scholarly journals Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors

2017 ◽  
Author(s):  
Brian K Mannakee ◽  
Uthra Balaji ◽  
Agnieszka K. Witkiewicz ◽  
Ryan N. Gutenkunst ◽  
Erik S. Knudsen
Keyword(s):  
Sensitivity And Specificity ◽  
Genome Sequencing ◽  
Genetic Variants ◽  
Great Promise ◽  
Multiple Sources ◽  
Genome Sequences ◽  
Primary Tumors ◽  
Tumor Genome

AbstractMotivationTumor genome sequencing offers great promise for guiding research and therapy, but spurious variant calls can arise from multiple sources. Mouse contamination can generate many spurious calls when sequencing patient-derived xenografts (PDXs). Paralogous genome sequences can also generate spurious calls when sequencing any tumor. We developed a BLAST-based algorithm, MAPEX, to identify and filter out spurious calls from both these sources.ResultsWhen calling variants from xenografts, MAPEX has similar sensitivity and specificity to more complex algorithms. When applied to any tumor, MAPEX also automatically flags calls that potentially arise from paralogous sequences. Our implementation, mapexr, runs quickly and easily on a desktocomputer. MAPEX is thus a useful addition to almost any pipeline for calling genetic variants in tumors.

scholarly journals The Identification of the SARS-CoV-2 Whole Genome: Nine Cases Among Patients in Banten Province, Indonesia

2021 ◽  
Author(s):  
Chris Adhiyanto ◽  
Laifa A. Hendarmin ◽  
Erike A. Suwarsono ◽  
Zeti Harriyati ◽  
Suryani ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Genetic Variants ◽  
Viral Genome ◽  
Genetic Background ◽  
Respiratory Illness ◽  
Whole Genome ◽  
Sequencing Data ◽  
Rt Pcr ◽  
Genome Sequences ◽  
Severe Patient

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the strain of virus that causes coronavirus disease 2019 (COVID-19), the respiratory illness responsible for the current pandemic. Viral genome sequencing has been widely applied during outbreaks to study the relatedness of this virus to other viruses, its transmission mode, pace, evolution and geographical spread, and also its adaptation to human hosts. To date, more than 90,000 SARS-CoV-2 genome sequences have been uploaded to the GISAID database. The availability of sequencing data along with clinical and geographical data may be useful for epidemiological investigations. In this study, we aimed to analyse the genetic background of SARS-CoV-2 from patients in Indonesia by whole genome sequencing. We examined nine samples from COVID-19 patients with RT-PCR cycle threshold (Ct) of less than 25 using ARTIC Network protocols for Oxford Nanopore’s Gridi On sequencer. The analytical methods were based on the ARTIC multiplex PCR sequencing protocol for COVID-19. In this study, we found that several genetic variants within the nine COVID-19 patient samples. We identified a mutation at position 614 P323L mutation in the ORF1ab gene often found in our severe patient samples. The number of SNPs and their location within the SARS-CoV-2 genome seems to vary. This diversity might be responsible for the virulence of the virus and its clinical manifestation.

scholarly journals PathFinder: Bayesian inference of clone migration histories in cancer

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i675-i683
Author(s):  
Sudhir Kumar ◽  
Antonia Chroni ◽  
Koichiro Tamura ◽  
Maxwell Sanderford ◽  
Olumide Oladeinde ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Cancer Cells ◽  
Bayesian Approach ◽  
Genetic Variants ◽  
Cancer Development ◽  
Posterior Probabilities ◽  
Migration Routes ◽  
Primary Tumors ◽  
History Of ◽  
The Web

Abstract Summary Metastases cause a vast majority of cancer morbidity and mortality. Metastatic clones are formed by dispersal of cancer cells to secondary tissues, and are not medically detected or visible until later stages of cancer development. Clone phylogenies within patients provide a means of tracing the otherwise inaccessible dynamic history of migrations of cancer cells. Here, we present a new Bayesian approach, PathFinder, for reconstructing the routes of cancer cell migrations. PathFinder uses the clone phylogeny, the number of mutational differences among clones, and the information on the presence and absence of observed clones in primary and metastatic tumors. By analyzing simulated datasets, we found that PathFinder performes well in reconstructing clone migrations from the primary tumor to new metastases as well as between metastases. It was more challenging to trace migrations from metastases back to primary tumors. We found that a vast majority of errors can be corrected by sampling more clones per tumor, and by increasing the number of genetic variants assayed per clone. We also identified situations in which phylogenetic approaches alone are not sufficient to reconstruct migration routes. In conclusion, we anticipate that the use of PathFinder will enable a more reliable inference of migration histories and their posterior probabilities, which is required to assess the relative preponderance of seeding of new metastasis by clones from primary tumors and/or existing metastases. Availability and implementation PathFinder is available on the web at https://github.com/SayakaMiura/PathFinder.

scholarly journals Draft Genome Sequences of Lactobacillus salivarius A3iob and Lactobacillus johnsonii CRL1647, Novel Potential Probiotic Strains for Honeybees (Apis mellifera L.)

2018 ◽  
Vol 7 (6) ◽  
Author(s):  
Marcela Carina Audisio ◽  
Leonardo Albarracín ◽  
Maria Julia Torres ◽  
Lucila Saavedra ◽  
Elvira Maria Hebert ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Genome Sequencing ◽  
Draft Genome ◽  
Illumina Miseq ◽  
Whole Genome ◽  
Genome Sequences ◽  
Lactobacillus Johnsonii ◽  
Lactobacillus Salivarius ◽  
Content Type ◽  
Probiotic Strains

This report describes the draft genome sequences of Lactobacillus salivarius A3iob and Lactobacillus johnsonii CRL1647, probiotic strains isolated from the gut of honeybee Apis mellifera workers. The reads were generated by a whole-genome sequencing (WGS) strategy on an Illumina MiSeq sequencer and were assembled into contigs with total sizes of 2,054,490 and 2,137,413 bp for the A3iob and CRL1647 strains, respectively.

scholarly journals You can’t judge a book by its cover or a tumor by its expression profile

2012 ◽  
Vol 2 (1) ◽  
pp. 21
Author(s):  
Steven M. Sorscher ◽  
Theodore Thomas
Keyword(s):  
Expression Profile ◽  
Expression Profiling ◽  
Radiographic Progression ◽  
Clinical Course ◽  
Unknown Primary ◽  
Great Promise ◽  
Primary Tumors ◽  
Remarkable Case ◽  
Rate Of Progression ◽  
Poorly Differentiated

Expression profiling has shown great promise in matching cancers of unknown primary to likely primary tumors of origin based on patterns of mRNA expression. However, it remains uncertain as to whether even well matched tumors will demonstrate the clinical features, such as rate of progression, of their matched counterparts. In this case report, we note that based on histology, immunohistochemistry and expression profile this patient’s poorly differentiated neuroendocrine tumor would have been expected to grow very rapidly on no therapy. Instead, this cancer was very indolent, with only very little radiographic progression over several years. We believe this report represents a remarkable case of a tumor where features, including expression profile, would not at all have accurately predicted the clinical course seen. While some series have suggested that matching by expression profiling predicts outcome, this case shows a dramatically different result.

scholarly journals Complete Genome Sequences of Three African Foot-and-Mouth Disease Viruses from Clinical Samples Isolated in 2009 and 2010

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Steven Van Borm ◽  
Toon Rosseel ◽  
Andy Haegeman ◽  
Mpolokang Elliot Fana ◽  
Latoa Seoke ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Complete Genome ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Clinical Samples ◽  
Full Genome ◽  
Full Genome Sequencing ◽  
Genome Sequences ◽  
Foot And Mouth

The complete genome sequences of three foot-and-mouth disease viruses (one virus of each serotype SAT1, SAT2 and O) were directly sequenced from RNA extracted from clinical bovine samples, demonstrating the feasibility of full-genome sequencing from strong positive samples taken from symptomatic animals.

scholarly journals Whole-Genome Sequencing of Nontyphoidal Salmonella enterica Isolates Obtained from Various Meat Types in Ghana

2019 ◽  
Vol 8 (15) ◽  
Author(s):  
Moon Y. F. Tay ◽  
Frederick Adzitey ◽  
Stella Amelia Sultan ◽  
Joseph Makija Tati ◽  
Kelyn L. G. Seow ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Draft Genome ◽  
Protein Source ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Important Protein ◽  
Retail Meats

Here, we report the draft genome sequences of 16 nontyphoidal Salmonella enterica isolates obtained from locally produced meats in Tamale, Ghana, which are commonly consumed by most natives as an important protein source. The draft genomes will help provide a molecular snapshot of Salmonella enterica isolates found in these retail meats in Tamale.

scholarly journals Draft Genome Sequences of Six Strains Isolated from the InSight Spacecraft and Associated Surfaces Using Oxford Nanopore- and Illumina-Based Sequencing

2020 ◽  
Vol 9 (21) ◽  
Author(s):  
Daniel L. Vera ◽  
Arman Seuylemezian ◽  
Kyle S. Landry ◽  
Ryan Hendrickson
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Draft Genome ◽  
Whole Genome ◽  
Genome Sequences ◽  
Planetary Protection ◽  
Functional Capabilities ◽  
Oxford Nanopore ◽  
Associated Surfaces ◽  
Insight Mission

ABSTRACT Whole-genome sequencing and annotation have allowed planetary protection engineers to assess the functional capabilities of microorganisms isolated from spacecraft hardware and associated surfaces. Here, we report draft genomes of six strains isolated from the InSight mission, determined using Oxford Nanopore- and Illumina-based sequencing.

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