scholarly journals Diagnostics of hereditary cancer syndromes by NGS. Process of creating a database.

2021 ◽  
Author(s):  
Ivan S. Abramov ◽  
Tatyana S. Lisitsa ◽  
Anna M. Stroganova ◽  
Oxana O. Ryabaya ◽  
Anastasiya M. Danishevich ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Malignant Neoplasms ◽  
Sequence Variants ◽  
Coding Region ◽  
Dna Libraries ◽  
Oncological Diseases ◽  
Custom Panel ◽  
Brca1 Brca2 ◽  
The Moment ◽  
Ngs Data

Background:more than 500 thousand new cases of malignant neoplasms are registered annually in the Russian Federation, of which more than 50 thousand new cases are due to hereditary forms.Improving the diagnosis of these diseases will make it possible to detect tumors in the early stages and take timely preventive and therapeutic measures. Aims:creation of a database and development of software for NGS data analysis for the prevention and early diagnosis of hereditary forms of oncological diseases. Methods:the present study used 636 DNA samples obtained from cancer patients with a high hereditary risk or a burdened family history. DNA was isolated from blood lymphocytes. DNA libraries were prepared with a KAPA Target Enrichment Custom Panel (Roche). The panel included probes for targeted enrichment of the coding region of 44 genes. NGS was performed on the MiSeq platform (Illumina). Results:we identified 65 pathogenic/ probably pathogenic nucleotide sequence variants in 96 patients in theATM, BLM, BRCA1, BRCA2, CHEK2, EPCAM, MEN1, MLH1, MSH2, MSH3, MSH6, MUTYH, PALB2, TP53genes. We also identified 2858 nucleotide sequence variants of unknown clinical significance. Conclusions:we have created a local database that contains both genetic variants and clinical and anamnestic data. The database contains 4763 nucleotide sequence variants at the moment, among which 2522 are unique variants identified in a single patient.

Sequence variants in the FcεRI alpha chain gene

2002 ◽  
Vol 93 (1) ◽  
pp. 37-41 ◽  
Author(s):  
Toshiki Shikanai ◽  
Eric S. Silverman ◽  
Brian W. Morse ◽  
Craig M. Lilly ◽  
Hiroshi Inoue ◽  
...  
Keyword(s):  
Promoter Region ◽  
Population Substructure ◽  
Chain Gene ◽  
Polymorphism Analysis ◽  
Sequence Variants ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Alpha Chain ◽  
Asthmatic Patients ◽  
Single Stranded Conformational Polymorphism

There is a relationship between IgE levels and expression of high-affinity IgE receptors (FcεRI). Because the alpha chain is the only portion of the receptor that binds directly to IgE, we reasoned that sequence variants in the FcεRI alpha gene may exist that alter these binding events. We screened all of the exons and the promoter region of the FcεRI alpha chain gene with genomic DNA from 389 asthmatic and 341 normal control subjects for mutations by using single-stranded conformational polymorphism analysis. No nonsynonomous single nucleotide polymorphisms (SNPs) were identified in the coding region. Three SNPs were found in the promoter region: an A/C transversion at −770 from the translation start site; a G/A transition at −664; and a T/C transition at −335. No differences in allele frequencies were detected between asthmatic subjects and controls. Homozygosity for the C variant at locus −335 was more common in Caucasian asthmatic patients with IgE levels in the lower quartile than in the upper quartile ( P = 0.032). An analysis of highly polymorphic SNPs indicated that this association is unlikely to be due to population substructure. We conclude that homozygosity for the C allele of FcεRI alpha chain variant is associated with lower IgE levels.

scholarly journals Nucleotide sequence of the two rat cellular rasH genes.

1986 ◽  
Vol 6 (5) ◽  
pp. 1706-1710 ◽  
Author(s):  
M Ruta ◽  
R Wolford ◽  
R Dhar ◽  
D Defeo-Jones ◽  
R W Ellis ◽  
...  
Keyword(s):  
Amino Acids ◽  
Nucleotide Sequence ◽  
Coding Region ◽  
3T3 Cells ◽  
Ras Gene ◽  
P21 Protein ◽  
Murine Sarcoma Virus ◽  
Sarcoma Virus ◽  
Nih 3T3 ◽  
Murine Sarcoma

We present the nucleotide sequence of the coding region of the rat c-rasH-1 gene and a partial sequence analysis of the rat c-rasH-2 gene. By comparing these sequences with the Harvey murine sarcoma virus ras gene, we predict that the p21 protein encoded by the Harvey virus differs from the cellular c-rasH-1-encoded p21 at only two amino acids; those at positions 12 and 59. Alterations at each of these positions may play a role in activating the viral p21 protein. The c-rasH-2 gene is likely to be a nonfunctional pseudogene because it lacks introns, cannot be activated to transform NIH 3T3 cells, and differs in sequence from both c-rasH-1 and v-rasH at several base pair positions.

RAD3 gene of Saccharomyces cerevisiae: nucleotide sequence of wild-type and mutant alleles, transcript mapping, and aspects of gene regulation

1985 ◽  
Vol 5 (1) ◽  
pp. 17-26
Author(s):  
L Naumovski ◽  
G Chu ◽  
P Berg ◽  
E C Friedberg
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Nucleotide Sequence ◽  
Coding Region ◽  
Base Pairs ◽  
S1 Nuclease ◽  
Calculated Molecular Weight ◽  
Base Pair Deletion ◽  
S1 Nuclease Mapping ◽  
Essential Function ◽  
Nuclease Mapping

We determined the complete nucleotide sequence of the RAD3 gene of Saccharomyces cerevisiae. The coding region of the gene contained 2,334 base pairs that could encode a protein with a calculated molecular weight of 89,796. Analysis of RAD3 mRNA by Northern blots and by S1 nuclease mapping indicated that the transcript was approximately 2.5 kilobases and did not contain intervening sequences. Fusions between the RAD3 gene and the lac'Z gene of Escherichia coli were constructed and used to demonstrate that the RAD3 gene was not inducible by DNA damage caused by UV radiation or 4-nitroquinoline-1-oxide. Two UV-sensitive chromosomal mutant alleles of RAD3, rad3-1 and rad3-2, were rescued by gap repair of a centromeric plasmid, and their sequences were determined. The rad3-1 mutation changed a glutamic acid to lysine, and the rad3-2 mutation changed a glycine to arginine. Previous studies have shown that disruption of the RAD3 gene results in loss of an essential function and is associated with inviability of haploid cells. In the present experiments, plasmids carrying the rad3-1 and rad3-2 mutations were introduced into haploid cells containing a disrupted RAD3 gene. These plasmids expressed the essential function of RAD3 but not its DNA repair function. A 74-base-pair deletion at the 3' end of the RAD3 coding region or a fusion of this deletion to the E. coli lac'Z gene did not affect either function of RAD3.

scholarly journals cDNA cloning, expression and chromosomal localization of the human sarco/endoplasmic reticulum Ca2+-ATPase 3 gene

1996 ◽  
Vol 318 (2) ◽  
pp. 689-699 ◽  
Author(s):  
Leonard DODE ◽  
Frank WUYTACK ◽  
Patrick F. J. KOOLS ◽  
Fouzia BABA-AISSA ◽  
Luc RAEYMAEKERS ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Nucleotide Sequence ◽  
Blot Hybridization ◽  
Cdna Probe ◽  
Human Platelets ◽  
Gene Transcript ◽  
Northern Blot Hybridization ◽  
Dna Encoding ◽  
Coding Region ◽  
Cos Cells

cDNA and genomic clones encoding human sarco/endoplasmic reticulum Ca2+-ATPase 3 (SERCA3) were isolated. The composite nucleotide sequence of the 4.6 kb cDNA, as well as the partial structure of 25 kb of genomic DNA encoding all but the 5´ region of the gene, was determined. The nucleotide sequence coding for the last six amino acids of the pump and the 3´-untranslated region were identified within the sequence of the last exon. Northern blot hybridization analysis using cDNA probes derived from this exon detected a 4.8 kb transcript in several human tissues. Using a cDNA probe derived from the 5´-coding region an unexpected mRNA distribution pattern, consisting of two mRNA species of 4.8 and 4.0 kb, was detected in thyroid gland and bone marrow only. This is the first indication of an alternative splicing mechanism operating on the SERCA3 gene transcript, which most likely generates SERCA3 isoforms with altered C-termini. Human SERCA3 expressed in platelets and in COS cells transfected with the corresponding cDNA was detected with the previously described antibody N89 (directed against the N-terminal region of rat SERCA3) and with a new SERCA3-specific antiserum C91, directed against the extreme C-terminus of the human isoform. A monoclonal antibody PL/IM430, previously assumed to recognize SERCA3 in human platelets, does not react with the 97 kDa human SERCA3 transiently expressed in COS cells. Therefore the 97 kDa isoform detected by PL/IM430 more likely represents a novel SERCA pump, as recently suggested [Kovács, Corvazier, Papp, Magnier, Bredoux, Enyedi, Sarkadi and Enouf (1994) J. Biol. Chem. 269, 6177–6184]. Finally, by fluorescence in situ hybridization and chromosome G-banding analyses, the SERCA3 gene was assigned to human chromosome 17p13.3.

Molecular cloning and nucleotide sequence analysis of the putative cDNA for the precursor molecule of the chicken LH-β subunit

1989 ◽  
Vol 3 (2) ◽  
pp. 129-137 ◽  
Author(s):  
T. Noce ◽  
H. Ando ◽  
T. Ueda ◽  
K. Kubokawa ◽  
T. Higashinakagawa ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Cdna Clone ◽  
Rabbit Antiserum ◽  
Nucleotide Sequence Analysis ◽  
Cdna Expression Library ◽  
Β Subunit ◽  
Coding Region ◽  
Precursor Molecule ◽  
Cdna Insert ◽  
Hybridization Probe

ABSTRACT A cDNA expression library was constructed from poly(A)+ RNA of broiler chicken adenohypophyses using λ gt11 as a vector. After screening with a rabbit antiserum against chicken LH, a cDNA clone (L12) containing a 436 bp insert was obtained. Using a subclone of L12 in pUC19 (pL12) as the hybridization probe, another cDNA clone (LF127) with a 533 bp insert was isolated. The LF127 contained the full-length cDNA encoding the putative chicken LH-β subunit precursor molecule. Hybridization of the pL12 cDNA insert to adenohypophysial RNA showed that chicken and Japanese quail adenohypophyses contained RNA species of about 0·8 and 1·0 kb respectively. The amount of this RNA species was ten times higher in adult male quails kept under long days at room temperature than in those kept under short days at 7 °C. In-situ hybridization experiments showed the exclusive distribution of the signal in the LH cells of the adenohypophysis. The similarity of the nucleotide sequence of the apoprotein-coding region of LH-β cDNA of the chicken to that of mammals is lower than that among mammals. The deduced amino acid sequence of the chicken LH-β subunit supports the hypothesis that the number of proline residues increases in the LH-β subunit the closer phylogenetically the vertebrate is to mammals.

Radiation Contribution Assessment to Development of Multiple Oncological Diseases in the Late Period of Acute Radiation Disease

2021 ◽  
Vol 66 (1) ◽  
pp. 44-48
Author(s):  
I. Galstyan ◽  
M. Konchalovsky ◽  
M. Kozlova ◽  
V. Nugis
Keyword(s):  
Radiation Effects ◽  
Acute Radiation ◽  
Malignant Neoplasms ◽  
Early Diagnostics ◽  
Adequate Treatment ◽  
Clinical Observations ◽  
Oncological Diseases ◽  
The Given

Purpose: On clinical examples to estimate a probable contribution of the postponed earlier external radiation of all body in the doses exceeding 1 Gy at development of multiple malignant neoplasms of different localization and a leukaemia. Material and methods: At 8 of 164 patients, it is long observed after the postponed acute radiation syndrome (ARS), multiple oncological diseases are revealed. Dynamics of consecutive forming of solid tumors at 2 patients and also malignant neoplasms and a myelodysplastic syndrome (MDS) with transformation in an acute leukamia at 1 patient is tracked. Observation duration – 31 years, 43 years and 32 years. Results: Availability of medical care to the patients who transferred ARS and high quality of its rendering at all stages (out-patient, stationary) allowed to reveal malignant neoplasms at early stages of development and to achieve an absolute recovery. However eventually at these patients development and other oncological diseases was observed. The given clinical observations allow to assume that at presented cases radiation acted on various stages of carcinogenesis, and its contribution to development of different oncological diseases in all patients was not identical. Conclusion: The analysis of clinical observations allows to assume that radiation contribution to genesis of various oncological diseases at the persons which underwent radiation in the doses causing development of ARS is various. Now in our country there are no approaches to quantitative assessment of a contribution of radiation effects to development of malignant neoplasms in each case. The patients who underwent acute single exposition in doses over 1 Gy have to be considered as having predisposition to development of multiple tumors in the remote terms. In this regard they for life need medical follow up for the purpose of early diagnostics and adequate treatment of the developing malignant neoplasms.

Current methods of radiological diagnosis of kidney neoplasms (literature review)

2021 ◽  
pp. 14-22
Author(s):  
Oleg N. YAMSHIKOV ◽  
Natalia V. YEMELYANOVA ◽  
Daria S. ZAGORODNOVA
Keyword(s):  
Kidney Neoplasms ◽  
Diagnostic Methods ◽  
Malignant Neoplasms ◽  
Kidney Tumors ◽  
The Past ◽  
New Methods ◽  
Total Incidence ◽  
Oncological Diseases ◽  
Working Age ◽  
Medical Disciplines

We presented an overview of domestic and foreign studies on the diagnosis of renal malignancies published in publicly available electronic specialized medical publications. Taking into account that every year the share of oncological diseases in the structure of the total incidence is constantly growing, and that cancer is one of the main causes of death and disability in the working age population, currently, the search for new diagnostic methods to detect kidney tumors still remains a pressing problem located at the junction of several medical disciplines, in particular, oncology, urology, radiation diagnostics and radiation therapy. Over the past decade, the diagnosis of malignant kidney neoplasms has undergone significant changes and has stepped far forward. Because of that the ability to detect the disease in the early stages of development increases. In the study, we examined the most widespread methods, methods that have already lost relevance, as well as new methods, such as magnetic resonance imaging, computed tomography ultrasonography, radiography, etc. We also considered the possibilities of differential diagnosis of benign and malignant neoplasms.

scholarly journals Nucleotide and derived amino acid sequences of a cDNA coding for pre-uteroglobin from the lung of the hare (Lepus capensis)

1986 ◽  
Vol 235 (3) ◽  
pp. 895-898 ◽  
Author(s):  
M S López de Haro ◽  
A Nieto
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Amino Acid Sequence ◽  
Amino Acid Sequences ◽  
Untranslated Regions ◽  
Coding Region ◽  
Homologous Proteins ◽  
Lepus Capensis ◽  
Rabbit Gene

An almost full-length cDNA coding for pre-uteroglobin from hare lung was cloned and sequenced. The derived amino acid sequence indicated that hare pre-uteroglobin contained 91 amino acids, including a signal peptide of 21 residues. Comparison of the nucleotide sequence of hare pre-uteroglobin cDNA with that previously reported for the rabbit gene indicated five silent point substitutions and six others leading to amino acid changes in the coding region. The untranslated regions of both pre-uteroglobin mRNAs were very similar. The amino acid changes observed are discussed in relation to the different progesterone-binding abilities of both homologous proteins.

scholarly journals Organization, transcription and regulation of the Leishmania infantum histone H3 genes

1996 ◽  
Vol 318 (3) ◽  
pp. 813-819 ◽  
Author(s):  
Manuel SOTO ◽  
Jose M REQUENA ◽  
Luis QUIJADA ◽  
Carlos ALONSO
Keyword(s):  
Nucleotide Sequence ◽  
Leishmania Infantum ◽  
Histone H3 ◽  
State Level ◽  
Protozoan Parasite ◽  
Control Mechanisms ◽  
Mrna Levels ◽  
Coding Region ◽  
Genes Encoding ◽  
Multiple Copies

The genomic organization and transcription of the genes encoding the histone H3 of the protozoan parasite Leishmania infantum have been studied. It was found that there are multiple copies of the histone H3 genes distributed in chromosomal bands XIX and XIV. The nucleotide sequence of two of the L. infantum H3 genes, each one located in a different chromosome, is reported. Although the nucleotide sequence of the coding region of both genes is identical, the sequence of the 3´ untranslated region is highly divergent. It was found also that there exist two different size classes of histone H3 transcripts, each one derived from a different gene, and that they are polyadenylated. The steady-state level of the transcripts dramatically decreases when the parasites enter the stationary phase of growth, suggesting a mode of regulation which is linked to the proliferation status of the cell. Unlike the replication-dependent histones, the L. infantum H3 mRNA levels do not decrease after treatment with DNA synthesis inhibitors. A comparative analysis of the sensitivity of the histone mRNA levels to DNA inhibition in the parasites L. infantum and Trypanosoma cruzi revealed the existence of different control mechanisms in histone expression in these two phylogenetically related protozoan parasites.

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