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  1. AU="Schellenberg, Gerard"
  2. AU="N. M. Kalinina"
  3. AU=Jalava Jari
  4. AU="Taylor, Lorna"
  5. AU="Eric C Ip"

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  1. Artikel: The role of structural variations in Alzheimer's disease and other neurodegenerative diseases.

    Wang, Hui / Wang, Li-San / Schellenberg, Gerard / Lee, Wan-Ping

    Frontiers in aging neuroscience

    2023  Band 14, Seite(n) 1073905

    Abstract: Dozens of single nucleotide polymorphisms (SNPs) related to Alzheimer's disease (AD) have been discovered by large scale genome-wide association studies (GWASs). However, only a small portion of the genetic component of AD can be explained by SNPs ... ...

    Abstract Dozens of single nucleotide polymorphisms (SNPs) related to Alzheimer's disease (AD) have been discovered by large scale genome-wide association studies (GWASs). However, only a small portion of the genetic component of AD can be explained by SNPs observed from GWAS. Structural variation (SV) can be a major contributor to the missing heritability of AD; while SV in AD remains largely unexplored as the accurate detection of SVs from the widely used array-based and short-read technology are still far from perfect. Here, we briefly summarized the strengths and weaknesses of available SV detection methods. We reviewed the current landscape of SV analysis in AD and SVs that have been found associated with AD. Particularly, the importance of currently less explored SVs, including insertions, inversions, short tandem repeats, and transposable elements in neurodegenerative diseases were highlighted.
    Sprache Englisch
    Erscheinungsdatum 2023-02-08
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article ; Review
    ZDB-ID 2558898-9
    ISSN 1663-4365
    ISSN 1663-4365
    DOI 10.3389/fnagi.2022.1073905
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel: Polygenic burden of short tandem repeat expansions promote risk for Alzheimer's disease.

    Guo, Michael H / Lee, Wan-Ping / Vardarajan, Badri / Schellenberg, Gerard D / Phillips-Cremins, Jennifer

    medRxiv : the preprint server for health sciences

    2023  

    Abstract: Studies of the genetics of Alzheimer's disease (AD) have largely focused on single nucleotide variants and short insertions/deletions. However, most of the disease heritability has yet to be uncovered, suggesting that there is substantial genetic risk ... ...

    Abstract Studies of the genetics of Alzheimer's disease (AD) have largely focused on single nucleotide variants and short insertions/deletions. However, most of the disease heritability has yet to be uncovered, suggesting that there is substantial genetic risk conferred by other forms of genetic variation. There are over one million short tandem repeats (STRs) in the genome, and their link to AD risk has not been assessed. As pathogenic expansions of STR cause over 30 neurologic diseases, it is important to ascertain whether STRs may also be implicated in AD risk. Here, we genotyped 321,742 polymorphic STR tracts genome-wide using PCR-free whole genome sequencing data from 2,981 individuals (1,489 AD case and 1,492 control individuals). We implemented an approach to identify STR expansions as STRs with tract lengths that are outliers from the population. We then tested for differences in aggregate burden of expansions in case versus control individuals. AD patients had a 1.19-fold increase of STR expansions compared to healthy elderly controls (p=8.27×10
    Sprache Englisch
    Erscheinungsdatum 2023-11-16
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2023.11.16.23298623
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel: 50,000 years of Evolutionary History of India: Insights from ~2,700 Whole Genome Sequences.

    Kerdoncuff, Elise / Skov, Laurits / Patterson, Nick / Zhao, Wei / Lueng, Yuk Yee / Schellenberg, Gerard D / Smith, Jennifer A / Dey, Sharmistha / Ganna, Andrea / Dey, A B / Kardia, Sharon L R / Lee, Jinkook / Moorjani, Priya

    bioRxiv : the preprint server for biology

    2024  

    Abstract: India has been underrepresented in whole genome sequencing studies. We generated 2,762 high coverage genomes from India-including individuals from most geographic regions, speakers of all major languages, and tribal and caste groups-providing a ... ...

    Abstract India has been underrepresented in whole genome sequencing studies. We generated 2,762 high coverage genomes from India-including individuals from most geographic regions, speakers of all major languages, and tribal and caste groups-providing a comprehensive survey of genetic variation in India. With these data, we reconstruct the evolutionary history of India through space and time at fine scales. We show that most Indians derive ancestry from three ancestral groups related to ancient Iranian farmers, Eurasian Steppe pastoralists and South Asian hunter-gatherers. We uncover a common source of Iranian-related ancestry from early Neolithic cultures of Central Asia into the ancestors of Ancestral South Indians (ASI), Ancestral North Indians (ANI), Austro-asiatic-related and East Asian-related groups in India. Following these admixtures, India experienced a major demographic shift towards endogamy, resulting in extensive homozygosity and identity-by-descent sharing among individuals. At deep time scales, Indians derive around 1-2% of their ancestry from gene flow from archaic hominins, Neanderthals and Denisovans. By assembling the surviving fragments of archaic ancestry in modern Indians, we recover ~1.5 Gb (or 50%) of the introgressing Neanderthal and ~0.6 Gb (or 20%) of the introgressing Denisovan genomes, more than any other previous archaic ancestry study. Moreover, Indians have the largest variation in Neanderthal ancestry, as well as the highest amount of population-specific Neanderthal segments among worldwide groups. Finally, we demonstrate that most of the genetic variation in Indians stems from a single major migration out of Africa that occurred around 50,000 years ago, with minimal contribution from earlier migration waves. Together, these analyses provide a detailed view of the population history of India and underscore the value of expanding genomic surveys to diverse groups outside Europe.
    Sprache Englisch
    Erscheinungsdatum 2024-02-17
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2024.02.15.580575
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: MitoH3: Mitochondrial Haplogroup and Homoplasmic/Heteroplasmic Variant Calling Pipeline for Alzheimer's Disease Sequencing Project.

    Zhu, Congcong / Tong, Tong / Farrell, John J / Martin, Eden R / Bush, William S / Pericak-Vance, Margaret A / Wang, Li-San / Schellenberg, Gerard D / Haines, Jonathan L / Lunetta, Kathryn L / Farrer, Lindsay A / Zhang, Xiaoling

    Journal of Alzheimer's disease reports

    2024  Band 8, Heft 1, Seite(n) 575–587

    Abstract: Background: Mitochondrial DNA (mtDNA) is a double-stranded circular DNA and has multiple copies in each cell. Excess heteroplasmy, the coexistence of distinct variants in copies of mtDNA within a cell, may lead to mitochondrial impairments. Accurate ... ...

    Abstract Background: Mitochondrial DNA (mtDNA) is a double-stranded circular DNA and has multiple copies in each cell. Excess heteroplasmy, the coexistence of distinct variants in copies of mtDNA within a cell, may lead to mitochondrial impairments. Accurate determination of heteroplasmy in whole-genome sequencing (WGS) data has posed a significant challenge because mitochondria carrying heteroplasmic variants cannot be distinguished during library preparation. Moreover, sequencing errors, contamination, and nuclear mtDNA segments can reduce the accuracy of heteroplasmic variant calling.
    Objective: To efficiently and accurately call mtDNA homoplasmic and heteroplasmic variants from the large-scale WGS data generated from the Alzheimer's Disease Sequencing Project (ADSP), and test their association with Alzheimer's disease (AD).
    Methods: In this study, we present MitoH3-a comprehensive computational pipeline for calling mtDNA homoplasmic and heteroplasmic variants and inferring haplogroups in the ADSP WGS data. We first applied MitoH3 to 45 technical replicates from 6 subjects to define a threshold for detecting heteroplasmic variants. Then using the threshold of 5% ≤variant allele fraction≤95%, we further applied MitoH3 to call heteroplasmic variants from a total of 16,113 DNA samples with 6,742 samples from cognitively normal controls and 6,183 from AD cases.
    Results: This pipeline is available through the Singularity container engine. For 4,311 heteroplasmic variants identified from 16,113 samples, no significant variant count difference was observed between AD cases and controls.
    Conclusions: Our streamlined pipeline, MitoH3, enables computationally efficient and accurate analysis of a large number of samples.
    Sprache Englisch
    Erscheinungsdatum 2024-04-08
    Erscheinungsland Netherlands
    Dokumenttyp Journal Article
    ISSN 2542-4823
    ISSN (online) 2542-4823
    DOI 10.3233/ADR-230120
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: Genomic variants, genes, and pathways of Alzheimer's disease: An overview.

    Naj, Adam C / Schellenberg, Gerard D

    American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics

    2016  Band 174, Heft 1, Seite(n) 5–26

    Abstract: Alzheimer's disease (AD) (MIM: 104300) is a highly heritable disease with great complexity in its genetic contributors, and represents the most common form of dementia. With the gradual aging of the world's population, leading to increased prevalence of ... ...

    Abstract Alzheimer's disease (AD) (MIM: 104300) is a highly heritable disease with great complexity in its genetic contributors, and represents the most common form of dementia. With the gradual aging of the world's population, leading to increased prevalence of AD, and the substantial cost of care for those afflicted, identifying the genetic causes of disease represents a critical effort in identifying therapeutic targets. Here we provide a comprehensive review of genomic studies of AD, from the earliest linkage studies identifying monogenic contributors to early-onset forms of AD to the genome-wide and rare variant association studies of recent years that are being used to characterize the mosaic of genetic contributors to late-onset AD (LOAD), and which have identified approximately ∼20 genes with common variants contributing to LOAD risk. In addition, we explore studies employing alternative approaches to identify genetic contributors to AD, including studies of AD-related phenotypes and multi-variant association studies such as pathway analyses. Finally, we introduce studies of next-generation sequencing, which have recently helped identify multiple low-frequency and rare variant contributors to AD, and discuss on-going efforts with next-generation sequencing studies to develop statistically well- powered and comprehensive genomic studies of AD. Through this review, we help uncover the many insights the genetics of AD have provided into the pathways and pathophysiology of AD. © 2016 Wiley Periodicals, Inc.
    Mesh-Begriff(e) Alzheimer Disease/genetics ; Alzheimer Disease/physiopathology ; Dementia/genetics ; Genetic Linkage/genetics ; Genetic Predisposition to Disease/genetics ; Genetic Variation/genetics ; Genome-Wide Association Study/methods ; Genomics ; Humans ; Polymorphism, Single Nucleotide/genetics
    Sprache Englisch
    Erscheinungsdatum 2016-11-25
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Review ; Research Support, N.I.H., Extramural
    ZDB-ID 2108616-3
    ISSN 1552-485X ; 1552-4841 ; 0148-7299
    ISSN (online) 1552-485X
    ISSN 1552-4841 ; 0148-7299
    DOI 10.1002/ajmg.b.32499
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel: Region-based analysis with functional annotation identifies genes associated with cognitive function in South Asians from India.

    Abu-Amara, Hasan / Zhao, Wei / Li, Zheng / Leung, Yuk Yee / Schellenberg, Gerard D / Wang, Li-San / Moorjani, Priya / Dey, A B / Dey, Sharmitha / Zhou, Xiang / Gross, Alden L / Lee, Jinkook / Kardia, Sharon L R / Smith, Jennifer A

    medRxiv : the preprint server for health sciences

    2024  

    Abstract: The prevalence of dementia among South Asians across India is approximately 7.4% in those 60 years and older, yet little is known about genetic risk factors for dementia in this population. Most known risk loci for Alzheimer's disease (AD) have been ... ...

    Abstract The prevalence of dementia among South Asians across India is approximately 7.4% in those 60 years and older, yet little is known about genetic risk factors for dementia in this population. Most known risk loci for Alzheimer's disease (AD) have been identified from studies conducted in European Ancestry (EA) but are unknown in South Asians. Using whole-genome sequence data from 2680 participants from the Diagnostic Assessment of Dementia for the Longitudinal Aging Study of India (LASI-DAD), we performed a gene-based analysis of 84 genes previously associated with AD in EA. We investigated associations with the Hindi Mental State Examination (HMSE) score and factor scores for general cognitive function and five cognitive domains. For each gene, we examined missense/loss-of-function (LoF) variants and brain-specific promoter/enhancer variants, separately, both with and without incorporating additional annotation weights (e.g., deleteriousness, conservation scores) using the variant-Set Test for Association using Annotation infoRmation (STAAR). In the missense/LoF analysis without annotation weights and controlling for age, sex, state/territory, and genetic ancestry, three genes had an association with at least one measure of cognitive function (FDR q<0.1).
    Sprache Englisch
    Erscheinungsdatum 2024-01-18
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.1101/2024.01.18.24301482
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel ; Online: Report of the APOE4 National Institute on Aging/Alzheimer Disease Sequencing Project Consortium Working Group: Reducing APOE4 in Carriers is a Therapeutic Goal for Alzheimer's Disease.

    Vance, Jeffery M / Farrer, Lindsay A / Huang, Yadong / Cruchaga, Carlos / Hyman, Bradley T / Pericak-Vance, Margaret A / Goate, Alison M / Greicius, Michael D / Griswold, Anthony J / Haines, Jonathan L / Tcw, Julia / Schellenberg, Gerard D / Tsai, Li-Huei / Herz, Joachim / Holtzman, David M

    Annals of neurology

    2024  Band 95, Heft 4, Seite(n) 625–634

    Abstract: Alzheimer's disease (AD) is the most common neurodegenerative disorder and one of the leading causes of disability worldwide. The apolipoprotein E4 gene (APOE4) is the strongest genetic risk factor for AD. In 2023, the APOE4 National Institute on Aging/ ... ...

    Abstract Alzheimer's disease (AD) is the most common neurodegenerative disorder and one of the leading causes of disability worldwide. The apolipoprotein E4 gene (APOE4) is the strongest genetic risk factor for AD. In 2023, the APOE4 National Institute on Aging/Alzheimer's Disease Sequencing Project working group came together to gather data and discuss the question of whether to reduce or increase APOE4 as a therapeutic intervention for AD. It was the unanimous consensus that cumulative data from multiple studies in humans and animal models support that lowering APOE4 should be a target for therapeutic approaches for APOE4 carriers. ANN NEUROL 2024;95:625-634.
    Mesh-Begriff(e) Animals ; United States ; Humans ; Alzheimer Disease/therapy ; Alzheimer Disease/drug therapy ; Apolipoprotein E4/genetics ; Goals ; National Institute on Aging (U.S.)
    Chemische Substanzen Apolipoprotein E4
    Sprache Englisch
    Erscheinungsdatum 2024-01-05
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Review
    ZDB-ID 80362-5
    ISSN 1531-8249 ; 0364-5134
    ISSN (online) 1531-8249
    ISSN 0364-5134
    DOI 10.1002/ana.26864
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Buch: The genetics of tauopathies

    Schellenberg, Gerard

    modifying genes and the mechanisms they reveal

    (NIH neuroscience seminar)

    2010  

    Körperschaft National Institutes of Health (U.S.)
    Verfasserangabe Gerard Schellenberg
    Serientitel NIH neuroscience seminar
    Mesh-Begriff(e) Supranuclear Palsy, Progressive/genetics ; Alzheimer Disease/genetics ; tau Proteins/genetics
    Sprache Englisch
    Verlag National Institutes of Health
    Erscheinungsort Bethesda, Md
    Dokumenttyp Buch
    Anmerkung Open-captioned. ; Title from title screen. ; Streaming video (1 hr., 7 min. : sd., col.).
    Datenquelle Katalog der US National Library of Medicine (NLM)

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  9. Artikel: Structural Variation Detection and Association Analysis of Whole-Genome-Sequence Data from 16,905 Alzheimer's Diseases Sequencing Project Subjects.

    Lee, Wan-Ping / Wang, Hui / Dombroski, Beth / Cheng, Po-Liang / Tucci, Albert / Si, Ya-Qin / Farrell, John / Tzeng, Jung-Ying / Leung, Yuk Yee / Malamon, John / Wang, Li-San / Vardarajan, Badri / Farrer, Lindsay / Schellenberg, Gerard

    Research square

    2023  

    Abstract: Structural variations (SVs) are important contributors to the genetics of human diseases. However, their role in Alzheimer's disease (AD) remains largely unstudied due to challenges in accurately detecting SVs. We analyzed whole-genome sequencing data ... ...

    Abstract Structural variations (SVs) are important contributors to the genetics of human diseases. However, their role in Alzheimer's disease (AD) remains largely unstudied due to challenges in accurately detecting SVs. We analyzed whole-genome sequencing data from the Alzheimer's Disease Sequencing Project (N = 16,905) and identified 400,234 (168,223 high-quality) SVs. Laboratory validation yielded a sensitivity of 82% (85% for high-quality). We found a significant burden of deletions and duplications in AD cases, particularly for singletons and homozygous events. On AD genes, we observed the ultra-rare SVs associated with the disease, including protein-altering SVs in
    Sprache Englisch
    Erscheinungsdatum 2023-10-05
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.21203/rs.3.rs-3353179/v1
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  10. Artikel ; Online: DNA from multiple viral species is associated with Alzheimer's disease risk.

    Tejeda, Marlene / Farrell, John / Zhu, Congcong / Wetzler, Lee / Lunetta, Kathryn L / Bush, William S / Martin, Eden R / Wang, Li-San / Schellenberg, Gerard D / Pericak-Vance, Margaret A / Haines, Jonathan L / Farrer, Lindsay A / Sherva, Richard

    Alzheimer's & dementia : the journal of the Alzheimer's Association

    2023  Band 20, Heft 1, Seite(n) 253–265

    Abstract: Introduction: Multiple infectious agents, including viruses, bacteria, fungi, and protozoa, have been linked to Alzheimer's disease (AD) risk by independent lines of evidence. We explored this association by comparing the frequencies of viral species ... ...

    Abstract Introduction: Multiple infectious agents, including viruses, bacteria, fungi, and protozoa, have been linked to Alzheimer's disease (AD) risk by independent lines of evidence. We explored this association by comparing the frequencies of viral species identified in a large sample of AD cases and controls.
    Methods: DNA sequence reads that did not align to the human genome in sequences were mapped to viral reference sequences, quantified, and then were tested for association with AD in whole exome sequences (WES) and whole genome sequences (WGS) datasets.
    Results: Several viruses were significant predictors of AD according to the machine learning classifiers. Subsequent regression analyses showed that herpes simplex type 1 (HSV-1) (odds ratio [OR] = 3.71, p = 8.03 × 10-4) and human papillomavirus 71 (HPV-71; OR = 3.56, p = 0.02), were significantly associated with AD after Bonferroni correction. The phylogenetic-related cluster of Herpesviridae was significantly associated with AD in several strata of the data (p < 0.01).
    Discussion: Our results support the hypothesis that viral infection, especially HSV-1, is associated with AD risk.
    Mesh-Begriff(e) Humans ; Alzheimer Disease/complications ; Phylogeny ; Herpes Simplex ; Herpesvirus 1, Human/genetics ; DNA
    Chemische Substanzen DNA (9007-49-2)
    Sprache Englisch
    Erscheinungsdatum 2023-08-14
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2211627-8
    ISSN 1552-5279 ; 1552-5260
    ISSN (online) 1552-5279
    ISSN 1552-5260
    DOI 10.1002/alz.13414
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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