Indian, Turkish, Australian, Tunisian, American, German, and Italian populations. In addition, one FCGR3Bnull , which represents a gene deletion, was also found in this study. This information is important not only for the assessment of neutrophil antibody-mediated clinical conditions and for disease association studies but also for anthropological studies.

Chronotype and a PERIOD3 variable number tandem repeat polymorphism in Han Chinese pilots

An association has been determined between variable number tandem-repeat (VNTR) polymorphisms in the PERIOD3 gene (PER3, rs57875989) and chronotype. An association has been found in which the longer PER3(5) allele is correlated with diurnal preference and shorter PER3(4) allele is linked with preference for evening, respectively. In this study, we explored the genotype frequency and relationship to the chronotype of a PER3 VNTR polymorphism in Han Chinese pilots compared to other populations to further develop aviation safety research. DNA samples were genotyped with respect to the 4-repeat and 5-repeat alleles of the PER3 VNTR polymorphism. We compared and analyzed PER3 VNTR genotype frequencies of a general Han Chinese population and Han Chinese pilots. The chronotypes of our subjects were evaluated by the morningness-eveningness questionnaire (MEQ). The distribution of PER3 VNTR genotype frequencies from 240 Han Chinese was determined (PER3(4/4), 78.3%; PER3(4/5), 20.0%; PER3(5/5), 1.7%) and compared to the genotype frequencies of 126 Han Chinese pilots (PER3(4/4), 71.4%; PER3(4/5), 26.1%; PER3(5/5), 2.4%). Statistical analysis revealed no significant difference between the general Han Chinese population and Han Chinese pilots regarding the PER3 VNTR genotype and allele frequencies (x(2) = 2.170, p > 0.05). Furthermore, MEQ results showed no association between the PER3 VTNR polymorphism and chronotype. However, PER3 VNTR genotype frequencies differed significantly between Han Chinese and other ethnic groups previously reported, such as Caucasians, African Americans and Italians. These data indicate that the proposed role of the PER3 VNTR needs further clarification and the role of PER3(5) allele in sleep regulation needs to be investigated in more detail. In particular, a study of PER3 polymorphisms with a larger sample size of Han Chinese individuals and Han Chinese pilots may be required.

Association of human leukocyte antigen gene polymorphism and mesangial proliferative glomerulonephritis in a large population-based study

The aim of the present study was to investigate the association of human leukocyte antigen (HLA) gene polymorphism and clinical phenotypes of patients with mesangial proliferative glomerulonephritis (MsPGN). The genotyping of HLA-A, HLA-B and HLA-DRB1 alleles was detected in 1,536 consecutive MsPGN patients during the previous five years and 2,027 age- and gender-matched healthy individuals by using the polymerase chain reaction-sequence-specific primers method. The clinical and pathological data of the patients were collected and the genotype frequencies (GF) and odds ratio (OR) were analyzed. The allele frequencies of HLA-A*23, A*25, B*15, B*40, B*53 and DRB1*18 were significantly higher in MsPGN patients than in the controls (P<0.05). These alleles were considered as the suspected susceptibility genes (SSG) for MsPGN. Of note, results of the follow-up survey study demonstrated poorer prognosis of patients with SSG than those without SSG. On the other hand, the frequencies of A*32, A*33, B*50, B*58, B*60, B*71, DRB1*16 were lower in MsPGN patients than in the controls (P<0.05). However, the alleles A*20, A*22, A*35, A*36, A*38, B*21, B*73 and B*78 were not expressed in MsPGN patients. HLA gene polymorphism is associated with hereditary susceptibility to MsPGN. Therefore, there might be corresponding susceptibility and protective genes associated with MsPGN.

Changes in TcpA gene frequency explain 2,4,6-trichlorophenol degradation in mesocosms

Soils are often polluted by chlorophenols in timber production areas in the northern hemisphere. The tcpA gene encodes the first step of 2,4,6-trichlorophenol (246-TCP) degradation. We tested tcpA gene frequency in three natural pristine soils with different 246-TCP degradation capacity. Gene tcpA frequency increased more in spiked than non-spiked 10-L pails containing coniferous humus soil with high degradation capacity, in contrast to soils where degradation was slower. As the soil in each mesocosm originated from a spatially separate field plot, changes in tcpA gene frequency affected 246-TCP degradation over a range of soil origins. This indicates that the abundance of and changes in tcpA gene frequency could be utilized in estimating the efficacy of natural attenuation and biostimulation treatments in controlled conditions.

Allelic frequencies of 20 visible phenotype variants in the korean population

The prediction of externally visible characteristics from DNA has been studied for forensic genetics over the last few years. Externally visible characteristics include hair, skin, and eye color, height, and facial morphology, which have high heritability. Recent studies using genome-wide association analysis have identified genes and variations that correlate with human visible phenotypes and developed phenotype prediction programs. However, most prediction models were constructed and validated based on genotype and phenotype information on Europeans. Therefore, we need to validate prediction models in diverse ethnic populations. In this study, we selected potentially useful variations for forensic science that are associated with hair and eye color, iris pattern, and facial morphology, based on previous studies, and analyzed their frequencies in 1,920 Koreans. Among 20 single nucleotide polymorphisms (SNPs), 10 SNPs were polymorphic, 6 SNPs were very rare (minor allele frequency < 0.005), and 4 SNPs were monomorphic in the Korean population. Even though the usability of these SNPs should be verified by an association study in Koreans, this study provides 10 potential SNP markers for forensic science for externally visible characteristics in the Korean population.

Human platelet-specific antigen frequencies in Indonesian population

BACKGROUND

Alloantibodies against human platelet antigens (HPAs) are responsible for the development of alloimmune thrombocytopenia including platelet transfusion refractoriness (PTR) and neonatal alloimmune thrombocytopenia (NAIT). Therefore, transfusion of HPA-compatible platelets is of importance for the management of these diseases.

AIM

Determination of the allele frequency of the major HPA systems for Indonesian blood donors and the development of the first HPA-typed donor registry in Indonesia.

METHODS

DNA derived from 500 Indonesian healthy blood donors was genotyped for HPA-1 to HPA-6 and HPA-15 alleles by the use of polymerase chain reaction sequence-specific primer method.

RESULTS

The gene frequencies of the rare allelic variants HPA-1b, -2b, -3b, -4b, -5b, -6b and -15b were 0·023, 0·060, 0·493, 0·052, 0·032, 0·044 and 0·049, respectively. However, donors homozygous for the HPA-1b, -2b and -6b were not found in this cohort, indicating that the risks of alloimmunisation caused by incompatibility of these three HPA systems are extremely low. In contrast, alloimmunisation against HPA-3, -4, -5 and -15 systems is anticipated.

CONCLUSION

The development of an HPA-genotyped registry for donors homozygous for HPA-1b, -2b and -6b is desired for the optimum management of PTR patients and children with NAIT.

Oestrogen receptor polymorphisms and late-life depression

BACKGROUND

Evidence suggests a role for oestrogen in depression but the involvement of oestrogen receptor polymorphisms remains unknown.

AIMS

To determine the association between oestrogen receptor polymorphisms and late-life depression and the modifying effect of hormone treatment.

METHOD

Depression was assessed using the Mini-International Neuropsychiatric Interview, according to DSM-IV criteria and the Centre for Epidemiologic Studies - Depression Scale. The association between oestrogen receptor α and β (ER-α and ER-β) polymorphisms with severe depression was examined in 6017 community-dwelling elderly people using multivariate logistic regression.

RESULTS

In women, the ER-α rs2234693 and rs9340799 polymorphisms were significantly associated with the risk of late-life depression. The A allele of ER-β rs1256049 increased the risk of depression, but only for non-current users of hormone treatment. In men, only the ER-β rs4986938 polymorphism showed a weak association with depression risk.

CONCLUSIONS

Oestrogen receptor polymorphisms are associated with severe late-life depression risk in women only.

Variants in interferon-alpha pathway genes and response to pegylated interferon-Alpha2a plus ribavirin for treatment of chronic hepatitis C virus infection in the hepatitis C antiviral long-term treatment against cirrhosis trial

Combination treatment with pegylated-interferon-alpha (PEG IFN-alpha) and ribavirin, the current recommended therapy for chronic hepatitis C virus (HCV) infection, results in a sustained virological response (SVR) in only about half of patients. Because genes involved in the interferon-alpha pathway may affect antiviral responses, we analyzed the relationship between variants in these genes and SVR among participants in the Hepatitis C Antiviral Long-Term treatment Against Cirrhosis (HALT-C) trial. Patients had advanced chronic hepatitis C that had previously failed to respond to interferon-based treatment. Participants were treated with peginterferon-alpha2a and ribavirin during the trial. Subjects with undetectable HCV RNA at week 72 were considered to have had an SVR. Subjects with detectable HCV RNA at week 20 were considered nonresponders. We used TaqMan assays to genotype 56 polymorphisms found in 13 genes in the interferon-alpha pathway. This analysis compares genotypes for participants with an SVR to nonresponders. The primary analysis was restricted to European American participants because a priori statistical power was low among the small number (n = 131) of African American patients. We used logistic regression to control the effect of other variables that are associated with treatment response. Among 581 European American patients, SVR was associated with IFNAR1 IVS1-22G (adjusted odds ratio, 0.57; P = 0.02); IFNAR2 Ex2-33C (adjusted odds ratio, 2.09; P = 0.02); JAK1 IVS22+112T (adjusted odds ratio, 1.66; P = 0.04); and ADAR Ex9+14A (adjusted odds ratio, 1.67; P = 0.03). For the TYK2-2256A promoter region variant, a borderline association was present among European American participants (OR, 1.51; P = 0.05) and a strong relationship among African American patients; all 10 with SVR who were genotyped for TYK2 -2256 carried the A variant compared with 68 of 120 (57%) nonresponders (P = 0.006).

CONCLUSION

Genetic polymorphisms in the interferon-alpha pathway may affect responses to antiviral therapy of chronic hepatitis C.

DNA polymorphisms and response to treatment in patients with chronic hepatitis C: results from the HALT-C trial

BACKGROUND/AIMS

Certain host genetic polymorphisms reportedly affect the likelihood of a sustained virological response (SVR) to interferon treatment in subjects infected with hepatitis C virus (HCV). As part of the HALT-C trial we evaluated genetic associations among patients infected with HCV genotype 1 who had failed previous interferon treatment.

METHODS

SVR was determined 24 weeks after completing treatment with pegylated interferon alfa-2a and ribavirin. Eight single nucleotide polymorphisms (SNPs) were selected on the basis of previously reported associations with treatment response. Genotypes were assessed by polymerase chain reaction-based assays. The percentage of patients who achieved SVR was determined for each genotype and for an IL10 promoter diplotype.

RESULTS

Among 637 non-Hispanic Caucasian patients there were no significant associations between genotype for any individual SNP (IL10-1082, IL10-592, TNF-308, TNF-238, TGFB1 codon 25, CCL2-2518, EPHX1 codon 113 and AGT-6) and SVR, but SVR was more common among the patients who were homozygous for the ACC IL10 promoter diplotype (adjusted odds ratio, 3.24; 95% confidence interval, 1.33-7.78; p=0.001).

CONCLUSIONS

Among non-Hispanic Caucasian patients treated with peginterferon and ribavirin after failing previous treatment with interferon, homozygosity for the ACC IL10 promoter diplotype was associated with SVR.

Phylogenetic studies of dogs with emphasis on Japanese and Asian breeds

The first domestication of the dog occurred in East Asia, and major ancestor of the dog was a wolf subspecies, Canis lupus chanco. This finding derives from data on the nucleotide sequences of mtDNA and the frequency of genes controlling blood protein polymorphisms in various subspecies of wolves and dog breeds around the world. The results of the allele frequency distribution of genes controlling 16 blood protein polymorphisms, and the incidence of dogs possessing erythrocytes with high potassium (HK) in Japan, East Asia and Europe allowed us to posturate the following hypothesis about the origins of Japanese dogs and the history of their development. In the Jomon period the first dogs entered the Japanese archipelago from southern or northern continental Asia. These dogs eventually spread throughout Japan. Then, during the Yayoi and Kofun periods, other dogs were brought over via the Korean Peninsula, and crossbreeding occurred with the original dogs. The resulted offspring can be assumed to be the ancestors of most of the Japanese breeds that exist today. Ethological studies have revealed a significant breed difference in behavioral traits among canine breeds with Japanese dogs, showing more aggressive dispositions than most of European dogs.

Lack of influence of COMT and NET genes variants on executive functions in schizophrenic and bipolar patients, their first-degree relatives and controls

Abnormal dopaminergic function in the prefrontal cortex (PFC) may be a key factor in the etiopathogeny of schizophrenia and bipolar disorder. Both schizophrenic and bipolar subjects have executive functions (EF) deficits, thought to reflect abnormal PFC function. The main inactivation pathways for dopamine in the PFC are enzymatic cleavage by the Carboxy-O-Methyl-Transferase (COMT) and reuptake by the nor-epinephrine transporter (NET). Our aim in this study was to replicate previous studies that investigated influence of the COMT genotype on EF in schizophrenic subjects, their relatives and controls and extend their scope by including bipolar patients, and their relatives and by exploring NET gene polymorphisms influence on executive performances. We investigated one functional polymorphism of the COMT gene and two polymorphisms of the NET gene. EF were assessed by means of the Trail Making Test (TMT) and the Wisconsin Card Sorting Test (WCST). We assessed the effect of each of the three genotypes on EF for the whole sample (N = 318) and separately in schizophrenic (N = 66), bipolar (N = 94) and healthy subjects (i.e., relatives and controls N = 158). Separate analyses were performed because of the presence, in patients samples, of potentially confounding factors, especially medication. Genotype had no significant effect on the cognitive measures in any of the analyses (for the two EF measures, the three polymorphisms, and the four groups). In our sample we found no evidence in favor of a major effect of COMT or NET polymorphisms on the two tests of EF.

Expression and genetic variability of PCDH11Y, a gene specific to Homo sapiens and candidate for susceptibility to psychiatric disorders

Synaptogenesis, the formation of functional synapses, is a crucial step for the development of the central nervous system. Among the genes involved in this process are cell adhesion molecules, such as protocadherins and neuroligins, which are essential factors for the identification of the appropriate partner cell and the formation of synapses. In this work, we studied the expression and the genetic variability of two closely related members of the protocadherin family PCDH11X/Y, located on the X and the Y chromosome, respectively. PCDH11Y is one of the rare genes specific to the hominoid lineage, being absent in other primates. Expression analysis indicated that transcripts of the PCDH11X/Y genes are mainly detected in the cortex of the human brain. Mutation screening of 30 individuals with autism identified two PCDH11Y polymorphic amino acid changes, F885V and K980N. These variations are in complete association, appeared during human evolution approximately 40,000 years ago and represent informative polymorphisms to study Y chromosome variability in populations. We studied the frequency of these variants in males with autism spectrum disorders (n = 110), attention deficit hyperactivity disorder (ADHD; n = 61), bipolar disorder (n = 61), obsessive-compulsive disorder (n = 51), or schizophrenia (n = 61) and observed no significant differences when compared to ethnically-matched control populations. These findings do not support the role of PCDH11Y, or more generally of a frequent specific Y chromosome, in the susceptibility to these neuropsychiatric disorders.

Newborn HLA-DR,DQ genotype screening: age- and ethnicity-specific type 1 diabetes risk estimates

OBJECTIVE

Certain human leukocyte antigen (HLA)-DR,DQ genotypes have been associated with type 1 diabetes mellitus (T1DM) risk, although it is unknown whether the association is due to alleles, haplotypes, genotypes, the formation of heterodimers, or all of the above. To characterize the role of the HLA-DR,DQ genotype and ethnicity on the onset age of T1DM, we analyzed these factors in patients with T1DM and the general population.

METHODS

One thousand three hundred twenty-two well-characterized patients with T1DM were compared with 3339 children from the general population of Denver, Colorado, USA. Because of the extensive available data across age and ethnic groups, this study population is unique.

RESULTS

The HLA-DR3/4,DQB1*0302, DRX/4,DQB1*0302 (where X=1, 4, 8, and 9), and HLA--DR3/3 genotypes were associated with T1DM, supporting previous research. Additionally, the DR3/9 genotype showed a positive association with T1DM, which has not previously been described in Caucasian populations. The HLA-DR3/4*0302 genotype was most strongly associated with T1DM in diabetic individuals with the youngest onset age. Genotype frequencies were similar between Hispanics and non-Hispanic whites, except for the DR3/3 genotype, which was more likely to be found in non-Hispanic whites.

CONCLUSIONS

These results indicate that there are multiple alleles and genotypes associated with T1DM and that the risk associated with different genetic markers depends on the age of disease onset, suggesting that some markers may be involved in more rapid disease progression.

Relationship of tobacco smoking with GSTM1 gene polymorphism in laringeal cancer

This paper aimed to analyze the association of polymorphism of GSTM1 0/0 genotype with laryngeal cancer along a hospital based case-control study. Polymorphisms of GSTM1 0/0 of samples from 36 patients with laryngeal cancer and 35 healthy controls were detected by PCR method. The reaction used as GSTM1 primers, using the sequence sense: 5'-CTGCCCTACTTGGATTGATGGG-3' and antisense: 5'-TGGATTGTAGCAGATCATGC-3'. N Acetyl transferase 1 (NAT1) gene using the primers sense: 5'-TAAAAGTAAAATGATTTGCTTTCG-3' and antisense: 5'- GCTTTCTAGCATAAATCACCAA-3' was used as internal positive control. Two sided 2 and multivariation analysis were used to analyse the results. The proportions of GSTM1 deleted genotype in cases and controls were 47.2% and 54.3%, respectively. There was significant increment of GSTM 0/0 genotype frequency in moderate smokers group of patients compared to control (P=0.033, OR= 4.78, 95% CI = 1.30-7.13). We conclude that GSTM1 deleted genotype may be a genetic susceptibility marker for laryngeal cancer whose exposed to low doses carcinogens. The absence of this enzyme seems to have a role in the development of laryngeal cancer, in which the mechanism still needs further investigation.

Selection Against Heterodera glycines Males by Soybean Lines with Genes for Resistance

Soybeans with genes for resistance select against Heterodera glycines with the corresponding genes for avirulence. There may be a differential effect of sex with some specific gene interactions, which would influence the magnitude of gene frequency changes. No effect on H. glycines males was detected with one selected nematode population and the resistant soybean line PI88788. The selective effect of PI89772 against male nematodes was greater with two inbred nematode populations than with one selected (on PI88788) population, presumably due to differences in H. glycines gene frequencies. 'Peking' also had few males with the one inbred nematode population, whereas Forrest and 'Pickett 71' had intermediate numbers. Apparently Forrest and Pickett 71 did not get all the Peking genes for resistance that affect male as well as female nematode development. Other H. glycines-soybean genes stop only females, since there were few or no cysts, except on the susceptible soybean Williams. The number of males' phenotype will help identify specific genes in both organisms.