Fifteen novel microsatellite loci, developed using next-generation sequencing, reveal the lack of genetic structure in Donax vittatus from Iberian Peninsula

2019 ◽  
Vol 217 ◽  
pp. 218-225 ◽  
Author(s):  
Jenyfer Fernández-Pérez ◽  
Ana Nantón ◽  
Alberto Arias-Pérez ◽  
Ana Insua ◽  
Josefina Méndez
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Structure ◽  
Iberian Peninsula ◽  
Microsatellite Loci ◽  
Next Generation ◽  
Generation Sequencing

Microsatellite instability detection using a large next-generation sequencing cancer panel across diverse tumour types

2019 ◽  
Vol 73 (2) ◽  
pp. 83-89 ◽  
Author(s):  
Jiuhong Pang ◽  
Tatyana Gindin ◽  
Mahesh Mansukhani ◽  
Helen Fernandes ◽  
Susan Hsiao
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Instability ◽  
Microsatellite Loci ◽  
Clinical Samples ◽  
Next Generation ◽  
Diverse Range ◽  
Tree Classifier ◽  
Generation Sequencing ◽  
Cancer Panel ◽  
Clinical Cases

AimMicrosatellite instability (MSI), a hallmark of DNA mismatch repair deficiency, is a key molecular biomarker with multiple clinical implications including the selection of patients for immunotherapy, identifying patients who may have Lynch syndrome and predicting prognosis in patients with colorectal tumours. Next-generation sequencing (NGS) provides the opportunity to interrogate large numbers of microsatellite loci concurrently with genomic variants. We sought to develop a method to detect MSI that would not require paired normal tissue and would leverage the sequence data obtained from a broad range of tumours tested using our 467-gene NGS Columbia Combined Cancer Panel (CCCP).MethodsAltered mononucleotide and dinucleotide microsatellite loci across the CCCP region of interest were evaluated in clinical samples encompassing a diverse range of tumour types. The number of altered loci was used to develop a decision tree classifier model trained on the retrospectively collected cohort of 107 clinical cases sequenced by the CCCP assay.ResultsThe classifier was able to correctly classify all cases and was then used to analyse a test set of clinical cases (n=112) and was able to correctly predict their MSI status with 100% sensitivity and specificity. Analysis of recurrently altered loci identified alterations in genes involved in DNA repair, signalling and transcriptional regulation pathways, many of which have been implicated in MSI tumours.ConclusionThis study highlights the utility of this approach, which should be applicable to laboratories performing similar testing.

Development and characterization of 15 polymorphic microsatellite loci in Sonneratia alba (Lythraceae) using next-generation sequencing

2012 ◽  
Vol 4 (3) ◽  
pp. 811-814 ◽  
Author(s):  
Yoshimi Shinmura ◽  
Alison K. S. Wee ◽  
Koji Takayama ◽  
Takeshi Asakawa ◽  
Orlex Baylen Yllano ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Loci ◽  
Next Generation ◽  
Sonneratia Alba ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing

scholarly journals Next Generation Sequencing, Isolation and Characterization of 14 Microsatellite Loci of Canthon Cyanellus (Coleoptera: Scarabaeidae)

2021 ◽  
Author(s):  
Luis R. Arce-Valdés ◽  
Rosa Ana Sánchez-Guillén ◽  
Janet Nolasco-Soto ◽  
Mario E. Favila
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Loci ◽  
Dung Beetle ◽  
Distribution Range ◽  
Next Generation ◽  
Isolation And Characterization ◽  
Paired End Sequencing ◽  
Generation Sequencing

Abstract BackgroundWe used Illumina paired-end-sequencing to isolate and characterize microsatellites of Canthon cyanellus, a Neotropical roller dung beetle encompassing several lineages within its distribution range.Methods and ResultsWe examined C. cyanellus specimens collected at eight different localities in Mexico (two or three specimens per locality). We initially made amplification tests with 16 loci, but two of these showed amplification problems; thus, we evaluated 14 loci. The 14 microsatellites were polymorphic, with 2–16 alleles each. The expected and observed heterozygosity ranged from 0.11 to 0.76 and from 0.20 to 0.78, respectively. ConclusionsThese microsatellites will help to assess structure at the population and lineage levels, identify zones of potential hybridization between lineages, and draw a more precise geographic delimitation of Canthon cyanellus lineages.

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