Sequence Variants Of Significance Research Articles

Use of dry-matter intake recorded at multiple time periods during lactation increases the accuracy of genomic prediction for dry-matter intake and residual feed intake in dairy cattle

Context Feed is the largest expense on a dairy farm, therefore improving feed efficiency is important. Recording dry-matter intake (DMI) is a prerequisite for calculating feed efficiency. Genetic variation of feed intake and feed efficiency varies across lactation stages and parities. DMI is an expensive and difficult-to-measure trait. This raises the question of which time periods during lactation would be most appropriate to measure DMI. Aims The aim was to evaluate whether sequence variants selected from genome-wide association studies (GWAS) for DMI recorded at multiple lactation time periods and parities would increase the accuracy of genomic estimated breeding values (GEBVs) for DMI and residual feed intake (RFI). Methods Data of 2274 overseas lactating cows were used for the GWAS to select sequence variants. GWAS was performed using the average of the DMI phenotypes in a 30-day window of six different time periods across the lactation. The most significant sequence variants were selected from the GWAS at each time period for either first or later parities. GEBVs for DMI and RFI in Australian lactating cows were estimated using BayesRC with 50 k single nucleotide polymorphisms (SNPs) and selected GWAS sequence variants. Key results There were differences in DMI genomic correlations and heritabilities between first and later parities and within parity across lactation time periods. Compared with using 50 k single-nucleotide polymorphisms (SNPs) only, the accuracy of DMI GEBVs increased by up to 11% by using the 50 k SNPs plus the selected sequence variants. Compared with DMI, the increase in accuracy for RFI was lower (by 6%) likely because the sequence variants were selected from GWAS for DMI not RFI. The accuracies for DMI and RFI GEBVs were highest by using selected sequence variants from the DMI GWAS in the mid- to late-lactation periods in later parity. Conclusions Our results showed that DMI phenotypes in late lactation time periods could capture more genetic variation and increase genomic prediction accuracy through the use of custom genotype panels in genomic selection. Implications Collecting DMI at the optimal time period(s) of lactation may help develop more accurate and cost-effective breeding values for feed efficiency in dairy cattle.

A rare case of hairy cell leukemia variant with ATM nonsense mutation and ATM deletion, resulting in complete loss of function

Abstract Introduction/Objective Hairy cell leukemia variant (HCL-v) is a rare B cell lymphoproliferative disorder. Although HCL- v shares some overlapping features with classic HCL, it lacks the characteristic immune-morphology and pathogenic BRAF V600E mutation seen in classic HCL and recognized as a distinct entity in the 2017 WHO classification. Approximately half of HCL-v harbors MAPK2 mutation and one third has TP53 mutation. Cytogenetic abnormalities include gain of chromosome 5, loss of chromosome 7q, and deletion of 17p13/TP53 and 11q/22 ATM gene Methods/Case Report We report a case of HCL-v with total loss of ATM gene function. A 71-year-old male with splenomegaly presented with an outside diagnosis of splenic marginal zone lymphoma and underwent splenectomy. Flow cytometry on spleen demonstrated mature clonal B lymphoid cells and was positive for CD11c and CD103. However, unlike classical HCL, it was CD25 negative, which supports the diagnosis of HCL-v. Sections of spleen revealed most of the red pulp replaced by hairy cell leukemic infiltrate with minimal preservation of the normal lymphoid stroma. Peripheral blood smear showed atypical lymphocytosis with prominent nucleoli but most lacking circumferential shaggy contours, seen in classic HCL. Cytogenetic analysis identified a deletion in chromosome 11(q13q23), which deletes the ATM gene. NGS analysis demonstrated a nonsense variant in ATM (p. E888*). No significant sequence variants were identified in BRAF, MAP2K1 or TP53. This is the first case report of HCL-v with a deletion as well as a non-sense mutation in the ATM gene. ATM gene belongs to the PI3/PI4-kinase family, and is an important cell cycle checkpoint kinase that phosphorylates downstream proteins, including TP53, BRCA1 etc. Although detection of the ATM has therapeutic application for prostate cancer patient for poly [ADP]-ribose polymerase inhibitor treatment, the significance of loss of ATM function in hairy cell leukemia variant is unknown. Results (if a Case Study enter NA) N/A Conclusion In conclusion, our case demonstrates that molecular test in hairy cell leukemia variant can be helpful for confirming the diagnosis as well as providing predictive information for potential target therapy. In our case, lack of MAP2K1 mutation precludes the patient for targeted therapy. In addition, the finding of novel mutation might help to understand the molecular pathogenesis in this rare entity.

Eleven genomic loci affect plasma levels of chronic inflammation marker soluble urokinase-type plasminogen activator receptor

Soluble urokinase-type plasminogen activator receptor (suPAR) is a chronic inflammation marker associated with the development of a range of diseases, including cancer and cardiovascular disease. The genetics of suPAR remain unexplored but may shed light on the biology of the marker and its connection to outcomes. We report a heritability estimate of 60% for the variation in suPAR and performed a genome-wide association meta-analysis on suPAR levels measured in Iceland (N = 35,559) and in Denmark (N = 12,177). We identified 13 independently genome-wide significant sequence variants associated with suPAR across 11 distinct loci. Associated variants were found in and around genes encoding uPAR (PLAUR), its ligand uPA (PLAU), the kidney-disease-associated gene PLA2R1 as well as genes with relations to glycosylation, glycoprotein biosynthesis, and the immune response. These findings provide new insight into the causes of variation in suPAR plasma levels, which may clarify suPAR’s potential role in associated diseases, as well as the underlying mechanisms that give suPAR its prognostic value as a unique marker of chronic inflammation.

Patients with coronary heart disease, dilated cardiomyopathy and idiopathic ventricular tachycardia share overlapping patterns of pathogenic variation in cardiac risk genes

BackgroundVentricular tachycardia (VT) is a major cause of sudden cardiac death (SCD). Clinical investigations can sometimes fail to identify the underlying cause of VT and the event is classified as idiopathic (iVT). VT contributes significantly to the morbidity and mortality in patients with coronary artery disease (CAD) and dilated cardiomyopathy (DCM). Since mutations in arrhythmia-associated genes frequently determine arrhythmia susceptibility screening for disease-predisposing variants could improve VT diagnostics and prevent SCD in patients.MethodsNinety-two patients diagnosed with coronary heart disease (CHD), DCM, or iVT were included in our study. We evaluated genetic profiles and variants in known cardiac risk genes by targeted next generation sequencing (NGS) using a newly designed custom panel of 96 genes. We hypothesized that shared morphological and phenotypical features among these subgroups may have an overlapping molecular base. To our knowledge, this was the first study of the deep sequencing of 96 targeted cardiac genes in Kazakhstan. The clinical significance of the sequence variants was interpreted according to the guidelines developed by the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) in 2015. The ClinVar and Varsome databases were used to determine the variant classifications.ResultsTargeted sequencing and stepwise filtering of the annotated variants identified a total of 307 unique variants in 74 genes, totally 456 variants in the overall study group. We found 168 mutations listed in the Human Genome Mutation Database (HGMD) and another 256 rare/unique variants with elevated pathogenic potential. There was a predominance of high- to intermediate pathogenicity variants in LAMA2, MYBPC3, MYH6, KCNQ1, GAA, and DSG2 in CHD VT patients. Similar frequencies were observed in DCM VT, and iVT patients, pointing to a common molecular disease association. TTN, GAA, LAMA2, and MYBPC3 contained the most variants in the three subgroups which confirm the impact of these genes in the complex pathogenesis of cardiomyopathies and VT. The classification of 307 variants according to ACMG guidelines showed that nine (2.9%) variants could be classified as pathogenic, nine (2.9%) were likely pathogenic, 98 (31.9%) were of uncertain significance, 73 (23.8%) were likely benign, and 118 (38.4%) were benign. CHD VT patients carry rare genetic variants with increased pathogenic potential at a comparable frequency to DCM VT and iVT patients in genes related to sarcomere function, nuclear function, ion flux, and metabolism.ConclusionsIn this study we showed that in patients with VT secondary to coronary artery disease, DCM, or idiopathic etiology multiple rare mutations and clinically significant sequence variants in classic cardiac risk genes associated with cardiac channelopathies and cardiomyopathies were found in a similar pattern and at a comparable frequency.

NextGen nuclear DNA sequencing in cyclic vomiting syndrome reveals a significant association with the stress-induced calcium channel (RYR2).

Cyclic vomiting syndrome (CVS) is a common, frequently disabling, 'functional' condition characterized by recurring, stereotypical attacks of intense nausea, vomiting, and lethargy, with the essential absence of these symptoms between episodes. Although the pathogenesis of CVS is yet unexplained, evidence has accumulated which suggest pathogenic roles for stress-related, autonomic, neuroendocrine, and mitochondrial factors. The objective of this pilot study was to elucidate mechanism(s) by identifying genes involved in the presumed multifactorial pathogenesis of CVS. In this pilot study, DNA from 75 unrelated CVS cases and 60 healthy controls were assayed by Courtagen Life Science's next-generation sequencing platform (nucSEEK(™) ), including over 1100 nuclear-encoded genes involved with mitochondria, metabolism, or ion channels. Significant sequence variants were defined as evolutionary conservation at least to Xenopus (frog) per the UCSC Genome Browser. The RYR2 gene, encoding a stress-induced calcium channel present in many neurons, was the only gene demonstrating a statistically significant difference in the proportion of conserved sequence variants among the groups (18/75 CVS, 24%, vs 3/60 controls, 5%; p = 0.0018, OR = 6.0, 95% CI = 1.7-22). We propose a mechanism in which RYR2 sequence variants result in aberrant stress-induced calcium release into the mitochondria of autonomic neurons, resulting in an increased risk to develop autonomic/functional disease such as CVS, and related conditions such as migraine and gut dysmotility. This model incorporates the existing hypotheses regarding CVS pathogenesis into a cohesive mechanism, and might have treatment implications.

Abstract 781: Sequence variations in TP53 3′UTR affect p53 protein expression and function and patient survival in diffuse large B-cell lymphoma.

Abstract Diffuse large B-cell lymphoma (DLBCL) is the most common form of non-Hodgkin lymphoma and represents ∼80% of all aggressive lymphomas. DLBCL can be classified into two major subtypes by gene expression profiling. The germinal center B-cell (GCB) subtype possesses gene expression patterns that resemble non-malignant B-cells that have entered the germinal center. The activated B-cell (ABC) subtype expresses many genes that are regulated by NF-κB activation. This agrees with the concept of cell of origin (COO) that subtypes of DLBCL originate from various stages of B-cell differentiation. The TP53 tumor suppressor gene encodes a transcription factor that acts as a sensor of cellular stressors and responds by upregulating various target genes to promote cell cycle arrest, initiate apoptosis, inhibit angiogenesis, and initiate DNA repair. Because approximately 50% of all cancers possess wild-type TP53 coding sequence (CDS), we reasoned that mutations outside the CDS may also promote tumorigenesis and help explain how cancers with wild-type p53 escape p53-regulated pathways. In this study, we determined the nucleotide sequence of the TP53 gene, including the 5′UTR and 3′UTR, in 244 de novo DLBCL tumors with a hypothesis that the TP53 3′UTR is altered in cancer. We sought to evaluate the prognostic importance and functional significance of sequence variation in the TP53 3′UTR in combination with CDS mutation and COO. We found a large number of single nucleotide variants (SNV) in the TP53 3′UTR with the majority of them previously unreported. There was no difference in overall survival and progression-free survival between patients with SNVs and those without. Similarly, no significant difference was found in COO subgroups between patients with and without SNVs. However, when patients are divided into two sets according to their TP53 CDS status, we found that patients carrying a wild-type TP53 CDS and a 3′UTR variant have a better 5-year overall survival than patients carrying a wild-type CDS and a native 3′UTR. In contrast, for patients with mutant TP53 CDS, 3′UTR variation predicts poor survival. Most of the unreported 3′UTR SNVs are located in the sites that are complementary to seed sequences of microRNA that are predicted or experimentally validated to target TP53. We found that three SNVs disrupting the seed match between miR-125b and the TP53 3′UTR affect p53 regulation by this microRNA. Additionally, an annotated SNP (rs78378222) in the TP53 polyadenylation signal (PAS) was uncovered in 3 of 244 patient samples (1.29%). Results from Northern and Western blots indicated that the presence of this SNP significantly affects p53 mRNA production and consequently results in downregulation of p53 protein. Using TUNEL assays, we demonstrate that cells harboring the TP53 PAS mutation exhibit reduced apoptosis upon UV treatment when compared to wild-type control cells. Citation Format: Michael Gordon, Ken H. Young, Yong Li. Sequence variations in TP53 3′UTR affect p53 protein expression and function and patient survival in diffuse large B-cell lymphoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 781. doi:10.1158/1538-7445.AM2013-781 Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.

Sequence analysis of the 5' untranslated region in isolates of at least four genotypes of hepatitis C virus in The Netherlands.

The RNAs of hepatitis C virus (HCV) isolates from 62 patients with chronic HCV infection were analyzed by direct sequencing of the 5' untranslated region. Two important sequence motifs were recognized: one between positions -170 and -155 and the other between positions -132 and -117. These motifs are partly complementary. All three previously published genotypes were observed; 34 (55%) isolates were classified as type 1 (including prototype [from the United States] and HCV-BK [from Japan] sequences), 11 (18%) were classified as type 2 (including HC-J6 and HC-J8), and 12 (19%) were classified as type 3 (including EB1); one patient was infected with genotypes 1 and 2. Four (6%) isolates showed aberrant sequences and were therefore provisionally classified as genotype 4. These results indicate the significance of sequence variation among the 5' untranslated regions of different HCV genotypes and indicate that this region could possibly be used for consistent genotyping of HCV isolates.