What is MSK-ACCESS?

It is a hybrid capture panel designed for Analysis of Circulating cfDNA to Evaluate Somatic Status using the Unique Molecular Index (UMIs) for high sensitivity. MSK-ACCESS is 13% as large, captures 47% of all mutations detected by MSK-IMPACT.

Brannon, A. R. et al. Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell- free DNA via paired normal sequencing using MSK-ACCESS. Nat Commun 12, 3770 (2021).

What is the panel design?

Selected exons of 129 genes for mutation detection

• Level 1-4

• High rates of mutations

SNPs of & of 12 genes

Common for

Introns for of 10 genes

genes

What are the Design Implications?

• Matched cfDNA-WBC (”tumor-normal”) assay to detect somatic alterations

• Sensitivity for mutation calling depends on ‘duplex’ collapsed coverage

• Different sensitivities for different classes of alterations

BAM Generation & Quality Control

Github Location -> https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/ACCESS_pipeline.cwl

Tools Used:

Variant Calling

Small Variants

Github Location ->

Tools Used:

Copy Number Variant (CNV)

Github Location ->

Refer to Bioinformatics Pipeline to Detect CNA's section in this paper for details:

Structural Variant (SV)

Github Location ->

Tool Used:

Microsatellite Instability Status (MSI)

Github Location ->

Tool Used:

Configurations

Voyager has all our configurations in the jinja template, it includes all the paths for various files and tools associated with the workflows, all location are on JUNO:

snps_indels:

CNV:

Fastq_to_bam:

MSI:

SV :