Micro-costing diagnostics in oncology: from single-gene testing to whole- genome sequencing

Figures & data

Table 1. Base case assumptions for cost calculations of diagnostic applications based on the standard case perspective

^aThe standard case perspective implies that an average Dutch lab practice was assumed and suppliers’ standard list prices were used, in respect of all techniques.

^bAdditional equipment refers to sample preparation platforms for NGS gene panels and WGS, whereby the unit of sample preparation is sample.

^cThe average coverage (sequencing depth) is based on the standard techniques’ specifications of the relevant suppliers. The 120× coverage for WGS corresponds to two samples (also one cancer patient) and consists of 90× tumor coverage (three times for heterogeneity) and 30× blood coverage (1 time as a reference genome).

^dThe unit of 1 flow cell is 30× coverage. In 1 run 2 flow cells of each 30× coverage fit. So, in 2 runs 4 flow cells fit, which corresponds to the 120× coverage for WGS.

^eData processing and data storage are outsourced for WGS.

^fData storage time concerns sixmonths of hot storage of a BAM file, VCF file, and patient report for WGS.

^gThe sample preparation and primary data analysis is done by a laboratory and bioinformatics technician for the standard techniques, and by a laboratory technician only for WGS. Sample and report administration is incorporated for all techniques.

^hThe data interpretation and report is done by a clinical molecular geneticist and pathologist for the standard techniques, and by a clinical molecular geneticist and a bioinformatics technician for WGS.

ⁱIn-house refers to in-house pipeline experience, for example, Burrows-Wheeler Aligner (BWA), Genome Analysis Toolkit (GATK), Strelka, BLCtoFASTQ, sebamba, PURPLE for WGS.

^jIncluding immunohistochemistry (IHC), Fluorescence In Situ Hybridization (FISH), pyrosequencing (Pyro seq), High Resolution Melting (HRM), Sanger sequencing (Sanger), next generation sequencing (NGS), and whole genome sequencing (WGS).

Table 2. Process-based cost calculations of diagnostic applications based on the standard case perspective

^aThe standard case perspective implies that an average Dutch lab practice was assumed and suppliers’ standard list prices were used, in respect of all techniques.

^bThe cost of the platforms, software, and consumables all exclude Value-Added Taxes (VAT).

^cFor the standard diagnostic techniques, lifecycles varying between 5 and 10 years, annuity factors ranging between 4.39 to 7.91, and an interest rate of 4.5% are maintained for both types of equipment (if applicable). The annual capital costs of the additional equipment (sample preparation platform) and the sequencing platform for WGS are calculated by taking into account a lifecycle of 5 years, an annuity factor of 4.45 and an interest rate of 4%.

^dThe capital, maintenance and operational costs per sample calculations are based on two times sample preparation and four times genome sequencing (90× coverage tumor and 30× coverage blood) for WGS. For WGS application, two samples are needed (tumor biopsy and blood) to do the analysis, whereas for the standard used techniques one sample (tumor) suffices.

^eDuring the first year, no maintenance costs occur as the platforms have a warranty for the first year.

^fSoftware management/maintenance incorporates daily supervision and maintenance of the pipeline for WGS. It takes up 0.2 FTE (of a 40-h working week) for a bioinformatics technician with a gross hourly salary of € 50.

^gData processing and data storage are outsourced for WGS. The cost of data processing covers the complete analysis of raw data to BAM file, VCF file, and patient report. The cost of data storage is estimated based on hot storage of the BAM file, VCF file, and patient report for sixmonths (€ 4 per month per 200 GB).

^hThe sample preparation and primary data analysis is done by a laboratory technician (gross hourly salary of € 22) and bioinformatics technician (gross hourly salary of € 29) for the standard techniques. For WGS, this is performed by a laboratory technician (gross hourly salary of €25). Sample and report administration are incorporated for all techniques.

ⁱThe data interpretation and report per sample are done by a clinical molecular biologist (gross hourly salary of € 41) and pathologist (gross hourly salary of € 61) for the standard techniques. For WGS, this is performed by a clinical molecular biologist and a bioinformatics technician, both with a gross hourly salary of €50.

^jThe total cost per cancer patient represents a total cost per target gene separately for IHC (ALK or ROS1) and FISH (ALK, ROS1 or RET). A combined total cost per cancer patient of the specified target genes per technique is given for Pyro seq, HRM (EGFR + KRAS + BRAF; BRAF + NRAS) and Biocartis (BRAF + NRAS), and for Sanger (10, 3, 6, and 9 amplicons) and NGS hotspot panels.

^kIncluding immunohistochemistry (IHC), Fluorescence In Situ Hybridization (FISH), pyrosequencing (Pyro seq), High-Resolution Melting (HRM), Sanger sequencing (Sanger), next generation sequencing (NGS), and whole genome sequencing (WGS).

Table 3. Costs of frequently applied combinations of techniques per cancer type

^aOverall, included standard techniques were performed in ≥ 2 labs (inventory labs) and included ≥ 5% of the analyses in total for the respective cancer types (PALGA data) (Supplementary Table 1). These techniques covered at least 80% of the performed analyses per cancer type (PALGA data). WGS usage is a potential future practice expectation for all cancer types. The total cost per technique represents a combined total cost, which is calculated based on their analysis of target genes (IHC, FISH, HRM) or hotspot panels (Sanger, NGS). For NGS, an average of the total cost of the three different platforms was used for the calculations.

^bTests 1, 2 (and 3) show the descending order of frequency usage of technique (combinations).

^cFor NSCLC, the techniques included in test 1 are concomitantly applied (100%) and those incorporated in test algorithms 2 and 3 are sequential applied (< 100%), only when the prior test is negative.

^dThe total cost for FISH is based on 60% frequency usage of ALK, ROS1 and RET (sequential testing: in 40% of cases a mutation in EGFR or KRAS is observed, and consequently FISH is not performed) [24,25].

^eThe genes tested with Sanger are EGFR, KRAS, BRAF, ERBB2, and MET (10 amplicons) for NSCLC; BRAF and NRAS (three amplicons) for melanoma; KRAS, NRAS, and BRAF (six amplicons) for CRC; KIT, PDGFRA, and BRAF (nine amplicons) for GIST.

^fIncluding non-small cell lung carcinoma (NSCLC), colorectal cancer (CRC), and gastrointestinal stromal tumor (GIST).

^gIncluding next-generation sequencing (NGS), Sanger sequencing (Sanger), High Resolution Melting (HRM), immunohistochemistry (IHC), Fluorescence In Situ Hybridization (FISH) and whole-genome sequencing (WGS).

Table 4. Sensitivity analysis

	Techniques^a
	NGS^b	Sanger				HRM	IHC	FISH	WGS
	PGM 316, 318 chip; MiSeq	ABI3500 (10 amplicons)	ABI3500 (3 amplicons)	ABI3500 (6 amplicons)	ABI3500 (9 amplicons)	BRAF+NRAS	ALK+ROS1	ALK+ROS1+ RET
Standard case perspective	€ 283,95	€ 71,19	€ 57,68	€ 63,47	€ 69,26	€ 74,56	€ 203,77	€ 403,45	€ 2.925,25
Range of practice^c	€ 250.11–216.01	€ 65.98–65.07	€ 56.52–55.62	€ 60.57–59.67	€ 64.63–63.72	€ 73.86–64.36	€ 166.06–161.06	€ 369.96–323.00	€ 2.820,66

ᵅCurrently, most frequently used techniques in cancer types of focus.

ᵇThe average total cost of the cost calculation outcomes for the NGS platforms and different hotspot panels is used.

ᶜThe utilization of the platforms varied from 17 to 47% for NGS (average 32%), 39 to 69% for Sanger (average 54%), 13 to 43% for HRM (average 28%), 15 to 45% for IHC (average 30%), 9 to 39% for FISH (average 24%), and 60% to 90% for WGS. The cost of consumables were reduced by 30% for all the techniques.

ᵈIncluding next-generation sequencing (NGS), Sanger sequencing (Sanger), High Resolution Melting (HRM), immunohistochemistry (IHC), Fluorescence In Situ Hybridization (FISH) and whole-genome sequencing (WGS).

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