“Somatic” and “pathogenic” - is the classification strategy applicable in times of large-scale sequencing?

Baer, Constance; Walter, Wencke; Hütter, Stephan; Twardziok, Sven; Meggendorfer, Manja; Kern, Wolfgang; Haferlach, Torsten; Haferlach, Claudia

doi:10.3324/haematol.2019.218917

Cited by 11 publications

(7 citation statements)

References 49 publications

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“…Future studies may also benefit from the use of an expanded bioinformatics pipeline which will ultimately provide a greater wealth of information to the clinician, such as the indication of variant germline/somatic status, the identification of clonal haematopoiesis of indeterminate potential (CHIP, which shows evidence of clonal expansion), monitoring of minimal residual disease, determination of disease predisposition, as well as accurate prediction of treatment response/outcome [ 63 , 64 ]. A larger study cohort as well as the collection of samples and clinical data at follow-up as well as data on response to therapy and survival will allow for better genotype–phenotype associations and contribute towards the better understanding of MPNs.…”

Section: Discussionmentioning

confidence: 99%

Analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel

Tan

Chow

Abidin³

et al. 2022

BMC Med Genomics

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Background The Philadelphia (Ph)-negative myeloproliferative neoplasms (MPNs), namely essential thrombocythaemia (ET), polycythaemia vera (PV) and primary myelofibrosis (PMF), are a group of chronic clonal haematopoietic disorders that have the propensity to advance into bone marrow failure or acute myeloid leukaemia; often resulting in fatality. Although driver mutations have been identified in these MPNs, subtype-specific markers of the disease have yet to be discovered. Next-generation sequencing (NGS) technology can potentially improve the clinical management of MPNs by allowing for the simultaneous screening of many disease-associated genes. Methods The performance of a custom, in-house designed 22-gene NGS panel was technically validated using reference standards across two independent replicate runs. The panel was subsequently used to screen a total of 10 clinical MPN samples (ET n = 3, PV n = 3, PMF n = 4). The resulting NGS data was then analysed via a bioinformatics pipeline. Results The custom NGS panel had a detection limit of 1% variant allele frequency (VAF). A total of 20 unique variants with VAFs above 5% (4 of which were putatively novel variants with potential biological significance) and one pathogenic variant with a VAF of between 1 and 5% were identified across all of the clinical MPN samples. All single nucleotide variants with VAFs ≥ 15% were confirmed via Sanger sequencing. Conclusions The high fidelity of the NGS analysis and the identification of known and novel variants in this study cohort support its potential clinical utility in the management of MPNs. However, further optimisation is needed to avoid false negatives in regions with low sequencing coverage, especially for the detection of driver mutations in MPL.

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Section: Discussionmentioning

confidence: 99%

Analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel

Tan

Chow

Abidin³

et al. 2022

BMC Med Genomics

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“…The expected VAF for heterozygous germline variants is around 50%, with the distribution from 40 to 60%. For the somatic variants, VAF deviates from the germline and is usually lower (<40%), because the acquired variant is not present in all cells ( Montgomery et al, 2018 ; Baer et al, 2019 ). This together indicates that JAK2 p.(Asn589Lys) could be of somatic origin; however, further testing of different type of sample (e.g., buccal swab) is required to confirm that.…”

Section: Discussionmentioning

confidence: 99%

Identification of Variants Associated With Rare Hematological Disorder Erythrocytosis Using Targeted Next-Generation Sequencing Analysis

Kristan

Pajič²,

Maver³

et al. 2021

Front. Genet.

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An erythrocytosis is present when the red blood cell mass is increased, demonstrated as elevated hemoglobin and hematocrit in the laboratory evaluation. Congenital predispositions for erythrocytosis are rare, with germline variants in several genes involved in oxygen sensing (VHL, EGLN1, and EPAS1), signaling for hematopoietic cell maturation (EPOR and EPO), and oxygen transfer (HBB, HBA1, HBA2, and BPGM) that were already associated with the eight congenital types (ECYT1–8). Screening for variants in known congenital erythrocytosis genes with classical sequencing approach gives a correct diagnosis for only up to one-third of the patients. The genetic background of erythrocytosis is more heterogeneous, and additional genes involved in erythropoiesis and iron metabolism could have a putative effect on the development of erythrocytosis. This study aimed to detect variants in patients with yet unexplained erythrocytosis using the next-generation sequencing (NGS) approach, targeting genes associated with erythrocytosis and increased iron uptake and implementing the diagnostics of congenital erythrocytosis in Slovenia. Selected 25 patients with high hemoglobin, high hematocrit, and no acquired causes were screened for variants in the 39 candidate genes. We identified one pathogenic variant in EPAS1 gene and three novel variants with yet unknown significance in genes EPAS1, JAK2, and SH2B3. Interestingly, a high proportion of patients were heterozygous carriers for two variants in HFE gene, otherwise pathogenic for the condition of iron overload. The association between the HFE variants and the development of erythrocytosis is not clearly understood. With a targeted NGS approach, we determined an actual genetic cause for the erythrocytosis in one patient and contributed to better management of the disease for the patient and his family. The effect of variants of unknown significance on the enhanced production of red blood cells needs to be further explored with functional analysis. This study is of great significance for the improvement of diagnosis of Slovenian patients with unexplained erythrocytosis and future research on the etiology of this rare hematological disorder.

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“…A germline mutation is considered to have an allele frequency of 50 to 100% [16]. A somatic mutation is usually present with a lower allele frequency because it is not present in all cells [17]. Four mutations were identified in the first patient's sample, and three mutations were identified in the second patient's sample.…”

Section: Discussionmentioning

confidence: 99%

Intermediate between Idiopathic Hypereosinophilia and Chronic Eosinophilic Leukemia: A Report of Two Hypereosinophilic Cases with Possible Novel Molecular Mutations

Choudhuri

Eskandari

Shi

et al. 2021

Case Reports in Hematology

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To distinguish a reactive eosinophilia from its malignant counterpart is challenging. Establishing clonality of the eosinophils is crucial and considered the determining factor for establishing a diagnosis. Cases of hypereosinophilia without clear reactive etiologies, no evidence of end-organ damage, normal cytogenetics, and no molecular mutations are termed as “Idiopathic Hypereosinophilia (IHE).” For cases which lie between the spectrum of chronic eosinophilic leukemia (CEL) and IHE, identification of underlying molecular abnormalities might be helpful in better understanding the disease process and prognosis. Here, we report two cases of hypereosinophilia in which five possible novel molecular mutations were identified by targeted next-generation sequencing (NGS) analysis. They were FBXW7, KM2A, TCF3, ERBB4, and MET. With multiple genetic mutations, these cases could be classified as chronic eosinophilic leukemia. Both these young patients responded well to steroid therapy. While targeted NGS is a useful tool in identifying new molecular mutation associated with hypereosinophilia, our cases raise the question of further investigating this entity and if there is a possibility of an intermediate category lying between the spectrum of CEL and IHE. Defining hypereosinophilia with clonal molecular abnormality as a malignant process may need to be revisited. Even though attempts are being made to identify mutations in IHE, it might be more significant clinically to differentiate them based on response to steroid therapy and prognosis.

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“Somatic” and “pathogenic” - is the classification strategy applicable in times of large-scale sequencing?

Cited by 11 publications

References 49 publications

Analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel

Analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel

Identification of Variants Associated With Rare Hematological Disorder Erythrocytosis Using Targeted Next-Generation Sequencing Analysis

Intermediate between Idiopathic Hypereosinophilia and Chronic Eosinophilic Leukemia: A Report of Two Hypereosinophilic Cases with Possible Novel Molecular Mutations

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