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Brain Tumor Pathology Jan 2023Pleomorphic xanthoastrocytoma (PXA) is a rare tumor ranging from World Health Organization (WHO) grades 2-3 and can potentially recur and metastasize throughout the...
Pleomorphic xanthoastrocytoma (PXA) is a rare tumor ranging from World Health Organization (WHO) grades 2-3 and can potentially recur and metastasize throughout the central nervous system (CNS). Cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) deletion is a frequent genomic alteration of PXA. Methylthioadenosine phosphorylase (MTAP) immunohistochemistry is a promising surrogate marker for CDKN2A homozygous deletion in different cancers but has not been examined in PXA. Therefore, we performed CDKN2A fluorescence in situ hybridization and MTAP immunohistochemistry on specimens from 23 patients with CNS WHO grades 2 (n = 10) and 3 (n = 13) PXAs, including specimens from primary and recurrent tumors, and determined whether MTAP immunohistochemistry correlated with CDKN2A homozygous deletion and clinicopathological features. CDKN2A homozygous deletion was detected in 30% (3/10) and 76.9% (10/13) of CNS WHO grades 2 and 3 PXAs, respectively. In addition, MTAP loss was inconsistent with CDKN2A homozygous deletion (sensitivity = 86.7%, specificity = 100%). Furthermore, CDKN2A homozygous deletion was correlated with WHO grade (p = 0.026) and the Ki-67 labeling index (p = 0.037). Therefore, MTAP immunostaining can be a suitable surrogate marker for CDKN2A homozygous deletions in PXAs, and CDKN2A homozygous deletions may be an important prognostic factor for PXAs.
Topics: Humans; Homozygote; In Situ Hybridization, Fluorescence; Gene Deletion; Sequence Deletion; Cyclin-Dependent Kinase Inhibitor p16; Astrocytoma
PubMed: 36550382
DOI: 10.1007/s10014-022-00447-0 -
Molecular Medicine Reports Jan 2020Wilson disease (WD) is a rare autosomal recessive genetic disorder that causes abnormal copper metabolism, resulting in pathological accumulation of copper in the liver,...
A novel gross deletion and breakpoint junction sequence analysis of ATP7B in a Chinese family with Wilson disease using next‑generation sequencing and Sanger sequencing.
Wilson disease (WD) is a rare autosomal recessive genetic disorder that causes abnormal copper metabolism, resulting in pathological accumulation of copper in the liver, brain and other organs. Mutations in the ATPase copper transporter 7B (ATP7B) gene, which encodes a membrane P‑type adenosine triphosphatase, have been identified as being responsible for WD. The present study analyzed clinical data and collected DNA samples from a pediatric patient with WD and her healthy parents. Mutation screening for ATP7B was performed using direct sequencing, multiplex ligation‑dependent probe amplification(MLPA), next‑generation sequencing (NGS) and Sanger sequencing of the breakpoint junction sequence. The patient (age, 2.7 years) presented with early‑onset hepatic disease. The present study identified compound heterozygous mutations of ATP7B, including a heterozygous mutation (p.Arg1,041Trp) and a novel heterozygous gross deletion of a 57,771 bp fragment (chr13: 52490972‑52548742) (GRCh37) from partial exon2‑ exon21 to external ATP7B sequence (15.833bp) in the patient. Analysis of the family members of the patient showed that the missense mutation and the gross deletion mutation were inherited from her mother and father, respectively. Microhomology and inverted repeat sequences, which may mediate the deletion mutation, were identified through sequence analysis on both sides of the breakpoints of this deletion. The present study provided additional information on the genotypic spectrum of the ATP7B gene, particularly with regard to early onset hepatic disease, as observed in the present patient with WD. The identification of the precise breakpoint junction sequence warrants further investigation of DNA break and recombination mechanisms. In detecting precise deletions, the NGS associated with Sanger sequencing of breakpoint junction sequence have been found to have more advantages than MLPA.
Topics: Adult; Age of Onset; Child, Preschool; Copper; Copper-Transporting ATPases; Female; Genetic Predisposition to Disease; Hepatolenticular Degeneration; Heterozygote; High-Throughput Nucleotide Sequencing; Humans; Male; Mutation; Pedigree; Sequence Deletion
PubMed: 31746411
DOI: 10.3892/mmr.2019.10830 -
Animal Biotechnology Apr 2023A-kinase anchoring protein 13 (AKAP13) is one of the AKAP protein family members, which is correlated with estrogen receptors (ERs) and progesterone receptor (PR)...
A-kinase anchoring protein 13 (AKAP13) is one of the AKAP protein family members, which is correlated with estrogen receptors (ERs) and progesterone receptor (PR) activity. Consequently, the gene is considered to be one of the candidate genes for regulating female fertility. Hence, the objectives of this study were to discover the potential insertion/deletion (indel) variants within the gene and evaluate their associations with litter size of Shaanbei white cashmere goats (SBWC) to screen candidate genes for the molecular marker-assisted selection (MAS). Ultimately, we found the 16-bp deletion of gene which displayed three genotypes (II, ID and DD). However, it was not confirmed to Hardy-Weinberg equilibrium (HWE) in the tested population. Statistical analysis demonstrated that this 16-bp indel locus was significantly associated with litter size in goats ( < 0.05), in which the ID genotype was a key genotype for increasing litter size in goats. Besides, independent tests between different genotypes and litter size showed that high-prolific groups had higher frequency of the 'D' allele ( < 0.05). Briefly, gene is a candidate gene for improving fertility, and its 16-bp indel locus can be used as a valid DNA molecular marker for the MAS in goat breeding.
Topics: Pregnancy; Female; Animals; Litter Size; Goats; Genotype; Fertility; Sequence Deletion
PubMed: 34431749
DOI: 10.1080/10495398.2021.1968418 -
International Journal of Molecular... Mar 2023The UCD 67-385 genome harbors a 7873 bp cluster containing , and , encoding 2-desmethy-4-deoxygadusol synthase, O-methyl transferase, and ATP-grasp ligase,...
The UCD 67-385 genome harbors a 7873 bp cluster containing , and , encoding 2-desmethy-4-deoxygadusol synthase, O-methyl transferase, and ATP-grasp ligase, respectively, of the mycosporine glutaminol (MG) biosynthesis pathway. Homozygous deletion mutants of the entire cluster, single-gene mutants, and the Δ;Δ and Δ;Δ double-gene mutants did not produce mycosporines. However, Δ accumulated the intermediate 4-deoxygadusol. Heterologous expression of the and or , and cDNAs in led to 4-deoxygadusol or MG production, respectively. Genetic integration of the complete cluster into the genome of the non-mycosporine-producing CBS 6938 wild-type strain resulted in a transgenic strain (CBS 6938_MYC) that produced MG and mycosporine glutaminol glucoside. These results indicate the function of , and in the mycosporine biosynthesis pathway. The transcription factor gene mutants Δ, Δcyc8, and Δ showed upregulation, Δ and Δ showed downregulation, and Δ and Δ showed no effect on mycosporinogenesis in glucose-containing medium. Finally, comparative analysis of the cluster sequences in several strains and the four newly described species of the genus showed the phylogenetic relationship of the strains and their differentiation from the other species of the genus .
Topics: Phylogeny; Homozygote; Sequence Deletion; Basidiomycota; Saccharomyces cerevisiae
PubMed: 36983003
DOI: 10.3390/ijms24065930 -
The Indian Journal of Medical Research Sep 2019Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder and is caused mainly by deletion, duplication and point mutations in the DMD gene. Diagnosis of DMD...
BACKGROUND & OBJECTIVES
Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder and is caused mainly by deletion, duplication and point mutations in the DMD gene. Diagnosis of DMD has been a challenge as the mutations in the.
DMD
gene are heterogeneous and require more than one diagnostic strategy for the validation of the mutation. This study was planned to evaluate the targeted next-generation sequencing (NGS) as a single platform to detect all types of mutations in the DMD gene, thereby reducing the time and costs compared to conventional sequential testing and also provide precise genetic information for emerging gene therapies.
METHODS
The study included 20 unrelated families and 22 patients from an Indian population who were screened for DMD based on phenotypes such as scoliosis, toe walking and loss of ambulation. Peripheral blood DNA was isolated and subjected to multiplex ligation-dependent probe amplification (MLPA) and targeted NGS of the DMD gene to identify the nature of the mutation.
RESULTS
In the study patients, 77 per cent of large deletion mutations and 23 per cent single-nucleotide variations (SNVs) were identified. Novel mutations were also identified along with reported deletions, point mutations and partial deletions within the exon of the DMD gene.
INTERPRETATION & CONCLUSIONS
Our findings showed the importance of NGS in the routine diagnostic practice in the identification of DMD mutations over sequential testing. It may be used as a single-point diagnostic strategy irrespective of the mutation type, thereby reducing the turnaround time and cost for multiple diagnostic tests such as MLPA and Sanger sequencing. Though MLPA is a sensitive technique and is the first line of a diagnostic test, the targeted NGS of the DMD gene may have an advantage of having a single diagnostic test. A study on a larger number of patients is needed to highlight NGS as a single, comprehensive platform for the diagnosis of DMD.
Topics: Adolescent; Child; Child, Preschool; DNA Mutational Analysis; Dystrophin; Exons; Gene Deletion; Genome, Human; High-Throughput Nucleotide Sequencing; Humans; India; Male; Multiplex Polymerase Chain Reaction; Muscular Dystrophy, Duchenne; Mutation; Phenotype; Point Mutation; Polymorphism, Single Nucleotide; Sequence Deletion
PubMed: 31719299
DOI: 10.4103/ijmr.IJMR_290_18 -
Journal of Virology Aug 2020Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus first identified in December 2019. Notable features that make SARS-CoV-2 distinct...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus first identified in December 2019. Notable features that make SARS-CoV-2 distinct from most other previously identified betacoronaviruses include a receptor binding domain and a unique insertion of 12 nucleotides or 4 amino acids (PRRA) at the S1/S2 boundary. In this study, we identified two deletion variants of SARS-CoV-2 that either directly affect the polybasic cleavage site itself (NSPRRAR) or a flanking sequence (QTQTN). These deletions were verified by multiple sequencing methods. results showed that the deletion of NSPRRAR likely does not affect virus replication in Vero and Vero-E6 cells; however, the deletion of QTQTN may restrict late-phase viral replication. The deletion of QTQTN was detected in 3 of 68 clinical samples and 12 of 24 -isolated viruses, while the deletion of NSPRRAR was identified in 3 -isolated viruses. Our data indicate that (i) there may be distinct selection pressures on SARS-CoV-2 replication or infection and ; (ii) an efficient mechanism for deleting this region from the viral genome may exist, given that the deletion variant is commonly detected after two rounds of cell passage; and (iii) the PRRA insertion, which is unique to SARS-CoV-2, is not fixed during virus replication These findings provide information to aid further investigation of SARS-CoV-2 infection mechanisms and a better understanding of the NSPRRAR deletion variant observed here. The spike protein determines the infectivity and host range of coronaviruses. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has two unique features in its spike protein, the receptor binding domain and an insertion of 12 nucleotides at the S1/S2 boundary resulting in a furin-like cleavage site. Here, we identified two deletion variants of SARS-CoV-2 that either directly affect the furin-like cleavage site itself (NSPRRAR) or a flanking sequence (QTQTN), and we investigated these deletions in cell isolates and clinical samples. The absence of the polybasic cleavage site in SARS-CoV-2 did not affect virus replication in Vero or Vero-E6 cells. Our data indicate the PRRAR sequence and the flanking QTQTN sequence are not fixed thus, there appears to be distinct selection pressures on SARS-CoV-2 sequences and Further investigation of the mechanism of generating these deletion variants and their infectivity in different animal models would improve our understanding of the origin and evolution of this virus.
Topics: Amino Acid Sequence; Animals; Base Sequence; Betacoronavirus; COVID-19; Cell Line; Chlorocebus aethiops; Coronavirus Infections; Furin; Genome, Viral; Host Specificity; Kinetics; Models, Molecular; Pandemics; Pneumonia, Viral; Protein Conformation; SARS-CoV-2; Sequence Analysis; Sequence Deletion; Spike Glycoprotein, Coronavirus; Vero Cells; Virus Replication
PubMed: 32571797
DOI: 10.1128/JVI.00790-20 -
Communications Biology Jan 2021Leishmania infantum causes visceral leishmaniasis, a deadly vector-borne disease introduced to the Americas during the colonial era. This non-native trypanosomatid...
Leishmania infantum causes visceral leishmaniasis, a deadly vector-borne disease introduced to the Americas during the colonial era. This non-native trypanosomatid parasite has since established widespread transmission cycles using alternative vectors, and human infection has become a significant concern to public health, especially in Brazil. A multi-kilobase deletion was recently detected in Brazilian L. infantum genomes and is suggested to reduce susceptibility to the anti-leishmanial drug miltefosine. We show that deletion-carrying strains occur in at least 15 Brazilian states and describe diversity patterns suggesting that these derive from common ancestral mutants rather than from recurrent independent mutation events. We also show that the deleted locus and associated enzymatic activity is restored by hybridization with non-deletion type strains. Genetic exchange appears common in areas of secondary contact but also among closely related parasites. We examine demographic and ecological scenarios underlying this complex L. infantum population structure and discuss implications for disease control.
Topics: Brazil; DNA, Protozoan; Evolution, Molecular; Gene Deletion; Genes, Protozoan; Genome, Protozoan; Leishmania infantum; Leishmaniasis, Visceral; Molecular Epidemiology; Phylogeny; Sequence Deletion; Whole Genome Sequencing
PubMed: 33514858
DOI: 10.1038/s42003-021-01658-5 -
Clinical Lymphoma, Myeloma & Leukemia Jul 2021
Topics: Antineoplastic Combined Chemotherapy Protocols; Bone Marrow; Chromosomes, Human, Pair 17; Drug Resistance, Neoplasm; Humans; Lymphoma, Follicular; Male; Middle Aged; Mutation, Missense; Neoplasm Grading; Sequence Deletion; Tumor Suppressor Protein p53
PubMed: 33867306
DOI: 10.1016/j.clml.2021.03.003 -
Journal of Clinical Laboratory Analysis Sep 2019Hb H disease is a serious type of α-thalassemia which cause moderate anemia while misdiagnosis by routine genetic analysis in a rare or novel Hb H disease.
BACKGROUND
Hb H disease is a serious type of α-thalassemia which cause moderate anemia while misdiagnosis by routine genetic analysis in a rare or novel Hb H disease.
METHODS
The study was done on three patients and one fetus in a suspected Hb H disease family. Hb analysis was carried out using capillary electrophoresis (CE), and hematological analysis was conducted with an automated cell counter. Common α- and β-thalassemia mutations were detected by routine genetic analysis (gap-PCR and RDB-PCR). Novel mutation diagnostic methods were based on DNA sequencing.
RESULTS
Capillary electrophoresis revealed clinical feature of classic Hb H disease in the proband, and hematology analysis showed moderate anemia (Hb 87 g/L). But routine genetic analysis was found that it was only a heterozygote for the -- deletion. DNA sequencing of α-globin genes (α1 and α2) identified the breakpoints between nts 34162 and 34171 at α2 gene, named CD 90-93 (-AGCTTCGG) mutation. The genotype of proband and fetus was the same -- /-α . His father was homozygous for the novel mutation (-α /-α ), and his mother was heterozygote for the -- deletion.
CONCLUSIONS
Our study for the first time described the novel mutation CD 90-93 (-AGCTTCGG). CE is a way to avoid misdiagnosis of rare or novel Hb H disease.
Topics: Base Sequence; Child, Preschool; Electrophoresis, Capillary; Hemoglobins, Abnormal; Humans; Male; Mutation; Sequence Analysis, DNA; Sequence Deletion; alpha-Thalassemia
PubMed: 31199523
DOI: 10.1002/jcla.22949 -
Genes Jan 2020Understanding mitochondrial DNA (mtDNA) evolution and inheritance has broad implications for animal speciation and human disease models. However, few natural models...
Understanding mitochondrial DNA (mtDNA) evolution and inheritance has broad implications for animal speciation and human disease models. However, few natural models exist that can simultaneously represent mtDNA transmission bias, mutation, and copy number variation. Certain isolates of the nematode harbor large, naturally-occurring mtDNA deletions of several hundred basepairs affecting the () gene that can be functionally detrimental. These deletion variants can behave as selfish DNA elements under genetic drift conditions, but whether all of these large deletion variants are transmitted in the same preferential manner remains unclear. In addition, the degree to which transgenerational mtDNA evolution profiles are shared between isolates that differ in their propensity to accumulate the deletion is also unclear. We address these knowledge gaps by experimentally bottlenecking two isolates of with different deletion frequencies for up to 50 generations and performing total DNA sequencing to identify mtDNA variation. We observed multiple mutation profile differences and similarities between isolates, a potentially species-specific pattern of copy number dysregulation, and some evidence for genetic hitchhiking in the deletion-bearing isolate. Our results further support as a practical model for characterizing naturally-occurring mtgenome variation and contribute to the understanding of how mtgenome variation persists in animal populations and how it presents in mitochondrial disease states.
Topics: Animals; Bacterial Proteins; Base Sequence; Caenorhabditis; DNA Copy Number Variations; DNA, Mitochondrial; Gene Deletion; Genetic Variation; Genome, Mitochondrial; Mitochondria; Mutation; NADH Dehydrogenase; Phylogeny; Repetitive Sequences, Nucleic Acid; Sequence Analysis, DNA; Sequence Deletion
PubMed: 31936803
DOI: 10.3390/genes11010077