Genotyping Of Mutations Research Articles

Progression and application of circulating tumor DNA in lymphoma

Lymphomas are a highly heterogeneous group of tumors that are classified into several subtypes. The gold standard method for the molecular profiling of lymphoma is based on invasive lymph node or tissue biopsy. However, this method cannot accurately capture spatial tumor heterogeneity in each patient as well as systemic tumor invasion and tumor burden. Circulating tumor DNA (ctDNA) is an emerging and highly versatile biomarker that overcomes the basic limitations of imaging scanning and tissue biopsy; has the characteristics of being simple, rapid, and non-invasive; and has good specificity and high sensitivity. ctDNA testing has been applied to a variety of subtypes of lymphoma and has been used for somatic mutation genotyping, efficacy monitoring during treatment, detection of minimal residual disease, and the prediction of survival, which may help clinicians make better clinical decisions in the diagnosis and treatment of lymphoma patients. Furthermore, this study also aims to review the different methods of ctDNA analysis and describe the specific applications of ctDNA in different lymphoma subtypes.

Genotyping single point mutations in rd1 and rd8 mice using melting curve analysis of qPCR fragments

PCR is tolerant to single nucleotide mismatches. Therefore, genotyping of point mutations by PCR requires special conditions for the amplification of allele-specific PCR fragments. MS-PCR (mutagenically separated PCR) is an improved version of ARMS (amplification refractory mutation system) in which additional nucleotide mismatches near the mutation site are used to separate the wt fragments from the mutant fragments in a single-tube PCR. In the originally described procedure, the resulting fragments are resolved on agarose gels according to differences in size introduced by different lengths of the allele-specific primers. In order to evaluate the PCR fragments by melting curve analysis, we enlarged the difference in the melting temperatures of the fragments of the two alleles by increasing the GC content of the longer allele-specific primer resulting in a higher melting temperature of the corresponding fragment. Using the murine retinal degeneration mutations rd1 and rd8 as an example, we show that such primers result in an easy to handle genotyping procedure: qPCR followed by melting curve analysis. In summary, MS-PCR is a simple and easy-to-use method for detecting single nucleotide variants.

Longitudinal survey of insecticide resistance in a village of central region of Burkina Faso reveals co-occurrence of 1014F, 1014S and 402L mutations in Anopheles coluzzii and Anopheles arabiensis

BackgroundPyrethroid resistance is one of the major threats for effectiveness of insecticide-treated bed nets (ITNs) in malaria vector control. Genotyping of mutations in the voltage gated sodium channel (VGSC) gene is widely used to easily assess the evolution and spread of pyrethroid target-site resistance among malaria vectors. L1014F and L1014S substitutions are the most common and best characterized VGSC mutations in major African malaria vector species of the Anopheles gambiae complex. Recently, an additional substitution involved in pyrethroid resistance, i.e. V402L, has been detected in Anopheles coluzzii from West Africa lacking any other resistance alleles at locus 1014. The evolution of target-site resistance mutations L1014F/S and V402L was monitored in An. coluzzii and Anopheles arabiensis specimens from a Burkina Faso village over a 10-year range after the massive ITN scale-up started in 2010.MethodsAnopheles coluzzii (N = 300) and An. arabiensis (N = 362) specimens collected both indoors and outdoors by different methods (pyrethrum spray catch, sticky resting box and human landing collections) in 2011, 2015 and 2020 at Goden village were genotyped by TaqMan assays and sequencing for the three target site resistance mutations; allele frequencies were statistically investigated over the years.ResultsA divergent trend in resistant allele frequencies was observed in the two species: 1014F decreased in An. coluzzii (from 0.76 to 0.52) but increased in An. arabiensis (from 0.18 to 0.70); 1014S occurred only in An. arabiensis and slightly decreased over time (from 0.33 to 0.23); 402L increased in An. coluzzii (from 0.15 to 0.48) and was found for the first time in one An. arabiensis specimen. In 2020 the co-occurrence of different resistance alleles reached 43% in An. coluzzii (alleles 410L and 1014F) and 32% in An. arabiensis (alleles 1014F and 1014S).ConclusionsOverall, an increasing level of target-site resistance was observed among the populations with only 1% of the two malaria vector species being wild type at both loci, 1014 and 402, in 2020. This, together with the co-occurrence of different mutations in the same specimens, calls for future investigations on the possible synergism between resistance alleles and their phenotype to implement local tailored intervention strategies.

Genotyping and Antiretroviral Drug Resistance Mutations among HIV Patients in Southern Santa Catarina, Brazil.

Therapeutic measures have been successful in increasing survival rates and quality of life of HIV/AIDS-infected people. However, some people fail to respond to antiretroviral therapy (HAART) because of viral resistance-associated mutations. To identify virus genotype and the presence of mutations that alter the susceptibility to HAART, and factors associated with the occurrence of these mutations. A cross-sectional study was conducted on adults living with HIV attending a specialized outpatient clinic in southern Santa Catarina, Brazil. The participants were interviewed and had blood samples collected for analysis. Those with detectable viral load were genotyped. Out of the 629 patients recruited, 127 subjects were included due to having a detectable viral load. The most common mutations were M184V and K103N. HIV-1 subtype C was the most prevalent strain. Resistance to HAART was associated with modification in the treatment regimen (p <0.001). This study concluded that the circulating subtype virus was subtype C and that the mutations K103N and M184V were the most prevalent strains in southern Santa Catarina, Brazil.

Detection and population genetic analysis of Aedes albopictus (Diptera: Culicidae) based on knockdown resistance (kdr) mutations in the Yangtze River basin of China

BackgroundAedes albopictus is an important vector of chikungunya, dengue, yellow fever and Zika viruses. Insecticides are often the most effective tools for rapidly decreasing the density of vector populations, especially during arbovirus disease outbreaks. However, the intense use of insecticides, particularly pyrethroids, has led to the selection of resistant mosquito populations worldwide. Mutations in the voltage-gated sodium channel (VGSC) gene are one of the main drivers of insecticide resistance in Ae. albopictus and are also known as “knockdown resistance” (kdr) mutations. Knowledge about genetic mutations associated with insecticide resistance is a prerequisite for developing techniques for rapid resistance diagnosis. Here, we report studies on the origin and dispersion of kdr haplotypes in samples of Ae. albopictus from the Yangtze River Basin, China; MethodsHere, we report the results of PCR genotyping of kdr mutations in 541 Ae. albopictus specimens from 22 sampling sites in 7 provinces and municipalities in the Yangtze River Basin. Partial DNA sequences of domain II and domain III of the VGSC gene were amplified. These DNA fragments were subsequently sequenced to discover the possible genetic mutations mediating knockdown resistance (kdr) to pyrethroids. The frequency and distribution of kdr mutations were assessed in 22 Ae. albopictus populations. Phylogenetic relationships among the haplotypes were used to infer whether the kdr mutations had a single or multiple origins; ResultsThe kdr mutation at the 1016 locus had 2 alleles with 3 genotypes: V/V (73.38%), V/G (26.43%) and G/G (0.18%). The 1016G homozygous mutation was found in only one case in the CQSL strain in Chongqing, and no 1016G mutations were detected in the SHJD (Shanghai), NJDX (Jiangsu) or HBQN (Hubei) strains. A total of 1532 locus had two alleles and three genotypes, I/I (88.35%), I/T (8.50%) and T/T (3.14%). A total of 1534 locus had four alleles and six genotypes: F/F (49.35%), F/S (19.96%), F/C (1.48%) and F/L (0.18%); S/S (23.66%); and C/C (5.36%). Haplotypes with the F1534C mutation were found only in Ae. albopictus populations in Chongqing and Hubei, and C1534C was found only in three geographic strains in Chongqing. Haplotypes with the 1534S mutation were found only in Ae. albopictus populations in Sichuan and Shanghai. F1534L was found only in HBYC. The Ae. albopictus populations in Shanghai were more genetically differentiated from those in the other regions (except Sichuan), and the genetic differentiation between the populations in Chongqing and those in the middle-lower reaches of the Yangtze River (Huber, Jiangsu, Jiangxi, and Anhui) was lower. Shanghai and Sichuan displayed low haplotype diversity and low nucleotide diversity. Phylogenetic analysis and sequence comparison revealed that the 1016 locus was divided into three branches, with the Clade A and Clade B branches bearing the 1016 mutation occurring mostly in Jiangsu and the Clade C branch bearing the 1016 mutation occurring mostly in Chongqing, suggesting at least two origins for 1016G. IIIS6 phylogenetic analysis and sequence comparison revealed that F1534S, F1534C and I1532T can be divided into two branches, indicating that IIIS6 has two origins; ConclusionsCombined with the distribution of kdr mutations and the analysis of population genetics, we infer that besides the local selection of pyrethroid resistance mutations, dispersal and colonization of Ae. albopictus from other regions may explain why kdr mutations are present in some Ae. albopictus populations in the Yangtze River Basin.

Mutations with known links to pork quality defects in Norwegian and German pig populations

ABSTRACT With heritable PSE (hal+) being largely eradicated in many countries, pork quality defects and their linkage to known mutations have received less attention in the last decade. We address this by mapping the frequency of four known mutations (200Q, 199 V, hal+, PHKG1) in heterogenous Norwegian and German pig populations (n = 136/61). Genotyping for mutations was done by PCR-RFLP analyses and Illumina chip genotyping. We found a high prevalence of pigs with at least one of the four tested mutations for Norwegian and German samples (60%, 77%). For Norwegian samples, we confirm known links of 200Q and PHKG1 with Hampshire and Duroc genetics, respectively. For Germany, we show that Piétrain pigs can still be heterozygous carriers of hal + . In all, our data points to a relatively high abundance of mutations that affect pork quality in both countries. The high prevalence of individual mutations may contribute to recent ham quality defects.

Carrying SNP rs17506395 (T > G) in TP63 gene and CCR5Δ32 mutation associated with the occurrence of breast cancer in Burkina Faso.

Genetic alterations in the TP63 (GenBank: NC_000003.12, ID: 8626) and CCR5 (receptor 5 chemokine co-receptor) (GenBank: NC_000003.12, ID: 1234) genes may increase the risk of developing breast cancer. The aim of this study was to investigate the probable involvement of polymorphisms rs17506395 in the TP63 (tumour protein 63) gene and the CCR5Δ32 mutation in the occurrence of breast cancer in Burkina Faso. This case-control study included 72 patients and 72 controls. Genotyping of SNP rs17506395 (TP63) was performed by polymerase chain reaction-restriction fragment length polymorphism, and genotyping of the CCR5Δ32 mutation was performed by allele-specific oligonucleotide polymerase chain reaction. For SNP rs17506395 (TP63), the genotypic frequencies of wild-type homozygotes (TT) and heterozygotes (TG) were, respectively, 27.72 and 72.22% in cases and 36.11 and 63.89% in controls. No mutated homozygotes (GG) were observed. For the CCR5Δ32 mutation, the genotypic frequencies of wild-type homozygotes (WT/WT) and heterozygotes (WT/Δ32) were 87.5 and 13.5%, respectively, in the cases and 89.29 and 10.71%, respectively, in the controls. No mutated homozygotes (Δ32/Δ32) were observed. None of the polymorphisms rs17506395 of the TP63 gene (OR = 1.47, 95% CI = 0.69-3.17, P = 0.284) and the CCR5Δ32 mutation (OR = 1.32, 95% CI = 0.46-3.77; P = 0.79) were associated with the occurrence of breast cancer in this study.

Abstract 5828: The genomic architecture of ibrutinib resistance in CLL: Oligoclonal progression with variable anatomical distribution

Abstract Progressive disease (PD) in patients with chronic lymphocytic leukemia (CLL) on ibrutinib often presents with acquired mutations in BTK and/or PLCG2. Reported variant allele frequencies (VAF) are often low, leading some to question the role of these mutations. Further, several co-existing mutations are often identified. Here we investigated the clonal composition of PD on single cell level, across time, and different anatomic compartments. 84 CLL patients (52 treatment-naïve; 32 relapsed/refractory) with either a TP53 aberration or age ≥65 years received single-agent ibrutinib 420 mg once daily until PD or limiting side effects on a phase 2 study (NCT01500733). The median progression-free survival was 86.6 months. 39 (46.4%) patients progressed, 31 with CLL (PD-CLL), and 8 with Richter’s transformation. Median time to PD-CLL was 57.2 months. In PD-CLL patients, peripheral blood (PB) was sent for genotyping of known hotspot mutations in BTK/PLCG2 (Neogenomics). We then designed digital droplet PCR probes to test for BTK C481S/R/Y and PLCG2 R665W/L845/S707F mutations in samples collected at baseline, during response to ibrutinib and at PD in 29 patients. 26 (89.7%) patients had detectable BTK/PLCG2 mutations (VAF range 0.04 - 0.96). 12 (41%) patients carried multiple BTK/PLCG2 mutations. In 11 evaluable cases single-cell DNA sequencing (Mission Bio) showed individual mutations present in separate cells consistent with branching evolution. Having confirmed oligoclonality, we calculated the cumulative cell fraction (cCF) of BTK/PLCG2 mutations in the 29 PD-CLL patients. 16 (55%) patients had cCF &amp;gt;0.5 (range 0.59-0.96), 10 patients (35%) had cCF &amp;lt; 0.5 (range 0.04-0.43) and 3 patients (10%) had no detectable mutations. BTK/PLCG2 mutations were detected in samples collected at median 21.6 months (range 0 - 75) prior to PD. In 11 cases, we tested lymph node (LN) biopsies at PD. In 6 cases with cCF &amp;lt;0.5 in PB, 4 corresponding LN samples had higher cCF (0.01/0.92; 0/0.85; 0.06/0.69; 0.46/0.99 for PB/LN, respectively). In 5 cases, PB contained 2-6 distinct subclones with cCF &amp;gt;0.5, in 3 cases the corresponding LN harbored fewer subclones than PB (6/3; 3/2; 3/0 for PB/LN, respectively). To characterize the genomic background of PD-CLL, we performed whole-exome sequencing of longitudinal samples from 26 patients. In addition to BTK/PLCG2, the most frequently mutated genes were TP53, SF3B1, NOTCH1, and POT1. Furthermore, copy number variations (CNA), such as del17p, del13q, del14q, del3p, and del8p, were common. In summary, in our cohort BTK/PLCG2 mutations were identified in 89.7% of PD-CLL patients. These mutations arise in oligoclonal populations with variable distribution across anatomical sites. In rare patients without BTK/PLCG2 mutations, the co-evolution of putative driver mutations and multiple CNAs generated genomic complexity reminiscent of lymphoma transformation. Citation Format: Chingiz Underbayev, Jonathan Chen, Hailey M. Harris, Lauren T. Vaughn, Andy Itsara, Adrian Wiestner. The genomic architecture of ibrutinib resistance in CLL: Oligoclonal progression with variable anatomical distribution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5828.

Abstract 960: Improved cfDNA methylation profiling through correction of misrepaired jagged-ends

Abstract Background: Profiling cfDNA methylation enables early cancer detection and classification, but challenges arise from "jagged ends" (JEs) for ~90% of cfDNA molecules, as well as for FFPE samples and partially degraded genomic DNA. Repair of these jagged ends introduces erroneous methylation signals, especially in shorter cfDNA fragments enriched for tumor derived molecules. Separately, DNA conversions during 5mC profiling hamper accurate simultaneous ctDNA genotyping of somatic mutations. To meet these needs, we developed a method preserving double-stranded cfDNA molecules without error-prone end-repair at jagged ends. This enables superior methylation profiling including hemimethylation detection, and simultaneous ctDNA SNV genotyping. Methods: We present JEEPERS (Jagged-End Error Polishing of Enzymatically misRepaired Sequences), a novel method for correcting errors in double-stranded library preparation for methylation profiling. JEEPERS detects and quantifies enzymatic repair errors at JEs, correcting them in silico. Leveraging duplex UMIs, it utilizes complementary strands and sibling reads from cfDNA families without jagged ends. The method exploits the 5' to 3' polarity of ER-associated errors and JE length profiles for correction. JEEPERS introduces anchor CpGs for precise correction of rare signals and enables accurate SNV calling at non CpG sites, addressing the challenge of differentiating true SNVs from conversion artifacts leading to C&amp;gt;T/G&amp;gt;A changes in sequencing data. Results: Analyzing 248 cfDNA samples (139 NSCLC patients, 109 healthy controls) by methylation profiling (EM-Seq) and ctDNA mutation genotyping (CAPP-Seq), JEEPERS correction efficiently addressed distortions, even at low tumor concentrations. Limiting dilution experiments demonstrated JEEPERS achieving a LOD95 of ~0.2% with 95% specificity (n=300). Despite ~50% lower molecular depth, JEEPERS-corrected cfDNA EM-Seq enabled accurate simultaneous methylation profiling and ctDNA genotyping, correlating strongly with CAPP-Seq genotypes (R=0.998, n=30). As expected, mutant ctDNA molecules were shorter than wild-type in both CAPP-Seq and EM-Seq data. cfDNA methylation patterns varied by oncogene vs. tumor suppressor status; EGFR mutants showed increased methylation (p&amp;lt;0.01), while TP53 mutants had lower methylation levels (p&amp;lt;0.05). Conclusions: Our method effectively corrects cfDNA methylation data, even at low tumor concentration, ensuring enhanced methylation signal accuracy and proficient SNV calling capabilities. This integrated approach offers a powerful means for investigating the link between SNVs and DNA methylation, significantly enhancing the accuracy of cancer detection using cfDNA, especially for early-stage tumors. This paves the way for a deeper understanding of the molecular mechanisms driving cancer initiation and progression. Citation Format: Rui Wang, Emily G. Hamilton, Diego Almanza, Angela Hui, Maximilian Diehn, Ash A. Alizadeh. Improved cfDNA methylation profiling through correction of misrepaired jagged-ends [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 960.

High carrier frequency of CYP21A2 gene mutations in Southern India - underscoring the need for genetic testing in Congenital Adrenal Hyperplasia.

Congenital Adrenal Hyperplasia (CAH) is one of the highly prevalent autosomal recessive endocrine disorders. The majority of CAH cases result from mutations in the CYP21A2 gene, leading to 21-hydroxylase deficiency. However, with the pseudogene-associated challenges in CYP21A2 gene analysis, routine genetic diagnostics and carrier screening in CAH are not a part of the first-tier investigations in a clinical setting. Furthermore, there is a lack of data on the carrier frequency for 21-OH deficiency. Therefore, this study is aimed at investigating the carrier frequency of common pseudogene derived CYP21A2 mutations in Southern India. Recently, a cost-effective Allele-specific PCR based genotyping for CYP21A2 hotspot mutations has been demonstrated to be a highly specific and sensitive assay at the authors' center. Leveraging this approach, a total of 1034 healthy individuals from South India underwent screening to identify the carrier frequency of nine hotspot mutations in the CYP21A2 gene. In this study, it was observed that 9.76% of the subjects were carriers for one or more of the nine different CYP21A2 mutations. Among the carriers, the most common was the large 30 kb deletion, followed by II72N, E6 CLUS, and I2G mutations. We have identified a high prevalence of CYP21A2 mutation carriers in Southern India. These findings emphasize the importance of implementing and expanding cost-effective genetic diagnostics and carrier screening throughout India. Such initiatives would play a crucial role in managing the disease burden, enabling early intervention, and establishing guidelines for CAH newborn genetic screening in the country. This study represents the first carrier screening data on CYP21A2 hotspot mutations from India and is the largest study conducted till date in this context.

Pyrethroid resistance status and co-occurrence of V1016G, F1534C and S989P mutations in the Aedes aegypti population from two dengue outbreak counties along the China-Myanmar border

BackgroundOver the past two decades, dengue fever (DF) has emerged as a significant arboviral disease in Yunnan province, China, particularly in the China-Myanmar border area. Aedes aegypti, an invasive mosquito species, plays a crucial role in transmitting the dengue virus to the local population. Insecticide-based vector control has been the primary tool employed to combat DF, but the current susceptibility status of Ae. aegypti to commonly used insecticides is unknown. Assessment of Ae. aegypti resistance to pyrethroid insecticides and an understanding of the underlying mechanisms of this resistance in the China-Myanmar border region is of significant strategic importance for effectively controlling the DF epidemic in the area.MethodsAedes aegypti larvae collected from Ruili and Gengma counties in Yunnan Province were reared to adults in the laboratory and tested for susceptibility to three pyrethroid insecticides (3.20% permethrin, 0.08% lambda-cyhalothrin and 0.20% deltamethrin) by the standard WHO susceptibility bioassay. Genotyping of mutations in the knockdown gene (kdr), namely S989P, V1016G and F1534C, that are responsible for resistance to pyrethroid insecticides was performed using allele-specific PCR methods. A possible association between the observed resistant phenotype and mutations in the voltage-gated sodium channel gene (VGSC) was also studied.ResultsAedes aegypti mosquitoes collected from the two counties and reared in the laboratory were resistant to all of the pyrethroids tested, with the exception of Ae. aegypti from Gengma County, which showed sensitivity to 0.20% deltamethrin. The mortality rate of Ae. aegypti from Ruili county exposed to 3.20% permethrin did not differ significantly from that of Ae. aegypti from Gengma County (χ2 = 0.311, P = 0.577). By contrast, the mortality rate of Ae. aegypti from Ruili County exposed to 0.08% lambda-cyhalothrin and 0.20% deltamethrin, respectively, was significantly different from that of Ae. aegypti from Gengma. There was no significant difference in the observed KDT50 of Ae. aegypti from the two counties to various insecticides. Four mutation types and 12 genotypes were detected at three kdr mutation sites. Based on results from all tested Ae. aegypti, the V1016G mutation was the most prevalent kdr mutation (100% prevalence), followed by the S989P mutation (81.6%) and the F1534C mutation (78.9%). The constituent ratio of VGSC gene mutation types was significantly different in Ae. aegypti mosquitoes from Ruili and those Gengma. The triple mutant S989P + V1016G + F1534C was observed in 274 Ae. aegypti mosquitoes (60.8%), with the most common genotype being SP + GG + FC (31.4%). The prevalence of the F1534C mutation was significantly higher in resistant Ae. aegypti from Ruili (odds ratio [OR] 7.43; 95% confidence interval [CI] 1.71–32.29; P = 0.01) and Gengma (OR 9.29; 95% CI 3.38–25.50; P = 0.00) counties than in susceptible Ae. aegypti when exposed to 3.20% permethrin and 0.08% lambda-cyhalothrin, respectively. No significant association was observed in the triple mutation genotypes with the Ae. aegypti population exposed to 3.20% permethrin and 0.20% deltamethrin resistance (P > 0.05), except for Ae. aegypti from Gengma County when exposed to 0.08% lambda-cyhalothrin (OR 2.86; 95% CI 1.20–6.81; P = 0.02).ConclusionsAedes aegypti from Ruili and Gengma counties have developed resistance to various pyrethroid insecticides. The occurrence of multiple mutant sites in VGSC strongly correlated with the high levels of resistance to pyrethroids in the Ae. aegypti populations, highlighting the need for alternative strategies to manage the spread of resistance. A region-specific control strategy for dengue vectors needs to be implemented in the future based on the status of insecticide resistance and kdr mutations.Graphical

Polymorphisms of the BMPR1B, BMP15 and GDF9 fecundity genes in four Chinese sheep breeds

Abstract. Numerous studies on prolific sheep breeds have shown that the transforming growth factor beta (TGF-β) superfamily members, including bone morphogenetic protein receptor type 1B (BMPR1B), bone morphogenetic protein 15 (BMP15) and growth differentiation factor 9 (GDF9), are the essential regulators of ovulation rate and litter size. In total, 11 known mutations (1 in BMPR1B, 6 in BMP15 and 4 in GDF9) are able to increase the ovulation rate and litter size, respectively. In this study, the genomic DNA was isolated from 512 high-prolificacy sheep (including the Small-tailed Han, Hu and Wadi sheep breeds) and 164 low-prolificacy sheep (Tan sheep), and genotyping of the specific mutations of the three fecundity-related genes was carried out by sequencing. The results showed that the FecB mutation in BMPR1B was detected in all four sheep breeds, and the frequency of B allele was significantly higher in the high-prolificacy breeds than that in the low-prolificacy breed (P&lt;0.001). A novel mutation, c.T755C (named S1), was found in BMP15 from the four sheep breeds. However, known mutations such as FecXI, FecXH, FecXB, FecXG, FecXL and FecXR were not detected in these breeds. Three known loci (G1, G3 and G4) and a new mutation, c.A1515G (named S2), were found in GDF9, and the other three known mutations (FecGH (G8), FecGE and FecTT) were not detected in all four sheep breeds. The genotype distribution at the G1 and G4 loci had significant differences between the low-prolificacy sheep breed and the other three high-prolificacy sheep breeds. There was no difference in the genotype distribution at the G1 and G4 loci between the three high-prolificacy sheep breeds. Haplotype analysis of the four polymorphic loci in GDF9 suggested that H4 (GGAA) was the preponderant haplotype in the three high-prolificacy sheep breeds, but H1 (GGGG) was in the low-prolificacy sheep breed. These results preliminarily showed that the BMPR1B and GDF9 might be major genes influencing the prolificacy of Chinese sheep breeds.

The Exploring of Growth Differentiation Factor-15 and H63D Gene Polymorphisms in β-thalassemia Major: Implications for Cardiovascular Risk and Iron Overload

BACKGROUND: β-thalassemia major (βTM) is a genetic disorder characterized by a deficiency in hemoglobin production, ineffective erythropoiesis, chronic hemolysis, lifelong blood transfusions, iron overload, and increased risk of cardiac complications. OBJECTIVE: The study aimed to evaluate the growth differentiation factor-15 (GDF-15) concentration in βTM patients and its correlation with cardiac complications. H63D refers to a specific mutation in the HFE gene, which is associated with hereditary hemochromatosis (HH), a genetic disorder characterized by excessive accumulation of iron in the body. This mutation involves a change of histidine (H) to aspartic acid (D) at position 63 in the HFE protein. This mutation is often only written abbreviated as (H63D). MATERIALS AND METHODS: This case–control study was done on 120 subjects. A total of 60 patient samples were randomly collected from the Genetic Hematology Center at the Babylon Hospital, with an age range of 10–26 years. In addition, 60 samples were collected from healthy children in the same age range as the control group; patients and controls were subdivided into (10–18) and (18–26) year groups. GDF-15 was measured by enzyme-linked immunosorbent assay, and the genotyping of mutation was done by amplification refractory mutation system-polymerase chain reaction technique. RESULTS: The study revealed a significant increase in ferritin (FER) and GDF-15 levels in the patients compared to controls (P &lt; 0.001). GDF-15 showed a direct correlation with age (r = 0.244, P = 0.02) and FER (r = 0.215, P = 0.04). There was a significant difference in H63D mutations between controls and patients (P = 0.044), with a higher proportion of the C-G (heterozygous for the mutant allele) genotype observed in βTM patients (31.67%). Additionally, a notable effect of the H63D mutation on serum ferritin (higher) levels within the βTM group was observed. CONCLUSION: Elevations of the GDF-15 in βTM patients indicate a high risk of cardiovascular complications in patients with βTM. The H63D mutation of the hemostatic iron regulator (HFE) gene is frequently found in βTM. Although a significant effect of the mutation was obtained on serum FER levels, it did not act as a risk factor in βTM patients. However, the frequent presence of the H63D mutation in patients indicated a possible association between single-nucleotide polymorphism and the iron regulation pathway.

Hybrid deep multi-task learning radiomics approach for predicting EGFR mutation status of non-small cell lung cancer in CT images

Objective. Epidermal growth factor receptor (EGFR) mutation genotyping plays a pivotal role in targeted therapy for non-small cell lung cancer (NSCLC). We aimed to develop a computed tomography (CT) image-based hybrid deep radiomics model to predict EGFR mutation status in NSCLC and investigate the correlations between deep image and quantitative radiomics features. Approach. First, we retrospectively enrolled 818 patients from our centre and 131 patients from The Cancer Imaging Archive database to establish a training cohort (N = 654), an independent internal validation cohort (N = 164) and an external validation cohort (N = 131). Second, to predict EGFR mutation status, we developed three CT image-based models, namely, a multi-task deep neural network (DNN), a radiomics model and a feature fusion model. Third, we proposed a hybrid loss function to train the DNN model. Finally, to evaluate the model performance, we computed the areas under the receiver operating characteristic curves (AUCs) and decision curve analysis curves of the models. Main results. For the two validation cohorts, the feature fusion model achieved AUC values of 0.86 ± 0.03 and 0.80 ± 0.05, which were significantly higher than those of the single-task DNN and radiomics models (all P < 0.05). There was no significant difference between the feature fusion and the multi-task DNN models (P > 0.8). The binary prediction scores showed excellent prognostic value in predicting disease-free survival (P = 0.02) and overall survival (P < 0.005) for validation cohort 2. Significance. The results demonstrate that (1) the feature fusion and multi-task DNN models achieve significantly higher performance than that of the conventional radiomics and single-task DNN models, (2) the feature fusion model can decode the imaging phenotypes representing NSCLC heterogeneity related to both EGFR mutation and patient NSCLC prognosis, and (3) high correlations exist between some deep image and radiomics features.

A Gradual Transition Toward Anaplasia in Wilms Tumor Through Tolerance to Genetic Damage

Patients with Wilms tumor (WT) in general have excellent survival, but the prognosis of patients belonging to the subgroup of WT with diffuse anaplasia (DA) is poor due to frequent resistance to chemotherapy. We hypothesized that DA WT cells might undergo changes, such as acquiring a persistent tolerance to DNA damage and copy number aberrations (CNAs), which could eventually lead to their resistance to chemotherapy treatment. Tissue sections from chemotherapy-treated DA WTs (n = 12) were compared with chemotherapy-treated nonanaplastic WTs (n = 15) in a tissue microarray system, enabling analysis of 769 tumor regions. All regions were scored for anaplastic features and immunohistochemistry was used to quantify p53 expression, proliferation index (Ki67), and DNA double-strand breaks (γH2AX). CNAs were assessed by array-based genotyping and TP53 mutations using targeted sequencing. Proliferation index and the frequency of DNA double-strand breaks (γH2AX dot expression) increased with higher anaplasia scores. Almost all (95.6%) areas with full-scale anaplasia had TP53 mutations or loss of heterozygosity, along with an increased amount of CNAs. Interestingly, areas with wild-type TP53 with loss of heterozygosity and only one feature of anaplasia (anaplasia score 1) also had significantly higher proliferation indices, more DNA double-strand breaks, and more CNAs than regions without any anaplastic features (score 0); such areas may be preanaplastic cell populations under selective pressure for TP53 mutations. In conclusion, we suggest that chemoresistance of DA WTs may be partly explained by a high proliferative capability of anaplastic cells, which also have a high burden of double-stranded DNA breaks and CNAs, and that there is a gradual emergence of anaplasia in WT.

PDL1 and molecular biomarkers expression in non-small cell lung cancer in Tunisian patients.

In cancer treatment, programmed death-1 (PD-1) and programmed death ligand-1 (PD-L1) inhibitors are thriving. Activated T lymphocytes expressed PD-1, it works with its ligand PD-L1 to limit T lymphocyte activation and prevent autoimmune disease. The expression of molecular biomarkers and PD-L1 in lung cancer determines the appropriate treatment strategy for patients with lung cancer. The purpose of this study was to look at the prevalence of molecular biomarkers and PD-L1 expression in a large group of Tunisian patients with advanced non-small cell lung cancer. We conducted an observational retrospective study in which medical/treatment history data were extracted retrospectively from medical records and archived tissue samples between January 1st 2019 and December 31st 2021. We gathered 157 patients who had recently been diagnosed with non-small cell lung carcinoma. In 36.9%of the cases, there was no molecular genotyping. EGFR (28.6%), KRAS (5.73%), and ALK gene rearrangement were the most common genotyping mutations (3.8%). ROS1 rearrangement was not present. There was a link between EGFR and gender, HER and age, and KRAS and biopsy tissue origin. Six of the tested cases with PD-L1 met the cut-off (³50%). PD-L1 positivity was more common in solid type adenocarcinoma (1.9%) than in acinar or papillary adenocarcinoma. There were no significant differences in PD-L1 expression across clinical and demographic parameters. High PD-L1 expression and molecular abnormalities were found in 1 case of EGFR, 1 case of BRAF, and 1 case of KRAS (3 cases). All of the other specimens with abnormalities had a PD-L1 <50%. ALK, ROS1, BRAF, KRAS, and MET were found to be significantly associated with PD-L1 expression. Our study is one of the country's largest, describing a large panel of biomarkers and their clinicopathologic/histopathologic associations in Tunisian lung cancer patients. We have the same molecular profile as European patients with an EGFR mutation, which is not the most common genotype abnormality in Tunisian patients. There is only one mutation at any given time. The expression of PD-L1 is determined by the histologic type and the origin of the biopsy tissue.

Single-Cell Genotyping of Single-Nucleotide Mutations Using In Situ Allele-Specific Loop-Mediated Isothermal Amplification.

Single-nucleotide mutations (SNMs) in the bacterial genome may cause antibiotic resistance. The visualization of SNMs can indicate antibiotic resistance phenotypes at the single-cell level but remains challenging. Herein, we proposed an in situ allele-specific isothermal amplification proceeded inside cells, allowing us to image bacterial genes with single-nucleotide resolution. The primer for loop-mediated isothermal amplification (LAMP) was designed with artificial mismatch bases to serve as an allele-specific probe, endowing LAMP to specifically amplify genes with SNMs. Due to the high amplification efficiency of LAMP, the method termed AlleLAMP can generate high gain for imaging SNMs and precisely quantify mutated quinolone-resistant Salmonella in bacterial mixture. We utilized AlleLAMP to survey the selection of antibiotic resistance under the preservative stress and found that the mutant quinolone-resistant strain owned a survival advantage over the wild-type quinolone-sensitive strain under the stress of preservatives. AlleLAMP can serve as a single-cell tool for analyzing the relationship between bacterial genotype and phenotype.

Deltamethrin and transfluthrin select for distinct transcriptomic responses in the malaria vector Anopheles gambiae

BackgroundThe widespread use of pyrethroid insecticides in Africa has led to the development of strong resistance in Anopheles mosquitoes. Introducing new active ingredients can contribute to overcome this phenomenon and ensure the effectiveness of vector control strategies. Transfluthrin is a polyfluorinated pyrethroid whose structural conformation was thought to prevent its metabolism by cytochrome P450 monooxygenases in malaria vectors, thus representing a potential alternative for managing P450-mediated resistance occurring in the field. In this study, a controlled selection was used to compare the dynamics of resistance between transfluthrin and the widely used pyrethroid deltamethrin in the mosquito Anopheles gambiae. Then, the associated molecular mechanisms were investigated using target-site mutation genotyping and RNA-seq.MethodsA field-derived line of An. gambiae carrying resistance alleles at low frequencies was used as starting material for a controlled selection experiment. Adult females were selected across 33 generations with deltamethrin or transfluthrin, resulting in three distinct lines: the Delta-R line (selected with deltamethrin), the Transflu-R line (selected with transfluthrin) and the Tiassale-S line (maintained without selection). Deltamethrin and transfluthrin resistance levels were monitored in each selected line throughout the selection process, as well as the frequency of the L1014F kdr mutation. At generation 17, cross-resistance to other public health insecticides was investigated and transcriptomes were sequenced to compare gene transcription variations and polymorphisms associated with adaptation to each insecticide.ResultsA rapid increase in resistance to deltamethrin and transfluthrin was observed throughout the selection process in each selected line in association with an increased frequency of the L1014F kdr mutation. Transcriptomic data support a broader response to transfluthrin selection as compared to deltamethrin selection. For instance, multiple detoxification enzymes and cuticle proteins were specifically over-transcribed in the Transflu-R line including the known pyrethroid metabolizers CYP6M2, CYP9K1 and CYP6AA1 together with other genes previously associated with resistance in An. gambiae.ConclusionThis study confirms that recurrent exposure of adult mosquitoes to pyrethroids in a public health context can rapidly select for various resistance mechanisms. In particular, it indicates that in addition to target site mutations, the polyfluorinated pyrethroid transfluthrin can select for a broad metabolic response, which includes some P450s previously associated to resistance to classical pyrethroids. This unexpected finding highlights the need for an in-depth study on the adaptive response of mosquitoes to newly introduced active ingredients in order to effectively guide and support decision-making programmes in malaria control.

Epidemiology of cytomegalovirus antiviral resistance testing for solid organ and bone marrow transplant patients from 2011 - 2019.

CMV reactivation post-transplantation is common, with need for prompt identification of patients most at-risk for CMV antiviral drug resistance (AVDR). This study describes CMV AVDR frequencies, antiviral prescribing practices, and AVDR risk factors in patients from 2011 to 2019 in British Columbia, Canada. Retrospective review of demographics, transplant type, viral loads, antiviral exposure duration, and 12-month mortality was conducted for all patients with samples submitted for CMV AVDR testing from 2011 to 2019. Genotyping of AVDR mutations occurred at the national reference laboratory. Mann-Whitney U, T-test or Fisher's exact tests examined differences between patients with and without AVDR. Fifty-three plasma and three tissue/fluid specimens successfully underwent CMV AVDR testing; of these samples, 27/56 (48%) had AVDR mutations detected. The commonest AVDR mutations were at UL97 loci A594 (20%), H596 (12%) and L595 (12%). Mutations occurred more frequently in requests from solid organ than hematopoietic stem cell transplant patients (58% vs. 27%, p=0.05). Previous resistance testing was a significant risk factor for AVDR (p<0.001). Patients with AVDR had approximately 51 more days of antiviral therapy (p=0.007) and took 9 days longer to clear viremia (p=0.23). The median turnaround time from sample send-out to reporting was nine days. However, empiric use of second-line antivirals occurred in most cases (39/53, 74%) before results were available. Laboratories should strive to provide timely CMV AVDR testing for transplant patients, to minimize unnecessary exposure to second-line antiviral agents. The findings of this study may help guide clinicians when selecting empiric antiviral therapy.

Contrasting Patterns of Asaia Association with Pyrethroid Resistance Escalation between the Malaria Vectors Anopheles funestus and Anopheles gambiae

Microbiome composition has been associated with insecticide resistance in malaria vectors. However, the contribution of major symbionts to the increasingly reported resistance escalation remains unclear. This study explores the possible association of a specific endosymbiont, Asaia spp., with elevated levels of pyrethroid resistance driven by cytochrome P450s enzymes and voltage-gated sodium channel mutations in Anopheles funestus and Anopheles gambiae. Molecular assays were used to detect the symbiont and resistance markers (CYP6P9a/b, 6.5 kb, L1014F, and N1575Y). Overall, genotyping of key mutations revealed an association with the resistance phenotype. The prevalence of Asaia spp. in the FUMOZ_X_FANG strain was associated with the resistance phenotype at a 5X dose of deltamethrin (OR = 25.7; p = 0.002). Mosquitoes with the resistant allele for the markers tested were significantly more infected with Asaia compared to those possessing the susceptible allele. Furthermore, the abundance correlated with the resistance phenotype at 1X concentration of deltamethrin (p = 0.02, Mann-Whitney test). However, for the MANGOUM_X_KISUMU strain, findings rather revealed an association between Asaia load and the susceptible phenotype (p = 0.04, Mann-Whitney test), demonstrating a negative link between the symbiont and permethrin resistance. These bacteria should be further investigated to establish its interactions with other resistance mechanisms and cross-resistance with other insecticide classes.