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Bureau A, Begum F, Taub MA, Hetmanski J, Parker MM, Albacha-Hejazi H, Scott AF, Murray JC, Marazita ML, Bailey-Wilson JE, Beaty TH, Ruczinski I. Inferring disease risk genes from sequencing data in multiplex pedigrees through sharing of rare variants. Genet Epidemiol 2019; 43:37-49. [PMID: 30246882 PMCID: PMC6330140 DOI: 10.1002/gepi.22155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 07/11/2018] [Accepted: 07/15/2018] [Indexed: 12/23/2022]
Abstract
We previously demonstrated how sharing of rare variants (RVs) in distant affected relatives can be used to identify variants causing a complex and heterogeneous disease. This approach tested whether single RVs were shared by all sequenced affected family members. However, as with other study designs, joint analysis of several RVs (e.g., within genes) is sometimes required to obtain sufficient statistical power. Further, phenocopies can lead to false negatives for some causal RVs if complete sharing among affected is required. Here, we extend our methodology (Rare Variant Sharing, RVS) to address these issues. Specifically, we introduce gene-based analyses, a partial sharing test based on RV sharing probabilities for subsets of affected relatives and a haplotype-based RV definition. RVS also has the desirable feature of not requiring external estimates of variant frequency or control samples, provides functionality to assess and address violations of key assumptions, and is available as open source software for genome-wide analysis. Simulations including phenocopies, based on the families of an oral cleft study, revealed the partial and complete sharing versions of RVS achieved similar statistical power compared with alternative methods (RareIBD and the Gene-Based Segregation Test), and had superior power compared with the pedigree Variant Annotation, Analysis, and Search Tool (pVAAST) linkage statistic. In studies of multiplex cleft families, analysis of rare single nucleotide variants in the exome of 151 affected relatives from 54 families revealed no significant excess sharing in any one gene, but highlighted different patterns of sharing revealed by the complete and partial sharing tests.
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Affiliation(s)
- Alexandre Bureau
- Département de Médecine Sociale et Préventive, Université Laval, Québec, Canada
- Centre de recherche CERVO, Québec, Canada
| | - Ferdouse Begum
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Margaret A. Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jacqueline Hetmanski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Margaret M. Parker
- Channing Division of Network Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Alan F. Scott
- Institute of Genetic Medicine, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, School of Medicine, University of Iowa, Iowa City, IA, USA
| | - Mary L. Marazita
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joan E. Bailey-Wilson
- Inherited Disease Research Branch, National Human Genome Research Institute, Baltimore, MD, USA
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Morlan Mairal M, Papadopoulos P, Hetmanski J, Caswell P, Krstic-Demonacos M, Aziz A. CALR mutations and their link with cellular calcium during megakaryocyte hyperplasia in MPNs. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx361.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Fu J, Beaty TH, Scott AF, Hetmanski J, Parker MM, Wilson JEB, Marazita ML, Mangold E, Albacha-Hejazi H, Murray JC, Bureau A, Carey J, Cristiano S, Ruczinski I, Scharpf RB. Whole exome association of rare deletions in multiplex oral cleft families. Genet Epidemiol 2016; 41:61-69. [PMID: 27910131 DOI: 10.1002/gepi.22010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 09/21/2016] [Accepted: 09/21/2016] [Indexed: 11/11/2022]
Abstract
By sequencing the exomes of distantly related individuals in multiplex families, rare mutational and structural changes to coding DNA can be characterized and their relationship to disease risk can be assessed. Recently, several rare single nucleotide variants (SNVs) were associated with an increased risk of nonsyndromic oral cleft, highlighting the importance of rare sequence variants in oral clefts and illustrating the strength of family-based study designs. However, the extent to which rare deletions in coding regions of the genome occur and contribute to risk of nonsyndromic clefts is not well understood. To identify putative structural variants underlying risk, we developed a pipeline for rare hemizygous deletions in families from whole exome sequencing and statistical inference based on rare variant sharing. Among 56 multiplex families with 115 individuals, we identified 53 regions with one or more rare hemizygous deletions. We found 45 of the 53 regions contained rare deletions occurring in only one family member. Members of the same family shared a rare deletion in only eight regions. We also devised a scalable global test for enrichment of shared rare deletions.
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Affiliation(s)
- Jack Fu
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, USA
| | - Alan F Scott
- Center for Inherited Disease Research, Johns Hopkins School of Medicine, Baltimore MD, USA.,Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore MD, USA
| | - Jacqueline Hetmanski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, USA
| | - Margaret M Parker
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Joan E Bailey Wilson
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
| | - Mary L Marazita
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, PA, USA
| | | | | | - Jeffrey C Murray
- Department of Pediatrics, School of Medicine, University of Iowa, IA, USA
| | - Alexandre Bureau
- Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec and Département de Médecine Sociale et Préventive, Université Laval, Québec, Canada
| | - Jacob Carey
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, USA
| | - Stephen Cristiano
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, USA
| | - Robert B Scharpf
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
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Wan ES, Qiu W, Morrow J, Beaty TH, Hetmanski J, Make BJ, Lomas DA, Silverman EK, DeMeo DL. Genome-wide site-specific differential methylation in the blood of individuals with Klinefelter syndrome. Mol Reprod Dev 2015; 82:377-86. [PMID: 25988574 DOI: 10.1002/mrd.22483] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 03/30/2015] [Indexed: 12/25/2022]
Abstract
Klinefelter syndrome (KS) (47 XXY) is a common sex-chromosome aneuploidy with an estimated prevalence of one in every 660 male births. Investigations into the associations between DNA methylation and the highly variable clinical manifestations of KS have largely focused on the supernumerary X chromosome; systematic investigations of the epigenome have been limited. We obtained genome-wide DNA methylation data from peripheral blood using the Illumina HumanMethylation450K platform in 5 KS (47 XXY) versus 102 male (46 XY) and 113 female (46 XX) control subjects participating in the COPDGene Study. Empirical Bayes-mediated models were used to test for differential methylation by KS status. CpG sites with a false-discovery rate < 0.05 in the discovery cohort which were available on the first-generation HumanMethylation 27 K platform were further examined in an independent replication cohort of 2 KS subjects, 590 male, and 495 female controls drawn from the International COPD Genetics Network (ICGN). Differential methylation at sites throughout the genome were identified, including 86 CpG sites that were differentially methylated in KS subjects relative to both male and female controls. CpG sites annotated to the HEN1 methyltransferase homolog 1 (HENMT1), calcyclin-binding protein (CACYBP), and GTPase-activating protein (SH3 domain)-binding protein 1 (G3BP1) genes were among the "KS-specific" loci that were replicated in ICGN. We conclude that site-specific differential methylation exists throughout the genome in KS. The functional impact and clinical relevance of these differentially methylated loci should be explored in future studies.
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Affiliation(s)
- Emily S Wan
- Channing Division of Network Medicine, Brigham & Women's Hospital, Boston, Massachusetts.,Division of Pulmonary and Critical Care, Brigham & Women's Hospital, Boston, Massachusetts
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham & Women's Hospital, Boston, Massachusetts
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham & Women's Hospital, Boston, Massachusetts
| | - Terri H Beaty
- Department of Biostatistics and Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Jacqueline Hetmanski
- Department of Biostatistics and Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Barry J Make
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, Colorado
| | - David A Lomas
- Wolfson Institute for Biomedical Research, University College London, London, United Kingdom
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham & Women's Hospital, Boston, Massachusetts.,Division of Pulmonary and Critical Care, Brigham & Women's Hospital, Boston, Massachusetts
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham & Women's Hospital, Boston, Massachusetts.,Division of Pulmonary and Critical Care, Brigham & Women's Hospital, Boston, Massachusetts
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Ingersoll RG, Hetmanski J, Park JW, Fallin MD, McIntosh I, Wu-Chou YH, Chen PK, Yeow V, Chong SS, Cheah F, Sull JW, Jee SH, Wang H, Wu T, Murray T, Huang S, Ye X, Jabs EW, Redett R, Raymond G, Scott AF, Beaty TH. Association between genes on chromosome 4p16 and non-syndromic oral clefts in four populations. Eur J Hum Genet 2010; 18:726-32. [PMID: 20087401 DOI: 10.1038/ejhg.2009.228] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Isolated cleft lip with or without cleft palate and cleft palate are among the most common human birth defects. Several candidate gene studies on MSX1 have shown significant association between markers in MSX1 and risk of oral clefts, and re-sequencing studies have identified multiple mutations in MSX1 in a small minority of cases, which may account for 1-2% of all isolated oral clefts cases. We explored the 2-Mb region around MSX1, using a marker map of 393 single nucleotide polymorphisms (SNPs) in 297 cleft lip, with or without cleft palate, case-parent trios and 84 cleft palate trios from Maryland, Taiwan, Singapore, and Korea. Both individual markers and haplotypes of two to five SNPs showed several regions yielding statistical evidence for linkage and disequilibrium. Two genes (STK32B and EVC) yielded consistent evidence from cleft lip, with or without cleft palate, trios in all four populations. These two genes plus EVC2 also yielded suggestive evidence for linkage and disequilibrium among cleft palate trios. This analysis suggests that several genes, not just MSX1, in this region may influence risk of oral clefts.
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Affiliation(s)
- Roxann G Ingersoll
- Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, MD 21287, USA.
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Maestri NE, Beaty TH, Hetmanski J, Smith EA, McIntosh I, Wyszynski DF, Liang KY, Duffy DL, VanderKolk C. Application of transmission disequilibrium tests to nonsyndromic oral clefts: including candidate genes and environmental exposures in the models. Am J Med Genet 1997; 73:337-44. [PMID: 9415696 DOI: 10.1002/(sici)1096-8628(19971219)73:3<337::aid-ajmg21>3.0.co;2-j] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Extensive epidemiological and genetic studies of the cause of oral clefts have demonstrated strong familial aggregation but have failed to yield definitive evidence of any single genetic mechanism. We used the transmission/disequilibrium test (TDT) to investigate the relationship between oral clefts and markers associated with five candidate genes by utilizing 160 parent-offspring trios. Conditional logistic regression models extended the TDT to include covariates as effect modifiers, thus permitting tests for gene-environment interactions. For four of these candidates [transforming growth factor alpha (TGFA), transforming growth factor beta 3 (TGFB3), retinoic acid receptor (RARA), and the proto-oncogene BCL3], we detected modestly elevated odds ratios for the transmission of one marker allele to cleft probands when all the trios were analyzed together. These odds ratios increased when information on type of cleft, race, family history, or maternal smoking were incorporated as effect modifiers. We detected significant interaction between maternal smoking and the transmission of alleles for markers near TGFA and TGFB3; excess transmission of allele 3 at BCL3 was most significant among cleft lip probands; and the odds ratios for transmission of alleles at D19S178 and THRA1 were significant when ethnic group was included in the model. We suggest that utilizing an analytical strategy that allows for stratification of data and incorporating environmental effects into a single analysis may be more effective for detecting genes of small effect.
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Affiliation(s)
- N E Maestri
- Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
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Abstract
Two resin-based processes and conventional culturing methods were compared in isolating organisms from blood specimens of patients given antimicrobial agents. Of 20 patients whose specimens were found to contain clinically relevant organisms, one or both of the resin-process methods isolated organisms in eight after conventional culturing was unsuccessful. Conventional cultures were successful in five cases in which the resin-process methods did not work, and both resin-process and conventional culturing were successful in seven cases. In eight cases in which other body fluids were cultured, only a resin-process method was successful in four, although they are intended for use only with blood specimens. Data indicate that resin-process methods should be used along with conventional culturing methods when patients have already been given an antimicrobial. A review of the literature shows that the devices improve the recovery of organisms but does not establish that detection time is decreased.
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Abstract
Blood subcultures repeated 3 days after the cultures were first identified as positives increased our detection of polymicrobic bacteremia in 9.1 to 27% of clinically significant patient episodes. Reincubation and repeated subculture of previously positive blood cultures had a direct impact on the therapeutic management of patients with polymicrobic bacteremia.
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