Low-Pass Genomic Instability Characterisation Assay Identifies Germline Mismatch Repair Deficiency and Risk of Cancer Onset

In a study conducted by the International Replication Repair Deficiency Consortium, the researchers used a well-annotated data set of childhood cancers and patients with cancer predisposition syndromes to provide evidence that low-pass genome analysis can be used to diagnose replication repair deficiency in cancerous and normal tissues. Low-pass Genomic Instability Characterisation (LOGIC) assay has been shown as a robust tool for the diagnosis of mismatch repair deficiency (MMRD) in multiple cancer types and in normal tissues. This functional genomic tool performs substantially better than currently used screening assays and is able to quantify the degree of MMRDness to enable risk stratification and precision-based decisions. The findings are published on 14 October 2022 in the Journal of Clinical Oncology.

The authors wrote in the background that diagnosis of MMRD is crucial for tumour management and early detection in patients with the cancer predisposition syndrome constitutional mismatch repair deficiency. Current diagnostic tools are limited and inconsistent both in childhood cancers and in determining germline MMRD. Constitutional mismatch repair deficiency results in an extremely aggressive cancer predisposition syndrome in which carriers are affected with cancer in early life, commonly brain, gastrointestinal, and haematopoietic malignancies. Both immunotherapy and early cancer detection through a surveillance protocol have recently been shown to improve survival for these patients. Therefore, a robust and affordable tool for MMRD detection in cancer and normal cells can enable both precision cancer therapy and genetic counselling for the patients and their family members.

Accumulation of microsatellite indels or instability (MSI) is a unique characteristic of MMRD cancers and has conventionally been used to diagnose such tumours. Several MSI-based diagnostic tests exist, such as the Microsatellite Instability Analysis System, which is a five microsatellite loci PCR-based panel. However, these five loci are not sufficient to detect MSI in non-epithelial tissues, such as brain and haematopoietic malignancies, even in the context of constitutional mismatch repair deficiency. Larger numbers of microsatellites may achieve better sensitivity and specificity.

Since the human genome harbours > 23 million microsatellites, the study team developed a LOGIC assay to test the diagnostic role of low-coverage genome sequencing in cancerous and normal tissues. The diagnostic performance of LOGIC was compared with that of current established assays including tumour mutational burden, immunohistochemistry, and the MSI panel. LOGIC was then applied to various normal tissues of patients with constitutional mismatch repair deficiency with comprehensive clinical data including age of cancer presentation.

LOGIC was 100% sensitive and specific in detecting MMRD in childhood cancers. It was more sensitive than the MSI panel (14%, p = 4.3 × 10−12), immunohistochemistry (86%, p = 4.6 × 10−3), or tumour mutational burden (80%, p = 9.1 × 10−4). LOGIC was able to distinguish constitutional mismatch repair deficiency from other cancer predisposition syndromes using blood and saliva DNA (p < 0.0001).

In normal cells, MMRDness scores differed between tissues (gastrointestinal > blood > brain), increased over time in the same individual, and revealed genotype-phenotype associations within the mismatch repair genes. Importantly, increased MMRDness score was associated with younger age of first cancer presentation in individuals with constitutional mismatch repair deficiency (p = 2.2 × 10−5).

The authors concluded that their results reveal that LOGIC is a sensitive and specific method to measure replication repair deficiency in both tumour and normal tissues with superior performance to currently used diagnostic assays. This rapid, robust, and economical functional genomic tool can be used in most laboratories worldwide.

LOGIC is especially advantageous as it enables fast (96 samples analyzed simultaneously), robust, and affordable (< 150 Canadian dollars) detection of germline MMRD. This contrasts with current tools that are cumbersome, reliant on local expertise, expensive, and less sensitive. Importantly, LOGIC is able to distinguish between Lynch Syndrome and constitutional mismatch repair deficiency using non-malignant (germline) tissue DNA, as patients with Lynch Syndrome retain MMR function from the unaffected allele. The biallelic loss of MMR in the cells of patients with constitutional mismatch repair deficiency is detected as an increase in the MMRDness score, in comparison with patients with Lynch Syndrome. This is critical, given the differences in screening and clinical management between the two syndromes.

The SickKids Cancer Sequencing program was supported by the Garron Family Cancer Centre with funds from the SickKids Foundation. This research was supported by Meagan’s Walk, b.r.a.i.n.child Canada, LivWise, SickKids Foundation donors, the Zane Cohen Center donors, the Canadian Institutes for Health Research (CIHR) grant, the CIHR Joint Canada-Israel Health Research Program, a Stand Up to Cancer—Bristol Myers Squibb Catalyst Research grant, a Genome Applications Partnership Program grant from Genome Canada, a COG NCORP Research Base Administrative Supplement Request: Landscape of somatic and inherited replication repair deficiency toward a childhood cancer vaccine, Spark Grants funded by both Canadian Cancer Society and Brain Canada, and St Baldrick’s Foundation International Scholar Award with generous support from the Team Campbell Foundation.

Reference

Chung J, Negm L, Bianchi V, et al. Genomic Microsatellite Signatures Identify Germline Mismatch Repair Deficiency and Risk of Cancer Onset. JCO; Published online 14 October 2022. DOI: 10.1200/JCO.21.02873

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