Next-Generation Sequencing

Agilent SLIMS

Agilent SLIMS for Biobanks brings a consistent, holistic approach to managing your lab’s biospecimen samples, improving the quality of research and the reliability of results. SLIMS provides a fast, easy way to manage your biological materials, and to implement quality control measures to be taken during sample collection, prior to sample accession, and upon sample use, ensuring the highest quality possible for your biobank.

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Agilent SLIMS for Biobanks

Oncotarget

Oncotarget published this trending research paper on March 21, 2023 in Volume 14, entitled, “Attenuation of cancer proliferation by suppression of glypican-1 and its pleiotropic effects in neoplastic behavior" by researchers from the Department of Experimental Medical Science, Glycobiology Group, Lund University, Biomedical Center A13, Lund, Sweden; Genevia Technologies Oy, Tampere 33100, Finland.

DOI - https://doi.org/10.18632/oncotarget.28388

Correspondence to - Katrin Mani - katrin.mani@med.lu.se

Abstract

Glypicans (GPC1-6) are associated with tumorigenic processes and their involvement in neoplastic behavior has been discussed in different cancer types. Here, a cancer-wide GPC expression study, using clinical cancer patient data in The Cancer Genome Atlas, reveals net upregulation of GPC1 and GPC2 in primary solid tumors, whereas GPC3, GPC5 and GPC6 display lowered expression pattern compared to normal tissues. Focusing on GPC1, survival analyses of the clinical cancer patient data reveal statistically significant correlation between high expression of GPC1 and poor prognosis in 10 particular cancer types i.e., bladder urothelial carcinoma, brain lower grade glioma, liver hepatocellular carcinoma, colon adenocarcinoma, kidney renal clear cell carcinoma, lung adenocarcinoma, mesothelioma, ovarian serous cystadenocarcinoma, uterine corpus endometrial carcinoma and uveal melanoma. In vitro studies targeting GPC1 expression by CRISPR/Cas9 or siRNA or treatment with an anti-GPC1 antibody resulted in attenuation of proliferation of cancer cells from bladder carcinoma, glioma and hepatocellular carcinoma patients (T24, U87 and HepG2 cells). Further, overexpression of GPC1 exhibited a significant and negative correlation between GPC1 expression and proliferation of T24 cells. Attempt to reveal the mechanism through which downregulation of GPC1 leads to attenuation of tumor growth using systematic Ingenuity Pathway Analysis indicate that suppression of GPC1 results in ECM-mediated inhibition of specific pro-cancer signaling pathways involving TGF-β and p38 MAPK. Identified differential expression and pleiotropic effects of GPCs in specific cancer types emphasize their potential as novel diagnostic tools and prognostic factors and open doors for future GPC targeted therapy.

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Keywords - Glypican-1, TCGA, bladder carcinoma, hepatocellular carcinoma, glioma

About Oncotarget

Oncotarget is a primarily oncology-focused, peer-reviewed, open access journal. Papers are published continuously within yearly volumes in their final and complete form, and then quickly released to Pubmed. On September 15, 2022, Oncotarget was accepted again for indexing by MEDLINE. Oncotarget is now indexed by Medline/PubMed and PMC/PubMed.

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Attenuation of Cancer Proliferation by Suppression of Glypican-1 and Pleiotropic Effects

Agilent Diagnostics & Genomics Group

The right sequencing data analysis and interpretation solution for your lab. With our suite of sequencing analysis tools, you can design a custom panel, analyze your genomic data, interpret your findings in the context of relevant databases, and manage your laboratory information with ease.  The Alissa Clinical Informatics Platform offers integrated sequencing analysis solutions to manage data, helping you to identify, triage and classify variants and generate customizable reports for clinical NGS and CGH.

[url][link]https://www.agilent.com/en/solutions/genomics-applications-solutions/informatics?utm_source=TechnologyNetworks&utm_medium=video&utm_campaign=DGG_23_Alissa_WE-01&utm_content=video
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Agilent Alissa Clinical Informatics Platform

CD Genomics

CD genomics can provide microorganism quantification amplicon sequencing based on 16S external standard sequences to obtain absolute abundance data for species in the sample. The 16S amplicon library is constructed and sequenced by adding a synthetic sequence of known copy number to the sample DNA, and then a standard curve is drawn according to the number of amplicon reads and the absolute copy number of the external standard sequence. And finally the absolute copy number of the 16S rRNA gene of the corresponding species of the OTU representative sequence in the sample is calculated. More information at https://www.cd-genomics.com/absolute-quantitative-16s-18s-its-amplicon-sequencing.html

Bioinformatics Analysis of 16s rRNA Amplicon Sequencing Data

CD Genomics has further optimized the process to exceed PacBio’s benchmarks in output and read length to support long-read metagenomic sequencing, and reduce some splicing errors and effectively improve the resolution of microbial community profiling. https://www.cd-genomics.com/Long-Read-Metagenomic-Sequencing.html

What is Metagenomics?

16S rRNA gene sequencing is commonly used for identification, classification and quantitation of microbes within complex biological mixture. In brief, the hypervariable regions of 16s rDNA in prokaryote are amplified by PCR.  The CD genomics can provide microorganism quantification amplicon sequencing based on 16S external standard sequences to obtain absolute abundance data for species in the sample. The 16S amplicon library is constructed and sequenced by adding a synthetic sequence of known copy number to the sample DNA, and then a standard curve is drawn according to the number of amplicon reads and the absolute copy number of the external standard sequence.  https://www.cd-genomics.com/absolute-quantitative-16s-18s-its-amplicon-sequencing.html

What Is 16s rRNA sequencing？

CD Genomics is committed to providing novel NGS services enabling researchers to explore structure and function of the microbial community in a high-resolution and culture-independent manner using technology from Illumina and PacBio. In addition, we also offer the service to sequence the genome of the individual cultured bacteria, fungi, phage or virus, whether do novo or re-sequencing. https://www.cd-genomics.com/Microbial-Genomics.html

Microbial Genomics Solutions at CD Genomics

Oncotarget published this research paper in Volume 14, entitled, “The 'extreme phenotype approach' applied to male breast cancer allows the identification of rare variants of ATR as potential breast cancer susceptibility alleles" by researchers from the Inserm UMR 1231 GAD Génétique des Anomalies du Développement, Université de Bourgogne, Dijon, France; Unité Fonctionnelle Innovation diagnostique dans les maladies rares, laboratoire de génétique chromosomique et moléculaire, Plateau Technique de Biologie, CHU Dijon Bourgogne, Dijon, France; Human DNA Damage Response Disorders Group, University of Sussex, Genome Damage and Stability Centre, Brighton, United Kingdom; Service d’Oncogénétique, Centre Georges François Leclerc, Dijon, France; Département de biologie et pathologie des tumeurs, Centre Georges François Leclerc, Dijon, France; Oncobiologie Génétique Bioinformatique, PCBio, CHU Besançon, Besançon, France; Centre de Génétique et Centre de Référence Maladies Rares Anomalies du Développement de l’Interrégion Est, Hôpital d’Enfants, CHU Dijon Bourgogne, Dijon, France; Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), CHU Dijon Bourgogne et Université de Bourgogne-Franche Comté, Dijon, France; Laboratoire de Génétique Médicale, INSERM U954, Hôpitaux de Brabois, Vandoeuvre les Nancy, France; Laboratoire d’Oncologie Moléculaire, Centre Jean Perrin, Clermont-Ferrand, France; Unité d’Oncogénétique, ICM Val d’Aurel, Montpellier, France; Université Bordeaux, IMB, UMR 5251, Talence, France; Service d’imagerie diagnostique et interventionnelle de l’adulte, Hôpital Pellegrin, CHU de Bordeaux, France; UF6948 oncogénétique, CHRU de Strasbourg, France; Service de génétique, CHU-Reims, France; Département d’oncologie médicale, INSERM LNC U1231, Centre Georges François Leclerc, Dijon, France.

DOI - https://doi.org/10.18632/oncotarget.28358

Correspondence to - Sophie Nambot - sophie.nambot@chu-dijon.fr

Abstract

In oncogenetics, some patients could be considered as “extreme phenotypes”, such as those with very early onset presentation or multiple primary malignancies, unusually high numbers of cancers of the same spectrum or rare cancer types in the same parental branch. For these cases, a genetic predisposition is very likely, but classical candidate gene panel analyses often and frustratingly remain negative. In the framework of the EX2TRICAN project, exploring unresolved extreme cancer phenotypes, we applied exome sequencing on rare familial cases with male breast cancer, identifying a novel pathogenic variant of ATR (p.Leu1808*). ATR has already been suspected as being a predisposing gene to breast cancer in women. We next identified 3 additional ATR variants in a cohort of both male and female with early onset and familial breast cancers (c.7762-2A>C; c.2078+1G>A; c.1A>G). Further molecular and cellular investigations showed impacts on transcripts for variants affecting splicing sites and reduction of ATR expression and phosphorylation of the ATR substrate CHEK1. This work further demonstrates the interest of an extended genetic analysis such as exome sequencing to identify very rare variants that can play a role in cancer predisposition in extreme phenotype cancer cases unexplained by classical cancer gene panels testing.

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Keywords - male breast cancer, genetic predisposition to cancer, exome sequencing, ATR, extreme phenotype

About Oncotarget

Oncotarget is a primarily oncology-focused, peer-reviewed, open access journal. Papers are published continuously within yearly volumes in their final and complete form, and then quickly released to Pubmed. On September 15, 2022, Oncotarget was accepted again for indexing by MEDLINE. Oncotarget is now indexed by Medline/PubMed and PMC/PubMed.

To learn more about Oncotarget, please visit https://www.oncotarget.com and connect with us:

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18009220957

“Extreme Phenotype Approach” Applied to Male Breast Cancer Allows ID of Rare Variants…

Aging (Aging-US)

Aging-US published this research paper in Volume 15, Issue 2, entitled, "Body weight influences musculoskeletal adaptation to long-term voluntary wheel running during aging in female mice" by the Department of Anatomy, Cell Biology and Physiology, School of Medicine, Indiana University, Indianapolis, IN; Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri, Kansas City, MO; Bone-Muscle Research Center, College of Nursing and Health Innovation, University of Texas, Arlington, TX; Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN; Department of Biomedical Sciences, School of Medicine, University of Missouri, Kansas City, MO; Department of Orthopaedic Surgery, School of Medicine, Indiana University, Indianapolis, IN.

DOI - https://doi.org/10.18632/aging.204390

Corresponding authors - Lynda Bonewald - lbonewal@iu.edu, Michael J. Wacker - wackerm@umkc.edu 

Abstract

Frailty is the hallmark of aging that can be delayed with exercise. The present studies were initiated based on the hypothesis that long-term voluntary wheel running (VWR) in female mice from 12 to 18 or 22 months of age would have beneficial effects on the musculoskeletal system. Mice were separated into high (HBW) and low (LBW) body weight based on final body weights upon termination of experiments. Bone marrow fat was significantly higher in HBW than LBW under sedentary conditions, but not with VWR. HBW was more protective for soleus size and function than LBW under sedentary conditions, however VWR increased soleus size and function regardless of body weight. VWR plus HBW was more protective against muscle loss with aging. Similar effects of VWR plus HBW were observed with the extensor digitorum longus, EDL, however, LBW with VWR was beneficial in improving EDL fatigue resistance in 18 mo mice and was more beneficial with regards to muscle production of bone protective factors. VWR plus HBW maintained bone in aged animals. In summary, HBW had a more beneficial effect on muscle and bone with aging especially in combination with exercise. These effects were independent of bone marrow fat, suggesting that intrinsic musculoskeletal adaptions were responsible for these beneficial effects.

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Keywords - body weight, musculoskeletal adaptation, long-term, voluntary wheel running, aging

About Aging-US

Launched in 2009, Aging-US publishes papers of general interest and biological significance in all fields of aging research and age-related diseases, including cancer—and now, with a special focus on COVID-19 vulnerability as an age-dependent syndrome. Topics in Aging-US go beyond traditional gerontology, including, but not limited to, cellular and molecular biology, human age-related diseases, pathology in model organisms, signal transduction pathways (e.g., p53, sirtuins, and PI-3K/AKT/mTOR, among others), and approaches to modulating these signaling pathways.

Please visit our website at https://www.Aging-US.com​​ and connect with us:

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Next-Generation Sequencing

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