TEST:

Archer® VariantPlex® Solid Tumor Kit

FUSIONPlex and VARIANTPlex libraries provide the same fusion and variant identification performance capability on all sequencing platforms tested, suggesting that both assays are sequencing platform agnostic.

When using 50ng SeraSeq® Myeloid DNA input (LGC Clinical Diagnostics, Inc.) and the VariantPlex Core Myeloid panel (37 gene targets), both the lyophilized VariantPlex and VariantPlex-HT detected 100% (22/22) known variants ranging from 3.8% to 20.4% allele frequency (AF). When using low-quality FFPE and the VariantPlex Complete Solid Tumor panel (430 gene targets), both workflows captured 28/28 (AF: 1.4%-20.2%) and 11/11 (AF:1.2%-18.9%) single nucleotide variants (SNVs) and Insertion and Deletions (InDels) when 50ng of SeraSeq compromised FFPE or 200ng Horizon Severe FFPE was used as input, respectively. The FusionPlex-HT workflow consistently showed increased library complexity using the FusionPlex Lung V2 panel with 20ng or 50ng of Seraseq RNA Fusion Mix v4 input.

The addition of TMB measurement to VariantPlex panels allows additional biomarker testing alongside MSI, SNV, indel, and CNV assessment using the same experimental workflow. Additionally, VariantPlex TMB assays function on FFPE samples over a range of qualities and without a paired normal sample.

The evolutional patterns in glioma depend on clonal selection caused by CNAs, mutations, genetic drift, intratumor heterogeneity and/or the patient’s treatment. Recurrence may arise from one major tumor clone or from one or more subclones within the primary tumor through. Integrated cytogenomic analyses of genetic/epigenetic profiles of primary and all recurrent tissues can contribute to a better understanding of mechanisms responsible for these processes and to identification of new alterations related to gliomas progression and/or resistance to treatment.

According to our data, the genomic profile of colorectal ASC is similar to that of conventional colorectal carcinoma, with significant druggable genetic alterations. Further studies are required to understand the more aggressive clinical behavior of this neoplasm.

"Integrated DNA Technologies, Inc....announced it closed on the purchase of Next Generation Sequencing (NGS) research assays from Invitae Corporation (NYSE: NVTA) under the trademarked name Archer. The integration of IDT’s portfolio with the acquired NGS research assays—which have been foundational in researching novel cancer fusions—will empower labs with an all-in-one solution to uncover biomarkers and advance cancer discoveries. The transaction enables IDT to expand its existing operations, build upon the legacy Archer portfolio, and welcome more than 100 new associates globally....Transaction Details-IDT purchased Archer NGS research assays—which reported high double-digit growth since 2019—from Invitae for cash consideration of approximately $48 million, subject to certain adjustments. The transaction is structured as an asset deal and includes a license to intellectual property related to the AMP technology."

Comparing the mutational patterns of the matched samples, we found that only one cfDNA had the same mutations (KRAS, SMAD4 and TP53) in the paired tissue. The results of the comparison between tumor tissue DNA and matched plasma cfDNA underline the importance of studying the paired solid tumor and plasma samples together.

The addition of TMB measurement to VariantPlex panels allows additional biomarker testing in addition to MSI, SNV, and CNV assessment using the same experimental workflow. Our TMB assay functions on FFPE samples over a range of qualities and without a paired normal sample. Additionally, there is also an ongoing development applying these TMB calling algorithms to a larger VariantPlex panel (>1.4 Mb genomic coverage and 430 genes) to increase gene coverage and improve TMB calling.

Interestingly, 5 out of 9 solid tumour exhibited gene mutations in the TP53; KRAS or MET genes which ones not revealed by the cfDNA Kit. Conclusion In summary, evidence suggests that liquid biopsy could provide relevant prognostic and predictive information in different phases of CRC progression, from early diagnosis and identification of minimal residual disease to the assessment of predictive biomarkers and the evaluation of the response to treatment and of the clonal evolution of the disease.

Round cell SFTs often correspond to IR or HR SFT risk groups. Unexpected/aberrant IHC expression is commonly encountered, with frequent BCOR and CK positivity being the most misleading. Since diffuse STAT6 expression is retained, awareness of this uncommon morphological variant of SFT, leading to the appropriate use of STAT6 IHC is the key to proper diagnosis.

This AMPchemistry based research assay enables detection of multiple mutation types and MSI status using FFPE-derived inputs across a range of input qualities without requiring a matched normal. Our assay and prototype MSI algorithm perform well on previously characterized FFPE samples from multiple tissue types. MSI status calls are strongly concordant with a PCR and CE assay without requiring a matched normal.

The applicability of using an integrated approach to detection of somatic tumor variants and MSI status has great clinical utility for a variety of tumor types. In addition, paired normal tissue is not required for NGS using an expanded panel of mononucleotide markers.

PFS >24 weeks was observed in 22% of patients treated with Fulv plus Enza, including 42% who had prior Fulv treatment, suggesting contribution of the anti-androgen. Response was significantly better when metastases were >10% for ER and AR. Poor response to Fulv plus Enza was significantly associated with mTOR pathway activation and patients with PIK3CA and or PTEN mutated metastases had a significantly shorter PFS.

"Our preliminary experience indicates that a focused NGS approach using low-throughput compatible assays is sufficient to guide molecular therapy in the majority of patients. More advanced plan ning of individualized targeted treatments and straightforward access to approved compounds for off-label use may be more effective than broader NGS analyzes to increase clinical benefits from precision oncology."