A main event and multiple introductions of SARS-CoV-2 initiated the COVID-19 epidemic in Greece.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Chains of infections starting from various countries worldwide seeded the outbreak of COVID-19 in Athens, capital city of Greece. A full-genome analysis of isolates from Athens' hospitals and other healthcare providers revealed the variety of SARS-CoV-2 that initiated the pandemic before lockdown and passenger flight restrictions. A dominant variant, encompassing the G614D amino acid substitution, spread through a major virus dispersal event, and sporadic introductions of rare variants characterized the local initiation of the epidemic. Mutations within the genome highlighted the genetic drift of the virus as rare variants emerged. An important variant contained a premature stop codon in orf7a leading to the truncation of a possibly important for viral pathogenesis domain. This study may serve as a reference for resolving future lines of infection in the area, especially after resumption of passenger flight connections to Athens and Greece during summer of 2020.

First applications of a targeted exome sequencing approach in fetuses with ultrasound abnormalities reveals an important fraction of cases with associated gene defects.

Background. Fetal malformations and other structural abnormalities are relatively frequent findings in the course of routine prenatal ultrasonographic examination. Due to their considerable genetic and clinical heterogeneity, the underlying genetic cause is often elusive and the resulting inability to provide a precise diagnosis precludes proper reproductive and fetal risk assessment. We report the development and first applications of an expanded exome sequencing-based test, coupled to a bioinformatics-driven prioritization algorithm, targeting gene disorders presenting with abnormal prenatal ultrasound findings. Methods. We applied the testing strategy to14 euploid fetuses, from 11 on-going pregnancies and three products of abortion, all with various abnormalities or malformations detected through prenatal ultrasound examination. Whole exome sequencing (WES) was followed by variant prioritization, utilizing a custom analysis pipeline (Fetalis algorithm), targeting 758 genes associated with genetic disorders which may present with abnormal fetal ultrasound findings. Results. A definitive or highly-likely diagnosis was made in 6 of 14 cases (43%), of which 3 were abortuses (Ellis-van Creveld syndrome, Ehlers-Danlos syndrome and Nemaline myopathy 2) and 3 involved on-going pregnancies (Citrullinemia, Noonan syndrome, PROKR2-related Kallmann syndrome). In the remaining eight on-going pregnancy cases (57%), a ZIC1 variant of unknown clinical significance was detected in one case, while in seven cases testing did not reveal any pathogenic variant(s). Pregnancies were followed-up to birth, resulting in one neonate harboring the PROKR2 mutation, presenting with isolated minor structural cardiac abnormalities, and in seven apparently healthy neonates. Discussion. The expanded targeted exome sequencing-based approach described herein (Fetalis), provides strong evidence suggesting a definite and beneficial increase in our diagnostic capabilities in prenatal diagnosis of otherwise chromosomally balanced fetuses with troubling ultrasound abnormalities. Furthermore, the proposed targeted exome sequencing strategy, designed primarily as a diagnostic rather than a research discovery tool, overcomes many of the problems and limitations associated with clinical wide-scale WES testing in a prenatal setting.

Clinical Evaluation of a Novel Nine-Gene Panel for Ion Torrent PGM Sequencing of Myeloid Malignancies.

BACKGROUND AND OBJECTIVE: In the last decade, a number of genes have been reported to be recurrently associated with myeloid malignancies. While some mutations are easily detectable by conventional molecular genetics methods, other mutations are more difficult to screen because of lower frequency and being scattered along large genomic ranges. However, newly developed approaches for next-generation sequencing provide an affordable solution for targeted multiplex resequencing of up to several hundreds of amplicons. Here, we aimed to develop and validate a novel custom panel for targeted resequencing of myeloid malignancy samples using the Ion PGM(™) System (Ion Torrent, Paisley, UK). METHODS: We designed a pool of 424 primers for the amplification of 212 amplicons covering 99.46 % of the exonic regions of nine human genes as follows: ASXL1, EZH2, CALR, RUNX1, SETBP1, SF3B1, SRSF2, TET2, and U2AF1. Initial testing of the panel performance was performed on an Ion PGM(™) machine using PGM(™) 316 v2 chips on 16 DNA samples from patients with myeloid malignancies. Sequence alignment, variant calling, and annotation were performed using Ion Reporter software. RESULTS: We identified a total of 14 nonsynonymous somatic coding variants in seven samples affecting six of the genes in the panel (ASXL1, CALR, RUNX1, SRSF2, TET2, and U2AF1). Notably, three of the identified mutations were not present in the Cosmic v.67 release. CONCLUSION: This proof-of-concept study confirms the feasibility of Ion Torrent systems for resequencing of clinically relevant mutations in myeloid malignancies. It can be particularly useful in cases without the most frequent clonal markers.

Evaluation of two highly-multiplexed custom panels for massively parallel semiconductor sequencing on paraffin DNA.

AIM: Massively parallel sequencing (MPS) holds promise for expanding cancer translational research and diagnostics. As yet, it has been applied on paraffin DNA (FFPE) with commercially available highly multiplexed gene panels (100s of DNA targets), while custom panels of low multiplexing are used for re-sequencing. Here, we evaluated the performance of two highly multiplexed custom panels on FFPE DNA. METHODS: Two custom multiplex amplification panels (B, 373 amplicons; T, 286 amplicons) were coupled with semiconductor sequencing on DNA samples from FFPE breast tumors and matched peripheral blood samples (n samples: 316; n libraries: 332). The two panels shared 37% DNA targets (common or shifted amplicons). Panel performance was evaluated in paired sample groups and quartets of libraries, where possible. RESULTS: Amplicon read ratios yielded similar patterns per gene with the same panel in FFPE and blood samples; however, performance of common amplicons differed between panels (p<0.001). FFPE genotypes were compared for 1267 coding and non-coding variant replicates, 999 out of which (78.8%) were concordant in different paired sample combinations. Variant frequency was highly reproducible (Spearman's rho 0.959). Repeatedly discordant variants were of high coverage / low frequency (p<0.001). Genotype concordance was (a) high, for intra-run duplicates with the same panel (mean±SD: 97.2±4.7, 95%CI: 94.8-99.7, p<0.001); (b) modest, when the same DNA was analyzed with different panels (mean±SD: 81.1±20.3, 95%CI: 66.1-95.1, p = 0.004); and (c) low, when different DNA samples from the same tumor were compared with the same panel (mean±SD: 59.9±24.0; 95%CI: 43.3-76.5; p = 0.282). Low coverage / low frequency variants were validated with Sanger sequencing even in samples with unfavourable DNA quality. CONCLUSIONS: Custom MPS may yield novel information on genomic alterations, provided that data evaluation is adjusted to tumor tissue FFPE DNA. To this scope, eligibility of all amplicons along with variant coverage and frequency need to be assessed.

Clonal expansion of B-cells in human systemic lupus erythematosus: evidence from studies before and after therapeutic B-cell depletion.

Anti-B-cell therapy may be beneficial for patients with SLE and active proliferative glomerulonephritis. Using genomic DNA, we examined how rituximab-induced transient B-cell depletion affected the composition of immunoglobulin heavy-chain (Ig-VH/DH/JH) repertoire at the time-point of 33-35% B-cell reconstitution in these patients. Clusters of clonaly-related Ig-VH/DH/JH sequences were evident in all 7 patients with active SLE but in none of 4 healthy subjects studied for comparison. In addition to original somatic mutation(s) shared in the majority of clonaly-related sequences, ongoing mutation suggested expansion of single B-cell precursors and clonal evolution. Otherwise, lupus repertoire was similar to that of healthy subjects with the exception of increased somatic hypermutation. The regenerating repertoire was diverse and comparable to baseline, albeit with fewer somatic mutations but more clonal expansions. Since clonal expansion may lead to preferential survival/growth of potentially autoreactive B-cells further studies are warranted, especially as therapies aiming to reduce B-cell survival emerge.

Serial determination of FLT3 mutations in myelodysplastic syndrome patients at diagnosis, follow up or acute myeloid leukaemia transformation: incidence and their prognostic significance.

The incidence of FLT3 mutations (internal tandem duplication and Asp835) was investigated in bone marrow samples from 97 patients with myelodysplastic syndrome [(MDS); excluding cases with refractory anaemia with excess blasts in transformation] at the time of diagnosis and several time points thereafter. Three patients had FLT3 mutations at presentation. Forty-two patients progressed to acute myeloid leukaemia (AML), including the three patients with FLT3 mutations at MDS diagnosis. Three additional patients acquired FLT3 mutations and progressed to AML in 1 month. FLT3 mutations seem to be a critical additional genetic event that transforms a minority of MDS patients to AML.

Hereditary hyperferritinemia cataract syndrome in three unrelated families of western Greek origin caused by the C39 > G mutation of L-ferritin IRE.

Hereditary hyperferritinemia-cataract syndrome (HHCS) is a well-characterized autosomal dominant disease caused by mutations in the iron responsive element (IRE) of ferritin L-chain (FTL) mRNA. Mutations in the IRE result in reduced binding of the trans-acting iron regulatory proteins (IRPs) and hence in upregulation of ferritin L-chain synthesis. The disease is characterized by increased L-ferritin in serum and tissues and early onset of bilateral cataracts. Iron metabolism is normal, and there is no tissue iron overload. At least 25 nucleotide substitutions and deletions in the L-ferritin IRE have been described in families with HHCS, originating from diverse European, Australian and North American populations. We studied the molecular pathogenesis of HHCS in three unrelated kinderships of western Greek origin, with 19 affected members. We identified a relatively rare C39G mutation located in the hexanucleotide loop of L-ferritin IRE. Computational analysis of mRNA folding of mutant FTL IRE predicted that the C39 > G mutation leads to a rearrangement of base pairing in this critical region, which is likely to modify the IRP binding affinity. All subjects with HHCS were heterozygotes for the same C39G mutation. Clinical and laboratory phenotypes were described. Moreover, there was evidence of an association between this FTL IRE stem-loop mutation and very high ferritin levels. Our findings broaden the list of populations where HHCS has been described.

Familial Mediterranean fever and E148Q pyrin gene mutation in Greece.

Familial Mediterranean fever (FMF) is an inherited disease characterized by recurrent inflammatory polyserositis. Although FMF is classically expected only in Middle East populations, it is becoming evident that the disease affects more groups than initially thought. The disease is associated with a number of mutations of the MEFV gene, which codes for a protein named pyrin. The role of E148Q pyrin gene mutation in the development of FMF remains inconclusive. Some authors believe it causes the disease, whereas others favor the concept of a noncausative role. To understand better the role of this mutation, gathering data from different populations may be of value. We studied 60 Greek cases fulfilling the criteria for FMF diagnosis, 30 cases being a definite FMF diagnosis and 30 a probable diagnosis. Twenty-one of the patients, carried mutation E148Q. One was a homozygote (E148Q/E148Q), and 20 carried mutation E148Q in combination with other mutations (compound heterozygotes). In 6 of the 60 cases studied, no mutations were found. Compared with the results for healthy controls, E148Q mutation is significantly frequent. Because different populations may exhibit different patterns of pyrin mutations, association of the E148Q mutation with FMF should be considered in connection with origin data.

Prevalence of the G320V mutation of the HJV gene, associated with juvenile hemochromatosis, in Greece.

Mutations of the HJV gene, which maps on chromosome 1q21, underlie most cases of juvenile hemochromatosis. We evaluated the frequency of the most common mutation (G320V) of the HJV gene in the Greek population, since 50% of cases of hereditary hemochromatosis in Greece carry mutations of the HJV gene.