{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T16:52:03Z","timestamp":1785516723369,"version":"3.56.0"},"reference-count":51,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2021,5,4]],"date-time":"2021-05-04T00:00:00Z","timestamp":1620086400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molec Gen &amp; Gen Med"],"published-print":{"date-parts":[[2021,6]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Pineal cyst is a benign lesion commonly occurring in people of any age. Until now, the underlying molecular alterations have not been explored.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We performed whole exome sequencing of 93 germline samples and 21 pineal cyst tissue samples to illustrate its genetic architecture and somatic mutations. The dominant and recessive inheritance modes were considered, and a probability was calculated to evaluate the significance of variant overrepresentation.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>By analyzing pineal cyst as a Mendelian disease with a dominant inheritance pattern, we identified 42,325 rare germline variants, and NM_001004711.1:c.476A&gt;G was highly enriched (FDR&lt;0.2). By analyzing it as a recessive disorder, we identified 753 homozygous rare variants detected in at least one pineal cyst sample each. One <jats:italic>STIM2<\/jats:italic> rare variant, NM_001169117.1:c.1652C&gt;T, was overrepresented (FDR&lt;0.05). Analyzing at a gene\u2010based level, we identified a list of the most commonlymutated germline genes, including <jats:italic>POP4<\/jats:italic>, <jats:italic>GNGT2<\/jats:italic> and <jats:italic>TMEM254<\/jats:italic>. A somatic mutation analysis of 21 samples identified 16 variants in 15 genes, which mainly participated in the biological processes of gene expression and epigenetic regulation, immune response modulation, and transferase activity.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>These molecular profiles are novel for this condition and provide data for investigators interested in pineal cysts.<\/jats:p><\/jats:sec>","DOI":"10.1002\/mgg3.1691","type":"journal-article","created":{"date-parts":[[2021,5,4]],"date-time":"2021-05-04T12:31:50Z","timestamp":1620131510000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Germline and somatic mutations in the pathology of pineal cyst: A whole\u2010exome sequencing study of 93 individuals"],"prefix":"10.1002","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0094-7726","authenticated-orcid":false,"given":"Yuanqing","family":"Yan","sequence":"first","affiliation":[{"name":"Vivian L. Smith Department of Neurosurgery McGovern Medical School The University of Texas Health Science Center at Houston Houston TX USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca","family":"Martinez","sequence":"additional","affiliation":[{"name":"Vivian L. Smith Department of Neurosurgery McGovern Medical School The University of Texas Health Science Center at Houston Houston TX USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria N.","family":"Rasheed","sequence":"additional","affiliation":[{"name":"Vivian L. Smith Department of Neurosurgery McGovern Medical School The University of Texas Health Science Center at Houston Houston TX USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joshua","family":"Cahal","sequence":"additional","affiliation":[{"name":"Vivian L. Smith Department of Neurosurgery McGovern Medical School The University of Texas Health Science Center at Houston Houston TX USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Xu","sequence":"additional","affiliation":[{"name":"Vivian L. Smith Department of Neurosurgery McGovern Medical School The University of Texas Health Science Center at Houston Houston TX USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanning","family":"Rui","sequence":"additional","affiliation":[{"name":"Vivian L. Smith Department of Neurosurgery McGovern Medical School The University of Texas Health Science Center at Houston Houston TX USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8815-6509","authenticated-orcid":false,"given":"Krista J.","family":"Qualmann","sequence":"additional","affiliation":[{"name":"Vivian L. Smith Department of Neurosurgery McGovern Medical School The University of Texas Health Science Center at Houston Houston TX USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John P.","family":"Hagan","sequence":"additional","affiliation":[{"name":"Vivian L. Smith Department of Neurosurgery McGovern Medical School The University of Texas Health Science Center at Houston Houston TX USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong H.","family":"Kim","sequence":"additional","affiliation":[{"name":"Vivian L. Smith Department of Neurosurgery McGovern Medical School The University of Texas Health Science Center at Houston Houston TX USA"},{"name":"Memorial Hermann Hospital Mischer Neuroscience Institute Houston TX USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2021,5,4]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth0410-248"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0165-4608(98)00220-9"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mce.2011.07.009"},{"key":"e_1_2_9_5_1","first-page":"355","article-title":"Pineal gland cysts\u2013an overview","volume":"48","author":"Bosnjak J.","year":"2009","journal-title":"Acta Clin Croat"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.biocel.2015.07.006"},{"issue":"3","key":"e_1_2_9_7_1","first-page":"405","article-title":"Ultrastructure of the pineal gland in the adult rat","volume":"138","author":"Calvo J.","year":"1984","journal-title":"Journal of Anatomy"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.3389\/fphys.2018.01673"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cancergen.2013.11.001"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1101\/gad.282145.116"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3118"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jaci.2015.08.039"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1080\/08880018.2016.1225326"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.RA118.003787"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-17121-0_99"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.toxlet.2019.02.014"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0161-6420(03)00484-6"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-020-0873-9"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"e_1_2_9_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp698"},{"key":"e_1_2_9_21_1","doi-asserted-by":"publisher","DOI":"10.1111\/bph.13659"},{"key":"e_1_2_9_22_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0307882100"},{"key":"e_1_2_9_23_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0205883"},{"key":"e_1_2_9_24_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.107524.110"},{"key":"e_1_2_9_25_1","doi-asserted-by":"publisher","DOI":"10.1007\/s007010200031"},{"key":"e_1_2_9_26_1","doi-asserted-by":"publisher","DOI":"10.1136\/jcp.49.3.267"},{"key":"e_1_2_9_27_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00441-002-0580-5"},{"key":"e_1_2_9_28_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mrfmmm.2006.09.003"},{"key":"e_1_2_9_29_1","doi-asserted-by":"publisher","DOI":"10.1097\/PAF.0000000000000107"},{"key":"e_1_2_9_30_1","doi-asserted-by":"publisher","DOI":"10.1177\/1535370218754524"},{"key":"e_1_2_9_31_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.wneu.2016.02.092"},{"key":"e_1_2_9_32_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg509"},{"key":"e_1_2_9_33_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1600-079X.1989.tb00407.x"},{"key":"e_1_2_9_34_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0189736"},{"key":"e_1_2_9_35_1","doi-asserted-by":"publisher","DOI":"10.1097\/MPH.0b013e3180308782"},{"key":"e_1_2_9_36_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1016"},{"key":"e_1_2_9_37_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1754"},{"key":"e_1_2_9_38_1","doi-asserted-by":"publisher","DOI":"10.3174\/ajnr.A2102"},{"key":"e_1_2_9_39_1","doi-asserted-by":"publisher","DOI":"10.1227\/00006123-199507000-00002"},{"key":"e_1_2_9_40_1","doi-asserted-by":"publisher","DOI":"10.1038\/336551a0"},{"key":"e_1_2_9_41_1","doi-asserted-by":"publisher","DOI":"10.1080\/09647049509525636"},{"key":"e_1_2_9_42_1","doi-asserted-by":"publisher","DOI":"10.1038\/cr.2017.15"},{"key":"e_1_2_9_43_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv009"},{"key":"e_1_2_9_44_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1601-183X.2011.00730.x"},{"key":"e_1_2_9_45_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jchemneu.2011.05.013"},{"key":"e_1_2_9_46_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12881-019-0922-8"},{"key":"e_1_2_9_47_1","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.CAN-19-3984"},{"key":"e_1_2_9_48_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq603"},{"key":"e_1_2_9_49_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2009-10-11-r130"},{"key":"e_1_2_9_50_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41374-018-0062-3"},{"key":"e_1_2_9_51_1","doi-asserted-by":"publisher","DOI":"10.1096\/fj.201701118R"},{"key":"e_1_2_9_52_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcp.29402"}],"container-title":["Molecular Genetics &amp; Genomic Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/mgg3.1691","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/mgg3.1691","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/mgg3.1691","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,30]],"date-time":"2023-08-30T02:22:35Z","timestamp":1693362155000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/mgg3.1691"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5,4]]},"references-count":51,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2021,6]]}},"alternative-id":["10.1002\/mgg3.1691"],"URL":"https:\/\/doi.org\/10.1002\/mgg3.1691","archive":["Portico"],"relation":{},"ISSN":["2324-9269","2324-9269"],"issn-type":[{"value":"2324-9269","type":"print"},{"value":"2324-9269","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,5,4]]},"assertion":[{"value":"2020-09-29","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-04-09","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-05-04","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e1691"}}