COLD-PCR Enriches Low-Level Variant DNA Sequences and Increases the Sensitivity of Genetic Testing

2013 ◽  
pp. 623-639 ◽  
Author(s):  
Elena Castellanos-Rizaldos ◽  
Coren A. Milbury ◽  
Minakshi Guha ◽  
G. Mike Makrigiorgos
Keyword(s):  
Genetic Testing ◽  
Dna Sequences ◽  
Low Level

Patterns of genetic screening for hereditary cancer syndromes: Effect of Supreme Court’s ruling invalidating single gene patent rights.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 1580-1580
Author(s):  
Zhen Ni Zhou ◽  
Melissa K Frey ◽  
Dimitrios Nasioudis ◽  
Ann Carlson ◽  
Jessica Fields ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Supreme Court ◽  
Dna Sequences ◽  
Single Gene ◽  
Categorical Variables ◽  
Court Ruling ◽  
Supreme Court Ruling ◽  
Gene Testing ◽  
The Supreme Court ◽  
Multigene Panels

1580 Background: In 6/2013 the Supreme Court ruled that isolated DNA sequences found in nature could not be patented, resulting in rapid uptake of multigene panels. We sought to explore trends in genetic testing since this ruling. Methods: Results of all patients undergoing genetic testing and counseling at a single institution between 7/1/13 and 12/31/16 were reviewed. Associations between categorical variables were evaluated by chi-square tests or Fisher's exact tests as appropriate for category size. Results: 1663 patients underwent genetic testing over the study period. The median age was 49 years (range 18-86). Use of multigene panels versus targeted gene testing increased significantly in the years following the Supreme Court ruling (Table 1, P<0.001). While the percentage of patients found to have pathogenic mutations remained stable over the study period (9%), detection of variants of uncertain significance (VUS) increased significantly (Table 1, P<0.001). In 2013 BRCA1/2 mutations accounted for 91% of identified mutations; however this number decreased over time (2014-83%, 2015-70%, 2016-58%, P=0.01). Use of multigene panels detected 71% of mutations in non- BRCA1/2 genes such as CHEK(19), APC(44), MSH6(1), P53(1), and PTEN(1). Patients with a personal history of breast and/or ovarian cancer were more likely to have targeted testing than patients with other cancer types (590, 66% vs. 9, 33%, P=0.001). Conclusions: The uptake of multigene panels has increased since the 2013 Supreme Court ruling. While this technology allowed for the identification of many cancer-related genes that would be missed on targeted BRCA1/2 testing, it also resulted in a significantly increased detection of VUS, a finding with unknown clinical implications. [Table: see text]

Autogenous regulation of the positive regulatory qa-1F gene in Neurospora crassa

1985 ◽  
Vol 5 (12) ◽  
pp. 3593-3599
Author(s):  
V B Patel ◽  
N H Giles
Keyword(s):  
Neurospora Crassa ◽  
Gene Cluster ◽  
Dna Sequences ◽  
Regulatory Gene ◽  
Quinic Acid ◽  
The Other ◽  
Wild Type ◽  
Low Level ◽  
Activator Protein ◽  
Autogenous Regulation

In Neurospora crassa, the qa-1F regulatory gene positively controls transcription of all genes in the quinic acid (qa) gene cluster. qa-1F is transcribed at a low, uninduced level but is subject to strong (50-fold), autogenous regulation as well as to control by the negative regulatory gene, qa-1S, and the inducer quinic acid. Cloned qa-1F DNA sequences hybridize to two related mRNAs of 2.9 and 3.0 kilobases. When wild-type (qa-1F+) cultures are transferred to inducing conditions, qa-1F mRNA increases for 4 h, remains somewhat level, and decreases after 8 to 10 h. That this control is autogenous, i.e., that the qa-1F gene controls the synthesis of its own mRNA, is indicated by the presence of approximately the same low level of qa-1F mRNA in poly(A)+ RNA from noninducible qa-1F- mutant cultures under inducing conditions as that observed in uninduced wild-type cultures. The qa-1S gene also regulates the transcription of qa-1F, since a qa-1S- mutant, whether in noninducing or inducing conditions, contains a level of qa-1F mRNA that corresponds to the low level observed in uninduced wild-type cultures. These results corroborate the hypothesis (M. E. Case and N. H. Giles, Proc. Natl. Acad. Sci. USA 72:553-557, 1975; V. B. Patel, M. Schweizer, C. C. Dykstra, S. R. Kushner, and N. H. Giles, Proc. Natl. Acad. Sci. USA 78:5783-5787, 1981; L. Huiet, Proc. Natl. Acad. Sci. USA 81:1174-1178, 1984) that the qa-1F gene encodes an activator protein and acts positively in controlling transcription of itself and the other qa genes.

scholarly journals Autogenous regulation of the positive regulatory qa-1F gene in Neurospora crassa.

1985 ◽  
Vol 5 (12) ◽  
pp. 3593-3599 ◽  
Author(s):  
V B Patel ◽  
N H Giles
Keyword(s):  
Neurospora Crassa ◽  
Gene Cluster ◽  
Dna Sequences ◽  
Regulatory Gene ◽  
Quinic Acid ◽  
The Other ◽  
Wild Type ◽  
Low Level ◽  
Activator Protein ◽  
Autogenous Regulation

In Neurospora crassa, the qa-1F regulatory gene positively controls transcription of all genes in the quinic acid (qa) gene cluster. qa-1F is transcribed at a low, uninduced level but is subject to strong (50-fold), autogenous regulation as well as to control by the negative regulatory gene, qa-1S, and the inducer quinic acid. Cloned qa-1F DNA sequences hybridize to two related mRNAs of 2.9 and 3.0 kilobases. When wild-type (qa-1F+) cultures are transferred to inducing conditions, qa-1F mRNA increases for 4 h, remains somewhat level, and decreases after 8 to 10 h. That this control is autogenous, i.e., that the qa-1F gene controls the synthesis of its own mRNA, is indicated by the presence of approximately the same low level of qa-1F mRNA in poly(A)+ RNA from noninducible qa-1F- mutant cultures under inducing conditions as that observed in uninduced wild-type cultures. The qa-1S gene also regulates the transcription of qa-1F, since a qa-1S- mutant, whether in noninducing or inducing conditions, contains a level of qa-1F mRNA that corresponds to the low level observed in uninduced wild-type cultures. These results corroborate the hypothesis (M. E. Case and N. H. Giles, Proc. Natl. Acad. Sci. USA 72:553-557, 1975; V. B. Patel, M. Schweizer, C. C. Dykstra, S. R. Kushner, and N. H. Giles, Proc. Natl. Acad. Sci. USA 78:5783-5787, 1981; L. Huiet, Proc. Natl. Acad. Sci. USA 81:1174-1178, 1984) that the qa-1F gene encodes an activator protein and acts positively in controlling transcription of itself and the other qa genes.

Replacing PCR with COLD-PCR enriches variant DNA sequences and redefines the sensitivity of genetic testing

2008 ◽  
Vol 14 (5) ◽  
pp. 579-584 ◽  
Author(s):  
Jin Li ◽  
Lilin Wang ◽  
Harvey Mamon ◽  
Matthew H Kulke ◽  
Ross Berbeco ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Dna Sequences

scholarly journals Construction of a novel phagemid to produce custom DNA origami scaffolds

2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Parsa M Nafisi ◽  
Tural Aksel ◽  
Shawn M Douglas
Keyword(s):  
Dna Sequences ◽  
Dna Origami ◽  
Single Strand ◽  
Base Pairs ◽  
Fixed Sequence ◽  
Design Processes ◽  
Low Level ◽  
Structural Details ◽  
Filamentous Bacteriophages ◽  
Fixed Region

Abstract DNA origami, a method for constructing nanoscale objects, relies on a long single strand of DNA to act as the ‘scaffold’ to template assembly of numerous short DNA oligonucleotide ‘staples’. The ability to generate custom scaffold sequences can greatly benefit DNA origami design processes. Custom scaffold sequences can provide better control of the overall size of the final object and better control of low-level structural details, such as locations of specific base pairs within an object. Filamentous bacteriophages and related phagemids can work well as sources of custom scaffold DNA. However, scaffolds derived from phages require inclusion of multi-kilobase DNA sequences in order to grow in host bacteria, and those sequences cannot be altered or removed. These fixed-sequence regions constrain the design possibilities of DNA origami. Here, we report the construction of a novel phagemid, pScaf, to produce scaffolds that have a custom sequence with a much smaller fixed region of 393 bases. We used pScaf to generate new scaffolds ranging in size from 1512 to 10 080 bases and demonstrated their use in various DNA origami shapes and assemblies. We anticipate our pScaf phagemid will enhance development of the DNA origami method and its future applications.

scholarly journals Construction of a novel phagemid to produce custom DNA origami scaffolds

2018 ◽  
Author(s):  
Parsa M. Nafisi ◽  
Tural Aksel ◽  
Shawn M. Douglas
Keyword(s):  
Dna Sequences ◽  
Dna Origami ◽  
Single Strand ◽  
Base Pairs ◽  
Fixed Sequence ◽  
Design Processes ◽  
Low Level ◽  
Structural Details ◽  
Filamentous Bacteriophages ◽  
Fixed Region

AbstractDNA origami, a method for constructing nanoscale objects, relies on a long single strand of DNA to act as the “scaffold” to template assembly of numerous short DNA oligonucleotide “staples”. The ability to generate custom scaffold sequences can greatly benefit DNA origami design processes. Custom scaffold sequences can provide better control of the overall size of the final object and better control of low-level structural details, such as locations of specific base pairs within an object. Filamentous bacteriophages and related phagemids can work well as sources of custom scaffold DNA. However, scaffolds derived from phages require inclusion of multi-kilobase DNA sequences in order to grow in host bacteria, and thus cannot be altered or removed. These fixed-sequence regions constrain the design possibilities of DNA origami. Here we report the construction of a novel phagemid, pScaf, to produce scaffolds that have a custom sequence with a much smaller fixed region of only 381 bases. We used pScaf to generate new scaffolds ranging in size from 1,512 to 10,080 bases and demonstrated their use in various DNA origami shapes and assemblies. We anticipate our pScaf phagemid will enhance development of the DNA origami method and its future applications.

Transcription factor/DNA interactions visualized by electron spectroscopic imaging

1992 ◽  
Vol 50 (1) ◽  
pp. 450-451
Author(s):  
David P. Bazett-Jones ◽  
Mark L. Brown
Keyword(s):  
Transcription Factor ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Phosphorus Content ◽  
Spectroscopic Imaging ◽  
Electron Spectroscopic Imaging ◽  
Dna Backbone ◽  
Two Parameters ◽  
High Level

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.

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