Genetic testing in autoinflammatory diseases - past, current and future perspectives.

INTRODUCTION: Autoinflammatory diseases (AID) are a group of rare monogenic illnesses, leading to uncontrolled activation of the innate immune system and presenting with recurrent flares of systemic and localized inflammation. Diagnosis is confirmed by the detection of a class IV or class V gene variant in an AID-related gene and improvements in sequencing techniques have enabled the discovery of new entities. The aim of our study is to explore the diagnostic yield of evolving genetic testing methods for AID and to determine whether increasing gene panels generate a higher diagnostic rate. METHODS: Retrospective study of 2620 patients that underwent sequencing for a clinical suspicion of AID in Belgium, between January 2015 and December 2020. Sequencing was performed through a 10-gene panel between 2015 and 2017, a 25-gene panel between 2018 and 2020 and mendeliome technology with a 66- and a 502- in silico gene panel in 2020. RESULTS: The rate of genetic diagnoses increased along with the expansion of the gene panel with a diagnostic yield of 15% with 10 genes, 16% with 25 genes and 23% with 502 genes. CONCLUSION: Our study is the first nationwide study for autoinflammatory genetic testing and the first use of mendeliome technology for AID diagnosis. Although we confirmed that the bigger the gene panel, the higher the diagnostic rate, this technology generated inevitably a higher financial and human cost although the majority of diagnoses remained amongst the four original hereditary recurrent fevers (HRFs).

Middle interhemispheric variant of holoprosencephaly: First prenatal report of a ZIC2 missense mutation.

We present a case of a middle interhemispheric variant of antenatal discovery associated with a de novo missense variant (NM_007129.5: c.1109G>A p.(Cys370Tyr)) in the ZIC2 gene. Our case represents the first prenatal description of a ZIC2 missense mutation found in association with syntelencephaly.

Novel features of PIK3CA-Related Overgrowth Spectrum: Lesson from an aborted fetus presenting a de novo constitutional PIK3CA mutation.

PIK3CA-Related Overgrowth Spectrum (PROS) encompass a group of disorders which are mainly characterized by segmental overgrowth of several tissues as well as venous and lymphatic malformations. It is caused by heterozygous, usually somatic mosaic, pathogenic variants in the PIK3CA gene. However, some patients presenting mainly isolated megalencephaly or "Cowden-like" features have been described harboring constitutional mutations of PIK3CA. Here, we report the case of a woman whose pregnancy was interrupted at 34 weeks of gestation after the detection of the following ultrasound abnormalities: left diaphragmatic hernia with intrathoracic stomach, right deviation of heart, intrathoracic double bubble sign, macrocephaly and polyhydramnios. Fetal autopsy contributed to better characterize the phenotype, showing megalencephaly, left diaphragmatic eventration, facial dysmorphism (hypertelorism, abnormal hair line implantation) and duplication of distal portion of the small bowel. Clinical exome sequencing identified a de novo constitutional variant c.1030G>A p.(Val344Met) in PIK3CA. Although this mutation has been previously described (as constitutional variant) in pediatric patients, our case represents the first detailed description of the prenatal features found in association with a constitutional PIK3CA mutation. Moreover, this case contributes to delineate novel features (diaphragmatic eventration and duplication of the distal part of the small bowel) which could be identified in association with PROS.

Undetectable circulating tumor DNA (ctDNA) levels correlate with favorable outcome in metastatic melanoma patients treated with anti-PD1 therapy.

BACKGROUND: Treatment with anti-PD1 monoclonal antibodies improves the survival of metastatic melanoma patients but only a subgroup of patients benefits from durable disease control. Predictive biomarkers for durable benefit could improve the clinical management of patients. METHODS: Plasma samples were collected from patients receiving anti-PD1 therapy for ctDNA quantitative assessment of BRAFV600 and NRASQ61/G12/G13 mutations. RESULTS: After a median follow-up of 84 weeks 457 samples from 85 patients were analyzed. Patients with undetectable ctDNA at baseline had a better PFS (Hazard ratio (HR) = 0.47, median 26 weeks versus 9 weeks, p = 0.01) and OS (HR = 0.37, median not reached versus 21.3 weeks, p = 0.005) than patients with detectable ctDNA. Additionally, the HR for death was lower after the ctDNA level became undetectable during follow-up (adjusted HR: 0.16 (95% CI 0.07-0.36), p-value < 0.001). ctDNA levels > 500 copies/ml at baseline or week 3 were associated with poor clinical outcome. Patients progressive exclusively in the central nervous system (CNS) had undetectable ctDNA at baseline and at subsequent assessments. In multivariate analysis adjusted for LDH, CRP, ECOG and number of metastatic sites, the ctDNA remained significant for PFS and OS. A positive correlation was observed between ctDNA levels and total metabolic tumor volume (TMTV), number of metastatic sites and total tumor burden. CONCLUSIONS: Assessment of ctDNA baseline and during therapy was predictive for tumor response and clinical outcome in metastatic melanoma patients and reflected the tumor burden. ctDNA evaluation provided reliable complementary information during anti-PD1 antibody therapy.

Detection of a Large Novel α-Thalassemia Deletion in an Autochthonous Belgian Family.

α-Thalassemia (α-thal) is a common hemoglobinopathy mainly caused by deletion of one or both α-globin genes. We describe an autochthonous Belgian family diagnosed with α-thal trait. Molecular analysis revealed a novel large deletion of at least 170 kb between 226.68 kb (0.2 Mb) and 402.68 kb (0.4 Mb) from the telomere of 16p, leaving the subtelomeric region intact. The deletion includes both α-globin genes (HBA1 and HBA2) but also flanking genes possibly related to non hematological effects: HBQ1, LUC7L, ITFG3, RGS11, ARHGDIG, PDIA2 and AXIN1. These genes are not contained in the region (0.9 and 1.7 Mb from the telomere of 16p) associated with α-thal intellectual disability (ATR-16) syndrome. However, further research is necessary to exclude other potential effects than α-thal in patients with a large deletion at 0.2-0.4 Mb from the telomere of 16p. Genetic counseling is important for carriers of this deletion as homozygosity for the α-globin (- -/) haplotype may lead to Hb Bart's (γ4) hydrops fetalis syndrome.

Case report: An infantile lethal form of Albright hereditary osteodystrophy due to a GNAS mutation.

Germline loss-of-function GNAS mutations are associated with multiple phenotypes, depending on the parental origin of the mutant allele. Here, we describe an infantile lethal form of atypical pseudohypoparathyroidism type 1a or 1c with severe Albright's hereditary osteodystrophy phenotype, underlying the extremely variable expressivity of this syndrome.

Illustrative cases for monitoring by quantitative analysis of BRAF/NRAS ctDNA mutations in liquid biopsies of metastatic melanoma patients who gained clinical benefits from anti-PD1 antibody therapy.

Anti-programmed death 1 (PD-1) monoclonal antibodies improve the survival of metastatic melanoma patients. Predictive or monitoring biomarkers for response to this therapy could improve the clinical management of these patients. To date, no established biomarkers are available for monitoring the response to immunotherapy. Tumor- specific mutations in circulating tumor DNA (ctDNA) such as BRAF and NRAS mutations for melanoma patients have been proposed for monitoring of immunotherapy response. We present seven illustrative cases for the use of ctDNA BRAF and NRAS mutations' monitoring in plasma. The cases described exemplify four distinct clinical benefit patterns: rapid and durable complete response (CR), early progression, followed by CR, CR followed by early progression after interrupting treatment and long-term disease stabilization. These representative cases suggest that comprehensive BRAF/NRAS ctDNA monitoring during anti-PD1 therapy is informative and can be of added value for the monitoring of melanoma patients gaining clinical benefit on anti-PD1 treatment. An important advantage of our approach is that using the cartridge system on the Idylla platform for mutation analysis, the results become available the same day 2 h after plasma collection. Therefore, in the future, the ctDNA level can be an element in the clinical management of the patients.

Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers.

OBJECTIVE: Recently, Next Generation Sequencing (NGS) has begun to supplant other technologies for gene mutation testing that is now required for targeted therapies. However, transfer of NGS technology to clinical daily practice requires validation. METHODS: We validated the Ion Torrent AmpliSeq Colon and Lung cancer panel interrogating 1850 hotspots in 22 genes using the Ion Torrent Personal Genome Machine. First, we used commercial reference standards that carry mutations at defined allelic frequency (AF). Then, 51 colorectal adenocarcinomas (CRC) and 39 non small cell lung carcinomas (NSCLC) were retrospectively analyzed. RESULTS: Sensitivity and accuracy for detecting variants at an AF >4% was 100% for commercial reference standards. Among the 90 cases, 89 (98.9%) were successfully sequenced. Among the 86 samples for which NGS and the reference test were both informative, 83 showed concordant results between NGS and the reference test; i.e. KRAS and BRAF for CRC and EGFR for NSCLC, with the 3 discordant cases each characterized by an AF <10%. CONCLUSIONS: Overall, the AmpliSeq colon/lung cancer panel was specific and sensitive for mutation analysis of gene panels and can be incorporated into clinical daily practice.