Table 1 Description of cancer projects for assessing costs of genomic sequencing
From: Estimating the costs of genomic sequencing in cancer control
| Â | Lung/Melanoma cancer | Breast cancer | Melanoma | Lung cancer | Oesophageal cancer | Mesothelioma |
|---|---|---|---|---|---|---|
Description | ||||||
 Project goal | Direct clinical application: treatment pathway | Direct clinical application: treatment pathway | Risk stratification, surveillance decisions | Determine personalised treatment paths | Determine tumour specific mutations | Determine tumour specific mutations |
 Setting | Statewide health service | Statewide health service | Clinical research | Clinical research | Research | Research |
 Type of sequencing | Panel | Panel | Exome | Exome | Genome | Genome |
 Number of patients | 745 | 192 | 383 | 10 | 100 | 3 |
 Commercial services | No, in-house | No, in-house | Yes, freight/sequencing | No, in-house | Yes, freight/sequencing | Yes, freight/sequencing |
 Location of sequencing testing | Pathology Queensland, Brisbane | Pathology Queensland, Brisbane | Australian Genomic Research Facility, Melbourne | Australian Translational Genomics Centre, Brisbane | Kinghorn Centre Clinical Genomics, Melbourne | Beijing Genomics Institute, Hong Kong |
 Setting/Location of bioinformatics | State government health service, Brisbane | State government health service, Brisbane | University, Brisbane | University, Brisbane | Medical Research Institute, Brisbane | Medical Research Institute, Brisbane |
Steps | ||||||
 1.Sampling | Biopsy sample (no blood) | Blood sample (no tumour) | Saliva - Oragene DNA self-collection kit | Biopsy sample & blood draw | Tumour biopsy & blood draw | Tumour biopsy & blood draw |
 2.DNA extraction | DNA 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 kit | QiaSymphony 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 preparation | Standardised in-house protocol | Standardised in-house protocol | AGRF - Illumina protocols, automated electrophoresis & qPCR | Pre-sequencing qPCR | GenomeOne – Illumina protocols | MGIEasy™ DNA Library Prep Kit V1, DNA nanoballs on BGISEQ-500 |
 4.Sequencing | Illumina MiSeq™/ NextSeq™ TruSeq 26-gene panel | Illumina MiSeq™/ NextSeq™,In-house panel, MLPA | Illumina NovaSeq™ | Illumina NextSeq™ | Illumina HiSeq XTen™ | BGISEQ-500™ |
Coverage depth | 1000X | 500X | >100X | 100-130X exome, 500-700X spiked-in gene panel | 30X blood, 60X tumour | 28X blood, 50X tumour |
 5. Analysis | In-house | In-house | In-house | Demultiplexed CASAVA | In-house | In-house |
Software for read mapping, variant calling/ annotation | VariantStudio | VariantStudio Next Gene Soft Genetics | BWA alignment, Picard, GATK Haplotype Caller. ANNOVAR | Novalign, GATK Haplotype Caller, VEP | SNPs, 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 clinicians | Standard report – paper and electronic, multidiscip team meeting 10% cases | Standard report – paper and electronic, multidisciplinary team meeting 10% cases | n/a pre-clinical work | Prep time for multidisciplinary team | n/a pre-clinical work | n/a pre-clinical work |
 7. Storage needs, 5 yrs | 107 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) |