Wilms Tumor Assay:Article Title: Genetic changes associated with relapse in favorable histology Wilms tumor: A Children’s Oncology Group AREN03B2 study
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Samples from normal blood or tissue, primary tumor, relapse tumor from patients with Wilms Tumor Children’s Oncology Group childrensoncologygroup.org Critical commercial assays AllPrep DNA/RNA kit Qiagen Cat# 80204 mirVana miRNA Isolation Kit Invitrogen Cat# AM1560 Roche High Pure miRNA Isolation Kit Roche Cat# 05080576001 QIAamp DNA Blood Midi kit Qiagen Cat# 51183 Quant-iT PicoGreen quantification assay kit Invitrogen Cat# P7589 RNA 6000 NanoChip Kit Agilent Cat # 5067-1511 Complex iPLEX Gold Genotyping Reagent Agena Cat #10158 Extend Primer Mix Integrated DNA Technologies (IDT) N/A Ampure XP SPRI Beads Beckman Coulter Cat# A63881 Hyper Prep without amplification KAPA Biosystems/Roche KK8505 Unique Dual-Indexed Adapter Plates KAPA Biosystems/Roche Cat# KK8727 Quantitative PCR kit (library quantification) KAPA Biosystems/Roche Cat# KK4835 Stranded Total RNA Prep with RiboZero Gold Illumina Cat# 20020599 IDT for Illumina – TruSeq RNA UD indexes Illumina Cat# 20022371 NEXTflex Small RNA-Seq Kit v.3 PerkinElmer Cat# NOVA-5132-06 HyperPrep Kit with Amplification KAPA Biosystems/Roche Cat # KK8504 xGenTM UDI-UMI adapters Integrated DNA Technologies N/A HiFi HotStart Ready Mix KAPA Biosystems/Roche KK2602 p5 and p7 primers Integrated DNA Technologies N/A Dual Index F&R primers Integrated DNA Technologies Cat# 100981K xGenTM Hybridization and Wash Kit Integrated DNA Technologies Cat# 1080584 xGenTM Universal Blockers Integrated DNA Technologies Cat# 1075476 CustomPanel bait Twist Biosciences Custom Platinum Hot-start PCR kit Invitrogen Cat# 13000012 ExoSAP-IT Applied Biosystems Cat# 78200.200.UL Quant-it dNA quantification assay kit (Picogreen) Invitrogen Thermo Science catalogue Q33130 BigDye XTerminator Purification Kit Applied Biosystems Cat# 4376486 Deposited data Raw and Analyzed Data (Project Publication Page: MP2PRT-WT) NCI Genomic Data Commons https://gdc.cancer.gov/about-data/ publications/MP2PRT-WT-2022; https://portal.gdc.cancer.gov/ projects/MP2PRT-WT gnomAD Karczewski et al.2020 gnomAD (broadinstitute.org) PharmGKB Whirl-Carrillo et al.2012 PharmGKB (pharmgkb.org) PGxMine Lever et al.2020 PGxMine (pharmgkb.org) Oligonucleotides Primers for verification of variants involving MGA, WT1, MCFC1, RBL1, COBLL1 This paper (Methods) N/A Primer Target locations for Validation set This paper (Table S4) N/A (Continued on next page) Cell Reports Medicine 3, 100644, June 21, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms Picard Broad Institute https://broadinstitute.github.io/picard/ CaVEman Nik-Zainal et al., 2016 https://github.com/cancerit/CaVEMan Pindel Ye et al., 2009 https://github.com/genome/pindel BRASS Campbell et al., 2008 https://github.com/cancerit/BRASS AscatNGS Raine et al., 2016 https://github.com/cancerit/ascatNgs bcl2fastq Illumina v.2.20.0 Bioionformatics Pipeline: mRNA analysis GDC https://docs.gdc.cancer.gov/Data/ Bioinformatics_Pipelines/ Expression_mRNA_Pipeline/ STAR two-pass Dobin et al. 2013 N/A HTSeq Anders et al. 2015 v.0.6.1.p1 Small RNA Quantification pipeline Chu et al. 2015 N/A GATK Mutect 2 tumor-only pipeline Van der Auwera et al.2020 Mutect2 – GATK (broadinstitute.org) Ensembl Variant Effect Predictor (VEP) McLaren et al. 2016 Variant Effect Predictor - Homo_sapiens - Ensembl genome browser 105 samtools mpileup Danecek et al. 2021 N/A Oncoprinter Cerami et al., 2012 cBioPortal for Cancer Genomics::Oncoprinter cBioPortal Gao et al., 2013 cBioPortal for Cancer Genomics DRAGEN Germline v.3 pipeline Ilumina DRAGEN Germline (illumina.com) GATK Haplotype Caller pipeline Van der Auwera et al.2020 HaplotypeCaller – GATK (broadinstitute. org) Sequencing Analysis Software v 6.0 ABI N/A TRACE/LASER Taliun et al.2017 LASER (umich.edu) ggplot2 Wickham 2016 https://ggplot2.tidyverse.org Other FilterMax F5 Multi Mode Microplate Reader Molecular Devices N/A Focused-ultrasonicator Covaris LE220-Plus Bravo liquid handling platform Agilent N/A ViiA qPCR machine Life Technologies (ABI) N/A NovaSeq 6000 Ilumina N/A Starlet Liquid Handling System Hamilton N/A Tape Station System Agilent N/A HiSeq 4000 Ilumina N/A Liquid Handling Workstation SciClone Pippin Prep system Sage Science Beverly, MA N/A SPE-DRY 96 Biotage N/A Veriti thermal cycler ABI N/A 3500XL Capillary sequencer ABI N/A Bioanalyzer Agilent N/A Agena’s MassARRAYTM System Agena N/A High Seq X Illumina SY-301-2002 Article ll OPEN ACCESS
Isolation:Article Title: Genetic changes associated with relapse in favorable histology Wilms tumor: A Children’s Oncology Group AREN03B2 study
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Samples from normal blood or tissue, primary tumor, relapse tumor from patients with Wilms Tumor Children’s Oncology Group childrensoncologygroup.org Critical commercial assays AllPrep DNA/RNA kit Qiagen Cat# 80204 mirVana miRNA Isolation Kit Invitrogen Cat# AM1560 Roche High Pure miRNA Isolation Kit Roche Cat# 05080576001 QIAamp DNA Blood Midi kit Qiagen Cat# 51183 Quant-iT PicoGreen quantification assay kit Invitrogen Cat# P7589 RNA 6000 NanoChip Kit Agilent Cat # 5067-1511 Complex iPLEX Gold Genotyping Reagent Agena Cat #10158 Extend Primer Mix Integrated DNA Technologies (IDT) N/A Ampure XP SPRI Beads Beckman Coulter Cat# A63881 Hyper Prep without amplification KAPA Biosystems/Roche KK8505 Unique Dual-Indexed Adapter Plates KAPA Biosystems/Roche Cat# KK8727 Quantitative PCR kit (library quantification) KAPA Biosystems/Roche Cat# KK4835 Stranded Total RNA Prep with RiboZero Gold Illumina Cat# 20020599 IDT for Illumina – TruSeq RNA UD indexes Illumina Cat# 20022371 NEXTflex Small RNA-Seq Kit v.3 PerkinElmer Cat# NOVA-5132-06 HyperPrep Kit with Amplification KAPA Biosystems/Roche Cat # KK8504 xGenTM UDI-UMI adapters Integrated DNA Technologies N/A HiFi HotStart Ready Mix KAPA Biosystems/Roche KK2602 p5 and p7 primers Integrated DNA Technologies N/A Dual Index F&R primers Integrated DNA Technologies Cat# 100981K xGenTM Hybridization and Wash Kit Integrated DNA Technologies Cat# 1080584 xGenTM Universal Blockers Integrated DNA Technologies Cat# 1075476 CustomPanel bait Twist Biosciences Custom Platinum Hot-start PCR kit Invitrogen Cat# 13000012 ExoSAP-IT Applied Biosystems Cat# 78200.200.UL Quant-it dNA quantification assay kit (Picogreen) Invitrogen Thermo Science catalogue Q33130 BigDye XTerminator Purification Kit Applied Biosystems Cat# 4376486 Deposited data Raw and Analyzed Data (Project Publication Page: MP2PRT-WT) NCI Genomic Data Commons https://gdc.cancer.gov/about-data/ publications/MP2PRT-WT-2022; https://portal.gdc.cancer.gov/ projects/MP2PRT-WT gnomAD Karczewski et al.2020 gnomAD (broadinstitute.org) PharmGKB Whirl-Carrillo et al.2012 PharmGKB (pharmgkb.org) PGxMine Lever et al.2020 PGxMine (pharmgkb.org) Oligonucleotides Primers for verification of variants involving MGA, WT1, MCFC1, RBL1, COBLL1 This paper (Methods) N/A Primer Target locations for Validation set This paper (Table S4) N/A (Continued on next page) Cell Reports Medicine 3, 100644, June 21, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms Picard Broad Institute https://broadinstitute.github.io/picard/ CaVEman Nik-Zainal et al., 2016 https://github.com/cancerit/CaVEMan Pindel Ye et al., 2009 https://github.com/genome/pindel BRASS Campbell et al., 2008 https://github.com/cancerit/BRASS AscatNGS Raine et al., 2016 https://github.com/cancerit/ascatNgs bcl2fastq Illumina v.2.20.0 Bioionformatics Pipeline: mRNA analysis GDC https://docs.gdc.cancer.gov/Data/ Bioinformatics_Pipelines/ Expression_mRNA_Pipeline/ STAR two-pass Dobin et al. 2013 N/A HTSeq Anders et al. 2015 v.0.6.1.p1 Small RNA Quantification pipeline Chu et al. 2015 N/A GATK Mutect 2 tumor-only pipeline Van der Auwera et al.2020 Mutect2 – GATK (broadinstitute.org) Ensembl Variant Effect Predictor (VEP) McLaren et al. 2016 Variant Effect Predictor - Homo_sapiens - Ensembl genome browser 105 samtools mpileup Danecek et al. 2021 N/A Oncoprinter Cerami et al., 2012 cBioPortal for Cancer Genomics::Oncoprinter cBioPortal Gao et al., 2013 cBioPortal for Cancer Genomics DRAGEN Germline v.3 pipeline Ilumina DRAGEN Germline (illumina.com) GATK Haplotype Caller pipeline Van der Auwera et al.2020 HaplotypeCaller – GATK (broadinstitute. org) Sequencing Analysis Software v 6.0 ABI N/A TRACE/LASER Taliun et al.2017 LASER (umich.edu) ggplot2 Wickham 2016 https://ggplot2.tidyverse.org Other FilterMax F5 Multi Mode Microplate Reader Molecular Devices N/A Focused-ultrasonicator Covaris LE220-Plus Bravo liquid handling platform Agilent N/A ViiA qPCR machine Life Technologies (ABI) N/A NovaSeq 6000 Ilumina N/A Starlet Liquid Handling System Hamilton N/A Tape Station System Agilent N/A HiSeq 4000 Ilumina N/A Liquid Handling Workstation SciClone Pippin Prep system Sage Science Beverly, MA N/A SPE-DRY 96 Biotage N/A Veriti thermal cycler ABI N/A 3500XL Capillary sequencer ABI N/A Bioanalyzer Agilent N/A Agena’s MassARRAYTM System Agena N/A High Seq X Illumina SY-301-2002 Article ll OPEN ACCESS
Amplification:Article Title: Genetic changes associated with relapse in favorable histology Wilms tumor: A Children’s Oncology Group AREN03B2 study
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Samples from normal blood or tissue, primary tumor, relapse tumor from patients with Wilms Tumor Children’s Oncology Group childrensoncologygroup.org Critical commercial assays AllPrep DNA/RNA kit Qiagen Cat# 80204 mirVana miRNA Isolation Kit Invitrogen Cat# AM1560 Roche High Pure miRNA Isolation Kit Roche Cat# 05080576001 QIAamp DNA Blood Midi kit Qiagen Cat# 51183 Quant-iT PicoGreen quantification assay kit Invitrogen Cat# P7589 RNA 6000 NanoChip Kit Agilent Cat # 5067-1511 Complex iPLEX Gold Genotyping Reagent Agena Cat #10158 Extend Primer Mix Integrated DNA Technologies (IDT) N/A Ampure XP SPRI Beads Beckman Coulter Cat# A63881 Hyper Prep without amplification KAPA Biosystems/Roche KK8505 Unique Dual-Indexed Adapter Plates KAPA Biosystems/Roche Cat# KK8727 Quantitative PCR kit (library quantification) KAPA Biosystems/Roche Cat# KK4835 Stranded Total RNA Prep with RiboZero Gold Illumina Cat# 20020599 IDT for Illumina – TruSeq RNA UD indexes Illumina Cat# 20022371 NEXTflex Small RNA-Seq Kit v.3 PerkinElmer Cat# NOVA-5132-06 HyperPrep Kit with Amplification KAPA Biosystems/Roche Cat # KK8504 xGenTM UDI-UMI adapters Integrated DNA Technologies N/A HiFi HotStart Ready Mix KAPA Biosystems/Roche KK2602 p5 and p7 primers Integrated DNA Technologies N/A Dual Index F&R primers Integrated DNA Technologies Cat# 100981K xGenTM Hybridization and Wash Kit Integrated DNA Technologies Cat# 1080584 xGenTM Universal Blockers Integrated DNA Technologies Cat# 1075476 CustomPanel bait Twist Biosciences Custom Platinum Hot-start PCR kit Invitrogen Cat# 13000012 ExoSAP-IT Applied Biosystems Cat# 78200.200.UL Quant-it dNA quantification assay kit (Picogreen) Invitrogen Thermo Science catalogue Q33130 BigDye XTerminator Purification Kit Applied Biosystems Cat# 4376486 Deposited data Raw and Analyzed Data (Project Publication Page: MP2PRT-WT) NCI Genomic Data Commons https://gdc.cancer.gov/about-data/ publications/MP2PRT-WT-2022; https://portal.gdc.cancer.gov/ projects/MP2PRT-WT gnomAD Karczewski et al.2020 gnomAD (broadinstitute.org) PharmGKB Whirl-Carrillo et al.2012 PharmGKB (pharmgkb.org) PGxMine Lever et al.2020 PGxMine (pharmgkb.org) Oligonucleotides Primers for verification of variants involving MGA, WT1, MCFC1, RBL1, COBLL1 This paper (Methods) N/A Primer Target locations for Validation set This paper (Table S4) N/A (Continued on next page) Cell Reports Medicine 3, 100644, June 21, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms Picard Broad Institute https://broadinstitute.github.io/picard/ CaVEman Nik-Zainal et al., 2016 https://github.com/cancerit/CaVEMan Pindel Ye et al., 2009 https://github.com/genome/pindel BRASS Campbell et al., 2008 https://github.com/cancerit/BRASS AscatNGS Raine et al., 2016 https://github.com/cancerit/ascatNgs bcl2fastq Illumina v.2.20.0 Bioionformatics Pipeline: mRNA analysis GDC https://docs.gdc.cancer.gov/Data/ Bioinformatics_Pipelines/ Expression_mRNA_Pipeline/ STAR two-pass Dobin et al. 2013 N/A HTSeq Anders et al. 2015 v.0.6.1.p1 Small RNA Quantification pipeline Chu et al. 2015 N/A GATK Mutect 2 tumor-only pipeline Van der Auwera et al.2020 Mutect2 – GATK (broadinstitute.org) Ensembl Variant Effect Predictor (VEP) McLaren et al. 2016 Variant Effect Predictor - Homo_sapiens - Ensembl genome browser 105 samtools mpileup Danecek et al. 2021 N/A Oncoprinter Cerami et al., 2012 cBioPortal for Cancer Genomics::Oncoprinter cBioPortal Gao et al., 2013 cBioPortal for Cancer Genomics DRAGEN Germline v.3 pipeline Ilumina DRAGEN Germline (illumina.com) GATK Haplotype Caller pipeline Van der Auwera et al.2020 HaplotypeCaller – GATK (broadinstitute. org) Sequencing Analysis Software v 6.0 ABI N/A TRACE/LASER Taliun et al.2017 LASER (umich.edu) ggplot2 Wickham 2016 https://ggplot2.tidyverse.org Other FilterMax F5 Multi Mode Microplate Reader Molecular Devices N/A Focused-ultrasonicator Covaris LE220-Plus Bravo liquid handling platform Agilent N/A ViiA qPCR machine Life Technologies (ABI) N/A NovaSeq 6000 Ilumina N/A Starlet Liquid Handling System Hamilton N/A Tape Station System Agilent N/A HiSeq 4000 Ilumina N/A Liquid Handling Workstation SciClone Pippin Prep system Sage Science Beverly, MA N/A SPE-DRY 96 Biotage N/A Veriti thermal cycler ABI N/A 3500XL Capillary sequencer ABI N/A Bioanalyzer Agilent N/A Agena’s MassARRAYTM System Agena N/A High Seq X Illumina SY-301-2002 Article ll OPEN ACCESS
Real-time Polymerase Chain Reaction:Article Title: Genetic changes associated with relapse in favorable histology Wilms tumor: A Children’s Oncology Group AREN03B2 study
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Samples from normal blood or tissue, primary tumor, relapse tumor from patients with Wilms Tumor Children’s Oncology Group childrensoncologygroup.org Critical commercial assays AllPrep DNA/RNA kit Qiagen Cat# 80204 mirVana miRNA Isolation Kit Invitrogen Cat# AM1560 Roche High Pure miRNA Isolation Kit Roche Cat# 05080576001 QIAamp DNA Blood Midi kit Qiagen Cat# 51183 Quant-iT PicoGreen quantification assay kit Invitrogen Cat# P7589 RNA 6000 NanoChip Kit Agilent Cat # 5067-1511 Complex iPLEX Gold Genotyping Reagent Agena Cat #10158 Extend Primer Mix Integrated DNA Technologies (IDT) N/A Ampure XP SPRI Beads Beckman Coulter Cat# A63881 Hyper Prep without amplification KAPA Biosystems/Roche KK8505 Unique Dual-Indexed Adapter Plates KAPA Biosystems/Roche Cat# KK8727 Quantitative PCR kit (library quantification) KAPA Biosystems/Roche Cat# KK4835 Stranded Total RNA Prep with RiboZero Gold Illumina Cat# 20020599 IDT for Illumina – TruSeq RNA UD indexes Illumina Cat# 20022371 NEXTflex Small RNA-Seq Kit v.3 PerkinElmer Cat# NOVA-5132-06 HyperPrep Kit with Amplification KAPA Biosystems/Roche Cat # KK8504 xGenTM UDI-UMI adapters Integrated DNA Technologies N/A HiFi HotStart Ready Mix KAPA Biosystems/Roche KK2602 p5 and p7 primers Integrated DNA Technologies N/A Dual Index F&R primers Integrated DNA Technologies Cat# 100981K xGenTM Hybridization and Wash Kit Integrated DNA Technologies Cat# 1080584 xGenTM Universal Blockers Integrated DNA Technologies Cat# 1075476 CustomPanel bait Twist Biosciences Custom Platinum Hot-start PCR kit Invitrogen Cat# 13000012 ExoSAP-IT Applied Biosystems Cat# 78200.200.UL Quant-it dNA quantification assay kit (Picogreen) Invitrogen Thermo Science catalogue Q33130 BigDye XTerminator Purification Kit Applied Biosystems Cat# 4376486 Deposited data Raw and Analyzed Data (Project Publication Page: MP2PRT-WT) NCI Genomic Data Commons https://gdc.cancer.gov/about-data/ publications/MP2PRT-WT-2022; https://portal.gdc.cancer.gov/ projects/MP2PRT-WT gnomAD Karczewski et al.2020 gnomAD (broadinstitute.org) PharmGKB Whirl-Carrillo et al.2012 PharmGKB (pharmgkb.org) PGxMine Lever et al.2020 PGxMine (pharmgkb.org) Oligonucleotides Primers for verification of variants involving MGA, WT1, MCFC1, RBL1, COBLL1 This paper (Methods) N/A Primer Target locations for Validation set This paper (Table S4) N/A (Continued on next page) Cell Reports Medicine 3, 100644, June 21, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms Picard Broad Institute https://broadinstitute.github.io/picard/ CaVEman Nik-Zainal et al., 2016 https://github.com/cancerit/CaVEMan Pindel Ye et al., 2009 https://github.com/genome/pindel BRASS Campbell et al., 2008 https://github.com/cancerit/BRASS AscatNGS Raine et al., 2016 https://github.com/cancerit/ascatNgs bcl2fastq Illumina v.2.20.0 Bioionformatics Pipeline: mRNA analysis GDC https://docs.gdc.cancer.gov/Data/ Bioinformatics_Pipelines/ Expression_mRNA_Pipeline/ STAR two-pass Dobin et al. 2013 N/A HTSeq Anders et al. 2015 v.0.6.1.p1 Small RNA Quantification pipeline Chu et al. 2015 N/A GATK Mutect 2 tumor-only pipeline Van der Auwera et al.2020 Mutect2 – GATK (broadinstitute.org) Ensembl Variant Effect Predictor (VEP) McLaren et al. 2016 Variant Effect Predictor - Homo_sapiens - Ensembl genome browser 105 samtools mpileup Danecek et al. 2021 N/A Oncoprinter Cerami et al., 2012 cBioPortal for Cancer Genomics::Oncoprinter cBioPortal Gao et al., 2013 cBioPortal for Cancer Genomics DRAGEN Germline v.3 pipeline Ilumina DRAGEN Germline (illumina.com) GATK Haplotype Caller pipeline Van der Auwera et al.2020 HaplotypeCaller – GATK (broadinstitute. org) Sequencing Analysis Software v 6.0 ABI N/A TRACE/LASER Taliun et al.2017 LASER (umich.edu) ggplot2 Wickham 2016 https://ggplot2.tidyverse.org Other FilterMax F5 Multi Mode Microplate Reader Molecular Devices N/A Focused-ultrasonicator Covaris LE220-Plus Bravo liquid handling platform Agilent N/A ViiA qPCR machine Life Technologies (ABI) N/A NovaSeq 6000 Ilumina N/A Starlet Liquid Handling System Hamilton N/A Tape Station System Agilent N/A HiSeq 4000 Ilumina N/A Liquid Handling Workstation SciClone Pippin Prep system Sage Science Beverly, MA N/A SPE-DRY 96 Biotage N/A Veriti thermal cycler ABI N/A 3500XL Capillary sequencer ABI N/A Bioanalyzer Agilent N/A Agena’s MassARRAYTM System Agena N/A High Seq X Illumina SY-301-2002 Article ll OPEN ACCESS
Library Quantification:Article Title: Genetic changes associated with relapse in favorable histology Wilms tumor: A Children’s Oncology Group AREN03B2 study
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Samples from normal blood or tissue, primary tumor, relapse tumor from patients with Wilms Tumor Children’s Oncology Group childrensoncologygroup.org Critical commercial assays AllPrep DNA/RNA kit Qiagen Cat# 80204 mirVana miRNA Isolation Kit Invitrogen Cat# AM1560 Roche High Pure miRNA Isolation Kit Roche Cat# 05080576001 QIAamp DNA Blood Midi kit Qiagen Cat# 51183 Quant-iT PicoGreen quantification assay kit Invitrogen Cat# P7589 RNA 6000 NanoChip Kit Agilent Cat # 5067-1511 Complex iPLEX Gold Genotyping Reagent Agena Cat #10158 Extend Primer Mix Integrated DNA Technologies (IDT) N/A Ampure XP SPRI Beads Beckman Coulter Cat# A63881 Hyper Prep without amplification KAPA Biosystems/Roche KK8505 Unique Dual-Indexed Adapter Plates KAPA Biosystems/Roche Cat# KK8727 Quantitative PCR kit (library quantification) KAPA Biosystems/Roche Cat# KK4835 Stranded Total RNA Prep with RiboZero Gold Illumina Cat# 20020599 IDT for Illumina – TruSeq RNA UD indexes Illumina Cat# 20022371 NEXTflex Small RNA-Seq Kit v.3 PerkinElmer Cat# NOVA-5132-06 HyperPrep Kit with Amplification KAPA Biosystems/Roche Cat # KK8504 xGenTM UDI-UMI adapters Integrated DNA Technologies N/A HiFi HotStart Ready Mix KAPA Biosystems/Roche KK2602 p5 and p7 primers Integrated DNA Technologies N/A Dual Index F&R primers Integrated DNA Technologies Cat# 100981K xGenTM Hybridization and Wash Kit Integrated DNA Technologies Cat# 1080584 xGenTM Universal Blockers Integrated DNA Technologies Cat# 1075476 CustomPanel bait Twist Biosciences Custom Platinum Hot-start PCR kit Invitrogen Cat# 13000012 ExoSAP-IT Applied Biosystems Cat# 78200.200.UL Quant-it dNA quantification assay kit (Picogreen) Invitrogen Thermo Science catalogue Q33130 BigDye XTerminator Purification Kit Applied Biosystems Cat# 4376486 Deposited data Raw and Analyzed Data (Project Publication Page: MP2PRT-WT) NCI Genomic Data Commons https://gdc.cancer.gov/about-data/ publications/MP2PRT-WT-2022; https://portal.gdc.cancer.gov/ projects/MP2PRT-WT gnomAD Karczewski et al.2020 gnomAD (broadinstitute.org) PharmGKB Whirl-Carrillo et al.2012 PharmGKB (pharmgkb.org) PGxMine Lever et al.2020 PGxMine (pharmgkb.org) Oligonucleotides Primers for verification of variants involving MGA, WT1, MCFC1, RBL1, COBLL1 This paper (Methods) N/A Primer Target locations for Validation set This paper (Table S4) N/A (Continued on next page) Cell Reports Medicine 3, 100644, June 21, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms Picard Broad Institute https://broadinstitute.github.io/picard/ CaVEman Nik-Zainal et al., 2016 https://github.com/cancerit/CaVEMan Pindel Ye et al., 2009 https://github.com/genome/pindel BRASS Campbell et al., 2008 https://github.com/cancerit/BRASS AscatNGS Raine et al., 2016 https://github.com/cancerit/ascatNgs bcl2fastq Illumina v.2.20.0 Bioionformatics Pipeline: mRNA analysis GDC https://docs.gdc.cancer.gov/Data/ Bioinformatics_Pipelines/ Expression_mRNA_Pipeline/ STAR two-pass Dobin et al. 2013 N/A HTSeq Anders et al. 2015 v.0.6.1.p1 Small RNA Quantification pipeline Chu et al. 2015 N/A GATK Mutect 2 tumor-only pipeline Van der Auwera et al.2020 Mutect2 – GATK (broadinstitute.org) Ensembl Variant Effect Predictor (VEP) McLaren et al. 2016 Variant Effect Predictor - Homo_sapiens - Ensembl genome browser 105 samtools mpileup Danecek et al. 2021 N/A Oncoprinter Cerami et al., 2012 cBioPortal for Cancer Genomics::Oncoprinter cBioPortal Gao et al., 2013 cBioPortal for Cancer Genomics DRAGEN Germline v.3 pipeline Ilumina DRAGEN Germline (illumina.com) GATK Haplotype Caller pipeline Van der Auwera et al.2020 HaplotypeCaller – GATK (broadinstitute. org) Sequencing Analysis Software v 6.0 ABI N/A TRACE/LASER Taliun et al.2017 LASER (umich.edu) ggplot2 Wickham 2016 https://ggplot2.tidyverse.org Other FilterMax F5 Multi Mode Microplate Reader Molecular Devices N/A Focused-ultrasonicator Covaris LE220-Plus Bravo liquid handling platform Agilent N/A ViiA qPCR machine Life Technologies (ABI) N/A NovaSeq 6000 Ilumina N/A Starlet Liquid Handling System Hamilton N/A Tape Station System Agilent N/A HiSeq 4000 Ilumina N/A Liquid Handling Workstation SciClone Pippin Prep system Sage Science Beverly, MA N/A SPE-DRY 96 Biotage N/A Veriti thermal cycler ABI N/A 3500XL Capillary sequencer ABI N/A Bioanalyzer Agilent N/A Agena’s MassARRAYTM System Agena N/A High Seq X Illumina SY-301-2002 Article ll OPEN ACCESS
RNA sequencing:Article Title: Genetic changes associated with relapse in favorable histology Wilms tumor: A Children’s Oncology Group AREN03B2 study
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Samples from normal blood or tissue, primary tumor, relapse tumor from patients with Wilms Tumor Children’s Oncology Group childrensoncologygroup.org Critical commercial assays AllPrep DNA/RNA kit Qiagen Cat# 80204 mirVana miRNA Isolation Kit Invitrogen Cat# AM1560 Roche High Pure miRNA Isolation Kit Roche Cat# 05080576001 QIAamp DNA Blood Midi kit Qiagen Cat# 51183 Quant-iT PicoGreen quantification assay kit Invitrogen Cat# P7589 RNA 6000 NanoChip Kit Agilent Cat # 5067-1511 Complex iPLEX Gold Genotyping Reagent Agena Cat #10158 Extend Primer Mix Integrated DNA Technologies (IDT) N/A Ampure XP SPRI Beads Beckman Coulter Cat# A63881 Hyper Prep without amplification KAPA Biosystems/Roche KK8505 Unique Dual-Indexed Adapter Plates KAPA Biosystems/Roche Cat# KK8727 Quantitative PCR kit (library quantification) KAPA Biosystems/Roche Cat# KK4835 Stranded Total RNA Prep with RiboZero Gold Illumina Cat# 20020599 IDT for Illumina – TruSeq RNA UD indexes Illumina Cat# 20022371 NEXTflex Small RNA-Seq Kit v.3 PerkinElmer Cat# NOVA-5132-06 HyperPrep Kit with Amplification KAPA Biosystems/Roche Cat # KK8504 xGenTM UDI-UMI adapters Integrated DNA Technologies N/A HiFi HotStart Ready Mix KAPA Biosystems/Roche KK2602 p5 and p7 primers Integrated DNA Technologies N/A Dual Index F&R primers Integrated DNA Technologies Cat# 100981K xGenTM Hybridization and Wash Kit Integrated DNA Technologies Cat# 1080584 xGenTM Universal Blockers Integrated DNA Technologies Cat# 1075476 CustomPanel bait Twist Biosciences Custom Platinum Hot-start PCR kit Invitrogen Cat# 13000012 ExoSAP-IT Applied Biosystems Cat# 78200.200.UL Quant-it dNA quantification assay kit (Picogreen) Invitrogen Thermo Science catalogue Q33130 BigDye XTerminator Purification Kit Applied Biosystems Cat# 4376486 Deposited data Raw and Analyzed Data (Project Publication Page: MP2PRT-WT) NCI Genomic Data Commons https://gdc.cancer.gov/about-data/ publications/MP2PRT-WT-2022; https://portal.gdc.cancer.gov/ projects/MP2PRT-WT gnomAD Karczewski et al.2020 gnomAD (broadinstitute.org) PharmGKB Whirl-Carrillo et al.2012 PharmGKB (pharmgkb.org) PGxMine Lever et al.2020 PGxMine (pharmgkb.org) Oligonucleotides Primers for verification of variants involving MGA, WT1, MCFC1, RBL1, COBLL1 This paper (Methods) N/A Primer Target locations for Validation set This paper (Table S4) N/A (Continued on next page) Cell Reports Medicine 3, 100644, June 21, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms Picard Broad Institute https://broadinstitute.github.io/picard/ CaVEman Nik-Zainal et al., 2016 https://github.com/cancerit/CaVEMan Pindel Ye et al., 2009 https://github.com/genome/pindel BRASS Campbell et al., 2008 https://github.com/cancerit/BRASS AscatNGS Raine et al., 2016 https://github.com/cancerit/ascatNgs bcl2fastq Illumina v.2.20.0 Bioionformatics Pipeline: mRNA analysis GDC https://docs.gdc.cancer.gov/Data/ Bioinformatics_Pipelines/ Expression_mRNA_Pipeline/ STAR two-pass Dobin et al. 2013 N/A HTSeq Anders et al. 2015 v.0.6.1.p1 Small RNA Quantification pipeline Chu et al. 2015 N/A GATK Mutect 2 tumor-only pipeline Van der Auwera et al.2020 Mutect2 – GATK (broadinstitute.org) Ensembl Variant Effect Predictor (VEP) McLaren et al. 2016 Variant Effect Predictor - Homo_sapiens - Ensembl genome browser 105 samtools mpileup Danecek et al. 2021 N/A Oncoprinter Cerami et al., 2012 cBioPortal for Cancer Genomics::Oncoprinter cBioPortal Gao et al., 2013 cBioPortal for Cancer Genomics DRAGEN Germline v.3 pipeline Ilumina DRAGEN Germline (illumina.com) GATK Haplotype Caller pipeline Van der Auwera et al.2020 HaplotypeCaller – GATK (broadinstitute. org) Sequencing Analysis Software v 6.0 ABI N/A TRACE/LASER Taliun et al.2017 LASER (umich.edu) ggplot2 Wickham 2016 https://ggplot2.tidyverse.org Other FilterMax F5 Multi Mode Microplate Reader Molecular Devices N/A Focused-ultrasonicator Covaris LE220-Plus Bravo liquid handling platform Agilent N/A ViiA qPCR machine Life Technologies (ABI) N/A NovaSeq 6000 Ilumina N/A Starlet Liquid Handling System Hamilton N/A Tape Station System Agilent N/A HiSeq 4000 Ilumina N/A Liquid Handling Workstation SciClone Pippin Prep system Sage Science Beverly, MA N/A SPE-DRY 96 Biotage N/A Veriti thermal cycler ABI N/A 3500XL Capillary sequencer ABI N/A Bioanalyzer Agilent N/A Agena’s MassARRAYTM System Agena N/A High Seq X Illumina SY-301-2002 Article ll OPEN ACCESS
Hybridization:Article Title: Genetic changes associated with relapse in favorable histology Wilms tumor: A Children’s Oncology Group AREN03B2 study
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Samples from normal blood or tissue, primary tumor, relapse tumor from patients with Wilms Tumor Children’s Oncology Group childrensoncologygroup.org Critical commercial assays AllPrep DNA/RNA kit Qiagen Cat# 80204 mirVana miRNA Isolation Kit Invitrogen Cat# AM1560 Roche High Pure miRNA Isolation Kit Roche Cat# 05080576001 QIAamp DNA Blood Midi kit Qiagen Cat# 51183 Quant-iT PicoGreen quantification assay kit Invitrogen Cat# P7589 RNA 6000 NanoChip Kit Agilent Cat # 5067-1511 Complex iPLEX Gold Genotyping Reagent Agena Cat #10158 Extend Primer Mix Integrated DNA Technologies (IDT) N/A Ampure XP SPRI Beads Beckman Coulter Cat# A63881 Hyper Prep without amplification KAPA Biosystems/Roche KK8505 Unique Dual-Indexed Adapter Plates KAPA Biosystems/Roche Cat# KK8727 Quantitative PCR kit (library quantification) KAPA Biosystems/Roche Cat# KK4835 Stranded Total RNA Prep with RiboZero Gold Illumina Cat# 20020599 IDT for Illumina – TruSeq RNA UD indexes Illumina Cat# 20022371 NEXTflex Small RNA-Seq Kit v.3 PerkinElmer Cat# NOVA-5132-06 HyperPrep Kit with Amplification KAPA Biosystems/Roche Cat # KK8504 xGenTM UDI-UMI adapters Integrated DNA Technologies N/A HiFi HotStart Ready Mix KAPA Biosystems/Roche KK2602 p5 and p7 primers Integrated DNA Technologies N/A Dual Index F&R primers Integrated DNA Technologies Cat# 100981K xGenTM Hybridization and Wash Kit Integrated DNA Technologies Cat# 1080584 xGenTM Universal Blockers Integrated DNA Technologies Cat# 1075476 CustomPanel bait Twist Biosciences Custom Platinum Hot-start PCR kit Invitrogen Cat# 13000012 ExoSAP-IT Applied Biosystems Cat# 78200.200.UL Quant-it dNA quantification assay kit (Picogreen) Invitrogen Thermo Science catalogue Q33130 BigDye XTerminator Purification Kit Applied Biosystems Cat# 4376486 Deposited data Raw and Analyzed Data (Project Publication Page: MP2PRT-WT) NCI Genomic Data Commons https://gdc.cancer.gov/about-data/ publications/MP2PRT-WT-2022; https://portal.gdc.cancer.gov/ projects/MP2PRT-WT gnomAD Karczewski et al.2020 gnomAD (broadinstitute.org) PharmGKB Whirl-Carrillo et al.2012 PharmGKB (pharmgkb.org) PGxMine Lever et al.2020 PGxMine (pharmgkb.org) Oligonucleotides Primers for verification of variants involving MGA, WT1, MCFC1, RBL1, COBLL1 This paper (Methods) N/A Primer Target locations for Validation set This paper (Table S4) N/A (Continued on next page) Cell Reports Medicine 3, 100644, June 21, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms Picard Broad Institute https://broadinstitute.github.io/picard/ CaVEman Nik-Zainal et al., 2016 https://github.com/cancerit/CaVEMan Pindel Ye et al., 2009 https://github.com/genome/pindel BRASS Campbell et al., 2008 https://github.com/cancerit/BRASS AscatNGS Raine et al., 2016 https://github.com/cancerit/ascatNgs bcl2fastq Illumina v.2.20.0 Bioionformatics Pipeline: mRNA analysis GDC https://docs.gdc.cancer.gov/Data/ Bioinformatics_Pipelines/ Expression_mRNA_Pipeline/ STAR two-pass Dobin et al. 2013 N/A HTSeq Anders et al. 2015 v.0.6.1.p1 Small RNA Quantification pipeline Chu et al. 2015 N/A GATK Mutect 2 tumor-only pipeline Van der Auwera et al.2020 Mutect2 – GATK (broadinstitute.org) Ensembl Variant Effect Predictor (VEP) McLaren et al. 2016 Variant Effect Predictor - Homo_sapiens - Ensembl genome browser 105 samtools mpileup Danecek et al. 2021 N/A Oncoprinter Cerami et al., 2012 cBioPortal for Cancer Genomics::Oncoprinter cBioPortal Gao et al., 2013 cBioPortal for Cancer Genomics DRAGEN Germline v.3 pipeline Ilumina DRAGEN Germline (illumina.com) GATK Haplotype Caller pipeline Van der Auwera et al.2020 HaplotypeCaller – GATK (broadinstitute. org) Sequencing Analysis Software v 6.0 ABI N/A TRACE/LASER Taliun et al.2017 LASER (umich.edu) ggplot2 Wickham 2016 https://ggplot2.tidyverse.org Other FilterMax F5 Multi Mode Microplate Reader Molecular Devices N/A Focused-ultrasonicator Covaris LE220-Plus Bravo liquid handling platform Agilent N/A ViiA qPCR machine Life Technologies (ABI) N/A NovaSeq 6000 Ilumina N/A Starlet Liquid Handling System Hamilton N/A Tape Station System Agilent N/A HiSeq 4000 Ilumina N/A Liquid Handling Workstation SciClone Pippin Prep system Sage Science Beverly, MA N/A SPE-DRY 96 Biotage N/A Veriti thermal cycler ABI N/A 3500XL Capillary sequencer ABI N/A Bioanalyzer Agilent N/A Agena’s MassARRAYTM System Agena N/A High Seq X Illumina SY-301-2002 Article ll OPEN ACCESS
Hot Start PCR:Article Title: Genetic changes associated with relapse in favorable histology Wilms tumor: A Children’s Oncology Group AREN03B2 study
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Samples from normal blood or tissue, primary tumor, relapse tumor from patients with Wilms Tumor Children’s Oncology Group childrensoncologygroup.org Critical commercial assays AllPrep DNA/RNA kit Qiagen Cat# 80204 mirVana miRNA Isolation Kit Invitrogen Cat# AM1560 Roche High Pure miRNA Isolation Kit Roche Cat# 05080576001 QIAamp DNA Blood Midi kit Qiagen Cat# 51183 Quant-iT PicoGreen quantification assay kit Invitrogen Cat# P7589 RNA 6000 NanoChip Kit Agilent Cat # 5067-1511 Complex iPLEX Gold Genotyping Reagent Agena Cat #10158 Extend Primer Mix Integrated DNA Technologies (IDT) N/A Ampure XP SPRI Beads Beckman Coulter Cat# A63881 Hyper Prep without amplification KAPA Biosystems/Roche KK8505 Unique Dual-Indexed Adapter Plates KAPA Biosystems/Roche Cat# KK8727 Quantitative PCR kit (library quantification) KAPA Biosystems/Roche Cat# KK4835 Stranded Total RNA Prep with RiboZero Gold Illumina Cat# 20020599 IDT for Illumina – TruSeq RNA UD indexes Illumina Cat# 20022371 NEXTflex Small RNA-Seq Kit v.3 PerkinElmer Cat# NOVA-5132-06 HyperPrep Kit with Amplification KAPA Biosystems/Roche Cat # KK8504 xGenTM UDI-UMI adapters Integrated DNA Technologies N/A HiFi HotStart Ready Mix KAPA Biosystems/Roche KK2602 p5 and p7 primers Integrated DNA Technologies N/A Dual Index F&R primers Integrated DNA Technologies Cat# 100981K xGenTM Hybridization and Wash Kit Integrated DNA Technologies Cat# 1080584 xGenTM Universal Blockers Integrated DNA Technologies Cat# 1075476 CustomPanel bait Twist Biosciences Custom Platinum Hot-start PCR kit Invitrogen Cat# 13000012 ExoSAP-IT Applied Biosystems Cat# 78200.200.UL Quant-it dNA quantification assay kit (Picogreen) Invitrogen Thermo Science catalogue Q33130 BigDye XTerminator Purification Kit Applied Biosystems Cat# 4376486 Deposited data Raw and Analyzed Data (Project Publication Page: MP2PRT-WT) NCI Genomic Data Commons https://gdc.cancer.gov/about-data/ publications/MP2PRT-WT-2022; https://portal.gdc.cancer.gov/ projects/MP2PRT-WT gnomAD Karczewski et al.2020 gnomAD (broadinstitute.org) PharmGKB Whirl-Carrillo et al.2012 PharmGKB (pharmgkb.org) PGxMine Lever et al.2020 PGxMine (pharmgkb.org) Oligonucleotides Primers for verification of variants involving MGA, WT1, MCFC1, RBL1, COBLL1 This paper (Methods) N/A Primer Target locations for Validation set This paper (Table S4) N/A (Continued on next page) Cell Reports Medicine 3, 100644, June 21, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms Picard Broad Institute https://broadinstitute.github.io/picard/ CaVEman Nik-Zainal et al., 2016 https://github.com/cancerit/CaVEMan Pindel Ye et al., 2009 https://github.com/genome/pindel BRASS Campbell et al., 2008 https://github.com/cancerit/BRASS AscatNGS Raine et al., 2016 https://github.com/cancerit/ascatNgs bcl2fastq Illumina v.2.20.0 Bioionformatics Pipeline: mRNA analysis GDC https://docs.gdc.cancer.gov/Data/ Bioinformatics_Pipelines/ Expression_mRNA_Pipeline/ STAR two-pass Dobin et al. 2013 N/A HTSeq Anders et al. 2015 v.0.6.1.p1 Small RNA Quantification pipeline Chu et al. 2015 N/A GATK Mutect 2 tumor-only pipeline Van der Auwera et al.2020 Mutect2 – GATK (broadinstitute.org) Ensembl Variant Effect Predictor (VEP) McLaren et al. 2016 Variant Effect Predictor - Homo_sapiens - Ensembl genome browser 105 samtools mpileup Danecek et al. 2021 N/A Oncoprinter Cerami et al., 2012 cBioPortal for Cancer Genomics::Oncoprinter cBioPortal Gao et al., 2013 cBioPortal for Cancer Genomics DRAGEN Germline v.3 pipeline Ilumina DRAGEN Germline (illumina.com) GATK Haplotype Caller pipeline Van der Auwera et al.2020 HaplotypeCaller – GATK (broadinstitute. org) Sequencing Analysis Software v 6.0 ABI N/A TRACE/LASER Taliun et al.2017 LASER (umich.edu) ggplot2 Wickham 2016 https://ggplot2.tidyverse.org Other FilterMax F5 Multi Mode Microplate Reader Molecular Devices N/A Focused-ultrasonicator Covaris LE220-Plus Bravo liquid handling platform Agilent N/A ViiA qPCR machine Life Technologies (ABI) N/A NovaSeq 6000 Ilumina N/A Starlet Liquid Handling System Hamilton N/A Tape Station System Agilent N/A HiSeq 4000 Ilumina N/A Liquid Handling Workstation SciClone Pippin Prep system Sage Science Beverly, MA N/A SPE-DRY 96 Biotage N/A Veriti thermal cycler ABI N/A 3500XL Capillary sequencer ABI N/A Bioanalyzer Agilent N/A Agena’s MassARRAYTM System Agena N/A High Seq X Illumina SY-301-2002 Article ll OPEN ACCESS
Purification:Article Title: Genetic changes associated with relapse in favorable histology Wilms tumor: A Children’s Oncology Group AREN03B2 study
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Samples from normal blood or tissue, primary tumor, relapse tumor from patients with Wilms Tumor Children’s Oncology Group childrensoncologygroup.org Critical commercial assays AllPrep DNA/RNA kit Qiagen Cat# 80204 mirVana miRNA Isolation Kit Invitrogen Cat# AM1560 Roche High Pure miRNA Isolation Kit Roche Cat# 05080576001 QIAamp DNA Blood Midi kit Qiagen Cat# 51183 Quant-iT PicoGreen quantification assay kit Invitrogen Cat# P7589 RNA 6000 NanoChip Kit Agilent Cat # 5067-1511 Complex iPLEX Gold Genotyping Reagent Agena Cat #10158 Extend Primer Mix Integrated DNA Technologies (IDT) N/A Ampure XP SPRI Beads Beckman Coulter Cat# A63881 Hyper Prep without amplification KAPA Biosystems/Roche KK8505 Unique Dual-Indexed Adapter Plates KAPA Biosystems/Roche Cat# KK8727 Quantitative PCR kit (library quantification) KAPA Biosystems/Roche Cat# KK4835 Stranded Total RNA Prep with RiboZero Gold Illumina Cat# 20020599 IDT for Illumina – TruSeq RNA UD indexes Illumina Cat# 20022371 NEXTflex Small RNA-Seq Kit v.3 PerkinElmer Cat# NOVA-5132-06 HyperPrep Kit with Amplification KAPA Biosystems/Roche Cat # KK8504 xGenTM UDI-UMI adapters Integrated DNA Technologies N/A HiFi HotStart Ready Mix KAPA Biosystems/Roche KK2602 p5 and p7 primers Integrated DNA Technologies N/A Dual Index F&R primers Integrated DNA Technologies Cat# 100981K xGenTM Hybridization and Wash Kit Integrated DNA Technologies Cat# 1080584 xGenTM Universal Blockers Integrated DNA Technologies Cat# 1075476 CustomPanel bait Twist Biosciences Custom Platinum Hot-start PCR kit Invitrogen Cat# 13000012 ExoSAP-IT Applied Biosystems Cat# 78200.200.UL Quant-it dNA quantification assay kit (Picogreen) Invitrogen Thermo Science catalogue Q33130 BigDye XTerminator Purification Kit Applied Biosystems Cat# 4376486 Deposited data Raw and Analyzed Data (Project Publication Page: MP2PRT-WT) NCI Genomic Data Commons https://gdc.cancer.gov/about-data/ publications/MP2PRT-WT-2022; https://portal.gdc.cancer.gov/ projects/MP2PRT-WT gnomAD Karczewski et al.2020 gnomAD (broadinstitute.org) PharmGKB Whirl-Carrillo et al.2012 PharmGKB (pharmgkb.org) PGxMine Lever et al.2020 PGxMine (pharmgkb.org) Oligonucleotides Primers for verification of variants involving MGA, WT1, MCFC1, RBL1, COBLL1 This paper (Methods) N/A Primer Target locations for Validation set This paper (Table S4) N/A (Continued on next page) Cell Reports Medicine 3, 100644, June 21, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms Picard Broad Institute https://broadinstitute.github.io/picard/ CaVEman Nik-Zainal et al., 2016 https://github.com/cancerit/CaVEMan Pindel Ye et al., 2009 https://github.com/genome/pindel BRASS Campbell et al., 2008 https://github.com/cancerit/BRASS AscatNGS Raine et al., 2016 https://github.com/cancerit/ascatNgs bcl2fastq Illumina v.2.20.0 Bioionformatics Pipeline: mRNA analysis GDC https://docs.gdc.cancer.gov/Data/ Bioinformatics_Pipelines/ Expression_mRNA_Pipeline/ STAR two-pass Dobin et al. 2013 N/A HTSeq Anders et al. 2015 v.0.6.1.p1 Small RNA Quantification pipeline Chu et al. 2015 N/A GATK Mutect 2 tumor-only pipeline Van der Auwera et al.2020 Mutect2 – GATK (broadinstitute.org) Ensembl Variant Effect Predictor (VEP) McLaren et al. 2016 Variant Effect Predictor - Homo_sapiens - Ensembl genome browser 105 samtools mpileup Danecek et al. 2021 N/A Oncoprinter Cerami et al., 2012 cBioPortal for Cancer Genomics::Oncoprinter cBioPortal Gao et al., 2013 cBioPortal for Cancer Genomics DRAGEN Germline v.3 pipeline Ilumina DRAGEN Germline (illumina.com) GATK Haplotype Caller pipeline Van der Auwera et al.2020 HaplotypeCaller – GATK (broadinstitute. org) Sequencing Analysis Software v 6.0 ABI N/A TRACE/LASER Taliun et al.2017 LASER (umich.edu) ggplot2 Wickham 2016 https://ggplot2.tidyverse.org Other FilterMax F5 Multi Mode Microplate Reader Molecular Devices N/A Focused-ultrasonicator Covaris LE220-Plus Bravo liquid handling platform Agilent N/A ViiA qPCR machine Life Technologies (ABI) N/A NovaSeq 6000 Ilumina N/A Starlet Liquid Handling System Hamilton N/A Tape Station System Agilent N/A HiSeq 4000 Ilumina N/A Liquid Handling Workstation SciClone Pippin Prep system Sage Science Beverly, MA N/A SPE-DRY 96 Biotage N/A Veriti thermal cycler ABI N/A 3500XL Capillary sequencer ABI N/A Bioanalyzer Agilent N/A Agena’s MassARRAYTM System Agena N/A High Seq X Illumina SY-301-2002 Article ll OPEN ACCESS
Biomarker Discovery:Article Title: Genetic changes associated with relapse in favorable histology Wilms tumor: A Children’s Oncology Group AREN03B2 study
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Samples from normal blood or tissue, primary tumor, relapse tumor from patients with Wilms Tumor Children’s Oncology Group childrensoncologygroup.org Critical commercial assays AllPrep DNA/RNA kit Qiagen Cat# 80204 mirVana miRNA Isolation Kit Invitrogen Cat# AM1560 Roche High Pure miRNA Isolation Kit Roche Cat# 05080576001 QIAamp DNA Blood Midi kit Qiagen Cat# 51183 Quant-iT PicoGreen quantification assay kit Invitrogen Cat# P7589 RNA 6000 NanoChip Kit Agilent Cat # 5067-1511 Complex iPLEX Gold Genotyping Reagent Agena Cat #10158 Extend Primer Mix Integrated DNA Technologies (IDT) N/A Ampure XP SPRI Beads Beckman Coulter Cat# A63881 Hyper Prep without amplification KAPA Biosystems/Roche KK8505 Unique Dual-Indexed Adapter Plates KAPA Biosystems/Roche Cat# KK8727 Quantitative PCR kit (library quantification) KAPA Biosystems/Roche Cat# KK4835 Stranded Total RNA Prep with RiboZero Gold Illumina Cat# 20020599 IDT for Illumina – TruSeq RNA UD indexes Illumina Cat# 20022371 NEXTflex Small RNA-Seq Kit v.3 PerkinElmer Cat# NOVA-5132-06 HyperPrep Kit with Amplification KAPA Biosystems/Roche Cat # KK8504 xGenTM UDI-UMI adapters Integrated DNA Technologies N/A HiFi HotStart Ready Mix KAPA Biosystems/Roche KK2602 p5 and p7 primers Integrated DNA Technologies N/A Dual Index F&R primers Integrated DNA Technologies Cat# 100981K xGenTM Hybridization and Wash Kit Integrated DNA Technologies Cat# 1080584 xGenTM Universal Blockers Integrated DNA Technologies Cat# 1075476 CustomPanel bait Twist Biosciences Custom Platinum Hot-start PCR kit Invitrogen Cat# 13000012 ExoSAP-IT Applied Biosystems Cat# 78200.200.UL Quant-it dNA quantification assay kit (Picogreen) Invitrogen Thermo Science catalogue Q33130 BigDye XTerminator Purification Kit Applied Biosystems Cat# 4376486 Deposited data Raw and Analyzed Data (Project Publication Page: MP2PRT-WT) NCI Genomic Data Commons https://gdc.cancer.gov/about-data/ publications/MP2PRT-WT-2022; https://portal.gdc.cancer.gov/ projects/MP2PRT-WT gnomAD Karczewski et al.2020 gnomAD (broadinstitute.org) PharmGKB Whirl-Carrillo et al.2012 PharmGKB (pharmgkb.org) PGxMine Lever et al.2020 PGxMine (pharmgkb.org) Oligonucleotides Primers for verification of variants involving MGA, WT1, MCFC1, RBL1, COBLL1 This paper (Methods) N/A Primer Target locations for Validation set This paper (Table S4) N/A (Continued on next page) Cell Reports Medicine 3, 100644, June 21, 2022 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms Picard Broad Institute https://broadinstitute.github.io/picard/ CaVEman Nik-Zainal et al., 2016 https://github.com/cancerit/CaVEMan Pindel Ye et al., 2009 https://github.com/genome/pindel BRASS Campbell et al., 2008 https://github.com/cancerit/BRASS AscatNGS Raine et al., 2016 https://github.com/cancerit/ascatNgs bcl2fastq Illumina v.2.20.0 Bioionformatics Pipeline: mRNA analysis GDC https://docs.gdc.cancer.gov/Data/ Bioinformatics_Pipelines/ Expression_mRNA_Pipeline/ STAR two-pass Dobin et al. 2013 N/A HTSeq Anders et al. 2015 v.0.6.1.p1 Small RNA Quantification pipeline Chu et al. 2015 N/A GATK Mutect 2 tumor-only pipeline Van der Auwera et al.2020 Mutect2 – GATK (broadinstitute.org) Ensembl Variant Effect Predictor (VEP) McLaren et al. 2016 Variant Effect Predictor - Homo_sapiens - Ensembl genome browser 105 samtools mpileup Danecek et al. 2021 N/A Oncoprinter Cerami et al., 2012 cBioPortal for Cancer Genomics::Oncoprinter cBioPortal Gao et al., 2013 cBioPortal for Cancer Genomics DRAGEN Germline v.3 pipeline Ilumina DRAGEN Germline (illumina.com) GATK Haplotype Caller pipeline Van der Auwera et al.2020 HaplotypeCaller – GATK (broadinstitute. org) Sequencing Analysis Software v 6.0 ABI N/A TRACE/LASER Taliun et al.2017 LASER (umich.edu) ggplot2 Wickham 2016 https://ggplot2.tidyverse.org Other FilterMax F5 Multi Mode Microplate Reader Molecular Devices N/A Focused-ultrasonicator Covaris LE220-Plus Bravo liquid handling platform Agilent N/A ViiA qPCR machine Life Technologies (ABI) N/A NovaSeq 6000 Ilumina N/A Starlet Liquid Handling System Hamilton N/A Tape Station System Agilent N/A HiSeq 4000 Ilumina N/A Liquid Handling Workstation SciClone Pippin Prep system Sage Science Beverly, MA N/A SPE-DRY 96 Biotage N/A Veriti thermal cycler ABI N/A 3500XL Capillary sequencer ABI N/A Bioanalyzer Agilent N/A Agena’s MassARRAYTM System Agena N/A High Seq X Illumina SY-301-2002 Article ll OPEN ACCESS
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