publication . Article . Preprint . 2018

Evaluation of Gene-Based Family-Based Methods to Detect Novel Genes Associated With Familial Late Onset Alzheimer Disease

Fernández, Maria Victoria; Budde, John; Del-Aguila, Jorge; Ibañez, Laura; Deming, Yuetiva; Harari, Oscar; Norton, Joanne; Morris, John C; Goate, Alison; Cruchaga, Carlos;
Open Access English
  • Published: 08 Jan 2018 Journal: Frontiers in Neuroscience, volume 12 (issn: 1662-4548, eissn: 1662-453X, Copyright policy)
  • Publisher: Frontiers Media S.A.
Abstract
Abstract Gene-based tests to study the combined effect of rare variants towards a particular phenotype have been widely developed for case-control studies, but their evolution and adaptation for family-based studies, especially for complex incomplete families, has been slower. In this study, we have performed a practical examination of all the latest gene-based methods available for family-based study designs using both simulated and real datasets. We have examined the performance of several collapsing, variance-component and transmission disequilibrium tests across eight different software and twenty-two models utilizing a cohort of 285 families (N=1,235) with ...
Subjects
free text keywords: Neuroscience, Original Research, gene-based, family-based, clustering, variance-component, transmission disequilibrium, rare variants, whole exome sequencing, Alzheimer's disease
Funded by
NIH| Collaborative GWAS of Dementia, AD and related MRI and Cognitive Endophenotypes
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R01AG033193-01
  • Funding stream: NATIONAL INSTITUTE ON AGING
,
NIH| CORONARY HEART DISEASE AND STROKE
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: N01HC085079-023
  • Funding stream: DIVISION OF EPIDEMIOLOGY AND CLINICAL APPLICATIONS
,
NIH| ARIC Neurocognitive Study (ARIC-NCS) 1 of 5
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01HL096812-08
  • Funding stream: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
,
NIH| CHS research resources for the cardiovascular health of older adults
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3U01HL130114-03S1
  • Funding stream: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
,
NWO| NCHA Subsidiebesluit 2008-2012
Project
  • Funder: Netherlands Organisation for Scientific Research (NWO) (NWO)
  • Project Code: 2300155116
62 references, page 1 of 5

Aly T. A.Baschal E. E.Jahromi M. M.Fernando M. S.Babu S. R.Fingerlin T. E.. (2008). Analysis of single nucleotide polymorphisms identifies major type 1A diabetes locus telomeric of the major histocompatibility complex. Diabetes 57, 770–776. 10.2337/db07-0900 18065518 [OpenAIRE] [PubMed] [DOI]

Balding D. J.Nichols R. A. (1995). A method for quantifying differentiation between populations at Multi-Allelic Loci and Its implications for investigating identity and paternity. Genetica 96, 3–12. 10.1007/BF01441146 7607457 [OpenAIRE] [PubMed] [DOI]

Bansal V.Libiger O.Torkamani A.Schork N. J. (2010). Statistical analysis strategies for association studies involving rare variants. Nat. Rev. Genet. 11, 773–785. 10.1038/nrg2867 20940738 [OpenAIRE] [PubMed] [DOI]

Baranzini S. E.Wang J.Gibson R. A.Galwey N.Naegelin Y.Barkhof F.. (2009). Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. Hum. Mo l. Genet.18, 767–778. 10.1093/hmg/ddn388 19010793 [OpenAIRE] [PubMed] [DOI]

Beecham G. W.Hamilton K.Naj A. C.Martin E. R.Huentelman M.Myers A. J.. (2014). Genome-wide association meta-analysis of neuropathologic features of Alzheimer's disease and related dementias. PLoS Genet. 10:e1004606. 10.1371/journal.pgen.1004606 25188341 [OpenAIRE] [PubMed] [DOI]

Chen C.Manichaikul A.Rich S. S. (2009). A generalized family-based association test for dichotomous traits. Am. J. Hum. Genet. 85, 364–376. 10.1016/j.ajhg.2009.08.003 19732865 [OpenAIRE] [PubMed] [DOI]

Cheong C.Hentschel L.Davidson A. E.Gerrelli D.Davie R.Rizzo R.. (2016). Mutations in CPAMD8 cause a unique form of autosomal-recessive anterior segment dysgenesis. Am. J. Hum. Genet.99, 1338–1352. 10.1016/j.ajhg.2016.09.022 27839872 [OpenAIRE] [PubMed] [DOI]

Choi S.Lee S.Cichon S.Nöthen M. M.Lange C.Park T.. (2014). FARVAT: a family-based rare variant association test. Bioinformatics 30, 3197–3205. 10.1093/bioinformatics/btu496 25075118 [OpenAIRE] [PubMed] [DOI]

Cingolani P.Platts A.Wang le L.Melissa Coon W.Nguyen T.Wang L.. (2012). A Program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of drosophila melanogaster strain w1118; Iso-2; Iso-3. Fly (Austin)6, 80–92. 10.4161/fly.19695 22728672 [OpenAIRE] [PubMed] [DOI]

Cirulli E. T.Goldstein D. B. (2010). Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat. Rev. Genet. 11, 415–425. 10.1038/nrg2779 20479773 [OpenAIRE] [PubMed] [DOI]

Cruchaga C.Celeste M. K.Jin S. C.Benitez B. A.Cai Y.Guerreiro R.. (2014). Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer's disease. Nature 505, 550–554. 10.1038/nature12825 24336208 [OpenAIRE] [PubMed] [DOI]

Cruchaga C.Del-Aguila J. L.Saef B.Black K.Fernandez M. V.Budde J.. (2017). Polygenic risk score of sporadic late-onset Alzheimer's disease reveals a shared architecture with the familial and early-onset forms. Alzheimers Dement. 14, 205–214. 10.1016/j.jalz.2017.08.013 28943286 [OpenAIRE] [PubMed] [DOI]

Cruchaga C.Haller G.Chakraverty S.Mayo K.Vallania F. L.M.Mitra R. D.. (2012). Rare variants in APP, PSEN1 and PSEN2 increase risk for AD in Late-onset Alzheimer's disease families. PLoS ONE 7:e31039. 10.1371/journal.pone.0031039 22312439 [OpenAIRE] [PubMed] [DOI]

Cukier H. N.Dueker N. D.Slifer S. H.Lee J. M.Whitehead P. L.Lalanne E.. (2014). Exome sequencing of extended families with autism reveals genes shared across neurodevelopmental and neuropsychiatric disorders. Mol. Autism 5:1. 10.1186/2040-2392-5-1 24410847 [OpenAIRE] [PubMed] [DOI]

De G.Yip W.Ionita-Laza I.Laird N.Amos C. I. (2013). Rare variant analysis for family-based design. PLoS ONE 8:e48495. 10.1371/journal.pone.0048495 23341868 [OpenAIRE] [PubMed] [DOI]

62 references, page 1 of 5
Abstract
Abstract Gene-based tests to study the combined effect of rare variants towards a particular phenotype have been widely developed for case-control studies, but their evolution and adaptation for family-based studies, especially for complex incomplete families, has been slower. In this study, we have performed a practical examination of all the latest gene-based methods available for family-based study designs using both simulated and real datasets. We have examined the performance of several collapsing, variance-component and transmission disequilibrium tests across eight different software and twenty-two models utilizing a cohort of 285 families (N=1,235) with ...
Subjects
free text keywords: Neuroscience, Original Research, gene-based, family-based, clustering, variance-component, transmission disequilibrium, rare variants, whole exome sequencing, Alzheimer's disease
Funded by
NIH| Collaborative GWAS of Dementia, AD and related MRI and Cognitive Endophenotypes
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1R01AG033193-01
  • Funding stream: NATIONAL INSTITUTE ON AGING
,
NIH| CORONARY HEART DISEASE AND STROKE
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: N01HC085079-023
  • Funding stream: DIVISION OF EPIDEMIOLOGY AND CLINICAL APPLICATIONS
,
NIH| ARIC Neurocognitive Study (ARIC-NCS) 1 of 5
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01HL096812-08
  • Funding stream: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
,
NIH| CHS research resources for the cardiovascular health of older adults
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3U01HL130114-03S1
  • Funding stream: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
,
NWO| NCHA Subsidiebesluit 2008-2012
Project
  • Funder: Netherlands Organisation for Scientific Research (NWO) (NWO)
  • Project Code: 2300155116
62 references, page 1 of 5

Aly T. A.Baschal E. E.Jahromi M. M.Fernando M. S.Babu S. R.Fingerlin T. E.. (2008). Analysis of single nucleotide polymorphisms identifies major type 1A diabetes locus telomeric of the major histocompatibility complex. Diabetes 57, 770–776. 10.2337/db07-0900 18065518 [OpenAIRE] [PubMed] [DOI]

Balding D. J.Nichols R. A. (1995). A method for quantifying differentiation between populations at Multi-Allelic Loci and Its implications for investigating identity and paternity. Genetica 96, 3–12. 10.1007/BF01441146 7607457 [OpenAIRE] [PubMed] [DOI]

Bansal V.Libiger O.Torkamani A.Schork N. J. (2010). Statistical analysis strategies for association studies involving rare variants. Nat. Rev. Genet. 11, 773–785. 10.1038/nrg2867 20940738 [OpenAIRE] [PubMed] [DOI]

Baranzini S. E.Wang J.Gibson R. A.Galwey N.Naegelin Y.Barkhof F.. (2009). Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. Hum. Mo l. Genet.18, 767–778. 10.1093/hmg/ddn388 19010793 [OpenAIRE] [PubMed] [DOI]

Beecham G. W.Hamilton K.Naj A. C.Martin E. R.Huentelman M.Myers A. J.. (2014). Genome-wide association meta-analysis of neuropathologic features of Alzheimer's disease and related dementias. PLoS Genet. 10:e1004606. 10.1371/journal.pgen.1004606 25188341 [OpenAIRE] [PubMed] [DOI]

Chen C.Manichaikul A.Rich S. S. (2009). A generalized family-based association test for dichotomous traits. Am. J. Hum. Genet. 85, 364–376. 10.1016/j.ajhg.2009.08.003 19732865 [OpenAIRE] [PubMed] [DOI]

Cheong C.Hentschel L.Davidson A. E.Gerrelli D.Davie R.Rizzo R.. (2016). Mutations in CPAMD8 cause a unique form of autosomal-recessive anterior segment dysgenesis. Am. J. Hum. Genet.99, 1338–1352. 10.1016/j.ajhg.2016.09.022 27839872 [OpenAIRE] [PubMed] [DOI]

Choi S.Lee S.Cichon S.Nöthen M. M.Lange C.Park T.. (2014). FARVAT: a family-based rare variant association test. Bioinformatics 30, 3197–3205. 10.1093/bioinformatics/btu496 25075118 [OpenAIRE] [PubMed] [DOI]

Cingolani P.Platts A.Wang le L.Melissa Coon W.Nguyen T.Wang L.. (2012). A Program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of drosophila melanogaster strain w1118; Iso-2; Iso-3. Fly (Austin)6, 80–92. 10.4161/fly.19695 22728672 [OpenAIRE] [PubMed] [DOI]

Cirulli E. T.Goldstein D. B. (2010). Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat. Rev. Genet. 11, 415–425. 10.1038/nrg2779 20479773 [OpenAIRE] [PubMed] [DOI]

Cruchaga C.Celeste M. K.Jin S. C.Benitez B. A.Cai Y.Guerreiro R.. (2014). Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer's disease. Nature 505, 550–554. 10.1038/nature12825 24336208 [OpenAIRE] [PubMed] [DOI]

Cruchaga C.Del-Aguila J. L.Saef B.Black K.Fernandez M. V.Budde J.. (2017). Polygenic risk score of sporadic late-onset Alzheimer's disease reveals a shared architecture with the familial and early-onset forms. Alzheimers Dement. 14, 205–214. 10.1016/j.jalz.2017.08.013 28943286 [OpenAIRE] [PubMed] [DOI]

Cruchaga C.Haller G.Chakraverty S.Mayo K.Vallania F. L.M.Mitra R. D.. (2012). Rare variants in APP, PSEN1 and PSEN2 increase risk for AD in Late-onset Alzheimer's disease families. PLoS ONE 7:e31039. 10.1371/journal.pone.0031039 22312439 [OpenAIRE] [PubMed] [DOI]

Cukier H. N.Dueker N. D.Slifer S. H.Lee J. M.Whitehead P. L.Lalanne E.. (2014). Exome sequencing of extended families with autism reveals genes shared across neurodevelopmental and neuropsychiatric disorders. Mol. Autism 5:1. 10.1186/2040-2392-5-1 24410847 [OpenAIRE] [PubMed] [DOI]

De G.Yip W.Ionita-Laza I.Laird N.Amos C. I. (2013). Rare variant analysis for family-based design. PLoS ONE 8:e48495. 10.1371/journal.pone.0048495 23341868 [OpenAIRE] [PubMed] [DOI]

62 references, page 1 of 5
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publication . Article . Preprint . 2018

Evaluation of Gene-Based Family-Based Methods to Detect Novel Genes Associated With Familial Late Onset Alzheimer Disease

Fernández, Maria Victoria; Budde, John; Del-Aguila, Jorge; Ibañez, Laura; Deming, Yuetiva; Harari, Oscar; Norton, Joanne; Morris, John C; Goate, Alison; Cruchaga, Carlos;