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| 1 | Next-generation sequencing technology:A technology review and future perspective显示文摘As one of the most powerful tools in biomedical research,DNA sequencing not only has been improving its productivity at an exponential growth rate but has also been evolving into a new layout of technological territories toward engineering and physical disciplines over the past three decades.In this technical review,we look into technical characteristics of the next-generation sequencers and provide insights into their future development and applications.We envisage that some of the emerging platforms are capable of supporting the USD1000 genome and USD100 genome goals if given a few years for technical maturation.We also suggest that scientists from China should play an active role in this campaign that will have a profound impact on both scientific research and societal healthcare systems. | ZHOU XiaoGuang1,REN LuFeng1,LI YunTao2,ZHANG Meng1,YU YuDe2 & YU Jun1 1 Key Laboratory of Genome Sciences and Information,Beijing Institute of Genomics,Chinese Academy of Sciences,Beijing 100029,China 2 Institute of Semiconductors,Chinese Academy of Sciences,Beijing 100083,China | 2010 | Science China(Life Sciences)2010，53，1： | 27 |
| 2 | Perspectives of DNA microarray and next-generation DNA sequencing technologies显示文摘DNA microarray and next-generation DNA sequencing technologies are important tools for high-throughput genome research,in revealing both the structural and functional characteristics of genomes.In the past decade the DNA microarray technologies have been widely applied in the studies of functional genomics,systems biology and pharmacogenomics.The next-generation DNA sequencing method was first introduced by the 454 Company in 2003,immediately followed by the establishment of the Solexa and Solid techniques by other biotech companies.Though it has not been long since the first emergence of this technology,with the fast and impressive improvement,the application of this technology has extended to almost all fields of genomics research,as a rival challenging the existing DNA microarray technology.This paper briefly reviews the working principles of these two technologies as well as their application and perspectives in genome research. | TENG XiaoKun1 & XIAO HuaSheng1,2 1 National Engineering Center for Biochip at Shanghai,Shanghai 201203,China 2 Shanghai-MOST Key Laboratory of Health and Disease Genomics,Chinese National Human Genome Center,Shanghai 201203,China | 2009 | Science China(Life Sciences)2009，52，1： | 15 |
| 3 | Review of current diagnostic methods and advances in Helicobacter pylori diagnostics in the era of next generation sequencing显示文摘Helicobacter pylori(H.pylori)infection is highly prevalent in the human population and may lead to severe gastrointestinal pathology including gastric and duodenal ulcers,mucosa associated tissue lymphoma and gastric adenocarcinoma.In recent years,an alarming increase in antimicrobial resistance and subsequently failing empiric H.pylori eradication therapies have been noted worldwide,also in many European countries.Therefore,rapid and accurate determination of H.pylori’s antibiotic susceptibility prior to the administration of eradication regimens becomes ever more important.Traditionally,detection of H.pylori and its antimicrobial resistance is done by culture and phenotypic drug susceptibility testing that are cumbersome with a long turn-around-time.Recent advances in diagnostics provide new tools,like real-time polymerase chain reaction(PCR)and line probe assays,to diagnose H.pylori infection and antimicrobial resistance to certain antibiotics,directly from clinical specimens.Moreover,high-throughput whole genome sequencing technologies allow the rapid analysis of the pathogen’s genome,thereby allowing identification of resistance mutations and associated antibiotic resistance.In the first part of this review,we will give an overview on currently available diagnostic methods for detection of H.pylori and its drug resistance and their implementation in H.pylori management.The second part of the review focusses on the use of next generation sequencing technology in H.pylori research.To this end,we conducted a literature search for original research articles in English using the terms“Helicobacter”,“transcriptomic”,“transcriptome”,“next generation sequencing”and“whole genome sequencing”.This review is aimed to bridge the gap between current diagnostic practice(histology,rapid urease test,H.pylori culture,PCR and line probe assays)and new sequencing technologies and their potential implementation in diagnostic laboratory settings in order to complement the currently recommended H.pylori management guidelines and subsequently improve public health. | Daniel Pohl Peter M Keller Valentine Bordier Karoline Wagner | 2019 | World Journal of Gastroenterology2019，25，32： | 15 |
| 4 | Piglet gut microbial shifts early in life:causes and effects显示文摘The gut microbiome has long been known to play fundamentally important roles in the animal health and the well-being of its host. As such, the establishment and maintenance of a beneficial gut microbiota early in life is crucial in pigs, since early gut colonizers are pivotal in the establishment of permanent microbial community structures affecting the health and growth performance of pigs later in life. Emphasizing this importance of early gut colonizers, it is critical to understand the factors impacting the establishment of the piglet gut microbiome at weaning. Factors include, among others, diet, in-feed antibiotics, probiotics and prebiotic administration. The impact of these factors on establishment of the gut microbiome of piglets at weaning includes effects on piglet gut microbial diversity, structure, and succession. In this review, we thoroughly reviewed the most recent findings on the piglet gut microbiome shifts as influenced by weaning, and how these microbiome changes brought about by various factors that have been shown to affect the development of microbiota in piglets. This review will provide a general overview of recent studies that can help to facilitate the design of new strategies to modulate the gut microbiome in order to enhance gastrointestinal health, growth performance and well-being of piglets. | Robin B.Guevarra Jun Hyung Lee Sun Hee Lee Min-Jae Seok Doo Wan Kim Bit Na Kang Timothy J.Johnson Richard E.Isaacson Hyeun Bum Kim | 2019 | Journal of Animal Science and Biotechnology2019，10，3： | 13 |
| 5 | Quasispecies structure,cornerstone of hepatitis B virus infection: Mass sequencing approach显示文摘Hepatitis B virus(HBV)is a DNA virus with complex replication,and high replication and mutation rates,leading to a heterogeneous viral population.The population is comprised of genomes that are closely related,but not identical;hence,HBV is considered a viral quasispecies.Quasispecies variability may be somewhat limited by the high degree of overlapping between the HBV coding regions,which is especially important in the P and S gene overlapping regions,but is less significant in the X and preCore/Core genes.Despite this restriction,several clinically and pathologically relevant variants have been characterized along the viral genome.Next-generation sequencing(NGS)approaches enable high-throughput analysis of thousands of clonally amplified regions and are powerful tools for characterizing genetic diversity in viral strains.In the present review,we update the information regarding HBV variability and present a summary of the various NGS approaches available for research in this virus.In addition,we provide an analysis of the clinical implications of HBV variants and their study by NGS. | Francisco Rodriguez-Frias Maria Buti David Tabernero Maria Homs | 2013 | World Journal of Gastroenterology2013，19，41： | 11 |
| 6 | High throughput RNA sequencing utility for diagnosis and prognosis in colon diseases显示文摘RNA sequencing is the use of hight hroughput next generation sequencing technology to survey, characterize, and quantify the transcriptome of a genome. RNA sequencing has been used to analyze the pathogenesis of several malignancies such melanoma, lung cancer, and colorectal cancer. RNA sequencing can identify differential expression of genes(DEG's), mutated genes, fusion genes, and gene isoforms in disease states. RNA sequencing has been used in the investigation of several colorectal diseases such as colorectal cancer, inflammatory bowel disease(ulcerative colitis and Crohn's disease), and irritable bowel syndrome. | Mamie Gao Allen Zhong Neil Patel Chiraag Alur Dinesh Vyas | 2017 | World Journal of Gastroenterology2017，23，16： | 4 |
| 7 | Next generation sequencing reveals co-existence of hereditary spherocytosis and Dubin–Johnson syndrome in a Chinese gril: A case report显示文摘BACKGROUND Hereditary spherocytosis(HS)is a hereditary disease of hemolytic anemia that occurs due to the erythrocyte membrane defects.Dubin–Johnson syndrome(DJS),which commonly results in jaundice,is a benign hereditary disorder of bilirubin clearance that occurs only rarely.The co-occurrence of HS and DJS is extremely rare.We recently diagnosed and treated a case of co-occurring HS and DJS.CASE SUMMARY A 21-year-old female patient presented to our department because of severe jaundice,severe splenomegaly,and mild anemia since birth.We eventually confirmed the diagnosis of co-occurring DJS and HS by next generation sequencing(NGS).The treatment of ursodeoxycholic acid in combination with phenobarbital successfully increased hemoglobin and reduced total bilirubin and direct bilirubin.CONCLUSION The routine application of NGS can efficiently render a definite diagnosis when inherited disorders are suspected. | Yuan Li Yang Li Yang Yang Wen-Rui Yang Jian-Ping Li Guang-Xin Peng Lin Song Hui-Hui Fan Lei Ye You-Zhen Xiong Zhi-Jie Wu Kang Zhou Xin Zhao Li-Ping Jing Feng-Kui Zhang Li Zhang | 2019 | World Journal of Clinical Cases2019，7，20： | 3 |
| 8 | A novel PIK3CD C896T mutation detected in bilateral sudden sensorineural hearing loss using next generation sequencing:An indication of primary immunodeficiency显示文摘Objective: To investigate immune-related genetic background in bilateral sudden sensorineural hearing loss(SSNHL).Case report and methods: The case is a 45-year-old man presenting with a 7-year history of bilateral profound SSNHL. Blood biochemical testing demonstrated increased levels of total cholesterol(5.88 mmol/L). Tests for hepatitis B showed a positive antibody against the hepatitis B core antigen. Complement C3 was below the normal value, and complement C4 and Ig G were in the lower range of normal values. CT images showed a normal inner ear and vestibular aqueduct but round window membranous ossification on both sides. A total number of 232 immuneassociated genes were sequenced using the next generation sequencing technique.Results: Mutations were detected in 5 genes, including the phosphoinositide 3-kinase catalytic subunit delta(PIK3CD), caspase recruitment domain-containing protein 9(CARD9), complement factor H-related(CFHR2), immunoglobulin lambda-like polypeptide 1 Protein(IGLL1),and transmembrane channel-like gene family 8(TMC8). In the PIK3 CD gene, a C896 T substitute in exon 7 was detected. This mutation causes primary immunodeficiency and is an autosomal dominant disease.Conclusion: The PIK3 CD C896T mutation responsible for primary immunodeficiency may contribute to the onset of bilateral SSNHL with subsequent rapid progression. | Jing Zou Xiangqiang Duan Guiliang Zheng Zhen Zhao Shiyue Chen Pu Dai Hongliang Zheng | 2016 | Journal of Otology2016，11，2： | 3 |
| 9 | Confocal endomicroscopy and cyst fluid molecular analysis: Comprehensive evaluation of pancreatic cysts显示文摘Increases in the quality as well as utilization of cross-sectional imaging have led to rising diagnoses of pancreatic cystic lesions(PCL). Accurate presurgical diagnosis enables appropriate triage of PCLs. Unfortunately, current diagnostic approaches have suboptimal accuracy and may lead to unnecessary surgical resections or missed diagnoses of advanced neoplasia. Additionally, early detection represents an opportunity for intervention to prevent the progression to pancreatic adenocarcinoma. Our aim for this review is to systematically review the current literature on confocal endomicroscopy and molecular biomarkers in the evaluation of PCLs. Confocal laser endomicroscopy is a novel technology that allows for real-time in vivo microscopic imaging with multiple clinical trials identifying characteristic endomicroscopy findings of various pancreatic cystic lesions. DNA-based molecular markers have also emerged as another diagnostic modality as the pattern of genetic alternations present in cyst fluid can provide both diagnostic and prognostic data. We propose that both techniques can be utilized to improve patient outcomes. | Feng Li Ahmad Malli Zobeida Cruz-Monserrate Darwin L Conwell Somashekar G Krishna | 2018 | World Journal of Gastrointestinal Endoscopy2018，10，1： | 2 |
| 10 | Next generation sequencing in cardiovascular diseases显示文摘In the last few years,the advent of next generation sequencing(NGS) has revolutionized the approach to genetic studies,making whole-genome sequencing a possible way of obtaining global genomic information.NGS has very recently been shown to be successful in identifying novel causative mutations of rare or common Mendelian disorders.At the present time,it is expected that NGS will be increasingly important in the study of inherited and complex cardiovascular diseases(CVDs).However,the NGS approach to the genetics of CVDs represents a territory which has not been widely investigated.The identification of rare and frequent genetic variants can be very important in clinical practice to detect pathogenic mutations or to establish a profile of risk for the development of pathology.The purpose of this paper is to discuss the recent application of NGS in the study of several CVDs such as inherited cardiomyopathies,channelopathies,coronary artery disease and aortic aneurysm.We also discuss the future utility and challenges related to NGS in studying the genetic basis of CVDs in order to improve diagnosis,prevention,and treatment. | Francesca Faita Cecilia Vecoli Ilenia Foffa Maria Grazia Andreassi | 2012 | World Journal of Cardiology2012，4，10： | 2 |
| 11 | Novel frameshift mutation in the SACS gene causing spastic ataxia of charlevoix-saguenay in a consanguineous family from the Arabian Peninsula:A case report and review of literature显示文摘BACKGROUND Familial cases of autosomal recessive spastic ataxia of charlevoix-saguenay have not been reported in the Arabian Peninsula,although the consanguineous marriage rate is very high.We report the first family from the Arabian Peninsula harboring a novel frameshift mutation in the SACS gene.CASE SUMMARY A 33-year-old man presented to our neurology clinic with balance problems and weakness of distal upper and lower limbs.He was previously clinically diagnosed with Friedreich's ataxia.However,the severity of polyneuropathy and the electrodiagnostic studies(EDX)findings are atypical features of Friedreich’s ataxia,and the deterioration was attributed to diabetic neuropathy.Close examination of other family members identified cerebellar ataxia,lower-limb pyramidal signs,peripheral neuropathy,and magnetic resonance imaging findings characterized by pontine linear hypointensities.Genetic testing for Friedreich’s ataxia did not yield a diagnosis.Whole exome sequencing identified a novel frameshift germline mutation in the SACS gene termed c.5824_5827delTACT using the transcript NM_014363.5,which is predicted to cause premature termination of the sacsin protein at amino acid position 1942(p.Tyr1942Metfs*9)and disrupts the sacsin SRR3 and domains downstream from it.The mutation segregated with the disease in the family.CONCLUSION Our data add to the spectrum of mutations in the SACS gene and argues for a need to implement suitably integrated clinical and diagnostic services,including next generation sequencing technology,to better classify ataxia in this area of the world. | Abdullah Al-Ajmi Sarah Shamsah Aleksandar Janicijevic Michayla Williams Fahd Al-Mulla | 2020 | World Journal of Clinical Cases2020，8，8： | 2 |
| 12 | Integrative molecular characterization of Chinese prostate cancer specimens显示文摘Prostate cancer(PCa)exhibits epidemiological and molecular heterogeneity.Despite extensive studies of its phenotypic and genetic properties in Western populations,its molecular basis is not clear in Chinese patients.To determine critical molecular characteristics and explore correlations between genomic markers and clinical parameters in Chinese populations,we applied an integrative genetic/transcriptomic assay that combines targeted next-generation sequencing and quantitative real-time PCR(qRT-PCR)on samples from 46 Chinese patients with PCa.Lysine(K)-specific methyltransferase 2D(KMT2D),zinc finger homeobox 3(ZFHX3),A-kinase anchoring protein 9(AKAP9),and GLI family zinc finger 1(GLI1)were frequently mutated in our cohort.Moreover,a clinicopathological analysis showed that RB transcriptional corepressor 1(RB1)deletion was common in patients with a high risk of disease progression.Remarkably,four genomic events,MYC proto-oncogene(MYC)amplification,RB1 deletion,APC regulator of WNT signaling pathway(APC)mutation or deletion,and cyclin-dependent kinase 12(CDK12)mutation,were correlated with poor disease-free survival.In addition,a close link between KMT2D expression and the androgen receptor(AR)signaling pathway was observed both in our cohort and in The Cancer Genome Atlas Prostate Adenocarcinoma(TCGA-PRAD)data.In summary,our results demonstrate the feasibility and benefits of integrative molecular characterization of PCa samples in disease pathology research and personalized medicine. | Shi-Dong Lv Hong-Yi Wang Xin-Pei Yu Qi-Liang Zhai Yao-Bin Wu Qiang Wei Wen-Hua Huang | 2020 | Asian Journal of Andrology2020，22，2： | 1 |
| 13 | Metagenomic comparison of the rectal microbiota between rhesus macaques(Macaca mulatta) and cynomolgus macaques(Macaca fascicularis)显示文摘Rhesus macaques(Macaca mulatta) and cynomolgus macaques(Macaca fascicularis) are frequently used in establishing animal models for human diseases. To determine the differences in gut microbiota between these species, rectal swabs from 20 rhesus macaques and 21 cynomolgus macaques were collected, and the microbial composition was examined by deep sequencing of the 16 S rR NA gene. We found that the rectal microbiota of cynomolgus macaques exhibited significantly higher alpha diversity than that of rhesus macaques, although the observed number of operational taxonomic units(OTUs) was almost the same. The dominant taxa at both the phylum and genus levels were similar between the two species, although the relative abundances of these dominant taxa were significantly different between them. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States(PICRUSt) showed significant differences in the functional components between the microbiota of the two species, in particular the lipopolysaccharide(LPS) synthesis proteins. The above data indicated significant differences in microbial composition and function between these two closely related macaque species, which should be taken into consideration in the future selection of these animals for disease models. | Yan-Fang Cui Feng-Jie Wang Lei Yu Hua-Hu Ye Gui-Bo Yang | 2019 | Zoological Research2019，40，2： | 1 |
| 14 | Novel mutations in PDE6B causing human retinitis pigmentosa显示文摘AIM: To identify the genetic defects of a Chinese patient with sporadic retinitis pigmentosa(RP).METHODS: Ophthalmologic examinations were performed on the sporadic RP patient, 144 genes associated with retinal diseases were scanned with capture next generation sequencing(CNGS) approach.Two heterozygous mutations in PDE6B were confirmed in the pedigree by Sanger sequencing subsequently. The carrier frequency of PDE6B mutations of reported PDE6B mutations based on the available two public exome databases(1000 Genomes Project and ESP6500 Genomes Project) and one in-house exome database was investigated.RESULTS: We identified compound heterozygosity of two novel nonsense mutations c.1133G>A(p.W378X) and c.2395C>T(p.R799X) in PDE6B, one reported causative gene for RP. Neither of the two mutations in our study was presented in three exome databases. Two mutations(p.R74 C and p.T604I) in PDE6B have relatively high frequencies in the ESP6500 and in-house databases,respectively, while no common dominant mutation in each of the database or across all databases.CONCLUSION: We demonstrates that compound heterozygosity of two novel nonsense mutations in PDE6B could lead to RP. These results collectively point to enormous potential of next-generation sequencing in determining the genetic etiology of RP and how various mutations in PDE6B contribute to the genetic heterogeneity of RP. | Lu-Lu Cheng Ru-Yi Han Fa-Yu Yang Xin-Ping Yu Jin-Ling Xu Qing-Jie Min Jie Tian Xiang-Lian Ge Si-Si Zheng Ye-Wen Lin Yi-Han Zheng Jia Qu Feng Gu | 2016 | International Journal of Ophthalmology(English edition)2016，9，8： | 1 |
| 15 | Large scale identification of SSR marker in perilla by next generation sequencing显示文摘Perilla frutescens (L.) is an edible, medicinal crop, and most popular in East Asia. Its molecular breeding and research are hampered by the paucity of molecular markers. Simple sequence repeat (SSR) markers are ubiquitous and widely used in eukaryotic genomes. EST-SSRs identification of perilla was performed in 116,387 reads generated by Illumina paired-end sequencing technology. In total 25,449 unigenes containing SSR and 33,867 SSR loci were identified, and 19,400 primer pairs were designed. Polymorphism of SSR primers was conducted by searching for insertions and deletions (INDELs), and 1,567 unique SSRs were predicted. Totally, 200 SSR primer pairs were selected for polymorphic validation among 23 perilla accessions. Results showed that 175 primer pairs produced amplicons, and 30 pairs exhibited polymorphism. Polymorphic ratio was higher by using INDEL method than using conventional primers. Phylogenetic analysis showed the 2 distinct groups: P. frutescens var. frutescens and P. frutescens var. crispa. Wrinkled leaf trait and seed trait were distinct between these 2 groups. However, no clear leaf color or geographic relationship was detected. The large scale development and identification of SSR marker in this research laid a foundation for genetic analysis and marker assisted breeding of cultivated perilla. | Qi Shen He Wen Tianyuan Zhang Jing Xu Xianping Wang Shimei Yang Caifu Du Degang Zhao | 2019 | Oil Crop Science2019，4，2： | 1 |
| 16 | Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine显示文摘High-throughput next generation sequencing (NGS) is a shotgun approach applied in a parallel fashion by which the genome is fragmented and sequenced through small pieces and then analyzed either by aligning to a known reference genome or by de novo assembly without reference genome.This technology has led researchers to conduct an explosion of sequencing related projects in multidisciplinary fields of science.However,due to the limitations of sequencing-based chemistry,length of sequencing reads and the complexity of genes,it is difficult to determine the sequences of some portions of the human genome,leaving gaps in genomic data that frustrate further analysis.Particularly,some complex genes are difficult to be accurately sequenced or mapped because they contain high GC-content and/or low complexity regions,and complicated pseudogenes,such as the genes encoding xenobiotic metabolizing enzymes and transporters (XMETs).The genetic variants in XMET genes are critical to predicate interindividual variability in drug efficacy,drug safety and susceptibility to environmental toxicity.We summarized and discussed challenges,wet-lab methods,and bioinformatics algorithms in sequencing 'complex' XMET genes,which may provide insightful information in the application of NGS technology for implementation in toxicogenomics and pharmacogenomics. | Yaqiong Jin Geng Chen Wenming Xiao Huixiao Hong Joshua Xu Yongli Guo Wenzhong Xiao Tieliu Shi Leming Shi Weida Tong Baitang Ning | 2019 | Science China(Life Sciences)2019，62，7： | 1 |
| 17 | Mesenchymal stem cells: A new diagnostic tool?显示文摘Mesenchymal stem cells(MSCs) are progenitor cells capable of self-renewal that can differentiate in multiple tissues and, under specific and standardizedculture conditions, expand in vitro with little phenotypic alterations. In recent years, preclinical and clinical studies have focused on MSC analysis and understanding the potential use of these cells as a therapy in a wide range of pathologies, and many applications have been tested. Clinical trials using MSCs have been performed(e.g., for cardiac events, stroke, multiple sclerosis, blood diseases, auto-immune disorders, ischemia, and articular cartilage and bone pathologies), and for many genetic diseases, these cells are considered an important resource. Considering of the biology of MSCs, these cells may also be useful tools for understanding the physiopathology of different diseases, and they can be used to develop specific biomarkers for a broad range of diseases. In this editorial, we discuss the literature related to the use of MSCs for diagnostic applications and we suggest new technologies to improve their employment. | Maria Teresa Valenti Antonio Mori Giovanni Malerba Luca Dalle Carbonare | 2015 | World Journal of Stem Cells2015，7，5： | 0 |
| 18 | Artificially designed pathogens – a diagnostic option for future military deployments显示文摘Background: Diagnostic microbial isolates of bio-safety levels 3 and 4 are difficult to handle in medical field camps under military deployment settings. International transport of such isolates is challenging due to restrictions by the International Air Transport Association. An alternative option might be inactivation and sequencing of the pathogen at the deployment site with subsequent sequence-based revitalization in well-equipped laboratories in the home country for further scientific assessment. Methods: A literature review was written based on a Pub Med search. Results: First described for poliovirus in 2002, de novo synthesis of pathogens based on their sequence information has become a well-established procedure in science. Successful syntheses have been demonstrated for both viruses and prokaryotes. However, the technology is not yet available for routine diagnostic purposes. Conclusions: Due to the potential utility of diagnostic sequencing and sequence-based de novo synthesis of pathogens, it seems worthwhile to establish the technology for diagnostic purposes over the intermediate term. This is particularly true for resource-restricted deployment settings, where safe handling of harmful pathogens cannot always be guaranteed. | Andreas E.Zautner Wyclif e O.Masanta Rebecca Hinz Ralf Matthias Hagen Hagen Frickmann | 2015 | Journal of Medical Colleges of PLA(China)2015，30，2： | 0 |
| 19 | A novel PKHD1 mutation identified in a family affected by ARPKD显示文摘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://gffzz7ae24db238c44b66h6ouqp5nco9b66vqw.ffgz.tsg.suse.edu.cn) 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. | Ling Hou Yue Du Chengguang Zhao Yubin Wu | 2018 | Journal of Pediatric Diseases2018，2，1： | 0 |
| 20 | Development of Starfruit Simple Sequence Repeat (SSR) Using Next Generation Sequencing显示文摘Starfruit (Averrhoa carambola L.) is an important fruit for Malaysian export and great attention has been made to improve starfruit fruit quality at Malaysian Agricultural Research and Development Institute (MARDI). The current study used next generation sequencing (NGS) technologies to develop starfruit simple sequence repeat (SSR) from 2 varieties namely B11 and B17 using Illumina HiSeq. The pre-processed reads were de novo assembled to generate approximately 75,000 and 74,000 scaffolds respectively. Total genome size for B11 and B17 were around 345 Mbp and 342 Mbp based on K-mer distribution analysis. In-silico microsatellite mining of each variety has identified more than 17,000 SSR in B11 and B17 respectively. Dinucleotides were the most abundant, accounting for more than 70% of all SSR and repeat motif GA (49%) was most common. A total of 239 SSR primer pairs were designed from contigs larger than 350 nucleotides and tested for amplification. The 30 polymorphic SSRs were used to DNA fingerprint of 12 starfruit hybrids. Polymorphism information content (PIC) ranged from 0.1411 to 0.6838, with an average of 0.3919. The Unweighted Pair-Group Method for Arithmetic Averages (UPGMA) dendrogram clustered 12 starfruit accessions into 2 groups. | Khairun Hisam Nasir Muhammad Fairuz Mohd Yusof Mohd Shahril Firdaus Siti Zainab Jantan Mira Farzana Mohamad Moktar Siti Norsaidah Ibrahim Noor Baiti Abdul Aziz Joanna Cho Lee Ying | 2019 | Journal of Food Science and Engineering2019，9，3： | 0 |
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