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Table 1 Description of cancer projects for assessing costs of genomic sequencing

From: Estimating the costs of genomic sequencing in cancer control

 Lung/Melanoma cancerBreast cancerMelanomaLung cancerOesophageal cancerMesothelioma
Description
 Project goalDirect clinical application: treatment pathwayDirect clinical application: treatment pathwayRisk stratification, surveillance decisionsDetermine personalised treatment pathsDetermine tumour specific mutationsDetermine tumour specific mutations
 SettingStatewide health serviceStatewide health serviceClinical researchClinical researchResearchResearch
 Type of sequencingPanelPanelExomeExomeGenomeGenome
 Number of patients745192383101003
 Commercial servicesNo, in-houseNo, in-houseYes, freight/sequencingNo, in-houseYes, freight/sequencingYes, freight/sequencing
 Location of sequencing testingPathology Queensland, BrisbanePathology Queensland, BrisbaneAustralian Genomic Research Facility, MelbourneAustralian Translational Genomics Centre, BrisbaneKinghorn Centre Clinical Genomics, MelbourneBeijing Genomics Institute, Hong Kong
 Setting/Location of bioinformaticsState government health service, BrisbaneState government health service, BrisbaneUniversity, BrisbaneUniversity, BrisbaneMedical Research Institute, BrisbaneMedical Research Institute, Brisbane
Steps
 1.SamplingBiopsy sample (no blood)Blood sample (no tumour)Saliva - Oragene DNA self-collection kitBiopsy sample & blood drawTumour biopsy & blood drawTumour biopsy & blood draw
 2.DNA extractionDNA Investigator extraction kit,
Qubit dsDNA Broad Range Assay kit
QiaSymphony kit,
Qubit dsDNA Broad Range Assay kit
QiaQuick Gel Extraction Kit, Qubit dsDNA Broad Range Assay kit, Sangar seq validation, BigDye sequencing kitQiaSymphony kit, DNA midi kits (blood and tumour)Qiagen AllPrep DNA mini kit,
QiaAMP DNA blood mini kit, Qubit dsDNA Broad Range Assay kit
Qiagen AllPrep DNA/RNA/ miRNA Universal kit, Qubit, SNP arrays
 3.Library preparationStandardised in-house protocolStandardised in-house protocolAGRF - Illumina protocols, automated electrophoresis & qPCRPre-sequencing qPCRGenomeOne – Illumina protocolsMGIEasy™ DNA Library Prep Kit V1, DNA nanoballs on BGISEQ-500
 4.SequencingIllumina MiSeq™/ NextSeq™
TruSeq 26-gene panel
Illumina MiSeq™/ NextSeq™,In-house panel, MLPAIllumina NovaSeq™Illumina NextSeq™Illumina HiSeq XTen™BGISEQ-500™
Coverage depth1000X500X>100X100-130X exome, 500-700X spiked-in gene panel30X blood, 60X tumour28X blood, 50X tumour
 5. AnalysisIn-houseIn-houseIn-houseDemultiplexed CASAVAIn-houseIn-house
Software for read mapping, variant calling/ annotationVariantStudioVariantStudio
Next Gene Soft Genetics
BWA alignment, Picard, GATK Haplotype Caller.
ANNOVAR
Novalign, GATK Haplotype Caller, VEPSNPs, Dual caller qSNP and GATK Haplotype caller. Indels:Haplotype Caller, Structural rearrangements: qSV
Copy Number: ascatNGS
SNPs, Dual caller qSNP and GATK Haplotype caller. Indels:Haplotype Caller, Structural rearrangements: qSV
Copy Number: ascatNGS
 6. Reporting to cliniciansStandard report – paper and electronic, multidiscip team meeting 10% casesStandard report – paper and electronic, multidisciplinary team meeting 10% casesn/a pre-clinical workPrep time for multidisciplinary teamn/a pre-clinical workn/a pre-clinical work
 7. Storage needs, 5 yrs107 TB (2 GB/sample)28 TB (2 GB/sample)275 TB (10 GB/sample)29 TB (20 GB/sample)529 TB (150 GB/tumour, 72 GB/blood)26 TB (150 GB/tumour, 72 GB/blood)
  1. Abbreviations: DNA deoxyribose nucleic acid, GAKT Genome Analysis Toolkit, MLPA Multiplex ligation-dependent probe amplification, qPCR quantitative polymerase chain reaction, BWA Burrow-Wheeler Aligner, VEP Variant Effect Predictor