scholarly journals Frequent detection of CXCR4-using viruses among Brazilian blood donors with HIV-1 long-standing infection and unknown clinical stage: Analysis of massive parallel sequencing data

Data in Brief ◽  
2016 ◽  
Vol 6 ◽  
pp. 267-274
Author(s):  
Rodrigo Pessôa ◽  
Sabri S. Sanabani
Keyword(s):  
Blood Donors ◽  
Clinical Stage ◽  
Massive Parallel Sequencing ◽  
Sequencing Data ◽  
Parallel Sequencing ◽  
Stage Analysis ◽  
Hiv 1

scholarly journals Massive parallel sequencing in a family with rectal cancer

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Karin Wallander ◽  
Jessada Thutkawkorapin ◽  
Ellika Sahlin ◽  
Annika Lindblom ◽  
Kristina Lagerstedt-Robinson
Keyword(s):  
Rectal Cancer ◽  
Genetic Variant ◽  
Family Members ◽  
Wnt Signaling Pathway ◽  
Massive Parallel Sequencing ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Cancer Syndrome ◽  
Parallel Sequencing ◽  
Missense Variants

Abstract Background We have previously reported a family with a suspected autosomal dominant rectal and gastric cancer syndrome without any obvious causative genetic variant. Here, we focused the study on a potentially isolated rectal cancer syndrome in this family. Methods We included seven family members (six obligate carriers). Whole-exome sequencing and whole-genome sequencing data were analyzed and filtered for shared coding and splicing sequence and structural variants among the affected individuals. Results When considering family members with rectal cancer or advanced adenomas as affected, we found six new potentially cancer-associated variants in the genes CENPB, ZBTB20, CLINK, LRRC26, TRPM1, and NPEPL1. All variants were missense variants and none of the genes have previously been linked to inherited rectal cancer. No structural variant was found. Conclusion By massive parallel sequencing in a family suspected of carrying a highly penetrant rectal cancer predisposing genetic variant, we found six genetic missense variants with a potential connection to the rectal cancer in this family. One of them could be a high-risk genetic variant, or one or more of them could be low risk variants. The p.(Glu438Lys) variant in the CENPB gene was found to be of particular interest. The CENPB protein binds DNA and helps form centromeres during mitosis. It is involved in the WNT signaling pathway, which is critical for colorectal cancer development and its role in inherited rectal cancer needs to be further examined.

scholarly journals Assessment of the gene mosaicism burden in blood and its implications for immune disorders

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Manuel Solís-Moruno ◽  
Anna Mensa-Vilaró ◽  
Laura Batlle-Masó ◽  
Irene Lobón ◽  
Núria Bonet ◽  
...  
Keyword(s):  
Whole Blood ◽  
Genetic Load ◽  
Low Frequency ◽  
Massive Parallel Sequencing ◽  
Sequencing Data ◽  
Somatic Variation ◽  
Low Frequencies ◽  
Parallel Sequencing ◽  
Negative Results ◽  
Relevant Role

AbstractThere are increasing evidences showing the contribution of somatic genetic variants to non-cancer diseases. However, their detection using massive parallel sequencing methods still has important limitations. In addition, the relative importance and dynamics of somatic variation in healthy tissues are not fully understood. We performed high-depth whole-exome sequencing in 16 samples from patients with a previously determined pathogenic somatic variant for a primary immunodeficiency and tested different variant callers detection ability. Subsequently, we explored the load of somatic variants in the whole blood of these individuals and validated it by amplicon-based deep sequencing. Variant callers allowing low frequency read thresholds were able to detect most of the variants, even at very low frequencies in the tissue. The genetic load of somatic coding variants detectable in whole blood is low, ranging from 1 to 2 variants in our dataset, except for one case with 17 variants compatible with clonal haematopoiesis under genetic drift. Because of the ability we demonstrated to detect this type of genetic variation, and its relevant role in disorders such as primary immunodeficiencies, we suggest considering this model of gene mosaicism in future genetic studies and considering revisiting previous massive parallel sequencing data in patients with negative results.

Autoantibodies to Phospholipids and to the Coagulation Proteins in AIDS

1997 ◽  
Vol 77 (05) ◽  
pp. 0856-0861 ◽  
Author(s):  
N Abuaf ◽  
S Laperche ◽  
B Rajoely ◽  
R Carsique ◽  
A Deschamps ◽  
...  
Keyword(s):  
Lupus Erythematosus ◽  
Antiphospholipid Antibodies ◽  
Blood Donors ◽  
Heterogeneous Mixture ◽  
Systemic Lupus ◽  
Hematological Disorders ◽  
False Positive Test ◽  
Glycoprotein I ◽  
Coagulation Proteins ◽  
Hiv 1

SummaryIn HIV-1 infection, an increased prevalence of anticardiolipin autoantibodies (aCL) and lupus anticoagulant (LA) has been described. In order to see if these antibodies are isolated or, like in autoimmune diseases, associated with hematological disorders and with antibodies to other phospholipids and to proteins of coagulation, we investigated 3 groups of patients: 1. 342 HIV-1 infected patients, 2. 145 control patients including 61 systemic lupus erythematosus (SLE) patients, 58 patients with a connective tissue disease, 15 patients with stroke, 11 patients with syphilis and 3.100 blood donors. In HIV-1 infection antiprothrombin (aPrT) antibodies were present in 25% of patients, the prevalence of antiphosphatidylcholine antibodies (aPC) (50%) was almost as high as aCL (64%), and 39% had both antibodies. Absorption on liposomes of the latter revealed an heterogeneous mixture of aCL and aPC or cross-reacting antibodies. In contrast with SLE, anti-β2-glycoprotein I (4%), LA (1%), biological false positive test for syphilis (0.3%), thrombosis (p <0.001) were uncommon. In HIV-1 infection, antiphospholipid antibodies do not associate with features linked to them in SLE or syphilis.

Exploring the usefulness of microhaplotypes in forensic identification using massive parallel sequencing technology

2020 ◽  
Vol 140 (1) ◽  
Author(s):  
Chiara Turchi ◽  
Filomena Melchionda ◽  
Mauro Pesaresi ◽  
Eleonora Ciarimboli ◽  
Carla Bini ◽  
...  
Keyword(s):  
Forensic Identification ◽  
Massive Parallel Sequencing ◽  
Sequencing Technology ◽  
Parallel Sequencing

scholarly journals Development of a User-Friendly Pipeline for Mutational Analyses of HIV Using Ultra-Accurate Maximum-Depth Sequencing

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1338
Author(s):  
Morgan E. Meissner ◽  
Emily J. Julik ◽  
Jonathan P. Badalamenti ◽  
William G. Arndt ◽  
Lauren J. Mills ◽  
...  
Keyword(s):  
Error Rates ◽  
Maximum Depth ◽  
Sequencing Data ◽  
Background Error ◽  
High Background ◽  
Immunodeficiency Virus ◽  
User Friendly ◽  
Viral Mutagenesis ◽  
Hiv 1

Human immunodeficiency virus type 2 (HIV-2) accumulates fewer mutations during replication than HIV type 1 (HIV-1). Advanced studies of HIV-2 mutagenesis, however, have historically been confounded by high background error rates in traditional next-generation sequencing techniques. In this study, we describe the adaptation of the previously described maximum-depth sequencing (MDS) technique to studies of both HIV-1 and HIV-2 for the ultra-accurate characterization of viral mutagenesis. We also present the development of a user-friendly Galaxy workflow for the bioinformatic analyses of sequencing data generated using the MDS technique, designed to improve replicability and accessibility to molecular virologists. This adapted MDS technique and analysis pipeline were validated by comparisons with previously published analyses of the frequency and spectra of mutations in HIV-1 and HIV-2 and is readily expandable to studies of viral mutation across the genomes of both viruses. Using this novel sequencing pipeline, we observed that the background error rate was reduced 100-fold over standard Illumina error rates, and 10-fold over traditional unique molecular identifier (UMI)-based sequencing. This technical advancement will allow for the exploration of novel and previously unrecognized sources of viral mutagenesis in both HIV-1 and HIV-2, which will expand our understanding of retroviral diversity and evolution.

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