Costs Down, Solve Rates Up
How a cost-effective targeted sequencing panel could provide accessible and affordable genetic diagnoses for patients and clinicians the world over
Daan Panneman | | 4 min read | News
Genetic screening techniques, such as whole exome sequencing (WES), and, more recently, whole genome sequencing (WGS), have rapidly developed, showing excellent solve rates for inherited retinal diseases (IRDs) over the last 10–15 years. But the costs are still too high. For instance, a commercial WES costs around US$200-300 – and that is without taking into account any bioinformatic processing and other personnel costs, such as for data analysis. Especially for low- and middle-income countries, a cost-effective alternative is needed. Additionally, because gene specific therapies, such as Luxturna – for RPE65-associated disease – are available on the market now, a genetic diagnosis is essential for a patient affected by a blinding condition.
Many genes have been associated with IRDs; however, ongoing research continues to identify new genotype–phenotype correlations and further explore how these genes are implicated in retinal degenerations. In our publication (1), we established a novel cost-effective targeted sequencing panel, and showed that single molecule molecular inversion probes (smMIPs) can be used to target regions of 114 genes and loci associated with retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA). With this technique, we sequenced 1,192 probands to establish the genetic cause of disease. This technique will also enable further studies into genotype–phenotype correlations and implications of the ascertained genes.
Our approach enables massive parallel sequencing of multiple genomic targets to identify genetic variants associated with RP and LCA. And the identification of novel variants offers patients a genetic diagnosis, which is significant to patient care outcomes. Furthermore, the detection of novel variants and the genetic diagnosis has the potential to provide further therapeutic options for patients. By reaching a 55.6 percent diagnostic yield (although noting that a portion of cases already had prior genetic testing), we show that this method provides higher cost-efficiency than other panel sequencing techniques, such as WES and WGS.
Our publication describes a first series of 1,192 patients that have been screened. But in total, we have around 4,500 patients included in our studies from all over the world, and we managed to achieve the same solve rate as described in the paper for a fraction of the costs it would take to sequence all these patients using WES or WGS. To keep sequencing costs down, we need to sequence 360 patients in one experiment. This means that, in a diagnostic setting, this approach may be less suitable as one would have to wait until there are 360 samples before sequencing could start, increasing turnover time in comparison to WES, which can be requested straight away. But the converse is also true; it is a great tool to diminish the “backlog” of patients who have not received genetic testing.
Alongside its cost-effectiveness, our method of solving also has great sensitivity, enabling large-scale single nucleotide variant and copy number variant detection for clinical diagnosis and counselling of RP and LCA patients. Furthermore, we were able to validate that pathogenic variants of rare disease-associated genes – that recently were deemed to be underlying disease in patients of our cohort – such as KIAA1549, do indeed significantly contribute to the patient population with IRDs. Currently, we are working on notifying our collaborators from all over the world about the genetic findings of the probands they submitted. More interesting and novel variants will be investigated further, as well as new genotype–phenotype correlations.
It is important to note that a genetic diagnosis is becoming increasingly important for patients. This diagnosis was already important information for ophthalmologists because it allowed them to inform individuals about disease progression and expectations, as well as for family planning. Now that therapies directed against specific genes are being developed and implemented, the importance is further highlighted – as is the importance of making sure that such genetic diagnoses are accessible and affordable to all.
In principle, our approach could facilitate cost-effective sequencing of IRD-associated genes in regions of the world that now lack adequate sequencing capacity for IRDs – and that is definitely a step in the right direction.
Funding for this research was provided by Novartis. The author would like to thank all of the co-authors of the study:
Rebekkah J. Hitti-Malin, Lara K. Holtes, Suzanne E. de Bruijn, Janine Reurink, Erica G.M. Boonen, Muhammad Imran Khan, Manir Ali, Sten Andréasson, Elfride De Baere, Sandro Banfi, Miriam Bauwens, Tamar Ben-Yosef, Béatrice Bocquet, Marieke De Bruyne, Berta de la Cerda, Frauke Coppieters, Pietro Farinelli, Thomas Guignard, Chris F. Inglehearn, Marianthi Karali, Ulrika Kjellström, Robert Koenekoop, Bart de Koning, Bart P. Leroy, Martin McKibbin, Isabelle Meunier, Konstantinos Nikopoulos, Koji M. Nishiguchi, James A. Poulter, Carlo Rivolta, Enrique Rodríguez de la Rúa, Patrick Saunders, Francesca Simonelli, Yasmin Tatour, Francesco Testa, Alberta A.H.J. Thiadens, Carmel Toomes, Anna M. Tracewska, Hoai Viet Tran, Hiroaki Ushida, Veronika Vaclavik, Virginie J.M. Verhoeven, Maartje van de Vorst, Christian Gilissen, Alexander Hoischen, Frans P.M . Cremers, Susanne Roosing
- DM Panneman et al., “Cost-effective sequence analysis of 113 genes in 1,192 probands with retinitis pigmentosa and Leber congenital amaurosis,” Front Cell Dev Biol, 11, 1112270 (2023). PMID: 36819107.