Methods of Gene Enrichment and Massively Parallel Sequencing Technologies

2013 ◽  
pp. 39-58 ◽  
Author(s):  
Hong Cui
Keyword(s):  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Parallel Sequencing ◽  
Sequencing Technologies ◽  
Gene Enrichment

scholarly journals Assessing genotyping errors in mammalian museum study skins using high-throughput genotyping-by-sequencing

2021 ◽  
Author(s):  
Stella C. Yuan ◽  
Eric Malekos ◽  
Melissa T. R. Hawkins
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Museum Specimens ◽  
Museum Specimen ◽  
Genotyping Errors ◽  
Allelic Dropout ◽  
Parallel Sequencing ◽  
Sequencing Technologies

AbstractThe use of museum specimens held in natural history repositories for population and conservation genetic research is increasing in tandem with the use of massively parallel sequencing technologies. Short Tandem Repeats (STRs), or microsatellite loci, are commonly used genetic markers in wildlife and population genetic studies. However, they traditionally suffered from a host of issues including length homoplasy, high costs, low throughput, and difficulties in reproducibility across laboratories. Massively parallel sequencing technologies can address these problems, but the incorporation of museum specimen derived DNA suffers from significant fragmentation and exogenous DNA contamination. Combatting these issues requires extra measures of stringency in the lab and during data analysis, yet there have not been any high-throughput sequencing studies evaluating microsatellite allelic dropout from museum specimen extracted DNA. In this study, we evaluate genotyping errors derived from mammalian museum skin DNA extracts for previously characterized microsatellites across PCR replicates utilizing high-throughput sequencing. We found it useful to classify samples based on DNA concentration, which determined the rate by which genotypes were accurately recovered. Longer microsatellites performed worse in all museum specimens. Allelic dropout rates across loci were dependent on sample quantity, with high concentration museum specimens performing as well and recovering quality metrics nearly as high as the frozen tissue sample. Based on our results, we provide a set of best practices for quality assurance and incorporation of reliable genotypes from museum specimens.

scholarly journals Genomic and epigenomic heterogeneity in chronic lymphocytic leukemia

Blood ◽  
2015 ◽  
Vol 126 (4) ◽  
pp. 445-453 ◽  
Author(s):  
Romain Guièze ◽  
Catherine J. Wu
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Clinical Course ◽  
Massively Parallel Sequencing ◽  
Clinical Impact ◽  
Lymphocytic Leukemia ◽  
Massively Parallel ◽  
Rapid Progress ◽  
Parallel Sequencing ◽  
Sequencing Technologies ◽  
Over Time

Abstract Defining features of chronic lymphocytic leukemia (CLL) are not only its immunophenotype of CD19+CD5+CD23+sIgdim expressing clonal mature B cells but also its highly variable clinical course. In recent years, advances in massively parallel sequencing technologies have led to rapid progress in our understanding of the CLL genome and epigenome. Overall, these studies have clearly demarcated not only the vast degree of genetic and epigenetic heterogeneity among individuals with CLL but also even within individual patient leukemias. We herein review the rapidly growing series of studies assessing the genetic and epigenetic features of CLL within clinically defined periods of its growth. These studies strongly suggest an evolving spectrum of lesions over time and that these features may have clinical impact.

scholarly journals The application of massively parallel sequencing technologies in diagnostics

10.3410/b2-59 ◽  
2010 ◽  
Vol 2 ◽  
Author(s):  
Andreas Dahl ◽  
Florian Mertes ◽  
Bernd Timmermann ◽  
Hans Lehrach
Keyword(s):  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Parallel Sequencing ◽  
Sequencing Technologies
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