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Exome sequencing for simultaneous mutation screening in children with hemophagocytic lymphohistiocytosis
In the present study, we used exome sequencing to analyze PRF1, UNC13D, STX11, and STXBP2, as well as genes associated with primary immunodeficiency disease (RAB27A, LYST, AP3B1, SH2D1A, ITK, CD27, XIAP, and MAGT1) in Thai children with hemophagocytic lymphohistiocytosis (HLH). We performed mutation...
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Published in: | International journal of hematology 2017-08, Vol.106 (2), p.282-290 |
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creator | Mukda, Ekchol Trachoo, Objoon Pasomsub, Ekawat Tiyasirichokchai, Rawiphorn Iemwimangsa, Nareenart Sosothikul, Darintr Chantratita, Wasun Pakakasama, Samart |
description | In the present study, we used exome sequencing to analyze PRF1, UNC13D, STX11, and STXBP2, as well as genes associated with primary immunodeficiency disease (RAB27A, LYST, AP3B1, SH2D1A, ITK, CD27, XIAP, and MAGT1) in Thai children with hemophagocytic lymphohistiocytosis (HLH). We performed mutation analysis of HLH-associated genes in 25 Thai children using an exome sequencing method. Genetic variations found within these target genes were compared to exome sequencing data from 133 healthy individuals. Variants identified with minor allele frequencies |
doi_str_mv | 10.1007/s12185-017-2223-3 |
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n
= 1), likely pathogenic (
n
= 16), variant of unknown significance (
n
= 12), or benign variant (
n
= 72). Homozygous, compound heterozygous, and double-gene heterozygous variants, involving mutations in PRF1 (
n
= 3), UNC13D (
n
= 2), STXBP2 (
n
= 3), LYST (
n
= 3), XIAP (
n
= 2), AP3B1 (
n
= 1), RAB27A (
n
= 1), and MAGT1 (
n
= 1), were demonstrated in 12 patients. Novel mutations were found in most patients in this study. In conclusion, exome sequencing demonstrated the ability to identify rare genetic variants in HLH patients. This method is useful in the detection of mutations in multi-gene associated diseases.</description><identifier>ISSN: 0925-5710</identifier><identifier>EISSN: 1865-3774</identifier><identifier>DOI: 10.1007/s12185-017-2223-3</identifier><identifier>PMID: 28353193</identifier><language>eng</language><publisher>Tokyo: Springer Japan</publisher><subject>Benign ; CD27 antigen ; Child ; Children ; DNA Mutational Analysis - methods ; Exome - genetics ; Gene frequency ; Gene sequencing ; Genes ; Genetic Association Studies ; Genetic diversity ; Genetic Testing - methods ; Hematology ; Histiocytosis ; Humans ; Immunodeficiency ; Indexing ; Itk protein ; Lymphatic diseases ; Lymphocytosis ; Lymphohistiocytosis, Hemophagocytic - diagnosis ; Lymphohistiocytosis, Hemophagocytic - genetics ; Medical diagnosis ; Medical screening ; Medicine ; Medicine & Public Health ; Membrane Proteins - genetics ; Molecular Diagnostic Techniques ; Multigene Family - genetics ; Mutation ; Oncology ; Original Article ; Patients ; Perforin - genetics ; Polymorphism, Single Nucleotide ; Primary immunodeficiencies ; Qa-SNARE Proteins - genetics ; rab GTP-Binding Proteins - genetics ; rab27 GTP-Binding Proteins ; Sequence Analysis, DNA - methods ; SH2D1A protein ; Single-nucleotide polymorphism ; Vesicular Transport Proteins - genetics ; XIAP protein</subject><ispartof>International journal of hematology, 2017-08, Vol.106 (2), p.282-290</ispartof><rights>The Japanese Society of Hematology 2017</rights><rights>International Journal of Hematology is a copyright of Springer, 2017.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c396t-afa1a23d441484f9fb1bfb3371d57c53d4780e2539cab73d0e0979fcfa45686f3</citedby><cites>FETCH-LOGICAL-c396t-afa1a23d441484f9fb1bfb3371d57c53d4780e2539cab73d0e0979fcfa45686f3</cites><orcidid>0000-0001-8118-163X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27922,27923</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28353193$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mukda, Ekchol</creatorcontrib><creatorcontrib>Trachoo, Objoon</creatorcontrib><creatorcontrib>Pasomsub, Ekawat</creatorcontrib><creatorcontrib>Tiyasirichokchai, Rawiphorn</creatorcontrib><creatorcontrib>Iemwimangsa, Nareenart</creatorcontrib><creatorcontrib>Sosothikul, Darintr</creatorcontrib><creatorcontrib>Chantratita, Wasun</creatorcontrib><creatorcontrib>Pakakasama, Samart</creatorcontrib><title>Exome sequencing for simultaneous mutation screening in children with hemophagocytic lymphohistiocytosis</title><title>International journal of hematology</title><addtitle>Int J Hematol</addtitle><addtitle>Int J Hematol</addtitle><description>In the present study, we used exome sequencing to analyze PRF1, UNC13D, STX11, and STXBP2, as well as genes associated with primary immunodeficiency disease (RAB27A, LYST, AP3B1, SH2D1A, ITK, CD27, XIAP, and MAGT1) in Thai children with hemophagocytic lymphohistiocytosis (HLH). We performed mutation analysis of HLH-associated genes in 25 Thai children using an exome sequencing method. Genetic variations found within these target genes were compared to exome sequencing data from 133 healthy individuals. Variants identified with minor allele frequencies <5% and novel mutations were confirmed using Sanger sequencing. Exome sequencing data revealed 101 non-synonymous single nucleotide polymorphisms (SNPs) in all subjects. These SNPs were classified as pathogenic (
n
= 1), likely pathogenic (
n
= 16), variant of unknown significance (
n
= 12), or benign variant (
n
= 72). Homozygous, compound heterozygous, and double-gene heterozygous variants, involving mutations in PRF1 (
n
= 3), UNC13D (
n
= 2), STXBP2 (
n
= 3), LYST (
n
= 3), XIAP (
n
= 2), AP3B1 (
n
= 1), RAB27A (
n
= 1), and MAGT1 (
n
= 1), were demonstrated in 12 patients. Novel mutations were found in most patients in this study. In conclusion, exome sequencing demonstrated the ability to identify rare genetic variants in HLH patients. This method is useful in the detection of mutations in multi-gene associated diseases.</description><subject>Benign</subject><subject>CD27 antigen</subject><subject>Child</subject><subject>Children</subject><subject>DNA Mutational Analysis - methods</subject><subject>Exome - genetics</subject><subject>Gene frequency</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic Association Studies</subject><subject>Genetic diversity</subject><subject>Genetic Testing - methods</subject><subject>Hematology</subject><subject>Histiocytosis</subject><subject>Humans</subject><subject>Immunodeficiency</subject><subject>Indexing</subject><subject>Itk protein</subject><subject>Lymphatic diseases</subject><subject>Lymphocytosis</subject><subject>Lymphohistiocytosis, Hemophagocytic - diagnosis</subject><subject>Lymphohistiocytosis, Hemophagocytic - genetics</subject><subject>Medical diagnosis</subject><subject>Medical screening</subject><subject>Medicine</subject><subject>Medicine & Public Health</subject><subject>Membrane Proteins - genetics</subject><subject>Molecular Diagnostic Techniques</subject><subject>Multigene Family - genetics</subject><subject>Mutation</subject><subject>Oncology</subject><subject>Original Article</subject><subject>Patients</subject><subject>Perforin - genetics</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Primary immunodeficiencies</subject><subject>Qa-SNARE Proteins - genetics</subject><subject>rab GTP-Binding Proteins - genetics</subject><subject>rab27 GTP-Binding Proteins</subject><subject>Sequence Analysis, DNA - methods</subject><subject>SH2D1A protein</subject><subject>Single-nucleotide polymorphism</subject><subject>Vesicular Transport Proteins - genetics</subject><subject>XIAP protein</subject><issn>0925-5710</issn><issn>1865-3774</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><recordid>eNp1kU-LFDEQxYMo7rjrB_AiAS97aU3lzyQ5yrKuwoIX9xzS6WQ6S3cyJt3ofHsz9CoieCpI_d6rVD2E3gB5D4TIDxUoKNERkB2llHXsGdqB2ouOScmfox3RVHRCArlAr2p9JA0kXL5EF1QxwUCzHRpvf-bZ4-q_rz65mA445IJrnNdpscnnteJ5XewSc8LVFe_TmYkJuzFOQ_EJ_4jLiEc_5-NoD9mdlujwdJqPYx5jbbr2kmusV-hFsFP1r5_qJXr4dPvt5nN3__Xuy83H-84xvV86GyxYygbOgSsedOihDz1jEgYhnWgNqYingmlne8kG4omWOrhgudirfWCX6HrzPZbcdqqLmWN1fpq2bQwoRYnUhEND3_2DPua1pPY7AxoU1ZLrMwUb5UqutfhgjiXOtpwMEHOOwWwxmHZdc47BsKZ5--S89rMf_ih-370BdANqa6WDL3-N_q_rL64OlNw</recordid><startdate>20170801</startdate><enddate>20170801</enddate><creator>Mukda, Ekchol</creator><creator>Trachoo, Objoon</creator><creator>Pasomsub, Ekawat</creator><creator>Tiyasirichokchai, Rawiphorn</creator><creator>Iemwimangsa, Nareenart</creator><creator>Sosothikul, Darintr</creator><creator>Chantratita, Wasun</creator><creator>Pakakasama, Samart</creator><general>Springer Japan</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7RV</scope><scope>7T5</scope><scope>7T7</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>BENPR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>H94</scope><scope>K9.</scope><scope>KB0</scope><scope>M0S</scope><scope>M1P</scope><scope>NAPCQ</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-8118-163X</orcidid></search><sort><creationdate>20170801</creationdate><title>Exome sequencing for simultaneous mutation screening in children with hemophagocytic lymphohistiocytosis</title><author>Mukda, Ekchol ; Trachoo, Objoon ; Pasomsub, Ekawat ; Tiyasirichokchai, Rawiphorn ; Iemwimangsa, Nareenart ; Sosothikul, Darintr ; Chantratita, Wasun ; Pakakasama, Samart</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c396t-afa1a23d441484f9fb1bfb3371d57c53d4780e2539cab73d0e0979fcfa45686f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Benign</topic><topic>CD27 antigen</topic><topic>Child</topic><topic>Children</topic><topic>DNA Mutational Analysis - methods</topic><topic>Exome - genetics</topic><topic>Gene frequency</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genetic Association Studies</topic><topic>Genetic diversity</topic><topic>Genetic Testing - methods</topic><topic>Hematology</topic><topic>Histiocytosis</topic><topic>Humans</topic><topic>Immunodeficiency</topic><topic>Indexing</topic><topic>Itk protein</topic><topic>Lymphatic diseases</topic><topic>Lymphocytosis</topic><topic>Lymphohistiocytosis, Hemophagocytic - diagnosis</topic><topic>Lymphohistiocytosis, Hemophagocytic - genetics</topic><topic>Medical diagnosis</topic><topic>Medical screening</topic><topic>Medicine</topic><topic>Medicine & Public Health</topic><topic>Membrane Proteins - genetics</topic><topic>Molecular Diagnostic Techniques</topic><topic>Multigene Family - genetics</topic><topic>Mutation</topic><topic>Oncology</topic><topic>Original Article</topic><topic>Patients</topic><topic>Perforin - genetics</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Primary immunodeficiencies</topic><topic>Qa-SNARE Proteins - genetics</topic><topic>rab GTP-Binding Proteins - genetics</topic><topic>rab27 GTP-Binding Proteins</topic><topic>Sequence Analysis, DNA - methods</topic><topic>SH2D1A protein</topic><topic>Single-nucleotide polymorphism</topic><topic>Vesicular Transport Proteins - genetics</topic><topic>XIAP protein</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mukda, Ekchol</creatorcontrib><creatorcontrib>Trachoo, Objoon</creatorcontrib><creatorcontrib>Pasomsub, Ekawat</creatorcontrib><creatorcontrib>Tiyasirichokchai, Rawiphorn</creatorcontrib><creatorcontrib>Iemwimangsa, Nareenart</creatorcontrib><creatorcontrib>Sosothikul, Darintr</creatorcontrib><creatorcontrib>Chantratita, Wasun</creatorcontrib><creatorcontrib>Pakakasama, Samart</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Nursing & Allied Health Database (ProQuest)</collection><collection>Immunology Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Health & Medical Collection (ProQuest Medical & Health Databases)</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Nursing & Allied Health Premium</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>MEDLINE - Academic</collection><jtitle>International journal of hematology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mukda, Ekchol</au><au>Trachoo, Objoon</au><au>Pasomsub, Ekawat</au><au>Tiyasirichokchai, Rawiphorn</au><au>Iemwimangsa, Nareenart</au><au>Sosothikul, Darintr</au><au>Chantratita, Wasun</au><au>Pakakasama, Samart</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Exome sequencing for simultaneous mutation screening in children with hemophagocytic lymphohistiocytosis</atitle><jtitle>International journal of hematology</jtitle><stitle>Int J Hematol</stitle><addtitle>Int J Hematol</addtitle><date>2017-08-01</date><risdate>2017</risdate><volume>106</volume><issue>2</issue><spage>282</spage><epage>290</epage><pages>282-290</pages><issn>0925-5710</issn><eissn>1865-3774</eissn><abstract>In the present study, we used exome sequencing to analyze PRF1, UNC13D, STX11, and STXBP2, as well as genes associated with primary immunodeficiency disease (RAB27A, LYST, AP3B1, SH2D1A, ITK, CD27, XIAP, and MAGT1) in Thai children with hemophagocytic lymphohistiocytosis (HLH). We performed mutation analysis of HLH-associated genes in 25 Thai children using an exome sequencing method. Genetic variations found within these target genes were compared to exome sequencing data from 133 healthy individuals. Variants identified with minor allele frequencies <5% and novel mutations were confirmed using Sanger sequencing. Exome sequencing data revealed 101 non-synonymous single nucleotide polymorphisms (SNPs) in all subjects. These SNPs were classified as pathogenic (
n
= 1), likely pathogenic (
n
= 16), variant of unknown significance (
n
= 12), or benign variant (
n
= 72). Homozygous, compound heterozygous, and double-gene heterozygous variants, involving mutations in PRF1 (
n
= 3), UNC13D (
n
= 2), STXBP2 (
n
= 3), LYST (
n
= 3), XIAP (
n
= 2), AP3B1 (
n
= 1), RAB27A (
n
= 1), and MAGT1 (
n
= 1), were demonstrated in 12 patients. Novel mutations were found in most patients in this study. In conclusion, exome sequencing demonstrated the ability to identify rare genetic variants in HLH patients. This method is useful in the detection of mutations in multi-gene associated diseases.</abstract><cop>Tokyo</cop><pub>Springer Japan</pub><pmid>28353193</pmid><doi>10.1007/s12185-017-2223-3</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0001-8118-163X</orcidid></addata></record> |
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language | eng |
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source | Springer Nature |
subjects | Benign CD27 antigen Child Children DNA Mutational Analysis - methods Exome - genetics Gene frequency Gene sequencing Genes Genetic Association Studies Genetic diversity Genetic Testing - methods Hematology Histiocytosis Humans Immunodeficiency Indexing Itk protein Lymphatic diseases Lymphocytosis Lymphohistiocytosis, Hemophagocytic - diagnosis Lymphohistiocytosis, Hemophagocytic - genetics Medical diagnosis Medical screening Medicine Medicine & Public Health Membrane Proteins - genetics Molecular Diagnostic Techniques Multigene Family - genetics Mutation Oncology Original Article Patients Perforin - genetics Polymorphism, Single Nucleotide Primary immunodeficiencies Qa-SNARE Proteins - genetics rab GTP-Binding Proteins - genetics rab27 GTP-Binding Proteins Sequence Analysis, DNA - methods SH2D1A protein Single-nucleotide polymorphism Vesicular Transport Proteins - genetics XIAP protein |
title | Exome sequencing for simultaneous mutation screening in children with hemophagocytic lymphohistiocytosis |
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