Jon Kemppainen

Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies

The formalin-fixed, paraffin-embedded (FFPE) biopsy is a challenging sample for molecular assays such as targeted next-generation sequencing (NGS). We compared three methods for FFPE DNA quantification, including a novel PCR assay (‘QFI-PCR’) that measures the absolute copy number of amplifiable DNA, across 165 residual clinical specimens. The results reveal the limitations of commonly used approaches, and demonstrate the value of an integrated workflow using QFI-PCR to improve the accuracy of NGS mutation detection and guide changes in input that can rescue low quality FFPE DNA. These findings address a growing need for improved quality measures in NGS-based patient testing.

A STREAMLINED PCR-BASED FRAGMENT ANALYSIS ASSAY THAT RESOLVES BOTH SINGLE NUCLEOTIDE AND POLY-T LENGTH POLYMORPHISMS AT APOE AND TOMM40 SUSCEPTIBILITY LOCI IN ALZHEIMER’S DISEASE

(0.82, 0.68-0.99, p1⁄40.03), SAM (0.62,0.40-0.98, p1⁄40.04), cobalamin/B12 (0.90,0.81-1.0), p1⁄40.04, taurine (0.88,0.770.99, p1⁄40.04), and 5-MTHF (0.91,0.82-1.00, p1⁄40.05). Conclusions: This meta-analysis provides support for the vascular hypothesis of AD, and suggests that cardiovascular and glial mechanisms (homocysteine, 24(s)hydroxycholesterol, and YKL-40) play an important role in AD pathogenesis. Reduced perfusion due to atherosclerosis is also suggested (homocysteine and 24(s)hydroxycholersterol). Homocysteine is associated with cognitive decline and brain atrophy. It can be inferred that vitamin B supplementation, and reduction of homocysteine levels prevent cognitive loss.