The essence of SNPs

Brookes, Anthony J.

doi:10.1016/s0378-1119(99)00219-x

Cited by 1,199 publications

(751 citation statements)

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“…4 Single nucleotide polymorphisms (SNPs) are among the most abundant variation class in human genome being responsible for approximately 83.6% of the total detected genetic variation in gene expression. 5 SNPs have a potential to impact phenotypic variation in different and independent ways: directly modulating gene expression, 5 creating or abolishing binding sites for microRNAs, 6 modifying splicing patterns, 7 or spatial conformations and/or functions of proteins due to amino-acid alterations in the protein sequence 8 or by altering protein translation kinetics.…”

Section: Introductionmentioning

confidence: 99%

DNA polymorphisms as tools for spinal cord injury research

et al. 2008

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Study Design: Data mining of single nucleotide polymorphisms (SNPs) in gene pathways related to spinal cord injury (SCI). Objectives: To identify gene polymorphisms putatively implicated with neuronal damage evolution pathways, potentially useful to SCI study. Setting: Departments of Psychiatry and Orthopedics, Faculdade de Medicina, Universidade de São Paulo, Brazil. Methods: Genes involved with processes related to SCI, such as apoptosis, inflammatory response, axonogenesis, peripheral nervous system development and axon ensheathment, were determined by evaluating the 'Biological Process' annotation of Gene Ontology (GO). Each gene of these pathways was mapped using MapViewer, and gene coordinates were used to identify their polymorphisms in the SNP database. As a proof of concept, the frequency of subset of SNPs, located in four genes (ALOX12, APOE, BDNF and NINJ1) was evaluated in the DNA of a group of 28 SCI patients and 38 individuals with no SC lesions. Results: We could identify a total of 95 276 SNPs in a set of 588 genes associated with the selected GO terms, including 3912 nucleotide alterations located in coding regions of genes. The five nonsynonymous SNPs genotyped in our small group of patients, showed a significant frequency, reinforcing their potential use for the investigation of SCI evolution. Conclusion: Despite the importance of SNPs in many aspects of gene expression and protein activity, these gene alterations have not been explored in SCI research. Here we describe a set of potentially useful SNPs, some of which could underlie the genetic mechanisms involved in the post trauma spinal cord damage.

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Section: Introductionmentioning

confidence: 99%

DNA polymorphisms as tools for spinal cord injury research

et al. 2008

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“…SNPs consist of the most abundant form of genetic variation and have a great potential for mapping complex genetic traits [for review, see Kruglyak, 1997Kruglyak, , 1999Brookes, 1999;Chakravarti, 1999]. Due to the potential for being used as genetic markers, scientists in the public and private sectors have begun to focus their attention on searching for SNPs throughout the human genome [Marshall, 1997;Collins et al, 1997Collins et al, , 1998Wang et al, 1998;Buetow et al, 1999;Marshall, 1999].…”

Section: Introductionmentioning

confidence: 99%

“…Due to the potential for being used as genetic markers, scientists in the public and private sectors have begun to focus their attention on searching for SNPs throughout the human genome [Marshall, 1997;Collins et al, 1997Collins et al, , 1998Wang et al, 1998;Buetow et al, 1999;Marshall, 1999]. For whole-genome association studies, it is estimated that approximately 100,000-500,000 SNPs would be required [Brookes, 1999;Kruglyak, 1999]. Currently a great deal of effort is invested in the identifica-tion of SNPs.…”

Section: Introductionmentioning

confidence: 99%

Characterization of publicly available SNPs in the Korean population

et al. 2001

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“…Many projects in current human genetics aim to dissect complex traits by making use of DNA markers, mainly by single nucleotide polymorphisms (SNPs) [1]. Currently, around 10 million SNPs are stored in public databases.…”

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confidence: 99%

Typing of single nucleotide polymorphisms by MALDI mass spectrometry: Principles and diagnostic applications

Sauer

2006

Clinica Chimica Acta

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Background: After the completion of the human genome sequencing project human genetics has now shifted its focus to DNA variation. DNA variation analysis is considered to be a key in partly understanding the mechanisms of complex diseases or varying patient responses in drug treatment. One of the major goals in genetics is finding the DNA variants that can act as diagnostic markers for predisposition to specific diseases. Moreover, in microbiology DNA variation has long been known to help discriminate and identify bacterial strains and viruses. Diagnostics based on DNA or RNA detection might be advantageous as an early-stage indication can be provided. Methods: Many simple and efficient methods for the analysis of nucleic acids are already available. Consequently, the last few years have seen an increased in the use of large-scale analysis of nucleic acids, in basic DNA variation studies along with diagnostics. Mass spectrometry techniques such as matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) can be of great use for genome variation analysis. In particular high-throughput SNP analysis by MALDI can be performed using fully integrated platforms. Conclusions: Mass spectrometry-based procedures have promise for SNPs analysis especially for clinical diagnostics. D

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The essence of SNPs

Cited by 1,199 publications

References 63 publications

DNA polymorphisms as tools for spinal cord injury research

DNA polymorphisms as tools for spinal cord injury research

Characterization of publicly available SNPs in the Korean population

Typing of single nucleotide polymorphisms by MALDI mass spectrometry: Principles and diagnostic applications

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