Deletion Genotype Research Articles

The risk of recurrence of breast cancer in the presence of deletion polymorphism of the GSTT1 and GSTM1 genes

Objective: The aim of the study was to establish the relationship between the effectiveness of chemotherapy (CMT) in case of breast cancer and the risk of recurrence with polymorphism of glutathione-S-transferase (GSTT1, GSTM1) genes.Methods: The study involved 132 women having breast cancer diagnosed, aged 23 to 79 years (average age 48 ± 13 years). They received chemotherapy treatment (neoadjuvant (NACMT), adjuvant (ACMT)). The detection of deletion (null) genotypes GSTM1 and GSTT1 was carried out using multiplex PCR followed by analysis of the melting curves of the reaction products.Results: Statistically significant connection between the presence of a null genotype GSTM1-0 and a reduced risk of breast cancer recurrence in patients having stage III BC (RR = 0.721; 95% CI: 0.524-0.992, p = 0.034). At the same time, the precense of GSTT1-0 genotype didn't have statistically significant effect on the risk of recurrence (RR = 0.543; 95% CI: 0.274– 1.077, p = 0.015). However, the tendency of the prevalence of GSTT1 0/0 among patients without recurrnece of breast cancer persisted.Conclusions: The lack of activity of the GSTT1 or GSTM1 enzymes in carriers of null genotypes can lead to a decrease in detoxification capacity and, accordingly, to a longer circulation of active metabolites of medicine and reactive oxygen species. It prolongs the time of exposure of chemotherapy drugs on tumor cells. The functionally active enzymes may increase the risk of breast cancer recurrence due to rapid elimination of drugs.

Progression of Obstructive Sleep Apnea Syndrome in Pediatric Patients with Prader-Willi Syndrome.

Obstructive sleep apnea syndrome (OSAS) is one of the most common comorbidities in patients with Prader–Willi syndrome (PWS) and causes significant consequences. This observational study was conducted to investigate the progression of OSAS in pediatric patients with PWS, who had not undergone upper airway surgery, through a longitudinal follow-up of their annual polysomnography results. Annual body mass index (BMI), BMI z-score, sleep efficiency and stages, central apnea index (CAI), obstructive apnea–hypopnea index (OAHI), and oxygen saturation nadir values were longitudinally analyzed. At enrollment, of 22 patients (10 boys and 12 girls) aged 11.7 ± 3.9 years, 20 had OSAS. During the 4-year follow-up, only two patients had a spontaneous resolution of OSAS. The average BMI and BMI z-score increased gradually, but CAI and OAHI showed no significant differences. After statistical adjustment for sex, age, genotype, growth hormone use, and BMI z-score, OAHI was associated with the BMI z-score and deletion genotype. In conclusion, OSAS is common in patients with PWS, and rarely resolved spontaneously. Watchful waiting may not be the best OSAS management strategy. Weight maintenance and careful selection of surgical candidates are important for OSAS treatment in patients with PWS.

Electrophoretic and molecular profile of the hemoglobinopathies in newborns at a reference hospital in Mozambique

Hemoglobinopathies are monogenic diseases with a significant impact on public health. It is estimated that 5.2% of the world population has at least one genetic alteration in the genes that code for globins and in Africa, 18.2% of the population have hemoglobinopathies of clinical relevance. Using hemoglobin capillary electrophoresis, we screen newborns from the Central Maputo Hospital in Mozambique for hemoglobinopathies and then used various PCR to genotype-affected newborns. Screening of newborns revealed that 35.8% had hemoglobinopathy traits, with variants running in the position of Hb Bart (33.2%), Hb C (1.7%), Hb D (0.8%), and Hb S (sickle cell) (0.4%). The molecular test identified that 9.9% of the newborns were homozygous for 3.7 kb and/or 4.2 kb deletion genotype and that there may be an uncharacterized deletion of MCS-R located on chromosome 16. This study also confirmed the presence of hemoglobin variants, Hb Maputo and Hb S, through the identification of their defining mutations. No mutations for Hb C were found; thus, we believe that it was a result of a screening error or contamination. This study successfully identified hemoglobinopathies of clinical significance within the Mozambican population, α-thalassemia and hemoglobin S, as well as their associated genotypes. Future research should include samples from other regions of the country and the use of a more comprehensive molecular diagnostic tool. With the confirmation of clinically significant genotypes, the local health system should promote the importance of screening of hemoglobinopathies in Mozambican newborns and adults.

Proteomics‐informed physiologically‐based pharmacokinetic (PBPK) modeling revealed differential effects of UGT2B17 variability on the pharmacokinetics of diclofenac following intravenous and oral administration

Uridine 5′‐diphospho‐glucuronosyltransferase 2B17 (UGT2B17) demonstrates dramatic inter‐individual variability (>3000‐fold) in the activity and expression in humans, which is associated with age, sex, genotype, and ethnicity.1We recently found that diclofenac is a UGT2B17 substrate, however, the quantitative contribution of UGT2B17 in the metabolism and pharmacokinetics (PK) of diclofenac is not well studied. Moreover, we hypothesized that the higher intestinal abundance of UGT2B17 could further amplify the magnitude and variability in its in vivo PK. We first investigated diclofenac glucuronide (DG) formation kinetics in human liver microsomes (HLM) and human intestinal microsomes (HIM) that were isolated from human donors containing the deletion genotype and the highest‐expressor of UGT2B17 in our tissue bank. Diclofenac showed 4‐ and 16‐fold difference in maximum DG formation rate (Vmax) in UGT2B17 highest‐expressor versus deletion in HLM and HIM, respectively (Fig. 1). Proteomics‐informed PBPK modeling2 estimated the quantitative contribution (fm) of UGT2B17 in the intestinal and hepatic glucuronidation of diclofenac, which revealed fm of 0.77, 0.24, and 0.0 in the highest, average, and null UGT2B17 expressors, respectively. Interestingly, intestinal fm of UGT2B17 was 0.94, 0.90, and 0.0 in the highest, average, and null expressors, respectively. The organ‐specific changes in the fm were also substantiated by the predicted fraction gut escaped (fg), which was primarily associated with UGT2B17 abundance in the enterocytes. A PBPK model was first developed and validated in the UGT2B17 average expressor and then extended to other populations utilizing UGT2B17 abundance data. Predicted plasma levels (AUC) of diclofenac were 20 % and 100 % higher following an IV dose (50 mg) in UGT2B17 deletion versus the average and the highest expressor subjects, respectively. Similalry, after 50 mg oral dose, ~2‐fold and 8.5‐fold higher AUC was observed in UGT2B17 deletion as compared to that in the average and the highest UGT2B17 expressors, respectively. Sex differences in UGT2B17 abundance explained ~2‐fold higher diclofenac AUC in females after oral administration. In summary, the unique intestinal abundance and the highly prevalent gene deletion of UGT2B17 could likely contribute to the variable bioavailability of its substrate drugs. Similarly, poor metabolism of diclofenac in children and in UGT2B17 deletion subjects could predispose these patients to high GI discomfort.References Bhatt et al., Drug Metab. Dispos. (2018). Parvez Md M et al., Drug Metab. Dispos.(2021).

Assessment of NKG2C copy number variation in HIV-1 infection susceptibility, and considerations about the potential role of lacking receptors and virus infection.

Human Immunodeficiency Virus (HIV) infection dynamics is strongly influenced by the host genetic background. NKG2C is an activating receptor expressed mainly on Natural Killer (NK) cells, and a polymorphism of copy number variation in the gene coding for this molecule has been pointed as a potential factor involved in HIV infection susceptibility. We evaluated the impact of the NKG2C deletion on HIV-1 susceptibility, with or without HBV/HCV co-infection, in a total of 780 individuals, including 385 HIV-infected patients and 395 healthy blood donors. NKG2C deletion genotyping was performed by standard PCR. To our knowledge, this is the first study to access the impact of complete NKG2C deletion among HIV-infected Brazilian individuals. The frequency of NKG2C deletion (range: 19–22%) was similar in cases and controls. No association of NKG2C deletion with HIV-1 susceptibility or influence on clinical features, HBV or HCV co-infection was observed in the evaluated population. Our findings suggest that NKG2C deletion, and the consequent absence of this receptor expression, does not directly impact HIV susceptibility, HBV/HCV-co-infection in the studied population, suggesting that other signaling pathways might be triggered and perform similar functions in cell activity in the absence of this specific receptor, preventing the development of disadvantageous phenotypes. Larger cohorts and studies involving protein expression are necessary to confirm our findings.

Polymorphisms in lncRNA MIR2052HG and susceptibility to breast cancer in Chinese population.

Background: Published studies based on pharmacokinetics have explored the relationship between the lncRNA MIR2052HG and the prognosis of breast cancer (BC) resistance and recurrence. However, the underlying association of MIR2052HG SNPs with BC development remains unclear.Methods: Combining bioinformatics and databases, SNPs (Single Nucleotide Polymorphisms) in the MIR2052HG gene were screened, and SNPs in the lncRNA MIR2052HG were selected for genotyping among 504 Chinese Han patients and 505 healthy controls, which were frequency-matched for age (±2 years). Logistic regression analysis was used to explore the association between MIR2052HG SNPs and the BC risk. Interactions between the MIR2052HG SNPs and reproductive factors were further evaluated using the multifactor dimensionality reduction (MDR) method. qRT–PCR was performed to detect MIR2052HG expression in individuals with different genotypes of rs34841297. The target miRNA, miR-4456 of MIR2052HG rs34841297 was predicted by websites and confirmed by performing dual luciferase gene reporter assays. CCK-8 and Transwell experiments were designed to explore the effects of miR-4456 on the proliferation, invasion and migration of BC cells.Results: In this study, nine SNPs were screened. After adjusting for age, menarche age, menopausal status, number of pregnancies, history of abortions, breast feeding history and family history of BC, the results of the logistic regression analysis showed the rs34841297 A/- gene polymorphism was positively correlated with the incidence of BC. Compared with the AA genotype, patients with the A-+-- genotype of rs34841297 at age<50 years, and menarche age<14 years, Premenopausal status, history of abortion, no history of breastfeeding and no family history of tumors in first-degree relatives had an increased risk of BC. MDR results revealed that individuals with rs34841297 - (homozygous deletion) of the A allele who were not menopausal and had no history of breastfeeding had a higher risk of BC. qRT–PCR results revealed that homozygous deletion (1.68±1.37) of the rs34841297 A- genotype resulted in higher MIR2052HG expression than the heterozygous deletion genotype (0.95±0.94) and wild AA genotype (0.26±0.12). Binding between MIR2052HG and miR-4456 was occurred when rs34841297 carried the AA genotype. Moreover, preliminary functional studies indicated that the overexpression of miR-4456 increased the proliferation, invasion and migration of BC cells.Conclusion: Our study showed that the MIR2052HG gene polymorphism may be related to BC susceptibility, and the MIR2052HG rs34841297 A/- genotype may probably affect the proliferation, invasion and migration of BC cells by modulating the interactions with of miR-4456.

Application of DNA Microarray in Genetic Mutation Detection in Patients with Thalassemia

To perform dried blood spots thalassemia gene detection in patients with positive blood phenotypes by microarray technology, and evaluate its value in clinical detection. DNA samples were extracted from dried blood spots of 410 patients. Microarray technology was used to detect 3 deletion and 3 non-deletion types of α-thalassemia and 19 β-thalassemia point mutations which were common gene mutions in China. There were 357 positive cases in all the 410 tested samples with the positive rate 87.07%, among which 299 cases (72.93%) carried deletion or point mutations of α-thalassemia, 29 cases (7.07%) carried point mutations of β-thalassemia and 29 cases (7.07%) carried gene mutations of complex αβ-thalassemia syndrome. The mutations of α-thalassemia were involved with --SEA heterozygous deletion (177 cases, 59.2%), αCS heterozygote (60 cases, 20.07%) and several other genotypes. The common mutations of β- thalassemia were involved with βCD41-42 heterozygote (10 cases, 34.48%) and βCD17 heterozygote (9 cases, 31.03%). The mutations of complex αβ-thalassemia syndrome were mainly involved with --SEA/αα+βCD17/βN (7 cases, 24.14%), αCSα/αα + βCD41-42/βN (3 cases, 10.34%) and -α4.2/αα + βCD17/βN (3 cases, 10.34%). The most common genetic mutations are --SEA for α-thalassemia and CD41-42 for β-thalassemia in Liuzhou, Guangxi Zhuang Autonomous Region. A and β-thalassemia can be detected at the same time by microarray chip technology in a high throughput manner.

Relation of phosphatase and tensin homolog gene polymorphism with hepatocellular carcinoma among hepatitis C-infected patients

Objective To study the significance of two phosphatase and tensin homolog (PTEN) gene polymorphisms, PTEN IVS4 rs3830675 and rs701848, as a risk factor for hepatocellular carcinoma (HCC) in chronic hepatitis C-infected patients. Background PTEN polymorphisms have been reported to be involved in multiple cancers. There are few reports concerning the linkage between the PTEN gene and liver cancer risk. Patients and methods The study was conducted on 200 participants. Of them, 80 had proven HCC, 60 were cirrhotic patients with no evidence of focal lesion, and 60 were healthy age-matched and sex-matched volunteers, enrolled in the study as a control group. PTEN IVS4 rs3830675 and rs701848 assessments by PCR-restricted fragment length polymorphism technique were done for all participants. Results The frequency of IVS4 rs3830675(––) genotype in patients with HCC was 56%, which is significantly increased compared with cirrhotic group (11.7%) and control group (10%). The combined dominant model (––/–+) was significantly higher than (++) genotype in patients with HCC compared with cirrhotic and control groups. The PTEN rs701848 polymorphisms (TT, TC, or CC) showed no significant difference among the three studied groups as well as allele distributions (T or C). Conclusion PTEN (IVS4 rs3830675) deletion (––) genotype may be a risk factor for HCC in chronic hepatitis C-infected patients more than (++) genotype. However, PTEN polymorphism (rs701848) was of no significance.

Variants in the Myostatin Gene and Physical Performance Phenotype of Elite Athletes.

The MSTN gene is a negative regulator of muscle growth that is attracting attention as a candidate gene for physical performance traits. We hypothesised that variants of MSTN might be associated with the status of elite athlete. We therefore sought to study the potential role of MSTN in the physical performance of athletes by analysing the whole coding sequence of the MSTN gene in a cohort of Lithuanian elite athletes (n = 103) and non-athletes (n = 127). Consequently, two genetic variants were identified: the deletion of one of three adenines in the first intron (c.373+90delA, rs11333758) and a non-synonymous variant in the second exon (c.458A>G, p.Lys(K)153Arg(R), rs1805086). Among all samples, the MSTN rs1805086 Lys(K) allele was the most common form in both groups. Homozygous genotype for the less common Arg(R) allele was identified in only one elite canoe rower, and we could find no direct association between rs1805086 and successful results in elite athletes. Surprisingly, the intronic variant (rs11333758) was abundant among all samples. The main finding was that endurance-oriented athletes had 2.1 greater odds of being MSTN deletion genotype than non-athletes (13.6% vs. 0.8%). The present study confirms the association of the polymorphism rs11333758 with endurance performance status in Lithuanian elite athletes.

Fetal-haemoglobin enhancing genotype at BCL11A reduces HbA2 levels in patients with sickle cell anaemia.

Understanding the interplay of genetic factors with haemoglobin expression and pathological processes in sickle cell disease is important for pharmacological and gene‐therapeutic interventions. In our nascent study cohort of Nigerian patients, we found that three major disease‐modifying factors, HbF levels, α‐thalassaemia deletion and BCL11A genotype, had expected beneficial haematological effects. A key BCL11A variant, while improving HbF levels (5.7%–9.0%), also led to a small, but significant decrease in HbA2. We conclude that in general, interventions boosting HbF are likely to reduce HbA2 in patients’ erythroid cells and that such therapeutic strategies might benefit from a parallel stimulation of HbA2 through independent mechanisms.

HRP2 and HRP3 cross-reactivity and implications for HRP2-based RDT use in regions with Plasmodium falciparum hrp2 gene deletions

BackgroundThe Plasmodium falciparum antigen histidine rich protein 2 (HRP2) is a preferred target for malaria rapid diagnostic tests (RDTs) because of its abundant production by the parasite and thermal stability. As a result, a majority of RDTs procured globally target this antigen. However, previous reports from South America and recent reports from sub-Saharan Africa and Asia indicate that certain P. falciparum parasites have deletions of the gene coding for HRP2. The HRP2 antigen is paralogous to another P. falciparum antigen HRP3 and some antibodies to HRP2 cross-react with HRP3. Multiple parasites have been described with deletions of one or both hrp2 and hrp3 genes. It is unclear how the various combinations of hrp2 and hrp3 deletion genotypes affect clinical sensitivity of HRP2-based RDTs.MethodsCross-reactivity between HRP2 and HRP3 was tested on malaria RDTs using culture-adapted P. falciparum parasites with both hrp2 and hrp3 intact or with one or both genes deleted. Ten-fold serial dilutions of four culture-adapted P. falciparum parasites [3D7 (hrp2+/hrp3+), Dd2 (hrp2−/hrp3+), HB3 (hrp2+/hrp3−) and 3BD5 (hrp2−/hrp3−)] ranging from 100,000 to 0.01 parasites/µL were prepared. HRP2, Plasmodium lactate dehydrogenase (pLDH) and aldolase concentrations were determined for the diluted samples using a multiplex bead assay. The samples were subsequently tested on three RDT products designed to detect P. falciparum by HRP2 alone or in combination with pLDH.ResultsAt parasite densities of approximately 1000 parasites/µL, parasites that expressed either hrp2 or hrp3 were detected by all three RDTs. Multiplex based antigen measurement using HRP2- conjugated beads demonstrated higher antigen concentration when both hrp2 and hrp3 genes were intact (3D7 parasites, 47.9 ng/ml) compared to HB3 (3.02 ng/mL) and Dd2 (0.20 ng/mL) strains that had one gene deleted. 3D7 at 10 parasites/µL (0.45 ng/mL) was reactive on all three RDT products whereas none of the other parasites were reactive at that density.ConclusionsAbove a certain antigen threshold, HRP3 cross-reactivity on HRP2-based RDTs is sufficient to mask the effects of deletions of hrp2 only. Studies of hrp2 deletion and its effects on HRP2-based RDTs must be studied alongside hrp3 deletions and include clinical sample reactivity on HRP2-based tests.

Influence of genetic polymorphisms in glutathione-S-transferases gene in response to imatinib among Brazilian patients with chronic myeloid leukemia

Polymorphism in metabolizing enzymes can influence drug response as well as the risk for adverse drug reactions. Nevertheless, there are still few studies analyzing the consequence of polymorphisms for the Glutathione-S-transferases (GST) gene to drug response in chronic myeloid leukemia (CML). This study reports, the influence of GSTP1*B and GSTT1/GSTM1null polymorphisms in response to imatinib in CML patients in a Brazilian population. One hundred thirty-nine CML patients from the Clinical Hospital of Goiânia, Goiás, Brazil, treated with imatinib were enrolled in this study. Genotyping of GSTT1 and GSTM1 genes deletions were performed by qPCR and of GSTP1 gene was performed by RFLP-PCR. The frequency of GSTP1*1B, GSTT1 and GSTM1null polymorphisms were determined for all patients. The influence of each patient's genotypes was analyzed with the patient's response to imatinib treatment. Brazilian CML patients revealed GSTT1 and GSTM1 genes deletions. GSTT1 deletion was found in 19.3% of patients and GSTM1 deletion in 48.7% of patients with CML. GSTT1/GSTM1 deletion was found in 11.7% in Brazilian CML patients. The "G allele" of GSTP1*B, is associated with later cytogenetic response in imatinib therapy. While, the gene presence combined with GG genotype (GSTM1 present/GSTPI-GG) conferred a tend to a later cytogenetic response to patients. GSTP1*B and GSTT1/GSTM1null polymorphisms influence treatment response in CML. Brazilian CML patients presenting GSTP1 AA/AG genotypes alone and in combination with GSTT1 null reach the cytogenetic response faster, while patients presenting GSTP1-GG and GSTMI positive genotypes may take longer to achieve cytogenetic response. As a result, it allows a better prognosis, with the use of an alternative therapy, other than reducing treatment cost.

Deletion polymorphism of glutathione S-transferases genes (GSTT1, GSTM1) in patients with breast cancer in Primorye region

Background. Breast cancer (BC) refers to multifactorial polygenic diseases that occur as a result of the combined interaction of genetic and environmental factors. Glutathione-mediated detoxification is of key importance in ensuring the resistance of body cells to the damaging effect of xenobiotics.Objective: to study the prevalence of deletion polymorphisms of the GSTM1 and GSTT1 genes and to establish their influence on the formation of cancer risk in patients with BC in the Primorye region (Russia).Materials and methods. The study involved 176 women with BC, aged 23 to 79 years (mean age 48 ± 13 years) and 66 conditionally healthy individuals without cancer. The detection of deletion (null) genotypes of the GSTM1 and GSTT1 was carried out using multiplex PCR followed by analysis of the melting curves of the reaction products.Results. The frequency of GSTT1-0 genotype among BC patients was higher than in the control group (14.77 % versus 6.06 %), significantly exceeding the indicators in the control group by more than 2.5 times (p &lt;0.1), indicating an association between the carriage of the GSTT1-0 genotype and the risk of developing BC. At the same time, the frequencies of the GSTM1-0 genotype in the study groups were comparable; no statistically significant association with the risk of developing BC was found.Conclusions. Homozygous deletion of GSTT1 (GSTT1-0) can potentially be considered as a low-penetrant risk factor for developing BC in the population of Primorye region.

Deletion polymorphism of GSTT1 gene and lipid peroxidation hyperactivation in menopausal insomnia

A comparative analysis of the parameters of lipid peroxidation - antioxidant defense system in menopausal women with- and without insomnia, depending on the GSTT1 polymorphism. The study included 181 menopausal Caucasian women (ethnic group - Russians), who according to the results of the clinical-anamnestic examinations were divided into insomnia group (n=120, age 53.68±4.61 years, body mass index 26.47±3.73 kg/m2) and control group (n=61, age 52.64±4.91 years, body mass index 27.69±3.11 kg/m2). The insomnia group was formed according to the clinical guidelines for the diagnosis and treatment of chronic insomnia in adults, and scores of the Insomnia Severity Index. The study of the GSTT1 gene polymorphism was carried out using polymerase chain reaction. The lipid peroxidation - antioxidant system parameters were determined by spectrofluorophotometric methods. In the insomnia group, carriers of the normal GSTT1 genotype had higher diene conjugates with lower glutathione peroxidase activity as compared to controls. When comparing groups of women with the deletion in GSTT1, an increase in the content of substrates and lipid peroxidation products was observed at all stages of lipid peroxidation, oxidized glutathione, glutathione S-transferase activity with a decrease in the content of reduced glutathione and retinol in the insomnia group as compared to controls. In the insomnia group, carriers of the deletion genotype had a higher content of ketodienes/conjugated trienes and active products of thiobarbituric acid, a lower content of retinol and α-tocopherol as compared to the patients with normal GSTT1 genotype. Conclusions. Insomnia in the menopausal women is accompanied with the intensification of lipid peroxidation only in the carriers of the GSTT1 deletion genotype.

ROLE OF GENETIC PREDISPOSITION, GENE POLYMORPHISM OF GLUTATHIONE-S-TRANSFERASE (GSTT1, GSTM1, GSTP1) AND SOME ADVERSE FACTORS IN DEVELOPMENT OF BRONCHIAL ASTHMA IN CHILDREN - RESIDENTS OF RADIOACTIVELY CONTAMINATED AREAS.

to determine the influence of hereditary predisposition, polymorphism of GSTT1, GSTM1, GSTP1 genes andenvironmental factors on the development of bronchial asthma in children - residents of radioactively contaminat-ed areas. School-age children-residents of radioactively contaminated areas with bronchial asthma,and those without clinical signs of respiratory pathology were examined. Genetic, medical, biological and social riskfactors were determined based on the study of anamnestic data and medical records. Ventilation lung capacity wasassessed by the method of computer spirometry. Molecular genetic studies were carried out using polymerase chainreaction (PCR) and restriction fragment length polymorphism (RFLP) for further analysis. Molecular genetic studies of the distribution of genotypes and frequencies of polymorphic variants of thegenes GSTT1, GSTM1, GSTP1 were performed in children living under long-term intake of 137Cs by food chains. It wasfound that in children with BA the tendency to frequency of the deletion variant of the GSTT1 and GSTM1 genes incomparison with children without bronchial and pulmonary pathology was increased. The study of distributing theGSTP1 A313G gene polymorphic variants revealed in children with BA a significant increase in the frequency of AG-genotype, compared with the data of reference group. Adverse factors that increase the risk of developing bron-choobstructive disorders and the probability of their implementation in the form of bronchial asthma in children -residents of RCA have been identified. It is established that among them the leading role is played by hereditarypredisposition to this disease. On the part of the child, such negative factors were unfavorable conditions of fetaldevelopment, the presence of signs of exudative-catarrhal diathesis, manifestations of allergies and frequent respi-ratory diseases from the first months of life. It was found that the risk of developing BA was significantly increasedin children with the GSTT1 and GSTM1 gene deletion genotypes; an increased risk of developing BA in children witha combination of the GSTP1 A313G gene polymorphism with deletion polymorphism of the GSTT1 or GSTM1 gene wasdetermined. Сonclusion. Оne of the leading mechanisms, due to which there is a realization of hereditary predisposition tobronchial asthma in children living under constant intake of radionuclides with a long half-life, is the polymorphismof certain glutathione-S-transferase genes, namely, GSTT1, GSTM1 and A313G gene deletion polymorphism and GSTP1gene polymorphism.

Genotype-phenotype correlation of HbH disease in northern Iraq

BackgroundHbH disease results from dysfunction of three, less commonly two, α-globin genes through various combinations of deletion and non-deletion mutations. Characterization of the mutations and the underlying genotypes is fundamental for proper screening and prevention of thalassaemia in any region. The aim of this study was to explore the genetic arrangements of HbH disease and to correlate the genotypes with the clinical phenotypes.MethodsA total of 44 HbH disease patients were enrolled in this study. They were clinically and haematologically assessed. The patients were tested for 21 common α-globin gene mutations using multiplex PCR and reverse hybridization. According to the genotype, the patients were categorized into two separate sub-groups, deletion and non-deletion types HbH disease.ResultsWithin the studied HbH disease patients, eight different α-globin gene mutations were detected in nine different genetic arrangements. The --MED and -α3.7 deletions were the two most frequently encountered mutations (37.5 and 35.2% respectively). Patients with deletion genotypes constituted 70.4%. The most common detected genotype was --MED/−α3.7 (59.1%), followed by αpoly-A1α/αpoly-A1α (13.6%). For the first time, coinheritance of two relatively mild mutations (−α3.7/ααAdana) was unpredictably detected in a 1.5 year-old child with Hb of 7.1 g/dL.ConclusionThe HbH disease patients’ clinical characteristics were variable with no ample difference between the deletion and non-deletion types. These results can be of benefit for the screening and management of thalassaemia in this region.

A Deletion Downstream of the CHCHD7 Gene Is Associated with Growth Traits in Sheep.

Simple SummaryThe genes CHCHD7 and PLAG1 are located on the same growth-related major quantitative trait locus of sheep. PLAG1 affects sheep growth, but no corresponding studies have been conducted on CHCHD7. However, polymorphisms in the CHCHD7 gene are associated with carcass weight and muscle formation in cattle, body height in cattle and humans, and weaning weight in Duroc pigs. In this study, the mathematical expectation method was used to analyze an 8-bp deletion mutation located downstream of the CHCHD7 gene in 2350 individuals from seven sheep breeds. The associations between wild-type and deletion genotypes and growth traits in Tan sheep were also analyzed. The 8-bp deletion locus was significantly associated with body length (p = 0.032), chest depth (p = 0.015), and chest width (p = 0.047) of Tan sheep. Additionally, wild-type genotype carriers were more numerous than those heterozygous for the deletion genotype. Thus, the genotyped 8-bp deletion downstream of the CHCHD7 gene may be associated with growth and development traits in sheep.In sheep, the coiled-coil-helix-coiled-coil-helix domain containing 7 (CHCHD7) gene and the pleiomorphic adenoma gene 1 (PLAG1) are on the same growth-related major quantitative trait locus, positioned head-to-head approximately 420 bp apart on chromosome 9. PLAG1 affects sheep growth, but the effects of CHCHD7 have not been determined. In this study, an 8-bp deletion downstream of CHCHD7 was analyzed in 2350 sheep from seven breeds. The associations between the deletion and growth traits of Tan sheep were also determined. Both genotypes (homozygous wild-type and heterozygous) for the 8-bp deletion were found in Tan (TS), Luxi Blackhead (LXBH), Small-Tail Han (STHS), and Lanzhou Fat-Tail (LFTS) sheep. However, there were no polymorphic sites for the mutation in Hu (HS), Sartuul (SS), and Australian White (AUW) sheep. In TS, LXBH, STHS, and LFTS sheep, the deletion genotype was less frequent than the wild-type genotype, and the allele frequencies of the deletion variant were 0.007 (TS), 0.011 (LBXH), 0.008 (STHS), and 0.010 (LFTS). The 8-bp deletion was significantly associated with body length (p = 0.032), chest depth (p = 0.015), and chest width (p = 0.047) in Tan sheep. Thus, the 8-bp deletion downstream of the CHCHD7 gene might be associated with growth and development traits of sheep.

Impact of UGT2B7 gene deletion genotype on human liver proteome

Background and objectivesUDP‐Glucuronosyltransferase 2B17 (UGT2B17) is a highly variable enzyme, which plays an important role in metabolism of endogenous steroids (e.g., testosterone), drugs or active metabolites (e.g., vorinostat, 17‐dihydroexemestane), and environmental chemicals (e.g., nicotine nitrosamine ketone, NNK). UGT2B17 is the most commonly deleted gene and we have previously demonstrated that age, sex, copy number variation, and certain single nucleotide polymorphisms can affect its abundance and activity (1). The aim of this study was to identify steroid and drug metabolism pathways that are impacted by UGT2B17 deletion using label‐free untargeted proteomics approach.MethodsThe untargeted proteomics study was performed on the liver S9 samples isolated from liver tissue of subjects with UGT2B17 gene deletion (n=3) and UGT2B17 high expression (n=3) (1). The proteins were reduced, alkylated, and digested with trypsin using an optimized protocol (1). Proteomics data were acquired in high resolution mode in QE‐HF (Thermo Scientific) coupled with Easy nano‐LC 1200. The tryptic digest was injected onto a nano‐column for peptide separation and the peptides were detected using data‐dependent acquisition (DDA) method. The survey scans of peptide precursors were performed from 375 to 1500 m/z at 120 K resolution with a 3e6 ion count target and a maximum injection time of 50 ms. The untargeted proteomic data was analyzed using MaxQuant with 1% FDR followed by data mining using Perseus and STRING analysis for pathway mapping.Results and conclusionA total of 1002 liver proteins were quantified based on the signature peptides. Out of 1002 proteins, 14 and 39 proteins were exclusively detected and quantified in UGT2B17 deletion and high expression groups, respectively (Fig. 1A), whereas 949 proteins were quantified in both the groups. The following pathways were upregulated in UGT2B17 deletion group: oxidation reduction process, drug metabolic process, steroid and fatty acid metabolic process. Notable proteins that were differentially expressed in the gene deletion groups were: a) AKR1D1, AKR1C4, AKR7DA3, AKR1A1, DHCR7, ADH6, ADH1C, ALDH1A1, ALDH9A1, and ALDH5A1 (upregulated) and b) CYP3A5, CYP1A2, LDHA, NNMT, Kynureninase, and ACACB (downregulated). A deeper molecular pathway analysis reveals that the enzymes associated with steroidal and bile acid homeostasis (e.g., aldo‐keto reductases (AKRs) and aldehyde dehydrogenases) were significantly elevated in the UGT2B17 deletion group. Interestingly, AKR1D1 acts as the sole Δ4‐3‐ketosteroid‐5β‐reductase, that metabolizes testosterone to inactive 5β‐dihydrotestosterone (2). In contrast, this pathway is a minor contributor to testosterone metabolism in the UGT2B17 high expressers. Similarly, AKR1C4 and UGT2B7, which are responsible for sequential conversion of 5β‐ dihydrotestosterone to 3α‐5β‐tetrahydrotestosterone (THT) to THT‐glucuronide (Fig. 1B), are upregulated in the UGT2B17 gene deletion groups. These novel findings of testosterone homeostasis in the UGT2B17 gene individuals can provide deeper insights into the mechanisms of UGT2B17 gene deletion‐associated pathophysiological conditions (osteoporosis, obesity, insulin sensitivity, and cancers).A) Number of hepatic proteins detected in UGT2B17 gene deletion (red) and high expressers (blue) individuals. B) Proposed compensatory mechanism of testosterone hepatic metabolism in UGT2B17 gene deletion individuals.Figure 1

VALOR2: characterization of large-scale structural variants using linked-reads

Most existing methods for structural variant detection focus on discovery and genotyping of deletions, insertions, and mobile elements. Detection of balanced structural variants with no gain or loss of genomic segments, for example, inversions and translocations, is a particularly challenging task. Furthermore, there are very few algorithms to predict the insertion locus of large interspersed segmental duplications and characterize translocations. Here, we propose novel algorithms to characterize large interspersed segmental duplications, inversions, deletions, and translocations using linked-read sequencing data. We redesign our earlier algorithm, VALOR, and implement our new algorithms in a new software package, called VALOR2.

GSTM1 and GSTT1 genetic polymorphisms and their association with antituberculosis drug-induced liver injury.

Antituberculosis (anti-TB) drugs are the most common cause of drug-induced liver injury (DILI). There are numerous studies revealing the associations between the polymorphisms of pharmacogenes and the risk of anti-TB DILI (ATDILI). In the present study, relevant studies regarding the pharmacogenes associated with ATDILI were systematically searched in PubMed and Scopus. A total of 24 genes associated with ATDILI were reported on and the top five reported genes in terms of frequency were revealed to be N-acetyltransferase 2, cytochrome P450 family 2 subfamily E member 1, glutathione S-transferases [glutathione S-transferase mu 1 (GSTM1) and glutathione S-transferase theta 1 (GSTT1)] and solute carrier organic anion transporter family member 1B1. As ATDILI may be the result of direct and indirect interactions, the encoded proteins were further analysed using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) to observe the protein-protein interactions and the associations amongst these proteins. The results suggested that only GSTT1 and GSTM1 were central proteins associated with all the other analysed proteins. Therefore, the association between GSTT1 or GSTM1 and the risk of developing ATDILI were further analysed. The results revealed that a GSTM1 deletion genotype was significantly associated with risk of ATDILI [odds ratio (OR), 1.28; 95% confidence interval (CI), 1.08-1.51; P=0.004], whereas the GSTT1 deletion genotype and GSTM1/GSTT1 dual-deletion genotype were not significantly associated with risk of ATDILI. Subgroup analysis based on ethnicity was performed and the results demonstrated a significant association between GSTM1 and ATDILI in South Asian individuals (OR, 1.48; 95% CI, 1.12-1.95; P=0.005), which has not been reported previously, to the best of our knowledge. In conclusion, GSTM1 was associated with ATDILI in South Asian individuals.