Advances in international newborn screening / 中华实用儿科临床杂志

Newborn screening is an important national public health policy and measure to reduce birth defects and improve the quality of China′s birth population.In the early 1960s, Dr.Robert Guthrie of the United States invented the first newborn screening test, namely, semi-quantitative determination of phenylalanine in dry blood filter paper for screening phenylketonuria.In the 1990s, tandem mass spectrometry (MS/MS) began to be applied to the screening of genetic metabolic diseases in newborns.This technology enabled the detection of multiple diseases by one test, and increased the types of diseases detected.In the past 10 years, with the development of screening technology, the invention of new drugs, the improvement of treatment methods, and especially the application of new technologies such as newborn genetic screening, the source of mutations can be identified at the molecular level.Moreover, newborn screening is extended to patients who are not candidates for MS/MS.Many genetic diseases are able to be screened and diagnosed early.Effective management and quality control of newborn disease screening are prerequisites for improving the quality and accuracy of results.Secondary and multi-level detection strategies, different biochemical or biochemical genetic testing methods, and the integration of targeted and non-targeted multi-omics data have a wide range of applications and great clinical value.

Genetics and muscle pathology in the diagnosis of muscular dystrophies: An update

Muscular dystrophies are a clinically and genetically heterogeneous group of disorders involving the skeletal muscles. They have a progressive clinical course and are characterized by muscle fiber degeneration. Congenital muscular dystrophies (CMD) include dystroglycanopathies, merosin-deficient CMD, collagen VI-deficient CMD, SELENON-related rigid spine muscular dystrophy, and LMNA-related CMD. Childhood and adult-onset muscular dystrophies include dystrophinopathies, limb-girdle muscular dystrophies, Emery-Dreifuss muscular dystrophy, facioscapulohumeral muscular dystrophy, and myotonic dystrophy. Traditionally, muscle biopsy and histopathology along with special pathology techniques such as immunohistochemistry or immunoblotting were used for the diagnosis of muscular dystrophies. However, recent advances in molecular genetic testing, especially the next-generation sequencing technology, have revolutionized the diagnosis of muscular dystrophies. Identification of the underlying genetic basis helps in appropriate management and prognostication of the affected individual and genetic counseling of the family. In addition, identification of the exact disease-causing mutations is necessary for accurate prenatal genetic testing and carrier testing, to prevent recurrence in the family. Mutation identification is also essential for initiating mutation-specific therapies (which have been developed recently, especially for Duchenne muscular dystrophy) and for enrolment of patients into ongoing therapeutic clinical trials. The 'genetic testing first' approach has now become the norm in most centers. Nonetheless, muscle biopsy-based testing still has an important role to play, especially for cases where genetic testing is negative or inconclusive for the etiology.

Distribution of bacteria infected by metagenomic sequencing technology in maxillofacial space / 华西口腔医学杂志

OBJECTIVES@#This study aimed to compare and analyze the consistency and difference between metageno-mic next-generation sequencing (mNGS) and conventional bacterial culture in the detection of pathogenic microorganisms in maxillofacial space infection, as well as to provide a new detection method for the early clinical identification of pathogenic bacteria in maxillofacial space infection.@*METHODS@#The clinical data of 16 patients with oral and maxillofacial space infections in the First Affiliated Hospital of Zhengzhou University from March 2020 to June 2020 were collected. mNGS and conventional bacterial culture methods were used to detect pus. We then analyzed and compared the test results of the two methods, including the test cycle, positive detection rate, anaerobic bacteria, facultative anaerobes and aerobic bacteria detection rates, distribution of pathogenic bacteria, relative species abundance, and resistance genes.@*RESULTS@#The average inspection period of mNGS was (18.81±3.73) h, and the average inspection period of bacterial culture was (83.25±11.64) h, the former was shorter than the latter (@*CONCLUSIONS@#Compared with conventional bacterial culture, mNGS has the characteristics of short test time, high sensitivity, and high accuracy. Thus, it is a new detection method for the early identification of pathogenic bacteria in maxillofacial space infection and is beneficial to the early clinical diagnosis and treatment of the disease.

Clinical characteristics and next generation sequencing of three cases of Listeria monocytogenes meningitis with complications / 中华儿科杂志

Objective@#To summarize the clinical characteristics of Listeria monocytogenes meningitis (LMM) with complications, and analyze the outcomes of next generation sequencing.@*Methods@#Clinical characteristics, laboratory findings, imaging features, antibiotics treatment, and next generation sequencing of cerebrospinal fluid were analyzed in 3 LMM patients who were hospitalized in the Department of Infectious Diseases of Beijing Children′s Hospital Affiliated to Capital Medical University from July 2015 to November 2017.@*Results@#The three patients were 1-year-old girl, 2-year-old girl, and 9-year-old boy, with normal immune function. They had eaten refrigerated food, milk or dairy products before onset. Symptoms included fever, headache, abdominal pain, diarrhea, vomiting, and convulsions, etc. The complications of two cases (case 2 and 3) were appendicitis and Meckel′s diverticulitis. The other one (case 1) was with sepsis and pneumonia. Leukocyte counts in cerebrospinal fluid were elevated in all the three cases, and cranial magnetic resonance imaging showed meningeal or periventricular involvement. All the children were diagnosed with LMM by positive CSF culture. CSF for next generation sequencing was sent after carbapenem antibiotics using, yet all the results were positive. The positive results were returned 2, 9, and 9 days earlier than culture results, respectively. The gene coverage was 5.00%, 7.00%, 0.04%, and the reads was 2 561, 1 011 and 8, respectively. All the three children had recurrent fever despite using cephalosporin. Levels of leukocytes in the blood and CSF further elevated. After using carbapenem antibiotics, patients improved eventually and were discharged from hospital.@*Conclusions@#LMM can occur in children with normal immune function and is usually associated with digestive system symptoms. Listeria monocytogenes can be detected quickly and accurately by the next generation sequencing technology, without being limited to sampling time and antibiotics application.

The correlation of the related signaling pathways and prognosis in patients with advanced cholangiocarcinoma / 中国肿瘤生物治疗杂志

@# Objective： ：To detect the gene mutation in cholangiocarcinoma patients using the next generation sequencing (NGS) technology, and to analyze its correlation to the prognosis of the patients. Methods: From June 2016 to June 2018, 40 patients diagnosed with cholangiocarcinoma received NGS examination to screen the possible mutations (single base mutation, structural variation, copy number variation and gene fusion, etc.). The disease control rates (DCR), progression-free survival (PFS) and overall survival (OS) of the patients, who received the first line therapy, were retrospectively reviewed to analyze the relationship between signaling pathway as well as its genetic variation and the prognosis of cholangiocarcinoma patients. Results: The median PFS of patients with and without TP53 mutation was 11.0 and 8.3 months, respectively (P=0.332), while OS was 14.3 and 32.9 months, respectively (P=0.041). The median PFS of patients with and without PI3K mutations was 8.3 and 11.0 months, respectively (P=0.285), while OS was 14.3 and 37.0 months, respectively (P=0.020). The median PFS of patients with and without mTOR pathway mutations was 6.3 and 10.3 months, respectively (P=0.020), while OS was 15.6 and 19.6 months, respectively (P=0.892). There was no significant effect of pathway-related gene mutations on patients’survival. Conclusion: The prognosis of cholangiocarcinoma patients with TP53 and PI3K pathway activation had obviously poor prognosis than those without. No significant difference was observed between the patients with and without mTOR pathway activation and IDH mutation.

Transcriptome analysis of female and male flower buds of Idesia polycarpa Maxim. var. vestita Diels

Background: Idesia polycarpa Maxim. var. vestita Diels, a dioecious plant, is widely used for biodiesel due to the high oil content of its fruits. However, it is hard to distinguish its sex in the seedling stage, which makes breeding and production problematic as only the female tree can produce fruits, and the mechanisms underlying sex determination and differentiation remain unknown due to the lack of available genomic and transcriptomic information. To begin addressing this issue, we performed the transcriptome analysis of its female and male flower. Results: 28,668,977 and 22,227,992 clean reads were obtained from the female and male cDNA libraries, respectively. After quality checks and de novo assembly, a total of 84,213 unigenes with an average length of 1179 bp were generated and 65,972 unigenes (78.34%) could be matched in at least one of the NR, NT, Swiss-Prot, COG, KEGG and GO databases. Functional annotation of the unigenes uncovered diverse biological functions and processes, including reproduction and developmental process, which may play roles in sex determination and differentiation. The Kyoto Encyclopedia of Genes and Genomes pathway analysis showed many unigenes annotated as metabolic pathways, biosynthesis of secondary metabolites pathways, plant­ pathogen interaction, and plant hormone signal transduction. Moreover, 29,953 simple sequence repeats were identified using the microsatellite software. Conclusion: This work provides the first detailed transcriptome analysis of female and male flower of I. polycarpa and lays foundations for future studies on the molecular mechanisms underlying flower bud development of I. polycarpa.

Research progress in the application of next-generation sequencing in forensic genetics / 中国法医学杂志

DNA typing of biological samples is an important step in performing individual identification and paternity testing in forensic applications. In practice, the detection of complex biological samples and the identification of complex kinships are challenging current biological technologies. Novel DNA technologies are also introduced into forensic genetics to improve the power of analysis. Next-generation sequencing (NGS) has several advantages, such as high-throughput and low cost, and can obtain detailed DNA sequences and relative contents of targeted regions, which will improve the detection of biological samples to help the analysis of forensic cases. The application of NGS in forensic genetics has received extensive attention and reports on the application of NGS in forensic genetics are increasing. In this study, we summarized the progress in the application research of NGS in the forensic genetics including the detection of genetic markers and their analytical methods. This will provide guides for related studies and forensic applications.

Application of gene capture technology combined with next generation sequencing technology on methylmalonic acidemia / 中华实用儿科临床杂志

Objective To assess the efficiency and reliability of clinical genetic diagnosis of methylmalonic acidemia(MMA) using new generation sequencing platform (HiSeq2000).Methods 1.Nine patients diagnosed with clinical signs of MMA were recruited.DNA library from the patients were mixed with designed gene capture probe.The whole exons region of 48 genes related to organic acid metabolism were screened using the gene capture combined with high-throughput sequencing.2.The joints were removed and the low quality data were filtered,the data were analyzed by means of SNP and InDel.To avoid the false positive,the abnormal sites were verified using the Sanger sequencing method.3.The detection of the organic acid in the urine was performed through gas chromatography-mass spectrometry and other auxiliary examinations.Results 1.Gene mutation:7 gene mutations of MMACHC were identified in 7 patients.Seven mutations:c.482G ＞ A,c.567_568insT,c.609G ＞ A,c.440_441del,c.80A ＞ G,c.315C ＞ G,c.90G ＞ Awere screened.The mutation c.440_441del had not been reported before,and others were all related to the disease.Two gene mutations of mutase apoenzyme(MUT) were identified in 1 case,all of which were introns:.c.754-1G ＞ C,c.1677-1G ＞ A.The novel mutation was c.754-1G ＞ C.No gene mutation was identified in 1 patient.2.Clinical manifestation:all of the patients were development delay,but the degrees were different;3 patients with convulsion; 1 patient with headache and central facial paralysis;1 patient with repeated intractable metabolic acidosis;1 patient with repeated hemolysis.Electroencephalogram of the all patients were abnormal;the result of cranial MRI of the 8 patients were abnormal;In all patients,urine level of methylmalonic acid significantly increased (273.4-146 022.8 times).Blood homo cysteine of 8 patients were significantly increased(27.13-396.84 μmol/L,normal ＜ 20 μmol/L).3.Sanger sequencing:there were no false positive exists.Conclusions 1.There were not a correlation between the clinical manifestation and gene mutation of the patients with MMA.The c.609G ＞ A was the hotspot mutation of MMACHC gene in Chinese patients with MMA and homocysteinemia.2.The mutations c.440_441del and c.754-1G ＞ C were presumed to be novel mutations.3.Gene capture technology combined with next-generation sequencing technology could be used to interrogate the wealth of data available in the human genome and lay the foundations for counseling of gene.This platform can be readily and timely adopted by clinical molecular diagnosis of MMA and represents a high throughput,high sensitivity,high efficiency and other characteristics approach for screening common genetic diseases.

Molecular Analysis of Duchenne muscular dystrophy / 中华实用儿科临床杂志

Objective To detect the mutation type and size variation of the dystrophy gene in Duchenne muscular dystrophy(DMD) patients,and discuss the strategy of molecular genetic diagnosis for DMD.Methods Multiplex ligation-dependent probe amplification(MLPA) and next-generation sequencing(NGS) were applied for genetic detection in patients with clinical suspected DMD.Sanger sequencing was performed to confirm the results.Results Pathogenic mutations were found in 28 cases with DMD.Twenty-two of the 28 cases were found to be positive with MLPA analysis,16 cases with deletion mutations,4 cases with duplication,and 2 cases with both deletion and duplication mutations.Then,NGS technology was performed to detect 5 cases with MLPA positive and 1 case with MLPA negative,which were chosen optionally,and 3 cases showed deletion (exon51 del,chrX:31779857-31795289; exon53 del,chrX:31685440-31747548; exon51-55 del,chrX:31632504-31827732) and 2 cases of duplication (exon45 dup,chrX:31970766-32023816 ; exon55 dup,chrX:31540860-31649750),which were consistent with MLPA analysis.Meanwhile,NGS could determine the location of break point and the size of DNA segments accurately and also detect one point mutation which was MLPA negative.In the end,Sanger sequencing was performed to confirm this point mutation.Conclusions The mutational spectrum of the DMD gene is complex,including deletion/duplication and point mutations,and MLPA is an efficient method for detecting paternal deletion and duplication of DMD,while NGS can not only detect both deletion/duplication and point mutations,but also determine the location of break point and the size of gene segments accurately.Next-generation sequencing may be a powerful technology for early clinical diagnosis,prognostic judgment and prenatal diagnosis of DMD.

Buscando agujaseen un pajar: viajes de rnas pequeños in silico e in vitro / Finding for a Neadle in a Haystack: Trips of Small RNAs from in silico to in vitro

Lo que se conoce tradicionalmente como análisis del transcriptoma comprende la caracterización y cuantificación del conjunto de RNAs transcritos en la célula. En los primeros años, los estudios del transcriptoma se enfocaron principalmente a RNA mensajeros o RNA codificantes. Más recientemente, debido a avances en la tecnología de secuenciammiento de última generación, los estudios del transcriptoma se han extendido a RNAs no codificantes. Estas moléculas presentan gran variedad de funciones en la regulación celular. Una caracterización completa del conjunto de ncRNAs no es alcanzable con las aproximaciones disponibles. Hoy en día la identificación de RNAs no codificantes y de sus RNA pequeños derivados, es un tema de vital importancia en el análisis genético. Uno de los avances recientes en el estudio del transcriptoma por ejemplo, se enfoca en la biología de RNA de interferencia y su aplicación clínica. Durante los últimos años se han desarrollado continuamente la capacidad de cómputo, eficiencia y capacidad de almacenamiento para modelar y procesar grandes volúmenes de información producto de secuenciamiento de última generación. Como consecuencia, esta revisión presenta el análisis del transcriptoma desde una perspectiva histórica unida a la modelación computacional de RNA no codificantes de datos de bibliotecas de RNAs pequeños.

What is commonly known about transcriptome studies encompass the characterization and quantification of the complete set of RNA transcripts produced by a cell. In its early days these analysis mainly focused on examination of messenger RNAs or coding RNAs. More recently, due to advances in next-generation sequencing technologies, transcriptome analysis has expanded to non-conding RNAs (ncRNAs). These molecules exhibit high variety of functions in cell regulation. Through characterization of complete sets of ncRNAs is not attainable with current approaches. At present de novo identification of ncRNAs and ncRNA-derived small RNAs is a major issue in genetic analysis. One of the most important recent advances of transcriptome analysis focuses, for example, on RNA interference (RNAi) biology and its clinical application. High-performance computing, storage capability and computational modeling have been continuously developed during last years to process and model large amounts of products of next generation sequencing methods. As consequence this review describes transcriptome sequencing analysis from a historical perspective to its link to computational approaches to model ncRNAs from small RNA library data.

Detection of hydin Gene Duplication in Personal Genome Sequence Data

Human personal genome sequencing can be done with high efficiency by aligning a huge number of short reads derived from various next generation sequencing (NGS) technologies to the reference genome sequence. One of the major obstacles is the incompleteness of human reference genome. We tried to analyze the effect of hidden gene duplication on the NGS data using the known example of hydin gene. Hydin2 , a duplicated copy of hydin on chromosome 16q22, has been recently found to be localized to chromosome 1q21, and is not included in the current version of standard human genome reference. We found that all of eight personal genome data published so far do not contain hydin2, and there is large number of nsSNPs in hydin. The heterozygosity of those nsSNPs was significantly higher than expected. The sequence coverage depth in hydin gene was about two fold of average depth. We believe that these unique finding of hydin can be used as useful indicators to discover new hidden multiplication in human genome.