{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T16:57:54Z","timestamp":1772211474596,"version":"3.50.1"},"reference-count":53,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2021,7,12]],"date-time":"2021-07-12T00:00:00Z","timestamp":1626048000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001412","name":"Council\u00a0of\u00a0Scientific and Industrial Research, India","doi-asserted-by":"publisher","award":["MLP1801"],"award-info":[{"award-number":["MLP1801"]}],"id":[{"id":"10.13039\/501100001412","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001843","name":"Science and Engineering Research Board","doi-asserted-by":"crossref","award":["EMR\/2016\/006828\/HS"],"award-info":[{"award-number":["EMR\/2016\/006828\/HS"]}],"id":[{"id":"10.13039\/501100001843","id-type":"DOI","asserted-by":"crossref"}]},{"name":"foundation for primary immunodeficiency diseases"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>\n                    X\u2014linked agammaglobulinemia (XLA, OMIM #300755) is a primary immunodeficiency disorder caused by pathogenic variations in the\n                    <jats:italic>BTK<\/jats:italic>\n                    gene, characterized by failure of development and maturation of B lymphocytes. The estimated prevalence worldwide is 1 in 190,000 male births. Recently, genome sequencing has been widely used in difficult to diagnose and familial cases. We report a large Indian family suffering from XLA with five affected individuals. We performed complete blood count, immunoglobulin assay, and lymphocyte subset analysis for all patients and analyzed Btk expression for one patient and his mother. Whole exome sequencing (WES) for four patients, and whole genome sequencing (WGS) for two patients have been performed. Carrier screening was done for 17 family members using Multiplex Ligation-dependent Probe Amplification (MLPA) and haplotype ancestry mapping using fineSTRUCTURE was performed. All patients had hypogammaglobulinemia and low CD19+ B cells. One patient who underwent Btk estimation had low expression and his mother showed a mosaic pattern. We could not identify any single nucleotide variants or small insertion\/ deletions from the WES dataset that correlates with the clinical feature of the patient. Structural variant analysis through WGS data identifies a novel large deletion of 5,296 bp at loci chrX:100,624,323\u2013100,629,619 encompassing exons 3\u20135 of the\n                    <jats:italic>BTK<\/jats:italic>\n                    gene. Family screening revealed seven carriers for the deletion. Two patients had a successful HSCT. Haplotype mapping revealed a South Asian ancestry. WGS led to identification of the accurate genetic mutation which could help in early diagnosis leading to improved outcomes, prevention of permanent organ damage and improved quality of life, as well as enabling genetic counselling and prenatal diagnosis in the family.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0254407","type":"journal-article","created":{"date-parts":[[2021,7,12]],"date-time":"2021-07-12T13:24:44Z","timestamp":1626096284000},"page":"e0254407","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["Whole genome sequencing identifies novel structural variant in a large Indian family affected with X-linked agammaglobulinemia"],"prefix":"10.1371","volume":"16","author":[{"given":"Abhinav","family":"Jain","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Geeta Madathil","family":"Govindaraj","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Athulya","family":"Edavazhippurath","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nabeel","family":"Faisal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rahul C.","family":"Bhoyar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vishu","family":"Gupta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ramya","family":"Uppuluri","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shiny Padinjare","family":"Manakkad","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Atul","family":"Kashyap","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anoop","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohit Kumar","family":"Divakar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohamed","family":"Imran","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sneha","family":"Sawant","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aparna","family":"Dalvi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Krishnan","family":"Chakyar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manisha","family":"Madkaikar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Revathi","family":"Raj","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sridhar","family":"Sivasubbu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7644-7181","authenticated-orcid":true,"given":"Vinod","family":"Scaria","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2021,7,12]]},"reference":[{"issue":"2","key":"pone.0254407.ref001","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1016\/0092-8674(93)90667-F","article-title":"Deficient expression of a B cell cytoplasmic tyrosine kinase in human X-linked agammaglobulinemia","volume":"72","author":"S Tsukada","year":"1993","journal-title":"Cell"},{"issue":"3\u20134","key":"pone.0254407.ref002","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1155\/2001\/28962","article-title":"Role of Bruton\u2019s tyrosine kinase in B cell development","volume":"8","author":"A Maas","year":"2001","journal-title":"Dev Immunol"},{"issue":"1","key":"pone.0254407.ref003","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1081\/IMM-120027687","article-title":"X-linked agammaglobulinemia: a survey of 33","volume":"33","author":"M Moin","year":"2004","journal-title":"Iranian patients. 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