Shruthi Mohan

Germline GATA2 deficiency is a pleiotropic condition 1-8 characterized by numerous phenotypes, including monocytopenia, immunodeficiency, microbial susceptibilities, and high rates of myeloid malignancies 1,8. Accurate curation of germline GATA2 variants is critical for patient care and requires well-defined phenotypes associated with GATA2 deficiency. The many phenotypes attributed to the condition render a simple description of GATA2 deficiency difficult, complicating the development of GATA2 variant curation rules. Therefore, the Myeloid Malignancy Variant Curation Expert Panel (MM-VCEP) sought to define GATA2 deficiency based on a statistical comparison of phenotype data. To do so, the MM-VCEP systematically analyzed phenotype data and applied statistical comparisons to define the phenotypic features of GATA2 deficiency to inform germline variant curation. The MM-VCEP assembled an international cohort of 339 people with clinically diagnosed GATA2 deficiency from 16 centers in seven countries. The 73 phenotypes of these individuals were compared statistically to those of control participants from the UK Biobank (UKBB). We compared single phenotypes as well as combinations of two, three, and four phenotypes in people with clinically diagnosed GATA2 deficiency to UKBB controls. We defined GATA2 deficiency as any of the 2,903 combinations of two or three phenotypes with log10Odds Ratio ≥3 (OR ≥ 1000). This definition of GATA2 deficiency will inform gene-specific phenotypic criteria used in GATA2 variant curation guidelines that will facilitate standardized variant curation by clinical laboratories worldwide.

Historically, the term “pseudodeficiency” has referred to individuals with significantly reduced activity of a specific enzyme in vitro but lacking phenotypic evidence of the associated disease. This phenomenon complicates the interpretation of enzyme activity-based laboratory testing, an issue that has become increasingly problematic with the expansion of newborn screening panels to include biochemical genetic conditions like lysosomal diseases that use measurement of enzyme activity as a first tier. While the term “pseudodeficiency” has been broadly used for over 40 years, it remains ill-defined and this has led to confusion. To better understand pseudodeficiency, and to create a platform for future work, we carried out a literature review. We identified 63 variants in 12 genes that have been reported as a probable or possible cause of pseudodeficiency. These variants have been demonstrated to result in enzyme deficiency through mechanisms such as altered gene expression, altered enzyme stability, or altered trafficking. As such, the term “pseudo”, which implies that the laboratory measurement was “false”, or artifactual, is misleading as many of these variants have been demonstrated to lead to measurable reduction of enzyme activity in vitro. Furthermore, evidence indicates that, when in cis with another missense variant, these variants can act synergistically to further lower enzyme activity. The implementation of systematized variant curation raises the risk of these pseudodeficiency variants being classified as “benign”, which could result in relevant variants being filtered by bioinformatic pipelines. We propose that further work is needed to better define “pseudodeficiency”, to generate an accepted nomenclature and framework to classify and report these variants, and to investigate whether these variants have any role in multifactorial disease.

Background Clinically important postoperative changes can be best evaluated through the minimal clinically important difference (MCID). Our study aims to evaluate risk factors associated with failure to achieve MCID following lumbar decompression (LD). Methods Demographics, perioperative characteristics, and patient-reported outcome measures (PROM) for pain, disability, and physical function were retrospectively reviewed and collected for patients undergoing LD. MCID achievement was calculated using established values. Relative risk of demographic and perioperative characteristics with failure to meet MCID for all PROMs was calculated. Least absolute shrinkage and selection operator (LASSO) was used to estimate individual risk factors, and postestimation logistic regression was performed. Results The study cohort included 811 patients. Comorbidity burden was associated with failed MCID for visual analog scale (VAS) back and leg pain and Oswestry Disability Index (ODI). Operative levels or duration was associated with failed MCID for VAS leg pain, 12-item short form physical component summary (SF-12 PCS), and the patient-reported outcomes measurement information system physical function (PROMIS PF). Preoperative spinal pathology was associated with failed MCID for VAS leg pain, ODI, SF-12 PCS, and PROMIS PF. Additional risk factors included the type of operation, insurance, age, and body mass index. LASSO selected insurance, age, comorbidity burden, blood loss, operative duration, and type of spinal pathology as significant risk factors for failure to reach MCID. Conclusion Failure to reach MCID was greatest for VAS back. Age, comorbidity burden, and prolonged procedures were significantly associated with risk for failure to reach MCID for a majority of PROMs. Comorbidity burden combined with operative outcomes may place patients at increased risk for failure to reach MCID for pain, disability, and physical function following LD. Level of Evidence 4. Clinical Relevance Establishes risk factors for failing to reach the threshold of meaningful difference in symptoms after LD surgery.

The broad use of next-generation sequencing and microarray platforms in the research and clinical laboratories has led to an increasing appreciation for the role of germline mutations in genes involved in hematopoiesis and lineage differentiation in contributing to myeloid neoplasms. Despite implementation of the American College of Medical Genetics and Genomics and Association for Molecular Pathology 2015 guidelines for sequence variant interpretation, the number of variants deposited in ClinVar, a genomic repository of genotype and phenotype data, and classified as having uncertain significance or being discordantly classified among clinical laboratories remains elevated and contributes to indeterminate or inconsistent patient care. In 2018, the American Society of Hematology and the Clinical Genome Resource co-sponsored the Myeloid Malignancy Variant Curation Expert Panel to develop rules for classifying gene variants associated with germline predisposition to myeloid neoplasia. Herein, we demonstrate application of our rules developed for the RUNX1 gene to variants in 6 examples to show how we would classify them within the proposed framework.

Glanzmann thrombasthenia (GT) is an autosomal recessive disorder of platelet aggregation caused by quantitative or qualitative defects in integrins αIIb and β3. These integrins are encoded by the ITGA2B and ITGB3 genes and form platelet glycoprotein (GP)IIb/IIIa, which acts as the principal platelet receptor for fibrinogen. Although there is variability in the clinical phenotype, most patients present with severe mucocutaneous bleeding at an early age. A classic pattern of abnormal platelet aggregation, platelet glycoprotein expression and molecular studies confirm the diagnosis. Management of bleeding is based on a combination of hemostatic agents including recombinant activated factor VII with or without platelet transfusions and antifibrinolytic agents. Refractory bleeding and platelet alloimmunization are common complications. Additionally, pregnant patients pose unique management challenges. This review highlights clinical and molecular aspects in the approach to patients with GT with particular emphasis on the significance of multidisciplinary care.

Standardized variant curation is essential for clinical care recommendations for patients with inherited disorders. Clinical Genome Resource (ClinGen) variant curation expert panels are developing disease-associated gene specifications using the 2015 American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) guidelines to reduce curation discrepancies. The ClinGen Myeloid Malignancy Variant Curation Expert Panel (MM-VCEP) was created collaboratively between the American Society of Hematology and ClinGen to perform gene- and disease-specific modifications for inherited myeloid malignancies. The MM-VCEP began optimizing ACMG/AMP rules for RUNX1 because many germline variants have been described in patients with familial platelet disorder with a predisposition to acute myeloid leukemia, characterized by thrombocytopenia, platelet functional/ultrastructural defects, and a predisposition to hematologic malignancies. The 28 ACMG/AMP codes were tailored for RUNX1 variants by modifying gene/disease specifications, incorporating strength adjustments of existing rules, or both. Key specifications included calculation of minor allele frequency thresholds, formulating a semi-quantitative approach to counting multiple independent variant occurrences, identifying functional domains and mutational hotspots, establishing functional assay thresholds, and characterizing phenotype-specific guidelines. Preliminary rules were tested by using a pilot set of 52 variants; among these, 50 were previously classified as benign/likely benign, pathogenic/likely pathogenic, variant of unknown significance (VUS), or conflicting interpretations (CONF) in ClinVar. The application of RUNX1-specific criteria resulted in a reduction in CONF and VUS variants by 33%, emphasizing the benefit of gene-specific criteria and sharing internal laboratory data.

Background & objectives: Subtelomeres are prone to deleterious rearrangements owing to their proximity to unique sequences on the one end and telomeric repetitive sequences, which increase their tendency to recombine, on the other end. These subtelomeric rearrangements resulting in segmental aneusomy are reported to contribute to the aetiology of idiopathic intellectual disability/developmental delay (ID/DD). We undertook this study to estimate the frequency of subtelomeric rearrangements in children with ID/DD. Methods: One hundred and twenty seven children with idiopathic ID/DD were tested for subtelomeric rearrangements using karyotyping and FISH. Blood samples were cultured, harvested, fixed and GTG-banded using the standard protocols. Results: Rearrangements involving the subtelomeres were observed in 7.8 per cent of the tested samples. Detection of rearrangements visible at the resolution of the karyotype constituted 2.3 per cent, while those rearrangements detected only with FISH constituted 5.5 per cent. Five deletions and five unbalanced translocations were detected. Analysis of parental samples wherever possible was informative regarding the inheritance of the rearrangement. Interpretation & conclusions: The frequency of subtelomeric rearrangements observed in this study was within the reported range of 0-35 per cent. All abnormal genotypes were clinically correlated. Further analysis with array technologies presents a future prospect. Our results suggest the need to test individuals with ID/DD for subtelomeric rearrangements using sensitive methods such as FISH.