{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T12:23:26Z","timestamp":1780316606894,"version":"3.54.1"},"reference-count":12,"publisher":"Wiley","issue":"7","license":[{"start":{"date-parts":[[2020,5,15]],"date-time":"2020-05-15T00:00:00Z","timestamp":1589500800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"name":"Grant-in-Aid for Early-Career Scientists by JSPS KAKENHI","award":["JP19K17342"],"award-info":[{"award-number":["JP19K17342"]}]},{"name":"Initiative on Rare and Undiagnosed Diseases","award":["JP17ek0109151"],"award-info":[{"award-number":["JP17ek0109151"]}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["American J of Med Genetics Pt A"],"published-print":{"date-parts":[[2020,7]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Shwachman\u2010Diamond syndrome characterized by metaphyseal dysplasia, pancreatic insufficiency, and pancytopenia is caused by biallelic mutations in <jats:italic>SBDS<\/jats:italic>. Gene conversion between <jats:italic>SBDS<\/jats:italic> and its pseudogene <jats:italic>SBDSP1<\/jats:italic> is the major cause. Here, we report two unrelated patients with Shwachman\u2010Diamond syndrome who were shown to be compound heterozygotes for relatively frequent pathogenic alleles (the 258+2T&gt;C allele and another allele composed of 183\u2010184TA&gt;CT and 201A&gt;G) using an established polymerase chain reaction sequencing assay with SBDS\u2010specific primers. Exome analysis of the patients showed discrepant results: 258+2T&gt;C with variant allele frequency around 0.85, and no variants detected for the 183\u2010184TA&gt;CT allele. Parental exome analysis of the two families further supported this notion. Confronted with two patients with an unexpected segregation pattern, we performed a transcriptome analysis of peripheral blood\u2010derived mRNA to demonstrate that the results were compatible with those obtained using SBDS\u2010specific PCR primers. Both alleles could be accounted for by gene conversion events. The diagnostic discrepancy can be accounted for by a decreased efficiency in the computational mapping of the reads with 183\u2010184TA&gt;CT and 201A&gt;G to the reference sequence of the <jats:italic>SBDS<\/jats:italic> locus during exome analysis. This report highlights the pitfall of exome analysis for genes with pseudogenes, such as <jats:italic>SBDS<\/jats:italic> and the alternative use of RNA\u2010seq is recommended to circumvent this problem.<\/jats:p>","DOI":"10.1002\/ajmg.a.61598","type":"journal-article","created":{"date-parts":[[2020,5,16]],"date-time":"2020-05-16T04:10:28Z","timestamp":1589602228000},"page":"1631-1636","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Shortfall of exome analysis for diagnosis of <scp>Shwachman\u2010Diamond<\/scp> syndrome: Mismapping due to the pseudogene <scp><i>SBDSP1<\/i><\/scp>"],"prefix":"10.1002","volume":"182","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4039-8899","authenticated-orcid":false,"given":"Mamiko","family":"Yamada","sequence":"first","affiliation":[{"name":"Center for Medical Genetics Keio University School of Medicine  Tokyo Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1497-7686","authenticated-orcid":false,"given":"Tomoko","family":"Uehara","sequence":"additional","affiliation":[{"name":"Center for Medical Genetics Keio University School of Medicine  Tokyo Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hisato","family":"Suzuki","sequence":"additional","affiliation":[{"name":"Center for Medical Genetics Keio University School of Medicine  Tokyo Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7311-4135","authenticated-orcid":false,"given":"Toshiki","family":"Takenouchi","sequence":"additional","affiliation":[{"name":"Department of Pediatrics Keio University School of Medicine  Tokyo Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayano","family":"Inui","sequence":"additional","affiliation":[{"name":"Department of Pediatric Hepatology and Gastroenterology Saiseikai Yokohama City Tobu Hospital  Kanagawa Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masako","family":"Ikemiyagi","sequence":"additional","affiliation":[{"name":"Department of Pediatrics National Hospital Organization Saitama Hospital  Saitama Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isamu","family":"Kamimaki","sequence":"additional","affiliation":[{"name":"Department of Pediatrics National Hospital Organization Saitama Hospital  Saitama Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenjiro","family":"Kosaki","sequence":"additional","affiliation":[{"name":"Center for Medical Genetics Keio University School of Medicine  Tokyo Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2020,5,15]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11632"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-40761-w"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng1062"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-0835-6_21"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1111\/cei.12042"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-015-0191-x"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.biopha.2016.11.036"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-3476(64)80150-5"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2004-04-1516"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymgmr.2019.100531"},{"key":"e_1_2_9_13_1","first-page":"3837","article-title":"Increased expression of long non\u2010coding RNA SBDSP1 correlates with poor survival in colorectal cancer","volume":"21","author":"Zhou H. 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