Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Molecular characterization of KRAS wild type tumors in patients with pancreatic adenocarcinoma

doi: 10.1158/1078-0432.CCR-21-3581

Figure Lengend Snippet: Molecular alterations seen in KRAS-WT tumors. 1A: Mutation rates detected by NGS. 1B: Alteration rates detected by immunohistochemistry, copy number amplification rates detected by NGS and fusion rates detected by RNA sequencing. Bars are color coded according to the oncogenic pathways of each biomarker. 1C: BRAF mutations seen in the cohort categorized into class 1, 2 and 3 based on mechanism of action.

Article Snippet: Treatment and survival information were available from a total of 5324 pancreatic cancer patients tested as either KRAS WT (N=705) or KRAS MT (N=4619) using NextGen sequencing platforms (NextSeq or Novaseq).

Techniques: Mutagenesis, Immunohistochemistry, Amplification, RNA Sequencing, Biomarker Discovery

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Molecular characterization of KRAS wild type tumors in patients with pancreatic adenocarcinoma

doi: 10.1158/1078-0432.CCR-21-3581

Figure Lengend Snippet: Volcano plot comparing molecular alterations of KRAS MT vs. WT tumors. NGS: Next-Gen Sequencing detected mutations. Only molecular alterations significantly different (adjusted p<0.05) are labeled. Full results can be found in Supplemental table 4.

Article Snippet: Treatment and survival information were available from a total of 5324 pancreatic cancer patients tested as either KRAS WT (N=705) or KRAS MT (N=4619) using NextGen sequencing platforms (NextSeq or Novaseq).

Techniques: Sequencing, Labeling

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Molecular characterization of KRAS wild type tumors in patients with pancreatic adenocarcinoma

doi: 10.1158/1078-0432.CCR-21-3581

Figure Lengend Snippet: An oncoprint displaying the molecular alteration patten of the 233 PDAC tumors. Each row represents a biomarker of either fusion, mutation or copy number amplification, as well as genomic signatures such as TMB or MSI/MMR. Red, blue and green represents TMB-H, MSI-high/MMR-deficient or mutations detected using DNA-sequencing; green represents copy number amplification detected by DNA sequencing, while navy blue represents fusions detected by RNA Sequencing. Grey represents no alteration detected while blanks represent unavailable data (indeterminate results due to low coverage or noisy signals). Bars on the right represents the prevalence of molecular alterations of each row.

Article Snippet: Treatment and survival information were available from a total of 5324 pancreatic cancer patients tested as either KRAS WT (N=705) or KRAS MT (N=4619) using NextGen sequencing platforms (NextSeq or Novaseq).

Techniques: Biomarker Discovery, Mutagenesis, Amplification, DNA Sequencing, RNA Sequencing

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Molecular characterization of KRAS wild type tumors in patients with pancreatic adenocarcinoma

doi: 10.1158/1078-0432.CCR-21-3581

Figure Lengend Snippet: Comparison of Tumor Microenvironment (TME) characteristics in KRAS MT vs. WT tumors. 5A: Lymphocyte cell fractions estimated by RNA sequencing using Quantiseq.5B: Stromal cell populations estimated by RNA sequencing using MCP counter.**: significantly different after correcting for multiple comparison; * trending differences.

Article Snippet: Treatment and survival information were available from a total of 5324 pancreatic cancer patients tested as either KRAS WT (N=705) or KRAS MT (N=4619) using NextGen sequencing platforms (NextSeq or Novaseq).

Techniques: Comparison, RNA Sequencing

Journal: The Journal of Experimental Medicine

Article Title: h CALCRL mutation causes autosomal recessive nonimmune hydrops fetalis with lymphatic dysplasia

doi: 10.1084/jem.20180528

Figure Lengend Snippet: Familial pedigree, placental histology and sequencing traces of family with NIHF. (A) Whole exome sequencing identified mutations in subject IV.3 in h CALCRL following the elimination of all previously implicated candidate genes. Parents, III.3 and III.4, and maternal grandmother were confirmed as heterozygous carriers of the hCALCRL(V205del) variant. Family history gives rise to two phenotypes dependent on haplotype: subfertility and nonimmune HF. (B) Placental histology from affected homozygous fetuses (IV.2 and IV.3) compared with a gestational-matched, normal placenta. The right column represents enlargements of boxed areas in the left column. Arrowheads indicate fetal vessels. In the case of the normal placenta, these vessels are completely filled with fetal erythrocytes and distributed both at the periphery and closer to the central villus core. In the case of the two affected placentas, the fetal vessels are more commonly found near the villus periphery, are compressed, and contain fewer erythrocytes. Arrows indicate presence of scattered Hofbauer cells. Asterisks indicate regions of severe edema within the chorionic villi of the affected placentas, a finding not seen in the normal placenta. (C) Whole exome sequencing traces for IV.3, III.4, and III.3 showing the amino acid residue valine 205 deletion (yellow). In individuals III.4 and III.3, the heterozygous allele (gray) is represented by the double peak.

Article Snippet: Whole-exome sequencing was performed on exon targets isolated from patient IV.3 by capture using nextSeq Exome sequencing Platform (Illumina) at CentoGene and an end-to-end bioinformatics pipeline was applied.

Techniques: Sequencing, Variant Assay, Residue