Comprehensive Genetic Analysis of RASopathy in the Era of Next-Generation Sequencing and Definition of a Novel Likely Pathogenic KRAS Variation

2022 ◽  
pp. 1-11
Author(s):  
Selma Demir ◽  
Hümeyra Yaşar Köstek ◽  
Aslıhan Sanrı ◽  
Ruken Yıldırım ◽  
Fatma Özgüç Çömlek ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Mapk Pathway ◽  
Mutation Screening ◽  
Genetic Diagnosis ◽  
Next Generation ◽  
Patient Cohort ◽  
Genes Encoding ◽  
Novel Variant ◽  
Mutation Distribution ◽  
Generation Sequencing

<b><i>Introduction:</i></b> Germline pathogenic variations of the genes encoding the components of the Ras-MAPK pathway are found to be responsible for RASopathies, a clinically and genetically heterogeneous group of diseases. In this study, we aimed to present the results of patients genetically investigated for RASopathy-related mutations in our Genetic Diagnosis Center. <b><i>Methods:</i></b> The results of 51 unrelated probands with RASopathy and 4 affected relatives (31 male, 24 female; mean age: 9.327 ± 8.214) were included in this study. Mutation screening was performed on DNA samples from peripheral blood of the patients either by Sanger sequencing of <i>PTPN11</i> hotspot regions (10/51 probands), or by a targeted amplicon next-generation sequencing panel (41/51 probands) covering the exonic regions of <i>BRAF</i>, <i>CBL</i>, <i>HRAS</i>, <i>KRAS</i>, <i>LZTR1</i>, <i>MAP2K1</i>, <i>MAP2K2</i>, <i>NF1</i>, <i>NRAS</i>, <i>PTPN11</i>, <i>RAF1</i>, <i>RASA2</i>, <i>RIT1</i>, <i>SHOC2</i>, <i>SOS1</i>, <i>SOS2</i>, <i>SPRED1</i>, and <i>KAT6B</i> genes. <b><i>Results:</i></b> Pathogenic/likely pathogenic variations found in 22 out of 51 probands (43.13%) and their 4 affected family members were located in <i>PTPN11</i>, <i>BRAF</i>, <i>KRAS</i>, <i>NF1</i>, <i>RAF1</i>, <i>SOS1</i>, and <i>SHOC2</i> genes. The c.148A&#x3e;C (p.Thr50Pro) variation in the <i>KRAS</i> gene was a novel variant detected in a sibling in our patient cohort. We found supportive evidence for the pathogenicity of the <i>NF1</i> gene c.5606G&#x3e;T (p.Gly1869Val) variation which we defined in an affected boy who inherited the mutation from his affected father. <b><i>Conclusion:</i></b> Although <i>PTPN11</i> is the most frequently mutated gene in our patient cohort, as in most previous reports, different mutation distribution among the other genes studied motivates the use of a next-generation sequencing gene panel including the possible responsible genes.

scholarly journals A novel PKHD1 mutation identified in a family affected by ARPKD Ling Hou, Yue Du, Chengguang Zhao, Yubin Wu

2018 ◽  
Vol 2 (1) ◽  
Author(s):  
Ling Hou ◽  
Yue Du ◽  
Chengguang Zhao ◽  
Yubin Wu
Keyword(s):  
Next Generation Sequencing ◽  
Single Gene ◽  
Mutation Screening ◽  
Genetic Diagnosis ◽  
Compound Heterozygous ◽  
Next Generation ◽  
Blood Leukocytes ◽  
Gene Capture ◽  
Renal Cystic Disease ◽  
Generation Sequencing

Objective Autosomal recessive polycystic kidney disease (ARPKD) is a rare inherited renal cystic disease involving multiple organs. It is caused by mutations in the PKHD1 gene. Here, we investigate the gene mutations in a family affected by ARPKD. Methods Genomic DNA was extracted from peripheral blood leukocytes obtained from the subjects, by means of targeted gene capture and next generation sequencing technologies for mutation screening, and were confirmed by Sanger sequencing. Results Two heterozygous mutations of PKHD1, c.6890T>C (p.Ile2297Thr) and c.11215C>T (p.Arg3739Trp), located in exons 43 and 62, respectively, were identified in the patient. Furthermore, the father and mother were revealed to be carriers of heterozygous c.6890T>C (p.Ile2297Thr) and c.11215C>T (p.Arg3739Trp) mutations, respectively. Mutation of c.11215C>T (p.Arg3739Trp) has been found in the ARPKD Mutation Database (http://www.humgen.rwth-aachen.de) but mutation of c.6890T>C (p.Ile2297Thr) has not been reported. Conclusions Compound heterozygous PKHD1 mutations were elucidated to be the molecular basis of ARPKD in this patient. The newly identified c.6890T>C (p.Ile2297Thr) mutation in the patient expands the mutation spectrum of the PKHD1 gene. Targeted gene capture and next generation sequencing are suitable for genetic diagnosis of single-gene inherited diseases like ARPKD, in which the pathogenic gene is large.

scholarly journals Frequency detection of BRAF V600E mutation in a cohort of pediatric langerhans cell histiocytosis patients by next-generation sequencing

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Shunqiao Feng ◽  
Lin Han ◽  
Mei Yue ◽  
Dixiao Zhong ◽  
Jing Cao ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Langerhans Cell Histiocytosis ◽  
Mutation Screening ◽  
Langerhans Cell ◽  
Braf V600e ◽  
P Value ◽  
Type I ◽  
Next Generation ◽  
Mutation Status ◽  
Generation Sequencing

Abstract Background Langerhans cell histiocytosis (LCH) is a rare neoplastic disease that occurs in both children and adults, and BRAF V600E is detected in up to 64% of the patients. Several studies have discussed the associations between BRAF V600E mutation and clinicopathological manifestations, but no clear conclusions have been drawn regarding the clinical significance of the mutation in pediatric patients. Results We retrieved the clinical information for 148 pediatric LCH patients and investigated the BRAF V600E mutation using next-generation sequencing alone or with droplet digital PCR. The overall positive rate of BRAF V600E was 60/148 (41%). The type of sample (peripheral blood and formalin-fixed paraffin-embedded tissue) used for testing was significantly associated with the BRAF V600E mutation status (p-value = 0.000 and 0.000). The risk of recurrence declined in patients who received targeted therapy (p-value = 0.006; hazard ratio 0.164, 95%CI: 0.046 to 0.583). However, no correlation was found between the BRAF V600E status and gender, age, stage, specific organ affected, TP53 mutation status, masses close to the lesion or recurrence. Conclusions This is the largest pediatric LCH study conducted with a Chinese population to date. BRAF V600E in LCH may occur less in East Asian populations than in other ethnic groups, regardless of age. Biopsy tissue is a more sensitive sample for BRAF mutation screening because not all of circulating DNA is tumoral. Approaches with low limit of detection or high sensitivity are recommended for mutation screening to avoid type I and II errors.

scholarly journals Development of a Next-Generation Sequencing Method for BRCA Mutation Screening

2012 ◽  
Vol 14 (6) ◽  
pp. 602-612 ◽  
Author(s):  
Maurice Chan ◽  
Shen Mo Ji ◽  
Zhen Xuan Yeo ◽  
Linda Gan ◽  
Eric Yap ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Brca Mutation ◽  
Mutation Screening ◽  
Next Generation ◽  
Sequencing Method ◽  
Generation Sequencing ◽  
Next Generation Sequencing Method

scholarly journals Next generation sequencing-based mutation screening of 86 patients with idiopathic short stature

2017 ◽  
Vol 64 (10) ◽  
pp. 947-954 ◽  
Author(s):  
Atsushi Hattori ◽  
Yuko Katoh-Fukui ◽  
Akie Nakamura ◽  
Keiko Matsubara ◽  
Tsutomu Kamimaki ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Short Stature ◽  
Mutation Screening ◽  
Idiopathic Short Stature ◽  
Next Generation ◽  
Generation Sequencing

Discovery of mutations in Chenopodium quinoa Willd through EMS mutagenesis and mutation screening using pre-selection phenotypic data and next-generation sequencing

2018 ◽  
Vol 156 (10) ◽  
pp. 1196-1204 ◽  
Author(s):  
Camilo Mestanza ◽  
Ricardo Riegel ◽  
Santiago C. Vásquez ◽  
Diana Veliz ◽  
Nicolás Cruz-Rosero ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Mutation Screening ◽  
Chenopodium Quinoa ◽  
Acetolactate Synthase ◽  
Screening Strategy ◽  
Next Generation ◽  
Induced Mutations ◽  
Phenotypic Data ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractQuinoa (Chenopodium quinoaWilld) is a dicotyledonous annual species belonging to the family Amaranthaceae, which is nutritionally well balanced in terms of its oil, protein and carbohydrate content. Targeting-induced local lesions in genomes (the TILLING strategy) was employed to find mutations in acetolactate synthase (AHAS) genes in a mutant quinoa population. TheAHASgenes were targeted because they are common enzyme target sites for five herbicide groups. Ethyl methane sulfonate (EMS) was used to induce mutations in theAHASgenes; it was found that 2% EMS allowed a mutation frequency of one mutation every 203 kilobases to be established. In the mutant population created, a screening strategy using pre-selection phenotypic data and next-generation sequencing (NGS) allowed identification of a mutation that alters the amino acid composition of this species (nucleotide 1231 codon GTT→ATT, Val→Ile); however, this mutation did not result in herbicide resistance. The current work shows that TILLING combined with the high-throughput of NGS technologies and an overlapping pool design provides an efficient and economical method for detecting induced mutations in pools of individuals.

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