Molecular features of 109 patients with chronic myelomonocytic leukemia in a single center / 中华血液学杂志

Objective: To explore the molecular features of chronic myelomonocytic leukemia (CMML) . Methods: According to 2022 World Health Organization (WHO 2022) classification, 113 CMML patients and 840 myelodysplastic syndrome (MDS) patients from March 2016 to October 2021 were reclassified, and the clinical and molecular features of CMML patients were analyzed. Results: Among 113 CMML patients, 23 (20.4%) were re-diagnosed as acute myeloid leukemia (AML), including 18 AML with NPM1 mutation, 3 AML with KMT2A rearrangement, and 2 AML with MECOM rearrangement. The remaining 90 patients met the WHO 2022 CMML criteria. In addition, 19 of 840 (2.3%) MDS patients met the WHO 2022 CMML criteria. At least one gene mutation was detected in 99% of CMML patients, and the median number of mutations was 4. The genes with mutation frequency ≥ 10% were: ASXL1 (48%), NRAS (34%), RUNX1 (33%), TET2 (28%), U2AF1 (23%), SRSF2 (21.1%), SETBP1 (20%), KRAS (17%), CBL (15.6%) and DNMT3A (11%). Paired analysis showed that SRSF2 was frequently co-mutated with ASXL1 (OR=4.129, 95% CI 1.481-11.510, Q=0.007) and TET2 (OR=5.276, 95% CI 1.979-14.065, Q=0.001). SRSF2 and TET2 frequently occurred in elderly (≥60 years) patients with myeloproliferative CMML (MP-CMML). U2AF1 mutations were often mutually exclusive with TET2 (OR=0.174, 95% CI 0.038-0.791, Q=0.024), and were common in younger (<60 years) patients with myelodysplastic CMML (MD-CMML). Compared with patients with absolute monocyte count (AMoC) ≥1×10(9)/L and <1×10(9)/L, the former had a higher median age of onset (60 years old vs 47 years old, P<0.001), white blood cell count (15.9×10(9)/L vs 4.4×10(9)/L, P<0.001), proportion of monocytes (21.5% vs 15%, P=0.001), and hemoglobin level (86 g/L vs 74 g/L, P=0.014). TET2 mutations (P=0.021) and SRSF2 mutations (P=0.011) were more common in patients with AMoC≥1×10(9)/L, whereas U2AF1 mutations (P<0.001) were more common in patients with AMoC<1×10(9)/L. There was no significant difference in the frequency of other gene mutations between the two groups. Conclusion: According to WHO 2022 classification, nearly 20% of CMML patients had AMoC<1×10(9)/L at the time of diagnosis, and MD-CMML and MP-CMML had different molecular features.

Gene mutation analysis of 12 families with congenital cataract / 中华实验眼科杂志

Objective:To analyze the clinical manifestations of congenital cataract in 12 families and gene variants causing the disease.Methods:The method of pedigree investigation was adopted.Clinical data of 27 patients from 12 Chinese Han families with congenital cataract were collected, and genomic DNA was extracted from peripheral blood samples of patients and family members.Candidate variants were screened by next generation sequencing and were verified by Sanger sequencing.Population frequency of the variants were obtained through the Genome Arrgregation Database (gnomAD).Pathogenicity of variants was analyzed through the Human Gene Mutation Database (HGMD), Database of Single Nucleotide Polymorphism (dbSNP) and PubMed, and the mutation effect was interpreted by protein prediction softwares including SIFT, PolyPhen_2 and MutationTaster.The conservation analysis of amino acid sequences of variants was performed by GERP+ + software.Diagnosis was confirmed by clinical ophthalmic phenotype, medical history and mutation analysis.This study adhered to the Declaration of Helsinki.The study protocol was approved by the Ethics Committee of the First Affiliated Hospital of Zhengzhou University (No.KS-2018-KY-36).Written informed consent was obtained from all subjects and their guardians.Results:Pathogenic genetic variants were found in all the 12 families, 9 of which had known pathogenic variants including MIP c.97C>T, GJA8 c.593G>A, CRYBA4 c.277T>C, CRYBB2 c.563G>A and c.436G>C, CRYGC c.470G>A, CRYGD c.70C>A, PAX2 c.70dupG as well as OCRL E5-E16dup, and 3 novel potential pathogenic variants including CRYGD c.422delG, ELP4 c.886C>A and CRYBB2 c.434G>C. CRYGD c.422delG could lead to the early termination of translation of protein products, which was pathogenic.The nucleotide and amino acid sites of ELP4 c.886C>A and CRYBB2 c.434G>C were highly conserved among species, and were predicted as harmful.The 12 families were consistent with co-segregation. Conclusions:CRYGD c.422delG, ELP4 c.886C>A and CRYBB2 c.434G>C may be novel pathogenic variants of congenital cataract.

Diagnosis of acanthosis nigricans in a family by targeted sequencing / 中华皮肤科杂志

A pedigree with familial acanthosis nigricans presenting with atypical clinical symptoms was reported. The 4-year-old female proband began to develop black patches on the neck and abdomen since the age of 1 year, which had gradually spread to the lips and front of the trunk in recent years. Reflectance confocal microscopy of the abdominal skin showed downward extension and twisting of dermal papillary rings with formation of gully-like structures, and moderately to highly refractive particles in the dermal papillary rings. The proband′s father and grandmother had similar medical history, but the pigmentation spontaneously subsided with age, leaving only local thickened skin lines. Peripheral blood samples were collected from the proband, her parents and grandmother, and panel-based targeted sequencing of peripheral blood DNA was performed for the proband. Sequencing showed a missense mutation c.1949A>C (p.Lys650Thr) in exon 14 of the FGFR3 gene in the proband, and Sanger sequencing confirmed the presence of this mutation in the proband and her father and grandmother. A diagnosis of familial acanthosis nigricans was made.

The utilization of biotinylated RNA baits on captured sequencing of cancer marker genes functional regions / Монголын Анагаах Ухаан

Background@#Nucleic acid sequencing is a multi-step process taken place in medical research or diagnostic laboratories. Since the emerge of second generation sequencing technology generally referred as next generation sequencing (NGS), the mass parallel reads covering human genome or transcriptome is achieved by cost cut down over thousand folds. Though the technology made tremendous push forward to various applications, its data analysis time and effort still takes worrisome time and human effort, bringing the emerge of next-step demand: targeted mass sequencing of only desired part from human genome or transcriptome with lower material cost and labor. By targeted sequencing, both run cost and data analysis process can be further cut down, and the read results are more reliable on changes such as determining varied number of repeats, heterozygote alleles, deletions, chromosomal scale abnormality and more. @*Objective@#In this study, we explored the utilization of biotinylated RNA baits on captured sequencing of cancer marker genes functional regions.@*Method@#Targeted NGS was achieved by capturing desired genomic regions using preparatory nucleic acid probes. RNA bait capturing of desired genomic regions has shown to have high specificity and quality. </br> The study was carried out with informed consent obtained from patients, with the approval №53 in 2018.03.15 by Medical Ethics committee, Ministry of Health, Mongolia.@*Result@#By preparing library of biotinylated RNA baits with 75000 unique sequences, we achieved mass parallel sequencing of human 410 cancer-marker-genes’ exons and UTRs with average read depth ~760, and covered thousands of SNPs on 5 genomic DNA samples. Tissue samples derived from breast cancer and ovary cancer had SNP and deletion on 7 marker genes (BRCA1, BRCA2, ATM, BRIP1, PTEN, TP53, RAD51C) not registered in database.@*Conclusion@#Experiments showed RNA baits with up to 117 nucleotide length, produced from ssDNA oligonucleotide stock, can be utilized to capture desired regions of human genome, and bring the cost of captured mass sequencing to 1500 USD, with 93.14-93.33% of Q30 read quality.

Mutation analysis in a pedigree with Rothmund-Thomson syndrome / 中华皮肤科杂志

Objective@#To detect gene mutations in a pedigree with Rothmund-Thomson syndrome (RTS) .@*Methods@#Clinical data were collected from two patients (an older sister and a younger brother) and their family members in a Chinese pedigree of Han nationality with RTS. Blood samples were obtained from the two patients, their unaffected older brother, their parents and 100 unrelated healthy controls. DNA was extracted, and all the exons in the encoding area of the RECQL4 gene were amplified by PCR. Gene mutations were detected by a skin-targeted next-generation sequencing panel, and verified by Sanger sequencing.@*Results@#Two heterozygous mutations were identified in the RECQL4 gene of the two patients, including a splice site mutation c.2886-1G>A and an insertion mutation c.1013_1014insC, which were inherited from the father and mother of the patients respectively. Meanwhile, neither of the two mutations was observed in 100 unrelated healthy controls or the older brother of the patients.@*Conclusion@#The splice site mutation c.2886-1G>A and the insertion mutation c.1013_1014insC in the RECQL4 gene may contribute to the clinical phenotype of the patients in this pedigree with RTS.

Mutation analysis in a pedigree with Rothmund-Thomson syndrome / 中华皮肤科杂志

Objective To detect gene mutations in a pedigree with Rothmund-Thomson syndrome (RTS).Methods Clinical data were collected from two patients (an older sister and a younger brother)and their family members in a Chinese pedigree of Han nationality with RTS.Blood samples were obtained from the two patients,their unaffected older brother,their parents and 100 unrelated healthy controls.DNA was extracted,and all the exons in the encoding area of the RECQL4 gene were amplified by PCR.Gene mutations were detected by a skin-targeted next-generation sequencing panel,and verified by Sanger sequencing.Results Two heterozygous mutations were identified in the RECQL4 gene of the two patients,including a splice site mutation c.2886-1G＞A and an insertion mutation c.1013_1014insC,which were inherited from the father and mother of the patients respectively.Meanwhile,neither of the two mutations was observed in 100 unrelated healthy controls or the older brother of the patients.Conclusion The splice site mutation c.2886-1G＞A and the insertion mutation c.1013_1014insC in the RECQL4 gene may contribute to the clinical phenotype of the patients in this pedigree with RTS.

Targeted sequencing analysis of hyper-eosinophilic syndrome and chronic eosinophilic leukemia / 中华血液学杂志

Objective@#Analysis of the molecular characteristics of eosinophilia. @*Methods@#Targeting sequence to 24 patients with chronic eosinophilic leukemia (CEL) with rearrangement of PDGFRA, PDGFRB, or FGFR1 and 62 patients with hyper-eosinophilic syndrome (HES). Mutation annotation and analysis of amino acid mutation using authoritative databases to speculate on possible pathogenic mutation. @*Results@#Thirty-seven kinds of clonal variant were detected from 17 patients with CEL, no recurrent mutation site and hot spot region were found. No pathogenic mutation was detected in 19 patients with PDGFRA rearrangement, but pathogenic mutations of ASXL1, RUNX1 and NRAS were detected from 2 patients with FGFR1 rearrangement who progressed to acute myeloid leukemia and 1 patient with PDGFRB rearrangement who progressed to T lymphoblastic lymphoma, respectively. One hundred and two kinds of clonal abnormalities were detected in 49 patients with HES. The main hot spot mutation regions included: CEBPA Exon1, TET2 Exon3, ASXL1 Exon12, IDH1 Y208C, and FGFR3 L164V. CRRLF2 P224L and PDGFRB R370C point mutations were detected separately in 2 patients with HES who treated with imatinib monotherapy and achieved hematologic remission. @*Conclusion@#The pathogenesis of CEL with PDGFRA, PDGFRB or FGFR1 rearrangement is usually single, and the progression of the disease may involve other driver mutation. A variety of genes with hot mutation regions may be involved in the pathogenesis of HES, and some mutation sites are sensitive to tyrosine kinase inhibitors.

Gene mutations from 511 myelodysplastic syndromes patients performed by targeted gene sequencing / 中华血液学杂志

Objective@#To study the characteristics of gene mutations in Chinese myelodysplastic syndromes (MDS) patients.@*Methods@#A total of 511 Chinese patients with MDS performed 112-gene targeted sequencing were retrospectively analyzed.@*Results@#Eighty-three distinct mutant genes were found in 511 patients with MDS. Amongst these, the most frequent mutations was associated with epigenetics (50%) , followed by spliceosome (37%) , signal transduction (34%) , transcription factors (24%) and cell cycle/apoptosis (17%) . 439 subjects (86%) had at least one gene mutation. The mean number of mutations in refractory anemia with unilineage dysplasia (RCUD) was 1.25, refractory anemia with multilineage dysplasia (RCMD) was 1.73, refractory anemia with ring sideroblasts (RARS) was 2.79, refractory anemia with excess blasts-1 (RAEB-1) was 2.22, RAEB-2 was 2.34, MDS with isolated 5q- was 2.67, MDS, unclassified (MDS-U) was 2.00. U2AF1 mutant subjects were more likely to have isolated+8[Q<0.001, OR=4.42 (95% CI 2.23-8.68) ]and less likely to have complex karyotypes[Q=0.005, OR=0.22 (95% CI 0.04-0.72) ]. According to the number of gene mutations, all subjects were categorized into three groups, namely group with 0-1 mutation, with 2 mutations and with three or more mutations. There was a significant difference in overall survival (OS) among three groups (P=0.041) .@*Conclusion@#About 90% patients with MDS have at least one gene mutation. Genes associated with epigenetics and spliceosome are most common mutated genes in MDS. The increased numbers of gene mutations accompany with disease evolution and associate with poor prognosis.