Ultra-low coverage whole genome sequencing of ccfDNA in multiple myeloma: A tool for laboratory routine?

Phenome-wide association study in 25,639 pregnant Chinese women reveals loci associated with maternal comorbidities and child health

Phenome-wide association studies (PheWAS) have been less focused on maternal diseases and maternal-newborn comorbidities, especially in the Chinese population. To enhance our understanding of the genetic basis of these related diseases, we conducted a PheWAS on 25,639 pregnant women and 14,151 newborns in the Chinese Han population using ultra-low-coverage whole-genome sequence (ulcWGS). We identified 2,883 maternal trait-associated SNPs associated with 26 phenotypes, among which 99.5% were near established genome-wide association study (GWAS) loci. Further refinement delineated these SNPs to 442 unique trait-associated loci (TALs) predicated on linkage disequilibrium R2 > 0.8, revealing that 75.6% demonstrated pleiotropy and 50.9% were located in genes implicated in analogous phenotypes. Notably, we discovered 21 maternal SNPs associated with 35 neonatal phenotypes, including two SNPs associated with identical complications in both mothers and children. These findings underscore the importance of integrating ulcWGS data to enrich the discoveries derived from traditional PheWAS approaches.

Sensitivity, specificity, and accuracy of molecular profiling on circulating cell-free DNA in refractory or relapsed multiple myeloma patients, results of MM-EP1 study

As a promising alternative to bone marrow aspiration (BMA), mutational profiling on blood-derived circulating cell-free tumor DNA (cfDNA) is a harmless and simple technique to monitor molecular response and treatment resistance of patients with refractory/relapsed multiple myeloma (R/R MM). We evaluated the sensitivity and specificity of cfDNA compared to BMA CD138 positive myeloma plasma cells (PCs) in a series of 45 R/R MM patients using the 29-gene targeted panel (AmpliSeq) NGS. KRAS, NRAS, FAM46C, DIS3, and TP53 were the most frequently mutated genes. The average sensitivity and specificity of cfDNA detection were 65% and 97%, respectively. The concordance per gene between the two samples was good to excellent according to Cohen's κ coefficients interpretation. An increased number of mutations detected in cfDNA were associated with a decreased overall survival. In conclusion, we demonstrated cfDNA NGS analysis feasibility and accuracy in R/R MM patients who may benefit from early phase clinical trial.

Basic ctDNA Panel Promises Affordable Clinical Validity in Colon Cancer Patients but Not in Pancreas Cancer Patients

The potential of circulating tumor DNA (ctDNA) as a biomarker to assess the progression of various solid tumors has been explored extensively. In this study, we investigated the feasibility of utilizing a ctDNA sequencing panel specifically designed to target the most frequently mutated genomic regions in colon and pancreas cancers. Through somatic analysis of colon and pancreas tumors, we targeted 27 regions within eight genes. By employing PCR amplification and Illumina NGS, we ensured that each region was adequately covered with a minimum of 5000 reads (with an average of 12,000 reads). Our method exhibited reproducibility with repetition and dilutions. The positive detection threshold for ctDNA was set at a cutoff value of 0.5% ctDNA of the total reads using IGV. Among the samples analyzed, 71% of colon cancer cases displayed somatic mutations covered by the targeted regions. Within this group, detectable ctDNA was observed in 34% of the cases. Conversely, in pancreatic cancer, 55% of mutations were covered by the panel's regions, but only 13% of these cases exhibited detectable ctDNA. In follow-ups with the patients, changes in ctDNA percentages demonstrated complete concordance with changes in the clinical condition in 88% of the cases. Our findings suggest that employing a basic ctDNA-targeted panel can serve as a cost-effective and reliable approach for repeated monitoring of the efficacy of colon cancer therapy. However, in the case of pancreatic cancer, ctDNA showed limited utility, and alternative biomarkers may offer superior diagnostic value. Additionally, we found that a negative ctDNA test is not a guarantee for a relapse-free recovery; thus, we recommend a continuous follow-up with the patient on a long-term basis.

Liquid biopsy by analysis of circulating myeloma cells and cell-free nucleic acids: a novel noninvasive approach of disease evaluation in multiple myeloma

Multiple myeloma (MM) is an incurable hematological cancer with high spatial- and temporal-heterogeneity. Invasive single-point bone marrow sampling cannot capture the tumor heterogeneity and is difficult to repeat for serial assessments. Liquid biopsy is a technique for identifying and analyzing circulating MM cells and cell products produced by tumors and released into the circulation, allowing for the minimally invasive and comprehensive detection of disease burden and molecular alterations in MM and monitoring treatment response and disease progression. Furthermore, liquid biopsy can provide complementary information to conventional detection approaches and improve their prognostic values. This article reviewed the technologies and applications of liquid biopsy in MM.