Hemophilia A with reduced coagulation factor Ⅺ: a case report and literature review / 中国输血杂志

【Objective】 To investigate the possible molecular pathogenesis of a child with hemophilia A accompanied by coagulation factor Ⅺ reduction by testing coagulation-related indicators and genotyping in the child and his family. 【Methods】 Peripheral blood from the patient and his parents for detection of coagulation factors Ⅷ, Ⅸ, Ⅺ, Ⅻ, VWF∶Ag, lupus anticoagulants and F VIII, F XI inhibitors were collected. All exons and flanking sequences of the genes encoding FⅧ and FⅪ were sequenced and bioinformatically analyzed. 【Results】 The child had low FⅧ and FⅪ activity and no parental abnormalities were observed. The sequencing results showed that there was a c. 1834(exon12) C>T heterozygous mutation in the FⅧ gene and a c. 1817 (exon15) G>A heterozygous mutation in the FⅪ gene, which was de novo. Bioinformatics analysis shows that the FⅪ mutation changes the original protein structure and increases the number of carboxyl groups. 【Conclusion】 For patients with prolonged APTT, in addition to excluding factors that interfere with APTT testing, all coagulation factors related to APTT should be tested to clarify the diagnosis.

Genetic Analysis of a Chinese Pedigree with Hereditary Spherocytosis Caused by Copy Number Variation Deletion of SPTB Gene / 中国实验血液学杂志

OBJECTIVE@#To investigate the molecular mechanism of the disease based on the clinical characterization and genetic mutation analysis in a family with hereditary spherocytosis.@*METHODS@#The proband with jaundice and anemia was referred to Yidu Central Hospital of Weifang in May 2021. Peripheral blood samples were collected from six members of the family. Second-generation sequencing was used to screen the pathological mutations, and the clinically significant variant sites were selected. Then the relevant databases were used to analyze the variant sites, and RT-qPCR was used to detect the relative mRNA levels of candidate gene. The structure and function of SPTB protein were analyzed by UniProt and SMART databases.@*RESULTS@#We infer that the SPTB gene copy number variation (CNV) deletion was co-segregated with the phenotype of the patients in this family based on the results of second-generation sequencing (about 700 target genes). The UCSC Genome Browser demonstrated that the deleted region was mainly located in exon2-3 of SPTB gene. The results of RT-qPCR showed that the relative SPTB mRNA levels of all patients were lower than the healthy control. UniProt and SMART databases analysis showed that SPTB protein without CH1 and CH2 domains could not bind to erythrocyte membrane actin.@*CONCLUSION@#The CNV deletion of SPTB gene may be the reason for the hereditary spherocytosis in this family.

Clinical characteristics of pneumocystis carinii pneumonia in children without human immunodeficiency virus infection / 中国小儿急救医学

Objective:To investigate the clinical characteristics and prognosis factors in children with pneumocystis carinii pneumonia (PCP) without human immunodeficiency virus (HIV) infected.Methods:From January 2017 to December 2020, 35 non-HIV infected patients with PCP were admitted to Hunan Children′s Hospital.According to the prognosis at discharge, they were divided into survival group and death group.The clinical characteristics of two groups were compared, and the prognostic factors were analyzed.Results:The age of 35 patients ranged from 1 month to 15 years, including 24 males and 11 females.Seven patients(20.0%) had primary immunodeficiency, 5 patients(14.2%) had autoimmune disease, and 4 patients(11.4%) had renal disease.Eighteen patients were treated with long-term hormone and 13 patients were treated with immunosuppressive agents before the onset of the disease.Clinical symptoms included shortness of breath or dyspnea, cough, fever and so on, while with few pulmonary signs.Peripheral blood lymphocyte count was less than 1.5×10 9/L in 18 cases.The median LDH was(654.94±57.66)U/L; Fungal D-glucan increased in 13 cases.The median P/F was(121.29±23.25)mmHg, and P/F was less than 200 mmHg in 16 cases.CD4 cells were less than 500/μL in 15 cases and less than 200/μL in 8 cases.The imaging findings were mainly consolidation or patellar shadow, diffuse ground glass shadow, 3 cases with pleural effusion, and 1 case with pneumothorax.Twenty-two cases survived and 13 died, with a mortality rate of 37.1%.There were statistically significant differences in hospitalization days, CD4 cell count, Fungal D-glucan, P/F, ICU admission and invasive mechanical ventilation between two groups( P<0.05). Logistic multivariate analysis showed that decreased P/F value was an independent risk factor affecting the prognosis of non-HIV infected children with PCP ( OR=0.006, 95% CI 0.975-1.000). Conclusion:The clinical manifestations, laboratory examinations and imaging examinations of non-HIV infected patients with PCP lack specificity.When a diagnosis is suspected, high-resolution CT should be performed based on the results of peripheral blood lymphocyte count, CD4 cell count, fungal D, LDH, and blood gas analysis results as soon as possible, compound sulfamethoxazole should be used timely.Decreased P/F value is an independent factor affecting the prognosis of non-HIV children with PCP.

Clinical characteristics of pneumocystis carinii pneumonia in children without human immunodeficiency virus infection / 中国小儿急救医学

Objective:To investigate the clinical characteristics and prognosis factors in children with pneumocystis carinii pneumonia (PCP) without human immunodeficiency virus (HIV) infected.Methods:From January 2017 to December 2020, 35 non-HIV infected patients with PCP were admitted to Hunan Children′s Hospital.According to the prognosis at discharge, they were divided into survival group and death group.The clinical characteristics of two groups were compared, and the prognostic factors were analyzed.Results:The age of 35 patients ranged from 1 month to 15 years, including 24 males and 11 females.Seven patients(20.0%) had primary immunodeficiency, 5 patients(14.2%) had autoimmune disease, and 4 patients(11.4%) had renal disease.Eighteen patients were treated with long-term hormone and 13 patients were treated with immunosuppressive agents before the onset of the disease.Clinical symptoms included shortness of breath or dyspnea, cough, fever and so on, while with few pulmonary signs.Peripheral blood lymphocyte count was less than 1.5×10 9/L in 18 cases.The median LDH was(654.94±57.66)U/L; Fungal D-glucan increased in 13 cases.The median P/F was(121.29±23.25)mmHg, and P/F was less than 200 mmHg in 16 cases.CD4 cells were less than 500/μL in 15 cases and less than 200/μL in 8 cases.The imaging findings were mainly consolidation or patellar shadow, diffuse ground glass shadow, 3 cases with pleural effusion, and 1 case with pneumothorax.Twenty-two cases survived and 13 died, with a mortality rate of 37.1%.There were statistically significant differences in hospitalization days, CD4 cell count, Fungal D-glucan, P/F, ICU admission and invasive mechanical ventilation between two groups( P<0.05). Logistic multivariate analysis showed that decreased P/F value was an independent risk factor affecting the prognosis of non-HIV infected children with PCP ( OR=0.006, 95% CI 0.975-1.000). Conclusion:The clinical manifestations, laboratory examinations and imaging examinations of non-HIV infected patients with PCP lack specificity.When a diagnosis is suspected, high-resolution CT should be performed based on the results of peripheral blood lymphocyte count, CD4 cell count, fungal D, LDH, and blood gas analysis results as soon as possible, compound sulfamethoxazole should be used timely.Decreased P/F value is an independent factor affecting the prognosis of non-HIV children with PCP.

Monomorphic epithelial intestinal T-cell lymphoma: a clinicopathological characteristic analysis / 白血病·淋巴瘤

Objective:To investigate the histopathological morphology, immunophenotype, molecular pathological features, clinical prognosis and treatment of monomorphic epithelial intestinal T-cell lymphoma (MEITL).Methods:The clinicopathological data of 5 patients with MEITL in Sichuan Jinyu Medical Laboratory Center Co., Ltd from March 2019 to February 2021 were retrospectively analyzed, and literatures were reviewed. All cases were tested by using histopathology, immunohistochemistry, in situ hybridization of Epstein-Barr virus (EBV) and T-cell clonability assessment, and 1 case had second-generation sequencing (NGS) test. Clinical follow-up was performed in 2 patients.Results:All 5 MEITL cases were middle-aged and old men. The histopathology showed that intestinal wall was diffuse with tumor cells infiltrating, and the cells were obviously epitheliophilic. All the tumor cells CD3, CD8, CD56, GrB were positively expressed, and expressions of other T-cell markers were different, among which 1 case had CD30 positive and 1 case had CD20 positive. All 5 cases were negative for EBV by in situ hybridization. Monoclonal rearrangement of T-cell receptor gene was detected in all 5 cases. Mutations of BCOR, JAK3, STAT5B and ATM were detected in 1 case by using NGS. Among 2 cases followed-up, 1 patient relapsed 7 months after he had the initial onset and underwent the first operation, and then he had another operation. This patient finally died of extensive metastasis in the lung, liver and abdominal cavity as well as ascites 13 months later; another patient died 1 month after emergency surgery for perforation.Conclusions:MEITL is a rare primary T-cell lymphoma of the digestive tract. The oncogenic event in the pathogenesis of MEITL mainly involves mutations in the tumor suppressor gene SETD2 and mutations in one or more genes of the JAK/STAT pathway. Currently, there is no standard treatment for MEITL. Most treatment options include surgical resection and anthracycline-based chemotherapy.

The prognostic value of cloned genetic mutations detected by second-generation sequencing in RUNX1-RUNX1T1 positive acute myeloid leukemia patients receiving intensive consolidation therapy / 中华血液学杂志

Objective: To investigate the prognostic value of clonal gene mutations detected by second-generation sequencing in patients with positive RUNX1-RUNX1T1 acute myeloid leukemia (AML) who received high-dose chemotherapy or autologous transplantation (intensive consolidation therapy) in the first complete remission (CR(1)) state. Methods: 79 AML patients with positive RUNX1-RUNX1T1 who received intensive consolidation therapy in CR(1) state from July 2011 to August 2017 were analyzed retrospectively. Kaplan-Meier curve and Cox regression model were used to figure out the effect of leukocyte counts at onset and gene mutations for prognosis. Results: C-KIT, FLT3, CEBPA and DNMT3A gene mutations were found in 25 (31.6%) , 6 (7.6%) , 7 (8.9%) and 1 (1.3%) patient among the population. Mutations in C-KIT exon17 and C-KIT exon8 were detected in 19 (24.1%) and 5 (6.3%) cases, respectively, and mutations of FLT3-ITD were confirmed in 5 (6.3%) cases. The higher leukocyte counts presented at onset of leukemia, the shorter overall survival (OS) was seen in these patients (P=0.03) . Patients with C-KIT exon17 mutation had significantly shorter OS (P=0.01) and disease free survival (DFS) (P=0.006) compared with those without gene mutations, and patients with FLT3-ITD gene mutation got the inferior OS (P=0.048) and DFS (P=0.071) . Conclusion: In AML patients with positive RUNX1-RUNX1T1 receiving intensive consolidation therapy, the white blood cell counts at onset of leukemia, C-KIT mutations in exon 17, and FLT3-ITD gene mutations suggest poor prognosis, which would contribute to elaborate risk stratification, personalized treatment and predict prognosis for these patients.

Ancestry Inference Using the ForenSeqTM DNA Signature Prep Kit / 法医学杂志

Objective To evaluate the effect of 56 ancestry informative single nucleotide polymorphism （aiSNP） genetic markers in the ForenSeqTM DNA Signature Prep Kit on ancestry inference. Methods A total of 85 samples from five populations including Hebei Han population, Inner Mongolia autonomous region Mongolian population, Tibet autonomous region Tibetan population, Xinjiang Uygur autonomous region Uygur population and Nigerian population were collected. The library was constructed with the ForenSeqTM DNA Signature Prep Kit and sequencing was performed based on the MiSeq FGx Forensic Genomics System. Using universal analysis software （UAS） of ForenSeqTM, principal component analysis （PCA）, Structure and likelihood ratio method was used on the genotyping data of 56 aiSNP markers, respectively, and the genetic relationships between populations and inference of the origin of ancestors were analyzed. Results Among the five populations tested, the four ethnic populations in China （Hebei Han population, Inner Mongolia autonomous region Mongolian population, Tibet autonomous region Tibetan population and Xinjiang Uygur autonomous region Uygur population） could be significantly distinguished from Nigerian population. Xinjiang Uygur autonomous region Uygur individuals were shown as having mixed origins of ancestors and could be distinguished from the other three Chinese populations. However, the other three populations in China （Hebei Han population, Inner Mongolia autonomous region Mongolian population and Tibet autonomous region Tibetan population） could not be effectively distinguished by the system. Conclusion The 56 aiSNP markers in the ForenSeqTM DNA Signature Prep Kit can make accurate ancestry inference from the intercontinental level, but it is not yet able to distinguish between Chinese subpopulations.

Application Prospect of Massively Parallel Sequencing in Mixed Stain Detection / 法医学杂志

Mixed stains is the common biological sample in sexual crime cases. Its analysis and DNA profiles interpretation are one of the difficulties in forensic examination. The current genetic marking of mixed stain detection mainly rely on capillary electrophoresis （CE） separation technology, and the analysis methods of the results are mainly inclusion rate and likelihood methods. Because CE has limited resolution and is not able to exploit the efficacy of each genetic marker, its ability to split mixed stain is limited. In recent years, the emerging massively parallel sequencing （MPS） technique not only can obtain the base sequence information of genetic markers, but also is capable of detecting multiple genetic markers simultaneously, and thus derives new analytical methods, bringing new opportunities for forensic detection and analysis of mixed stain. This paper intends to review the application prospects of conventional mixed stain analyses and MPS technique, therefore to provide references for later research and practice.

Second generation sequencing detection breast cancer susceptibility gene variants for risk prediction and clinical treatment / 中国肿瘤临床

Objective:To investigate the function of breast cancer susceptibility gene variants in predicting breast cancer risk and guid-ing clinical treatment through DNA sequencing. Methods:This study involved 146 patients, 71 high-risk cases, and 55 healthy people, totaling 272 cases. The subjects were treated in Tianjin Medical University Cancer Institute and Hospital from November 2013 to July 2015. Genomic DNA was sequenced by a second generation sequencing platform. All exon areas of six common breast cancer suscepti-bility genes (BRCA1, BRCA2, PTEN, STK11, TP53, and RAP1) were sequenced through amplicon sequencing method. Meaningful vari-ants including single nucleotide variants (SNVs), insertion-deletions (InDels) and nonsense mutations were selected and statistical methods, such as t test andχ2 test, were used to analyze the statistical differences in incidence rates among three groups. Results:A total of 177 meaningful variants were confirmed, including 50 SNVs, 8 nonsense mutations, and 9 InDels. Among the variants, 31 were recorded in the Exome Aggregation Consortium (ExAC), 40 were noted in ClinVar database, and 21 were not encoded in the present da-tabase, which were defined as new variants in this study. Conversely, 57 variants (85.1%) were found in breast cancer patients and high-risk cases, and the incidence of axillary lymph node metastasis (P=0.010) and pathological stages (P=0.002) in mutation positive patients were both higher than mutation negative patients. Moreover, the percentage of family history of cancer (P=0.005) and triple negative breast cancer (P=0.009) were both higher in patients carrying pathogenic mutations than in nonpathogenic patients. Conclu-sion:Breast cancer susceptibility gene variants may not only be a tool used to predict the risk of getting breast cancer but also a mean-ingful guideline for the clinical treatment and prognosis evaluation.

Prediction of the target genes mediated by RYBP in the leukemic cell apoptosis / 实用医学杂志

Objective To investigate the target genes in RYBP-mediated leukemia cell apoptosis by high-flux sequencing. Methods The HL-60 cell line with knockdown of RYBP was set up. MRNA and microRNA sequencing was conducted by the next-generation sequencing technology. Result MRNAs and miRNAs were dys-regulated in HL-60 cell line with knockdown of RYBP. The results of KEGG analysis indicated that the down-regu-lated genes were associated with cancer transcription regulation and amino acid metabolism. SPI1 and miR-214-3p were shown downregulated after knockdown of RYBP. Conclusion The target genes in RYBP-mediated leukemia cell apoptosis include BBC3,BAI1,SESN2 ,CCNG2,JAK3,STAT4,SPI1,BCL6,CD11b and hsa-miR-214-3p.

Review of Second Generation Sequencing and Its Application in Forensic Genetics / 法医学杂志

The rapid development of second generation sequencing （SGS） within the past few years has led to the increasement of data throughput and read length while at the same time brought down substantially the sequencing cost. This made new breakthrough in the area of biology and ushered the forensic genetics into a new era. Based on the history of sequencing application in forensic genetics, this paper reviews the importance of sequencing technologies for genetic marker detection. The application status and potential of SGS in forensic genetics are discussed based on the already explored SGS platforms of Roche, Illumina and Life Technologies. With these platforms, DNA markers （SNP, STR）, RNA markers （mRNA, microRNA） and whole mtDNA can be sequenced. However, development and validation of application kits, maturation of analysis software, connection to the existing databases and the possible ethical issues occurred with big data will be the key factors that determine whether this technology can substitute or supplement PCR-CE, the mature technology, and be widely used for cases detection.