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At least 307 records · Page 17Linked to original sources
PubMed2017

Reanalysis of BRCA1/2 negative high risk ovarian cancer patients reveals novel germline risk loci and insights into missing heritability.

While up to 25% of ovarian cancer (OVCA) cases are thought to be due to inherited factors, the majority of genetic risk remains unexplained. To address this gap, we sought to identify previously undescribed OVCA risk variants through the whole exome sequencing (WES) and candidate gene analysis of 48 women with ovarian cancer and selected for high risk of genetic inheritance, yet negative for any known pathogenic variants in either BRCA1 or BRCA2. In silico SNP analysis was employed to identify suspect variants followed by validation using Sanger DNA sequencing. We identified five pathogenic variants in our sample, four of which are in two genes featured on current multi-gene panels; (RAD51D, ATM). In addition, we found a pathogenic FANCM variant (R1931*) which has been recently implicated in familial breast cancer risk. Numerous rare and predicted to be damaging variants of unknown significance were detected in genes on current commercial testing panels, most prominently in ATM (n = 6) and PALB2 (n = 5). The BRCA2 variant p.K3326*, resulting in a 93 amino acid truncation, was overrepresented in our sample (odds ratio = 4.95, p = 0.01) and coexisted in the germline of these women with other deleterious variants, suggesting a possible role as a modifier of genetic penetrance. Furthermore, we detected loss of function variants in non-panel genes involved in OVCA relevant pathways; DNA repair and cell cycle control, including CHEK1, TP53I3, REC8, HMMR, RAD52, RAD1, POLK, POLQ, and MCM4. In summary, our study implicates novel risk loci as well as highlights the clinical utility for retesting BRCA1/2 negative OVCA patients by genomic sequencing and analysis of genes in relevant pathways.

Adult↗
PubMed1985

Site-specific analysis of drug interactions and damage in DNA using sequencing techniques.

DNA-sequencing techniques can be adapted to provide powerful analytical tools for pinpointing the sites at which DNA is modified by either radiations or chemicals. Base modifications, covalent adducts, crosslinks, and noncovalent binding can all be detected. This review outlines the adaptions of the Maxam-Gilbert and Sanger dideoxy sequencing techniques which make such studies possible. Practical aspects and limitations of the various methods are given. Assays which test the ability of DNA polymerase to bypass damage and misincorporate bases are also discussed. It is concluded that these techniques constitute the most powerful method currently available for the study of sequence-specific DNA interactions.

Animals↗
PubMed1980

Primed synthesis methods of sequencing DNA and RNA.

Primed synthesis sequencing requires a partially single-stranded molecule in which a specific polynucleotide primer with a free 3' hydroxyl terminus is base paired to a single-stranded template. The template and primer strands can be DNA or RNA in any combination. A polymerase, either DNA polymerase for DNA/DNA or RNA/DNA primer-template combinations or reverse transcriptase for a DNA/RNA primer-template molecule, is used to copy the template by chain extension. In the chain termination method of sequencing (see Sanger et al., Proc. Natl. Acad. Sci. USA 74: 5463; 1977), nucleotide-specific chain terminators (dideoxy ATP(ddA), ddC, ddG, and ddT) are used to promote a nucleotide specific termination in the chain extension, so that some of the chains terminate at every position at which that nucleotide occurs in the sequence. By using each of the nucleotide specific-chain terminators in separate chain extension reactions and on the same primed template, the sequence of the template can be determined. This method is simple, rapid, and accurate and has been used to determine the sequences of whole DNA viruses (phi X174 and G4), plasmid cloned DNA, eukaryote mRNAs, and RNA viral genomes. These primed synthesis methods of sequencing are now being developed into methods for nucleotide mutagenesis.

Base Sequence↗
PubMed2005

Distribution, cloning and sequencing of GnRH, its receptor, and effects of gastric acid secretion of GnRH analogue in gastric parietal cells of rats.

Our objective was to study the distribution of gonadotropin-releasing hormone (GnRH) and its receptor, cloning and sequencing of GnRH and its receptor gene in cultured gastric parietal cells of rats. The distribution of GnRH and its receptor mRNA were investigated through immunocytochemical ABC methods and in situ hybridization methods in cultured gastric parietal cells of rats. After isolation of the total RNA from the parietal cells, RT-PCR was conducted to obtain GnRH and its receptor cDNA. Then, the products of PCR was purified, digested by the restriction enzyme of Hind III and EcoR I, and DNA fragments of interests were cloned into pUC19 vector. The products of PCR were analyzed by sequencing with Sanger's method after identified by PCR and digestion of restriction enzyme. Gastric parietal cells showed GnRH and its receptor immunoreactivity; positive material was located in cytoplasm other than in nuclei. GnRH and its receptor mRNA hybridized signals were also detected in cytoplasm with negative nuclei. The specific amplified band of GnRH and its receptor sequences were detected through Agarose gel electrophoresis, and GnRH gene sequence is identical to that of GnRH which has been reported in rat hypothalamus and GnRH receptor sequence is identical to that of the pituitary of rat. GnRH analogue (Alarelin) could inhibit the gastric acid secretion both by direct actions on parietal cells and by inhibiting vagous function. Our data suggest that GnRH could be produced by gastric parietal cells of rats and may modulate physiological function of gastric parietal cells of rats through autocrinal and paracrinal way.

Animals↗
PubMed2005

Genomic organization of zebrafish cone-rod homeobox gene and exclusion as a candidate gene for retinal degeneration in niezerka and mikre oko.

PURPOSE: To determine the genomic organization of the zebrafish crx gene and to evaluate if mutations in crx are responsible for the retinal degeneration phenotype in the zebrafish (Danio rerio) mutants niezerka (nie(m743)) and mikre oko (mok(m632)). METHODS: Overlapping fragments were PCR amplified from genomic DNA isolated from homozygous mutant embryos and wild-type siblings (sibs). Amplicons were sequenced and sequence data assembled into contigs. Genomic organization was determined by alignment of contigs with published cDNA sequences and zebrafish genomic sequence from Sanger and Ensembl databases. Linkage analysis used DNA from mapping panels of single homozygous mutant animals with mixed genetic backgrounds. RESULTS: The analysis indicated that the zebrafish crx gene consisted of three exons and 2 introns, and spans 3.8 kb of genomic DNA. The splice junctions were all located within the coding region. Highly repetitive sequences present in non-coding regions of crx and extended tetra-nucleotide repeats in intronic regions were associated with sequence variation between different strains. Homozygous mok(m632) or nie(m743) mutants and their respective wild-type sibs, showed identical patterns of heterozygosity and sequence variations within each line. No mutation in crx were identified in homozygous mok(m632) or nie(m743). Consistent with the absence of identified mutations, linkage analysis excluded linkage of the mutant phenotypes to crx. CONCLUSIONS: Despite the presence of sequence variations in their respective genetic backgrounds, within each line the sequence of crx was identical. Consistent with the absence of mutations, further analysis excluded linkage of the mutant phenotypes to crx. Analysis is in progress to map these loci and identify the genes responsible for the retinal degeneration phenotype in these mutant lines.

Animals↗
PubMed2000

[Cloning and sequence analysis of the light chain variable region gene of monoclonal anti-idiotypic antibody NP30 of Schistosoma japonicum].

OBJECTIVE: To amplify and sequence the light chain of anti-idiotypic monoclonal antibody NP30 of Schistosoma japonicum. METHODS: By comparing the conserved regions at each end of the nucleotide sequences of murine germ-line genes encoding FR1 and FR4 regions of immunoglobulin light chain variable regions, we designed a set of primers for amplification of VL gene. The hybridoma cells secreting anti-idiotypic monoclonal antibody NP30 of Schistosoma japonicum were cultured and their genome DNAs were extracted and used as templates for PCR. The PCR product was then cloned into pUC19 vector. The recombinants were sequenced by Sanger's method. The VL gene was compared with GenBank and published mouse VL genes. RESULTS: The full-length of VL gene was 318 bp. The VL gene was a member of mouse Ig kappa light chain subgroup IV and generated from rearrangement of germ line V and J kappa 4 genes. The VL gene sequence has been registered by GenBank(accession No. AF206720). CONCLUSION: The obtained VL gene was a potentially functional gene of anti-idiotypic monoclonal antibody NP30 of Schistosoma japonicum.

Amino Acid Sequence↗
PubMed1994

A calculation of all possible oligosaccharide isomers both branched and linear yields 1.05 x 10(12) structures for a reducing hexasaccharide: the Isomer Barrier to development of single-method saccharide sequencing or synthesis systems.

The number of all possible linear and branched isomers of a hexasaccharide was calculated and found to be > 1.05 x 10(12). This large number defines the Isomer Barrier, a persistent technological barrier to the development of a single analytical method for the absolute characterization of carbohydrates, regardless of sample quantity. Because of this isomer barrier, no single method can be employed to determine complete oligosaccharide structure in 100 nmol amounts with the same assurance that can be achieved for 100 pmol amounts with single-procedure Edman peptide or Sanger DNA sequencing methods. Difficulties in the development of facile synthetic schemes for oligosaccharides are also explained by this large number. No current method of chemical or physical analysis has the resolution necessary to distinguish among 10(12) structures having the same mass. Therefore the 'characterization' of a middle-weight oligosaccharide solely by NMR or mass spectrometry necessarily contains a very large margin of error. Greater uncertainty accompanies results performed solely by sequential enzyme degradation followed by gel-permeation chromatography or electrophoresis, as touted by some commercial advertisements. Much of the literature which uses these single methods to 'characterize' complex carbohydrates is, therefore, in question, and journals should beware of publishing structural characterizations unless the authors reveal all alternate possible structures which could result from their analysis.(ABSTRACT TRUNCATED AT 250 WORDS)

Biological Evolution↗
PubMed1998

PCR-introduced loop structure as primer in DNA sequencing.

The need for a primer hybridization step before sequencing has been eliminated using a stem-loop structure generated by PCR. The loop structure is obtained by careful design of the PCR primer or by cloning the target DNA into a dedicated vector (pRIT 28HP). After solid-phase capture of the PCR product, the loop is formed by elution of the non-bound strand. Here, we show that both the immobilized and the eluted strand can be analyzed using conventional Sanger DNA sequencing and the novel pyrosequencing method as described previously. By using a stem-loop structure as a primer for DNA sequencing, the risk for mispriming is minimized.

Base Sequence↗
PubMed2001

[Construction and expression of single chain Fv antibody against human bladder carcinoma].

OBJECTIVE: To construct and express single chain Fv antibody against human bladder carcinoma, which was expected to have advantages in targeted diagnosis and therapy with the characteristics of lower immunogenicity. METHODS: Hybridoma BDI-1 cell, which secreted a monoclonal antibody against human bladder carcinoma, was used to isolate total RNA. By reverse transcription, the cDNA was synthesized and used as templates for amplifying the immunoglobulin heavy-and light-chain variable region genes by polymerase chain reaction (PCR). The amplified DNA was ligated into a sequencing vector pUC19 and sequenced with Sanger's method. The VH and VL genes were inserted into expression vector pFUW80. By inducing, the ScFv antibodies were expressed and secreted from Escherichia coli. Binding activities against the bladder carcinoma cells were detected by ELISA. The 5 x his-tagged ScFv antibodies were purified on IDA-Ni2+ resin by immobilized metal chelate affinity chromatography (IMAC). The purified ScFv antibodies were analyzed by SDS-PAGE. RESULTS: A full-length of VH and VL genes was 366 and 324 base pairs respectively. Comparing with other published sequences, the VH gene was a member of mouse heavy-chain VH subgroup II and originated from re-arrangement of VH, Dsp2.2 and JH4; the VL gene was VK subgroup IV and from Vk and Jk4. The ScFv antibodies could inhibit 84% of the antigen binding activity of original McAb BDI-1. The purified ScFv antibodies gave a single major band (Mr-29 000) on SDS-PAGE. CONCLUSION: The single chain Fv antibody against human bladder carcinoma was successfully constructed and expressed.

Amino Acid Sequence↗
PubMed2026

A novel hemizygous missense variant in the BEND2 gene is associated with nonobstructive azoospermia.

Nonobstructive azoospermia (NOA), the most severe form of male infertility, frequently arises from genetic defects that disrupt spermatogenesis. In this study, a novel hemizygous missense variant (NM_001184767.2 [c.G1069A; p.V357I]) is identified in the X-linked BEN domain-containing 2 ( BEND2 ) gene of a patient with NOA characterized by spermatocyte maturation arrest. Whole-exome sequencing and Sanger validation confirmed that this rare variant is absent in fertile controls and that no pathogenic variants were detected in established NOA genes. Computational analysis predicted potential structural alterations via AlphaFold modeling, leading to the hypothesis that the ability of BEND2 to recognize genomic targets may be compromised. The patient's phenotype phenocopies the meiotic arrest observed in Bend2 -knockout mice. Expression profiling confirmed predominant BEND2 transcription in human and mouse testes, peaking in early spermatocytes and coinciding with meiotic initiation, with reduced transcript levels detected in the proband's peripheral blood compared with those in an obstructive azoospermia control. This study reports a pathogenic BEND2 variant associated with NOA with spermatocyte arrest, highlighting its critical role in human meiosis and expanding the genetic etiology of male infertility.

Adult↗
PubMed2024

Analysis of human papillomavirus type 16 E4, E5 and L2 gene variations among women with cervical infection in Xinjiang, China.

BACKGROUND: There is a high incidence of cervical cancer in Xinjiang. Genetic variation in human papillomavirus may increase its ability to invade, spread, and escape host immune response. METHODS: HPV16 genome was sequenced for 90 positive samples of HPV16 infection. Sequences of the E4, E5 and L2 genes were analysed to reveal sequence variation of HPV16 in Xinjiang and the distribution of variation among the positive samples of HPV16 infection. RESULTS: Eighty-one of the 90 samples of HPV16 infection showed variation in HPV16 E4 gene with 18 nucleotide variation sites, of which 8 sites were synonymous variations and 11 missense variations. 90 samples of HPV16 infection showed variation in HPV16 E5 and L2 genes with 16 nucleotide variation sites (6 synonymous, 11 missense variations) in the E5 gene and 100 nucleotide variation sites in L2 gene (37 synonymous, 67 missense variations). The frequency of HPV16 L2 gene missense variations G3377A, G3599A, G3703A, and G3757A was higher in the case groups than in the control groups. CONCLUSIONS: Phylogenetic tree analysis showed that 87 samples were European strains, 3 cases were Asian strains, there were no other variations, and G4181A was related to Asian strains. HPV16 L2 gene missense variations G3377A, G3599A, G3703A, and G3757A were significantly more frequent in the case groups than in the control groups.

Humans↗
PubMed2002

Novel approach for the effective determination of DNA scission site using the Sanger method.

This paper describes the effective determination of DNA scission site using a novel approach that is based on the Sanger method of nucleotide sequencing. The DNA scission site is determined by contrast with the nucleotide sequence of the DNA. Here, instead of the traditional Maxam-Gilbert method for the determination of the DNA sequence, we utilized the Sanger method and studied its effectiveness in the determination of DNA scission sites. Using this method, the determination of DNA scission site becomes more facile and exact. And the total time for the determination is reduced nearly by half in comparison to the Maxam-Gilbert method. Further advantages of this novel approach include the reduced risks of radiation exposure for researchers and contamination of the apparatus.

Base Sequence↗
PubMed1997

Kaj Ulrik Linderstrøm-Lang (1896-1959).

The Carlsberg Laboratory in Copenhagen has had a long tradition of outstanding science. At the time covered by this discussion, Kjeldahl, Sørensen, and Linderstrøm-Lang had been consecutive directors of the Chemical Laboratory for 83 years. Lang's inspired leadership began in the 1930s with a number of innovations (study of metabolism in single cells, titrations in non-aqueous solvents, relation of proteolysis to structure) but it was not until the early 1950s that Denmark had sufficiently recovered from the war for the laboratory to enter world science again. During World War II, Lang had been active in the Danish resistance movement. After the war, a number of major advances were being made that would revolutionize the field of protein chemistry (Pauling and Corey's H-bonded structures, Sanger's sequencing techniques, chromatography, Watson and Crick structures, modern instrumentation). The time for the new field of the physical biochemistry of proteins had arrived. Lang, with his broad experience, adventurous spirit, and genius for innovation, created an environment that was ideal for the convergence of these disconnected advances into a uniform science. The emphasis was to be on quantitative measurements on proteins in solution with interpretations based on molecular structures. During an all-too-brief period of time, Lang's laboratory attracted a large fraction of those who were destined to be the leaders of the next generation of protein chemists. At this time, the Carlsberg Laboratory was probably the most scientifically exciting environment for a protein chemist. The methods developed at that time-hydrogen exchange, limited proteolysis, optical rotatory dispersion, volume changes accompanying protein reactions, automatic titrations-are still all in common use and many of the visitors to the laboratory in that period and their students are still playing major roles in protein research. Lang's other qualities should not be ignored. He was not only a great scientist but also a musician, raconteur, artist, and an exceptionally warm and compassionate human being.

Chemistry↗
PubMed2025

The functional study of novel KLHL3 missense mutations associated with pseudohypoaldosteronism type II.

BACKGROUND: Pseudohypoaldosteronism type II (PHA II) is an inherited tubulopathy, clinically defined by three hallmark features, including secondary hypertension, hyperchloremic metabolic acidosis, and persistent hyperkalemia occurring despite maintained glomerular filtration function. Herein, we aim to investigate the association of kelch like family member 3 (KLHL3) gene mutations with PHA II. METHODS: Compound heterozygous KLHL3 mutations were identified through whole-exome sequencing and Sanger validation. AlphaFold-based structural modeling, site-directed mutagenesis of Flag-tagged plasmids, and co-immunoprecipitation (Co-IP)/immunoblotting in vivo were combined to analyze mutant protein interactions and ubiquitination effects. RESULTS: A Chinese patient was identified with two previously unreported KLHL3 variants (c.131G > A [p.R44Q] and c.744 C > G [p.Y248*]), exhibiting a biochemical triad of asymptomatic hyperkalemia, mild metabolic acidosis, and borderline hypertension. Administration of thiazide diuretics effectively normalized the patient’s hyperkalemia and hypertension. A p.R44Q missense mutation predicted as variants of uncertain significance (VOUS) by American College of Medical Genetics and Genomics (ACMG) guidelines, and a p.Y248* nonsense mutation predicted as variants of likely pathogenic. Functional study revealed that the two KLHL3 mutations impair its ubiquitination of with-no-lysine kinase 1 (WNK1) and with-no-lysine kinase 4 (WNK4), and further increase phosphorylation of both SPAK (sterile20/sporulation-specific protein-1 related proline/alanine-rich kinase)/OSR1 (oxidative stress response kinase-1) and Na-Cl-cotransporter (NCC). CONCLUSIONS: Our study characterized two previously unreported KLHL3 mutations, followed by comprehensive in vitro functional analyses to elucidate their pathophysiological contributions at the molecular level.

Humans↗
PubMed1988

A DNA polymerase from a thermoacidophilic archaebacterium: evolutionary and technological interests.

The archaebacteria constitute a group of prokaryotes with an intermediate phylogenetic position between eukaryotes and eubacteria. The study of their DNA polymerases may provide valuable information about putative evolutionary relationships between prokaryotic and eukaryotic DNA polymerases. As a first step towards this goal, we have purified to near homogeneity a DNA polymerase from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius. This enzyme is a monomeric protein of 100 kDa which can catalyze DNA synthesis using either activated calf thymus DNA or oligonucleotide-primed single-stranded DNA as a template. The activity is optimal at 70 degrees C and the enzyme is thermostable up to 80 degrees C; however, it can still polymerize up to 200 nucleotides at 100 degrees C. These remarkable thermophilic properties and thermostability permit examination of the mechanism of DNA synthesis under conditions of decreased stability of the DNA helix. Furthermore, these properties make S. acidocaldarius DNA polymerase a very efficient enzyme to be used in DNA amplification by the recently developed polymerase chain reaction method (PCR) as well as in the Sanger DNA sequencing technique.

Archaea↗
PubMed2006

Multiplex single nucleotide polymorphism genotyping by adapter ligation-mediated allele-specific amplification.

An improved approach for increasing the multiplex level of single nucleotide polymorphism (SNP) typing by adapter ligation-mediated allele-specific amplification (ALM-ASA) has been developed. Based on an adapter ligation, each reaction requires n allele-specific primers plus an adapter-specific primer that is common for all SNPs. Thus, only n+1 primers are used for an n-plex PCR amplification. The specificity of ALM-ASA was increased by a special design of the adapter structure and PCR suppression. Given that the genetic polymorphisms in the liver enzyme cytochrome P450 CYP2D6 (debrisoquine 4-hydroxylase) have profound effects on responses of individuals to a particular drug, we selected 17 SNPs in the CYP2D6 gene as an example for the multiplex SNP typing. Without extensive optimization, we successfully typed 17-plex SNPs in the CYP2D6 gene by ALM-ASA. The results for genotyping 70 different genome samples by the 17-plex ALM-ASA were completely consistent with those obtained by both Sanger's sequencing and PCR restriction fragment length polymorphism (PCR-RFLP) analysis. ALM-ASA is a potential method for SNP typing at an ultra-low cost because of a high multiplex level and a simple optimization step for PCR. High-throughput SNP typing could be readily realized by coupling ALM-ASA with a well-developed automation device for sample processing.

Alleles↗
PubMed2006

Association of IL1B polymorphisms with gastric cancer in a Chinese population.

OBJECTIVES: To investigate the association between IL1B polymorphisms and risk of gastric cancer in a Chinese population, seven SNPs in the IL1B gene were selected for this study. METHODS: A multiplex genotyping method, which is based on adapter ligation and allele-specific amplification, was established to type seven SNPs on the IL1B gene simultaneously. One hundred and forty-one non-cancer outpatients and 97 patients with gastric cancer were genotyped, and the relation between IL1B polymorphisms and gastric cancer was statistically analyzed. RESULTS: The seven SNPs were successfully typed and the results were consistent with those obtained by both Sanger's sequencing and PCR-RFLP. Handling with statistical analysis, we observed significantly different genotype frequencies of 0794C>T (chi(2)=6.11, P=0.05), 1274C>T (chi(2)=6.86, P=0.03) and 2143T>C (chi(2)=6.86, P=0.03) between patients and controls. CONCLUSION: ALM-ASA is a potential method for multiplex SNP typing with a low consumption of genomic DNA. SNPs 0794C>T, 1274C>T, and 2143T>C are associated with gastric cancer.

Adolescent↗