Detection of rare reciprocal RUNX1 rearrangements by next‐generation sequencing in acute myeloid leukemia

Reciprocal RUNX1 fusions are traditionally found in up to 10% of acute myeloid leukemia (AML) patients, usually associated with a translocation (8;21)(q22;q22) corresponding to the RUNX1‐RUNX1T1 fusion gene. So far, alternative RUNX1 rearrangements have been reported only rarely in AML, and the few reports so far have focused on results based on cytogenetics, fluorescence in situ hybridization, and polymerase chain reaction. Acknowledging the inherent limitations of these diagnostic techniques, the true incidence of rare RUNX1 rearrangements may be underestimated. In this report, we present two cases of adult AML, in which we detected rare RUNX1 rearrangements not by conventional cytogenetics but rather by next‐generation panel sequencing. These include t(16;21)(q24;q22)/RUNX1‐CBFA2T3 and t(7;21)(p22;q22)/RUNX1‐USP42, respectively. In both patients the AML was therapy‐related and associated with additional structural and numerical alterations thereby conferring bad prognosis. This is in line with previous reports on rare RUNX1 fusions in AML and emphasizes the clinical importance of their detection. In summary, our report not only confirms the clinical utility of NGS for diagnostics of rare reciprocal rearrangements in AML in a real‐life scenario but also sheds light on the variety and complexity within AML. It further emphasizes the need for collection of additional cases for deepening insights on their clinical meaning as well as their frequency.     

Deleterious mutations in esophageal carcinoma cuniculatum detected by next generation sequencing

Esophageal carcinoma cuniculatum (ECC) is a rare form of extremely well-differentiated squamous cell carcinoma of esophagus that is often misdiagnosed preoperatively. The molecular changes underlying ECC remain unknown. This study aimed to explore the molecular signature of ECC using next-generation sequencing (NGS). Five cases of ECC were collected from our pathology database from 2014 to 2019. One patient received chemoradiation and the remaining four patients were treatment-naïve. Areas of normal squamous mucosa, non-invasive component, and invasive component of ECC were circled and macrodissected. Genomic DNA extracted from the macrodissected tissue was sequenced using GatorSeq NGS Panel. Deleterious mutations, predicted by Sorting Intolerant from Tolerant (SIFT), were identified using tumor/normal pairs and annotated by amino acid change. The normal-appearing squamous mucosa in the ECC harbored recurrent deleterious somatic mutations in ROS1 and POLE genes. ECC tumor-specific deleterious mutations were identified on TP53, NOTCH1, and PIK3CA genes. Our results support a mutually exclusive pattern in NOTCH1 and PIK3CA mutation. Non-invasive and invasive components in ECC had identical mutation profiles. Chemoradiation therapy led to disappearance of NOTCH1 mutation in one ECC case. Our results suggest molecular testing may help pre-operative diagnosis, and provide therapeutic targets in patients with advanced or unresectable ECC.     

Nebulin (NEB) mutations in a childhood onset distal myopathy with rods and cores uncovered by next generation sequencing

Recessive nebulin (NEB) mutations are a common cause of nemaline myopathy (NM), typically characterized by generalized weakness of early-onset and nemaline rods on muscle biopsy. Exceptional adult cases with additional cores and an isolated distal weakness have been reported. The large NEB gene with 183 exons has been an obstacle for the genetic work-up. Here we report a childhood-onset case with distal weakness and a core-rod myopathy, associated with recessive NEB mutations identified by next generation sequencing (NGS). This 6-year-old boy presented with a history of gross-motor difficulties following a normal early development. He had distal leg weakness with bilateral foot drop, as well as axial muscle weakness, scoliosis and spinal rigidity; additionally he required nocturnal respiratory support. Muscle magnetic resonance (MR) imaging showed distal involvement in the medial and anterior compartment of the lower leg. A muscle biopsy featured both rods and cores. Initial targeted testing identified a heterozygous Nebulin exon 55 deletion. Further analysis using NGS revealed a frameshifting 4 bp duplication, c.24372_24375dup (P.Val8126fs), on the opposite allele. This case illustrates that NEB mutations can cause childhood onset distal NM, with additional cores on muscle biopsy and proves the diagnostic utility of NGS for myopathies, particularly when large genes are implicated.     

Detection of novel germline mutations in six breast cancer predisposition genes by targeted next‐generation sequencing

In this study, a customized amplicon‐based target sequencing panel was designed to enrich the whole exon regions of six genes associated with the risk of breast cancer. Targeted next‐generation sequencing (NGS) was performed for 146 breast cancer patients (BC), 71 healthy women with a family history of breast cancer (high risk), and 55 healthy women without a family history of cancer (control). Sixteen possible disease‐causing mutations on four genes were identified in 20 samples. The percentages of possible disease‐causing mutation carriers in the BC group (8.9%) and in the high‐risk group (8.5%) were higher than that in the control group (1.8%). The BRCA1 possible disease‐causing mutation group had a higher prevalence in family history and triple‐negative breast cancer, while the BRCA2 possible disease‐causing mutation group was younger and more likely to develop axillary lymph node metastasis (P < 0.05). Among the 146 patients, 47 with a family history of breast cancer were also sequenced with another 14 moderate‐risk genes. Three additional possible disease‐causing mutations were found on PALB2, CHEK2, and PMS2 genes, respectively. The results demonstrate that the six‐gene targeted NGS panel may provide an approach to assess the genetic risk of breast cancer and predict the clinical prognosis of breast cancer patients.     

Complete blood count differences in a cohort of Down syndrome neonates with transient abnormal myelopoiesis screened for GATA1 pathogenic variants

Transient abnormal myelopoiesis (TAM) raises the risk for acute myeloid leukemia of Down syndrome (DS) (ML‐DS), and both are related to GATA1 pathogenic variants. Here, we analyzed which findings on complete blood count (CBC) are associated with TAM in a cohort of neonates with DS screened for GATA1 pathogenic variants. The CBCs were compared among 70 newborns with DS, including 16 patients (22.9%) with TAM (cases), and 54 patients (77.1%) without TAM (controls). TAM was defined as peripheral circulating blasts (PCBs) ≥ 1%. PCR and direct sequencing were used to screen DNA samples from peripheral blood for GATA1 exon 2 mutations. Multivariate logistic regression analyses determined that the mean count of lymphocytes was significantly higher in DS infants with TAM (p = .035) and that lymphocytosis confers a risk for TAM (adjusted odds ratio = 7.23, 95% confidence intervals: 2.02–25.92). Pathogenic variants of GATA1 were identified in 2 of 70 analyzed DS neonates (2.9%), of which one had ML‐DS and another had an asymptomatic TAM. Among those DS infants with TAM, the GATA1 pathogenic variant detection was 12.5%. Our results indicated that lymphocytosis is associated with TAM in neonates with DS. However, since not all infants with an abnormal CBC had TAM, and not all infants with TAM had GATA1 pathogenic variants, we emphasize that only the search for GATA1 pathogenic variants allows the proper identification of the subgroup of DS infants with a real increasing in risk for ML‐DS.     

Panel-based next generation sequencing as a reliable and efficient technique to detect mutations in unselected patients with retinal dystrophies

Hereditary retinal dystrophies (RD) constitute a group of blinding diseases that are characterized by clinical variability and pronounced genetic heterogeneity. The different forms of RD can be caused by mutations in >100 genes, including >1600 exons. Consequently, next generation sequencing (NGS) technologies are among the most promising approaches to identify mutations in RD. So far, NGS is not routinely used in gene diagnostics. We developed a diagnostic NGS pipeline to identify mutations in 170 genetically and clinically unselected RD patients. NGS was applied to 105 RD-associated genes. Underrepresented regions were examined by Sanger sequencing. The NGS approach was successfully established using cases with known sequence alterations. Depending on the initial clinical diagnosis, we identified likely causative mutations in 55% of retinitis pigmentosa and 80% of Bardet–Biedl or Usher syndrome cases. Seventy-one novel mutations in 40 genes were newly associated with RD. The genes USH2A, EYS, ABCA4, and RHO were more frequently affected than others. Occasionally, cases carried mutations in more than one RD-associated gene. In addition, we found possible dominant de-novo mutations in cases with sporadic RD, which implies consequences for counseling of patients and families. NGS-based mutation analyses are reliable and cost-efficient approaches in gene diagnostics of genetically heterogeneous diseases like RD.     

Acute encephalopathy in an immunocompromised boy with astrovirus-MLB1 infection detected by next generation sequencing

We report a case of an immunodeficient 4-year-old boy with acute encephalopathy possibly related to human astrovirus-MLB1 infection. The astrovirus-MLB1 genome was identified in his stool, serum, cerebrospinal fluid, urine, and throat swabs by next generation sequencing. We present additional evidence showing human astroviruses are important infectious agents, regardless of their clades, involving the central nervous system in immunocompromised hosts.     

应用下一代半导体靶向测序技术检测Marfan综合征致病突变

目的 应用Ion Torrent PGM半导体测序仪和Ion AmpliSeqTMInherited Disease Panel对3例马凡综合征(Marfan syndrome,MFS)进行致病基因突变检测,明确其致病突变,并评价下一代半导体靶向测序诊断复杂单基因遗传病的效果.方法 在知情同意的基础上采集3例MFS患者及1名正常志愿者外周血,提取基因组DNA,经多重PCR扩增富集目的基因片段.每个样本用特异性序列标签进行标记后,应用Ion One Touch系统进行模板制备、乳化PCR及磁珠颗粒富集;最后用318半导体测序芯片进行高通量测序.用Ion Torrent Suite 3.2软件进行序列比对及SNPs和Indels提取,再用dbSNP 137数据库过滤得到SNPs和indels,剩余的可疑突变经Sanger法测序验证.结果 用一张318芯片得到855.80Mb的总数据量,4个样本的平均测序深度均达到100×以上,对目的区域的覆盖度在98％以上.数据经软件分析及数据库过滤后,在3例MFS患者中分别得到3个FBN1基因可疑突变,并经Sanger法测序验证,一个为已报道FBN1基因错义突变(p.E1811K),另外两个为新发现的突变,包括一个无义突变(p.E2264X),1个插入突变(p.L871FfsX23).结论 在3例MFS患者中都成功检出FBN1基因致病突变,表明半导体靶向测序可对复杂单基因遗传病进行高效、准确的基因诊断.     

Detection of an activated JAK3 variant and a Xq26.3 microdeletion causing loss of PHF6 and miR-424 expression in myelodysplastic syndromes by combined targeted next generation sequencing and SNP array analysis

Myelodysplastic syndromes (MDS) are hematopoietic disorders characterized by ineffective hematopoiesis and progression to acute leukemia. In patients ineligible for hematopoietic stem cell transplantation, azacitidine is the only treatment shown to prolong survival. However, with the availability of a growing compendium of cancer biomarkers and related drugs, analysis of relevant genetic alterations for individual MDS patients might become part of routine evaluation.     

Next-generation sequencing in molecular diagnosis: NUBPL mutations highlight the challenges of variant detection and interpretation

Next-generation sequencing (NGS) is transitioning from being a research tool to being used in routine genetic diagnostics, where a major challenge is distinguishing which of many sequence variants in an individual are truly pathogenic. We describe some limitations of in silico analyses of NGS data that emphasize the need for experimental confirmation. Using NGS, we recently identified an apparently homozygous missense mutation in NUBPL in a patient with mitochondrial complex I deficiency. Causality was established via lentiviral correction studies with wild-type NUBPL cDNA. NGS data, however, provided an incomplete understanding of the genetic abnormality. We show that the maternal allele carries an unbalanced inversion, while the paternal allele carries a branch-site mutation in addition to the missense mutation. We demonstrate that the branch-site mutation, which is present in approximately one of 120 control chromosomes, likely contributes to pathogenicity and may be one of the most common autosomal mutations causing mitochondrial dysfunction. Had these analyses not been performed following NGS, the original missense mutation may be incorrectly annotated as pathogenic and a potentially common pathogenic variant not detected. It is important that locus-specific databases contain accurate information on pathogenic variation. NGS data, therefore, require rigorous experimental follow-up to confirm mutation pathogenicity.     

Next generation sequencing analysis of consecutive Russian patients with clinical suspicion of inborn errors of immunity

Primary immune deficiencies are usually attributed to genetic defects and, therefore, frequently referred to as inborn errors of immunity (IEI). We subjected the genomic DNA of 333 patients with clinical signs of IEI to next generation sequencing (NGS) analysis of 344 immunity-related genes and, in some instances, additional genetic techniques. Genetic causes of the disease were identified in 69/333 (21%) of subjects, including 11/18 (61%) of children with syndrome-associated IEIs, 45/202 (22%) of nonsyndromic patients with Jeffrey Modell Foundation (JMF) warning signs, 9/56 (16%) of subjects with periodic fever, 3/30 (10%) of cases of autoimmune cytopenia, 1/21 (5%) of patients with unusually severe infections and 0/6 (0%) of individuals with isolated elevation of IgE level. There were unusual clinical observations: twins with severe immunodeficiency carried a de novo CHARGE syndrome-associated SEMA3E c.2108C>T (p.S703L) allele; however, they lacked clinical features of CHARGE syndrome. Additionally, there were genetically proven instances of Netherton syndrome, Х-linked agammaglobulinemia, severe combined immune deficiency (SCID), IPEX and APECED syndromes, among others. Some patients carried recurrent pathogenic alleles, such as AIRE c.769C>T (p.R257*), NBN c.657del5, DCLRE1C c.103C>G (p.H35D), NLRP12 c.1054C>T (p.R352C) and c.910C>T (p.H304Y). NGS is a powerful tool for high-throughput examination of patients with malfunction of immunity.     

Molecular study of Nucleophosmin 1(NPM1) gene in acute myeloid leukemia in Kurdish population

BackgroundIn patients with Acute Myeloid Leukemia (AML) the most frequent acquired molecular abnormalities and important prognostic indicators is nucleophosmin-1 (NPM1) mutations. Our study aims was molecular study of Nucleophosmin -1 gene in Acute Myeloid Leukemia in Kurdish population.Patients &MethodsA total of 50 patients with AML, (36) of them attended Nanakaly Hospital and (14) attended Hiwa Hospital and 30 healthy subjects as control were selected randomly, all were matched of age and gender. Polymerase chain reaction (PCR) was used for detection of NPM1 gene mutation. Three samples of PCR product for NPM1 gene mutations were sequenced, and mutations were determined by comparison with the normal NPM1 sequence NCBI (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"NM_002520","term_id":"1838744830"}}NM_002520).ResultsOut of 50 patients with AML, 5 (10%) of them were NPM1 gene mutation positive, and 45 (90%) were negative. The mutation were a base substitution (C to A), (G to C), (G to T), transversion mutation in addition of frame shift mutation and all mutated cases were heterozygous and retained a wild type allele.ConclusionIdentification of NPM1 mutations in AML are important for prognostication, treatment decision and optimization of patient care.     

WT1 mutations and polymorphisms in Southeast Asian acute myeloid leukemia

Genomic alterations of the Wilms' Tumor 1 (WT1) gene have been reported to occur in patients with acute myeloid leukemia (AML). No data presently exists regarding the frequency of WT1 mutations in the Southeast Asian AML population. This study focused on WT1 exons 7–10 mutations and their correlation with other molecular markers and patients' characteristics. The zinc finger domain of WT1 gene covering exons 7–10 was directly sequenced. Six types of mutations were identified among 49 cases (12.24%); 4 localized on exon 7 and 2 on exon 9. Two novel mutations were identified including the insertion within codon 313 and codon 314. Patients harboring WT1 mutations seemed to have a younger age (29.5 vs 45.4 years), a higher white blood cell count (120.3 vs 19.8 × 10⁹/L), and a lower platelet count (54.2 vs 104.3 × 10⁹/L) as compared to those without the mutations although statistical differences could not be demonstrated. All exon 7 mutations were frameshift mutations and had NRAS mutation while exon 9 mutations were base substitutions and had FLT3-ITD mutation. Interestingly, the major allele for rs16754 single nucleotide polymorphism was G (25-homozygous and 6-heterozygous) which was in contrast to A in the Western reports. The frequency of WT1 mutation in the Southeast Asian AML was thus comparable to the figures reported from the West although the designated major allele for rs16754 polymorphism was different.     

Double CEBPA mutations are prognostically favorable in non-M3 acute myeloid leukemia patients with wild-type NPM1 and FLT3-ITD

This study is aimed to investigate the pattern of CEBPA mutations and its clinical significance in Chinese non-M3 acute myeloid leukemia (AML) patients. The entire coding region of CEBPA gene was amplified by PCR and then sequenced in samples from 233 non-M3 AML patients. Fifty mutations were identified in 37 (15.8%) patients with eleven (4.7%) double mutated CEBPA (dmCEBPA) and twenty-six (11.1%) single mutated CEBPA (smCEBPA). dmCEBPA was exclusively observed in M1 and M2 subtypes of FAB classification (P = 0.008), whereas smCEBPA occurred in almost all subtypes (P = 0.401). Patients with dmCEBPA had significantly younger age and higher WBC counts than those with wtCEBPA (P = 0.016 and 0.043, respectively). Both dmCEBPA and smCEBPA were mainly present in cytogenetically normal patients. Patients with dmCEBPA achieved higher rate of complete (CR) than wtCEBPA patients (88% vs. 51%, P = 0.037), whereas smCEBPA and wtCEBPA groups are similar (47% vs. 51%, P = 0.810). Patients with dmCEBPA had a superior overall survival (OS) compared with patients with wtCEBPA (P = 0.033), whereas patients with smCEBPA had a similar OS as patients with wtCEBPA (P = 0.976). dmCEBPA but not smCEBPA was also associated with favorable outcome in patients with wild-type NPM1 and FLT3-ITD (NPM1^wtFLT3-ITD^wt). Our data confirm that dmCEBPA but not smCEBPA is prognostically favorable in NPM1^wtFLT3-ITD^wt AML, and suggest that the entity AML with mutated CEBPA should be definitely designated as AML with dmCEBPA in WHO classification and smCEBPA should be excluded from the favorable risk of molecular abnormalities.     

Contribution of next generation sequencing to early detection of cytomegalovirus UL97 emerging mutants and viral subpopulations analysis in kidney transplant recipients

BackgroundCytomegalovirus (CMV) is the major opportunistic virus encountered after transplantation, and resistant variants challenge antiviral treatment. We studied the emergence and evolution of the canonical UL97 L595S mutation in four kidney recipients by comparing Sanger sequencing with a specific next-generation sequencing (NGS) assay, and assessed the global evolution of UL97 gene variability.Study designPlasmids harbouring wild-type and/or L595S mutated UL97 genes were used to assess the analytical performances of NGS assay. UL97 gene was retrospectively analysed in patients’ samples drawn during CMV infection follow-up, Shannon entropy (Sn) was calculated and phylogenetic analyses were performed.ResultsWild-type and L595S plasmids PCR products were mixed to obtain L595S concentrations of 0, 1, 2, 5, 10, 20 and 100%. Mean triplicate NGS results were 0, 0.71, 1.79, 5.30, 13.17, 17 and 100%, respectively, while Sanger sequencing only detected L595S when above 20%. The NGS mean error rate was 0.196 ± 0.07%. In the four patients, emergence of L595S mutation under ganciclovir treatment was followed-up. After foscarnet rescue therapy, leading to undetectable CMV viral load, in two patients, L595S mutant re-emerged, but was only detected by NGS technology (14% and 9.6%). Using NGS data, phylogenetic trees and Sn showed a complex evolution of concomitant viral subpopulations.ConclusionsNGS technology allowed a deeper discrimination of the emergence and persistence of a drug resistance mutation, which could be pertinent to investigate when routine Sanger sequencing detects only wild-type strains. Moreover, NGS improved sensitivity helps in studying viral abundance, dynamics and diversity, less approachable with Sanger sequencing.     

Novel mutations and their genotype-phenotype correlations in patients with Noonan syndrome,using next-generation sequencing

Purpose

Noonan Syndrome (NS) is an autosomal dominant disorder with many variable and heterogeneous conditions. The genetic basis for 20–30% of cases is still unknown. This study evaluates Iranian Noonan patients both clinically and genetically for the first time.