Repo locations: https://github.com/msk-access

Framework: https://github.com/mskcc-omics-workflows/modules/

Containers: https://github.com/mskcc-omics-workflows/containers

CMO onboarding

The first thing to do once you have joined is to visit https://mskcc.github.io/on-boarding/ and finish of task necessary for compliance & initiate the process of getting access to various systems.

Cluster Guide

To learn more about the cluster and its resources visit the MIRO board

CCI specific onboarding

Guides on Confluence

Welcome aboard!

Welcome to CCI wiki! Here you'll find everything you need to know about CCI.

You can read more about the Center for Molecular Oncology (CMO) here:

Access Data Analysis:

BAM Generation & Quality Control

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

Tools Used:

• BWA

• Trimgalore

Github Location ->

Tools Used:

Github Location ->

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

Github Location ->

Tool Used:

Github Location ->

Tool Used:

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:

👋 Lead Scientist — 💌 shahr2@mskcc.org — 🇺🇸 New York

I am responsible for leading a team of Computational Biologists and Bioinformatics Software Engineers who develop, maintain, and operate bioinformatics pipelines and databases in the . We also perform collaborative research with other labs and clinicians both within MSKCC and in the broader research community. On a daily basis, we analyze blood samples from patients with tissue-based cancers, using their circulating tumor DNA extracted from the blood, thereby avoiding the need for tumor biopsies. More specifically, I lead the team in designing, developing, and implementing software tools to process and analyze high-throughput next-generation sequencing data for liquid biopsy applications ( & Clonal Hematopoiesis Panel). Previously at MSK, I helped develop the workflow for analyzing MSK-IMACT data for both clinical and research implementation, which is still in use. You can read more about my background . Also, here is the link to my

👋 Senior Computational Biologist — 💌 sivaprk@mskcc.org — 🇺🇸 Texas

(Research)

Developed by scientists in the CMO Technology Innovation Lab and Department of Pathology, this high-sensitivity assay is offered by the CMO to MSK researchers for profiling circulating tumor DNA derived from blood plasma. The inclusion of matched buffy coat DNA enables the identification and elimination of germline variants and mutations associated with clonal hematopoiesis, a significant confounder of most commercial assays. The assay is available for clinical use in the Molecular Diagnostics Service and for research projects in the Integrated Genomics Operations (IGO). CCI supports the data processing and analysis of research projects utilizing MSK-ACCESS in IGO and leads the ongoing development of the MSK-ACCESS pipeline for all applications. The current version of the pipeline is available here: mskcc/ACCESS-Pipeline: cfDNA Sequencing Pipeline with UMI (github.com), and more details about the assay and analysis are described in this paper below as well as here:

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).

CMO-CH

Developed by scientists in the CMO Technology Innovation Lab in collaboration with CCI and Clonal Hematopoiesis (CH) program, Diagnostic Molecular Pathology, Precision Interception, and Prevention Initiative & CCI, this assay utilizes the same barcoding and ultra-deep sequencing technology as MSK-ACCESS to detect CH mutations in white blood cells at high sensitivity. CMO-CH is offered by the CMO to MSK researchers for profiling white blood cell DNA to detect mutations in the most commonly altered CH-associated genes. The assay is run in IGO, and CCI supports the data processing and analysis. You can learn more about it

For both projects, additional analysis packages and development versions of the workflows can be found here:

Our Mission

The CMO Cell-Free DNA Informatics (CCI) group’s mission is to develop and apply computational methods to organize, analyze and understand genomic data generated from cfDNA assays such as MSK-ACCESS. The group is responsible for all computational infrastructure needed to deploy, run, and deliver results for research cfDNA assays in a production setting for CMO.

Our Values

Be Compassionate

We treat everyone we encounter with compassion, seeing the humanity behind their problems and experiences.

Be Mindful

We do not take advantage of our users' attention and adopt mindful working practices so that we can create safe spaces both in our working environment and in our products themselves.

Research First

We challenge our own and others' assumptions through qualitative and quantitative research. Not sure about an idea? Test it.

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).

MSK-ACCESS v2: Expanding Genomic Profiling Capabilities

Memorial Sloan Kettering Cancer Center is currently validating MSK-ACCESS v2 (2021). Building on the foundation of our original 2017 assay, Version 2 streamlines processing into a single probe pool while significantly expanding our genomic target territory.

Version Comparison: Advancing from v1 to v2

The updated panel increases our gene coverage and bait territory while simplifying the workflow.

To ensure we capture the most clinically relevant genomic data, several key upgrades have been integrated into v2:

• Expanded Target List: 153 additional OncoKB targets.

• Refined Regions: Updated hotspots and high TMB (Tumor Mutational Burden) regions.

• New Tumor Suppressor Genes (TSGs): 5 additional TSGs have been included: CHEK2, ERCC2, PALB2, BAP1, and CDK12.

The MSK-ACCESS v2 panel consists of a carefully curated set of targets designed to provide comprehensive genomic insights. Below is the breakdown of targets, probes, and cumulative territory by category:

Note on Category A Exclusions: The OncoKB targets explicitly exclude Heme and L1 prostate markers (BARD1, BRIP1, CHEK1, RAD51B, RAD51C, RAD51D).

BAM Generation & Quality Control

Github Location -> https://github.com/msk-access/nucleo

Github Location -> https://github.com/msk-access/nucleo_qc

Tools Used:

• BWA

• fastp

• fgbio

• Multi-QC

Github Location ->

Tools Used:

Github Location ->

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

Github Location ->

Tool Used:

Github Location ->

Tool Used:

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:

CMO-CH is offered by the Center for Molecular Oncology (CMO) to MSK researchers for profiling white blood cell DNA to detect mutations in the most commonly altered (CH) associated genes.

• 596 targets capturing 58% of CH and 90.4% of CH-PD mutations identified in the latest CH dataset from 40K patients

• Total size = 1,143 probes (0.14 Mb)

• The best place to start is to learn more about MSK-ACCESS and for that please read the paper:

  • 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).

• Learn more about the current collapsing method Marianas

• Learn more about the new collapsing () method using

• Learn more about the

• Understand the updated version for the above using these

• Learn about scripts that help with downstream analysis

• Learn about for viewing BAM files to distinguish real variants from artifacts

• admie - Files used for microsatellite instability detection tool ADMIE for MSK-ACCESS

• cosmic - VCF file of cosmic used in MSK-ACCESS workflows

• dbSNP

CCI works closely with CMO project managers to track the progress of cfDNA projects submitted to CMO by MSK researchers. CMO project managers support CCI by facilitating and coordinating project initiation, sample collection, and metadata collection.

-> information associated with a sample. This is a current work-in-progress written in Java/Neo4J that is supposed to be the one source of truth for metadata associated with samples. Currently, these responsibilities are managed by Beagle.

LIMS -> Laboratory information management system -- when sequencing is complete, metadata and file information on the sequences is first input into this system.

-> triggers and monitors workflows. There's also a part of it that tracks files and metadata associated with those files which may be splintered out in the future. A request typically comes from LIMS which begins the workflow process.

-> a nicer interface for Beagle (sample workflow tracking) and soon the MDB (make updates to metadata)

-> An HTTP API for Toil which Beagle is reliant on for interacting with workflows.

-> A workflow engine that interfaces well with LSF.

Voyager -> The suite of applications built by the Voyager team, including Ridgeback, Beagle, and Hermes.

-> Distributed high-performance computing that's managed in-house. Most data processing and files are housed here.

-> IBM's Platform Computing (Load Sharing Facility) tool for scheduling workflows on HPC. It has a specific to managing workloads.

-> a YAML-like language for defining workflows.

-> Reactive workflow framework and a programming that eases the writing of data-intensive computational pipelines.

-> Sequencing of the Deoxyribonucleic acid ()

-> Sequencing of the Ribonucleic acid ()

-> Cell-Free DNA assay for patients with solid tumors

CMO-CH -> Assay for profiling clonal hematopoiesis mutations from blood

-> Assay for profiling patients tissue DNA for solid tumors

-> Assay for profiling patients blood DNA for Heme malignancies

-> Allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

-> Whole Exome Sequencing

-> Whole Genome Sequencing

-> Whole Transcriptome Sequencing

-> one of the companies that provides sequencing machine

-> Type of sequencer from Illumina

-> Type of sequencer from Illumina

-> Type of sequencer from Illumina

-> Type of sequencer from Illumina

-> a company that sells instruments for long-read sequencing based on

-> a company that sells instruments for long-read sequencing based on technology

It is a hybrid capture panel designed for Analysis of Circulating 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.

Selected exons of 129 genes for mutation detection

To get reimbursed for your expenses, just fill in the expense report online.

• The best place to start would be to understand the data flow:

  • LIMS/SMILE -> Voyager -> JUNO

• Learn more about the codebases listed below that form Voyager

To request time off, just fill in things at MSK TIME, and also please email your manager of the same.