VarGrouper: A Bioinformatic Tool for Local Haplotyping of Deletion–Insertion Variants from Next-Generation Sequencing Data after Variant Calling

Publication date: Available online 20 February 2019Source: The Journal of Molecular DiagnosticsAuthor(s): Ryan J. Schmidt, Allison Macleay, Long Phi LeAccurate genetic variant representation through nomenclature and annotation is essential for understanding functional consequence and properly noting the presence of variants across time, assays, and laboratories. Current variant calling algorithms detect single deletion–insertion variants as multiple indel and/or substitution variants from next-generation sequencing data. Consequently, these variants are separately annotated in bioinformatics pipelines, leading to inaccurate variant representation. We developed a bioinformatic solution to this problem—VarGrouper—that automatically recognizes individual variants that arise from a deletion–insertion variant and aggregates them into a single variant that can be properly annotated. This tool has been integrated into our routine clinical molecular diagnostics workflow for DNA sequencing of solid tumors. Over an 11-month period, VarGrouper variants were reported by all attending molecular pathologists involved in interpretation and represented 4.1% of all variants reported; 10.9% of cases with reportable variants contained at least one VarGrouper variant. VarGrouper improves the practice of molecular diagnostics by increasing the accuracy and consistency of variant annotation. VarGrouper is freely available for use by the molecular diagnostic community.
Source: The Journal of Molecular Diagnostics - Category: Pathology Source Type: research

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In this study, we found that TLR1/TLR2 expression predicted favorable prognosis of lung cancer patients. In the related mice tumor model, TLR1/TLR2 activation by synthetic bacterial lipoprotein (BLP), a TLR1/2 agonist, greatly inhibited tumor growth and selectively decreased monocytic MDSCs (M-MDSCs). Furthermore, BLP treatment redirected M-MDSC differentiation towards M1 macrophage through JNK pathway, and thus blocked the suppressive activity of M-MDSCs in a TLR2-dependent manner. Therefore, our data demonstrated that TLR2 could be a promising biomarker and a potential immunotherapeutic target for lung cancer.
Source: Molecular Immunology - Category: Allergy & Immunology Source Type: research
Publication date: August 2019Source: Molecular Immunology, Volume 112Author(s): Elizabeth A. Bemis, Jill M. Norris, Jennifer Seifert, Ashley Frazer-Abel, Yuko Okamoto, Marie L. Feser, M. Kristen Demoruelle, Kevin D. Deane, Nirmal K. Banda, V. Michael HolersAbstractRheumatoid arthritis (RA) is a complex autoimmune disease with an etiology that is not yet well understood, disproportionally affects women and also varies in incidence and prevalence by population. The presence of anti-citrullinated protein antibodies (ACPA) is a highly specific biomarker for the diagnosis of clinically apparent RA. ACPA are also present in the ...
Source: Molecular Immunology - Category: Allergy & Immunology Source Type: research
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Source: Analytic Methods in Accident Research - Category: Accident Prevention Source Type: research
Publication date: Available online 14 June 2019Source: Stem Cell ResearchAuthor(s): Nupur Bhargava, Shashank Jaitly, Sangam Giri Goswami, Suman Jain, Debojyoti Chakraborty, Sivaprakash RamalingamAbstractSickle cell disease (SCD) is an autosomal recessive disorder caused by a mutation in β-globin (HBB) gene. We have generated an induced pluripotent stem cell (iPSC) line, IGIBi001-A from an Indian sickle cell patient with a homozygous HBB gene mutation using Sendai virus reprogramming system. Characterization of IGIBi001-A showed that these iPSCs are transgene-free and expressed pluripotent stem cell markers. They had a...
Source: Stem Cell Research - Category: Stem Cells Source Type: research
Publication date: Available online 14 June 2019Source: Stem Cell ResearchAuthor(s): Nutnicha Tantarungsee, Zaukir Bostan Ali, Rungtip Soi-ampornkul, Chuda Rujitharanawong, Chanika Subchookul, Alisa Ritthaphai, Bootsakorn Boonkaew, Methichit Wattanapanitch, Kanchalit Thanomkitti, Daranporn Triwongwaranat, Chinnavuth Vatanashevanopakorn, Rattapon ThuangtongAbstractAn induced pluripotent stem cell (iPSC) line, MUSIi010-A, was established by Sendai virus (SeV) transduction of scalp fibroblasts from a 59-year-old male with androgenetic alopecia (AGA). Pluripotency of the iPSC line was verified by immunofluorescence staining of ...
Source: Stem Cell Research - Category: Stem Cells Source Type: research
Authors: Malergue MC, Ohanessian A, Zannis K, Bruneval P, Ennezat PV PMID: 31199198 [PubMed - as supplied by publisher]
Source: Acta Cardiologica - Category: Cardiology Tags: Acta Cardiol Source Type: research
This report could be used to provide guidance for both practical and economical approaches. PMID: 31190617 [PubMed - as supplied by publisher]
Source: Acta Cardiologica - Category: Cardiology Tags: Acta Cardiol Source Type: research
Authors: Lee JH, Nam JH, Park JS, Lee DH PMID: 31190481 [PubMed - as supplied by publisher]
Source: Korean Circulation Journal - Category: Cardiology Tags: Korean Circ J Source Type: research
CONCLUSIONS: These data provide the current PCI practice pattern with the use of FFR and IVUS in intermediate lesion. More common use of FFR for intermediate lesion should be encouraged. PMID: 31190480 [PubMed - as supplied by publisher]
Source: Korean Circulation Journal - Category: Cardiology Tags: Korean Circ J Source Type: research
CONCLUSIONS: Separate examination of control rates demonstrated different sex- and age-differential trends, which would have been overlooked in combined control rates. PMID: 31190479 [PubMed - as supplied by publisher]
Source: Korean Circulation Journal - Category: Cardiology Tags: Korean Circ J Source Type: research
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