Deep sequencing detects very-low-grade somatic mosaicism in the unaffected mother of siblings with nemaline myopathy

2014 ◽  
Vol 24 (7) ◽  
pp. 642-647 ◽  
Author(s):  
Satoko Miyatake ◽  
Eriko Koshimizu ◽  
Yukiko K. Hayashi ◽  
Kazushi Miya ◽  
Masaaki Shiina ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Somatic Mosaicism ◽  
Nemaline Myopathy ◽  
Low Grade

Determination of the mutant allele frequency in patients with neurofibromatosis type 2 and somatic mosaicism by means of deep sequencing

2015 ◽  
Vol 54 (8) ◽  
pp. 482-488 ◽  
Author(s):  
Melanie Spyra ◽  
Benjamin Otto ◽  
Gerhard Schön ◽  
Hildegard Kehrer-Sawatzki ◽  
Victor-Felix Mautner
Keyword(s):  
Allele Frequency ◽  
Deep Sequencing ◽  
Mutant Allele ◽  
Somatic Mosaicism ◽  
Neurofibromatosis Type ◽  
Neurofibromatosis Type 2 ◽  
Mutant Allele Frequency

scholarly journals Targeted Deep Sequencing Reveals No Definitive Evidence for Somatic Mosaicism in Atrial Fibrillation

2015 ◽  
Vol 8 (1) ◽  
pp. 50-57 ◽  
Author(s):  
Jason D. Roberts ◽  
James Longoria ◽  
Annie Poon ◽  
Michael H. Gollob ◽  
Thomas A. Dewland ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Deep Sequencing ◽  
Somatic Mosaicism ◽  
Definitive Evidence ◽  
Targeted Deep Sequencing

scholarly journals Detection of brain somatic variation in epilepsy-associated developmental lesions

2021 ◽  
Author(s):  
Tracy A Bedrosian ◽  
Katherine E Miller ◽  
Olivia E Grischow ◽  
Hyojung Yoon ◽  
Kathleen M Schieffer ◽  
...  
Keyword(s):  
Focal Epilepsy ◽  
Mapk Pathway ◽  
Focal Cortical Dysplasia ◽  
Somatic Mosaicism ◽  
Cortical Dysplasia ◽  
Disease Genes ◽  
Low Grade ◽  
Type I ◽  
Somatic Variation ◽  
Tissue Samples

Epilepsy-associated developmental lesions, including malformations of cortical development and low-grade developmental tumors, represent a major cause of drug-resistant seizures requiring surgical intervention in children. Brain-restricted somatic mosaicism has been implicated in the genetic etiology of these lesions; however, many contributory genes remain unidentified. We enrolled 50 children undergoing epilepsy surgery into a translational research study. We performed exome and RNA-sequencing of resected brain tissue samples to identify somatic variation. We uncovered candidate disease-causing somatic variation affecting 28 patients (56%), as well as candidate germline variants affecting 4 patients (8%). We confirmed somatic findings using high-depth targeted DNA sequencing. In agreement with previous studies, we identified somatic variation affecting SLC35A2 and MTOR pathway genes in patients with focal cortical dysplasia. Somatic gains of chromosome 1q were detected in 30% (3 of 10) Type I FCD patients. Somatic variation of MAPK pathway genes (i.e., FGFR1, FGFR2, BRAF, KRAS) was associated with low-grade epilepsy-associated developmental tumors. Somatic structural variation accounted for over one-half of epilepsy-associated tumor diagnoses. Sampling across multiple anatomic regions revealed that somatic variant allele fractions vary widely within epileptogenic tissue. Finally, we identified putative disease-causing variants in genes (EEF2, NAV2, PTPN11) not yet associated with focal cortical dysplasia. These results further elucidate the genetic basis of structural brain abnormalities leading to focal epilepsy in children and point to new candidate disease genes.

scholarly journals A KRT6A Mutation p.Ile462Asn In A Chinese Family With Pachyonychia Congenita, And Identification of Maternal Mosaicism

2021 ◽  
Author(s):  
Li Yue ◽  
Wang Yumeng ◽  
Yan Ming ◽  
Pan Chaolan ◽  
Zhang Jia ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Sanger Sequencing ◽  
Low Frequency ◽  
Gene Mutations ◽  
Chinese Family ◽  
Heterozygous Mutation ◽  
Low Grade ◽  
Autosomal Dominant Disorder ◽  
Keratin Gene ◽  
Pachyonychia Congenita

Abstract Background: Pachyonychia congenita (PC, OMIM #167200, #167210, #615726, #615728, and #615735) is a rare autosomal dominant disorder caused by keratin gene mutations in KRT6A, KRT6B, KRT6C, KRT16 or KRT17. It is characterized with nail dystrophy and palmoplantar keratoderma (PPK). The most prominent manifestation is plantar pain. This is the first reported case of maternal mosaicism in PC. Although very rare, germ cell mosaicism should be considered when providing genetic counselling for unaffected parents of a child with PC. Methods: Genomic DNA was extracted from peripheral blood samples, hair bulbs, buccal smears and the father’s germ cells. The entire coding and flanking intronic sequences of 5 keratin genes were screened for mutations in every individuals of the family by Sanger sequencing. We used whole exome sequencing (WES) to search for mosaicism in the parents who had no KRT6A mutation identified by Sanger sequencing. Mosaicism was confirmed by SNaPshot sequencing and HiSeq deep sequencing.Results: A previously reported heterozygous mutation, p.Ile462Asn, was identified in KRT6A in the proband and his affected sister. The variant was detected in one sequencing read from 86 sequencing reads from DNA from the mother’s blood by WES. The mutation was not identified in DNA from the father’s blood. Frequency of reads was 47% and 49% in proband and his sister, respectively. SNaPshot sequencing revealed mosaicism at a level of 2.5% and 4.7% in DNA from blood and hair bulbs from the unaffected mother. HiSeq deep sequencing demonstrated low-grade mosaicism in the patient’s younger sister and parents.Conclusion: These findings indicate the ability of WES and SNaPshot sequencing to detect low-frequency mosaic mutations. Although very rare, germinal mosaicism should be considered when genetic counseling is given to families with presumed spontaneous cases of PC.

Somatic mosaicism of a heterogeneous mutation of ACTA 1 in nemaline myopathy

2019 ◽  
Vol 61 (11) ◽  
pp. 1169-1171
Author(s):  
Takayuki Yokoi ◽  
Kenshi Sei ◽  
Yumi Enomoto ◽  
Takuya Naruto ◽  
Kenji Kurosawa
Keyword(s):  
Somatic Mosaicism ◽  
Nemaline Myopathy

Quantitative Ultra-Deep Sequencing of Non-Coding Regions to Characterize Clonal Evolution in Follicular Lymphoma

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 146-146
Author(s):  
Janice M Spence ◽  
John Spence ◽  
Richard Burack
Keyword(s):  
Population Dynamics ◽  
Genetic Variation ◽  
Follicular Lymphoma ◽  
Deep Sequencing ◽  
Low Frequency ◽  
Tumor Evolution ◽  
Evolutionary Trees ◽  
Low Grade ◽  
Coding Regions ◽  
Grade 3

Abstract Abstract 146 Background: Cancers are characterized by genomic instability, and the resulting intra-clonal diversity is thought to underlie the evolution of more aggressive clinical course behavior and therapy resistance. Intra-clonal heterogeneity in follicular lymphoma (FL) has been documented qualitatively by analysis of mutations induced by Activation Induced Deaminase (AID) in IGH coding regions. AID also aberrantly targets non-coding regions of the genome causing numerous “passenger” mutations. To obtain a quantitative measure of genetic variation and to characterize population dynamics in FL, we performed ultra-deep “next generation” sequencing of selected non-coding regions known to be aberrantly targeted by AID in FL. Herein, we quantify and characterize AID-induced genetic variation in FL and relate the extent of variation to grade. Method: An ultra-deep sequencing approach, able to identify sequences present at 0.3% frequency, was developed to quantify sub-clonal populations within a tumor so that the extent of intraclonal heterogeneity can be compared between tumors. Genomic DNA was obtained from fresh/frozen specimens (10 FL grade 1/2, 2 FL grade 3, 3 hyperplastic lymph nodes and 1 epithelial cell line). H&E sections and flow cytometry data were examined to corroborate the diagnosis and fraction of tumor (>50% in all cases). The ten sequenced (ABI-SoLID) regions were PCR amplicons of: 5'UTRs of BCL2, BCL6, MYC, PAX5, PIM1, RHOH, CD83 and SYK; IGH (mu enhancer-J6; clone-specific Vh-J6). Average mapped coverage was > 20,000-fold. To detect rare mutations while suppressing read noise, data were mapped using an algorithm (BFAST) designed to detect rare Single Nucleotide Variants (SNV); a novel recursive mapping pipeline enhanced detection of SNVs in heavily mutated regions. A novel filtering algorithm handled data as 34 base-pair “words” with confirmation based on partial assembly using independently obtained sequences from adjacent regions. Results: 656 mutations were detected in non-coding regions of the 12 FL specimens. FL specimens had more mutations in all 5' UTRs combined (range 14–193, median 47, n=12) than control specimens (range 2–7, n=4). The mutations were associated with AID-motifs (p<0.05). 8 regions (excluding SYK and MYC) had significantly more SNVs in FLs compared to controls. BCL2 had the largest number of SNVs and the number of SNVs in BCL2 predicted the sum of SNVs in the 9 other regions (r2=0.85). The specimens could be placed into 4 strata based on the number of BCL2 SNVs (Poisson ladder, p=0.005). No correlation was seen between the number of SNVs and grade, percent nodularity, percent tumor, or other histologic features. Of the 354 SNVs in BCL2, many were “rare”: 78 were present in less than 1% of alleles and 41 in less than 0.5%. Strikingly, all low frequency CNVs were found in cases of Grade 1/2 FL without any found in either of the Grade 3 FL specimens despite the abundance of higher frequency CNVs in these cases. Representing the data as evolutionary trees suggested that the grades have differing population dynamics: Grade 1/2 showed dominant populations from which similarly proliferative subpopulations were continuously derived while Grade 3 showed a dominant population with remnant evolutionarily antecedent cells but little evidence of continuing development of intraclonal variation. Conclusions: The number of SNVs in AID-targeted non-coding regions varied widely allowing stratification of FL cases into 4 groups. The number of SNVs in BCL2 non-coding regions correlated with the number of SNVs in the other 8 gene regions combined, suggesting that analysis of the BCL2 non-coding region is sufficient to characterize the genome-wide effects of aberrantly targeted AID. Furthermore, low frequency mutations (present in less than 10% of sequences) were found only in grade 1/2 but not in grade 3. Representing the data as evolutionary trees indicated that population dynamics also varied greatly, with evidence that in low grade FL there is active ongoing generation of diversity while in grade 3 FL the population is dominated by the most evolutionarily derived clone with relatively less ongoing diversification. In contrast to prior methods, this quantitative approach to tumor evolution may allow correlation of intraclonal genetic diversity with natural history, response to immune-chemotherapy and risk of transformation to diffuse large cell lymphoma. Disclosures: No relevant conflicts of interest to declare.

Direct Observation of Crystalline Ordering In Naturally Graphitized Carbon Produced by Low Grade Metamorphism

1977 ◽  
Vol 35 ◽  
pp. 162-163
Author(s):  
Thomas R. McKee ◽  
Peter R. Buseck
Keyword(s):  
Crystallite Size ◽  
Sedimentary Rocks ◽  
Carbonaceous Material ◽  
Low Grade ◽  
X Ray ◽  
Graphitized Carbon ◽  
Transmission Electron ◽  
Heat Treated ◽  
Commercial Carbon ◽  
Metamorphic Zone

Sediments commonly contain organic material which appears as refractory carbonaceous material in metamorphosed sedimentary rocks. Grew and others have shown that relative carbon content, crystallite size, X-ray crystallinity and development of well-ordered graphite crystal structure of the carbonaceous material increases with increasing metamorphic grade. The graphitization process is irreversible and appears to be continous from the amorphous to the completely graphitized stage. The most dramatic chemical and crystallographic changes take place within the chlorite metamorphic zone.The detailed X-ray investigation of crystallite size and crystalline ordering is complex and can best be investigated by other means such as high resolution transmission electron microscopy (HRTEM). The natural graphitization series is similar to that for heat-treated commercial carbon blacks, which have been successfully studied by HRTEM (Ban and others).

Scanning Electron Microscope Study of Bacteria on Mineral Surfaces

1976 ◽  
Vol 34 ◽  
pp. 130-131
Author(s):  
V.K. Berry
Keyword(s):  
Oxidation Reaction ◽  
Electron Microscope Study ◽  
Elemental Sulfur ◽  
Thiobacillus Ferrooxidans ◽  
Physical Contact ◽  
Metal Sulfides ◽  
Low Grade ◽  
Mineral Surfaces ◽  
Mineral Surface ◽  
Scanning Electron Microscope Study

There are two strains of bacteria viz. Thiobacillus thiooxidansand Thiobacillus ferrooxidanswidely mentioned to play an important role in the leaching process of low-grade ores. Another strain used in this study is a thermophile and is designated Caldariella .These microorganisms are acidophilic chemosynthetic aerobic autotrophs and are capable of oxidizing many metal sulfides and elemental sulfur to sulfates and Fe2+ to Fe3+. The necessity of physical contact or attachment by bacteria to mineral surfaces during oxidation reaction has not been fairly established so far. Temple and Koehler reported that during oxidation of marcasite T. thiooxidanswere found concentrated on mineral surface. Schaeffer, et al. demonstrated that physical contact or attachment is essential for oxidation of sulfur.

TEM/AEM characterization of fine-grained clay minerals in very-low-grade rocks: Evaluation of contamination by empa involving celadonite family minerals

1996 ◽  
Vol 54 ◽  
pp. 694-695
Author(s):  
Gejing Li ◽  
D. R. Peacor ◽  
D. S. Coombs ◽  
Y. Kawachi
Keyword(s):  
Electron Microscopy ◽  
Volcanic Rocks ◽  
Analytical Electron Microscopy ◽  
Metamorphic Rocks ◽  
New Mineral ◽  
Chemical Compositions ◽  
Low Grade ◽  
Fine Grained ◽  
Depth Analysis ◽  
Mineral Aggregates

Recent advances in transmission electron microscopy (TEM) and analytical electron microscopy (AEM) have led to many new insights into the structural and chemical characteristics of very finegrained, optically homogeneous mineral aggregates in sedimentary and very low-grade metamorphic rocks. Chemical compositions obtained by electron microprobe analysis (EMPA) on such materials have been shown by TEM/AEM to result from beam overlap on contaminant phases on a scale below resolution of EMPA, which in turn can lead to errors in interpretation and determination of formation conditions. Here we present an in-depth analysis of the relation between AEM and EMPA data, which leads also to the definition of new mineral phases, and demonstrate the resolution power of AEM relative to EMPA in investigations of very fine-grained mineral aggregates in sedimentary and very low-grade metamorphic rocks.Celadonite, having end-member composition KMgFe3+Si4O10(OH)2, and with minor substitution of Fe2+ for Mg and Al for Fe3+ on octahedral sites, is a fine-grained mica widespread in volcanic rocks and volcaniclastic sediments which have undergone low-temperature alteration in the oceanic crust and in burial metamorphic sequences.

Inflammageing in the cardiovascular system: mechanisms, emerging targets, and novel therapeutic strategies

2020 ◽  
Vol 134 (17) ◽  
pp. 2243-2262
Author(s):  
Danlin Liu ◽  
Gavin Richardson ◽  
Fehmi M. Benli ◽  
Catherine Park ◽  
João V. de Souza ◽  
...  
Keyword(s):  
Cardiovascular Diseases ◽  
Cardiovascular System ◽  
Nlrp3 Inflammasome ◽  
Molecular Mechanisms ◽  
Molecular Targets ◽  
Therapeutic Interventions ◽  
Low Grade ◽  
Cardiovascular Research ◽  
Inflammatory Processes ◽  
Ach Receptors

Abstract In the elderly population, pathological inflammation has been associated with ageing-associated diseases. The term ‘inflammageing’, which was used for the first time by Franceschi and co-workers in 2000, is associated with the chronic, low-grade, subclinical inflammatory processes coupled to biological ageing. The source of these inflammatory processes is debated. The senescence-associated secretory phenotype (SASP) has been proposed as the main origin of inflammageing. The SASP is characterised by the release of inflammatory cytokines, elevated activation of the NLRP3 inflammasome, altered regulation of acetylcholine (ACh) nicotinic receptors, and abnormal NAD+ metabolism. Therefore, SASP may be ‘druggable’ by small molecule therapeutics targeting those emerging molecular targets. It has been shown that inflammageing is a hallmark of various cardiovascular diseases, including atherosclerosis, hypertension, and adverse cardiac remodelling. Therefore, the pathomechanism involving SASP activation via the NLRP3 inflammasome; modulation of NLRP3 via α7 nicotinic ACh receptors; and modulation by senolytics targeting other proteins have gained a lot of interest within cardiovascular research and drug development communities. In this review, which offers a unique view from both clinical and preclinical target-based drug discovery perspectives, we have focused on cardiovascular inflammageing and its molecular mechanisms. We have outlined the mechanistic links between inflammageing, SASP, interleukin (IL)-1β, NLRP3 inflammasome, nicotinic ACh receptors, and molecular targets of senolytic drugs in the context of cardiovascular diseases. We have addressed the ‘druggability’ of NLRP3 and nicotinic α7 receptors by small molecules, as these proteins represent novel and exciting targets for therapeutic interventions targeting inflammageing in the cardiovascular system and beyond.

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