LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 5 of total 5

Search options

  1. Article ; Online: Admixture mapping implicates 13q33.3 as ancestry-of-origin locus for Alzheimer disease in Hispanic and Latino populations

    Horimoto, Andrea R.V.R. / Boyken, Lisa A. / Blue, Elizabeth E. / Grinde, Kelsey E. / Nafikov, Rafael A. / Sohi, Harkirat K. / Nato, Alejandro Q. / Bis, Joshua C. / Brusco, Luis I. / Morelli, Laura / Ramírez, Alfredo / Dalmasso, Maria Carolina / Temple, Seth / Satizabal, Claudia / Browning, Sharon R. / Sudha Seshadri / Wijsman, Ellen M. / Thornton, Timothy A.

    Human Genetics and Genomics Advances. 2023 May 20, p.100207-

    2023  , Page(s) 100207–

    Abstract: Alzheimer disease (AD) is the most common form of senile dementia, with high incidence late in life in many populations including Caribbean Hispanic (CH) populations. Such admixed populations, descended from more than one ancestral population, can ... ...

    Abstract Alzheimer disease (AD) is the most common form of senile dementia, with high incidence late in life in many populations including Caribbean Hispanic (CH) populations. Such admixed populations, descended from more than one ancestral population, can present challenges for genetic studies, including limited sample sizes and unique analytical constraints. Therefore, CH populations and other admixed populations have not been well represented in studies of AD, and much of the genetic variation contributing to AD risk in these populations remains unknown. Here, we conduct genome-wide analysis of AD in multiplex CH families from the Alzheimer Disease Sequencing Project (ADSP). We developed, validated, and applied an implementation of a logistic mixed model for admixture mapping with binary traits that leverages genetic ancestry to identify ancestry-of-origin loci contributing to AD. We identified three loci on chromosome 13q33.3 associated with reduced risk of AD, where associations were driven by Native American (NAM) ancestry. This AD admixture mapping signal spans the FAM155A, ABHD13, TNFSF13B, LIG4, and MYO16 genes and was supported by evidence for association in an independent sample from the Alzheimer's Genetics in Argentina-Alzheimer Argentina consortium (AGA-ALZAR) study with considerable NAM ancestry. We also provide evidence of NAM haplotypes and key variants within 13q33.3 that segregate with AD in the ADSP whole-genome sequencing data. Interestingly, the widely used genome-wide association study approach failed to identify associations in this region. Our findings underscore the potential of leveraging genetic ancestry diversity in recently admixed populations to improve genetic mapping, in this case for AD-relevant loci.
    Keywords Alzheimer disease ; Latinos ; ancestry ; genetic variation ; genome-wide association study ; genomics ; haplotypes ; human genetics ; loci ; risk ; risk reduction ; statistical models ; Argentina ; Caribbean
    Language English
    Dates of publication 2023-0520
    Publishing place Elsevier Inc.
    Document type Article ; Online
    Note Pre-press version ; Use and reproduction
    ISSN 2666-2477
    DOI 10.1016/j.xhgg.2023.100207
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  2. Article ; Online: Admixture mapping implicates 13q33.3 as ancestry-of-origin locus for Alzheimer disease in Hispanic and Latino populations.

    Horimoto, Andrea R V R / Boyken, Lisa A / Blue, Elizabeth E / Grinde, Kelsey E / Nafikov, Rafael A / Sohi, Harkirat K / Nato, Alejandro Q / Bis, Joshua C / Brusco, Luis I / Morelli, Laura / Ramirez, Alfredo / Dalmasso, Maria Carolina / Temple, Seth / Satizabal, Claudia / Browning, Sharon R / Seshadri, Sudha / Wijsman, Ellen M / Thornton, Timothy A

    HGG advances

    2023  Volume 4, Issue 3, Page(s) 100207

    Abstract: Alzheimer disease (AD) is the most common form of senile dementia, with high incidence late in life in many populations including Caribbean Hispanic (CH) populations. Such admixed populations, descended from more than one ancestral population, can ... ...

    Abstract Alzheimer disease (AD) is the most common form of senile dementia, with high incidence late in life in many populations including Caribbean Hispanic (CH) populations. Such admixed populations, descended from more than one ancestral population, can present challenges for genetic studies, including limited sample sizes and unique analytical constraints. Therefore, CH populations and other admixed populations have not been well represented in studies of AD, and much of the genetic variation contributing to AD risk in these populations remains unknown. Here, we conduct genome-wide analysis of AD in multiplex CH families from the Alzheimer Disease Sequencing Project (ADSP). We developed, validated, and applied an implementation of a logistic mixed model for admixture mapping with binary traits that leverages genetic ancestry to identify ancestry-of-origin loci contributing to AD. We identified three loci on chromosome 13q33.3 associated with reduced risk of AD, where associations were driven by Native American (NAM) ancestry. This AD admixture mapping signal spans the
    MeSH term(s) Humans ; Alzheimer Disease/genetics ; Genome-Wide Association Study ; Hispanic or Latino/genetics ; Genetic Loci/genetics ; Ethnicity
    Language English
    Publishing date 2023-05-20
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ISSN 2666-2477
    ISSN (online) 2666-2477
    DOI 10.1016/j.xhgg.2023.100207
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Article ; Online: PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers.

    Nato, Alejandro Q / Chapman, Nicola H / Sohi, Harkirat K / Nguyen, Hiep D / Brkanac, Zoran / Wijsman, Ellen M

    Bioinformatics (Oxford, England)

    2015  Volume 31, Issue 23, Page(s) 3790–3798

    Abstract: Motivation: Huge genetic datasets with dense marker panels are now common. With the availability of sequence data and recognition of importance of rare variants, smaller studies based on pedigrees are again also common. Pedigree-based samples often ... ...

    Abstract Motivation: Huge genetic datasets with dense marker panels are now common. With the availability of sequence data and recognition of importance of rare variants, smaller studies based on pedigrees are again also common. Pedigree-based samples often start with a dense marker panel, a subset of which may be used for linkage analysis to reduce computational burden and to limit linkage disequilibrium between single-nucleotide polymorphisms (SNPs). Programs attempting to select markers for linkage panels exist but lack flexibility.
    Results: We developed a pedigree-based analysis pipeline (PBAP) suite of programs geared towards SNPs and sequence data. PBAP performs quality control, marker selection and file preparation. PBAP sets up files for MORGAN, which can handle analyses for small and large pedigrees, typically human, and results can be used with other programs and for downstream analyses. We evaluate and illustrate its features with two real datasets.
    Availability and implementation: PBAP scripts may be downloaded from http://faculty.washington.edu/wijsman/software.shtml.
    Contact: wijsman@uw.edu.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Autism Spectrum Disorder/genetics ; Female ; Genetic Linkage ; Genetic Markers ; Humans ; Linkage Disequilibrium ; Male ; Pedigree ; Polymorphism, Single Nucleotide/genetics ; Quality Control ; Software
    Chemical Substances Genetic Markers
    Language English
    Publishing date 2015-07-30
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btv444
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2374: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  4. Article: Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project

    Naj, Adam C / Lin, Honghuang / Vardarajan, Badri N / White, Simon / Lancour, Daniel / Ma, Yiyi / Schmidt, Michael / Sun, Fangui / Butkiewicz, Mariusz / Bush, William S / Kunkle, Brian W / Malamon, John / Amin, Najaf / Choi, Seung Hoan / Hamilton-Nelson, Kara L / van der Lee, Sven J / Gupta, Namrata / Koboldt, Daniel C / Saad, Mohamad /
    Wang, Bowen / Nato, Alejandro Q / Sohi, Harkirat K / Kuzma, Amanda / Wang, Li-San / Cupples, L. Adrienne / van Duijn, Cornelia / Seshadri, Sudha / Schellenberg, Gerard D / Boerwinkle, Eric / Bis, Joshua C / Dupuis, Josée / Salerno, William J / Wijsman, Ellen M / Martin, Eden R / DeStefano, Anita L

    Genomics. 2019 July, v. 111, no. 4

    2019  

    Abstract: The Alzheimer's Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants ( ... ...

    Institution Alzheimer's Disease Sequencing Project (ADSP)
    Abstract The Alzheimer's Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants (indels) was performed centrally using GATK-HaplotypeCaller and Atlas V2. The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each pipeline, and developed and implemented a novel protocol, termed “consensus calling,” to combine genotype calls from both pipelines into a single high-quality set. QC was applied to autosomal bi-allelic SNVs and indels, and included pipeline-recommended QC filters, variant-level QC, and sample-level QC. Low-quality variants or genotypes were excluded, and sample outliers were noted. Quality was assessed by examining Mendelian inconsistencies (MIs) among 67 parent-offspring pairs, and MIs were used to establish additional genotype-specific filters for GATK calls. After QC, 578 subjects remained. Pipeline-specific QC excluded ~12.0% of GATK and 14.5% of Atlas SNVs. Between pipelines, ~91% of SNV genotypes across all QCed variants were concordant; 4.23% and 4.56% of genotypes were exclusive to Atlas or GATK, respectively; the remaining ~0.01% of discordant genotypes were excluded. For indels, variant-level QC excluded ~36.8% of GATK and 35.3% of Atlas indels. Between pipelines, ~55.6% of indel genotypes were concordant; while 10.3% and 28.3% were exclusive to Atlas or GATK, respectively; and ~0.29% of discordant genotypes were. The final WGS consensus dataset contains 27,896,774 SNVs and 3,133,926 indels and is publicly available.
    Keywords Alzheimer disease ; data collection ; filters ; genotype ; pipelines ; protocols ; quality control ; sequence analysis
    Language English
    Dates of publication 2019-07
    Size p. 808-818.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 356334-0
    ISSN 1089-8646 ; 0888-7543
    ISSN (online) 1089-8646
    ISSN 0888-7543
    DOI 10.1016/j.ygeno.2018.05.004
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2367: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  5. Article ; Online: Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project.

    Naj, Adam C / Lin, Honghuang / Vardarajan, Badri N / White, Simon / Lancour, Daniel / Ma, Yiyi / Schmidt, Michael / Sun, Fangui / Butkiewicz, Mariusz / Bush, William S / Kunkle, Brian W / Malamon, John / Amin, Najaf / Choi, Seung Hoan / Hamilton-Nelson, Kara L / van der Lee, Sven J / Gupta, Namrata / Koboldt, Daniel C / Saad, Mohamad /
    Wang, Bowen / Nato, Alejandro Q / Sohi, Harkirat K / Kuzma, Amanda / Wang, Li-San / Cupples, L Adrienne / van Duijn, Cornelia / Seshadri, Sudha / Schellenberg, Gerard D / Boerwinkle, Eric / Bis, Joshua C / Dupuis, Josée / Salerno, William J / Wijsman, Ellen M / Martin, Eden R / DeStefano, Anita L

    Genomics

    2018  Volume 111, Issue 4, Page(s) 808–818

    Abstract: The Alzheimer's Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants ( ... ...

    Abstract The Alzheimer's Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants (indels) was performed centrally using GATK-HaplotypeCaller and Atlas V2. The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each pipeline, and developed and implemented a novel protocol, termed "consensus calling," to combine genotype calls from both pipelines into a single high-quality set. QC was applied to autosomal bi-allelic SNVs and indels, and included pipeline-recommended QC filters, variant-level QC, and sample-level QC. Low-quality variants or genotypes were excluded, and sample outliers were noted. Quality was assessed by examining Mendelian inconsistencies (MIs) among 67 parent-offspring pairs, and MIs were used to establish additional genotype-specific filters for GATK calls. After QC, 578 subjects remained. Pipeline-specific QC excluded ~12.0% of GATK and 14.5% of Atlas SNVs. Between pipelines, ~91% of SNV genotypes across all QCed variants were concordant; 4.23% and 4.56% of genotypes were exclusive to Atlas or GATK, respectively; the remaining ~0.01% of discordant genotypes were excluded. For indels, variant-level QC excluded ~36.8% of GATK and 35.3% of Atlas indels. Between pipelines, ~55.6% of indel genotypes were concordant; while 10.3% and 28.3% were exclusive to Atlas or GATK, respectively; and ~0.29% of discordant genotypes were. The final WGS consensus dataset contains 27,896,774 SNVs and 3,133,926 indels and is publicly available.
    MeSH term(s) Algorithms ; Alzheimer Disease/genetics ; Female ; Genome-Wide Association Study/methods ; Genome-Wide Association Study/standards ; Genotype ; Genotyping Techniques/methods ; Genotyping Techniques/standards ; Humans ; Male ; Polymorphism, Genetic ; Quality Control ; Whole Genome Sequencing/methods ; Whole Genome Sequencing/standards
    Language English
    Publishing date 2018-05-29
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 356334-0
    ISSN 1089-8646 ; 0888-7543
    ISSN (online) 1089-8646
    ISSN 0888-7543
    DOI 10.1016/j.ygeno.2018.05.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2367: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top