Journal: Frontiers in Genetics

Article Title: Analytical validation and implementation of a pan cancer next-generation sequencing panel, CANSeq TM Kids for molecular profiling of childhood malignancies

doi: 10.3389/fgene.2023.1067457

Figure Lengend Snippet: Study Cohort. Summary of clinical specimens and commercial controls used in study (n = 65).

Article Snippet: Three Coriell HapMap DNA samples NA12878, NA18507, NA19240 and two normal colon and lung RNA samples (SeraCare Life Sciences, Milford, MA) were used to determine assay specificity by evaluating positive and negative variant calls of SNV/MNV, INDELs across all targeted hotspots and fusions covered by the assay.

Techniques:

Journal: Frontiers in Genetics

Article Title: Analytical validation and implementation of a pan cancer next-generation sequencing panel, CANSeq TM Kids for molecular profiling of childhood malignancies

doi: 10.3389/fgene.2023.1067457

Figure Lengend Snippet: Study Cohort. Details of specimens used in study.

Article Snippet: Three Coriell HapMap DNA samples NA12878, NA18507, NA19240 and two normal colon and lung RNA samples (SeraCare Life Sciences, Milford, MA) were used to determine assay specificity by evaluating positive and negative variant calls of SNV/MNV, INDELs across all targeted hotspots and fusions covered by the assay.

Techniques: Biomarker Discovery, Mutagenesis, Control

Journal: Frontiers in Genetics

Article Title: Analytical validation and implementation of a pan cancer next-generation sequencing panel, CANSeq TM Kids for molecular profiling of childhood malignancies

doi: 10.3389/fgene.2023.1067457

Figure Lengend Snippet: Quality metrics and thresholds.

Article Snippet: Three Coriell HapMap DNA samples NA12878, NA18507, NA19240 and two normal colon and lung RNA samples (SeraCare Life Sciences, Milford, MA) were used to determine assay specificity by evaluating positive and negative variant calls of SNV/MNV, INDELs across all targeted hotspots and fusions covered by the assay.

Techniques:

Journal: Frontiers in Genetics

Article Title: Analytical validation and implementation of a pan cancer next-generation sequencing panel, CANSeq TM Kids for molecular profiling of childhood malignancies

doi: 10.3389/fgene.2023.1067457

Figure Lengend Snippet: Accuracy. The LOI of DNA and RNA.

Article Snippet: Three Coriell HapMap DNA samples NA12878, NA18507, NA19240 and two normal colon and lung RNA samples (SeraCare Life Sciences, Milford, MA) were used to determine assay specificity by evaluating positive and negative variant calls of SNV/MNV, INDELs across all targeted hotspots and fusions covered by the assay.

Techniques: Variant Assay, Control

Journal: Frontiers in Genetics

Article Title: Analytical validation and implementation of a pan cancer next-generation sequencing panel, CANSeq TM Kids for molecular profiling of childhood malignancies

doi: 10.3389/fgene.2023.1067457

Figure Lengend Snippet: Specificity. Analytical specificity of RNA samples.

Article Snippet: Three Coriell HapMap DNA samples NA12878, NA18507, NA19240 and two normal colon and lung RNA samples (SeraCare Life Sciences, Milford, MA) were used to determine assay specificity by evaluating positive and negative variant calls of SNV/MNV, INDELs across all targeted hotspots and fusions covered by the assay.

Techniques: Control

Journal: Journal of Gastrointestinal Oncology

Article Title: The roles and mechanisms of APOL1 in the development of colorectal cancer

doi: 10.21037/jgo-24-275

Figure Lengend Snippet: Effect of APOL1 on the biological behavior of CRC cells. (A) qRT-PCR was used to determine the APOL1 mRNA levels in HCT116, SW1116, and NCM460 cells. (B) In HCT116 cells, qRT-PCR was used to determine the interference efficacy of shAPOL1#1/2/3. (C) CCK8 assay was used to evaluate the proliferative capacity of HCT116 and SW1116 cells. (D) The count of clones in HCT116 and SW1116 cells was determined using the colony formation test. Staining method: crystal violet. Magnification: ×100. (E) Wound healing test was used to assess the migratory capacity of HCT116 and SW1116 cells (magnification: ×40). (F) The Transwell test was used to determine HCT116 and SW1116 cells’ invasion ability (magnification: ×100). Staining method: crystal violet. Each group, n=3. *, P<0.05 vs. NCM460 group; **, P<0.01; ***, P<0.001 vs . sh-NC group. sh-NC, shRNA-negative control; sh-APOL1, shRNA-apolipoprotein L1; OD, optical density; CRC, colorectal cancer; qRT-PCR, quantitative real-time polymerase chain reaction; CCK8, Cell Counting Kit 8.

Article Snippet: Shanghai iCell Bioscience Inc. (Shanghai, China) provided the human normal colon epithelial cells NCM460 (iCell-h373) and CRC cell lines [HCT116 (iCell-h071) and SW1116 cells (iCell-h201)].

Techniques: Quantitative RT-PCR, CCK-8 Assay, Clone Assay, Staining, shRNA, Negative Control, Real-time Polymerase Chain Reaction, Cell Counting