1
|
Wang P, Lynn A, Miskimen K, Song YE, Wisniewski T, Cohen M, Appleby BS, Safar JG, Haines JL. Genome-wide association studies identify novel loci in rapidly progressive Alzheimer's disease. Alzheimers Dement 2024; 20:2034-2046. [PMID: 38184787 PMCID: PMC10984493 DOI: 10.1002/alz.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/14/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 01/08/2024]
Abstract
INTRODUCTION Recent data suggest that distinct prion-like amyloid beta and tau strains are associated with rapidly progressive Alzheimer's disease (rpAD). The role of genetic factors in rpAD is largely unknown. METHODS Previously known AD risk loci were examined in rpAD cases. Genome-wide association studies (GWAS) were performed to identify variants that influence rpAD. RESULTS We identified 115 pathology-confirmed rpAD cases and 193 clinical rpAD cases, 80% and 69% were of non-Hispanic European ancestry. Compared to the clinical cohort, pathology-confirmed rpAD had higher frequencies of apolipoprotein E (APOE) ε4 and rare missense variants in AD risk genes. A novel genome-wide significant locus (P < 5×10-8 ) was observed for clinical rpAD on chromosome 21 (rs2832546); 102 loci showed suggestive associations with pathology-confirmed rpAD (P < 1×10-5 ). DISCUSSION rpAD constitutes an extreme subtype of AD with distinct features. GWAS found previously known and novel loci associated with rpAD. Highlights Rapidly progressive Alzheimer's disease (rpAD) was defined with different criteria. Whole genome sequencing identified rare missense variants in rpAD. Novel variants were identified for clinical rpAD on chromosome 21.
Collapse
Affiliation(s)
- Ping Wang
- Department of Population and Quantitative Health SciencesSchool of Medicine, Case Western Reserve UniversityClevelandOhioUSA
| | - Audrey Lynn
- Department of Population and Quantitative Health SciencesSchool of Medicine, Case Western Reserve UniversityClevelandOhioUSA
- Cleveland Institute for Computational BiologyClevelandOhioUSA
| | - Kristy Miskimen
- Department of Population and Quantitative Health SciencesSchool of Medicine, Case Western Reserve UniversityClevelandOhioUSA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health SciencesSchool of Medicine, Case Western Reserve UniversityClevelandOhioUSA
| | - Thomas Wisniewski
- Departments of NeurologyPathology and PsychiatryCenter for Cognitive Neurology, NYU Grossman School of MedicineNew YorkNew YorkUSA
| | - Mark Cohen
- Department of PathologyCase Western Reserve UniversityClevelandOhioUSA
- National Prion Disease Pathology Surveillance CenterCase Western Reserve UniversityClevelandOhioUSA
| | - Brian S. Appleby
- Department of PathologyCase Western Reserve UniversityClevelandOhioUSA
- National Prion Disease Pathology Surveillance CenterCase Western Reserve UniversityClevelandOhioUSA
- Department of NeurologyCase Western Reserve UniversityClevelandOhioUSA
- Department of PsychiatryCase Western Reserve UniversityClevelandOhioUSA
| | - Jiri G. Safar
- Department of PathologyCase Western Reserve UniversityClevelandOhioUSA
- Department of NeurologyCase Western Reserve UniversityClevelandOhioUSA
- Department of NeurosciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Jonathan L. Haines
- Department of Population and Quantitative Health SciencesSchool of Medicine, Case Western Reserve UniversityClevelandOhioUSA
- Cleveland Institute for Computational BiologyClevelandOhioUSA
| |
Collapse
|
2
|
Ho P, Yu WH, Tee BL, Lee W, Li C, Gu Y, Yokoyama JS, Reyes‐Dumeyer D, Choi Y, Yang H, Vardarajan BN, Tzuang M, Lieu K, Lu A, Faber KM, Potter ZD, Revta C, Kirsch M, McCallum J, Mei D, Booth B, Cantwell LB, Chen F, Chou S, Clark D, Deng M, Hong TH, Hwang L, Jiang L, Joo Y, Kang Y, Kim ES, Kim H, Kim K, Kuzma AB, Lam E, Lanata SC, Lee K, Li D, Li M, Li X, Liu C, Liu C, Liu L, Lupo J, Nguyen K, Pfleuger SE, Qian J, Qian W, Ramirez V, Russ KA, Seo EH, Song YE, Tartaglia MC, Tian L, Torres M, Vo N, Wong EC, Xie Y, Yau EB, Yi I, Yu V, Zeng X, St George‐Hyslop P, Au R, Schellenberg GD, Dage JL, Varma R, Hsiung GR, Rosen H, Henderson VW, Foroud T, Kukull WA, Peavy GM, Lee H, Feldman HH, Mayeux R, Chui H, Jun GR, Ta Park VM, Chow TW, Wang L. Asian Cohort for Alzheimer's Disease (ACAD) pilot study on genetic and non-genetic risk factors for Alzheimer's disease among Asian Americans and Canadians. Alzheimers Dement 2024; 20:2058-2071. [PMID: 38215053 PMCID: PMC10984480 DOI: 10.1002/alz.13611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/17/2023] [Revised: 09/25/2023] [Accepted: 11/27/2023] [Indexed: 01/14/2024]
Abstract
INTRODUCTION Clinical research in Alzheimer's disease (AD) lacks cohort diversity despite being a global health crisis. The Asian Cohort for Alzheimer's Disease (ACAD) was formed to address underrepresentation of Asians in research, and limited understanding of how genetics and non-genetic/lifestyle factors impact this multi-ethnic population. METHODS The ACAD started fully recruiting in October 2021 with one central coordination site, eight recruitment sites, and two analysis sites. We developed a comprehensive study protocol for outreach and recruitment, an extensive data collection packet, and a centralized data management system, in English, Chinese, Korean, and Vietnamese. RESULTS ACAD has recruited 606 participants with an additional 900 expressing interest in enrollment since program inception. DISCUSSION ACAD's traction indicates the feasibility of recruiting Asians for clinical research to enhance understanding of AD risk factors. ACAD will recruit > 5000 participants to identify genetic and non-genetic/lifestyle AD risk factors, establish blood biomarker levels for AD diagnosis, and facilitate clinical trial readiness. HIGHLIGHTS The Asian Cohort for Alzheimer's Disease (ACAD) promotes awareness of under-investment in clinical research for Asians. We are recruiting Asian Americans and Canadians for novel insights into Alzheimer's disease. We describe culturally appropriate recruitment strategies and data collection protocol. ACAD addresses challenges of recruitment from heterogeneous Asian subcommunities. We aim to implement a successful recruitment program that enrolls across three Asian subcommunities.
Collapse
Affiliation(s)
- Pei‐Chuan Ho
- Penn Neurodegeneration Genomics CenterDepartment of PathologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- The Leonard Davis Institute of Health EconomicsUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Wai Haung Yu
- Brain Health and Imaging Center and Geriatric Mental Health ServicesCentre for Addiction and Mental HealthTorontoOntarioCanada
- Department of Pharmacology and ToxicologyUniversity of TorontoTorontoOntarioCanada
| | - Boon Lead Tee
- Memory and Aging CenterDepartment of NeurologyWeill Institute for NeurosciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
- Global Brain Health InstituteUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Wan‐Ping Lee
- Penn Neurodegeneration Genomics CenterDepartment of PathologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Clara Li
- Alzheimer's Disease Research CenterDepartment of PsychiatryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Yian Gu
- Department of NeurologyColumbia University Medical CenterNew YorkNew YorkUSA
| | - Jennifer S. Yokoyama
- Memory and Aging CenterDepartment of NeurologyWeill Institute for NeurosciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
- Department of Radiology and Biomedical ImagingUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Dolly Reyes‐Dumeyer
- Gertrude H. Sergievsky CenterTaub Institute of Aging Brain and Department of Neurology at Columbia UniversityNew YorkNew YorkUSA
| | - Yun‐Beom Choi
- Englewood HealthEnglewoodNew JerseyUSA
- Department of NeurologyRutgers New Jersey Medical SchoolNewarkNew JerseyUSA
| | - Hyun‐Sik Yang
- Center for Alzheimer Research and TreatmentDepartment of NeurologyBrigham and Women's HospitalBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Badri N. Vardarajan
- Gertrude H. Sergievsky CenterTaub Institute of Aging Brain and Department of Neurology at Columbia UniversityNew YorkNew YorkUSA
| | - Marian Tzuang
- Department of Community Health SystemsUniversity of California San Francisco School of NursingSan FranciscoCaliforniaUSA
| | - Kevin Lieu
- Memory and Aging CenterDepartment of NeurologyWeill Institute for NeurosciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Anna Lu
- Alzheimer's Disease Cooperative StudyUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Kelley M. Faber
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Zoë D. Potter
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Carolyn Revta
- Alzheimer's Disease Cooperative StudyUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Maureen Kirsch
- Penn Neurodegeneration Genomics CenterDepartment of PathologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Jake McCallum
- Geriatric Mental Health Services, Centre for Addiction and Mental HealthTorontoOntarioCanada
| | - Diana Mei
- Memory and Aging CenterDepartment of NeurologyWeill Institute for NeurosciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Briana Booth
- Penn Neurodegeneration Genomics CenterDepartment of PathologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Laura B. Cantwell
- Penn Neurodegeneration Genomics CenterDepartment of PathologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Fangcong Chen
- Department of NeurologyColumbia University Medical CenterNew YorkNew YorkUSA
| | - Sephera Chou
- Geriatric Mental Health Services, Centre for Addiction and Mental HealthTorontoOntarioCanada
| | - Dewi Clark
- Geriatric Mental Health Services, Centre for Addiction and Mental HealthTorontoOntarioCanada
| | - Michelle Deng
- Geriatric Mental Health Services, Centre for Addiction and Mental HealthTorontoOntarioCanada
| | - Ting Hei Hong
- University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Ling‐Jen Hwang
- Stanford Alzheimer's Disease Research CenterStanfordCaliforniaUSA
| | - Lilly Jiang
- University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Yoonmee Joo
- Department of Community Health SystemsUniversity of California San Francisco School of NursingSan FranciscoCaliforniaUSA
| | - Younhee Kang
- College of NursingGraduate Program in System Health Science and EngineeringEwha Womans UniversitySeoulRepublic of Korea
| | - Ellen S. Kim
- Division of NeurologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Hoowon Kim
- Department of NeurologyChosun University Hospital, Dong‐guGwangjuRepublic of Korea
| | - Kyungmin Kim
- Department of Child Development and Family StudiesCollege of Human EcologySeoul National UniversityJongno‐guSeoulRepublic of Korea
| | - Amanda B. Kuzma
- Penn Neurodegeneration Genomics CenterDepartment of PathologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Eleanor Lam
- Geriatric Mental Health Services, Centre for Addiction and Mental HealthTorontoOntarioCanada
| | - Serggio C. Lanata
- Memory and Aging CenterDepartment of NeurologyWeill Institute for NeurosciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Kunho Lee
- Biomedical Science, College of Natural SciencesChosun UniversityGwanak‐guSeoulRepublic of Korea
| | - Donghe Li
- Department of Medicine (Biomedical Genetics)Boston University School of MedicineBostonMassachusettsUSA
| | - Mingyao Li
- Department of BiostatisticsEpidemiology and InformaticsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Xiang Li
- Geriatric Mental Health Services, Centre for Addiction and Mental HealthTorontoOntarioCanada
| | - Chia‐Lun Liu
- Penn Neurodegeneration Genomics CenterDepartment of PathologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Collin Liu
- Department of NeurologyKeck School of Medicine at University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Linghsi Liu
- Alzheimer's Disease Research CenterDepartment of PsychiatryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Jody‐Lynn Lupo
- Alzheimer's Disease Cooperative StudyUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Khai Nguyen
- Department of MedicineUniversity of California at San DiegoLa JollaCaliforniaUSA
| | - Shannon E. Pfleuger
- Division of NeurologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - James Qian
- Memory and Aging CenterDepartment of NeurologyWeill Institute for NeurosciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Winnie Qian
- Geriatric Mental Health Services, Centre for Addiction and Mental HealthTorontoOntarioCanada
| | - Veronica Ramirez
- Stanford Alzheimer's Disease Research CenterStanfordCaliforniaUSA
| | - Kristen A. Russ
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Eun Hyun Seo
- Premedical Science, College of MedicineChosun University, Dong‐guGwangjuRepublic of Korea
| | - Yeunjoo E. Song
- Department of Population & Quantitative Health SciencesSchool of MedicineCase Western Reserve UniversityClevelandOhioUSA
| | - Maria Carmela Tartaglia
- Tanz Centre for Research in Neurodegenerative DiseasesUniversity of TorontoTorontoOntarioCanada
| | - Lu Tian
- Department of Biomedical Data ScienceStanford University School of MedicineStanfordCaliforniaUSA
| | - Mina Torres
- Southern California Eye Institute, CHA Hollywood Presbyterian Medical CenterLos AngelesCaliforniaUSA
| | - Namkhue Vo
- Alzheimer's Disease Cooperative StudyUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Ellen C. Wong
- Department of NeurologyKeck School of Medicine at University of Southern CaliforniaLos AngelesCaliforniaUSA
- Department of NeurologyRancho Los Amigos National Rehabilitation CenterDowneyCaliforniaUSA
| | - Yuan Xie
- Department of NeurologyColumbia University Medical CenterNew YorkNew YorkUSA
| | - Eugene B. Yau
- Division of NeurologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Isabelle Yi
- Stanford Alzheimer's Disease Research CenterStanfordCaliforniaUSA
| | - Victoria Yu
- Department of OphthalmologyKeck School of Medicine at University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Xiaoyi Zeng
- Alzheimer's Disease Research CenterDepartment of PsychiatryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Peter St George‐Hyslop
- Tanz Centre for Research in Neurodegenerative DiseasesUniversity of TorontoTorontoOntarioCanada
- Department of Neurology and the Taub Institute for Research on Alzheimer's Disease and the Aging BrainColumbia UniversityNew YorkNew YorkUSA
| | - Rhoda Au
- Department of Anatomy and NeurobiologySlone Epidemiology CenterBoston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
- Department of EpidemiologyBoston University School of Public HealthBostonMassachusettsUSA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics CenterDepartment of PathologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Jeffrey L. Dage
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
- Department of NeurologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Rohit Varma
- Southern California Eye Institute, CHA Hollywood Presbyterian Medical CenterLos AngelesCaliforniaUSA
| | - Ging‐Yuek R. Hsiung
- Division of NeurologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Howard Rosen
- Memory and Aging CenterDepartment of NeurologyWeill Institute for NeurosciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Victor W. Henderson
- Department of Epidemiology and Population HealthStanford UniversityStanfordCaliforniaUSA
- Department of Neurology & Neurological SciencesStanford UniversityStanfordCaliforniaUSA
| | - Tatiana Foroud
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Walter A. Kukull
- Department of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Guerry M. Peavy
- Department of NeurosciencesUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Haeok Lee
- Rory Meyers College of NursingNew York UniversityNew YorkNew YorkUSA
| | - Howard H. Feldman
- Alzheimer's Disease Cooperative StudyUniversity of California, San DiegoLa JollaCaliforniaUSA
- Department of NeurosciencesUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Richard Mayeux
- Department of Neurology and the Taub Institute for Research on Alzheimer's Disease and the Aging BrainColumbia University, Vagelos College of Physicians and SurgeonsNew YorkNew YorkUSA
| | - Helena Chui
- Department of NeurologyKeck School of Medicine at University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Gyungah R. Jun
- Department of Medicine (Biomedical Genetics)Boston University School of MedicineBostonMassachusettsUSA
- Department of OphthalmologyBoston University School of MedicineBostonMassachusettsUSA
- Department of BiostatisticsBoston University School of Public HealthBostonMassachusettsUSA
| | - Van M. Ta Park
- Department of Community Health SystemsUniversity of California San Francisco School of NursingSan FranciscoCaliforniaUSA
- Asian American Research Center on Health (ARCH)University of California San Francisco School of NursingSan FranciscoCaliforniaUSA
| | - Tiffany W. Chow
- Penn Neurodegeneration Genomics CenterDepartment of PathologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Alector Inc.South San FranciscoCaliforniaUSA
| | - Li‐San Wang
- Penn Neurodegeneration Genomics CenterDepartment of PathologyPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| |
Collapse
|
3
|
Main LR, Song YE, Lynn A, Laux RA, Miskimen KL, Osterman MD, Cuccaro ML, Ogrocki PK, Lerner AJ, Vance JM, Fuzzell MD, Fuzzell SL, Hochstetler SD, Dorfsman DA, Caywood LJ, Prough MB, Adams LD, Clouse JE, Herington SD, Scott WK, Pericak-Vance MA, Haines JL. Genetic analysis of cognitive preservation in the midwestern Amish reveals a novel locus on chromosome 2. medRxiv 2023:2023.12.13.23299932. [PMID: 38168325 PMCID: PMC10760262 DOI: 10.1101/2023.12.13.23299932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
INTRODUCTION Alzheimer disease (AD) remains a debilitating condition with limited treatments and additional therapeutic targets needed. Identifying AD protective genetic loci may identify new targets and accelerate identification of therapeutic treatments. We examined a founder population to identify loci associated with cognitive preservation into advanced age. METHODS Genome-wide association and linkage analyses were performed on 946 examined and sampled Amish individuals, aged 76-95, who were either cognitively unimpaired (CU) or impaired (CI). RESULTS 12 SNPs demonstrated suggestive association (P≤5×10-4) with cognitive preservation. Genetic linkage analyses identified >100 significant (LOD≥3.3) SNPs, some which overlapped with the association results. Only one locus on chromosome 2 retained significance across multiple analyses. DISCUSSION A novel significant result for cognitive preservation on chromosome 2 includes the genes LRRTM4 and CTNNA2. Additionally, the lead SNP, rs1402906, impacts the POU3F2 transcription factor binding affinity, which regulates LRRTM4 and CTNNA2.
Collapse
Affiliation(s)
- Leighanne R Main
- Departments of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, USA, 44106
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
- Cleveland Institute of Computational Biology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
| | - Yeunjoo E Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
- Cleveland Institute of Computational Biology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
- Cleveland Institute of Computational Biology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
| | - Renee A Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Kristy L Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Michael D Osterman
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Michael L Cuccaro
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Paula K Ogrocki
- Department of Neurology, University Hospitals Cleveland Medical Center, 11100 Euclid Ave, Cleveland, OH, USA, 44106
- Department of Neurology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
| | - Alan J Lerner
- Department of Neurology, University Hospitals Cleveland Medical Center, 11100 Euclid Ave, Cleveland, OH, USA, 44106
- Department of Neurology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
| | - Jeffery M Vance
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - M Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Sarada L Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Sherri D Hochstetler
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
| | - Daniel A Dorfsman
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Laura J Caywood
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Michael B Prough
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Larry D Adams
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Jason E Clouse
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Sharlene D Herington
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - William K Scott
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Margaret A Pericak-Vance
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, USA, 33136
| | - Jonathan L Haines
- Departments of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, USA, 44106
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44016
- Cleveland Institute of Computational Biology, Case Western Reserve University School of Medicine, 10900 Euclid Ave, Cleveland, OH, USA, 44106
| |
Collapse
|
4
|
Osterman MD, Song YE, Lynn A, Miskimen K, Adams LD, Laux RA, Caywood LJ, Prough MB, Clouse JE, Herington SD, Slifer SH, Fuzzell SL, Hochstetler SD, Main LR, Dorfsman DA, Zaman AF, Ogrocki P, Lerner AJ, Vance JM, Cuccaro ML, Scott WK, Pericak-Vance MA, Haines JL. Founder population-specific weights yield improvements in performance of polygenic risk scores for Alzheimer disease in the Midwestern Amish. HGG Adv 2023; 4:100241. [PMID: 37742071 PMCID: PMC10565871 DOI: 10.1016/j.xhgg.2023.100241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/21/2023] [Revised: 09/16/2023] [Accepted: 09/16/2023] [Indexed: 09/25/2023] Open
Abstract
Alzheimer disease (AD) is the most common type of dementia and is estimated to affect 6 million Americans. Risk for AD is multifactorial, including both genetic and environmental risk factors. AD genomic research has generally focused on identification of risk variants. Using this information, polygenic risk scores (PRSs) can be calculated to quantify an individual's relative disease risk due to genetic factors. The Amish are a founder population descended from German and Swiss Anabaptist immigrants. They experienced a genetic bottleneck after arrival in the United States, making their genetic architecture different from the broader European ancestry population. Prior work has demonstrated the lack of transferability of PRSs across populations. Here, we compared the performance of PRSs derived from genome-wide association studies (GWASs) of Amish individuals to those derived from a large European ancestry GWAS. Participants were screened for cognitive impairment with further evaluation for AD. Genotype data were imputed after collection via Illumina genotyping arrays. The Amish individuals were split into two groups based on the primary site of recruitment. For each group, GWAS was conducted with account for relatedness and adjustment for covariates. PRSs were then calculated using weights from the other Amish group. PRS models were evaluated with and without covariates. The Amish-derived PRSs distinguished between dementia status better than the European-derived PRS in our Amish populations and demonstrated performance improvements despite a smaller training sample size. This work highlighted considerations for AD PRS usage in populations that cannot be adequately described by basic race/ethnicity or ancestry classifications.
Collapse
Affiliation(s)
- Michael D Osterman
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA.
| | - Yeunjoo E Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Kristy Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Larry D Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Renee A Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Laura J Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael B Prough
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jason E Clouse
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sharlene D Herington
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Susan H Slifer
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sarada L Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Sherri D Hochstetler
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Leighanne R Main
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA; Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Daniel A Dorfsman
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Andrew F Zaman
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Paula Ogrocki
- Department of Neurology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA; Department of Neurology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Alan J Lerner
- Department of Neurology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA; Department of Neurology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA.
| |
Collapse
|
5
|
Celis K, Zaman A, Adams LD, Gardner O, Farid R, Starks TD, Lacroix FC, Hamilton-Nelson K, Mena P, Tejada S, Laux R, Song YE, Caban-Holt A, Feliciano-Astacio B, Vance JM, Haines JL, Byrd GS, Beecham GW, Pericak-Vance MA, Cuccaro ML. Neuropsychiatric features in a multi-ethnic population with Alzheimer disease and mild cognitive impairment. Int J Geriatr Psychiatry 2023; 38:e5992. [PMID: 37655494 PMCID: PMC10518518 DOI: 10.1002/gps.5992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 08/12/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND Alzheimer disease (AD) is more prevalent in African American (AA) and Hispanic White (HIW) compared to Non-Hispanic White (NHW) individuals. Similarly, neuropsychiatric symptoms (NPS) vary by population in AD. This is likely the result of both sociocultural and genetic ancestral differences. However, the impact of these NPS on AD in different groups is not well understood. METHODS Self-declared AA, HIW, and NHW individuals were ascertained as part of ongoing AD genetics studies. Participants who scored higher than 0.5 on the Clinical Dementia Rating (CDR) Scale (CDR) were included. Group similarities and differences on Neuropsychiatric Inventory Questionnaire (NPI-Q) outcomes (NPI-Q total score, NPI-Q items) were evaluated using univariate ANOVAs and post hoc comparisons after controlling for sex and CDR stage. RESULTS Our sample consisted of 498 participants (26% AA; 30% HIW; 44% NHW). Overall, NPI-Q total scores differed significantly between our groups, with HIW having the highest NPI-Q total scores, and by AD stage as measured by CDR. We found no significant difference in NPI-Q total score by sex. There were six NPI-Q items with comparable prevalence in all groups and six items that significantly differed between the groups (Anxiety, Apathy, Depression, Disinhibition, Elation, and Irritability). Further, within the HIW group, differences were found between Puerto Rican and Cuban American Hispanics across several NPI-Q items. Finally, Six NPI-Q items were more prevalent in the later stages of AD including Agitation, Appetite, Hallucinations, Irritability, Motor Disturbance, and Nighttime Behavior. CONCLUSIONS We identified differences in NPS among HIW, AA, and NHW individuals. Most striking was the high burden of NPS in HIW, particularly for mood and anxiety symptoms. We suggest that NPS differences may represent the impact of sociocultural influences on symptom presentation as well as potential genetic factors rooted in ancestral background. Given the complex relationship between AD and NPS it is crucial to discern the presence of NPS to ensure appropriate interventions.
Collapse
Affiliation(s)
- Katrina Celis
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Andrew Zaman
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Larry Deon Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Olivia Gardner
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Rajabli Farid
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Takiyah D Starks
- Maya Angelou Center for Health Equity, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Faina C Lacroix
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Kara Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Pedro Mena
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Sergio Tejada
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Renee Laux
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yeunjoo E Song
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Allison Caban-Holt
- Maya Angelou Center for Health Equity, Wake Forest University, Winston-Salem, North Carolina, USA
| | | | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Jonathan L Haines
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Cleveland Institute for Computational Biology, Cleveland, Ohio, USA
| | - Goldie S Byrd
- Maya Angelou Center for Health Equity, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| |
Collapse
|
6
|
Grunin M, Igo RP, Song YE, Blanton SH, Pericak-Vance MA, Haines JL. Identifying X-Chromosome Variants Associated with Age-Related Macular Degeneration. medRxiv 2023:2023.08.28.23294688. [PMID: 37693625 PMCID: PMC10491266 DOI: 10.1101/2023.08.28.23294688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Purpose In genome-wide association studies (GWAS), X chromosome (ChrX) variants are often not investigated. Sex-specific effects and ChrX-specific quality control (QC) are needed to examine these effects. Previous analyses identified 52 autosomal variants associated with age-related macular degeneration (AMD) via the International AMD Genomics Consortium (IAMDGC), but did not analyze ChrX. Therefore, our goal was to investigate ChrX variants for association with AMD. Methods We genotyped 29,629 non-Hispanic White (NHW) individuals (M/F:10,404/18,865; AMD12,087/14723) via a custom chip and imputed after ChrX-specific QC (XWAS 3.0) using the Michigan Imputation Server. Imputation generated 1,221,623 variants on ChrX. Age, informative PCs, and subphenotyeps were covariates for logistic association analyses with Fishers correction. Gene/pathway analyses were performed with VEGAS, GSEASNP, ICSNPathway, DAVID, and mirPath. Results Logistic association on NHW individuals with sex correction, identified variants in/near the genes SLITRK4, ARHGAP6, FGF13 and DMD associated with AMD (P<1x10 -6 ,Fishers combined-corrected). Via association testing of subphenotypes of choroidal neovascularization and geographic atrophy (GA), variants in DMD associated with GA (P<1x10 -6 , Fishers combined-corrected). Via gene-based analysis with VEGAS, several genes were associated with AMD (P<0.05, both truncated tail strength/truncated product P) including SLITRK4 and BHLHB9 . Pathway analysis using GSEASNP and DAVID showed genes associated with nervous system development (FDR: P:0.02), and blood coagulation (FDR: P:0.03). Variants in the region of a microRNA (miR) were associated with AMD (P<0.05, truncated tail strength/truncated product P). Via DIANA mirPath analysis, downstream targets of miRs show association with brain disorders and fatty acid elongation (P<0.05). A long-non coding RNA on ChrX near the DMD locus was also associated with AMD (P=4x10 -7 ). Epistatic analysis (t-statistic) for a quantitative trait of AMD vs control including covariates found a suggestive association in the XG gene (P=2x10^-5). Conclusions Analysis of ChrX variants demonstrates association with AMD and these variants may be linked to novel pathways. Further analysis is needed to confirm results and to understand their biological significance and relationship with AMD development in worldwide populations.
Collapse
|
7
|
Rajabli F, Benchek P, Tosto G, Kushch N, Sha J, Bazemore K, Zhu C, Lee WP, Haut J, Hamilton-Nelson KL, Wheeler NR, Zhao Y, Farrell JJ, Grunin MA, Leung YY, Kuksa PP, Li D, Lucio da Fonseca E, Mez JB, Palmer EL, Pillai J, Sherva RM, Song YE, Zhang X, Iqbal T, Pathak O, Valladares O, Kuzma AB, Abner E, Adams PM, Aguirre A, Albert MS, Albin RL, Allen M, Alvarez L, Apostolova LG, Arnold SE, Asthana S, Atwood CS, Ayres G, Baldwin CT, Barber RC, Barnes LL, Barral S, Beach TG, Becker JT, Beecham GW, Beekly D, Benitez BA, Bennett D, Bertelson J, Bird TD, Blacker D, Boeve BF, Bowen JD, Boxer A, Brewer J, Burke JR, Burns JM, Buxbaum JD, Cairns NJ, Cantwell LB, Cao C, Carlson CS, Carlsson CM, Carney RM, Carrasquillo MM, Chasse S, Chesselet MF, Chin NA, Chui HC, Chung J, Craft S, Crane PK, Cribbs DH, Crocco EA, Cruchaga C, Cuccaro ML, Cullum M, Darby E, Davis B, De Jager PL, DeCarli C, DeToledo J, Dick M, Dickson DW, Dombroski BA, Doody RS, Duara R, Ertekin-Taner NI, Evans DA, Faber KM, Fairchild TJ, Fallon KB, Fardo DW, Farlow MR, Fernandez-Hernandez V, Ferris S, Foroud TM, Frosch MP, Fulton-Howard B, Galasko DR, Gamboa A, Gearing M, Geschwind DH, Ghetti B, Gilbert JR, Goate AM, Grabowski TJ, Graff-Radford NR, Green RC, Growdon JH, Hakonarson H, Hall J, Hamilton RL, Harari O, Hardy J, Harrell LE, Head E, Henderson VW, Hernandez M, Hohman T, Honig LS, Huebinger RM, Huentelman MJ, Hulette CM, Hyman BT, Hynan LS, Ibanez L, Jarvik GP, Jayadev S, Jin LW, Johnson K, Johnson L, Kamboh MI, Karydas AM, Katz MJ, Kauwe JS, Kaye JA, Keene CD, Khaleeq A, Kim R, Knebl J, Kowall NW, Kramer JH, Kukull WA, LaFerla FM, Lah JJ, Larson EB, Lerner A, Leverenz JB, Levey AI, Lieberman AP, Lipton RB, Logue M, Lopez OL, Lunetta KL, Lyketsos CG, Mains D, Margaret FE, Marson DC, Martin ERR, Martiniuk F, Mash DC, Masliah E, Massman P, Masurkar A, McCormick WC, McCurry SM, McDavid AN, McDonough S, McKee AC, Mesulam M, Miller BL, Miller CA, Miller JW, Montine TJ, Monuki ES, Morris JC, Mukherjee S, Myers AJ, Nguyen T, O'Bryant S, Olichney JM, Ory M, Palmer R, Parisi JE, Paulson HL, Pavlik V, Paydarfar D, Perez V, Peskind E, Petersen RC, Pierce A, Polk M, Poon WW, Potter H, Qu L, Quiceno M, Quinn JF, Raj A, Raskind M, Reiman EM, Reisberg B, Reisch JS, Ringman JM, Roberson ED, Rodriguear M, Rogaeva E, Rosen HJ, Rosenberg RN, Royall DR, Sager MA, Sano M, Saykin AJ, Schneider JA, Schneider LS, Seeley WW, Slifer SH, Small S, Smith AG, Smith JP, Sonnen JA, Spina S, St George-Hyslop P, Stern RA, Stevens AB, Strittmatter SM, Sultzer D, Swerdlow RH, Tanzi RE, Tilson JL, Trojanowski JQ, Troncoso JC, Tsuang DW, Van Deerlin VM, van Eldik LJ, Vance JM, Vardarajan BN, Vassar R, Vinters HV, Vonsattel JP, Weintraub S, Welsh-Bohmer KA, Whitehead PL, Wijsman EM, Wilhelmsen KC, Williams B, Williamson J, Wilms H, Wingo TS, Wisniewski T, Woltjer RL, Woon M, Wright CB, Wu CK, Younkin SG, Yu CE, Yu L, Zhu X, Kunkle BW, Bush WS, Wang LS, Farrer LA, Haines JL, Mayeux R, Pericak-Vance MA, Schellenberg GD, Jun GR, Reitz C, Naj AC. Multi-ancestry genome-wide meta-analysis of 56,241 individuals identifies LRRC4C, LHX5-AS1 and nominates ancestry-specific loci PTPRK , GRB14 , and KIAA0825 as novel risk loci for Alzheimer's disease: the Alzheimer's Disease Genetics Consortium. medRxiv 2023:2023.07.06.23292311. [PMID: 37461624 PMCID: PMC10350126 DOI: 10.1101/2023.07.06.23292311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Limited ancestral diversity has impaired our ability to detect risk variants more prevalent in non-European ancestry groups in genome-wide association studies (GWAS). We constructed and analyzed a multi-ancestry GWAS dataset in the Alzheimer's Disease (AD) Genetics Consortium (ADGC) to test for novel shared and ancestry-specific AD susceptibility loci and evaluate underlying genetic architecture in 37,382 non-Hispanic White (NHW), 6,728 African American, 8,899 Hispanic (HIS), and 3,232 East Asian individuals, performing within-ancestry fixed-effects meta-analysis followed by a cross-ancestry random-effects meta-analysis. We identified 13 loci with cross-ancestry associations including known loci at/near CR1 , BIN1 , TREM2 , CD2AP , PTK2B , CLU , SHARPIN , MS4A6A , PICALM , ABCA7 , APOE and two novel loci not previously reported at 11p12 ( LRRC4C ) and 12q24.13 ( LHX5-AS1 ). Reflecting the power of diverse ancestry in GWAS, we observed the SHARPIN locus using 7.1% the sample size of the original discovering single-ancestry GWAS (n=788,989). We additionally identified three GWS ancestry-specific loci at/near ( PTPRK ( P =2.4×10 -8 ) and GRB14 ( P =1.7×10 -8 ) in HIS), and KIAA0825 ( P =2.9×10 -8 in NHW). Pathway analysis implicated multiple amyloid regulation pathways (strongest with P adjusted =1.6×10 -4 ) and the classical complement pathway ( P adjusted =1.3×10 -3 ). Genes at/near our novel loci have known roles in neuronal development ( LRRC4C, LHX5-AS1 , and PTPRK ) and insulin receptor activity regulation ( GRB14 ). These findings provide compelling support for using traditionally-underrepresented populations for gene discovery, even with smaller sample sizes.
Collapse
|
8
|
Prough MB, Zaman A, Caywood LJ, Clouse JE, Herington SD, Slifer SH, Dorfsman DA, Adams LA, Laux RA, Song YE, Lynn A, Fuzzell D, Fuzzell SL, Miller SD, Miskimen K, Main LR, Osterman MD, Ogrocki P, Lerner AJ, Vance JM, Haines JL, Scott WK, Pericak-Vance M, Cuccaro ML. Visuospatial and Verbal Memory Differences in Amish Individuals With Alzheimer Disease and Related Dementias. Alzheimer Dis Assoc Disord 2023; 37:195-199. [PMID: 37561946 PMCID: PMC10529392 DOI: 10.1097/wad.0000000000000570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/07/2023] [Accepted: 06/13/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND Verbal and visuospatial memory impairments are common to Alzheimer disease and Related Dementias (ADRD), but the patterns of decline in these domains may reflect genetic and lifestyle influences. The latter may be pertinent to populations such as the Amish who have unique lifestyle experiences. METHODS Our data set included 420 Amish and 401 CERAD individuals. Sex-adjusted, age-adjusted, and education-adjusted Z-scores were calculated for the recall portions of the Constructional Praxis Delay (CPD) and Word List Delay (WLD). ANOVAs were then used to examine the main and interaction effects of cohort (Amish, CERAD), cognitive status (case, control), and sex on CPD and WLD Z-scores. RESULTS The Amish performed better on the CPD than the CERAD cohort. In addition, the difference between cases and controls on the CPD and WLD were smaller in the Amish and Amish female cases performed better on the WLD than the CERAD female cases. DISCUSSION The Amish performed better on the CPD task, and ADRD-related declines in CPD and WLD were less severe in the Amish. In addition, Amish females with ADRD may have preferential preservation of WLD. This study provides evidence that the Amish exhibit distinct patterns of verbal and visuospatial memory loss associated with aging and ADRD.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Reneé A Laux
- Department of Population and Quantitative Health Sciences
| | - Yeunjoo E Song
- Department of Population and Quantitative Health Sciences
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences
| | - Denise Fuzzell
- Department of Population and Quantitative Health Sciences
| | | | | | | | - Leighanne R Main
- Department of Genetics and Genome Sciences
- Cleveland Institute for Computational Biology, Case Western Reserve University
| | - Michael D Osterman
- Department of Population and Quantitative Health Sciences
- Cleveland Institute for Computational Biology, Case Western Reserve University
| | - Paula Ogrocki
- Department of Neurology, Case Western Reserve University School of Medicine
- Department of Neurology, University Hospitals Cleveland Medical Center, Cleveland, OH
| | - Alan J Lerner
- Department of Neurology, Case Western Reserve University School of Medicine
- Department of Neurology, University Hospitals Cleveland Medical Center, Cleveland, OH
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences
- Cleveland Institute for Computational Biology, Case Western Reserve University
| | - William K Scott
- John P. Hussman Institute for Human Genomics
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL
| | - Margaret Pericak-Vance
- John P. Hussman Institute for Human Genomics
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL
| |
Collapse
|
9
|
Ramos J, Caywood LJ, Prough MB, Clouse JE, Herington SD, Slifer SH, Fuzzell MD, Fuzzell SL, Hochstetler SD, Miskimen KL, Main LR, Osterman MD, Zaman AF, Whitehead PL, Adams LD, Laux RA, Song YE, Foroud TM, Mayeux RP, George-Hyslop PS, Ogrocki PK, Lerner AJ, Vance JM, Cuccaro ML, Haines JL, Pericak-Vance MA, Scott WK. Genetic variants in the SHISA6 gene are associated with delayed cognitive impairment in two family datasets. Alzheimers Dement 2023; 19:611-620. [PMID: 35490390 PMCID: PMC9622429 DOI: 10.1002/alz.12686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/23/2021] [Revised: 03/08/2022] [Accepted: 03/28/2022] [Indexed: 11/12/2022]
Abstract
INTRODUCTION Studies of cognitive impairment (CI) in Amish communities have identified sibships containing CI and cognitively unimpaired (CU) individuals. We hypothesize that CU individuals may carry protective alleles delaying age at onset (AAO) of CI. METHODS A total of 1522 individuals screened for CI were genotyped. The outcome studied was AAO for CI individuals or age at last normal exam for CU individuals. Cox mixed-effects models examined association between age and single nucleotide variants (SNVs). RESULTS Three SNVs were significantly associated (P < 5 × 10-8 ) with AAO on chromosomes 6 (rs14538074; hazard ratio [HR] = 3.35), 9 (rs534551495; HR = 2.82), and 17 (rs146729640; HR = 6.38). The chromosome 17 association was replicated in the independent National Institute on Aging Genetics Initiative for Late-Onset Alzheimer's Disease dataset. DISCUSSION The replicated genome-wide significant association with AAO on chromosome 17 is located in the SHISA6 gene, which is involved in post-synaptic transmission in the hippocampus and is a biologically plausible candidate gene for Alzheimer's disease.
Collapse
Affiliation(s)
- Jairo Ramos
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael B. Prough
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jason E. Clouse
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Susan H. Slifer
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - M. Denise Fuzzell
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Sarada L. Fuzzell
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | | | | | - Leighanne R. Main
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Michael D. Osterman
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Andrew F. Zaman
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Patrice L. Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Renee A. Laux
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Yeunjoo E. Song
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Tatiana M. Foroud
- Indiana Alzheimer’s Disease Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Richard P. Mayeux
- Taub Institute on Alzheimer’s Disease and the Aging Brain, Department of Neurology, Columbia University, New York, NY, USA
- Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
- Department of Neurology, Columbia University, New York, NY, USA
| | | | - Paula K. Ogrocki
- University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Alan J. Lerner
- University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jonathan L. Haines
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - William K. Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| |
Collapse
|
10
|
Main LR, Song YE, Laux RA, Miskimen KL, Cuccaro ML, Ogrocki PK, Lerner AJ, Vance JM, Fuzzell MD, Fuzzell SL, Hochstetler SD, Osterman MD, Lynn A, Dorfsman DA, Caywood LJ, Prough MB, Adams LD, Clouse JE, Herington SD, Scott WK, Pericak‐Vance MA, Haines JL. Detecting genetic loci for preservation of cognition in the Midwestern United States Amish. Alzheimers Dement 2022. [DOI: 10.1002/alz.061554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Leighanne R. Main
- Department of Genetics and Genome Sciences, Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
| | - Yeunjoo E. Song
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Kristy L. Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Paula K. Ogrocki
- Brain Health and Memory Center, University Hospital Cleveland OH USA
- Department of Neurology, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Alan J. Lerner
- Brain Health and Memory Center, University Hospital Cleveland OH USA
- Department of Neurology, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miami FL USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Sherri D. Hochstetler
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Michael D. Osterman
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Daniel A. Dorfsman
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Michael B. Prough
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Jason E. Clouse
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - William K. Scott
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Jonathan L. Haines
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| |
Collapse
|
11
|
Osterman MD, Song YE, Wheeler NR, Laux RA, Adams LD, Caywood LJ, Prough MB, Clouse JE, Herington SD, Slifer SH, Lynn A, Bartlett J, Fuzzell MD, Fuzzell SL, Hochstetler SD, Miskimen KL, Main LR, Dorfsman DA, Ogrocki PK, Lerner AJ, Vance JM, Cuccaro ML, Bush WS, Scott WK, Pericak‐Vance MA, Haines JL. Assessing a Network‐Specific Polygenic Risk Score for Alzheimer’s Disease in the Midwestern Amish and Across Diverse Ancestries. Alzheimers Dement 2022. [DOI: 10.1002/alz.067210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Michael D. Osterman
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | | | - Renee A. Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Larry D. Adams
- University of Miami Miller School of Medicine Miami FL USA
| | | | | | | | | | | | - Audrey Lynn
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | | | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | | | - Kristy L. Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Leighanne R. Main
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | | | - Paula K. Ogrocki
- Department of Neurology, Case Western Reserve University School of Medicine Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Alan J. Lerner
- Department of Neurology, Case Western Reserve University School of Medicine Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | | | | | - William S. Bush
- Case Western Reserve University School of Medicine Cleveland OH USA
| | | | | | - Jonathan L. Haines
- Case Western Reserve University School of Medicine, Department of Population & Quantitative Health Sciences, Cleveland Institute for Computational Biology Cleveland OH USA
| | | |
Collapse
|
12
|
Wang P, Lynn A, Song YE, Haines JL. Distinct features of rapidly progressive Alzheimer’s disease. Alzheimers Dement 2022. [DOI: 10.1002/alz.063951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ping Wang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Jonathan L. Haines
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| |
Collapse
|
13
|
Dorfsman DA, Prough MB, Caywood LJ, Clouse JE, Herington SD, Slifer SH, Adams LD, Laux RA, Song YE, Lynn A, Fuzzell MD, Fuzzell SL, Hochstetler SD, Miskimen KL, Main LR, Osterman MD, Ogrocki PK, Lerner AJ, Vance JM, Cuccaro ML, Haines JL, Pericak‐Vance MA, Scott WK. Association of mitochondrial haplogroups and cognitive impairment in the Amish. Alzheimers Dement 2022. [DOI: 10.1002/alz.067658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Daniel A. Dorfsman
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Michael B. Prough
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Jason E. Clouse
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Susan H. Slifer
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Sherri D. Hochstetler
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Kristy L. Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Leighanne R. Main
- Department of Genetics and Genome Sciences, Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
| | - Michael D. Osterman
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
| | - Paula K. Ogrocki
- University Hospitals Cleveland Medical Center Cleveland OH USA
- Department of Neurology, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Alan J. Lerner
- University Hospitals Cleveland Medical Center Cleveland OH USA
- Department of Neurology, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Jeffery M. Vance
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Michael L. Cuccaro
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Jonathan L. Haines
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | - Margaret A. Pericak‐Vance
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - William K. Scott
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| |
Collapse
|
14
|
Prough MB, Caywood LJ, Clouse JE, Herington SD, Slifer SH, Dorfsman DA, Adams LD, Laux RA, Song YE, Lynn A, Fuzzell MD, Fuzzell SL, Miller SD, Miskimen KL, Main LR, Osterman MD, Ogrocki PK, Lerner AJ, Vance JM, Cuccaro ML, Haines JL, Scott WK, Pericak‐Vance MA. Plasma pTau181 is associated with impaired cognition in the Old Order Amish and adds additional information beyond the known genetic risk factors for AD. Alzheimers Dement 2022. [DOI: 10.1002/alz.067752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Michael B. Prough
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Jason E. Clouse
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Susan H. Slifer
- University of Miami, Miller School of Medicine, John P. Hussman Institute for Human Genomics Miami FL USA
| | - Daniel A. Dorfsman
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Sherri D. Miller
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Kristy L. Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Leighanne R. Main
- Department of Genetics and Genome Sciences, Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
| | - Michael D. Osterman
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
| | - Paula K. Ogrocki
- Department of Neurology, Case Western Reserve University School of Medicine Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Alan J. Lerner
- Department of Neurology, Case Western Reserve University School of Medicine Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Jonathan L. Haines
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine Cleveland OH USA
| | - William K. Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Margaret A. Pericak‐Vance
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| |
Collapse
|
15
|
Naj AC, Reitz C, Rajabli F, Jun GR, Benchek P, Tosto G, Sha J, Zhu C, Kushch NA, Lee W, Haut J, Hamilton‐Nelson KL, Wheeler NR, Zhao Y, Farrell J, Chung J, Grunin M, Leung YY, Li D, da Fonseca EL, Mez JB, Palmer EL, Pillai JA, Sherva R, Song YE, Zhang X, Iqbal T, Pathak O, Valladares O, Kuzma AB, Kunkle BW, Bush WS, Wang L, Farrer LA, Haines JL, Mayeux R, Pericak‐Vance MA, Schellenberg GD. Multi‐Ancestry Genome‐wide Association Analysis of Late‐Onset Alzheimer’s Disease (LOAD) in 60,941 Individuals Identifies a Novel Cross‐Ancestry Association in
LRRC4C. Alzheimers Dement 2022. [DOI: 10.1002/alz.065822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Adam C. Naj
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Christiane Reitz
- Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University New York NY USA
- The Taub Institute for Research on Alzheimer’s Disease and The Aging Brain, Columbia University New York NY USA
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Gyungah R Jun
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine Boston MA USA
- Department of Biostatistics, Boston University School of Public Health Boston MA USA
| | - Penelope Benchek
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Giuseppe Tosto
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University New York NY USA
- G.H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University New York NY USA
| | - Jin Sha
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Congcong Zhu
- Boston University School of Medicine Boston MA USA
| | - Nicholas A. Kushch
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Wan‐Ping Lee
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Jacob Haut
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Kara L. Hamilton‐Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Nicholas R. Wheeler
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Yi Zhao
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - John Farrell
- Boston University School of Medicine Boston MA USA
| | | | - Michelle Grunin
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Yuk Yee Leung
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Donghe Li
- Boston University School of Medicine Boston MA USA
| | - Eder Lucio da Fonseca
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Jesse B. Mez
- Boston University School of Medicine Boston MA USA
- Boston University Alzheimer’s Disease Research Center Boston MA USA
| | - Ellen L Palmer
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Jagan A. Pillai
- Cleveland Clinic Neurological Institute Cleveland OH USA
- Cleveland Clinic Lou Ruvo Center for Brain Health Cleveland OH USA
| | - Richard Sherva
- Boston University School of Medicine Boston MA USA
- National Center for PTSD, VA Boston Healthcare System Boston MA USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Xiaoling Zhang
- Boston University School of Medicine Boston MA USA
- Boston University School of Public Health Boston MA USA
| | - Taha Iqbal
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Omkar Pathak
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Otto Valladares
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Amanda B Kuzma
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Brian W. Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - William S. Bush
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Li‐San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine Boston MA USA
- Department of Biostatistics, Boston University School of Public Health Boston MA USA
- Department of Ophthalmology, Boston University School of Medicine Boston MA USA
- Department of Neurology, Boston University School of Medicine Boston MA USA
- Department of Epidemiology, Boston University School of Public Health Boston MA USA
| | - Jonathan L. Haines
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University New York NY USA
- G.H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University New York NY USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | | |
Collapse
|
16
|
Caliebe A, Tekola‐Ayele F, Darst BF, Wang X, Song YE, Gui J, Sebro RA, Balding DJ, Saad M, Dubé M. Including diverse and admixed populations in genetic epidemiology research. Genet Epidemiol 2022; 46:347-371. [PMID: 35842778 PMCID: PMC9452464 DOI: 10.1002/gepi.22492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022]
Abstract
The inclusion of ancestrally diverse participants in genetic studies can lead to new discoveries and is important to ensure equitable health care benefit from research advances. Here, members of the Ethical, Legal, Social, Implications (ELSI) committee of the International Genetic Epidemiology Society (IGES) offer perspectives on methods and analysis tools for the conduct of inclusive genetic epidemiology research, with a focus on admixed and ancestrally diverse populations in support of reproducible research practices. We emphasize the importance of distinguishing socially defined population categorizations from genetic ancestry in the design, analysis, reporting, and interpretation of genetic epidemiology research findings. Finally, we discuss the current state of genomic resources used in genetic association studies, functional interpretation, and clinical and public health translation of genomic findings with respect to diverse populations.
Collapse
Affiliation(s)
- Amke Caliebe
- Institute of Medical Informatics and StatisticsKiel University and University Hospital Schleswig‐HolsteinKielGermany
| | - Fasil Tekola‐Ayele
- Epidemiology Branch, Division of Population Health Research, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaMarylandUSA
| | - Burcu F. Darst
- Center for Genetic EpidemiologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
- Public Health Sciences DivisionFred Hutchinson Cancer Research CenterSeattleWashingtonUSA
| | - Xuexia Wang
- Department of MathematicsUniversity of North TexasDentonTexasUSA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health SciencesCase Western Reserve UniversityClevelandOhioUSA
| | - Jiang Gui
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth CollegeOne Medical Center Dr.LebanonNew HampshireUSA
| | | | - David J. Balding
- Melbourne Integrative Genomics, Schools of BioSciences and of Mathematics & StatisticsUniversity of MelbourneMelbourneAustralia
| | - Mohamad Saad
- Qatar Computing Research InstituteHamad Bin Khalifa UniversityDohaQatar
- Neuroscience Research Center, Faculty of Medical SciencesLebanese UniversityBeirutLebanon
| | - Marie‐Pierre Dubé
- Department of Medicine, and Social and Preventive MedicineUniversité de MontréalMontréalQuébecCanada
- Beaulieu‐Saucier Pharmacogenomcis CentreMontreal Heart InstituteMontrealCanada
| | | |
Collapse
|
17
|
Waksmunski AR, Miskimen K, Song YE, Grunin M, Laux R, Fuzzell D, Fuzzell S, Adams LD, Caywood L, Prough M, Stambolian D, Scott WK, Pericak-Vance MA, Haines JL. Consequences of a Rare Complement Factor H Variant for Age-Related Macular Degeneration in the Amish. Invest Ophthalmol Vis Sci 2022; 63:8. [PMID: 35930268 PMCID: PMC9363678 DOI: 10.1167/iovs.63.9.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Genetic variants in the complement factor H gene (CFH) have been consistently implicated in age-related macular degeneration (AMD) risk. However, their functional effects are not fully characterized. We previously identified a rare, AMD-associated variant in CFH (P503A, rs570523689) in 19 Amish individuals, but its functional consequences were not investigated. Methods We performed genotyping for CFH P503A in 1326 Amish individuals to identify additional risk allele carriers. We examined differences for age at AMD diagnosis between carriers and noncarriers. In blood samples from risk allele carriers and noncarriers, we quantified (i) CFH RNA expression, (ii) CFH protein expression, and (iii) C-reactive protein (CRP) expression. Potential changes to the CFH protein structure were interrogated computationally with Phyre2 and Chimera software programs. Results We identified 39 additional carriers from Amish communities in Ohio and Indiana. On average, carriers were younger than noncarriers at AMD diagnosis, but this difference was not significant. CFH transcript and protein levels in blood samples from Amish carriers and noncarriers were also not significantly different. CRP levels were also comparable in plasma samples from carriers and noncarriers. Computational protein modeling showed slight changes in the CFH protein conformation that were predicted to alter interactions between the CFH 503 residue and other neighboring residues. Conclusions In total, we have identified 58 risk allele carriers for CFH P503A in the Ohio and Indiana Amish. Although we did not detect significant differences in age at AMD diagnosis or expression levels of CFH in blood samples from carriers and noncarriers, we observed modest structural changes to the CFH protein through in silico modeling. Based on our functional and computational observations, we hypothesize that CFH P503A may affect CFH binding or function rather than expression, which would require additional research to confirm.
Collapse
Affiliation(s)
- Andrea R Waksmunski
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States.,Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Kristy Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Yeunjoo E Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Michelle Grunin
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Renee Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Sarada Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| | - Larry D Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Laura Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Michael Prough
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Jonathan L Haines
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States.,Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States.,Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States
| |
Collapse
|
18
|
Osterman MD, Song YE, Adams LD, Laux RA, Caywood LJ, Prough MB, Clouse JE, Herington SD, Slifer SH, Lynn A, Fuzzell MD, Fuzzell SL, Hochstetler SD, Miskimen K, Main LR, Dorfsman DA, Ogrocki P, Lerner AJ, Ramos J, Vance JM, Cuccaro ML, Scott WK, Pericak-Vance MA, Haines JL. The genetic architecture of Alzheimer disease risk in the Ohio and Indiana Amish. HGG Adv 2022; 3:100114. [PMID: 35599847 PMCID: PMC9114685 DOI: 10.1016/j.xhgg.2022.100114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/22/2022] [Indexed: 11/26/2022] Open
Abstract
Alzheimer disease (AD) is the most common type of dementia and is currently estimated to affect 6.2 million Americans. It ranks as the sixth leading cause of death in the United States, and the proportion of deaths due to AD has been increasing since 2000, while the proportion of many other leading causes of deaths have decreased or remained constant. The risk for AD is multifactorial, including genetic and environmental risk factors. Although APOE ε4 remains the largest genetic risk factor for AD, more than 26 other loci have been associated with AD risk. Here, we recruited Amish adults from Ohio and Indiana to investigate AD risk and protective genetic effects. As a founder population that typically practices endogamy, variants that are rare in the general population may be of a higher frequency in the Amish population. Since the Amish have a slightly lower incidence and later age of onset of disease, they represent an excellent and unique population for research on protective genetic variants. We compared AD risk in the Amish and to a non-Amish population through APOE genotype, a non-APOE genetic risk score of genome-wide significant variants, and a non-APOE polygenic risk score considering all of the variants. Our results highlight the lesser relative impact of APOE and differing genetic architecture of AD risk in the Amish compared to a non-Amish, general European ancestry population.
Collapse
Affiliation(s)
- Michael D. Osterman
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael B. Prough
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jason E. Clouse
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Susan H. Slifer
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Sherri D. Hochstetler
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kristy Miskimen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Leighanne R. Main
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Daniel A. Dorfsman
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Paula Ogrocki
- Department of Neurology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Department of Neurology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Alan J. Lerner
- Department of Neurology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Department of Neurology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jairo Ramos
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - William K. Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jonathan L. Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| |
Collapse
|
19
|
Osterman MD, Song YE, Nittala M, Sadda SR, Scott WK, Stambolian D, Pericak-Vance MA, Haines JL. Genomewide Association Study of Retinal Traits in the Amish Reveals Loci Influencing Drusen Development and Link to Age-Related Macular Degeneration. Invest Ophthalmol Vis Sci 2022; 63:17. [PMID: 35857289 PMCID: PMC9315071 DOI: 10.1167/iovs.63.8.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Purpose The purpose of this study was to identify genetic risk loci for retinal traits, including drusen, in an Amish study population and compare these risk loci to known risk loci of age-related macular degeneration (AMD). Methods Participants were recruited from Amish communities in Ohio, Indiana, and Pennsylvania. Each participant underwent a basic health history, ophthalmologic examination, and genotyping. A genomewide association analysis (GWAS) was conducted for the presence and quantity of each of three retinal traits: geographic atrophy, drusen area, and drusen volume. The findings were compared to results from a prior large GWAS of predominantly European-ancestry individuals. Further, a genetic risk score for AMD was used to predict the presence and quantity of the retinal traits. Results After quality control, 1074 participants were included in analyses. Six single nucleotide polymorphisms (SNPs) met criteria for genomewide significance and 48 were suggestively associated across three retinal traits. The significant SNPs were not highly correlated with known risk SNPs for AMD. A genetic risk score for AMD provided significant predictive value of the retinal traits. Conclusions We identified potential novel genetic risk loci for AMD in a midwestern Amish study population. Additionally, we determined that there is a clear link between the genetic risk of AMD and drusen. Further study, including longitudinal data collection, may improve our ability to define this connection and improve understanding of the biological risk factors underlying drusen development.
Collapse
Affiliation(s)
- Michael D Osterman
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland Ohio, United States.,Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States
| | - Yeunjoo E Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland Ohio, United States
| | - Muneeswar Nittala
- Doheny Imaging Reading Center, Doheny Eye Institute, Los Angeles, California, United States
| | - SriniVas R Sadda
- Doheny Imaging Reading Center, Doheny Eye Institute, Los Angeles, California, United States
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States.,The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Dwight Stambolian
- Ophthalmology and Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States.,The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland Ohio, United States.,Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States
| |
Collapse
|
20
|
Zöller B, Pirouzifard M, Svensson PJ, Holmquist B, Stenman E, Elston RC, Song YE, Sundquist J, Sundquist K. Familial Segregation of Venous Thromboembolism in Sweden: A Nationwide Family Study of Heritability and Complex Segregation Analysis. J Am Heart Assoc 2021; 10:e020323. [PMID: 34913365 PMCID: PMC9075256 DOI: 10.1161/jaha.120.020323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Background This is the first nationwide segregation analysis that aimed to determine whether familial venous thromboembolism (VTE) is attributable to inheritance and/or shared environment, and the possible mode of inheritance. Methods and Results The Swedish Multi‐Generation Register was linked to the Swedish patient register for the period 1964 to 2015. Three generational families of Swedish‐born individuals were identified. Heritability was examined using Falconer regression. Complex segregation analysis was conducted using the Statistical Analysis for Genetic Epidemiology software (version 6.4, 64‐bit Linux). Among the 4 301 174 relatives from 450 558 pedigrees, 177 865 (52% women) individuals were affected with VTE. VTE occurred in 2 or more affected relatives in 61 217 (13.6%) of the pedigrees. Heritability showed age and sex dependence with higher heritability for men and young individuals. In 18 933 pedigrees, VTE occurred only in the first generation and was not inherited. Segregation analysis was performed in the remaining 42 284 pedigrees with inherited VTE and included 939 192 individuals. Prevalence constraints were imposed in the models to allow for the selection of the pedigrees analyzed. The sporadic nongenetic model could be discarded. The major‐type‐only model, with a correlation structure compatible with some polygenic effects, was the preferred model. Among the Mendelian models, the mixed codominant (plus polygenic) model was preferred. Conclusions This nationwide segregation analysis of VTE supports a genetic cause of the familial aggregation of VTE. Heritability was higher for men and younger individuals, suggesting a Carter effect, in agreement with a multifactorial threshold inheritance.
Collapse
Affiliation(s)
- Bengt Zöller
- Center for Primary Health Care Research Lund University/Region Skåne Malmö Sweden
| | - MirNabi Pirouzifard
- Center for Primary Health Care Research Lund University/Region Skåne Malmö Sweden
| | - Peter J Svensson
- Department of Coagulation Disorders Skåne University HospitalLund University Malmö Sweden
| | | | - Emelie Stenman
- Center for Primary Health Care Research Lund University/Region Skåne Malmö Sweden
| | - Robert C Elston
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH
| | - Yeunjoo E Song
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH
| | - Jan Sundquist
- Center for Primary Health Care Research Lund University/Region Skåne Malmö Sweden
| | - Kristina Sundquist
- Center for Primary Health Care Research Lund University/Region Skåne Malmö Sweden
| |
Collapse
|
21
|
Scott WK, Ramos J, Slifer SH, Caywood LJ, Prough MB, Clouse JE, Dorfsman DA, Herington SD, Fuzzell MD, Fuzzell SL, Sewell JL, Miller SD, Osterman MD, Main LR, Miskimen KL, Lynn A, Whitehead PL, Adams LD, Laux RA, Song YE, Foroud TM, Mayeux R, Ogrocki PK, Lerner AJ, Vance JM, Cuccaro ML, Haines JL, Pericak‐Vance MA. Association of a locus on chromosome 17 with earlier age at onset of cognitive impairment in a familial Amish dataset. Alzheimers Dement 2021. [DOI: 10.1002/alz.056288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- William K. Scott
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Jairo Ramos
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Susan H. Slifer
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Michael B. Prough
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jason E. Clouse
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Daniel A. Dorfsman
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Jane L. Sewell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sherri D. Miller
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Michael D. Osterman
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Leighanne R Main
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Kristy L. Miskimen
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Patrice L. Whitehead
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology Case Western Reserve University Cleveland OH USA
| | | | - Richard Mayeux
- The Taub Institute for Research on Alzheimer’s Disease and The Aging Brain Columbia University New York NY USA
| | - Paula K. Ogrocki
- Case Western Reserve University School of Medicine Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Alan J. Lerner
- Case Western Reserve University School of Medicine Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Jonathan L. Haines
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology Case Western Reserve University Cleveland OH USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| |
Collapse
|
22
|
Prough MB, Caywood LJ, Clouse JE, Herington SD, Slifer SH, Dorfsman DA, Adams LD, Laux RA, Song YE, Lynn A, Fuzzell MD, Fuzzell SL, Sewell JL, Miller SD, Miskimen KL, Main LR, Osterman MD, Ogrocki PK, Lerner AJ, Ramos J, Vance JM, Cuccaro ML, Haines JL, Scott WK, Pericak‐Vance MA. Preferential preservation of constructional praxis delayed recall compared to word list delayed recall in the Amish. Alzheimers Dement 2021. [DOI: 10.1002/alz.056386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Michael B. Prough
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jason E. Clouse
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Susan H. Slifer
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Daniel A. Dorfsman
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology Case Western Reserve University Cleveland OH USA
| | - Audrey Lynn
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Jane L. Sewell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sherri D. Miller
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Kristy L. Miskimen
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Leighanne R Main
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Michael D. Osterman
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Paula K. Ogrocki
- Case Western Reserve University School of Medicine Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Alan J. Lerner
- Case Western Reserve University School of Medicine Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Jairo Ramos
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Jonathan L. Haines
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
- Cleveland Institute for Computational Biology Case Western Reserve University Cleveland OH USA
| | - William K. Scott
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| |
Collapse
|
23
|
Main LR, Song YE, Laux RA, Miskimen KL, Cuccaro ML, Ogrocki PK, Lerner AJ, Vance JM, Fuzzell MD, Fuzzell SL, Sewell JL, Caywood LJ, Prough MB, Adams LD, Clouse JE, Herington SD, Scott WK, Pericak‐Vance MA, Haines JL. Genome‐wide association for protective variants in Alzheimer’s disease in the Midwestern Amish. Alzheimers Dement 2021. [DOI: 10.1002/alz.056363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Leighanne R Main
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Kristy L. Miskimen
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | | | - Alan J. Lerner
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Jane L. Sewell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Michael B. Prough
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jason E. Clouse
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - William K. Scott
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jonathan L. Haines
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| |
Collapse
|
24
|
Main LR, Song YE, Laux RA, Miskimen K, Cuccaro ML, Ogrocki P, Lerner AJ, Vance JM, Fuzzell MD, Fuzzell SL, Sewell JL, Lynn A, Caywood LJ, Prough M, Scott B, Adams LD, Clouse JE, Herington SD, Pericak‐Vance MA, Haines JL. Search for protective genetic variants in Alzheimer disease in the U.S. Midwestern Amish. Alzheimers Dement 2020. [DOI: 10.1002/alz.045350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Kristy Miskimen
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Michael L. Cuccaro
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Paula Ogrocki
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Alan J. Lerner
- Case Western Reserve University School of Medicine Cleveland OH USA
| | - Jeffery M. Vance
- Dr. John T. Macdonald Department of Genetics University of Miami Miller School of Medicine Miami FL USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Jane L. Sewell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Audrey Lynn
- Case Western Reserve University Cleveland OH USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Michael Prough
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | | | | | | | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | | | | |
Collapse
|
25
|
Song YE, Miskimen K, Laux RA, Fuzzell MD, Fuzzell SL, Sewell JL, Miller SD, Adams LD, Caywood LJ, Prough M, Close JE, Herington SD, Slifer SH, Ramos J, Vance JM, Cuccaro ML, Ogrocki PK, Lerner AJ, Scott WK, Pericak‐Vance MA, Haines JL. Longitudinal assessment of cognitive decline in the Amish. Alzheimers Dement 2020. [DOI: 10.1002/alz.043440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Kristy Miskimen
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Jane L. Sewell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sherri D. Miller
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Michael Prough
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jason E. Close
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Susan H. Slifer
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jairo Ramos
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | | | - Alan J. Lerner
- Brain Health and Memory Center University Hospital Cleveland OH USA
| | - William K. Scott
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Jonathan L. Haines
- Cleveland Institute for Computational Biology Case Western Reserve University Cleveland OH USA
- Case Western Reserve University School of Medicine Cleveland OH USA
| |
Collapse
|
26
|
Ramos J, Jaworski J, Adams LD, Laux RA, Caywood LJ, Prough M, Clouse JE, Herington SD, Slifer SH, Fuzzell MD, Fuzzell SL, Sewell JL, Miller SD, Song YE, Miskimen K, Main LR, Ogrocki P, Lerner AJ, Vance JM, Cuccaro ML, Haines JL, Pericak‐Vance MA, Scott WK. Joint linkage and association mapping of preserved cognition in the old‐order Amish. Alzheimers Dement 2020. [DOI: 10.1002/alz.046416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jairo Ramos
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - James Jaworski
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Renee A. Laux
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Laura J. Caywood
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Michael Prough
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | | | - Sharlene D. Herington
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Susan H. Slifer
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - M. Denise Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sarada L. Fuzzell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Jane L. Sewell
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Sherri D. Miller
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Yeunjoo E. Song
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Kristy Miskimen
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | | | - Paula Ogrocki
- University Hospitals Cleveland Medical Center Cleveland OH USA
| | - Alan J. Lerner
- Case Western Reserve University School of Medicine Cleveland OH USA
| | - Jeffery M. Vance
- Dr. John T. Macdonald Department of Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Michael L. Cuccaro
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | | | | | - William K. Scott
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| |
Collapse
|
27
|
Laville V, Kang JH, Cousins CC, Iglesias AI, Nagy R, Cooke Bailey JN, Igo RP, Song YE, Chasman DI, Christen WG, Kraft P, Rosner BA, Hu F, Wilson JF, Gharahkhani P, Hewitt AW, Mackey DA, Hysi PG, Hammond CJ, vanDuijn CM, Haines JL, Vitart V, Fingert JH, Hauser MA, Aschard H, Wiggs JL, Khawaja AP, MacGregor S, Pasquale LR. Genetic Correlations Between Diabetes and Glaucoma: An Analysis of Continuous and Dichotomous Phenotypes. Am J Ophthalmol 2019; 206:245-255. [PMID: 31121135 DOI: 10.1016/j.ajo.2019.05.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 05/03/2019] [Accepted: 05/09/2019] [Indexed: 01/05/2023]
Abstract
PURPOSE A genetic correlation is the proportion of phenotypic variance between traits that is shared on a genetic basis. Here we explore genetic correlations between diabetes- and glaucoma-related traits. DESIGN Cross-sectional study. METHODS We assembled genome-wide association study summary statistics from European-derived participants regarding diabetes-related traits like fasting blood sugar (FBS) and type 2 diabetes (T2D) and glaucoma-related traits (intraocular pressure [IOP], central corneal thickness [CCT], corneal hysteresis [CH], corneal resistance factor [CRF], cup-to-disc ratio [CDR], and primary open-angle glaucoma [POAG]). We included data from the National Eye Institute Glaucoma Human Genetics Collaboration Heritable Overall Operational Database, the UK Biobank, and the International Glaucoma Genetics Consortium. We calculated genetic correlation (rg) between traits using linkage disequilibrium score regression. We also calculated genetic correlations between IOP, CCT, and select diabetes-related traits based on individual level phenotype data in 2 Northern European population-based samples using pedigree information and Sequential Oligogenic Linkage Analysis Routines. RESULTS Overall, there was little rg between diabetes- and glaucoma-related traits. Specifically, we found a nonsignificant negative correlation between T2D and POAG (rg = -0.14; P = .16). Using Sequential Oligogenic Linkage Analysis Routines, the genetic correlations between measured IOP, CCT, FBS, fasting insulin, and hemoglobin A1c were null. In contrast, genetic correlations between IOP and POAG (rg ≥ 0.45; P ≤ 3.0 × 10-4) and between CDR and POAG were high (rg = 0.57; P = 2.8 × 10-10). However, genetic correlations between corneal properties (CCT, CRF, and CH) and POAG were low (rg range -0.18 to 0.11) and nonsignificant (P ≥ .07). CONCLUSION These analyses suggest that there is limited genetic correlation between diabetes- and glaucoma-related traits.
Collapse
|
28
|
Song YE, Lee S, Park K, Elston RC, Yang HJ, Won S. ONETOOL for the analysis of family-based big data. Bioinformatics 2019; 34:2851-2853. [PMID: 29596615 PMCID: PMC6084591 DOI: 10.1093/bioinformatics/bty180] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 03/26/2018] [Indexed: 11/25/2022] Open
Abstract
Motivation Despite the need for separate tools to analyze family-based data, there are only a handful of tools optimized for family-based big data compared to the number of tools available for analyzing population-based data. Results ONETOOL implements the properties of well-known existing family data analysis tools and recently developed methods in a computationally efficient manner, and so is suitable for analyzing the vast amount of variant data available from sequencing family members, providing a rich choice of analysis methods for big data on families. Availability and implementation ONETOOL is freely available from http://healthstat.snu.ac.kr/software/onetool/. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Yeunjoo E Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Sungyoung Lee
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, Korea
| | - Kyungtaek Park
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, Korea
| | - Robert C Elston
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Hyeon-Jong Yang
- SCH Biomedical Informatics Research Unit, Soonchunhyang University Hospital, Seoul, Korea.,Department of Pediatrics, Soonchunhyang University Hospital, Soonchunhyang University College of Medicine, Seoul, Korea
| | - Sungho Won
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, Korea.,Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Korea.,Institute of Health and Environment, Seoul National University, Seoul, Korea
| |
Collapse
|
29
|
Song YE, Kang H, Park H. Algorithm to Estimate the Extended Turnaround Time Including Outpatient Waiting Time for Blood Specimen Collection when a Stand-alone Queue Ticket System not Connectable to Laboratory Information System Is Used. Ann Clin Lab Sci 2018; 48:726-735. [PMID: 30610042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
BACKGROUND A queue ticket system (QTS) used in an outpatient phlebotomy clinic was unable to be directly integrated with the laboratory information system (LIS). To monitor patient's waiting time and extended turnaround time (TAT) as patient-centered quality indicators for outpatient laboratory services, we developed an algorithm to integrate data between the QTS and the LIS. METHODS Between June 1 to September 30, 2017, data files were exported from a QSYS-8000 (HION Tech, Seoul, Korea). Each calling event from the QTS data was matched to a barcode of test requests from the LIS if the following conditions were met: (1) time interval between "call time" from QTS and "barcode printing time" from LIS <90 s; (2) "Counter Number" from LIS="Counter Number" from QTS. Extended TAT was estimated as the interval between pulling the queue ticket and the reporting of the test result. RESULTS 82.66%±3.14% of the barcodes from the LIS were matched to issued tickets. Median waiting time (mean±SD) was 6.5±5.3 min. Median extended TAT was 84.7±11.2 min for non-STAT and 53.0±6.4 min for STAT. CONCLUSION When a stand-alone QTS was used in the outpatient phlebotomy clinic, data from the QTS and the LIS were integrated using a novel algorithm we developed.
Collapse
Affiliation(s)
- Yeunjoo E Song
- Department of Population and Quantitative Health Science, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Heechan Kang
- Department of Hospital Information, The Catholic University of Korea, Bucheon, Korea
| | - Haeil Park
- Department of Laboratory Medicine, Bucheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Bucheon, Korea
| |
Collapse
|
30
|
Bailey JNC, Gharahkhani P, Kang JH, Butkiewicz M, Sullivan DA, Weinreb RN, Aschard H, Allingham RR, Ashley-Koch A, Lee RK, Moroi SE, Brilliant MH, Wollstein G, Schuman JS, Fingert JH, Budenz DL, Realini T, Gaasterland T, Scott WK, Singh K, Sit AJ, Igo RP, Song YE, Hark L, Ritch R, Rhee DJ, Vollrath D, Zack DJ, Medeiros F, Vajaranant TS, Chasman DI, Christen WG, Pericak-Vance MA, Liu Y, Kraft P, Richards JE, Rosner BA, Hauser MA, Craig JE, Burdon KP, Hewitt AW, Mackey DA, Haines JL, MacGregor S, Wiggs JL, Pasquale LR. Testosterone Pathway Genetic Polymorphisms in Relation to Primary Open-Angle Glaucoma: An Analysis in Two Large Datasets. Invest Ophthalmol Vis Sci 2018; 59:629-636. [PMID: 29392307 PMCID: PMC5795896 DOI: 10.1167/iovs.17-22708] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Sex hormones may be associated with primary open-angle glaucoma (POAG), although the mechanisms are unclear. We previously observed that gene variants involved with estrogen metabolism were collectively associated with POAG in women but not men; here we assessed gene variants related to testosterone metabolism collectively and POAG risk. Methods We used two datasets: one from the United States (3853 cases and 33,480 controls) and another from Australia (1155 cases and 1992 controls). Both datasets contained densely called genotypes imputed to the 1000 Genomes reference panel. We used pathway- and gene-based approaches with Pathway Analysis by Randomization Incorporating Structure (PARIS) software to assess the overall association between a panel of single nucleotide polymorphisms (SNPs) in testosterone metabolism genes and POAG. In sex-stratified analyses, we evaluated POAG overall and POAG subtypes defined by maximum IOP (high-tension [HTG] or normal tension glaucoma [NTG]). Results In the US dataset, the SNP panel was not associated with POAG (permuted P = 0.77), although there was an association in the Australian sample (permuted P = 0.018). In both datasets, the SNP panel was associated with POAG in men (permuted P ≤ 0.033) and not women (permuted P ≥ 0.42), but in gene-based analyses, there was no consistency on the main genes responsible for these findings. In both datasets, the testosterone pathway association with HTG was significant (permuted P ≤ 0.011), but again, gene-based analyses showed no consistent driver gene associations. Conclusions Collectively, testosterone metabolism pathway SNPs were consistently associated with the high-tension subtype of POAG in two datasets.
Collapse
Affiliation(s)
- Jessica N Cooke Bailey
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - Puya Gharahkhani
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Australia
| | - Jae H Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States
| | - Mariusz Butkiewicz
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - David A Sullivan
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
| | - Robert N Weinreb
- Department of Ophthalmology, Hamilton Glaucoma Center and Shiley Eye Institute, University of California at San Diego, La Jolla, California, United States
| | - Hugues Aschard
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts, United States
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States
| | - Richard K Lee
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Sayoko E Moroi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United States
| | - Murray H Brilliant
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, Wisconsin, United States
| | - Gadi Wollstein
- Department of Ophthalmology, NYU Langone Medical Center, NYU School of Medicine, New York, New York, United States
| | - Joel S Schuman
- Department of Ophthalmology, NYU Langone Medical Center, NYU School of Medicine, New York, New York, United States
| | - John H Fingert
- Departments of Ophthalmology and Anatomy/Cell Biology, University of Iowa, College of Medicine, Iowa City, Iowa, United States
| | - Donald L Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, North Carolina, United States
| | - Tony Realini
- Department of Ophthalmology, WVU Eye Institute, Morgantown, West Virginia, United States
| | - Terry Gaasterland
- Scripps Genome Center, University of California at San Diego, San Diego, California, United States
| | - William K Scott
- Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Kuldev Singh
- Department of Ophthalmology, Stanford University, Palo Alto, California, United States
| | - Arthur J Sit
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Robert P Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - Yeunjoo E Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - Lisa Hark
- Wills Eye Hospital, Glaucoma Research Center, Philadelphia, Pennsylvania, United States
| | - Robert Ritch
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York, United States
| | - Douglas J Rhee
- Department of Ophthalmology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - Douglas Vollrath
- Department of Genetics, Stanford University, Palo Alto, California, United States
| | - Donald J Zack
- Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, Maryland, United States
| | - Felipe Medeiros
- Department of Ophthalmology, Hamilton Glaucoma Center and Shiley Eye Institute, University of California at San Diego, La Jolla, California, United States
| | - Thasarat S Vajaranant
- Department of Ophthalmology, University of Illinois College of Medicine at Chicago, Chicago, Illinois, United States
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - William G Christen
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Margaret A Pericak-Vance
- Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, United States
| | - Peter Kraft
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts, United States.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts, United States
| | - Julia E Richards
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United States
| | - Bernard A Rosner
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts, United States
| | - Michael A Hauser
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States.,Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Adelaide, SA, Australia
| | - Kathryn P Burdon
- School of Medicine, Menzies Research Institute of Tasmania, Hobart, Australia
| | - Alex W Hewitt
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - David A Mackey
- School of Medicine, Menzies Research Institute of Tasmania, Hobart, Australia.,Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, Australia
| | - Janey L Wiggs
- Department of Ophthalmology, Mass Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
| | - Louis R Pasquale
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States.,Department of Ophthalmology, Mass Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts, United States
| | | |
Collapse
|
31
|
Khawaja AP, Cooke Bailey JN, Wareham NJ, Scott RA, Simcoe M, Igo RP, Song YE, Wojciechowski R, Cheng CY, Khaw PT, Pasquale LR, Haines JL, Foster PJ, Wiggs JL, Hammond CJ, Hysi PG. Genome-wide analyses identify 68 new loci associated with intraocular pressure and improve risk prediction for primary open-angle glaucoma. Nat Genet 2018; 50:778-782. [PMID: 29785010 PMCID: PMC5985943 DOI: 10.1038/s41588-018-0126-8] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/27/2018] [Indexed: 01/10/2023]
Abstract
Glaucoma is the leading cause of irreversible blindness globally 1 . Despite its gravity, the disease is frequently undiagnosed in the community 2 . Raised intraocular pressure (IOP) is the most important risk factor for primary open-angle glaucoma (POAG)3,4. Here we present a meta-analysis of 139,555 European participants, which identified 112 genomic loci associated with IOP, 68 of which are novel. These loci suggest a strong role for angiopoietin-receptor tyrosine kinase signaling, lipid metabolism, mitochondrial function and developmental processes underlying risk for elevated IOP. In addition, 48 of these loci were nominally associated with glaucoma in an independent cohort, 14 of which were significant at a Bonferroni-corrected threshold. Regression-based glaucoma-prediction models had an area under the receiver operating characteristic curve (AUROC) of 0.76 in US NEIGHBORHOOD study participants and 0.74 in independent glaucoma cases from the UK Biobank. Genetic-prediction models for POAG offer an opportunity to target screening and timely therapy to individuals most at risk.
Collapse
Affiliation(s)
- Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Jessica N Cooke Bailey
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Robert A Scott
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Mark Simcoe
- Department of Ophthalmology, King's College London, St. Thomas' Hospital, London, UK
- Department of Twin Research & Genetic Epidemiology, King's College London, St. Thomas' Hospital, London, UK
| | - Robert P Igo
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Yeunjoo E Song
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Robert Wojciechowski
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Johns Hopkins Wilmer Eye Institute, Baltimore, MD, USA
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye-ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Peng T Khaw
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Louis R Pasquale
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Paul J Foster
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
- Division of Genetics and Epidemiology, UCL Institute of Ophthalmology, London, UK
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA, USA.
| | - Chris J Hammond
- Department of Ophthalmology, King's College London, St. Thomas' Hospital, London, UK.
| | - Pirro G Hysi
- Department of Ophthalmology, King's College London, St. Thomas' Hospital, London, UK.
- Department of Twin Research & Genetic Epidemiology, King's College London, St. Thomas' Hospital, London, UK.
| |
Collapse
|
32
|
Abstract
Linkage Analysis is a family-based method of analysis to examine whether any typed genetic markers cosegregate with a given trait, in this case a quantitative trait. If linkage exists, this is taken as evidence in support of a genetic basis for the trait. Historically, linkage analysis was performed using a binary disease trait, but has been extended to include quantitative disease measures. Quantitative traits are desirable as they provide more information than binary traits. Linkage analysis can be performed using single-marker methods (one marker at a time) or multipoint (using multiple markers simultaneously). In model-based linkage analysis the genetic model for the trait of interest is specified. There are many software options for performing linkage analysis. Here, we use the program package Statistical Analysis for Genetic Epidemiology (S.A.G.E.). S.A.G.E. was chosen because it also includes programs to perform data cleaning procedures and to generate and test genetic models for a quantitative trait, in addition to performing linkage analysis. We demonstrate in detail the process of running the program LODLINK to perform single-marker analysis, and MLOD to perform multipoint analysis using output from SEGREG, where SEGREG was used to determine the best fitting statistical model for the trait.
Collapse
Affiliation(s)
- Yeunjoo E Song
- Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road, Cleveland, OH, 44106-7281, USA.
| | - Sunah Song
- Case Western Reserve University, Wolstein Research Building, 2103 Cornell Road, Cleveland, OH, 44106-7281, USA
| | - Audrey H Schnell
- Cardiovascular Imaging Core Laboratory, Harrington Heart & Vascular Institute, University Hospitals Cleveland Medical Center, 11100 Euclid Avenue, Cleveland, OH, 44106, USA
| |
Collapse
|
33
|
Aschard H, Kang JH, Iglesias AI, Hysi P, Cooke Bailey JN, Khawaja AP, Allingham RR, Ashley-Koch A, Lee RK, Moroi SE, Brilliant MH, Wollstein G, Schuman JS, Fingert JH, Budenz DL, Realini T, Gaasterland T, Scott WK, Singh K, Sit AJ, Igo RP, Song YE, Hark L, Ritch R, Rhee DJ, Gulati V, Haven S, Vollrath D, Zack DJ, Medeiros F, Weinreb RN, Cheng CY, Chasman DI, Christen WG, Pericak-Vance MA, Liu Y, Kraft P, Richards JE, Rosner BA, Hauser MA, Klaver CCW, vanDuijn CM, Haines J, Wiggs JL, Pasquale LR. Genetic correlations between intraocular pressure, blood pressure and primary open-angle glaucoma: a multi-cohort analysis. Eur J Hum Genet 2017; 25:1261-1267. [PMID: 28853718 DOI: 10.1038/ejhg.2017.136] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 07/18/2017] [Accepted: 07/21/2017] [Indexed: 01/30/2023] Open
Abstract
Primary open-angle glaucoma (POAG) is the most common chronic optic neuropathy worldwide. Epidemiological studies show a robust positive relation between intraocular pressure (IOP) and POAG and modest positive association between IOP and blood pressure (BP), while the relation between BP and POAG is controversial. The International Glaucoma Genetics Consortium (n=27 558), the International Consortium on Blood Pressure (n=69 395), and the National Eye Institute Glaucoma Human Genetics Collaboration Heritable Overall Operational Database (n=37 333), represent genome-wide data sets for IOP, BP traits and POAG, respectively. We formed genome-wide significant variant panels for IOP and diastolic BP and found a strong relation with POAG (odds ratio and 95% confidence interval: 1.18 (1.14-1.21), P=1.8 × 10-27) for the former trait but no association for the latter (P=0.93). Next, we used linkage disequilibrium (LD) score regression, to provide genome-wide estimates of correlation between traits without the need for additional phenotyping. We also compared our genome-wide estimate of heritability between IOP and BP to an estimate based solely on direct measures of these traits in the Erasmus Rucphen Family (ERF; n=2519) study using Sequential Oligogenic Linkage Analysis Routines (SOLAR). LD score regression revealed high genetic correlation between IOP and POAG (48.5%, P=2.1 × 10-5); however, genetic correlation between IOP and diastolic BP (P=0.86) and between diastolic BP and POAG (P=0.42) were negligible. Using SOLAR in the ERF study, we confirmed the minimal heritability between IOP and diastolic BP (P=0.63). Overall, IOP shares genetic basis with POAG, whereas BP has limited shared genetic correlation with IOP or POAG.
Collapse
Affiliation(s)
- Hugues Aschard
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, MA, USA
| | - Jae H Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Adriana I Iglesias
- Department of Epidemiology, Genetic Epidemiology Unit, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Pirro Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jessica N Cooke Bailey
- Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Anthony P Khawaja
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA
| | | | - Richard K Lee
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sayoko E Moroi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Murray H Brilliant
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | - Gadi Wollstein
- Department of Ophthalmology, NYU Langone Medical Center, NYU School of Medicine, New York, NY, USA
| | - Joel S Schuman
- Department of Ophthalmology, NYU Langone Medical Center, NYU School of Medicine, New York, NY, USA
| | - John H Fingert
- Departments of Ophthalmology and Anatomy/Cell Biology, University of Iowa, College of Medicine, Iowa City, IO, USA
| | - Donald L Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, NC, USA
| | - Tony Realini
- Department of Ophthalmology, WVU Eye Institute, Morgantown, WV, USA
| | - Terry Gaasterland
- Scripps Genome Center, University of California at San Diego, San Diego, CA, USA
| | - William K Scott
- Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kuldev Singh
- Department of Ophthalmology, Stanford University, Palo Alto, CA, USA
| | - Arthur J Sit
- Department of Ophthalmology, Mayo Clinic, Rochester, MN, USA
| | - Robert P Igo
- Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Yeunjoo E Song
- Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Lisa Hark
- Wills Eye Hospital, Glaucoma Research Center, Philadelphia, PA, USA
| | - Robert Ritch
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, NY, USA
| | - Douglas J Rhee
- Department of Ophthalmology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Vikas Gulati
- Department of Ophthalmology &Visual Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Shane Haven
- Department of Ophthalmology &Visual Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Donald J Zack
- Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, MD, USA
| | - Felipe Medeiros
- Department of Ophthalmology, Hamilton Eye Center, University of California at San Diego, San Diego, CA, USA
| | - Robert N Weinreb
- Department of Ophthalmology, Hamilton Eye Center, University of California at San Diego, San Diego, CA, USA
| | - Ching-Yu Cheng
- Singapore National Eye Centre, Singapore Eye Research Institute, Singapore, Singapore.,Ophthalmology &Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - William G Christen
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Yutao Liu
- Department of Cellular Biology &Anatomy, Augusta University, Augusta, GA, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, MA, USA
| | - Julia E Richards
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Bernard A Rosner
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael A Hauser
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, USA.,Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | | | - Caroline C W Klaver
- Department of Epidemiology, Genetic Epidemiology Unit, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Cornelia M vanDuijn
- Department of Epidemiology, Genetic Epidemiology Unit, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jonathan Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Janey L Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Louis R Pasquale
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
34
|
Liu Y, Bailey JC, Helwa I, Dismuke WM, Cai J, Drewry M, Brilliant MH, Budenz DL, Christen WG, Chasman DI, Fingert JH, Gaasterland D, Gaasterland T, Gordon MO, Igo RP, Kang JH, Kass MA, Kraft P, Lee RK, Lichter P, Moroi SE, Realini A, Richards JE, Ritch R, Schuman JS, Scott WK, Singh K, Sit AJ, Song YE, Vollrath D, Weinreb R, Medeiros F, Wollstein G, Zack DJ, Zhang K, Pericak-Vance MA, Gonzalez P, Stamer WD, Kuchtey J, Kuchtey RW, Allingham RR, Hauser MA, Pasquale LR, Haines JL, Wiggs JL. A Common Variant in MIR182 Is Associated With Primary Open-Angle Glaucoma in the NEIGHBORHOOD Consortium. Invest Ophthalmol Vis Sci 2017; 57:4528-4535. [PMID: 27537254 PMCID: PMC4991020 DOI: 10.1167/iovs.16-19688] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Purpose Noncoding microRNAs (miRNAs) have been implicated in the pathogenesis of glaucoma. We aimed to identify common variants in miRNA coding genes (MIR) associated with primary open-angle glaucoma (POAG). Methods Using the NEIGHBORHOOD data set (3853 cases/33,480 controls with European ancestry), we first assessed the relation between 85 variants in 76 MIR genes and overall POAG. Subtype-specific analyses were performed in high-tension glaucoma (HTG) and normal-tension glaucoma subsets. Second, we examined the expression of miR-182, which was associated with POAG, in postmortem human ocular tissues (ciliary body, cornea, retina, and trabecular meshwork [TM]), using miRNA sequencing (miRNA-Seq) and droplet digital PCR (ddPCR). Third, miR-182 expression was also examined in human aqueous humor (AH) by using miRNA-Seq. Fourth, exosomes secreted from primary human TM cells were examined for miR-182 expression by using miRNA-Seq. Fifth, using ddPCR we compared miR-182 expression in AH between five HTG cases and five controls. Results Only rs76481776 in MIR182 gene was associated with POAG after adjustment for multiple comparisons (odds ratio [OR] = 1.23, 95% confidence interval [CI]: 1.11–1.42, P = 0.0002). Subtype analysis indicated that the association was primarily in the HTG subset (OR = 1.26, 95% CI: 1.08–1.47, P = 0.004). The risk allele T has been associated with elevated miR-182 expression in vitro. Data from ddPCR and miRNA-Seq confirmed miR-182 expression in all examined ocular tissues and TM-derived exosomes. Interestingly, miR-182 expression in AH was 2-fold higher in HTG patients than nonglaucoma controls (P = 0.03) without controlling for medication treatment. Conclusions Our integrative study is the first to associate rs76481776 with POAG via elevated miR-182 expression.
Collapse
Affiliation(s)
- Yutao Liu
- Department of Cellular Biology and Anatomy Augusta University, Augusta, Georgia, United States 2James & Jean Culver Vision Discovery Institute, Augusta University, Augusta, Georgia, United States 3Center for Biotechnology and Genomic Medicine, Augusta Uni
| | - Jessica Cooke Bailey
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States
| | - Inas Helwa
- Department of Cellular Biology and Anatomy Augusta University, Augusta, Georgia, United States
| | - W Michael Dismuke
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Jingwen Cai
- Department of Cellular Biology and Anatomy Augusta University, Augusta, Georgia, United States
| | - Michelle Drewry
- Department of Cellular Biology and Anatomy Augusta University, Augusta, Georgia, United States
| | - Murray H Brilliant
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, United States
| | - Donald L Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, North Carolina, United States
| | - William G Christen
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Daniel I Chasman
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - John H Fingert
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States
| | | | - Terry Gaasterland
- Scripps Genome Center, University of California at San Diego, San Diego, California, United States
| | - Mae O Gordon
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Robert P Igo
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States
| | - Jae H Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Michael A Kass
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Peter Kraft
- School of Public Health, Harvard University, Boston, Massachusetts, United States
| | - Richard K Lee
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Paul Lichter
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United States
| | - Sayoko E Moroi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United States
| | - Anthony Realini
- Department of Ophthalmology, West Virginia University Eye Institute, Morgantown, West Virginia, United States
| | - Julia E Richards
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United States
| | - Robert Ritch
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York, United States
| | - Joel S Schuman
- Department of Ophthalmology, UPMC Eye Center, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - William K Scott
- Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Kuldev Singh
- Department of Ophthalmology, Stanford University, Palo Alto, California, United States
| | - Arthur J Sit
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Yeunjoo E Song
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States
| | - Douglas Vollrath
- Department of Ophthalmology, Stanford University, Palo Alto, California, United States
| | - Robert Weinreb
- Department of Ophthalmology and Hamilton Glaucoma Center, University of California, San Diego, California, United States
| | - Felipe Medeiros
- Department of Ophthalmology and Hamilton Glaucoma Center, University of California, San Diego, California, United States
| | - Gadi Wollstein
- Department of Ophthalmology, UPMC Eye Center, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Donald J Zack
- Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, Maryland, United States
| | - Kang Zhang
- Department of Ophthalmology and Hamilton Glaucoma Center, University of California, San Diego, California, United States
| | - Margaret A Pericak-Vance
- Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Pedro Gonzalez
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - W Daniel Stamer
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - John Kuchtey
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Rachel W Kuchtey
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Michael A Hauser
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States 26Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States
| | - Louis R Pasquale
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States 27Department of Ophthalmology, Mass Eye & Ear, Boston, Massachusetts, United States
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States
| | - Janey L Wiggs
- Department of Ophthalmology, Mass Eye & Ear, Boston, Massachusetts, United States
| |
Collapse
|
35
|
Pasquale LR, Aschard H, Kang JH, Bailey JNC, Lindström S, Chasman DI, Christen WG, Allingham RR, Ashley-Koch A, Lee RK, Moroi SE, Brilliant MH, Wollstein G, Schuman JS, Fingert J, Budenz DL, Realini T, Gaasterland T, Gaasterland D, Scott WK, Singh K, Sit AJ, Igo RP, Song YE, Hark L, Ritch R, Rhee DJ, Gulati V, Havens S, Vollrath D, Zack DJ, Medeiros F, Weinreb RN, Pericak-Vance MA, Liu Y, Kraft P, Richards JE, Rosner BA, Hauser MA, Haines JL, Wiggs JL. Age at natural menopause genetic risk score in relation to age at natural menopause and primary open-angle glaucoma in a US-based sample. Menopause 2017; 24:150-156. [PMID: 27760082 PMCID: PMC5266624 DOI: 10.1097/gme.0000000000000741] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 07/18/2016] [Accepted: 07/18/2016] [Indexed: 12/04/2022]
Abstract
OBJECTIVE Several attributes of female reproductive history, including age at natural menopause (ANM), have been related to primary open-angle glaucoma (POAG). We assembled 18 previously reported common genetic variants that predict ANM to determine their association with ANM or POAG. METHODS Using data from the Nurses' Health Study (7,143 women), we validated the ANM weighted genetic risk score in relation to self-reported ANM. Subsequently, to assess the relation with POAG, we used data from 2,160 female POAG cases and 29,110 controls in the National Eye Institute Glaucoma Human Genetics Collaboration Heritable Overall Operational Database (NEIGHBORHOOD), which consists of 8 datasets with imputed genotypes to 5.6+ million markers. Associations with POAG were assessed in each dataset, and site-specific results were meta-analyzed using the inverse weighted variance method. RESULTS The genetic risk score was associated with self-reported ANM (P = 2.2 × 10) and predicted 4.8% of the variance in ANM. The ANM genetic risk score was not associated with POAG (Odds Ratio (OR) = 1.002; 95% Confidence Interval (CI): 0.998, 1.007; P = 0.28). No single genetic variant in the panel achieved nominal association with POAG (P ≥0.20). Compared to the middle 80 percent, there was also no association with the lowest 10 percentile or highest 90 percentile of genetic risk score with POAG (OR = 0.75; 95% CI: 0.47, 1.21; P = 0.23 and OR = 1.10; 95% CI: 0.72, 1.69; P = 0.65, respectively). CONCLUSIONS A genetic risk score predicting 4.8% of ANM variation was not related to POAG; thus, genetic determinants of ANM are unlikely to explain the previously reported association between the two phenotypes.
Collapse
Affiliation(s)
- Louis R. Pasquale
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary
- Channing Division of Network Medicine, Brigham and Women's Hospital
| | - Hugues Aschard
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard Medical School, Boston, MA
| | - Jae H. Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital
| | - Jessica N. Cooke Bailey
- Department of Epidemiology and Biostatistics
- Institute of Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Sara Lindström
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard Medical School, Boston, MA
| | - Daniel I. Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - William G. Christen
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | | | - Allison Ashley-Koch
- Department of Medicine, Duke University, Duke University Medical Center, Durham, NC
| | - Richard K. Lee
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL
| | - Sayoko E. Moroi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI
| | - Murray H. Brilliant
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI
| | - Gadi Wollstein
- Department of Ophthalmology, UPMC Eye Center, University of Pittsburgh, Pittsburgh, PA
| | - Joel S. Schuman
- Department of Ophthalmology, UPMC Eye Center, University of Pittsburgh, Pittsburgh, PA
| | - John Fingert
- Departments of Ophthalmology and Anatomy/Cell Biology, University of Iowa, College of Medicine, Iowa City, IO
| | - Donald L. Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, NC
| | - Tony Realini
- Department of Ophthalmology, WVU Eye Institute, Morgantown, WV
| | - Terry Gaasterland
- Scripps Genome Center, University of California at San Diego, San Diego, CA
| | | | - William K. Scott
- Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL
| | - Kuldev Singh
- Department of Ophthalmology, Stanford University, Palo Alto, CA
| | - Arthur J. Sit
- Department of Ophthalmology, Mayo Clinic, Rochester, MN
| | | | | | - Lisa Hark
- Wills Eye Institute, Philadelphia, PA
| | - Robert Ritch
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, NY
| | - Douglas J. Rhee
- Department of Ophthalmology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Vikas Gulati
- Department of Ophthalmology & Visual Sciences, University of Nebraska Medical Center, Omaha, NE
| | - Shane Havens
- Department of Ophthalmology & Visual Sciences, University of Nebraska Medical Center, Omaha, NE
| | | | - Donald J. Zack
- Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, MD
| | - Felipe Medeiros
- Department of Ophthalmology, Hamilton Eye Center; University of California at San Diego, San Diego, CA
| | - Robert N. Weinreb
- Department of Ophthalmology, Hamilton Eye Center; University of California at San Diego, San Diego, CA
| | | | - Yutao Liu
- Department of Cellular Biology & Anatomy, Augusta University, Augusta, GA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard Medical School, Boston, MA
| | - Julia E. Richards
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI
| | - Bernard A. Rosner
- Channing Division of Network Medicine, Brigham and Women's Hospital
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard Medical School, Boston, MA
| | - Michael A. Hauser
- Department of Ophthalmology
- Department of Medicine, Duke University, Duke University Medical Center, Durham, NC
| | - Jonathan L. Haines
- Department of Epidemiology and Biostatistics
- Institute of Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Janey L. Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary
| |
Collapse
|
36
|
Abstract
Structural equation modeling (SEM) has been used in a wide range of applied sciences including genetic analysis. The recently developed R package, strum, implements a framework for SEM for general pedigree data. We explored different SEM techniques using strum to analyze the multivariate longitudinal data and to ultimately test the association of genotypes on blood pressure traits. The quantitative blood pressure (BP) traits, systolic BP (SBP) and diastolic BP (DBP) were analyzed as the main traits of interest with age, sex, and smoking status as covariates. The single nucleotide polymorphism (SNP) genotype information from genome-wide association studies (GWAS) data was used for the test of association. The adjustment for hypertension treatment effect was done by the censored regression approach. Two different longitudinal data models, autoregressive model and latent growth curve model, were used to fit the longitudinal BP traits. The test of association for SNP was done using a novel score test within the SEM framework of strum. We found the 10 SNPs within the GWAS suggestive P value level, and among those 10, the most significant top 3 SNPs agreed in rank in both analysis models. The general SEM framework in strum is very useful to model and test for the association with massive genotype data and complex systems of multiple phenotypes with general pedigree data.
Collapse
Affiliation(s)
- Yeunjoo E Song
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Nathan J Morris
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106 USA ; Center for Clinical Investigation, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Catherine M Stein
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106 USA ; Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106 USA
| |
Collapse
|
37
|
Bailey JNC, Loomis SJ, Kang JH, Allingham RR, Gharahkhani P, Khor CC, Burdon KP, Aschard H, Chasman DI, Igo RP, Hysi PG, Glastonbury CA, Ashley-Koch A, Brilliant M, Brown AA, Budenz DL, Buil A, Cheng CY, Choi H, Christen WG, Curhan G, De Vivo I, Fingert JH, Foster PJ, Fuchs C, Gaasterland D, Gaasterland T, Hewitt AW, Hu F, Hunter DJ, Khawaja AP, Lee RK, Li Z, Lichter PR, Mackey DA, McGuffin P, Mitchell P, Moroi SE, Perera SA, Pepper KW, Qi Q, Realini T, Richards JE, Ridker PM, Rimm E, Ritch R, Ritchie M, Schuman JS, Scott WK, Singh K, Sit AJ, Song YE, Tamimi RM, Topouzis F, Viswanathan AC, Verma SS, Vollrath D, Wang JJ, Weisschuh N, Wissinger B, Wollstein G, Wong TY, Yaspan BL, Zack DJ, Zhang K, Study ENE, Weinreb RN, Pericak-Vance MA, Small K, Hammond CJ, Aung T, Liu Y, Vithana EN, MacGregor S, Craig JE, Kraft P, Howell G, Hauser MA, Pasquale LR, Haines JL, Wiggs JL. Genome-wide association analysis identifies TXNRD2, ATXN2 and FOXC1 as susceptibility loci for primary open-angle glaucoma. Nat Genet 2016; 48:189-94. [PMID: 26752265 PMCID: PMC4731307 DOI: 10.1038/ng.3482] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 12/09/2015] [Indexed: 12/13/2022]
Abstract
Primary open angle glaucoma (POAG) is a leading cause of blindness world-wide. To identify new susceptibility loci, we meta-analyzed GWAS results from 8 independent studies from the United States (3,853 cases and 33,480 controls) and investigated the most significant SNPs in two Australian studies (1,252 cases and 2,592 controls), 3 European studies (875 cases and 4,107 controls) and a Singaporean Chinese study (1,037 cases and 2,543 controls). A meta-analysis of top SNPs identified three novel loci: rs35934224[T] within TXNRD2 (odds ratio (OR) = 0.78, P = 4.05×10−11 encoding a mitochondrial protein required for redox homeostasis; rs7137828[T] within ATXN2 (OR = 1.17, P = 8.73×10−10), and rs2745572[A] upstream of FOXC1 (OR = 1.17, P = 1.76×10−10). Using RT-PCR and immunohistochemistry, we show TXNRD2 and ATXN2 expression in retinal ganglion cells and the optic nerve head. These results identify new pathways underlying POAG susceptibility and suggest novel targets for preventative therapies.
Collapse
Affiliation(s)
- Jessica N Cooke Bailey
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Stephanie J Loomis
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
| | - Jae H Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, USA
| | - Puya Gharahkhani
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Chiea Chuen Khor
- Division of Human Genetics, Genome Institute of Singapore, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia.,Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Hugues Aschard
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Robert P Igo
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Craig A Glastonbury
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Murray Brilliant
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, USA
| | - Andrew A Brown
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Donald L Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Alfonso Buil
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Ching-Yu Cheng
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.,Eye Academic Clinical Program, Duke-National University of Singapore Graduate Medical School, Singapore
| | - Hyon Choi
- Section of Rheumatology and Clinical Epidemiology Unit, Boston University School of Medicine, Boston, Massachusetts, USA
| | - William G Christen
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Gary Curhan
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Renal Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Immaculata De Vivo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - John H Fingert
- Department of Ophthalmology, University of Iowa, College of Medicine, Iowa City, Iowa, USA.,Department of Anatomy and Cell Biology, University of Iowa, College of Medicine, Iowa City, Iowa, USA
| | - Paul J Foster
- National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital, London, UK.,Department of Ophthalmology, University College London, London, UK
| | - Charles Fuchs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Terry Gaasterland
- Scripps Genome Center, University of California at San Diego, San Diego, California, USA
| | - Alex W Hewitt
- Centre for Eye Research Australia, University of Melbourne, Melbourne, Victoria, Australia.,Department of Ophthalmology, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
| | - Frank Hu
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA.,Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
| | - David J Hunter
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA.,Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Anthony P Khawaja
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Richard K Lee
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Zheng Li
- Division of Human Genetics, Genome Institute of Singapore, Singapore
| | - Paul R Lichter
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - David A Mackey
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia.,Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Peter McGuffin
- Medical Research Council Social Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, King's College London, London, UK
| | - Paul Mitchell
- Centre for Vision Research, Westmead Millennium Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Sayoko E Moroi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Shamira A Perera
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.,Duke-National University of Singapore Graduate Medical School, Singapore
| | | | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Tony Realini
- Department of Ophthalmology, West Virginia University Eye Institute, Morgantown, West Virginia, USA
| | - Julia E Richards
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, USA.,Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Eric Rimm
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA.,Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Robert Ritch
- Einhorn Clinical Research Center, Department of Ophthalmology, New York Eye and Ear Infirmary of Mount Sinai, New York, New York, USA
| | - Marylyn Ritchie
- Center for Systems Genomics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Joel S Schuman
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - William K Scott
- Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Kuldev Singh
- Department of Ophthalmology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Arthur J Sit
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - Yeunjoo E Song
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Rulla M Tamimi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Fotis Topouzis
- Department of Ophthalmology, School of Medicine, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece
| | - Ananth C Viswanathan
- National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital, London, UK
| | - Shefali Setia Verma
- Center for Systems Genomics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Douglas Vollrath
- Department of Genetics, Stanford University School of Medicine, Palo Alto, California, USA
| | - Jie Jin Wang
- Centre for Vision Research, Westmead Millennium Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Nicole Weisschuh
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Gadi Wollstein
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Tien Y Wong
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | | | - Donald J Zack
- Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, Maryland, USA
| | - Kang Zhang
- Hamilton Glaucoma Center, Shiley Eye Institute, University of California, San Diego, San Diego, California, USA
| | - Epic-Norfolk Eye Study
- Department of Cellular Biology and Anatomy, Georgia Regents University, Augusta, Georgia, USA
| | | | - Robert N Weinreb
- Hamilton Glaucoma Center, Shiley Eye Institute, University of California, San Diego, San Diego, California, USA
| | - Margaret A Pericak-Vance
- Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Kerrin Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Christopher J Hammond
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.,Eye Academic Clinical Program, Duke-National University of Singapore Graduate Medical School, Singapore
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Georgia Regents University, Augusta, Georgia, USA.,James and Jean Culver Vision Discovery Institute, Georgia Regents University, Augusta, Georgia, USA
| | - Eranga N Vithana
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.,Eye Academic Clinical Program, Duke-National University of Singapore Graduate Medical School, Singapore
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA.,Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, Massachusetts, USA
| | | | - Michael A Hauser
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, USA.,Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Louis R Pasquale
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
| |
Collapse
|
38
|
Ginns EI, Galdzicka M, Elston RC, Song YE, Paul SM, Egeland JA. Disruption of sonic hedgehog signaling in Ellis-van Creveld dwarfism confers protection against bipolar affective disorder. Mol Psychiatry 2015; 20:1212-8. [PMID: 25311364 DOI: 10.1038/mp.2014.118] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/06/2014] [Accepted: 08/21/2014] [Indexed: 01/30/2023]
Abstract
Ellis-van Creveld syndrome, an autosomal recessively inherited chondrodysplastic dwarfism, is frequent among Old Order Amish of Pennsylvania. Decades of longitudinal research on bipolar affective disorder (BPAD) revealed cosegregation of high numbers of EvC and Bipolar I (BPI) cases in several large Amish families descending from the same pioneer. Despite the high prevalence of both disorders in these families, no EvC individual has ever been reported with BPI. The proximity of the EVC gene to our previously reported chromosome 4p16 BPAD locus with protective alleles, coupled with detailed clinical observations that EvC and BPI do not occur in the same individuals, led us to hypothesize that the genetic defect causing EvC in the Amish confers protection from BPI. This hypothesis is supported by a significant negative association of these two disorders when contrasted with absence of disease (P=0.029, Fisher's exact test, two-sided, verified by permutation to estimate the null distribution of the test statistic). As homozygous Amish EVC mutations causing EvC dwarfism do so by disrupting sonic hedgehog (Shh) signaling, our data implicate Shh signaling in the underlying pathophysiology of BPAD. Understanding how disrupted Shh signaling protects against BPI could uncover variants in the Shh pathway that cause or increase risk for this and related mood disorders.
Collapse
Affiliation(s)
- E I Ginns
- Departments of Clinical Labs, Neurology, Pediatrics, Pathology and Psychiatry, University of Massachusetts Medical School/UMass Memorial Medical Center, Worcester, MA, USA
| | - M Galdzicka
- Departments of Clinical Labs and Pathology, University of Massachusetts Medical School/UMass Memorial Medical Center, Worcester, MA, USA
| | - R C Elston
- Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Y E Song
- Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - S M Paul
- Departments of Neuroscience, Psychiatry and Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - J A Egeland
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| |
Collapse
|
39
|
Ge L, Shi B, Song YE, Li Y, Wang S, Wang X. Clinical value of real-time elastography quantitative parameters in evaluating the stage of liver fibrosis and cirrhosis. Exp Ther Med 2015; 10:983-990. [PMID: 26622426 DOI: 10.3892/etm.2015.2628] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 07/18/2014] [Accepted: 03/19/2015] [Indexed: 02/06/2023] Open
Abstract
The aim of the present study was to assess the value of real-time elastography (RTE) quantitative parameters, namely the liver fibrosis (LF) index and the ratio of blue area (%AREA), in evaluating the stage of liver fibrosis. RTE quantitative analysis software was used to examine 120 patients with chronic hepatitis in order to obtain the values for 12 quantitative parameters from the elastic images. The diagnostic performance of two such parameters, the LF index and %AREA, were assessed with a receiver operating characteristic (ROC) curve to determine the optimal diagnostic cut-off values for liver cirrhosis and fibrosis. A good correlation was observed between the LF index and %AREA with the fibrosis stage. The areas under the ROC curve for the LF index were 0.985 for the diagnosis of liver cirrhosis and 0.790 for liver fibrosis. With regard to %AREA, the areas under the ROC curve for the diagnosis of liver cirrhosis and fibrosis were 0.963 and 0.770, respectively. An LF index of >3.25 and a %AREA of >28.83 for the diagnosis of cirrhosis stage resulted in sensitivity values of 100 and 100%, specificity values of 88.9 and 85.9% and accuracy values of 90.8 and 88.3%, respectively. The LF index and %AREA parameters exhibited higher reliability in the diagnosis of liver cirrhosis compared with the diagnosis of the liver fibrosis stage. However, the two parameters possessed a similar efficacy in the diagnosis of liver cirrhosis and the stage of liver fibrosis. Therefore, the quantitative RTE parameters of the LF index and %AREA may be clinically applicable as reliable indices for the early diagnosis of liver cirrhosis, without the requirement of an invasive procedure.
Collapse
Affiliation(s)
- Lan Ge
- Department of Ultrasound, Tongji Hospital, Tongji University, Shanghai 200065, P.R. China
| | - Baomin Shi
- Department of Ultrasound, Tongji Hospital, Tongji University, Shanghai 200065, P.R. China
| | - Y E Song
- Department of Ultrasound, Tongji Hospital, Tongji University, Shanghai 200065, P.R. China
| | - Yuan Li
- Department of Ultrasound, Tongji Hospital, Tongji University, Shanghai 200065, P.R. China
| | - Shuo Wang
- Department of Ultrasound, Tongji Hospital, Tongji University, Shanghai 200065, P.R. China
| | - Xiuyan Wang
- Department of Ultrasound, Tongji Hospital, Tongji University, Shanghai 200065, P.R. China
| |
Collapse
|
40
|
Abstract
BACKGROUND Structural equation modeling (SEM) is an extremely general and powerful approach to account for measurement error and causal pathways when analyzing data, and it has been used in wide range of applied sciences. There are many commercial and freely available software packages for SEM. However, it is difficult to use any of the packages to analyze general pedigree data, and SEM packages for genetics are limited in their application. RESULTS We present the new R package strum to serve the need of a suitable SEM software tool for genetic analysis. It implements a general framework for SEM within the context of general pedigree data. This context requires specialized considerations such as familial correlations and ascertainment. Our package is an extraordinarily flexible tool capable of modeling genetic association, linkage analysis, polygenic effects, shared environment, and ascertainment combined with confirmatory factor analysis and general SEM. It also provides a convenient tool for model visualization, and integrates tools for simulating pedigree data. The various features of this package are tested through a simulation study to evaluate performance, and our results show that strum is very reliable and robust in terms of the accuracy and coverage of parameter estimates. CONCLUSIONS strum is a valuable new tool for genetic analysis. It can be easily used with general pedigree data, incorporating both measurement and structural models, giving it some significant advantages over other software packages. It also includes a built-in approach for handling ascertainment, a helpful integrated tool for genetic data simulation, and built-in tools for model visualization, providing a significant addition to biomedical research.
Collapse
Affiliation(s)
- Yeunjoo E Song
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - Catherine M Stein
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - Nathan J Morris
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, 44106, USA.
- Center for Clinical Investigation, Case Western Reserve University, Cleveland, OH, 44106, USA.
| |
Collapse
|
41
|
Song YE, Elston RC. The null distribution of likelihood-ratio statistics in the conditional-logistic linkage model. Front Genet 2013; 4:244. [PMID: 24312121 PMCID: PMC3832807 DOI: 10.3389/fgene.2013.00244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 10/26/2013] [Indexed: 12/25/2022] Open
Abstract
Olson's conditional-logistic model retains the nice property of the LOD score formulation and has advantages over other methods that make it an appropriate choice for complex trait linkage mapping. However, the asymptotic distribution of the conditional-logistic likelihood-ratio (CL-LR) statistic with genetic constraints on the model parameters is unknown for some analysis models, even in the case of samples comprising only independent sib pairs. We derive approximations to the asymptotic null distributions of the CL-LR statistics and compare them with the empirical null distributions by simulation using independent affected sib pairs. Generally, the empirical null distributions of the CL-LR statistics match well the known or approximated asymptotic distributions for all analysis models considered except for the covariate model with a minimum-adjusted binary covariate. This work will provide useful guidelines for linkage analysis of real data sets for the genetic analysis of complex traits, thereby contributing to the identification of genes for disease traits.
Collapse
Affiliation(s)
- Yeunjoo E Song
- Department of Epidemiology and Biostatistics, Case Western Reserve University Cleveland, OH, USA
| | | |
Collapse
|
42
|
Song YE, Wang X, Shen ZW, Xu Y, Li JY. Expressing the maize anthocyanin regulatory gene Lc increased flavonoid content in the seed of white pericarp rice and purple pericarp rice. Genetika 2013; 49:1292-9. [PMID: 25470930 DOI: 10.7868/s0016675813100123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The colour of red, purple, brown and white occurs in pericarp of rice. Here, the maize anthocyanin regulatory gene Lc under control of the promoter of the rice glutelin gene Gt1 was introduced in the white pericarp rice "Chao2-10" and purple pericarp rice "Qingjiaozidao". The results demonstrated that some transgenic "Chao2-10" rice pericarps became brown, and the total flavonoid contents in the unpolished rice of the two transgenic rices increased significantly compared with their respective controls. Unpolished rice kernel thickness and weight in the two transgenic rices decreased slightly.
Collapse
|
43
|
Abstract
A novel web-based tool PedWiz that pipelines the informatics process for pedigree data is introduced. PedWiz is designed to assist researchers in the analysis of pedigree data. It provides a convenient tool for pedigree informatics: descriptive statistics, relative pairs, genetic similarity coefficients, the variance-covariance matrix for three estimated coefficients of allele identical-by-descent sharing as well as mean allele sharing, a plot of the pedigree structures, and a visualization of the identity coefficients. With a renewed interest in linkage and other family based methods, PedWiz will be a valuable tool for the analysis of family data.
Collapse
Affiliation(s)
- Yeunjoo E Song
- Department of Epidemiology and Biostatistics, Case Western Reserve University Cleveland, OH, USA
| | | |
Collapse
|
44
|
Song YE, Namkung J, Shields RW, Baechle DJ, Song S, Elston RC. A method to detect single-nucleotide polymorphisms accounting for a linkage signal using covariate-based affected relative pair linkage analysis. BMC Proc 2011; 5 Suppl 9:S84. [PMID: 22373405 PMCID: PMC3287925 DOI: 10.1186/1753-6561-5-s9-s84] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We evaluate an approach to detect single-nucleotide polymorphisms (SNPs) that account for a linkage signal with covariate-based affected relative pair linkage analysis in a conditional-logistic model framework using all 200 replicates of the Genetic Analysis Workshop 17 family data set. We begin by combining the multiple known covariate values into a single variable, a propensity score. We also use each SNP as a covariate, using an additive coding based on the number of minor alleles. We evaluate the distribution of the difference between LOD scores with the propensity score covariate only and LOD scores with the propensity score covariate and a SNP covariate. The inclusion of causal SNPs in causal genes increases LOD scores more than the inclusion of noncausal SNPs either within causal genes or outside causal genes. We compare the results from this method to results from a family-based association analysis and conclude that it is possible to identify SNPs that account for the linkage signals from genes using a SNP-covariate-based affected relative pair linkage approach.
Collapse
Affiliation(s)
- Yeunjoo E Song
- Department of Epidemiology and Biostatistics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
| | | | | | | | | | | |
Collapse
|
45
|
Baker AR, Goodloe RJ, Larkin EK, Baechle DJ, Song YE, Phillips LS, Gray-McGuire CL. Multivariate association analysis of the components of metabolic syndrome from the Framingham Heart Study. BMC Proc 2009; 3 Suppl 7:S42. [PMID: 20018034 PMCID: PMC2795941 DOI: 10.1186/1753-6561-3-s7-s42] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Metabolic syndrome, by definition, is the manifestation of multiple, correlated metabolic impairments. It is known to have both strong environmental and genetic contributions. However, isolating genetic variants predisposing to such a complex trait has limitations. Using pedigree data, when available, may well lead to increased ability to detect variants associated with such complex traits. The ability to incorporate multiple correlated traits into a joint analysis may also allow increased detection of associated genes. Therefore, to demonstrate the utility of both univariate and multivariate family-based association analysis and to identify possible genetic variants associated with metabolic syndrome, we performed a scan of the Affymetrix 50 k Human Gene Panel data using 1) each of the traits comprising metabolic syndrome: triglycerides, high-density lipoprotein, systolic blood pressure, diastolic blood pressure, blood glucose, and body mass index, and 2) a composite trait including all of the above, jointly. Two single-nucleotide polymorphisms within the cholesterol ester transfer protein (CETP) gene remained significant even after correcting for multiple testing in both the univariate (p < 5 x 10-7) and multivariate (p < 5 x 10-9) association analysis. Three genes met significance for multiple traits after correction for multiple testing in the univariate analysis, while five genes remained significant in the multivariate association. We conclude that while both univariate and multivariate family-based association analysis can identify genes of interest, our multivariate approach is less affected by multiple testing correction and yields more significant results.
Collapse
Affiliation(s)
- Allison R Baker
- Department of Epidemiology and Biostatistics, Division of Genetic and Molecular Epidemiology, Case Western Reserve University, 11400 Euclid Avenue, Suite 260, Cleveland, Ohio 44106, USA
| | - Robert J Goodloe
- Department of Epidemiology and Biostatistics, Division of Genetic and Molecular Epidemiology, Case Western Reserve University, 11400 Euclid Avenue, Suite 260, Cleveland, Ohio 44106, USA
- Center for Clinical Investigation, Case Western Reserve University, 11400 Euclid Avenue, Suite 260, Cleveland, Ohio 44106, USA
| | - Emma K Larkin
- Department of Epidemiology and Biostatistics, Division of Genetic and Molecular Epidemiology, Case Western Reserve University, 11400 Euclid Avenue, Suite 260, Cleveland, Ohio 44106, USA
- Center for Clinical Investigation, Case Western Reserve University, 11400 Euclid Avenue, Suite 260, Cleveland, Ohio 44106, USA
| | - Dan J Baechle
- Department of Epidemiology and Biostatistics, Division of Genetic and Molecular Epidemiology, Case Western Reserve University, 11400 Euclid Avenue, Suite 260, Cleveland, Ohio 44106, USA
| | - Yeunjoo E Song
- Department of Epidemiology and Biostatistics, Division of Genetic and Molecular Epidemiology, Case Western Reserve University, 11400 Euclid Avenue, Suite 260, Cleveland, Ohio 44106, USA
| | - Lynette S Phillips
- Department of Epidemiology and Biostatistics, Division of Genetic and Molecular Epidemiology, Case Western Reserve University, 11400 Euclid Avenue, Suite 260, Cleveland, Ohio 44106, USA
| | - Courtney L Gray-McGuire
- Department of Epidemiology and Biostatistics, Division of Genetic and Molecular Epidemiology, Case Western Reserve University, 11400 Euclid Avenue, Suite 260, Cleveland, Ohio 44106, USA
| |
Collapse
|
46
|
Abstract
In this study we compared the effects of radiofrequency (RF) energy applied to the swine endocardium in a unipolar fashion and in a bipolar one with two different interelectrode distances (5 mm, 10 mm). RF energy (500 kHz) delivered to the swine endocardium was divided into eight categories: 100 J, 101-200 J, 201-300 J, 301-400 J, 401-500 J, 501-600 J, 601-1000 J, and > 1000 J. The results showed that when RF energy was applied in a bipolar fashion, the lesions involved the catheter/tissue interface and partly the interelectrode spacing, while in a unipolar fashion. They were found in the catheter/tissue interface only. At any energy level, there were no statistically significant differences in lesion depths among all the three fashions, and the lesion surface areas produced by the bipolar fashion (with 5 mm or 10 mm interelectrode spacing) were all greater than those by the unipolar fashion (P < 0.05). When the delivered energy was under 500 joules, a greater lesion surface area was found in 5 mm bipolar fashion than in 10mm bipolar fashion (P < 0.05), while energy exceeded 500 joules, the differences in the lesion surface areas were no longer significant between these two bipolar fashions.
Collapse
Affiliation(s)
- Y G Wang
- Department of Cardiology, Tongji Hospital, Tongji Medical University, Wuhan
| | | | | | | | | |
Collapse
|