Sequence microsatellite. Medical search. Frequent questions

Despite this variation, we provide an indication of what number of sequences and consequent proportion of a 454 run are required for the development of 40 designable, unique microsatellite loci for a typical molecular ecological study. (datadryad.org)
Finally, to address the challenges of choosing loci from the vast array of microsatellite loci typically available from partial genome runs (average for this study, 2341 loci), we provide a microsatellite development flowchart as a procedural guide for application once the results of a partial genome run are obtained. (datadryad.org)
MSI status was determined from over 7,000 target microsatellite loci covered by NGS. (carislifesciences.com)
Here we describe a new set of novel polymorphic microsatellite loci to facilitate the investigation of genetic structure and artificial breeding. (biomedcentral.com)
Eighty-five microsatellite loci were selected for microsatellite marker optimization. (biomedcentral.com)
2013) Discretized Gaussian Mixture for Genotyping of microsatellite loci containing homopolymer runs. (omictools.com)
Microsatellite-based FST estimates appeared much smaller than ITS-based estimates and not significantly correlated, likely due to microsatellite allele size homoplasy typical of these highly polymorphic loci. (unibo.it)
We used the partial control region (CR) of mitochondrial DNA (mtDNA) and seven microsatellite loci to investigate the intra-species structure, differentiation, and demographic history of hog deer populations from three landscapes, the Terai Arc, Northeast, and Indo-Burma (Keibul Lamjao National Park (KLNP), Manipur, India) landscapes. (nature.com)
The results of the investigations of the microsatellite loci supported the mtDNA results unambiguously. (nature.com)
Loci of interests in the X-chromosome (DXS9895, GATA172D05 and DXS9898) were amplified in a single PCR with primers of published sequences (1-3). (astm.org)
Population Structure and Genetic Diversity of Sporothrix globosa in China According to 10 Novel Microsatellite Loci. (cdc.gov)

SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. (usgs.gov)
Microsatellites are also known as simple sequence repeats (SSRs). (wikipedia.org)
BES analyses identified 6,848 simple sequence repeats (SSRs), of which 3,854 had high quality flanking sequences for PCR primers design. (biomedcentral.com)
The genetic structure and variability was described among 52 oil palm inter-population crosses after two selection cycles using simple sequence repeats markers (SRR). (academicjournals.org)

The microsatellite search algorithm is extremely efficient, and we have used it to identify repeats with motifs from 2 to 25bp in length. (usgs.gov)
Microsatellite instability structure consists of repeated nucleotides, most often seen as GT/CA repeats. (wikipedia.org)
Although researchers do not agree on a specific threshold for the number of tandem repeats that constitute a microsatellite, there is a consensus around their relative size. (wikipedia.org)
Microsatellites (Short sequence repeats, SSRs, Short tandem repeats): are short (1-6bp) repeating sequences in genetic code. (flashcardmachine.com)

Next generation sequencing (NGS) is revolutionizing molecular ecology by simplifying the development of molecular genetic markers, including microsatellites. (datadryad.org)
In this study, we describe a new set of 30 EST-derived microsatellite markers which would aid in characterizing population structure, genetic diversity and constructing linkage map in E. sinensis . (biomedcentral.com)
Microsatellite instability (MSI) is the condition of genetic hypermutability (predisposition to mutation) that results from impaired DNA mismatch repair (MMR). (wikipedia.org)
These newly developed microsatellite markers will be useful for investigating the genetic diversity and population genetic structure of V. vulpes and will aid in developing conservation strategies for this species. (geneticsmr.com)
A strategy is introduced by which physical and genetic map inconsistencies can be resolved using the preliminary 4x assembly of the whole genome sequence of soybean. (arizona.edu)
A codon is a DNA or RNA sequence of three nucleotides (a trinucleotide) that forms a unit of genetic information encoding a particular amino acid. (genome.gov)
In order to investigate the spatial genetic structuring of C. rubrum, five microsatellite markers and the ribosomal internal transcribed spacer 1 (ITS-1) sequences were analysed in 11 samples from the northwestern Mediterranean Sea. (unibo.it)
If [they're] microsatellite instable, then do genetic analysis to confirm and make sure you do germline testing to see if the patient is has Lynch syndrome. (ajmc.com)
As part of the multicenter, population-based Ohio Colorectal Cancer Prevention Initiative, tumor DNA was sequenced for 419 consecutive CRC cases undergoing standard universal tumor screening and germline genetic testing, and 46 patients with CRC known to have LS due to a germline mutation in a mismatch repair gene. (cdc.gov)

Design and test primers for this sequence using Primer-BLAST. (nih.gov)
Primers flanking microsatellite were designed using the PRIMER PREMIER 5.0 program. (biomedcentral.com)

To facilitate this integration of maps, we screened 3290 microsatellites (SSRs) identified from BAC end sequences of clones comprising the 'Williams 82' physical map. (arizona.edu)
We also identified 216,232 SSRs and 138,856 microsatellite markers. (biorxiv.org)

Allelic diversity of 22 Sampoerna Agro's oil palm Pisifera based on Microsatellite markers. (academicjournals.org)

The mismatch repair (MMR) system plays a major role in removing DNA polymerization errors, and loss of this pathway results in hereditary cancers characterized by microsatellite instability. (nih.gov)

The discovery of specific repeat elements will facilitate analyses of sequence content (e.g. for SNPs discovery and for transcriptome characterization) and future genome sequence assemblies. (biomedcentral.com)

Whole-genome sequencing of the soybean (Glycine max (L.) Merr. (arizona.edu)
Compared to whole genome sequencing (WGS), exome sequencing covers only the 1% of the genome that is translated into protein, greatly reducing the technical burden of data collection and analysis. (frontiersin.org)
performed the first whole-genome sequencing study on AML cells collected from a single patient. (frontiersin.org)
Here, we report first de novo whole genome sequencing and assembly of an early flowering gamma mutant of Emma White hybrid for developing a genomics resource for further studies. (biorxiv.org)
Use whole genome sequencing to study how and why certain fungi spread and make people sick. (cdc.gov)
Conjugal Transfer, Whole Genome Sequencing, and Plasmid Analysis of Four mcr-1 -bearing Isolates from U.S. Patients. (cdc.gov)

Microsatellite density increases with genome size and is seen twice as much at the ends of chromosome arms than in the chromosome bodies. (wikipedia.org)
pUPD was detected in 11p15 and next in the entire chromosome 11 with microsatellite markers. (lu.se)
Quantitative fluorescent PCR with amplification of chromosome-specific DNA sequences for chromosomes 13, 18, 21 and X indicated GW-pUPD. (lu.se)

In the absence of hPMS2, a greater number of microsatellite expansion versus deletion mutations was observed, and expansion rates of the tetranucleotide alleles were similar. (nih.gov)
PCR and Sanger sequencing were used to confirm mutations in and screen other family members where they were available. (molvis.org)
In a study of 450 CRC diagnosed under 50 years via the Ohio Colorectal Cancer Prevention Initiative, germline DNA analysis for mutations in 25 cancer susceptibility genes was done in addition to assessing microsatellite instability and/or immunohistochemistry for MMR deficiency. (cdc.gov)

Exome sequencing was performed in one affected family member. (molvis.org)
While whole exome sequencing (WES) remains popular and effective as a method of genetically profiling different cancers, advances in sequencing technology has enabled an increasing number of whole-genome based studies. (frontiersin.org)

These informative microsatellite markers will be useful in studies of genetics, genomics and marker-assisted selection breeding in E. sinensis . (biomedcentral.com)
NEW YORK (GenomeWeb) - 10x Genomics has announced two new sequencing partnerships with Qiagen and Illumina. (genomeweb.com)
Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome. (biomedcentral.com)
The methods treated cover a large number of topics from traditional population genetics to large-scale genomics with high-throughput sequencing data. (routledge.com)
As the integration of NGS in the study and treatment of cancer continues to mature, we believe that the field of cancer genomics will need to move toward more complete 100% genome sequencing. (frontiersin.org)
First, this article summarizes the history of massively parallel next-generation sequencing (NGS) in the context of cancer genomics and reviews recent research and clinical applications. (frontiersin.org)

Microsatellite-based high density linkage map in oil palm (Elaeis guineensis Jacq. (academicjournals.org)

10x's microfluidics-based molecular barcoding long read solutions, built on the GemCode platform, can be used with Illumina sequencers to give researchers a wider range of sequencing applications to choose from, the company said. (genomeweb.com)
Genomic sequencing, evolution and molecular epidemiology of rabies virus. (cdc.gov)

7] Full gene sequencing, albeit expensive, can detect all of the defective mismatch repair genes in HNPCC. (medscape.com)
Pembrolizumab, a PD-1 inhibitor, gained accelerated approval from the FDA in May 2017 for unresectable or metastatic colon cancer that has tested positive for microsatellite instability-high (MSI-H) or deficient mismatch repair (dMMR), and has progressed following treatment with a fluoropyrimidine, oxaliplatin, and irinotecan. (medscape.com)
It has been also hypothesized that mismatch repair-deficient/microsatellite-unstable tumors are more responsive to PD-L1 blockade. (medscape.com)

We have used gamma-ray induced 'early flowering mutant' to generate draft genome sequences with total length (bp) with 678,650,699 and contigs at 447,500 with N50 at 1,423 using the Illumina HiSeqX10 sequencing platform. (biorxiv.org)

An allele is one of two or more versions of DNA sequence (a single base or a segment of bases) at a given genomic location. (genome.gov)

This article will review recent impact of massively parallel next-generation sequencing (NGS) in our understanding and treatment of cancer. (frontiersin.org)

A protein consists of one or more chains of amino acids (called polypeptides) whose sequence is encoded in a gene. (genome.gov)
field gene bank accessions using microsatellite markers. (academicjournals.org)
Preliminary tests, such as BRAF mutation testing, may be useful in determining which patients are likely to benefit from full gene sequencing. (medscape.com)
9] Thus, persons with colorectal cancers with the BRAF mutation may be unlikely to have HNPCC, and further testing with full gene sequencing is probably unwarranted. (medscape.com)

Microsatellite markers provide a powerful tool in genome researches due to their wide distribution, codominant inheritance and high polymorphism. (biomedcentral.com)

The proteins involved in MMR correct polymerase errors by forming a complex that binds to the mismatched section of DNA, excises the error, and inserts the correct sequence in its place. (wikipedia.org)
REPLI‑g Kits provide DNA polymerase, buffers and reagents for highly uniform whole genome amplification with minimal sequence bias and can be used with various starting materials, including genomic DNA, fresh or dried blood, buccal swabs, fresh or frozen tissue and cells. (qiagen.com)

It can be tested by immunohistochemistry, next-generation sequencing, and fragment analyses. (ajmc.com)
A recent study compared the performance of tumor next-generation sequencing to the current multistep approach (using microsatellite instability (MSI) testing and/or immunohistochemistry (IHC) for MMR proteins). (cdc.gov)

Using a shuttle vector assay, we measured mutation rates at reporter cassettes containing defined mononucleotide, dinucleotide, and tetranucleotide microsatellite sequences. (nih.gov)
The most common microsatellite in humans is a dinucleotide repeat of the nucleotides C and A, which occurs tens of thousands of times across the genome. (wikipedia.org)

The objectives of this study were to construct a normalized cDNA library for efficient EST analysis, to generate thousands of ESTs, and to analyze the ESTs for microsatellites and potential single nucleotide polymorphisms (SNPs). (nih.gov)
A next generation sequencing panel with 303 SNPs on 21 chromosomes showed pUPD in both blood and pancreatic tissue. (lu.se)

Cluster analysis indicated the presence of 635 contigs and 4,053 singletons, generating a total of 4,688 unique sequences. (nih.gov)

The numerous microsatellites will facilitate integration of the linkage and physical maps and serve as valuable resource for fine mapping QTL and positional cloning of genes affecting aquaculture production traits. (biomedcentral.com)
Linkage analysis can help determine regions of interest in whole-genome sequence studies. (karger.com)
However, many linkage studies rely on older microsatellite (MSAT) panels. (karger.com)

Longer sequences are called minisatellite, and even longer sequences are called satellite DNA sites. (wikipedia.org)

In order to enrich the genomic tools already available in this species and provide further insight on the complexity of its genome, we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their contents. (biomedcentral.com)
In the meantime, new genomic research could be changing clinical and public health approaches to reducing the burden of colorectal cancer from LS and in general, by shifting the laboratory testing approach toward tumor next generation sequencing. (cdc.gov)

The REPLI-g Screening kit is intended for rapid screening using a range of genotyping, PCR, sequencing or microarray assays. (qiagen.com)

Although the length of microsatellites can vary from person to person and contributes to the individual DNA "fingerprint", each individual has microsatellites of a set length. (wikipedia.org)

Dr Marshall describes the impacts of microsatellite stability and instability on metastatic colorectal cancer. (ajmc.com)
Universal Screening for Lynch Syndrome: Can Tumor Sequencing Have a Larger Public Health Impact on Treatment and Prevention of Colorectal Cancer? (cdc.gov)

Every patient with colon cancer and every physician treating colon cancer needs to know the microsatellite status of all patients. (ajmc.com)
Although promising, no immunotherapy drugs have been approved by the FDA to treat gastrointestinal malignancies outside of the recent approval of pembrolizumab for the treatment of patients with colon cancer with microsatellite instability (MSI). (medscape.com)

Microsatellite genotyping was used for haplotype analysis. (molvis.org)

Treangen and Salzberg, 2012) Repetitive DNA and next-generation sequencing: computational challenges and solutions. (omictools.com)
The first rainbow trout repeat elements database (INRA RT rep1.0) containing 735 putative repeat elements was developed, and identified almost 59.5% of the BES database in base-pairs as repetitive sequence. (biomedcentral.com)
Approximately 55% of the BES reads (97,846) had more than 100 base pairs of contiguous non-repetitive sequences. (biomedcentral.com)
Second, we highlight the importance and potential of complete or 100% genome sequencing, i.e., the ability to sequence highly repetitive non-coding sequences beyond the reach of current NGS technologies. (frontiersin.org)

The adenoma carcinoma sequence: an indoctrinated model for tumorigenesis, but is it always a clinical reality? (unboundmedicine.com)
TY - JOUR T1 - The adenoma carcinoma sequence: an indoctrinated model for tumorigenesis, but is it always a clinical reality? (unboundmedicine.com)
What is the clinical significance of microsatellites? (flashcardmachine.com)
First Draft Genome Sequence of Leishmania (Viannia) lainsoni Strain 216-34, Isolated from a Peruvian Clinical Case. (cdc.gov)

A total of 35 microsatellites were identified from the ESTs, with 18 having sufficient flanking sequences for primer design. (nih.gov)
A total of 5,542 ESTs were generated representing 4,688 unique sequences. (nih.gov)

A total of 6,528 clones were sequenced from this library generating 5,542 high-quality EST sequences. (nih.gov)

Each of the 3 analysis modules can also be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc. (usgs.gov)
Yesterday, 10x said that it is partnering with Qiagen to co-develop and co-market next-generation sequencing and single-cell biology analysis workflows and informatics solutions. (genomeweb.com)
Transferability of Cucumber Microsatellite Markers Used for Phylogenetic Analysis and Population Structure Study in Bottle Gourd (Lagenaria siceraria (Mol. (springer.com)
Phylogenetic reconstructions obtained from ITS-1 sequences analysis showed that samples from Minorca and Sardinia islands were the most divergent while the three samples from the Tuscan archipelago (Argentario, Giannutri and Elba) appeared genetically homogeneous. (unibo.it)

Microsatellites make up approximately three percent of the human genome, or more than one million fragments of DNA. (wikipedia.org)

populations detected by microsatellite markers: implication for conservation. (academicjournals.org)

The modules are used to 1) identify the subset of paired-end sequences that pass Illumina quality standards, 2) align paired-end reads into a single composite DNA sequence, and 3) identify sequences that possess microsatellites (both simple and compound) conforming to user-specified parameters. (usgs.gov)

In this study, we developed 25 polymorphic microsatellite markers that included 3-13 (mean = 6.32) alleles per locus using 22 red fox individuals. (geneticsmr.com)
In a phase II study of pembrolizumab in patients with microsatellite-high (MSI-H) solid tumors, the objective response rate was 39.6% (95% CI = 31.7% to 47.9%), including 7.4% complete responses (CRs) and 32.2% partial responses (PRs). (medscape.com)

An anticodon is a trinucleotide sequence located at one end of a transfer RNA (tRNA) molecule, which is complementary to a corresponding codon in a messenger RNA (mRNA) sequence. (genome.gov)

recommendations for ecologists when using next generation sequencing for microsatellite development. (datadryad.org)
Data from: Rise of the machines - recommendations for ecologists when using next generation sequencing for microsatellite development. (datadryad.org)
Here we summarize the results of the large scale development of microsatellites for 54 non-model species using NGS and show there are clear differences amongst plants, invertebrates and vertebrates for the number and proportion of motif types recovered that are able to be utilised as markers. (datadryad.org)
This data set represents the sequence data generated during the development of microsatellite markers for Sitka spruce. (data.gov.uk)
The rapid development of DNA sequencing technologies has driven a revolution in our understanding of this highly complex and diverse group of diseases ( Devita and Rosenberg, 2012 ). (frontiersin.org)

The tool works with standard single letter nucleotide or protein codes including ambiguities and can match Prosite patterns in protein sequences. (nih.gov)
The sequence of the four nucleotide bases encodes DNA's information. (genome.gov)

We further show that the Illumina platform is capable of identifying large numbers of microsatellites, even when using unenriched sample libraries and a very small percentage of the sequencing capacity from a single DNA sequencing run. (usgs.gov)
Separately, 10x and Illumina said today that they are partnering to co-market Illumina's sequencing systems and 10x's linked-read sequencing products. (genomeweb.com)

Anatomy22

Organisms20

Diseases16

Chemicals and Drugs19

Analytical, Diagnostic and Therapeutic Techniques and Equipment23

Psychiatry and Psychology1

Phenomena and Processes97

Disciplines and Occupations4

Anthropology, Education, Sociology and Social Phenomena3

Technology, Industry, Agriculture2

Information Science3

Health Care10

Geographicals7

Loci11

Simple sequenc4

Repeats4

Genetic9

Primers2

SSRs2

Based on microsatellite markers1

Characterized by microsatellite instability1

Characterization1

Whole Genome Sequencing6

Chromosome3

Mutations3

Exome Sequencing2

Genomics6

Elaeis guineensis Jacq1

Molecular2

Mismatch repair3

Genome Sequences1

Allele1

Massively parallel1

Gene4

Polymorphism1

Polymerase2

Immunohistochemistry2

Dinucleotide2

SNPs2

Contigs1

Linkage3

Minisatellite1

Genomic2

Assays1

Fingerprint1

Colorectal cancer2

Colon cancer2

Haplotype1

Repetitive4

Clinical4

ESTs2

Clones1

Analysis4

Approximately1

Populations1

Parameters1

Study2

MRNA1

Development5

Nucleotide2

Illumina2