REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
Raw sequencing files	This paper	dbGaP study accession phs001939.v3.p1
Raw sequencing files (processed by GDC)	This paper	https://portal.gdc.cancer.gov/projects/CMI-MPC
Processed and deidentified sequencing and clinical data	This paper	https://www.cbioportal.org/study/summary?id=mpcproject_broad_2021
Processed and deidentified figure data and code	This paper	https://github.com/vanallenlab/mpcproject-paper
Study information and materials seen by patients	This paper	https://mpcproject.org/
Rural-area continuum codes (2010)	USDA66	https://www.ers.usda.gov/data-products/rural-urban-commuting-area-codes.aspx
Information on MPC patients nationwide (2018)	SEER21	https://seer.cancer.gov/data-software/
Medically underserved and health-physician shortage areas (accessed Dec 2021)	HRSA23	https://data.hrsa.gov/tools/shortage-area
National Area Deprivation Index 2019 data	Kind and Buckingham, 201867	https://www.neighborhoodatlas.medicine.wisc.edu/
ClinVar (2019)	Landrum et al., 201832	https://www.ncbi.nlm.nih.gov/clinvar/
Variant Effect Predictor GRCh37 Cache	McLaren et al., 201668	https://useast.ensembl.org/info/docs/tools/vep/script/vep_cache.html
COSMIC germline cancer census gene set v86	Sondka et al., 201869	https://cancer.sanger.ac.uk/census
Software and algorithms
Python 3.8	Python Software Foundation, 202170	https://www.python.org/
R 3.5.1	R Core Team, 202171	https://www.r-project.org/
BWA	Li and Durbin, 200972	http://bio-bwa.sourceforge.net/
GATK 3.7	McKenna et al., 201073	https://github.com/broadinstitute/gatk/releases
Sequence alignment and alteration calling (component algorithms detailed below)	The Getz Laboratory	https://portal.firecloud.org/#methods/getzlab/CGA_WES_Characterization_Pipeline_v0.1_Dec2018/
Mutect v1.1.6	Cibulskis et al., 201374	http://archive.broadinstitute.org/cancer/cga/mutect
FilterByOrientationBias	McKenna et al., 201073	https://gatk.broadinstitute.org/hc/en-us/articles/360037060232
Strelka v2.8.0	Saunders et al., 201275	https://github.com/Illumina/strelka
Oncotator v1.9.9.0	Ramos et al., 201576	https://github.com/broadinstitute/oncotator
MutSig2CV	Lawrence et al., 201477	https://github.com/getzlab/MutSig2CV
GATK 3.7 (CNV)	McKenna et al., 201073	https://gatk.broadinstitute.org/hc/en-us/articles/360035531092
ABSOLUTE v1.5	Carter et al., 201278	https://software.broadinstitute.org/cancer/cga/absolute_download
FACETS v0.6.2	Shen and Seshan, 201679	https://github.com/mskcc/facets
GISTIC2.0 v2.0.23	Mermel et al., 201128	https://github.com/broadinstitute/gistic2
DeTiN v2.0.1	Taylor-Weiner et al., 201880	https://github.com/getzlab/deTiN
ContEst	Cibulskis et al., 201181	https://software.broadinstitute.org/cancer/cga/contest
CrossCheckFingerprints (GATK 3.7)	McKenna et al., 201073	https://gatk.broadinstitute.org/hc/en-us/articles/360037594711
ichorCNA	Adalsteinsson et al., 201756	https://github.com/broadinstitute/ichorCNA
deconstructSigs (COSMIC v2 signatures, v1.9.0)	Rosenthal et al., 201633	https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0893-4
DeepVariant v0.8.0	Poplin et al., 201882	https://github.com/google/deepvariant
PhylogicNDT	Leshchiner et al., 201846	https://github.com/broadinstitute/PhylogicNDT
Other
Repository for regenerating main study findings and figures of this paper	This paper	https://github.com/vanallenlab/mpcproject-paper, https://doi.org/10.5281/zenodo.6816267