SNP Web Resources and Their Potential Applications in Personalized Medicine

Wang, Jingbo; Pang, Grace Su Yin; Chong, Samuel S.; Lee, Caroline

doi:10.2174/138920012802138552

Cited by 34 publications

(21 citation statements)

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“…Evidences show that through SNPs a wide range of human diseases such as cancer or autoimmunity can be triggered [10, 11]. SNPs also might affect the pharmacokinetics and pharmacodynamics of certain drugs in cancer therapy [12]. The transcriptional regulation of a protein, its structure and its function can be affected by a single base substitution, deletion or insertion.…”

Section: Introductionmentioning

confidence: 99%

In silico SNP analysis of the breast cancer antigen NY-BR-1

et al. 2016

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BackgroundBreast cancer is one of the most common malignancies with increasing incidences every year and a leading cause of death among women. Although early stage breast cancer can be effectively treated, there are limited numbers of treatment options available for patients with advanced and metastatic disease. The novel breast cancer associated antigen NY-BR-1 was identified by SEREX analysis and is expressed in the majority (>70%) of breast tumors as well as metastases, in normal breast tissue, in testis and occasionally in prostate tissue. The biological function and regulation of NY-BR-1 is up to date unknown.MethodsWe performed an in silico analysis on the genetic variations of the NY-BR-1 gene using data available in public SNP databases and the tools SIFT, Polyphen and Provean to find possible functional SNPs. Additionally, we considered the allele frequency of the found damaging SNPs and also analyzed data from an in-house sequencing project of 55 breast cancer samples for recurring SNPs, recorded in dbSNP.ResultsOver 2800 SNPs are recorded in the dbSNP and NHLBI ESP databases for the NY-BR-1 gene. Of these, 65 (2.07%) are synonymous SNPs, 191 (6.09%) are non-synoymous SNPs, and 2430 (77.48%) are noncoding intronic SNPs. As a result, 69 non-synoymous SNPs were predicted to be damaging by at least two, and 16 SNPs were predicted as damaging by all three of the used tools. The SNPs rs200639888, rs367841401 and rs377750885 were categorized as highly damaging by all three tools. Eight damaging SNPs are located in the ankyrin repeat domain (ANK), a domain known for its frequent involvement in protein-protein interactions. No distinctive features could be observed in the allele frequency of the analyzed SNPs.ConclusionConsidering these results we expect to gain more insights into the variations of the NY-BR-1 gene and their possible impact on giving rise to splice variants and therefore influence the function of NY-BR-1 in healthy tissue as well as in breast cancer.

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Section: Introductionmentioning

confidence: 99%

In silico SNP analysis of the breast cancer antigen NY-BR-1

et al. 2016

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“…For instance, a SNP would look like this: subject 1: ...AGATAGC...; subject 2: ...AGATAGC.... Known SNPs amount to thousands and can be strongly associated with individual traits, including for instance height or differences in the response to therapies [26]. …”

Section: Overview Of Available Methods For Cfdna Testing In Maternal mentioning

confidence: 99%

Clinical Perspective of Cell-Free DNA Testing for Fetal Aneuploidies

Gratacós

Nicolaides²

2014

Fetal Diagn Ther

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Cell-free DNA testing in maternal blood provides the most effective method of screening for trisomy 21, with a reported detection rate of 99% and a false positive rate of less than 0.1%. After many years of research, this method is now commercially available and is carried out in an increasing number of patients, and there is an expanding number of conditions that can be screened for. However, the application of these methods in clinical practice requires a careful analysis. Current first-trimester screening strategies are based on a complex combination of tests, aiming at detecting fetal defects and predicting the risk of main pregnancy complications. It is therefore necessary to define the optimal way of combining cell-free DNA testing with current first-trimester screening methods. In this concise review we describe the basis of cell-free DNA testing and discuss the potential approaches for its implementation in combination with current tests in the first trimester.

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“…The input beam is 3D Gaussian and it is worthy to study its higher order detuning effects to explain why there is no resonance for  > 90° and to explain the maximum emittance growth at  = 87°. We resort to the available analytical expression of the space charge Hamiltonian for the 2D Gaussian beam [27,25], which is given by…”

Section: Characteristics Of Fourth Order Resonancementioning

confidence: 99%

Characteristics of the fourth order resonance in high intensity linear accelerators

Jeon

Hwang

2017

Physics of Plasmas

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For the 4= 360° space-charge resonance in high intensity linear accelerators, the emittance growth is surveyed for input Gaussian beams, as a function of the depressed phase advance per cell  and the initial tune depression ( o  ). For each data point, the linac lattice is designed such that the fourth order resonance dominates over the envelope instability. The data show that the maximum emittance growth takes place at   87° over a wide range of the tune depression (or beam current), which confirms that the relevant parameter for the emittance growth is  and that for the bandwidth is. An interesting four-fold phase space structure is observed that cannot be explained with the fourth order resonance terms alone. Analysis attributes this effect to a small negative sixth order detuning term as the beam is redistributed by the resonance. Analytical studies show that the tune increases monotonically for the Gaussian beam which prevents the resonance for  > 90. Frequency analysis indicates that the four-fold structure observed for input KV beams when  < 90 is not the fourth order resonance but a fourth order envelope instability because the 1/4 = 90/360 component is missing in the frequency spectrum.

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SNP Web Resources and Their Potential Applications in Personalized Medicine

Cited by 34 publications

References 0 publications

In silico SNP analysis of the breast cancer antigen NY-BR-1

In silico SNP analysis of the breast cancer antigen NY-BR-1

Clinical Perspective of Cell-Free DNA Testing for Fetal Aneuploidies

Characteristics of the fourth order resonance in high intensity linear accelerators

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