ribo zero human mouse rat set b illumina 20020612 qubit dna high sensitivity kit thermo fisher scientific q32851 sureselect xt hs2 dna kits  (Illumina Inc)

Journal: Technology in Cancer Research & Treatment

Article Title: Combined DNA Analysis from Stool and Blood Samples Improves Tumor Tracking and Assessment of Clonal Heterogeneity in Localized Rectal Cancer Patients

doi: 10.1177/15330338241252706

Figure Lengend Snippet: Sampling process. Timeline of biopsy, blood, and stool specimen collection. Tumor biopsies were taken before any treatment was initiated. Blood and stool samples were collected before neoadjuvant chemoradiotherapy (CRT) and optionally in the interval between CRT completion and curative surgery (up to eight weeks after CRT completion). Biopsy samples were analyzed using the SureSelect TM XT HS-focused exome panel comprising 4800 genes and regions, whereas blood and stool samples were investigated using the AVENIO TM ctDNA surveillance panel covering 197 genes and regions. FFPE: formalin-fixed, paraffin-embedded; cfDNA: cell-free DNA, ctDNA: cell-free tumor DNA, CRT: chemoradiotherapy. Figure created with Biorender.com.

Article Snippet: Because the AVENIO TM Tumor Tissue targeted kit was not available at the time, which covers the same genetic regions as the AVENIO TM ctDNA Library Prep Kit used for plasma and stool samples, the SureSelect TM XT HS Target Enrichment Kit in combination with the SureSelect TM XT HS Focused Exome capture library (Agilent, Santa Clara, USA, cat. no. G9702A; 5190-7787) was used for tissue and resection mutation analysis.

Techniques: Sampling, Formalin-fixed Paraffin-Embedded

Journal: Technology in Cancer Research & Treatment

Article Title: Combined DNA Analysis from Stool and Blood Samples Improves Tumor Tracking and Assessment of Clonal Heterogeneity in Localized Rectal Cancer Patients

doi: 10.1177/15330338241252706

Figure Lengend Snippet: Sequencing Metrics of Individual Sequencing Approaches.

Article Snippet: Because the AVENIO TM Tumor Tissue targeted kit was not available at the time, which covers the same genetic regions as the AVENIO TM ctDNA Library Prep Kit used for plasma and stool samples, the SureSelect TM XT HS Target Enrichment Kit in combination with the SureSelect TM XT HS Focused Exome capture library (Agilent, Santa Clara, USA, cat. no. G9702A; 5190-7787) was used for tissue and resection mutation analysis.

Techniques: Sequencing, Mutagenesis

Journal: Technology in Cancer Research & Treatment

Article Title: Combined DNA Analysis from Stool and Blood Samples Improves Tumor Tracking and Assessment of Clonal Heterogeneity in Localized Rectal Cancer Patients

doi: 10.1177/15330338241252706

Figure Lengend Snippet: Mutational allelic frequencies, numbers, and direct comparisons of identified mutations in different specimens. (A) Allelic frequencies (AF) of mutations identified in different sample specimens. (B) Comparison of AF of detected mutations in paired plasma and stool samples derived from the same patients. (C) Number of identified mutations per patient within different sample specimens. (D) Number of shared and non-shared mutations in the same patient across different specimen comparisons. (E) Number of intersecting mutations in different specimens across all patients (n = 9) from whom all three specimens were analyzed. Only mutations that are covered by both the SureSelect TM (biopsy) and AVENIO TM (plasma and stool) panel are depicted. Numbers above lines in graphs (A–C) represent p-values.

Article Snippet: Because the AVENIO TM Tumor Tissue targeted kit was not available at the time, which covers the same genetic regions as the AVENIO TM ctDNA Library Prep Kit used for plasma and stool samples, the SureSelect TM XT HS Target Enrichment Kit in combination with the SureSelect TM XT HS Focused Exome capture library (Agilent, Santa Clara, USA, cat. no. G9702A; 5190-7787) was used for tissue and resection mutation analysis.

Techniques: Comparison, Derivative Assay

Journal: Technology in Cancer Research & Treatment

Article Title: Combined DNA Analysis from Stool and Blood Samples Improves Tumor Tracking and Assessment of Clonal Heterogeneity in Localized Rectal Cancer Patients

doi: 10.1177/15330338241252706

Figure Lengend Snippet: Comparison of identified mutations across different sample specimens in individual patients. (A) Mutational lesions detected in either tumor biopsy, plasma, or stool samples in individual patients. (B) Mutational analysis in patients from whom plasma and stool samples were available before (plasma/stool) and after (plasma_T2/stool_T2) therapeutic intervention. (C) Comparison of variants detected in tumor biopsies and liquid biopsies (plasma) in patients from whom stool mutational analysis was not available. (D) Comparison of mutations in different sample specimens of patient 1462 whose plasma and stool mutation profile is compared to a resection of the whole tumor (resection). Timeline of the course of disease, sample collection, and therapeutic interventions of Pat 1462 are depicted. Genes marked with X in tissue samples are not covered by the SureSelect TM sequencing panel used for biopsy specimen analysis. Gene names represent individual mutational positions within a certain gene. Grey gene names represent synonymous mutations. Color code represents allelic frequency. CRT: chemoradiotherapy; cfDNA: cell-free DNA.

Article Snippet: Because the AVENIO TM Tumor Tissue targeted kit was not available at the time, which covers the same genetic regions as the AVENIO TM ctDNA Library Prep Kit used for plasma and stool samples, the SureSelect TM XT HS Target Enrichment Kit in combination with the SureSelect TM XT HS Focused Exome capture library (Agilent, Santa Clara, USA, cat. no. G9702A; 5190-7787) was used for tissue and resection mutation analysis.

Techniques: Comparison, Mutagenesis, Sequencing