Allele Frequencies Of Variants Research Articles

Repurposing non-invasive prenatal testing data: Population study of single nucleotide variants associated with colorectal cancer and Lynch syndrome.

In our previous work, genomic data generated through non-invasive prenatal testing (NIPT) based on low-coverage massively parallel whole-genome sequencing of total plasma DNA of pregnant women in Slovakia was described as a valuable source of population specific data. In the present study, these data were used to determine the population allele frequency of common risk variants located in genes associated with colorectal cancer (CRC) and Lynch syndrome (LS). Allele frequencies of identified variants were compared with six world populations to detect significant differences between populations. Finally, variants were interpreted, functional consequences were searched for and clinical significance of variants was investigated using publicly available databases. Although the present study did not identify any pathogenic variants associated with CRC or LS in the Slovak population using NIPT data, significant differences were observed in the allelic frequency of risk CRC variants previously reported in genome-wide association studies and common variants located in genes associated with LS. As Slovakia is one of the leading countries with the highest incidence of CRC among male patients in the world, there is a need for studies dedicated to investigating the cause of such a high incidence of CRC in Slovakia. The present study also assumed that extensive cross-country data aggregation of NIPT results would represent an unprecedented source of information concerning human genome variation in cancer research.

Type and frequency of genetic variants for cardiovascular riskin patients with type 2 diabetes mellitus

Introduction and Aim:Type 2 diabetes mellitus (T2DM) is associated with a wide range of cardiovascular diseases that comprise the largest cause of both morbidity and mortality for the diabetic patients. The aim is to study the allelic and genotypic frequencies of genetic variants associated with cardiovascular disease (CVD) in T2DM and to assess their contribution to the risk ofcardiovascular complications in the patients. Materials and Methods:The genotyping was performed by usingCardiovascular disease StripAssay kit (Vienna Lab) based on polymerase chain reaction and reverse hybridization. The following mutations were studied: FV G1691A (Leiden), FV H1299R (R2),Prothrombin G20210A, Factor XIII V34L, ?-Fibrinogen ? 455 G/A, PAI-1 4G/5G, GPIIIa L33P (HPA-1), MTHFR C677T, MTHFR A1298C, ACE I/D, Apo B R3500Q, Apo E2/E3/E4. Diabetic patients were divided in 2groups: 1) patients with cardiovascular complications(N=20) and 2) patientswithout cardiovascular complications (N=16). Results:In all diabetic patients, we found higher than population frequency for FV Leiden allele (5.5%), FVR2 allele (9.7%), PAI-1 4G allele (58.9%), ?-Fibrinogen genotype -455G/A (38.9%) andACE D/D genotype (36.1%). Statistically higher frequency was established for ?-Fibrinogen ?455 G/A genotype in the patients with cardiovascular complications compared to non-cardiovascular patients (55% vs. 18.7%). Conclusion:We detected significantly higher frequency of ?-Fibrinogen ?455 G/A genotype in diabetic patients, especially in these with cardiovascular disease. Based on its pro-inflammatory role and its connection to possiblethrombotic events, we assumed that patients would benefit from anti-inflammatory treatment.

Statistical Modelling of Population-Level Exonic Variant Frequency Data with an Emphasis on Rare Variants

Introduction & Objective: Rare variants with allele frequency smaller than 1% are postulated to be associated with disease susceptibility. Since allele frequencies vary globally, the use of population control data that does not match the study population can produce bias. The research question is to identify factors that explain variation in allele frequency across populations. The secondary question is to evaluate the potential bias in using population as control data when studying variants. We use data from gnomAD (Genome Aggregation Database) to answer these questions.
 Methods: We apply each of three model formulations: Linear, Logistic, and Poisson to explain how the frequency or count of variants depends on population subgroup/ancestry, functional annotation, sex, and disease status. We also evaluate interactions between population subgroups and functional annotation.
 Results: For very rare variants (allele frequency < 0.1%), likelihood ratio testing (LRT) provides evidence that allele frequencies vary with functional annotation and population in all three model formulations. By LRT, interactions of population and functional annotation are significant in the Logistic model and the Poisson model. The goodness-of-fit statistics show a better fit in the linear model compared to low frequency variants.
 Conclusion: We observe that population & functional annotation affect variant frequencies, and conclude that detection of differences across populations and annotations is model scale-dependent, especially for different degrees of rareness. Therefore, statisticians need to carefully consider the potential for bias when using gnomAD as control data. Moreover, gnomAD is a great resource for studies dealing with rare variants.

The genomics of heart failure: design and rationale of the HERMES consortium.

AimsThe HERMES (HEart failure Molecular Epidemiology for Therapeutic targetS) consortium aims to identify the genomic and molecular basis of heart failure.Methods and resultsThe consortium currently includes 51 studies from 11 countries, including 68 157 heart failure cases and 949 888 controls, with data on heart failure events and prognosis. All studies collected biological samples and performed genome‐wide genotyping of common genetic variants. The enrolment of subjects into participating studies ranged from 1948 to the present day, and the median follow‐up following heart failure diagnosis ranged from 2 to 116 months. Forty‐nine of 51 individual studies enrolled participants of both sexes; in these studies, participants with heart failure were predominantly male (34–90%). The mean age at diagnosis or ascertainment across all studies ranged from 54 to 84 years. Based on the aggregate sample, we estimated 80% power to genetic variant associations with risk of heart failure with an odds ratio of ≥1.10 for common variants (allele frequency ≥ 0.05) and ≥1.20 for low‐frequency variants (allele frequency 0.01–0.05) at P < 5 × 10−8 under an additive genetic model.ConclusionsHERMES is a global collaboration aiming to (i) identify the genetic determinants of heart failure; (ii) generate insights into the causal pathways leading to heart failure and enable genetic approaches to target prioritization; and (iii) develop genomic tools for disease stratification and risk prediction.

Is BRD7 associated with spermatogenesis impairment and male infertility in humans? A case-control study in a Han Chinese population

BackgroundBromodomain-containing protein 7 (BRD7), a member of the bromodomain-containing protein family, plays important roles in chromatin modification and transcriptional regulation. A recent model of Brd7-knockout mice presented azoospermia and male infertility, implying the potential role of BRD7 in spermatogenic failure in humans. This case-control study aimed to explore the association of the BRD7 gene with spermatogenic efficiency and the risk of spermatogenic defects in humans.ResultsA total of six heterozygous variants were detected in the coding and splicing regions of the BRD7 gene in patients with azoospermia. For each of four rare variants predicted to potentially damage BRD7 function, we further identified these four variants in oligozoospermia and normozoospermia as well. However, no difference in the allele and genotype frequencies of rare variants were observed between cases with spermatogenic failure and controls with normozoospermia; the sperm products of variant carriers were similar to those of noncarriers. Moreover, similar distribution of the alleles, genotypes and haplotypes of seven tag single nucleotide polymorphisms (tagSNPs) was observed between the cases with azoospermia and oligozoospermia and controls with normozoospermia; associations of tagSNP-distinguished BRD7 alleles with sperm products were not identified.ConclusionsThe lack of an association of BRD7-linked rare and common variants with spermatogenic failure implied a limited contribution of the BRD7 gene to spermatogenic efficiency and susceptibility to male infertility in humans.

Interleukin-1 Receptor Antagonist (IL-1RN) Gene Variable Number Tandem Repeats (VNTR) Polymorphism Association in men Infertility in Erbil City /Kurdistan Iraq

The interleukin-1 family has multifaceted roles in men٫s reproductive syste. Out of these is interleukin-1 receptor antagonist (IL-1RN) which exists in men gonads, and in case of infection and inflammatory process, its activity is increased. The current study aims to verify a possible linkage of Variable Number Tandem Repeat (VNTR) polymorphism of the IL-1RN gene with human men infertility. The study groups enrolled included 100 infertile men and 100 fertile and healthy men. Their seminal fluids were subjected to analysis. Also peripheral blood samples were collected for the assessment or detection of polymorphic Variable Number Tandem Repeats (VNTR) polymorphism of interleukin-1 receptor antagonist gene (IL-1RN). Two alleles, namely IL-1RN1 allele corresponding to 410bp fragment and IL-11RN2 that corresponding to 240bp fragments, are a marker for human men infertility, detected by PCR technique. The results delineated a high frequency of IL-1RN2 allelic gene variants (26%), and two VNTR allelic gene variants carriers IL-1RN1 and IL-1RN2 (16%) among infertile men with significant impacts on sperm motility and morphology (P&lt; 0.000-0.002) respectively. This prospective study inKurdistan region (Erbil –Iraq) defined a significant impact of VNTR polymorphism of IL-1RN gene in the etiology of men infertility especially on sperm motility and morphology; particularly carriers of IL-1RN2 allelic variants

Phenotypic Expression and Outcomes in Individuals With Rare Genetic Variants of Hypertrophic Cardiomyopathy

BackgroundHypertrophic cardiomyopathy (HCM) is caused by rare variants in sarcomere-encoding genes, but little is known about the clinical significance of these variants in the general population. ObjectivesThe goal of this study was to compare lifetime outcomes and cardiovascular phenotypes according to the presence of rare variants in sarcomere-encoding genes among middle-aged adults. MethodsThis study analyzed whole exome sequencing and cardiac magnetic resonance imaging in UK Biobank participants stratified according to sarcomere-encoding variant status. ResultsThe prevalence of rare variants (allele frequency <0.00004) in HCM-associated sarcomere-encoding genes in 200,584 participants was 2.9% (n = 5,712; 1 in 35), and the prevalence of variants pathogenic or likely pathogenic for HCM (SARC-HCM-P/LP) was 0.25% (n = 493; 1 in 407). SARC-HCM-P/LP variants were associated with an increased risk of death or major adverse cardiac events compared with controls (hazard ratio: 1.69; 95% confidence interval [CI]: 1.38-2.07; P < 0.001), mainly due to heart failure endpoints (hazard ratio: 4.23; 95% CI: 3.07-5.83; P < 0.001). In 21,322 participants with both cardiac magnetic resonance imaging and whole exome sequencing, SARC-HCM-P/LP variants were associated with an asymmetric increase in left ventricular maximum wall thickness (10.9 ± 2.7 mm vs 9.4 ± 1.6 mm; P < 0.001), but hypertrophy (≥13 mm) was only present in 18.4% (n = 9 of 49; 95% CI: 9%-32%). SARC-HCM-P/LP variants were still associated with heart failure after adjustment for wall thickness (hazard ratio: 6.74; 95% CI: 2.43-18.7; P < 0.001). ConclusionsIn this population of middle-aged adults, SARC-HCM-P/LP variants have low aggregate penetrance for overt HCM but are associated with an increased risk of adverse cardiovascular outcomes and an attenuated cardiomyopathic phenotype. Although absolute event rates are low, identification of these variants may enhance risk stratification beyond familial disease.

Pharmacogenetic markers of chemotherapy toxicity in gastrointestinal tumors: a preliminary analysis

Aim. To assess the association between the carriage of minor allelic variants of 8 genes that encode key enzymes involved in the metabolism of anticancer drugs (DPYD, GSTP1, MTHFR, UGT1A1) and cell repair (XPC, ERCC1, TYMP, NQO1) and the severity of adverse drug events in patients with common gastrointestinal tumors. Tasks. To study the frequency of minor allelic variants of the DPYD, GSTP1, MTHFR, UGT1A1, XPC, ERCC1, TYMP, NQO1 genes; to assess the frequency and severity of adverse drug events of chemotherapy treatment in the study population. Materials and methods. For the period from October 2020 to April 2021, 56 patients (women 29, men 27) with verified malignant tumors of the gastrointestinal tract were included in a prospective clinical study as a part of the RSF grant No. 20-75-10158. The mean age was 62.311.4 years. Colon cancer was detected in 24 patients, tumors of the esophagus and stomach in 19 patients, tumors of pancreas and biliary tract in 13 patients. First-line palliative chemotherapy was given to 27 patients, adjuvant 19 patients, neoadjuvant 10 patients. All patients had not previously received cytotoxic or radiation treatment. Point nucleotide variants of genes DPYD, XPC, GSTP1, MTHFR, ERCC1, UGT1A1, TYMPS, NQO1 were determined by hybridization analysis on biological microchips. Differences in the tolerance of cytotoxic therapy (5-fluorouracil, platinum preparations, irinotecan) depending on the genotype were assessed using Fishers exact test. Results. The average number of chemotherapy courses received was 4.22.6 (112). There was a statistically significant difference in the tolerability of chemotherapy in patients with minor allelic variants of the GSTP1 rs1695 (p=0.03), ERCC1 rs11615 (p=0.01), and UGT1A1 rs8175347 (p=0.003) genes. Conclusion. The use of hybridization analysis on biological microchips to assess allelic variants responsible for the tolerability of cytotoxic therapy is reasonable and requires further prospective assessment.

Role of WNT4, HOXA10 and TWIST1 genes in the pathogenesis of external genital endometriosis and uterine leiomyoma

BACKGROUND: Uterine leiomyoma and endometriosis are the most common gynecological diseases in women of reproductive age. A number of data indicate that there are common elements in the pathogenesis of these hyperproliferative conditions. This article is devoted to comparative analysis of the role of the WNT4, HOXA10 and TWIST1 genes in the development of uterine leiomyoma and external genital endometriosis.&#x0D; AIM: The aim of this study was to evaluate the frequency of polymorphic variants rs7521902 (WNT4) and rs4721745 (TWIST1) in patients with uterine leiomyoma, external genital endometriosis and in the comparison group; to determine the frequency of rare allelic variants of the HOXA10 gene in patients with external genital endometriosis; and to study the expression of these genes in the endometrium in patients with uterine leiomyoma, EGE and in the comparison group.&#x0D; MATERIALS AND METHODS: The polymorphic variants of the WNT4 and TWIST1 genes were studied by real-time PCR in patients with external genital endometriosis, uterine leiomyoma and in the comparison group. In patients with EGE and women in the comparison group, the second exon of the HOXA10 gene was sequenced. Real-time PCR with reverse transcription analysis of the expression of the WNT4, TWIST1 and HOXA10 genes in endometrial samples from the patients of the study groups was performed.&#x0D; RESULTS: The frequencies of polymorphic variants rs7521902 (WNT4) and rs4721745 (TWIST1) in patients with uterine leiomyoma, external genital endometriosis and in the comparison group did not differ significantly. Minor alleles of the HOXA10 gene were not identified in patients with external genital endometriosis. Expression of the WNT4 gene in the endometrium of patients with external genital endometriosis was independent of menstrual cycle phase and was reduced by 1.9 times compared to the endometrium of women with uterine leiomyoma. Expression of the HOXA10 gene in the endometrium of endometriosis patients on days 20-23 of the menstrual cycle was significantly reduced compared to the women in the comparison group. Expression of the TWIST1 gene was not altered in the endometrium of patients with uterine leiomyoma and external genital endometriosis.&#x0D; CONCLUSIONS: We did not identify associations of the studied polymorphic variants of the WNT4 and TWIST genes and minor variants of the HOXA10 gene with uterine leiomyoma and external genital endometriosis. The expression of the WNT4 and HOXA10 genes is reduced in the endometrium in patients with external genital endometriosis, but not in women with uterine leiomyoma. Changes in expression patterns of the studied genes in the endometrium differ significantly in these two diseases.

Variant of TSHR is Not a Frequent Cause of Congenital Hypothyroidism in Chinese Han Patients.

PurposeTo screen variants of the thyroid stimulating hormone receptor (TSHR) gene among congenital hypothyroidism (CH) patients.Patients and MethodsWe conducted a genetic screening of the TSHR gene in a cohort of 125 Chinese CH patients. Variants were detected by customized targeted next-generation sequencing.ResultsA total of 11 TSHR missense heterozygous variants were identified in 14 CH patients. Six variants were in the transmembrane domains, four variants were in the leucine-rich repeats and one variant was located in the hinge region of the TSHR protein. p.F525S was the most prevalent variant with an allele frequency of 0.016, followed by p.R450H with an allele frequency of 0.012. The allele frequency of most variants was higher in our cohort than those of other populations.ConclusionThe prevalence of TSHR variants was 11.2%. Variant p.F525S was the most prevalent variant with an allele frequency of 0.016. The prevalence of TSHR variants was different from other populations.

Association between the Trp64Arg polymorphism of the ADRB3 gene and overactive bladder.

The β3 -adrenergic receptor (ADRB3) is very important in the regulation of the human detrusor muscle function. The well-known tryptophan64arginine polymorphism of the ADRB3 gene alters the response of the receptor to various stimuli, including adrenalin and noradrenalin, and may increase the susceptibility to develop overactive bladder (OAB). Therefore, this study was performed to determine whether ADRB3 Trp64Arg polymorphism is associated with the pathophysiology of OAB syndrome. The study group (n = 150) consists of 72 patients with OAB and 78 controls without OAB. Venous blood samples were taken from all participants to analyze the ADRB3 gene Trp64Arg polymorphism using polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) assay. We compared the distribution of Trp64Arg polymorphism and symptom severity in both OAB and non-OAB subjects using χ2 test and Mann-Whitney's U test, respectively. The frequency of the 64Arg variant (heterozygous plus homozygous) in OAB and non-OAB subjects was 15.3% and 14.1%, respectively. There was no statistically significant difference between the OAB and non-OAB groups in regard to the distribution frequency of ADRB3 Trp64Arg polymorphism. The total frequency (OAB + non-OAB, 76 women and 74 men) of the Arg64 variant allele was 5.9% and 10.8% in women and in men, respectively. Although the frequency of the Arg64 variant was nearly twofold higher in men compared to women, the difference was not statistically significant. These results demonstrated that the ADRB3 Trp64Arg polymorphism is not significantly associated with OAB syndrome in a sample of Turkish OAB patients.

GWAS-Top Polymorphisms Associated With Late-Onset Alzheimer Disease in Brazil: Pointing Out Possible New Culprits Among Non-Coding RNAs.

Several genome-wide association studies (GWAS) have been carried out with late-onset Alzheimer’s disease (LOAD), mainly in European and Asian populations. Different polymorphisms were associated, but several of them without a functional explanation. GWAS are fundamental for identifying loci associated with diseases, although they often do not point to causal polymorphisms. In this sense, functional investigations are a fundamental tool for discovering causality, although the failure of this validation does not necessarily indicate a non-causality. Furthermore, the allele frequency of associated genetic variants may vary widely between populations, requiring replication of these associations in other ethnicities. In this sense, our study sought to replicate in 150 AD patients and 114 elderly controls from the South Brazilian population 18 single-nucleotide polymorphisms (SNPs) associated with AD in European GWAS, with further functional investigation using bioinformatic tools for the associated SNPs. Of the 18 SNPs investigated, only four were associated in our population: rs769449 (APOE), rs10838725 (CELF1), rs6733839, and rs744373 (BIN1–CYP27C1). We identified 54 variants in linkage disequilibrium (LD) with the associated SNPs, most of which act as expression or splicing quantitative trait loci (eQTLs/sQTLs) in genes previously associated with AD or with a possible functional role in the disease, such as CELF1, MADD, MYBPC3, NR1H3, NUP160, SPI1, and TOMM40. Interestingly, eight of these variants are located within long non-coding RNA (lncRNA) genes that have not been previously investigated regarding AD. Some of these polymorphisms can result in changes in these lncRNAs’ secondary structures, leading to either loss or gain of microRNA (miRNA)-binding sites, deregulating downstream pathways. Our pioneering work not only replicated LOAD association with polymorphisms not yet associated in the Brazilian population but also identified six possible lncRNAs that may interfere in LOAD development. The results lead us to emphasize the importance of functional exploration of associations found in large-scale association studies in different populations to base personalized and inclusive medicine in the future.

Genomic Profiling Reveals Spatial Intra-Tumor Heterogeneity in Follicular Lymphoma

Background and Aims: Follicular lymphoma (FL) is an incurable B cell malignancy characterized by advanced stage disease and a heterogeneous clinical course. Despite recent genomic studies focused on profiling single FL biopsies over several time-points, little is known about the spatial heterogeneity as multi-site sampling is rarely conducted in lymphomas. However, in solid cancers, this approach has demonstrated profound spatial intra-tumor heterogeneity (ITH), impacting mechanisms of drug resistance and compromising precision-based strategies. As the majority of FL patients manifest disseminated tumor involvement, we sought to characterize the extent and clinical importance of spatial genetic heterogeneity in FL.Methods: Our study cohort comprised 9 FL patients (SP1-9) from which 22 synchronously removed spatially-separated samples from several tissue sources (lymph node (LN), bone marrow (BM), skin (SK), pleural effusion (PE), ascites (AS), spleen (SP)) were collected. For patients SP3 and SP4, both spatial and longitudinal samples at 2 time-points; at FL and histological transformation, were included. FL B-cells and normal T-cells were enriched by fluorescence activated cell sorting (FACS) in most cases. Each sample was subjected to whole exome sequencing and we defined somatic variants, copy number alterations (CNAs) and mutation signatures using established bioinformatic tools. We employed a statistical clustering model (mclust) for clonal density estimation and together with ultra-deep targeted sequencing, reconstructed each tumor's subclonal architecture.Results: Whilst spatially-separated FL tumors shared identical BCL2 - IGH breakpoints, we observed variable degrees of ITH. On average, 82% (range 50%-99%) of variants were shared between sites with two patterns of spatial ITH observed: high (SP1, SP8, SP9) and low (SP5, SP6, SP7). Copy number analyses showed a high level of concordance in most cases, except for SP4, SP7 and SP8. The overall distribution of known mutational signatures between spatially shared and discordant variants was different. Shared variants were predominantly enriched for mutational signature 1, representing age-related changes. In contrast signatures 6 and 24, both suggestive of defective DNA mismatch repair, were more pronounced in the spatially-discordant variants (χ2 test, p <0.0001), indicating that distinct mutagenic processes operate at different times during a tumor's evolution. Clonal architecture analyses revealed that some tumors comprised multiple competing subclones, with distinct clusters of mutations demonstrating differential expansions within spatially-separated sites, exemplified in SP2 (Figure 1). Importantly, for cases where spatial tumors were examined at two time-points, the degree of heterogeneity markedly increased with transformation. Detailed mutation analysis showed that apart from CREBBP mutations, that were clonally maintained throughout spatially separated biopsies, there were several instances of site-specific alterations in genes encoding proteins known to activate signaling pathways amenable to targeted therapies such as, TNFAIP3 (SP3 and SP9), TNFRSF14 (SP1), PIK3CD (SP4) and copy number loss of PTEN (SP8). In depth characterization of these variants using deep-sequencing techniques confirmed their discordant nature, suggesting ongoing genetic diversification driving evolution after widespread tumor dissemination.Conclusion: Collectively, our results demonstrate that spatial ITH is prevalent in FL. The existence of site-specific aberrations suggests a single biopsy insufficiently captures the full genomic complexity present and these spatial variations need to be considered in biomarker-led clinical studies.Figure 1: Dot plot demonstrating variants allele frequencies (VAFs) of all non-synonymous variants in SP2. Three distinct subclones circled in purple, orange and green can be inferred. The purple cluster includes ATP 6V1B2 and KMT2D variants classified as clonal in the BM and subclonal in the LN. The orange cluster includes different variants in KMT2D classified as subclonal in the BM and clonal in the LN. The green cluster includes variants in EZH2 and BCL2 that have a higher VAF in the LN compared to the BM. VAFs for selected variants in each of these putative subclones are shown in the horizontal bar graphs. [Display omitted] DisclosuresAuer:Janssen: Consultancy. Gribben:Kite: Honoraria; Karyopharm: Honoraria; Pharmacyclics: Honoraria; TG Therapeutics: Honoraria; Celgene: Honoraria; Acerta: Honoraria; Janssen: Honoraria; Genentech/Roche: Honoraria; Abbvie: Honoraria.

Granulomonocytic Progenitors (GMPs) Are Key Target Cells of Azacitidine in MDS and AML

Context: Azacitidine (AZA) prolongs overall survival (OS) but does not cure higher-risk MDS and AML (MDS/AML) patients (pts). Conversely, response to AZA in MDS/AML has been linked with a slow reduction in the clonal burden of bone marrow nucleated cells (BMNCs, Uy, Leukemia 2016) and reduced frequency of phenotypic Leukemic stem/progenitor cells (LSPCs; Craddock, Leukemia 2013). MDS progenitor quiescence could also explain resistance to AZA (Unnikrishnan, Cell Rep 2017). Whether the clonal composition and quiescence of LSCPs can predict long-term response to AZA and herald the relapse clone has never been investigated.Methods: We obtained bone marrow (BM) samples from higher-risk (IPSS int-2/high) or AML pts at onset of AZA, response evaluation, and relapse when available, and sorted LSCPs defined as GMPs (Lin-CD34+CD38+CD123+CD45RA+) or Lymphoid-primed multipotent progenitor (LMPPs, Lin-CD34+CD38-CD90-CD45RA+), as well as Hematopoietic Stem Cells (HSC, Lin-CD34+CD38-CD90+) when available, and performed sequencing of 57 genes recurrently mutated in MDS/AML (Agilent SureSelect, Illumina MiSeq) after whole genome amplification (WGA, Repli-G, Qiagen). We compared the resulting clonal composition to that of pre-AZA unamplified DNA from BM mononuclear cells (BMNCs). In an independent cohort of AML pts treated with AZA, we interrogated the cell cycle status (Ki67/Hoescht 33343) of GMPs and total blasts from thawed BMNCs collected prior to AZA.Results: WGA did not alter the Variant Allele Frequency (VAF) of single nucleotide variants (R²=0.96) or small insertions/deletions (R²=0.99), enabling the clonal interrogation of as few as 300 cells. We studied a cohort of 11 pts (5 MDS, 6 AML) with a median of 6 mutations treated with AZA (median 9 cycles), including 7 responders (CR in 4, PR in 1, marrow CR in 2). We compared clonal burden of BMNCs, HSCs (mean 0.1% of BMNCs), LMPPs (mean 0.6%) and GMPs (mean 9.7%) in 4 pts prior to AZA. Of the 3 immature fractions, the GMP fraction had the highest abundance among BMNCs and the highest clonal burden (median VAF 24.2% vs 10.0% in BMNCs, P=0.001), representing an ideal leukemic population for the monitoring of clonal evolution with AZA.We next analyzed the clonal composition of GMPs at the time of AZA response evaluation in all 11 pts, after a median of 6 cycles. GMPs represented 0.78% of BMNCs at evaluation. While there was no change in VAFs in BMNCs at evaluation compared to pre-AZA samples (p=0.48), a lower clonal burden in GMPs was seen in responders (n=7) compared to non-responders (n=4, P=0.002). This difference reflected clearance of secondary lesions (eg. genes involved in signaling) in responders (median VAF 1.8% vs 38.2% in non-responders, p=0.007), while ancestral lesions (eg. genes involved in DNA methylation) retained high clonality irrespective of response (p=0.2). BMNCs at relapse were obtained in 5/7 responders (CR n=4, mCR n=1) and compared to samples collected before AZA or after 6 cycles. In two pts who relapsed after 9 and 12 cycles, GMP clonal architecture added no information compared to BMNC in predicting the composition of the relapse clone. Conversely, in 3 pts relapsing after 15, 16 and 23 total cycles, GMP clonal composition predicted the relapse clone composition better than BMNC because of contamination of BMNCs by a passenger clone (n=1), or over-representation of a FLT3 + relapse clone in GMPs compared to BMNCs (n=2). In pt SLS008, the relapse NPM1 +/ FLT3 + clone was detected only in GMPs before AZA and never in BMNCs with a detection limit of 1% (Figure).We interrogated the cycling of GMPs compared to CD45dim/SSClow blasts in an independent cohort of 28 AML pts treated with AZA in first line (n=13) or in the relapsed/refractory setting (n=15). A lower proportion of quiescent (Ki67low) blasts predicted response (p=0.03) but had no impact on OS. Conversely, the proportion of quiescent GMP predicted progressive disease (p=0.04) and was also a prognostic factor for OS, with a median OS of 15.1 months in pts with <60% quiescent GMPs vs 4.2 months in those with ≥60% quiescent GMPs (p=0.04).Conclusion: Our pilot study shows that clearance of secondary lesions in GMPs is associated with response to AZA and that GMP quiescence can predict long-term outcome of MDS/AML pts treated with AZA. Our results suggest that GMPs constitute key target cells for AZA in MDS/AML and warrant prospective validation of GMP-based biomarkers for hypomethylating agents. [Display omitted] DisclosuresRenneville:CELGENE: Research Funding. Pimanda:Celgene: Research Funding. Fenaux:Celgene: Honoraria, Research Funding; Janssen: Honoraria, Research Funding; Janssen: Honoraria, Research Funding; Celgene: Honoraria, Research Funding; Novartis: Honoraria, Research Funding; Novartis: Honoraria, Research Funding; Amgen: Honoraria, Research Funding; Astex: Honoraria, Research Funding; Astex: Honoraria, Research Funding; Amgen: Honoraria, Research Funding. Itzykson:Novartis: Research Funding; Janssen: Research Funding.

Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus

Understanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics. Based on genome-wide Fst (pairwise fixation index) and Vst analyses, which compared the variance in allele frequencies of single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs), respectively, we found a high level of genetic differentiation between two populations. CNV patterns revealed population-specific expansions and contractions. Interestingly, we identified a ~20 kbp genomic island of high divergence with a strong sign of positive selection. This region contains a melanin-biosynthetic polyketide synthase gene cluster linked to six additional genes likely involved in biosynthesis, membrane trafficking, regulation, and localization of melanin. Differences in growth yield and melanin biosynthesis between the two populations grown under 2% NaCl stress suggested that this genomic island contributes to the observed differences in melanin accumulation. Our findings provide a better understanding of the genetic and evolutionary mechanisms underlying the adaptation to saline conditions of the L. rhizohalophila–S. salsa symbiosis.

Genome-wide association study on blood pressure traits in the Iranian population suggests ZBED9 as a new locus for hypertension

High blood pressure is the heritable risk factor for cardiovascular and kidney diseases. Genome-wide association studies(GWAS) on blood pressure traits increase our understanding of its underlying genetic basis. However, a large proportion of GWAS was conducted in Europeans, and some roadblocks deprive other populations to benefit from their results. Iranians population with a high degree of genomic specificity has not been represented in international databases to date, so to fill the gap, we explored the effects of 652,919 genomic variants on Systolic Blood Pressure (SBP), Diastolic Blood Pressure (DBP), and Hypertension (HTN) in 7694 Iranian adults aged 18 and over from Tehran Cardiometabolic Genetic Study (TCGS). We identified consistent signals on ZBED9 associated with HTN in the genome-wide borderline threshold after adjusting for different sets of environmental predictors. Moreover, strong signals on ABHD17C and suggestive signals on FBN1 were detected for DBP and SBP, respectively, while these signals were not consistent in different GWA analysis. Our finding on ZBED9 was confirmed for all BP traits by linkage analysis in an independent sample. We found significant associations with similar direction of effects and allele frequency of genetic variants on ZBED9 with DBP (genome-wide threshold) and HTN (nominal threshold) in GWAS summary data of UK Biobank. Although there is no strong evidence to support the function of ZBED9 in blood pressure regulation, it provides new insight into the pleiotropic effects of hypertension and other cardiovascular diseases.

Influence of APOE locus on poor prognosis of COVID-19

The COVID-19 pandemic has infected over 25 million of people worldwide, 5% of whom evolved to death and, among of the active cases, more than 60 thousand are classified as critical or severe. Recent studies revealed that ApoE, a protein encoded by APOE gene, may increase the risk of severe COVID-19 cases. ApoE has been involved with prevention of tissue damage and promotion of adaptative immune response in the lungs. This study investigated frequencies distribution of alleles that alter the ApoE expression in lung tissues to trace a profile of these variants and associate them to COVID-19 clinical outcomes. Data about APOE expression levels was obtained from the Genotype-Tissue Expression Project and the allele frequencies of APOE variants was acquired from the populations included in the phase 3 release of the 1000 Genomes Project. A total of 128 variants showed a significant impact on the APOE expression in lung tissues (p < 0.0001). Linkage Disequilibrium analysis revealed that 98 variants were closely grouped into seven distinct haplotype blocks, of which six were composed of variants that significantly decrease APOE gene expression in the lungs. Most of the haplotypes with higher impact on APOE expression showed greater frequencies in Europeans and lower in Africans, which implies that European populations might be more susceptible to SARS-CoV-2 infection. The present study indicates a potential genetic contribution of APOE expression-modifying variants in modulating the prognosis of COVID-19.

Analysis of Genomic DNA from Medieval Plague Victims Suggests Long-Term Effect of Yersinia pestis on Human Immunity Genes.

Pathogens and associated outbreaks of infectious disease exert selective pressure on human populations, and any changes in allele frequencies that result may be especially evident for genes involved in immunity. In this regard, the 1346-1353 Yersinia pestis-caused Black Death pandemic, with continued plague outbreaks spanning several hundred years, is one of the most devastating recorded in human history. To investigate the potential impact of Y. pestis on human immunity genes, we extracted DNA from 36 plague victims buried in a mass grave in Ellwangen, Germany in the 16th century. We targeted 488 immune-related genes, including HLA, using a novel in-solution hybridization capture approach. In comparison with 50 modern native inhabitants of Ellwangen, we find differences in allele frequencies for variants of the innate immunity proteins Ficolin-2 and NLRP14 at sites involved in determining specificity. We also observed that HLA-DRB1*13 is more than twice as frequent in the modern population, whereas HLA-B alleles encoding an isoleucine at position 80 (I-80+), HLA C*06:02 and HLA-DPB1 alleles encoding histidine at position 9 are half as frequent in the modern population. Simulations show that natural selection has likely driven these allele frequency changes. Thus, our data suggest that allele frequencies of HLA genes involved in innate and adaptive immunity responsible for extracellular and intracellular responses to pathogenic bacteria, such as Y. pestis, could have been affected by the historical epidemics that occurred in Europe.

The influence of RS738409 I148M polymorphism of patatin-like phospholipase domain containing 3 gene on the susceptibility of non-alcoholic fatty liver disease

We aimed to elucidate the frequency of polymorphic genotypes and alleles of patatin-like phospholipase domain containing 3 rs738409 polymorphism and its possible associations with non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis in a cohort from Turkey.We enrolled 200 patients diagnosed with NAFLD and genotyped for rs738409 I148M polymorphism by real-time polymerase chain reaction, particularly by melting curve analysis. SPSS analysis software was used for statistical significance. Continuous variable values were expressed as mean ± standard deviation. Significant statistical level was chosen as p = 0.05.Our results demonstrate in a cohort from Turkey that rs738409 C > G polymorphism (I148M) of patatin-like phospholipase domain containing 3 gene is significantly able to affect individuals to have NAFLD in unadjusted regression model.Consistent with the previous studies in other populations, our study group showed a significantly higher risk of having NAFLD in unadjusted regression model but not in the adjusted model indicating that non-genetic factors such as age and sex may be responsible for the association. However, independent studies need to validate our findings with a larger group of NAFLD patients, as well as in different ethnic cohorts.

Familial pseudohyperkalemia induces significantly higher levels of extracellular potassium in early storage of red cell concentrates without affecting other standard measures of quality: A case control and allele frequency study

Familial pseudohyperkalemia (FP) is characterized by an increased rate of potassium leakage in refrigerated red cells and is associated with the minor allele of the single nucleotide polymorphism rs148211042 (R723Q) in the ABCB6 gene. The study aims were to obtain the minor allele frequencies of ABCB6 variants and to measure supernatant potassium accumulation, and other red cell storage parameters, in red cell concentrates (RCC) from carriers of variant rs148211042 under standard blood bank conditions. Whole blood units were collected from 6 FP individuals and 11 controls and processed into RCC in additive solution. RCC were sampled and tested over cold storage for full blood count, extracellular potassium, glucose, lactate, microvesicle release, deformability, hemolysis, pH, adenosine triphosphate, and 2,3-diphosphoglycerate. Screening of genotyped cohorts identified that variant rs148211042 is present in 1 in 394 British citizens of European ancestry. FP RCC had significantly higher supernatant potassium at all time points from day 3 onwards (p < .001) and higher mean cell volume (p=.032) than controls. The initial rate of potassium release was higher in FP RCC; supernatant potassium reached 46.0 (23.8-57.6) mmol/L (mean [range]) by day 5, increasing to 68.9 (58.8-73.7) mmol/L by day 35. Other quality parameters were not significantly different between FP RCC and controls. These data suggest that if a blood donor has FP, reducing the RCC shelf-life to 5 days may be insufficient to reduce the risk of hyperkalemia in clinical scenarios such as neonatal large volume transfusion.