Allele Levels Research Articles

Antioxidant Genetic Variants Modify Echocardiography Indices in Long COVID.

Although disturbance of redox homeostasis might be responsible for COVID-19 cardiac complications, this molecular mechanism has not been addressed yet. We have proposed modifying the effects of antioxidant proteins polymorphisms (superoxide dismutase 2 (SOD2), glutathione peroxidase 1 (GPX1), glutathione peroxidase 3 (GPX3) and nuclear factor erythroid 2-related factor 2, (Nrf2)) in individual susceptibility towards the development of cardiac manifestations of long COVID-19. The presence of subclinical cardiac dysfunction was assessed via echocardiography and cardiac magnetic resonance imaging in 174 convalescent COVID-19 patients. SOD2, GPX1, GPX3 and Nrf2 polymorphisms were determined via the appropriate PCR methods. No significant association of the investigated polymorphisms with the risk of arrhythmia development was found. However, the carriers of variant GPX1*T, GPX3*C or Nrf2*A alleles were more than twice less prone for dyspnea development in comparison with the carriers of the referent ones. These findings were even more potentiated in the carriers of any two variant alleles of these genes (OR = 0.273, and p = 0.016). The variant GPX alleles were significantly associated with left atrial and right ventricular echocardiographic parameters, specifically LAVI, RFAC and RV-EF (p = 0.025, p = 0.009, and p = 0.007, respectively). Based on the relation between the variant SOD2*T allele and higher levels of LV echocardiographic parameters, EDD, LVMI and GLS, as well as troponin T (p = 0.038), it can be proposed that recovered COVID-19 patients, who are the carriers of this genetic variant, might have subtle left ventricular systolic dysfunction. No significant association between the investigated polymorphisms and cardiac disfunction was observed when cardiac magnetic resonance imaging was performed. Our results on the association between antioxidant genetic variants and long COVID cardiological manifestations highlight the involvement of genetic propensity in both acute and long COVID clinical manifestations.

Evaluation of Population Characteristic Differences between the Largemouth Bass and Its Backcross Following a Long‐Term Florida Bass Stocking Effort

AbstractManagement agencies throughout the southern United States widely stock Florida Bass (FLB) Micropterus floridanus into extant Largemouth Bass (LMB) M. salmoides populations, with the intent of increasing the trophy potential of those water bodies. These stockings commonly lead to a shift in the systemwide genetic composition toward a population dominated by hybrids, which are predominantly LMB with low levels of FLB alleles (FX‐LMB). Despite the increasing prevalence of FX‐LMB throughout the Southeast, little work has examined FX‐LMB population vital rates and whether these hybrids increase the trophy potential of a water body. Our study fills a void in existing research by comparing the population characteristics of FX‐LMB and LMB using a common garden experimental design. Lake Ouachita is a large Arkansas reservoir that was stocked with over 800,000 fingerling FLB between 2007 and 2015. In 2019, we collected 1,000 bass from throughout the reservoir and determined the level of FLB introgression for each fish by using a panel of species‐diagnostic single‐nucleotide polymorphisms. We then tested for relationships between the percentage of FLB alleles or genotype and the age at 50% maturity, total annual mortality rate, size structure, condition, and growth. In addition, we compared tournament catches of large bass during the pre‐ and poststocking time periods to test whether catch rates of 2.3‐kg and larger bass increased after FLB stockings. Our results indicated that FX‐LMB hybrids likely do not mature earlier, survive longer, have better body condition, or have greater growth potential than native LMB in Lake Ouachita. We also did not observe differences in the number of hours to catch a 2.3‐kg or larger bass or in the number of 2.3‐kg and larger bass captured per tournament between the pre‐ and poststocking time periods. We conclude that a stocking program resulting in a subtle shift in the genetic composition toward the FX‐LMB genotype will not effectively increase the trophy potential of a population.

Plasma lipid signature as an indicator of the risk and rate of progression from mild cognitive impairment to Alzheimer’s disease

AbstractBackgroundOur knowledge about the importance of lipids in progression and the rate of progression from Mild Cognitive Impairment (MCI) to AD is limited. Our objective was to determine plasma lipids that could be implicated in the progression or rate of progression from MCI to AD.MethodWe analyzed the plasma lipid profile of MCI patients (N = 90) by liquid chromatography coupled with mass spectrometry. The association of lipids with progression was studied by logistic regression and a Cox regression model was used to assess lipids associated with the speed of progression. We adjusted our analyses for age, sex, CSF core AD biomarkers, APOE4 status, and Mini‐Mental State Examination (MMSE).ResultForty‐seven (52%) MCI patients progressed to AD during follow‐up (58 ± 12.5 months). Regression analysis detected that presence of APOE4 allele and high levels of four lipids – two as risk factors (p = 0.002) and two as protectors (p = 0.002 and p = 0.003)– were associated with progression (AUC 0.972, p < 0.001). The effect of these lipids in separating progressive from non‐progressive patients was significant when compared with the regression model without them (AUC 0.729 vs 0.972, z = 4.595, |z|>2.575, p < 0.01). Seven lipids were associated with the rate of progression, of which two were associated with a shorter time to progression (OR 9.88, 99% CI [3.08 –31.71], p < 0.001 and OR 34.81, CI 99% [4.88 – 248.3], p < 0.001) and five with a longer time to progression (OR 0.34, 99% CI [0.135 – 0.870], p = 0.003; OR 0.164, CI 99% [0.056 – 0.479], p < 0.001; OR 0.153, 99% CI [0.056 – 0.419], p < 0.001; OR 0.148, CI 99% [0.034 – 0.644], p = 0.001; and OR 0.029, 99% CI [0.007 – 0.131], p < 0.001).ConclusionOur results suggest that lipid dysregulation could have an important role in progression and rate of progression from MCI to AD. Our data also indicate that AD lipid alterations could have clinical implications as circulating biomarkers of progression and progression speed.

Abstract 1045: RePhyNER: Overcoming limitations of access to matched germline for serial liquid biopsy applications

Abstract Background: Comparison of a blood or tissue sample with a matched germline control is a key step for accurate detection of somatic mutations. This is particularly important for tracking minimal residual disease (MRD), since alterations erroneously considered to be tumor derived may lead to false detection. Use of blood leukocytes as a germline control is critical not only for appropriate censoring of constitutional allelic variants, but also for addressing those associated with clonal hematopoiesis (CH). However, such matched germline is not always available, or may be suboptimal when contaminated with tumor cells. We hypothesized that accurate tumor genotyping might be feasible without a matched germline, using a dedicated algorithmic framework relying on clonal relationships of alleles of interest (i.e., phylons). Methods: Here, we introduce RePhyNER (Recursive Phylon Nomination, Enumeration, and Recovery), an algorithm for addressing this challenge in serial liquid biopsies. RePhyNER relies on the assumption that when comparing two specimens from the same individual (e.g., before and after therapy), the genomic variants of interests (e.g., tumor somatic mutations) behave differently in their allelic levels when compared to variants needing to be censored (e.g., germline constitutional alleles or CH). Using the change in mean allelic level of all variants in ≥2 samples, RePhyNER relies on a recursive approach to test each candidate somatic variant’s corresponding change gradient against this distribution using count-based statistics. Results: We used simulations to assess the importance of multiple parameters including fraction of contaminating variants or alleles and mean allelic fold-change. These simulations showed substantially superior performance of a recursive approach and revealed that for ≥2-fold changes in the mean VAF in a pair of samples, RePhyNER accurately removed >99% of contaminating alleles while preserving ~100% of true variants. We then applied RePhyNER to 108 plasma cell-free DNA (cfDNA) samples from 47 patients with classic Hodgkin Lymphoma (cHL) profiled by PhasED-Seq and compared MRD-detection performance with or without matched germline. RePhyNER substantially improved specificity by ~30% (68% vs 99%), and Precision by ~50% (46% vs 96%), while only modestly reducing sensitivity (100% vs 91%). We next applied PhasED-Seq to a cohort of cHL patients (n=65) without matched germline information. MRD positivity within the first 2 cycles of therapy was associated with inferior outcome when using RePhyNER (P<0.05 vs ns), correctly reclassifying 26% of detected patients to undetected. Conclusions: RePhyNER enables germline-free and accurate genotyping for MRD detection. Notably, RePhyNER obviates the need for additional germline profiling overcoming key limitations described above and avoids the additional associated costs of sequencing. Citation Format: Mohammad Shahrokh Esfahani, Stefan Alig, Emily Hamilton, Joseph Schroers-Martin, Brian Sworder, Jan Boegeholz, Mari Olsen, Chih Long Liu, David Kurtz, Maximilian Diehn, Ash Alizadeh. RePhyNER: Overcoming limitations of access to matched germline for serial liquid biopsy applications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1045.

Abstract 36: Comparing twenty-two matched patient-derived cell lines developed from either patient, PDX, or organoid tumor cell material

Abstract The National Cancer Institute has developed a Patient-Derived Models Repository (NCI PDMR; https://pdmr.cancer.gov) comprised of quality-controlled, early passage, and clinically-annotated patient-derived tumor xenografts (PDXs), organoids (PDOrgs), cell cultures (PDCs), and cancer associated fibroblasts (CAFs) available with genomic data to the extramural community for research use. Models are developed by the NCI PDMR in decreasing order of complexity, specifically 1) patient material can be used to develop PDXs, PDOrgs, PDCs, and CAFs, 2) PDX material for PDOrgs and PDCs, and 3) PDOrg material for PDCs, but a PDC is never used to develop a PDOrg or PDX. Eleven pairs of 22 matched PDCs have been developed in parallel from either patient, PDX, patient-derived organoid, or PDX-derived organoid tumor material and sequenced by WES and RNASeq. Genetic stability was assessed using multiple approaches including microsatellite instability (MSI) generated from MSISensor2, percentage of genomic loss of heterozygosity (LOH) using a set of ~800k heterozygous SNPs from a population level genomic database (gnomAD), pairwise Spearman correlation based on BIN level copy number (CN)/RNA expression profiles, and OncoKB annotated oncogenic/likely oncogenic variants. No systematic differences were observed within PDC pairs derived from different origins or compared to their patient and/or PDX material in MSI, LOH% and RNA expression profile but pairwise Spearman correlation (0.66-0.88) in CNV profiles were somewhat variable, likely due to low sequencing depth. In one PDC pair (299254), 3 out of 12 OncoKB annotated Indels and CNV showed opposite level of variant allele frequencies/CN when comparing a model derived from patient material to one developed from a PDX-derived organoid, possibly driven by a lineage-specific subclonal outgrowth when compared to patient and PDX data. Phenotypic characteristics of matched PDCs also overall show no major differences, though variability in growth rates and the ability to form spheroids in serum-free medium were noted. In one pair (919269), the PDC derived from patient material was able to form a cell line xenograft (CLX) in NSG mice but not the PDC developed from a patient-derived organoid. Overall, these models demonstrate a high degree of concordance at the genetic and phenotypic level when compared to the originating patient and/or PDX tumor. Though further characterization (e.g., preclinical drug testing) may be needed to define differences between matched PDC pairs, lack of access to patient tissue or failure to generate tumor cell cultures from one source of material should not hamper development of preclinical in vitro models from other patient-derived model types as long as the source-of-origin is clearly defined. Funded by NCI Contract No. HHSN261200800001E Citation Format: Cindy R. Timme, Ting-Chia Chang, Sergio Y. Alcoser, Gareth Bliss, Carrie Bonomi, Suzanne Borgel, John Carter, Alice Chen, Li Chen, Kevin Cooper, Biswajit Das, Kelly Dougherty, Lindsay Dutko, Marion Gibson, Michelle M. Gottholm-Ahalt, Tara Grinnage-Pulley, Shahanawaz Jiwani, Keegan Kalmbach, Chris Karlovich, Kimberly Klarmann, Tiffanie Chase, Michael Mullendore, Matthew Murphy, Kevin Plater, Gloryvee Rivera, Jessica Steed, Luke Stockwin, Yvonne A. Evrard, Mickey Williams, Dianne L. Newton, Melinda G. Hollingshead, James H. Doroshow. Comparing twenty-two matched patient-derived cell lines developed from either patient, PDX, or organoid tumor cell material [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 36.

Mutation screening of AOPEP variants in a large dystonia cohort.

Recently, AOPEP has been identified to be a novel causative gene of autosomal-recessive dystonia. However, no large cohort study has been conducted to confirm the association. We aimed to systematically evaluate the genetic associations of AOPEP with dystonia in a large Chinese dystonia cohort. We analyzed rare variants of AOPEP in 878 dystonia patients with whole-exome sequencing. The over-representation of rare variants in patients was examined with Fisher's exact test at allele and gene levels. Among the 878 patients with dystonia, we found two patients with biallelic likely pathogenic variants in the AOPEP gene. One patient carried putative compound heterozygous variants (p.A212D and p.G216R) and presented with childhood-onset segmental dystonia involving the upper limbs and craniocervical muscles accompanied by myoclonus of the dystonia affected areas. One patient carried homozygote of p.M291Nfs*68 and presented with adult-onset isolated cervical dystonia. Another 15 patients were identified to carry heterozygous rare variants in AOPEP, including 2 loss-of-function variants (p.M291Nfs*68 and p.R493X) and 6 missense variants. One loss-of-function variant (p.R493X) was the same as previously reported. Nearly, all of the 15 patients carrying heterozygous variants in AOPEP presented with isolated dystonia with only craniocervical muscles affected, except for one patient who carried the p.R493X variant presented with segmental dystonia affecting the neck and right upper limb combined with parkinsonism. Gene-based burden analysis detected enrichment of rare variants and rare damaging variants of AOPEP in dystonia. Our study supplemented the evidence on the role of AOPEP in autosomal-recessive dystonia in Chinese population, and expanded the genotypic and phenotypic spectrum of AOPEP.

Lineage and hybridization effects on size potential in the Largemouth Bass complex

AbstractObjectiveIntroductions of Florida Bass Micropterus floridanus (FB) to Texas resulted in prevalent hybridization with Largemouth Bass M. salmoides (LB) and the creation of hybrid‐dominated fisheries. However, little was known about the size potential of these hybrids relative to each other or relative to the parental taxa.MethodsSampling of these taxa and their hybrids in Texas (populations = 166; n = 8685) and genotyping at taxon‐diagnostic microsatellite loci facilitated comparisons of allele and genotype frequencies among weight‐classes.ResultResults indicated that per capita, fish that were 100% FB were much more likely to attain moderate (≥3.63‐kg) to large (≥5.9‐kg) size than any other genotype in the species complex. Among hybrids, F1 genotypes were likely to reach moderate to large sizes at rates similar to hybrids with high levels of FB alleles; otherwise, the likelihood of reaching large size scaled positively with levels of FB alleles. Hybrids with <50% FB alleles and fish that were 100% LB were almost non‐existent in the moderate and large size‐classes. A case study in Lake Fork (n = 510) provided similar results, although F1 genotypes were more likely to reach large size than any other hybrid.ConclusionThese findings provide evidence for positive size‐related heterosis in the F1 generation and suggest that absent heterotic effects, size potential in hybrids is driven by many small additive‐effect loci.

Frequent use of IGHV3-30-3 in SARS-CoV-2 neutralizing antibody responses.

The antibody response to SARS-CoV-2 shows biased immunoglobulin heavy chain variable (IGHV) gene usage, allowing definition of genetic signatures for some classes of neutralizing antibodies. We investigated IGHV gene usage frequencies by sorting spike-specific single memory B cells from individuals infected with SARS-CoV-2 early in the pandemic. From two study participants and 703 spikespecific B cells, the most used genes were IGHV1-69, IGHV3-30-3, and IGHV3-30. Here, we focused on the IGHV3-30 group of genes and an IGHV3-30-3-using ultrapotent neutralizing monoclonal antibody, CAB-F52, which displayed broad neutralizing activity also in its germline-reverted form. IGHV3-30-3 is encoded by a region of the IGH locus that is highly variable at both the allelic and structural levels. Using personalized IG genotyping, we found that 4 of 14 study participants lacked the IGHV3-30-3 gene on both chromosomes, raising the question if other, highly similar IGHV genes could substitute for IGHV3-30-3 in persons lacking this gene. In the context of CAB-F52, we found that none of the tested IGHV3-33 alleles, but several IGHV3-30 alleles could substitute for IGHV3-30-3, suggesting functional redundancy between the highly homologous IGHV3-30 and IGHV3-30-3 genes for this antibody.

Contributions of NR1H3 genetic polymorphisms to susceptibility and effects of narrowband UVB phototherapy to nonsegmental vitiligo

Vitiligo is the most common depigmenting disorder to which both genetic and environmental factors contribute. The aim of the current work was to evaluate the relationship between polymorphisms of the gene nuclear receptor subfamily 1 Group H member 3 (NR1H3) and the risk of vitiligo and phototherapy effects in the Chinese Han population. Two independent samples were enrolled to form the discovery set (comprised of 1668 nonsegmental vitiligo [NSV] patients and 2542 controls) and the validation set (comprised of 745 NSV patients and 1492 controls). A total of 13 tag single nucleotide polymorphisms (SNPs) were genotyped in the samples from the discovery stage. SNPs that achieved nominal significance were validated in another independent sample set. The serum level of NR1H3 protein was assayed using enzyme-linked immunosorbent assay kits in the validation set. Genetic association analysis was carried out at allelic and genotypic levels. The therapeutic effects of significant SNPs were examined in the validation set. The SNP rs3758672 was significantly associated with NSV. The A allele was correlated with NSV risk and poorer therapeutic effects. The A allele was strongly correlated with the increased level of serum NR1H3 in both controls and patients. In summary, SNP rs3758672 in NR1H3 was significantly associated with both disease susceptibility and individualized therapeutic effects of NSV in study participants with Han Chinese ancestry.

Validation of Genome-Wide SSR Markers Developed for Genetic Diversity and Population Structure Study in Grain Amaranth (Amaranthus hypochondriacus)

Grain Amaranth is the most promising C4 dicotyledonous pseudocereal and is distributed globally. It has an excellent nutritional profile and adaptability against a broad range of environmental factors. These traits have renewed the interest of researchers and breeders in exploring this underutilized orphan crop. The present study aimed to validate the genome-wide SSR to assess the genetic diversity among 94 Amaranthus hypochondriacus accessions using 57 genomic SSR (g-SSR) markers developed in-house. A total of 36 g-SSRs were recorded as polymorphic and amplified 138 alleles, with an average of 3.83 alleles per locus. Major allele frequency ranged from 0.29 to 0.98, with an average of 0.63 per marker. The expected heterozygosity ranged from 0.03 to 0.81, with an average of 0.46 per locus. Polymorphism information content (PIC) ranged from 0.03 to 0.79, with an average of 0.40, indicating a high level of polymorphism across amaranth accessions. Population structure analysis resulted into two major genetic clusters irrespective of their geographical origin, which suggests there may be sharing of common genomic regions across the accessions. High allelic frequency and heterozygosity levels indicate significant genetic variability in the germplasm, which can be further used in future breeding programs.

MIR149 rs2292832 and MIR499 rs3746444 Genetic Variants Associated with the Risk of Rheumatoid Arthritis.

MicroRNAs (miRNAs) are small non-coding RNAs that play a key role in post-transcriptional modulation of individual genes' expression. Several miRNA variants from different populations are known to be associated with an increased risk of rheumatoid arthritis (RA). This study was undertaken with the aim to investigate the association of single nucleotide variants; namely, rs2292832, rs3746444, rs11614913, rs1044165, and rs767649 of MIR149, MIR499, MIR196, MIR223, and MIR155, respectively, with RA in the Pakistani population. A case-control study was performed by recruiting and genotyping a total of 600 individuals (300 cases and 300 controls) for these five variants using a TaqMan single-nucleotide polymorphism (SNP) genotyping assay. The resultant genotypic data was statistically analyzed through a chi-squared test for its association with RA under different inheritance models. We found a significant association of rs2292832 with RA at genotypic (co-dominant (p < 0.0001), dominant (CC vs. TT + CT: OR 2.063 (1.437-2.962); p = 0.0001), recessive (TT vs. CT + CC: OR 0.376 (0.259-0.548); p < 0.0001)), and allelic (allele C) levels ((OR 0.506 (0.402-0637); p < 0.0001)). Similarly, the rs3746444 showed a significant association with RA under co-dominant (p = 0.0001), dominant (GG vs. AA + AG: OR 5.246 (3.414-8.061); p < 0.0001), recessive (AA vs. GG + AG: OR 0.653 (0.466-0.916); p = 0.014), and additive models (G vs. A; OR 0.779 (0.620-0.978); p = 0.03). However, we did not observe any significant association of rs11614913, rs1044165, or rs767649 with RA in our subjects. To our knowledge, this was the first study that investigated and found an association between functional polymorphisms in miRNAs and RA in the Pakistani population.

Mutation Screening of MED27 in a Large Dystonia Cohort

Objectives. Recently, biallelic variants in MED27 have been identified to correlate with complex dystonia. However, no replicative study has been conducted in larger dystonia cohorts. In this study, we aimed to systematically evaluate the genetic associations of MED27 with dystonia in a large dystonia cohort. Materials and Methods. We analyzed rare variants (minor allele frequency &lt; 0.01 ) of MED27 in a large Chinese dystonia cohort with whole exome sequencing. The overrepresentation of rare variants in patients was examined with Fisher’s exact test at allele and gene levels. Results. A total of 688 patients with dystonia were included in the study, including 483 isolated dystonia, 133 combined dystonia, and 72 complex dystonia. The average age at onset (SD) was 34.3 (19.1) years old. After applying filtering criteria, five rare variants, namely, p.R247H, p.P174A, p.P123A, p.L120F, and p.F56C, were identified in six individuals. All of them carried the variant in the heterozygous form, and no patients with compound heterozygous or homozygous alleles were identified. At allele level, no variant was associated with risk of dystonia. Gene-based burden analysis did not detect enrichment of rare variants of MED27 in dystonia either. Conclusion. Variants of MED27 were rare in Chinese dystonia patients, probably because that mutations in MED27 are more associated with more complex neurodevelopmental disorders that can also include dystonia among the various neurological features. Further studies are needed to confirm the role of MED27 in dystonia and other neurological disorders.

Cyclodextrin-Based Nanoparticles for Delivery of Antisense Oligonucleotides Targeting Huntingtin.

Huntington's disease (HD) is a progressive inherited neurodegenerative disease caused by a CAG repeat expansion in the huntingtin gene, which is translated into the pathologic mutant huntingtin (mHTT) protein. Despite the great potential of HTT lowering strategies and the numerous antisense oligonucleotides (ASOs) in pre- and clinical trials, sustained silencing of mHTT has not been achieved. As a strategy to improve ASO delivery, cyclodextrin-based nanoparticles (CDs) offer a promising approach. Here, three CDs with distinct chemical structures were designed and their efficacies were compared as potential platforms for the delivery of ASO targeting HTT. Results using striatal neurons and HD patient-derived fibroblasts indicate that modified γ-CDs exhibited the best uptake efficiency and successfully downregulated mHTT at protein and allele levels. The incorporation of the brain-targeting peptide RVG into the modified γ-CDs showed greater downregulation of mHTT protein and HD-causing allele SNP1 than untargeted ones in an in vitro blood-brain barrier model. Although the ASO sequence was designed as a nonallele-specific therapeutic approach, our strategy gives an additional benefit of some mHTT selectivity. Overall, this study demonstrated the CD platform's feasibility for delivering ASO-based therapeutics for HD treatment.

Analysis of CYP2C19 gene polymorphism and influencing factors of pharmacological response of clopidogrel in patients with cerebral infarction in Zhejiang, China.

Certain genetic and non-genetic factors may cause damaged platelet inhibition by clopidogrel. We aimed to determine the effect of cytochrome P4502C19 (CYP2C19) polymorphism, along with other clinical factors, on the platelet response to clopidogrel in patients with acute ischemic stroke (AIS). A total of 214 patients with AIS receiving clopidogrel at a maintenance dose of 75 mg daily admitted to the Ningbo First Hospital between 1 January 2020, and 31 December 2021, were enrolled. Platelet aggregation analysis was performed to determine clopidogrel resistance. Quantitative real-time polymerase chain reaction (QRT-PCR) was used to determine CYP2C19 genotype. Other laboratory data on complete blood count and biochemical parameters were taken from patient medical files. Among the 214 AIS patients treated with clopidogrel in the Ningbo population, the incidence of clopidogrel resistance was approximately 43.9%, and the distribution of CYP2C19 genotypes was highest for CYP2C19(*1/*2) (43.0%), followed by CYP2C19 (*1/*1) (38.8%). The distribution of alleles *1, *2, *3, and *17 was 62.1, 32.5, 4.9, and 0.5%, respectively. A chi-squared test showed that the gene frequencies of alleles *2 and *3 were significantly higher in the clopidogrel-resistant group than in the clopidogrel-sensitive group (p < 0.001), and a Mann-Whitney U-test showed that high HCY levels were significantly correlated with clopidogrel resistance (p < 0.001). Multi-factor logistic regression analysis demonstrated that mutant heterozygous genotype [OR 2.893; 95% confidence interval (CI) 1.456-5.748; p = 0.002], mutant homozygous genotype (OR 4.741; 95% CI 1.828-12.298; p = 0.001), and high HCY levels (OR 1.209; 95% CI 1.072-1.362; p = 0.002) were significantly associated with clopidogrel resistance. According to our results, carrying the CYP2C19*2/*3 allele and high HCY levels are independent risk factors for clopidogrel resistance after clopidogrel therapy in patients with AIS. These two factors should be considered prior to clopidogrel administration.

Rare variants in IMPDH2 cause autosomal dominant dystonia in Chinese population.

Recently, IMPDH2 has been linked to dystonia. However, no replication study from other cohorts has been conducted to confirm the association. We aimed to systematically evaluate the genetic associations of IMPDH2 with dystonia in a large dystonia cohort. We analyzed rare variants (minor allele frequency < 0.01) of IMPDH2 in 688 Chinese dystonia patients with whole exome sequencing. The over-representation of rare variants in patients was examined with Fisher's exact test at allele and gene levels. Four rare variants were detected in IMPDH2 in four patients with dystonia in our cohort, including three missense variants (p.Ser508Leu, p.Ala396Thr, and p.Phe24Val) and one splice acceptor variant (c.1296-1G>T). Two of them (c.1296-1G>T and p.Ser508Leu) were co-segregated in the family co-segregation analysis and were classified as pathogenic and likely pathogenic variant according to the American College of Medical Genetics and Genomics (ACMG) guidelines, respectively. Gene burden analysis revealed enrichment of rare variants in IMPDH2 in dystonia. Our work supplemented the evidence on the role of IMPDH2 in autosomal dominant dystonia in Chinese population, and expanded the genetic and phenotypic spectrum of IMPDH2, paving way for future studies.

Schizophrenia, Human Leukocyte Antigen (HLA), and Herpes Viruses: Immunogenetic Associations at the Population Level

Several factors have been implicated in schizophrenia (SZ), including human herpes viruses (HHV) and the adaptive immunity Human Leukocyte Antigen (HLA) genes. Here we investigated these issues in 2 complementary ways. In one analysis, we evaluated SZ-HLA and HHV-HLA associations at the level of a single allele by computing (a) a SZ-HLA protection/susceptibility (P/S) score based on the covariance between SZ and 127 HLA allele prevalences in 14 European countries, (b) estimating in silico HHV-HLA best binding affinities for the 9 HHV strains, and (c) evaluating the dependence of P/S score on HHV-HLA binding affinities. These analyses yielded (a) a set of 127 SZ-HLA P/S scores, varying by >200× (maximum/minimum), which could not be accounted for by chance, (b) a set of 127 alleles × 9 HHV best-estimated affinities, varying by >600×, and (c) a set of correlations between SZ-HLA P/S scores and HHV-HLA binding which indicated a prominent role of HHV1. In a subsequent analysis, we extended these findings to the individual person by taking into account the fact that every individual carries 12 HLA alleles and computed (a) the average SZ-HLA P/S scores of 12 randomly chosen alleles (2 per gene), an indicator of HLA-based SZ P/S for an individual, and (b) the average of the corresponding HHV estimated affinities for those alleles, an indicator of overall effectiveness of HHV-HLA binding. We found (a) that HLA protection for SZ was significantly more prominent than susceptibility, and (b) that protective SZ-HLA scores were associated with higher HHV-HLA binding affinities, indicating that HLA binding and subsequent elimination of several HHV strains may confer protection against schizophrenia.

Insertion of a TRIM-like sequence in MdFLS2-1 promoter is associated with its allele-specific expression in response to Alternaria alternata in apple.

Alternaria blotch disease, caused by Alternaria alternata apple pathotype (AAAP), is one of the major fungal diseases in apple. Early field observations revealed, the anther-derived homozygote Hanfu line (HFTH1) was highly susceptible to AAAP, whereas Hanfu (HF) exhibited resistance to AAAP. To understand the molecular mechanisms underlying the difference in sensitivity of HF and HFTH1 to AAAP, we performed allele-specific expression (ASE) analysis and comparative transcriptomic analysis before and after AAAP inoculation. We reported an important immune gene, namely, MdFLS2, which displayed strong ASE in HF with much lower expression levels of HFTH1-derived alleles. Transient overexpression of the dominant allele of MdFLS2-1 from HF in GL-3 apple leaves could enhance resistance to AAAP and induce expression of genes related to salicylic acid pathway. In addition, MdFLS2-1 was identified with an insertion of an 85-bp terminal-repeat retrotransposon in miniature (TRIM) element-like sequence in the upstream region of the nonreference allele. In contrast, only one terminal direct repeat (TDR) from TRIM-like sequence was present in the upstream region of the HFTH1-derived allele MdFLS2-2. Furthermore, the results of luciferase and β-glucuronidase reporter assays demonstrated that the intact TRIM-like sequence has enhancer activity. This suggested that insertion of the TRIM-like sequence regulates the expression level of the allele of MdFLS2, in turn, affecting the sensitivity of HF and HFTH1 to AAAP.

Eplet-Predicted Antigens: An Attempt to Introduce Eplets into Unacceptable Antigen Determination and Calculated Panel-Reactive Antibody Calculation Facilitating Kidney Allocation.

(1) Calculated panel-reactive antibody (CPRA) is a measure of sensitization based on unacceptable antigens (UAs). Determination of UAs based on single-antigen bead assays at allele or antigen levels may be inappropriate. We aimed to introduce eplets for better assessment of sensitization; (2) 900 recipients and 1427 donors were enrolled for candidate or donor pools, respectively. Eplets were from the HLA Epitope Registry. UAs were determined by anti-HLA antibodies identified using LIFECODES Single Antigen (LSA) kits. CPRA values were calculated using a simplified method of donor filtering; (3) HLA antigens containing all eplets of an HLA antigen in LSA kits (LSA antigen) were defined as eplet-predicted (EP) antigens, the reactivity of which could be predicted by that LSA antigen. High reactivity concordance was found between LSA and EP antigens. More HLA antigens were covered by EP antigens in the population than LSA antigens. CPRA values at the EP level were higher than at the allele level and lower than at the antigen level. The EP antigens facilitated UA determination for non-LSA antigens and avoided acute rejection; (4) UA determination using EP antigens can lead to more accurate assessment of sensitization, enabling a high probability of compatible organs and a low risk of adverse outcomes.

Increased Prevalence of Unstable HLA-C Variants in HIV-1 Rapid-Progressor Patients

HIV-1 infection in the absence of treatment results in progression toward AIDS. Host genetic factors play a role in HIV-1 pathogenesis, but complete knowledge is not yet available. Since less-expressed HLA-C variants are associated with poor HIV-1 control and unstable HLA-C variants are associated with higher HIV-1 infectivity, we investigated whether there was a correlation between the different stages of HIV-1 progression and the presence of specific HLA-C allotypes. HLA-C genotyping was performed using allele-specific PCR by analyzing a treatment-naïve cohort of 96 HIV-1-infected patients from multicentric cohorts in the USA, Canada, and Brazil. HIV-1-positive subjects were classified according to their different disease progression status as progressors (Ps, n = 48), long-term non-progressors (LTNPs, n = 37), and elite controllers (ECs, n = 11). HLA-C variants were classified as stable or unstable according to their binding stability to β2-microglobulin/peptide complex. Our results showed a significant correlation between rapid progression to AIDS and the presence of two or one unstable HLA-C variants (p-value: 0.0078, p-value: 0.0143, respectively). These findings strongly suggest a link between unstable HLA-C variants both at genotype and at allele levels and rapid progression to AIDS. This work provides further insights into the impact of host genetic factors on AIDS progression.

Epigenetic and Genetic Contribution for Expression Bias of Homologous Alleles in Polyploid Sugarcane

DNA methylation regulates gene expression in eukaryotes, but their roles in gene expression changes in polyploids are poorly understood. Here, we comparatively analyzed the DNA methylation profiles and transcriptome maps of four tissues (leaf, rind, pith, and root) in autopolyploid sugarcane (Saccharum spontaneum). The overall DNA methylation levels were relatively equal and were consistent with the similar genome-wide expression levels of homologous alleles among different homologous chromosomes. However, tetrad alleles showed a large proportion of non-balanced alleles (85–89%) compared with balanced alleles (11–15%). For tetrad alleles, highly-expressed alleles showed lower Ka/Ks values than those in lowly-expressed alleles, indicating that dominant (and non-suppressed) alleles were under strong purifying selection pressure compared to non-dominant (and suppressed) alleles. Specifically, higher DNA methylation levels were found in non-balanced alleles compared to balanced alleles, as well as a higher CG to TG substitution rate, suggesting epigenetic and genetic variation associated with transcription divergence. Moreover, among non-balanced alleles, which were associated with DNA methylation changes, many were involved in several processes relevant to agronomic traits, such as responses to stress and carbohydrate transport. Taken together, our results provide unique epigenetic insights into the transcriptional regulation of homologous alleles, which contribute to the key agronomic traits in sugarcane and facilitate epigenetic studies in other polyploid crops.