Clinical and molecular characterization of 17q21.31 microdeletion syndrome in 14 French patients with mental retardation.

International audienceChromosome 17q21.31 microdeletion was one of the first genomic disorders identified by chromosome microarrays. We report here the clinical and molecular characterization of a new series of 14 French patients with this microdeletion syndrome. The most frequent clinical features were hypotonia, developmental delay and facial dysmorphism, but scaphocephaly, prenatal ischemic infarction and perception deafness were also described. Genotyping of the parents showed that the parent from which the abnormality was inherited carried the H2 inversion polymorphism, confirming that the H2 allele is necessary, but not sufficient to generate the 17q21.31 microdeletion. Previously reported molecular analyses of patients with 17q21.31 microdeletion syndrome defined a 493 kb genomic fragment that was deleted in most patients after taking into account frequent copy number variations in normal controls, but the deleted interval was significantly smaller (205 kb) in one of our patients, encompassing only the MAPT, STH and KIAA1267 genes. As this patient presents the classical phenotype of 17q21.31 syndrome, these data make it possible to define a new minimal critical region of 160.8 kb, strengthening the evidence for involvement of the MAPT gene in this syndrome

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

Abstract 146: Performance of a Chromogenic Thrombin Generation Assay in the Thrombophilia Screening in 597 Unselected Patients with a History of VenousThromboembolism

The HemosIL ThromboPath assay (Instrumentation Laboratory) is a chromogenic assay designed to globally evaluate the functionality of the protein C (PC) pathway. It is based on the ability of endogenous APC generated after activation of PC by a snake venom extract (Protac) to reduce the thrombin generation induced by a reagent containing tissue factor. Briefly, optical density is measured after addition of a thrombin-specific chromogenic substrate in the presence (OD A) or absence (OD B) of Protac. Test results are expressed as the Protac-Induced Coagulation Inhibition percentage (PICI%) that corresponds to the ratio [OD B-OD A]/OD B x 100. A normal test result corresponds to a PICI% above a cut-off level defined as the mean-1 SD of the values measured in 30 healthy controls. To determine the performance of that assay, we retrospectively tested frozen plasma samples from 597 consecutive patients referred for screening of biological risk factors for venous thrombosis (209 M and 388 F, mean age=45.6 years, range 15-100). None was on vitamin K-antagonist or had evidence of liver failure. PICI% was significantly lower in patients who presented with than in those without any PC pathway abnormality [median=69.0% (range: 15.3-96.8), n=101 vs. 89.8 (range: 38.5-98.0), n=496; p&lt;0.0001]. All carriers of the Factor V Leiden mutation (32 heterozygotes, and 1 homozygote) had a PICI% below the cut-off level (88.5%). The same applied to all patients with either a PC deficiency (n=14) or a lupus anticoagulant (n=8). The test sensitivity to congenital and acquired PS deficiency was 97.7% (n=45/46). 41.5% of the patients without abnormality of the PC pathway had a decreased test result (n=206/496). The overall test sensitivity to tested thrombophilia was 99.0% (95%CI=94.6-100), its specificity 58.5% (95%CI=54.0-62.9), its negative predictive value (NPV) 99.7% (95%CI=98.1-100) and its PPV 32.7% (95%CI=27.4-38.2). The high sensitivity of the HemosIL ThromboPath assay to PC pathway abnormalities together with a high NPV, closed to 100%, associated with a normal test result, suggest the potential interest of that assay as part of the screening strategy of PC pathway abnormalities. In that connection, the economic impact of its introduction is currently evaluated.</jats:p

Economic Impact of a Screening Strategy for Protein C Pathway Abnormalities Based on a New Global Chromogenic Assay (HemosIL ThromboPath) as a First Step Screening Assay In a Series of 597 Unselected Consecutive Patients.

Abstract Abstract 3822 To date, screening for biological risk factors for thrombosis has been based on the measurement of individual parameters such as Protein C, PS, activated PC resistance and/or identification of the causative mutation R506Q (Factor V Leiden), and lupus anticoagulant (LA) in the case of PC pathway abnormalities. As FVL mutation can de demonstrated in around 20% of the patients of Caucasian origin with a history of thrombosis, and less than 5% of them presented with either PC or PS deficiency or LA, any of such abnormalities is found in less than one third of the tested samples. This suggests that the current screening strategy is costly and time-consuming and highlights the potential usefulness of a simple assay to screen globally for these abnormalities, as this would rationalize the use of expensive individual assays. The HemosIL ThromboPath assay (Instrumentation Laboratory) is a new chromogenic assay designed to globally evaluate the functionality of the PC pathway. It is based on the ability of endogenous APC generated after activation of PC by a snake venom extract (Protac) to reduce the thrombin generation induced by a reagent containing tissue factor. Briefly, optical density is measured after addition of a thrombin-specific chromogenic substrate in the presence (OD A) or absence (OD B) of Protac. It is recommended by the manufacturer to express test results as the Protac-Induced Coagulation Inhibition percentage (PICI%) which corresponds to the ratio [OD B-OD A]/OD B × 100 and to consider as normal, test results above the cut-off level defined as the mean minus 1 SD of the PICI% measured in the plasma of 30 healthy controls. The aim of this retrospective study was to evaluate the economic impact of a screening strategy for PC pathway abnormalities based on that new global assay as a first step screening assay, in a series of unselected consecutive patients referred to our laboratory for screening of biological risk factors for thrombosis, during a 6-month period. At the time of the study, 697 frozen plasma samples were still available, and 597 samples were further evaluated after excluding those obtained from patients on oral anticoagulant treatment (n=83) or with evidence of liver failure (n=17), both situations being associated with a decreased response to the global assay. There were 215 M and 382 F with a mean age of 45.6 years (range: 15–100). PICI% was significantly lower in patients who presented with any PC pathway abnormality than in those without [median=69.0% (range: 15.3–88.3), n=100 vs. 89.8 (range: 38.5–98.0), n=497; p&lt;0.0001]. All patients with PC pathway abnormality i.e. FVL mutation (1 homozygous and 32 heterozygous carriers), PC deficiency (activity &lt;70%, n=14), PS deficiency (free antigen concentration&lt;50%, n=45) and LA (n=8) had a PICI% below the cut-off level (88.5%) and the same applied to 41.5% of the patients without PC pathway abnormality (n=206/496). As the test performed well in those patients, with an overall sensitivity to PC pathway abnormalities of 100% (95%CI=96.4-100), a specificity of 58.5% (95%CI=54.1-63.0), negative predictive value (NPV) of 100% (95%CI=98.7-100) and a PPV of 32.7% (95%CI=27.4-38.2), a screening strategy could be proposed in which the HemosIL ThromboPath assay would be used as a first-step screening test for all these PC pathway abnormalities, and the corresponding individual assays be performed only in the case of an abnormal test result. If applied to our series, such a screening strategy would have leaded to a 28.6% decrease in the total number of tests performed and to a 30.1% reduction in the screening costs (incl. reagents and labor) when compared to the routine strategy. In conclusion, the high sensitivity of the HemosIL ThromboPath assay to PC pathway abnormalities and the high NPV (100%) associated with a normal test result, suggest its potential interest as part of a screening strategy for these abnormalities. In our technical conditions and with a 16.8% frequency of PC pathway abnormalities in our population, such a strategy, in which the HemosIL ThromboPath would be performed as a first screening assay and specific assays only performed when test result was abnormal, would have been associated with a 28.6% reduction in the number of tests performed and a 30.1% reduction in the total screening costs. However, these results deserve to be confirmed in larger scale studies involving populations of different origins and/or in different technical conditions. Disclosures: No relevant conflicts of interest to declare. </jats:sec