Further Confirmation of Germline Glioma Risk Variant rs78378222 in TP53 and Its Implication in Tumor Tissues via Integrative Analysis of TCGA Data

Zhaoming Wang, Preetha Rajaraman, Beatrice S. Melin, Charles C. Chung, Weijia Zhang, Roberta Mckean-Cowdin, Dominique Michaud, Meredith Yeager, Anders Ahlbom, Demetrius Albanes, Ulrika Andersson, Laura E Beane Freeman, Julie E. Buring, Mary Ann Butler, Tania Carreón, Maria Feychting, Susan M. Gapstur, J. Michael Gaziano, Graham G. Giles, Goran Hallmans & 24 others Roger Henriksson, Judith Hoffman-Bolton, Peter D. Inskip, Cari M. Kitahara, Loic Le Marchand, Martha S. Linet, Shengchao Li, Ulrike Peters, Mark P. Purdue, Nathaniel Rothman, Avima M. Ruder, Howard D. Sesso, Gianluca Severi, Meir Stampfer, Victoria L. Stevens, Kala Visvanathan, Sophia S. Wang, Emily White, Anne Zeleniuch-Jacquotte, Robert Hoover, Joseph F. Fraumeni, Nilanjan Chatterjee, Patricia Hartge, Stephen J. Chanock

Research output: Contribution to journalArticle

Abstract

We confirmed strong association of rs78378222:A>C (per allele odds ratio [OR] = 3.14; P = 6.48 × 10-11), a germline rare single-nucleotide polymorphism (SNP) in TP53, via imputation of a genome-wide association study of glioma (1,856 cases and 4,955 controls). We subsequently performed integrative analyses on the Cancer Genome Atlas (TCGA) data for GBM (glioblastoma multiforme) and LUAD (lung adenocarcinoma). Based on SNP data, we imputed genotypes for rs78378222 and selected individuals carrying rare risk allele (C). Using RNA sequencing data, we observed aberrant transcripts with ~3 kb longer than normal for those individuals. Using exome sequencing data, we further showed that loss of haplotype carrying common protective allele (A) occurred somatically in GBM but not in LUAD. Our bioinformatic analysis suggests rare risk allele (C) disrupts mRNA termination, and an allelic loss of a genomic region harboring common protective allele (A) occurs during tumor initiation or progression for glioma.

Original languageEnglish (US)
Pages (from-to)684-688
Number of pages5
JournalHuman Mutation
Volume36
Issue number7
DOIs
StatePublished - Jul 1 2015

Fingerprint

Atlases
Glioma
Alleles
Genome
Neoplasms
Glioblastoma
Single Nucleotide Polymorphism
Exome
RNA Sequence Analysis
Loss of Heterozygosity
Genome-Wide Association Study
Computational Biology
Haplotypes
Odds Ratio
Genotype
Messenger RNA
Adenocarcinoma of lung

Keywords

  • Glioma
  • Rare SNP
  • TCGA
  • TP53

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Wang, Z., Rajaraman, P., Melin, B. S., Chung, C. C., Zhang, W., Mckean-Cowdin, R., ... Chanock, S. J. (2015). Further Confirmation of Germline Glioma Risk Variant rs78378222 in TP53 and Its Implication in Tumor Tissues via Integrative Analysis of TCGA Data. Human Mutation, 36(7), 684-688. https://doi.org/10.1002/humu.22799

Further Confirmation of Germline Glioma Risk Variant rs78378222 in TP53 and Its Implication in Tumor Tissues via Integrative Analysis of TCGA Data. / Wang, Zhaoming; Rajaraman, Preetha; Melin, Beatrice S.; Chung, Charles C.; Zhang, Weijia; Mckean-Cowdin, Roberta; Michaud, Dominique; Yeager, Meredith; Ahlbom, Anders; Albanes, Demetrius; Andersson, Ulrika; Freeman, Laura E Beane; Buring, Julie E.; Butler, Mary Ann; Carreón, Tania; Feychting, Maria; Gapstur, Susan M.; Gaziano, J. Michael; Giles, Graham G.; Hallmans, Goran; Henriksson, Roger; Hoffman-Bolton, Judith; Inskip, Peter D.; Kitahara, Cari M.; Marchand, Loic Le; Linet, Martha S.; Li, Shengchao; Peters, Ulrike; Purdue, Mark P.; Rothman, Nathaniel; Ruder, Avima M.; Sesso, Howard D.; Severi, Gianluca; Stampfer, Meir; Stevens, Victoria L.; Visvanathan, Kala; Wang, Sophia S.; White, Emily; Zeleniuch-Jacquotte, Anne; Hoover, Robert; Fraumeni, Joseph F.; Chatterjee, Nilanjan; Hartge, Patricia; Chanock, Stephen J.

In: Human Mutation, Vol. 36, No. 7, 01.07.2015, p. 684-688.

Research output: Contribution to journalArticle

Wang, Z, Rajaraman, P, Melin, BS, Chung, CC, Zhang, W, Mckean-Cowdin, R, Michaud, D, Yeager, M, Ahlbom, A, Albanes, D, Andersson, U, Freeman, LEB, Buring, JE, Butler, MA, Carreón, T, Feychting, M, Gapstur, SM, Gaziano, JM, Giles, GG, Hallmans, G, Henriksson, R, Hoffman-Bolton, J, Inskip, PD, Kitahara, CM, Marchand, LL, Linet, MS, Li, S, Peters, U, Purdue, MP, Rothman, N, Ruder, AM, Sesso, HD, Severi, G, Stampfer, M, Stevens, VL, Visvanathan, K, Wang, SS, White, E, Zeleniuch-Jacquotte, A, Hoover, R, Fraumeni, JF, Chatterjee, N, Hartge, P & Chanock, SJ 2015, 'Further Confirmation of Germline Glioma Risk Variant rs78378222 in TP53 and Its Implication in Tumor Tissues via Integrative Analysis of TCGA Data', Human Mutation, vol. 36, no. 7, pp. 684-688. https://doi.org/10.1002/humu.22799
Wang, Zhaoming ; Rajaraman, Preetha ; Melin, Beatrice S. ; Chung, Charles C. ; Zhang, Weijia ; Mckean-Cowdin, Roberta ; Michaud, Dominique ; Yeager, Meredith ; Ahlbom, Anders ; Albanes, Demetrius ; Andersson, Ulrika ; Freeman, Laura E Beane ; Buring, Julie E. ; Butler, Mary Ann ; Carreón, Tania ; Feychting, Maria ; Gapstur, Susan M. ; Gaziano, J. Michael ; Giles, Graham G. ; Hallmans, Goran ; Henriksson, Roger ; Hoffman-Bolton, Judith ; Inskip, Peter D. ; Kitahara, Cari M. ; Marchand, Loic Le ; Linet, Martha S. ; Li, Shengchao ; Peters, Ulrike ; Purdue, Mark P. ; Rothman, Nathaniel ; Ruder, Avima M. ; Sesso, Howard D. ; Severi, Gianluca ; Stampfer, Meir ; Stevens, Victoria L. ; Visvanathan, Kala ; Wang, Sophia S. ; White, Emily ; Zeleniuch-Jacquotte, Anne ; Hoover, Robert ; Fraumeni, Joseph F. ; Chatterjee, Nilanjan ; Hartge, Patricia ; Chanock, Stephen J. / Further Confirmation of Germline Glioma Risk Variant rs78378222 in TP53 and Its Implication in Tumor Tissues via Integrative Analysis of TCGA Data. In: Human Mutation. 2015 ; Vol. 36, No. 7. pp. 684-688.
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abstract = "We confirmed strong association of rs78378222:A>C (per allele odds ratio [OR] = 3.14; P = 6.48 × 10-11), a germline rare single-nucleotide polymorphism (SNP) in TP53, via imputation of a genome-wide association study of glioma (1,856 cases and 4,955 controls). We subsequently performed integrative analyses on the Cancer Genome Atlas (TCGA) data for GBM (glioblastoma multiforme) and LUAD (lung adenocarcinoma). Based on SNP data, we imputed genotypes for rs78378222 and selected individuals carrying rare risk allele (C). Using RNA sequencing data, we observed aberrant transcripts with ~3 kb longer than normal for those individuals. Using exome sequencing data, we further showed that loss of haplotype carrying common protective allele (A) occurred somatically in GBM but not in LUAD. Our bioinformatic analysis suggests rare risk allele (C) disrupts mRNA termination, and an allelic loss of a genomic region harboring common protective allele (A) occurs during tumor initiation or progression for glioma.",
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AU - Gaziano, J. Michael

AU - Giles, Graham G.

AU - Hallmans, Goran

AU - Henriksson, Roger

AU - Hoffman-Bolton, Judith

AU - Inskip, Peter D.

AU - Kitahara, Cari M.

AU - Marchand, Loic Le

AU - Linet, Martha S.

AU - Li, Shengchao

AU - Peters, Ulrike

AU - Purdue, Mark P.

AU - Rothman, Nathaniel

AU - Ruder, Avima M.

AU - Sesso, Howard D.

AU - Severi, Gianluca

AU - Stampfer, Meir

AU - Stevens, Victoria L.

AU - Visvanathan, Kala

AU - Wang, Sophia S.

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