Journal: Cancers

Article Title: Neuroblastoma Molecular Risk-Stratification of DNA Copy Number and ALK Genotyping via Cell-Free Circulating Tumor DNA Profiling

doi: 10.3390/cancers13133365

Figure Lengend Snippet: Blood collection tube type and time till processing affect the levels of cfDNA MNA detection. ( A ) Normal blood samples collected in EDTA (E), Streck (S), and PAXgene (P) tubes, spiked immediately with Kelly cell line DNA, and processed to plasma at the indicated time post venipuncture with or without agitation. ( B ) Matched samples collected from patients diagnosed with MNA-neuroblastoma at initial presentation prior to treatment (diagnosis) or at disease recurrence, and at after 1 cycle of chemotherapy. Blood was collected in EDTA (E) and Streck (S) tubes and processed at the indicated time post venipuncture (in brackets) after incubation at room temperature without agitation. Following cfDNA extraction from plasma MYCN copy number (navy, left Y axis, values showed on outside end) and THNSL2 concentrations (grey, right Y axis) assessed by duplex ddPCR and presented with 95% CI.

Article Snippet: Samples analyzed for MYCN , and THNSL2 genomic regions in the Rotor Gene Q (QIAGEN) real-time PCR, similarly to ddPCR: qPCR reactions consisted of 10 μL ddPCRTM Supermix for Probes (No dUTP) (Bio-Rad Laboratories), 0.8 μL of MYCN and THNSL2 PrimePCR Copy Number Assays (dHsaCP2506554, and dHsaCP2506297, respectively; final concentrations of primers and probes of 500 nM and 200 nM, respectively), 4 units of HaeIII restriction enzyme (New England BioLabs), and cfDNA/water for a final volume of 20 μL.

Techniques: Clinical Proteomics, Biomarker Discovery, Incubation, Extraction

Journal: Frontiers in Immunology

Article Title: Low unspliced cell-associated HIV RNA in early treated adolescents living with HIV on long suppressive ART

doi: 10.3389/fimmu.2024.1334236

Figure Lengend Snippet: Primers and probes used for detection of HIV CA-RNA and CA-DNA.

Article Snippet: PrimePCR Probe Assay : TBP, human, Hex-labeled, Bio-Rad , Assay ID: qHsaCIP0036255 , reference gene for CA-RNA assay (Bio-Rad).

Techniques: Sequencing

Journal: Cancers

Article Title: Neuroblastoma Molecular Risk-Stratification of DNA Copy Number and ALK Genotyping via Cell-Free Circulating Tumor DNA Profiling

doi: 10.3390/cancers13133365

Figure Lengend Snippet: Blood collection tube type and time till processing affect the levels of cfDNA MNA detection. ( A ) Normal blood samples collected in EDTA (E), Streck (S), and PAXgene (P) tubes, spiked immediately with Kelly cell line DNA, and processed to plasma at the indicated time post venipuncture with or without agitation. ( B ) Matched samples collected from patients diagnosed with MNA-neuroblastoma at initial presentation prior to treatment (diagnosis) or at disease recurrence, and at after 1 cycle of chemotherapy. Blood was collected in EDTA (E) and Streck (S) tubes and processed at the indicated time post venipuncture (in brackets) after incubation at room temperature without agitation. Following cfDNA extraction from plasma MYCN copy number (navy, left Y axis, values showed on outside end) and THNSL2 concentrations (grey, right Y axis) assessed by duplex ddPCR and presented with 95% CI.

Article Snippet: Duplex MYCN / THNSL2 ddPCR reaction consisted of 10 μL ddPCR™ Supermix for Probes (No dUTP) (Bio-Rad Laboratories), 1 μL of MYCN and THNSL2 PrimePCR assay (final concentrations of primers and probes of 900 nM and 250 nM, respectively), 4 units of HaeIII restriction enzyme (New England BioLabs, Notting Hill, VIC, Australia), and cfDNA/water for a final volume of 20 μL.

Techniques: Incubation