Syukri Shukor

Optical genome mapping enables accurate testing of large repeat expansions

Bart P. G. H. van der Sanden, Kornelia Neveling, Syukri Shukor, Michael D. Gallagher et autres

Short tandem repeats (STRs) are common variations in human genomes that frequently expand or contract, causing genetic disorders, mainly when expanded. Traditional diagnostic methods for identifying these expansions, such as repeat-primed PCR and Southern blotting, are often labor-intensive, locus-specific, and are unable …

nl, us, au (code pays fourni par la source)

Optical Genome Mapping for Applications in Repeat Expansion Disorders

Bart P. G. H. van der Sanden, Kornelia Neveling, Andy Wing Chun Pang, Syukri Shukor et autres

Short tandem repeat (STR) expansions are associated with more than 60 genetic disorders. The size and stability of these expansions correlate with the severity and age of onset of the disease. Therefore, being able to accurately detect the absolute length of STRs …

nl, us (code pays fourni par la source)

Optical genome mapping enables accurate repeat expansion testing

Bart P. G. H. van der Sanden, Kornelia Neveling, Syukri Shukor, Michael D. Gallagher et autres

ABSTRACT Short tandem repeats (STRs) are amongst the most abundant class of variations in human genomes and are meiotically and mitotically unstable which leads to expansions and contractions. STR expansions are frequently associated with genetic disorders, with the size of expansions often …

us, au (code pays fourni par la source)

521 GEN-009, a personalized neoantigen vaccine candidate, elicits diverse and durable immune responses associated with clinical efficacy outcomes

Mara G. Shainheit, Ece Bicak, Masoud Golshadi, Gabriella Santone et autres

Background GEN-009, a personalized vaccine candidate comprised of ATLAS™-prioritized neoantigens combined with Hiltonol®, is currently being evaluated in a Phase 1/2a clinical trial (NCT03633110). ATLAS™ is a cell-based recall assay that, without predictions, screens each patient‘s mutanome to identify neoantigens for vaccine …

us (code pays fourni par la source)

485 Long term results from a phase 1 trial of GEN-009, a personalized neoantigen vaccine, combined with PD-1 inhibition in advanced solid tumors

Maura L. Gillison, Mark Magdi Awad, Przemyslaw W. Twardowski, Ammar W. Sukari et autres

Background GEN-009 adjuvanted personalized cancer vaccine contains up to 20 neoantigens selected by ATLAS™, an ex vivo bioassay screening autologous T-cells for immune responses against both neoantigens and Inhibigens™. Inhibigen-specific T-cells suppress immunity, have been shown to accelerate tumor progression in mice, …

us (code pays fourni par la source)

413 GEN-009, a personalized neoantigen vaccine, elicits robust immune responses in individuals with advanced or metastatic solid tumors

Mara G. Shainheit, Devin Champagne, Gabriella Santone, Syukri Shukor et autres

Background ATLASTM is a cell-based bioassay that utilizes a cancer patient‘s own monocyte-derived dendritic cells and CD4+ and CD8+ T cells to screen their mutanome and identify neoantigens that elicit robust anti-tumor T cell responses, as well as, deleterious InhibigensTM.1 GEN-009, a …

us (code pays fourni par la source)

Tracking leukemic T‐cell transcriptional dynamics in vivo with a blood‐based reporter assay

Alfred G. Tamayo, Syukri Shukor, Alexandra Burr, Patrick Erickson et autres

Transcriptional dynamics of cancer cells govern cell fate decisions and are therapeutically actionable drug targets. In this study, we engineered a circulating cancer cell line that secretes a luciferase reporter to capture constitutive and circadian clock-driven transcription dynamics over the course of …

us (code pays fourni par la source)

Quantitative assessment of LASSO probe assembly and long-read multiplexed cloning

Syukri Shukor, Alfred G. Tamayo, Lorenzo Tosi, H. Benjamin Larman et autres

BACKGROUND: Long Adapter Single-Stranded Oligonucleotide (LASSO) probes were developed as a novel tool for massively parallel cloning of kilobase-long genomic DNA sequences. LASSO dramatically improves the capture length limit of current DNA padlock probe technology from approximately 150 bps to several kbps. …

us (code pays fourni par la source)

Computational Simulation of Adapter Length-Dependent LASSO Probe Capture Efficiency

Jingqian Liu, Syukri Shukor, Shuxiang Li, Alfred G. Tamayo et autres

Multiplexed cloning of long DNA sequences is a valuable technique in many biotechnology applications, such as long-read genome sequencing and the creation of open reading frame (ORF) libraries. Long-adapter single-stranded oligonucleotide (LASSO) probes have shown promise as a tool to clone long …

us (code pays fourni par la source)

Additional file 4: of Quantitative assessment of LASSO probe assembly and long-read multiplexed cloning

Syukri Shukor, Alfred G. Tamayo, Lorenzo Tosi, H. Benjamin Larman et autres

Table S3. Single Target Capture ImageJ Pixel Density Plot. Single target LASSO captures were visualized on PAGE gels and imaged. Major and minor bands were highlighted using ImageJ to obtain pixel density plots. (XLSX 8 kb)

Additional file 3: of Quantitative assessment of LASSO probe assembly and long-read multiplexed cloning

Syukri Shukor, Alfred G. Tamayo, Lorenzo Tosi, H. Benjamin Larman et autres

Table S2. NGS Read Accounting of Sequenced LASSO E. coli ORF-eome Captures. The table shows raw sequencing output (HiSeq 1 × 50 bp platform) of PCR amplified multiplexed ORF-eome capture. Reads were first aligned to both E. coli genome and LASSO probe …

Additional file 2: of Quantitative assessment of LASSO probe assembly and long-read multiplexed cloning

Syukri Shukor, Alfred G. Tamayo, Lorenzo Tosi, H. Benjamin Larman et autres

Table S1. NGS Read Accounting of Sequenced Assembled LASSO Probes The table shows raw sequencing output (MiSeq 2 × 75 bp platform) of inversion PCR products before and after read pairing, sequencing duplicate removal, and alignment using our NGS pipeline. (XLSX 8 …