Enhanced specificity of high sensitivity somatic variant profiling in cell-free DNA via paired normal sequencing: design, validation, and clinical experience of the MSK-ACCESS liquid biopsy assay

Brannon, A. R.; Jayakumaran, G.; Diosdado, M.; Patel, J.; Razumova, A.; Hu, Y.; Meng, F.; Haque, M.; Sadowska, J.; Murphy, B.; Baldi, T.; Johnson, I.; Ptashkin, R.; Hasan, M.; Srinivasan, P.; Rema, A. B.; Rijo, I.; Agarunov, A.; Won, H.; Perera, D.; Brown, D. N.; Samolia, A.; Jing, X.; Gedvilaite, E.; Yang, J. L.; Stephens, D. P.; Dix, J.-M.; DeGroat, N.; Nafa, K.; Syed, A.; Li, A.; Lebow, E. S.; Bowman, A. S.; Ferguson, D. C.; Liu, Y.; Mata, D. A.; Sharma, R.; Yang, S.-R.; Bale, T.; Benhamida, J. K.; Chang, J. C.; Dogan, S.; Hameed, M. R.; Hechtman, J. F.; Moung, C.; Ross, D. S.

doi:10.1101/2020.06.27.175471

Home/Archive/bioRxiv

bioRxiv · 10.1101/2020.06.27.175471

Enhanced specificity of high sensitivity somatic variant profiling in cell-free DNA via paired normal sequencing: design, validation, and clinical experience of the MSK-ACCESS liquid biopsy assay

View original source ↗Export metadata ↓

Abstract

Circulating cell-free DNA (cfDNA) from blood plasma of cancer patients can be used to interrogate somatic tumor alterations non-invasively or when adequate tissue is unavailable. We have developed and clinically implemented MSK-ACCESS (Analysis of Circulating cfDNA to Evaluate Somatic Status), an NGS assay for detection of very low frequency somatic alterations in select exons and introns of 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 98% for a priori mutation profiling. To evaluate the performance and utility of MSK-ACCESS, we report results from the first 681 prospective blood samples (617 patients) that underwent clinical analysis to guide patient management. Somatic mutations, copy number, and/or structural variants were detected in 73% of the samples, and 56% of these circulating-tumor DNA (ctDNA) positive samples had clinically actionable alterations. The utilization of matched white blood cell sequencing allowed retention of somatic alterations while filtering out over 10,000 germline and clonal hematopoiesis variants, thereby greatly enhancing the specificity of the assay. Taken together, our experience illustrates the importance of analyzing a matched normal sample when interpreting cfDNA results and highlights the potential of cfDNA profiling to guide treatment selection, monitor treatment response, and identify mechanisms of treatment resistance.

Explore related subjects

genomics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Brannon, A. R., Jayakumaran, G., Diosdado, M., Patel, J., Razumova, A., Hu, Y., Meng, F., Haque, M., Sadowska, J., Murphy, B., Baldi, T., Johnson, I., Ptashkin, R., Hasan, M., Srinivasan, P., Rema, A. B., Rijo, I., Agarunov, A., Won, H., Perera, D., Brown, D. N., Samolia, A., Jing, X., Gedvilaite, E., Yang, J. L., Stephens, D. P., Dix, J.-M., DeGroat, N., Nafa, K., Syed, A., Li, A., Lebow, E. S., Bowman, A. S., Ferguson, D. C., Liu, Y., Mata, D. A., Sharma, R., Yang, S.-R., Bale, T., Benhamida, J. K., Chang, J. C., Dogan, S., Hameed, M. R., Hechtman, J. F., Moung, C., Ross, D. S.. 2020-06-29. Enhanced specificity of high sensitivity somatic variant profiling in cell-free DNA via paired normal sequencing: design, validation, and clinical experience of the MSK-ACCESS liquid biopsy assay. https://doi.org/10.1101/2020.06.27.175471

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

The tiger shark, Galeocerdo cuvier (Peron & Lesueur, 1822), genome reveals genomic and epigenomic signatures of shark evolution and demographic history

Cartilaginous fishes (Chondrichthyes) represent one of the oldest extant vertebrate lineages, persisting for over 450 million years, yet genomic resources remain limited for many species despite widespread conservation concern. The tiger shark, Galeocerdo cuvier (Peron & Lesueur, 1822), the sole surviving member of the family Galeocerdonidae, is a circumglobally cosmopolitan predator vital in ecosystem regulation but is experiencing population declines. Here, we generated the first chromosome-scale haplotype-phased reference genome for the tiger shark and integrated comparative and population genomics with methylomics to characterise its genome architecture and evolutionary history. This assembly presented the first evidence of male heterogamety in this species. Comparative analyses revealed lineage-specific transposable element expansions across the chondrichthyan class suggesting ongoing genome restructuring in Carcharhiniform sharks. We report the first hydroxymethylome in a chondrichthyan, higher than that of other vertebrates, hinting at novel DNA evolutionary and regulatory pathways in an early-diverging lineage of jawed vertebrates. We identified genomic signatures of prolonged population decline that correlated with historical climate fluctuations and have resulted in sustained low levels of genetic heterozygosity in this species. These findings offer new insights into shark and broader vertebrate genomic and epigenomic evolution while providing valuable resources for conservation genomics of one of the world's most widespread top-order predators in the face of accelerating environmental change.

genomics↗

bioRxiv2026

A genomic prediction framework for growth traits in black soldier fly (Hermetia illucens) breeding programmes

Background Genomic prediction has been applied in livestock, plant and aquaculture species to accelerate genetic gain. However, its application and potential still remain unexplored in farmed black soldier fly (BSF), an emerging globally important insect production species. Due to the diversity of BSF feed sources, selection strategies need to be evaluated across various feedstocks and production environments to aid in building genomic selection into BSF breeding programmes. In this study, 2,083 BSF larvae from the base population were reared on three diets (SYK: Soy-okara, BSG: brewers' spent grain and FVW: fruit and vegetable waste), and 536 from the F7 population were reared on a chicken starter feed diet. Larvae were phenotyped for four growth traits (LBW, larval body weight; LL, larval length; LW, larval width; LSA, larval surface area) and genotyped across 4,680 SNPs. Genomic prediction was evaluated using seven methods under additive (A) and additive-dominance (AD) models, considering across- and within-diet effects, genotype by diet (G x D) interactions, differences amongst reference and test generations, and SNP densities. Results Performance varied across all scenarios, with LBW showing higher predictive ability (PA) among the growth traits. Accounting for dominance generally improved PA. Multivariate models accounting for G x D performed similarly to, or marginally better than, within-diet predictions. Cross-diet prediction was more variable and generally lower than within-diet prediction, showing reduced transferability across untested nutritional environments. Reducing the SNP density from 4,680 to 3,000 SNPs maintained comparable PA; however, PA decreased below 3,000 SNPs. Across multiple generations, predictive performance declined, resulting from reduced genetic connectivity and possible genotype-by-environment (G x E) interactions between the reference and testing populations. Conclusions Overall, these results provide an application-based framework for genomic prediction in BSF in semi- or commercial production settings. Results also highlight the importance of the genetic model, representative reference populations, and appropriate marker densities for genomic selection.

genomics↗

bioRxiv2026

SPACE-Tag Enables High-Throughput Spatial Chromatin Profiling With CUT&Tag

Spatial epigenomics maps chromatin states within intact tissues, yet current methods remain limited by accessibility and scale. We developed SPACE-Tag, a spatial CUT&Tag framework that converts epigenetic marks-associated DNA into polyadenylated RNA through T7 based linear amplification, enabling direct integration with standard spatial transcriptomic workflows. Applied to the mouse brain, SPACETag resolved activating and repressive chromatin landscapes, recovered region-specific gene regulatory programs across anatomical domains, and showed strong correlation with existing bulk and single cell reference data. We generated an integrated multimodal atlas of the aging mouse brain, profiling five histone modifications and the transcriptome in parallel across the adult lifespan to establish the largest spatial multimodal dataset to date. This analysis uncovered sharp regional divergence with aging in the brain: fiber tracts showed widespread transcriptional downregulation, often without nearby chromatin state transitions, whereas the isocortex showed coordinated chromatin transcriptome changes, including an H3K4me1 peak module that increased with age, was enriched at super-enhancers and linked to upregulation of neuronal plasticity regulators. These findings highlight the power of multimodal and high throughput spatial genomics in uncovering the divergent regulatory logic that governs tissue-specific vulnerability and resilience in the aging brain.

genomics↗